From 3be6e9c04ba59dcf33a53437828788e2db384510 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Fri, 25 Sep 2026 10:38:05 +0100
Subject: [PATCH 01/38] Claude suggestions for pulling VCFs from zarr datasets

---
 malariagen_data/anoph/to_vcf_cnv.py  | 401 +++++++++++++++++++++++++++
 malariagen_data/anopheles.py         |   2 +
 tests/anoph/test_vcf_exporter_cnv.py | 234 ++++++++++++++++
 3 files changed, 637 insertions(+)
 create mode 100644 malariagen_data/anoph/to_vcf_cnv.py
 create mode 100644 tests/anoph/test_vcf_exporter_cnv.py

diff --git a/malariagen_data/anoph/to_vcf_cnv.py b/malariagen_data/anoph/to_vcf_cnv.py
new file mode 100644
index 000000000..fbc16f520
--- /dev/null
+++ b/malariagen_data/anoph/to_vcf_cnv.py
@@ -0,0 +1,401 @@
+import gzip
+import os
+from datetime import date
+from typing import List, Optional, Sequence
+
+import numpy as np
+from numpydoc_decorator import doc  # type: ignore
+
+from .cnv_data import AnophelesCnvData
+from . import base_params
+from . import cnv_params
+from . import plink_params
+from . import vcf_params
+
+
+def _decode(value) -> str:
+    return value.decode() if hasattr(value, "decode") else str(value)
+
+
+def _write_vcf_header(
+    f,
+    *,
+    contigs: Sequence[str],
+    sample_ids: Sequence[str],
+    info_lines: Sequence[str],
+    format_lines: Sequence[str],
+    alt_lines: Sequence[str] = (),
+) -> None:
+    f.write("##fileformat=VCFv4.3\n")
+    f.write(f"##fileDate={date.today().strftime('%Y%m%d')}\n")
+    f.write("##source=malariagen_data\n")
+    for contig in contigs:
+        f.write(f"##contig=<ID={contig}>\n")
+    for line in alt_lines:
+        f.write(line + "\n")
+    for line in info_lines:
+        f.write(line + "\n")
+    for line in format_lines:
+        f.write(line + "\n")
+    header_cols = [
+        "#CHROM",
+        "POS",
+        "ID",
+        "REF",
+        "ALT",
+        "QUAL",
+        "FILTER",
+        "INFO",
+        "FORMAT",
+    ]
+    f.write("\t".join(header_cols + list(sample_ids)) + "\n")
+
+
+class CnvVcfExporter(
+    AnophelesCnvData,
+):
+    """
+    Export CNV calls to VCF.
+
+    N.B., unlike SNP calls, CNV calls are not fully standardised in VCF.
+    Here each CNV region or call is written as a single symbolic `<CNV>`
+    ALT allele (REF is written as "N", per the VCF specification for
+    imprecise/symbolic variants), with the relevant per-sample data
+    encoded in FORMAT fields. This is a draft representation intended
+    to give IGV something sensible to render, and to remove the
+    dependency on separately-hosted CNV VCF files; it is not intended
+    to be a fully general-purpose CNV VCF writer.
+    """
+
+    def __init__(
+        self,
+        **kwargs,
+    ):
+        # N.B., this class is designed to work cooperatively, and
+        # so it's important that any remaining parameters are passed
+        # to the superclass constructor.
+        super().__init__(**kwargs)
+
+    @doc(
+        summary="""
+            Export CNV HMM copy number calls to Variant Call Format (VCF).
+        """,
+        extended_summary="""
+            This function writes genome-wide CNV HMM calls to a VCF file.
+            Each CNV region is written as a symbolic `<CNV>` allele, with
+            the estimated copy number for each sample stored in the `CN`
+            FORMAT field. Data is written in chunks to avoid loading the
+            entire array into memory. Supports optional gzip compression
+            when the output path ends with `.gz`.
+        """,
+        returns="""
+        Path to the VCF output file.
+        """,
+    )
+    def cnv_hmm_to_vcf(
+        self,
+        output_path: vcf_params.vcf_output_path,
+        region: base_params.regions,
+        sample_sets: Optional[base_params.sample_sets] = None,
+        sample_query: Optional[base_params.sample_query] = None,
+        sample_query_options: Optional[base_params.sample_query_options] = None,
+        max_coverage_variance: cnv_params.max_coverage_variance = cnv_params.max_coverage_variance_default,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
+        chunks: base_params.chunks = base_params.native_chunks,
+        overwrite: plink_params.overwrite = False,
+    ) -> str:
+        if os.path.exists(output_path) and not overwrite:
+            return output_path
+
+        ds = self.cnv_hmm(
+            region=region,
+            sample_sets=sample_sets,
+            sample_query=sample_query,
+            sample_query_options=sample_query_options,
+            max_coverage_variance=max_coverage_variance,
+            inline_array=inline_array,
+            chunks=chunks,
+        )
+
+        sample_ids = ds["sample_id"].values
+        contigs = ds.attrs.get("contigs", self.contigs)
+        compress = output_path.endswith(".gz")
+        opener = gzip.open if compress else open
+
+        with opener(output_path, "wt") as f:
+            _write_vcf_header(
+                f,
+                contigs=contigs,
+                sample_ids=sample_ids,
+                alt_lines=[
+                    '##ALT=<ID=CNV,Description="Copy number variant region">',
+                ],
+                info_lines=[
+                    '##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the CNV region">',
+                ],
+                format_lines=[
+                    '##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number estimated from read coverage by HMM">',
+                ],
+            )
+
+            pos_data = ds["variant_position"].data
+            end_data = ds["variant_end"].data
+            contig_data = ds["variant_contig"].data
+            cn_data = ds["call_CN"].data
+
+            chunk_sizes = pos_data.chunks[0]
+            offsets = np.cumsum((0,) + chunk_sizes)
+
+            with self._spinner(f"Write VCF ({ds.sizes['variants']} CNV HMM regions)"):
+                for ci in range(len(chunk_sizes)):
+                    start = offsets[ci]
+                    stop = offsets[ci + 1]
+                    pos_chunk = pos_data[start:stop].compute()
+                    end_chunk = end_data[start:stop].compute()
+                    contig_chunk = contig_data[start:stop].compute()
+                    cn_chunk = cn_data[start:stop].compute()
+
+                    lines: List[str] = []
+                    for j in range(pos_chunk.shape[0]):
+                        chrom = contigs[contig_chunk[j]]
+                        pos = str(pos_chunk[j])
+                        end = int(end_chunk[j])
+                        info = f"END={end}"
+                        sample_fields = (
+                            "." if v < 0 else str(int(v)) for v in cn_chunk[j]
+                        )
+                        lines.append(
+                            f"{chrom}\t{pos}\t.\tN\t<CNV>\t.\t.\t{info}\tCN\t"
+                            + "\t".join(sample_fields)
+                            + "\n"
+                        )
+                    f.write("".join(lines))
+
+        return output_path
+
+    @doc(
+        summary="""
+            Export CNV coverage calls to Variant Call Format (VCF).
+        """,
+        extended_summary="""
+            This function writes CNV coverage calls (discrete CNV alleles
+            called from read coverage) to a VCF file. Each CNV allele is
+            written as a symbolic `<CNV>` allele, with the presence/absence
+            call for each sample stored in the `GT` FORMAT field (as a
+            haploid call: "1" if the CNV allele was called, "0" if not,
+            "." if missing). Data is written in chunks to avoid loading
+            the entire array into memory. Supports optional gzip
+            compression when the output path ends with `.gz`.
+        """,
+        returns="""
+        Path to the VCF output file.
+        """,
+    )
+    def cnv_coverage_calls_to_vcf(
+        self,
+        output_path: vcf_params.vcf_output_path,
+        region: base_params.regions,
+        sample_set: base_params.sample_set,
+        analysis: cnv_params.coverage_calls_analysis,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
+        chunks: base_params.chunks = base_params.native_chunks,
+        overwrite: plink_params.overwrite = False,
+    ) -> str:
+        if os.path.exists(output_path) and not overwrite:
+            return output_path
+
+        ds = self.cnv_coverage_calls(
+            region=region,
+            sample_set=sample_set,
+            analysis=analysis,
+            inline_array=inline_array,
+            chunks=chunks,
+        )
+
+        sample_ids = ds["sample_id"].values
+        contigs = ds.attrs.get("contigs", self.contigs)
+        compress = output_path.endswith(".gz")
+        opener = gzip.open if compress else open
+
+        with opener(output_path, "wt") as f:
+            _write_vcf_header(
+                f,
+                contigs=contigs,
+                sample_ids=sample_ids,
+                alt_lines=[
+                    '##ALT=<ID=CNV,Description="Copy number variant region">',
+                ],
+                info_lines=[
+                    '##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the CNV allele">',
+                    '##INFO=<ID=CIPOS,Number=1,Type=Integer,Description="Confidence interval half-width around POS">',
+                    '##INFO=<ID=CIEND,Number=1,Type=Integer,Description="Confidence interval half-width around END">',
+                ],
+                format_lines=[
+                    '##FORMAT=<ID=GT,Number=1,Type=String,Description="CNV call (1=called, 0=not called)">',
+                ],
+            )
+
+            pos_data = ds["variant_position"].data
+            end_data = ds["variant_end"].data
+            contig_data = ds["variant_contig"].data
+            id_data = ds["variant_id"].data
+            cipos_data = ds["variant_CIPOS"].data
+            ciend_data = ds["variant_CIEND"].data
+            filter_data = ds["variant_filter_pass"].data
+            gt_data = ds["call_genotype"].data
+
+            chunk_sizes = pos_data.chunks[0]
+            offsets = np.cumsum((0,) + chunk_sizes)
+
+            with self._spinner(
+                f"Write VCF ({ds.sizes['variants']} CNV coverage calls)"
+            ):
+                for ci in range(len(chunk_sizes)):
+                    start = offsets[ci]
+                    stop = offsets[ci + 1]
+                    pos_chunk = pos_data[start:stop].compute()
+                    end_chunk = end_data[start:stop].compute()
+                    contig_chunk = contig_data[start:stop].compute()
+                    id_chunk = id_data[start:stop].compute()
+                    cipos_chunk = cipos_data[start:stop].compute()
+                    ciend_chunk = ciend_data[start:stop].compute()
+                    filter_chunk = filter_data[start:stop].compute()
+                    gt_chunk = gt_data[start:stop].compute()
+
+                    lines: List[str] = []
+                    for j in range(pos_chunk.shape[0]):
+                        chrom = contigs[contig_chunk[j]]
+                        pos = str(pos_chunk[j])
+                        variant_id = _decode(id_chunk[j])
+                        end = int(end_chunk[j])
+                        filt = "PASS" if filter_chunk[j] else "."
+                        info = (
+                            f"END={end};CIPOS={int(cipos_chunk[j])}"
+                            f";CIEND={int(ciend_chunk[j])}"
+                        )
+                        sample_fields = (
+                            "." if v < 0 else str(int(v)) for v in gt_chunk[j]
+                        )
+                        lines.append(
+                            f"{chrom}\t{pos}\t{variant_id}\tN\t<CNV>\t.\t{filt}\t{info}\tGT\t"
+                            + "\t".join(sample_fields)
+                            + "\n"
+                        )
+                    f.write("".join(lines))
+
+        return output_path
+
+    @doc(
+        summary="""
+            Export CNV discordant read calls to Variant Call Format (VCF).
+        """,
+        extended_summary="""
+            This function writes CNV discordant read calls (CNV alleles
+            supported by discordant/paired-end read evidence) to a VCF
+            file. Each CNV allele is written as a symbolic `<CNV>` allele,
+            with the call for each sample stored in the `GT` FORMAT field
+            (as a haploid call: "1" if the CNV allele was called, "0" if
+            not, "." if missing). Data is written in chunks to avoid
+            loading the entire array into memory. Supports optional gzip
+            compression when the output path ends with `.gz`.
+        """,
+        returns="""
+        Path to the VCF output file.
+        """,
+    )
+    def cnv_discordant_read_calls_to_vcf(
+        self,
+        output_path: vcf_params.vcf_output_path,
+        contigs: base_params.contigs,
+        sample_sets: Optional[base_params.sample_sets] = None,
+        sample_query: Optional[base_params.sample_query] = None,
+        sample_query_options: Optional[base_params.sample_query_options] = None,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
+        chunks: base_params.chunks = base_params.native_chunks,
+        overwrite: plink_params.overwrite = False,
+    ) -> str:
+        if os.path.exists(output_path) and not overwrite:
+            return output_path
+
+        ds = self.cnv_discordant_read_calls(
+            contigs=contigs,
+            sample_sets=sample_sets,
+            sample_query=sample_query,
+            sample_query_options=sample_query_options,
+            inline_array=inline_array,
+            chunks=chunks,
+        )
+
+        sample_ids = ds["sample_id"].values
+        all_contigs = ds.attrs.get("contigs", self.contigs)
+        compress = output_path.endswith(".gz")
+        opener = gzip.open if compress else open
+
+        with opener(output_path, "wt") as f:
+            _write_vcf_header(
+                f,
+                contigs=all_contigs,
+                sample_ids=sample_ids,
+                alt_lines=[
+                    '##ALT=<ID=CNV,Description="Copy number variant region">',
+                ],
+                info_lines=[
+                    '##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the CNV allele">',
+                    '##INFO=<ID=REGION,Number=1,Type=String,Description="Identifier of the region covered by this call">',
+                    '##INFO=<ID=SBM,Number=1,Type=Integer,Description="Method used to determine the start breakpoint">',
+                    '##INFO=<ID=EBM,Number=1,Type=Integer,Description="Method used to determine the end breakpoint">',
+                ],
+                format_lines=[
+                    '##FORMAT=<ID=GT,Number=1,Type=String,Description="CNV call (1=called, 0=not called)">',
+                ],
+            )
+
+            pos_data = ds["variant_position"].data
+            end_data = ds["variant_end"].data
+            contig_data = ds["variant_contig"].data
+            id_data = ds["variant_id"].data
+            region_data = ds["variant_Region"].data
+            sbm_data = ds["variant_StartBreakpointMethod"].data
+            ebm_data = ds["variant_EndBreakpointMethod"].data
+            gt_data = ds["call_genotype"].data
+
+            chunk_sizes = pos_data.chunks[0]
+            offsets = np.cumsum((0,) + chunk_sizes)
+
+            with self._spinner(
+                f"Write VCF ({ds.sizes['variants']} CNV discordant read calls)"
+            ):
+                for ci in range(len(chunk_sizes)):
+                    start = offsets[ci]
+                    stop = offsets[ci + 1]
+                    pos_chunk = pos_data[start:stop].compute()
+                    end_chunk = end_data[start:stop].compute()
+                    contig_chunk = contig_data[start:stop].compute()
+                    id_chunk = id_data[start:stop].compute()
+                    region_chunk = region_data[start:stop].compute()
+                    sbm_chunk = sbm_data[start:stop].compute()
+                    ebm_chunk = ebm_data[start:stop].compute()
+                    gt_chunk = gt_data[start:stop].compute()
+
+                    lines: List[str] = []
+                    for j in range(pos_chunk.shape[0]):
+                        chrom = all_contigs[contig_chunk[j]]
+                        pos = str(pos_chunk[j])
+                        variant_id = _decode(id_chunk[j])
+                        end = int(end_chunk[j])
+                        region_val = _decode(region_chunk[j])
+                        info = (
+                            f"END={end};REGION={region_val}"
+                            f";SBM={int(sbm_chunk[j])};EBM={int(ebm_chunk[j])}"
+                        )
+                        sample_fields = (
+                            "." if v < 0 else str(int(v)) for v in gt_chunk[j]
+                        )
+                        lines.append(
+                            f"{chrom}\t{pos}\t{variant_id}\tN\t<CNV>\t.\t.\t{info}\tGT\t"
+                            + "\t".join(sample_fields)
+                            + "\n"
+                        )
+                    f.write("".join(lines))
+
+        return output_path
diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py
index 8342dbb88..b775dad1e 100644
--- a/malariagen_data/anopheles.py
+++ b/malariagen_data/anopheles.py
@@ -37,6 +37,7 @@
 from .anoph.to_plink import PlinkConverter
 from .anoph.ld import AnophelesLdAnalysis
 from .anoph.to_vcf import SnpVcfExporter
+from .anoph.to_vcf_cnv import CnvVcfExporter
 from .anoph.g123 import AnophelesG123Analysis
 from .anoph.fst import AnophelesFstAnalysis
 from .anoph.h12 import AnophelesH12Analysis
@@ -93,6 +94,7 @@ class AnophelesDataResource(
     PlinkConverter,
     AnophelesLdAnalysis,
     SnpVcfExporter,
+    CnvVcfExporter,
     AnophelesIgv,
     AnophelesKaryotypeAnalysis,
     AnophelesAimData,
diff --git a/tests/anoph/test_vcf_exporter_cnv.py b/tests/anoph/test_vcf_exporter_cnv.py
new file mode 100644
index 000000000..e111ce70b
--- /dev/null
+++ b/tests/anoph/test_vcf_exporter_cnv.py
@@ -0,0 +1,234 @@
+import gzip
+import os
+import random
+
+import pytest
+from pytest_cases import parametrize_with_cases
+
+from malariagen_data import af1 as _af1
+from malariagen_data import ag3 as _ag3
+
+from malariagen_data.anoph.to_vcf_cnv import CnvVcfExporter
+
+
+@pytest.fixture
+def ag3_sim_api(ag3_sim_fixture):
+    return CnvVcfExporter(
+        url=ag3_sim_fixture.url,
+        public_url=ag3_sim_fixture.url,
+        config_path=_ag3.CONFIG_PATH,
+        major_version_number=_ag3.MAJOR_VERSION_NUMBER,
+        major_version_path=_ag3.MAJOR_VERSION_PATH,
+        pre=True,
+        aim_metadata_dtype={
+            "aim_species_fraction_arab": "float64",
+            "aim_species_fraction_colu": "float64",
+            "aim_species_fraction_colu_no2l": "float64",
+            "aim_species_gambcolu_arabiensis": object,
+            "aim_species_gambiae_coluzzii": object,
+            "aim_species": object,
+        },
+        gff_gene_type="gene",
+        gff_gene_name_attribute="Name",
+        gff_default_attributes=("ID", "Parent", "Name", "description"),
+        results_cache=ag3_sim_fixture.results_cache_path.as_posix(),
+        default_coverage_calls_analysis="gamb_colu",
+        discordant_read_calls_analysis=ag3_sim_fixture.config[
+            "DEFAULT_DISCORDANT_READ_CALLS_ANALYSIS"
+        ],
+    )
+
+
+@pytest.fixture
+def af1_sim_api(af1_sim_fixture):
+    return CnvVcfExporter(
+        url=af1_sim_fixture.url,
+        public_url=af1_sim_fixture.url,
+        config_path=_af1.CONFIG_PATH,
+        major_version_number=_af1.MAJOR_VERSION_NUMBER,
+        major_version_path=_af1.MAJOR_VERSION_PATH,
+        pre=False,
+        gff_gene_type="protein_coding_gene",
+        gff_gene_name_attribute="Note",
+        gff_default_attributes=("ID", "Parent", "Note", "description"),
+        results_cache=af1_sim_fixture.results_cache_path.as_posix(),
+        default_coverage_calls_analysis="funestus",
+        discordant_read_calls_analysis=None,
+    )
+
+
+def case_ag3_sim(ag3_sim_fixture, ag3_sim_api):
+    return ag3_sim_fixture, ag3_sim_api
+
+
+def case_af1_sim(af1_sim_fixture, af1_sim_api):
+    return af1_sim_fixture, af1_sim_api
+
+
+def _check_basic_vcf_structure(output_path, expected_n_variants, expected_sample_ids):
+    assert os.path.exists(output_path)
+
+    opener = gzip.open if output_path.endswith(".gz") else open
+    with opener(output_path, "rt") as f:
+        lines = f.readlines()
+
+    header_lines = [line for line in lines if line.startswith("##")]
+    column_line = [line for line in lines if line.startswith("#CHROM")]
+    data_lines = [line for line in lines if not line.startswith("#")]
+
+    assert header_lines[0].strip() == "##fileformat=VCFv4.3"
+    assert len(column_line) == 1
+
+    col_fields = column_line[0].strip().split("\t")
+    vcf_samples = col_fields[9:]
+    assert list(vcf_samples) == list(expected_sample_ids)
+
+    assert len(data_lines) == expected_n_variants
+
+    for line in data_lines:
+        fields = line.rstrip("\n").split("\t")
+        assert len(fields) == 9 + len(expected_sample_ids)
+        ref, alt = fields[3], fields[4]
+        assert ref == "N"
+        assert alt == "<CNV>"
+
+    return data_lines
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_hmm_to_vcf(fixture, api: CnvVcfExporter, tmp_path):
+    region = random.choice(api.contigs)
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = random.sample(all_sample_sets, min(2, len(all_sample_sets)))
+
+    ds = api.cnv_hmm(region=region, sample_sets=sample_sets, max_coverage_variance=None)
+    n_variants = ds.sizes["variants"]
+    sample_ids = ds["sample_id"].values
+
+    output_path = str(tmp_path / "test_cnv_hmm.vcf")
+    api.cnv_hmm_to_vcf(
+        output_path=output_path,
+        region=region,
+        sample_sets=sample_sets,
+        max_coverage_variance=None,
+    )
+
+    data_lines = _check_basic_vcf_structure(output_path, n_variants, sample_ids)
+
+    # Check positions match.
+    vcf_positions = sorted([int(line.split("\t")[1]) for line in data_lines])
+    ds_positions = sorted(ds["variant_position"].values.tolist())
+    assert vcf_positions == ds_positions
+
+    # Check FORMAT is CN.
+    for line in data_lines:
+        fields = line.rstrip("\n").split("\t")
+        assert fields[8] == "CN"
+        assert fields[7].startswith("END=")
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_coverage_calls_to_vcf(fixture, api: CnvVcfExporter, tmp_path):
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_set = random.choice(all_sample_sets)
+    analysis = random.choice(api.coverage_calls_analysis_ids)
+    region = random.choice(api.contigs)
+
+    ds = api.cnv_coverage_calls(region=region, sample_set=sample_set, analysis=analysis)
+    n_variants = ds.sizes["variants"]
+    sample_ids = ds["sample_id"].values
+
+    output_path = str(tmp_path / "test_cnv_coverage_calls.vcf")
+    api.cnv_coverage_calls_to_vcf(
+        output_path=output_path,
+        region=region,
+        sample_set=sample_set,
+        analysis=analysis,
+    )
+
+    data_lines = _check_basic_vcf_structure(output_path, n_variants, sample_ids)
+
+    ds_ids = [
+        v.decode() if hasattr(v, "decode") else str(v) for v in ds["variant_id"].values
+    ]
+    vcf_ids = [line.split("\t")[2] for line in data_lines]
+    assert sorted(vcf_ids) == sorted(ds_ids)
+
+    for line in data_lines:
+        fields = line.rstrip("\n").split("\t")
+        assert fields[8] == "GT"
+        assert fields[6] in ("PASS", ".")
+        assert "CIPOS=" in fields[7]
+        assert "CIEND=" in fields[7]
+        for sample_val in fields[9:]:
+            assert sample_val in ("0", "1", ".")
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_discordant_read_calls_to_vcf(fixture, api: CnvVcfExporter, tmp_path):
+    contig = random.choice(api.contigs)
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = random.sample(all_sample_sets, min(2, len(all_sample_sets)))
+
+    ds = api.cnv_discordant_read_calls(contigs=contig, sample_sets=sample_sets)
+    n_variants = ds.sizes["variants"]
+    sample_ids = ds["sample_id"].values
+
+    output_path = str(tmp_path / "test_cnv_discordant.vcf")
+    api.cnv_discordant_read_calls_to_vcf(
+        output_path=output_path,
+        contigs=contig,
+        sample_sets=sample_sets,
+    )
+
+    data_lines = _check_basic_vcf_structure(output_path, n_variants, sample_ids)
+
+    for line in data_lines:
+        fields = line.rstrip("\n").split("\t")
+        assert fields[8] == "GT"
+        assert "REGION=" in fields[7]
+        assert "SBM=" in fields[7]
+        assert "EBM=" in fields[7]
+        for sample_val in fields[9:]:
+            assert sample_val in ("0", "1", ".")
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_hmm_to_vcf_overwrite(fixture, api: CnvVcfExporter, tmp_path):
+    region = api.contigs[0]
+    output_path = str(tmp_path / "test_cnv_hmm.vcf")
+
+    api.cnv_hmm_to_vcf(
+        output_path=output_path, region=region, max_coverage_variance=None
+    )
+    mtime_first = os.path.getmtime(output_path)
+
+    # Without overwrite, should return early.
+    api.cnv_hmm_to_vcf(
+        output_path=output_path, region=region, max_coverage_variance=None
+    )
+    assert os.path.getmtime(output_path) == mtime_first
+
+    # With overwrite, file should be rewritten.
+    api.cnv_hmm_to_vcf(
+        output_path=output_path,
+        region=region,
+        max_coverage_variance=None,
+        overwrite=True,
+    )
+    assert os.path.exists(output_path)
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_hmm_to_vcf_gzip(fixture, api: CnvVcfExporter, tmp_path):
+    region = api.contigs[0]
+    output_path = str(tmp_path / "test_cnv_hmm.vcf.gz")
+
+    api.cnv_hmm_to_vcf(
+        output_path=output_path, region=region, max_coverage_variance=None
+    )
+    assert os.path.exists(output_path)
+
+    with gzip.open(output_path, "rt") as f:
+        first_line = f.readline()
+    assert first_line.strip() == "##fileformat=VCFv4.3"

From 73f547f7364570f7fb9c35fa8f636f23234e72e4 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 28 Sep 2026 12:53:19 +0100
Subject: [PATCH 02/38] claude suggestions for BAM-replacement, not really
 possible for data in zarr datasets

---
 malariagen_data/anoph/igv.py         | 212 ++++++++++++++++++-
 malariagen_data/anoph/to_coverage.py | 293 +++++++++++++++++++++++++++
 malariagen_data/anopheles.py         |   2 +
 tests/anoph/conftest.py              |  38 ++--
 4 files changed, 530 insertions(+), 15 deletions(-)
 create mode 100644 malariagen_data/anoph/to_coverage.py

diff --git a/malariagen_data/anoph/igv.py b/malariagen_data/anoph/igv.py
index 59680640b..19c59ca48 100644
--- a/malariagen_data/anoph/igv.py
+++ b/malariagen_data/anoph/igv.py
@@ -1,3 +1,4 @@
+import os
 from typing import List, Optional
 
 import igv_notebook  # type: ignore
@@ -77,11 +78,97 @@ def _igv_site_filters_tracks(
             tracks.append(track_config)
         return tracks
 
+    def _igv_local_coverage_track(
+        self,
+        *,
+        region: Region,
+        sample: str,
+        visibility_window: int,
+        source: str = "cnv_hmm",
+        field: str = "NormCov",
+        output_path: Optional[str] = None,
+    ):
+        # Build a coverage track computed locally from the Zarr arrays
+        # rather than loaded from an externally-hosted file. This is not
+        # a substitute for an alignments track (there are no individual
+        # reads), but gives a fallback source of coverage information
+        # for a sample when the BAM file is not available. Two sources
+        # are supported: "cnv_hmm" gives windowed coverage genome-wide;
+        # "snp_calls" gives per-base read depth, but only at called SNP
+        # sites.
+        #
+        # N.B., this method is only usable when this class is combined
+        # (via cooperative multiple inheritance) with CoverageExporter,
+        # as is the case for the top-level Ag3/Af1 data resource classes.
+        # Methods are accessed via getattr rather than a direct import to
+        # avoid adding CoverageExporter as a base class of AnophelesIgv,
+        # which would conflict with the method resolution order of the
+        # combined data resource classes.
+        extra_kwargs: dict
+        if source == "cnv_hmm":
+            to_bedgraph = getattr(self, "cnv_hmm_coverage_to_bedgraph", None)
+            extra_kwargs = dict(field=field)
+            track_name = f"Coverage ({field}, local) - {sample}"
+            path_suffix = field
+        elif source == "snp_calls":
+            to_bedgraph = getattr(self, "snp_calls_coverage_to_bedgraph", None)
+            extra_kwargs = dict()
+            track_name = f"SNP read depth (local) - {sample}"
+            path_suffix = "AD"
+        else:
+            raise ValueError(
+                f"Unknown coverage source: {source!r}. "
+                "Valid sources are 'cnv_hmm', 'snp_calls'."
+            )
+
+        if to_bedgraph is None:
+            raise NotImplementedError(
+                "Local coverage tracks require this API object to also "
+                "provide CNV and SNP data (see CoverageExporter)."
+            )
+
+        if output_path is None:
+            if self._results_cache is None:
+                raise ValueError(
+                    "Cannot create a local coverage track without knowing "
+                    "where to write it. Either pass `coverage_track_path`, "
+                    "or configure `results_cache` when creating this API "
+                    "object."
+                )
+            safe_region = (
+                str(region).replace(":", "_").replace(",", "").replace("-", "_")
+            )
+            cache_dir = self._results_cache / "igv_coverage"
+            os.makedirs(cache_dir, exist_ok=True)
+            output_path = str(
+                cache_dir / f"{sample}_{safe_region}_{source}_{path_suffix}.bedgraph"
+            )
+
+        to_bedgraph(
+            output_path=output_path,
+            region=region,
+            sample=sample,
+            **extra_kwargs,
+        )
+
+        return {
+            "name": track_name,
+            "url": output_path,
+            "format": "bedgraph",
+            "type": "wig",
+            "visibilityWindow": visibility_window,  # bp
+            "height": 50,
+            "color": "#5e3c99",
+        }
+
     def _igv_view_alignments_tracks(
         self,
         region: Region,
         sample: str,
         visibility_window: int = 20_000,
+        local_coverage_fallback: bool = False,
+        coverage_source: str = "cnv_hmm",
+        coverage_track_path: Optional[str] = None,
     ):
         # Look up sample set for sample.
         try:
@@ -121,7 +208,10 @@ def _igv_view_alignments_tracks(
             }
         )
 
-        # Add alignments track.
+        # Add alignments track. N.B., this depends on the BAM file being
+        # hosted at `bam_url` and remaining reachable; if that URL stops
+        # working (e.g. following migration of raw data to ENA/EVA) this
+        # track will fail to load in the browser.
         tracks.append(
             {
                 "name": "Alignments",
@@ -134,6 +224,21 @@ def _igv_view_alignments_tracks(
             }
         )
 
+        # Optionally also add a coverage track computed locally from CNV
+        # HMM or SNP calls data, as a fallback source of coverage
+        # information that does not depend on the alignments BAM file
+        # remaining available.
+        if local_coverage_fallback:
+            tracks.append(
+                self._igv_local_coverage_track(
+                    region=region,
+                    sample=sample,
+                    visibility_window=visibility_window,
+                    source=coverage_source,
+                    output_path=coverage_track_path,
+                )
+            )
+
         return tracks
 
     @_check_types
@@ -183,6 +288,28 @@ def igv(
                 visible.
             """,
             init="If True, call igv_notebook.init().",
+            local_coverage_fallback="""
+                If True, also add a coverage track computed locally from
+                CNV HMM or SNP calls data. Unlike the alignments track,
+                this does not depend on the BAM file remaining available
+                at its hosted URL, so it provides a fallback source of
+                coverage information if that URL stops working. It is
+                not a substitute for the alignments track, since it
+                contains only summarised coverage values, not individual
+                reads.
+            """,
+            coverage_source="""
+                Which data to compute the local coverage track from, if
+                `local_coverage_fallback` is True. "cnv_hmm" gives
+                windowed coverage genome-wide; "snp_calls" gives
+                per-base read depth, but only at called SNP sites.
+            """,
+            coverage_track_path="""
+                Path to write the local coverage track file to, if
+                `local_coverage_fallback` is True. If not provided,
+                defaults to a location under `results_cache` (which must
+                therefore be configured).
+            """,
         ),
     )
     def view_alignments(
@@ -191,6 +318,9 @@ def view_alignments(
         sample: str,
         visibility_window: int = 20_000,
         init: bool = True,
+        local_coverage_fallback: bool = False,
+        coverage_source: str = "cnv_hmm",
+        coverage_track_path: Optional[str] = None,
     ):
         # Parse region.
         region_prepped: Region = _parse_single_region(self, region)
@@ -201,6 +331,86 @@ def view_alignments(
             region=region_prepped,
             sample=sample,
             visibility_window=visibility_window,
+            local_coverage_fallback=local_coverage_fallback,
+            coverage_source=coverage_source,
+            coverage_track_path=coverage_track_path,
+        )
+
+        # Create IGV browser.
+        self.igv(region=region_prepped, tracks=tracks, init=init)
+
+    @_check_types
+    @doc(
+        summary="""
+            Launch IGV and view sequence read coverage from the given
+            sample, computed locally from CNV HMM or SNP calls data.
+        """,
+        extended_summary="""
+            Unlike `view_alignments()`, this does not depend on an
+            externally-hosted BAM file, or on the WGS data catalog:
+            coverage is derived directly from data already available in
+            the Zarr arrays. It shows only summarised coverage depth,
+            not individual aligned reads, so it is a fallback source of
+            information about read coverage rather than a substitute for
+            viewing alignments.
+        """,
+        parameters=dict(
+            sample="Sample identifier.",
+            source="""
+                Which data to compute the coverage track from.
+                "cnv_hmm" gives windowed coverage genome-wide;
+                "snp_calls" gives per-base read depth, but only at
+                called SNP sites.
+            """,
+            field="""
+                Which coverage field to display, if `source` is
+                "cnv_hmm". "NormCov" is coverage normalised against a set
+                of reference windows; "RawCov" is unnormalised read
+                counts per window. Ignored if `source` is "snp_calls".
+            """,
+            visibility_window="""
+                Zoom level in base pairs at which SNP data will become
+                visible.
+            """,
+            init="If True, call igv_notebook.init().",
+            output_path="""
+                Path to write the local coverage track file to. If not
+                provided, defaults to a location under `results_cache`
+                (which must therefore be configured).
+            """,
+        ),
+    )
+    def view_coverage(
+        self,
+        region: base_params.region,
+        sample: str,
+        source: str = "cnv_hmm",
+        field: str = "NormCov",
+        visibility_window: int = 20_000,
+        init: bool = True,
+        output_path: Optional[str] = None,
+    ):
+        # Parse region.
+        region_prepped: Region = _parse_single_region(self, region)
+        del region
+
+        # Set up site filters tracks, consistent with view_alignments().
+        tracks = self._igv_site_filters_tracks(
+            contig=region_prepped.contig,
+            visibility_window=visibility_window,
+        )
+
+        # Add the locally-computed coverage track. N.B., this does not
+        # touch the WGS data catalog or any externally-hosted files.
+        tracks.append(
+            self._igv_local_coverage_track(
+                region=region_prepped,
+                sample=sample,
+                visibility_window=visibility_window,
+                source=source,
+                field=field,
+                output_path=output_path,
+            )
         )
 
         # Create IGV browser.
diff --git a/malariagen_data/anoph/to_coverage.py b/malariagen_data/anoph/to_coverage.py
new file mode 100644
index 000000000..dc5d1c234
--- /dev/null
+++ b/malariagen_data/anoph/to_coverage.py
@@ -0,0 +1,293 @@
+import gzip
+import os
+from typing import List, Optional
+
+import numpy as np
+from numpydoc_decorator import doc  # type: ignore
+
+from .cnv_data import AnophelesCnvData
+from .snp_data import AnophelesSnpData
+from . import base_params
+from . import cnv_params
+from . import plink_params
+
+_VALID_CNV_COVERAGE_FIELDS = {"NormCov", "RawCov"}
+
+
+def _bedgraph_opener(output_path: str):
+    compress = output_path.endswith(".gz")
+    return gzip.open if compress else open
+
+
+class CoverageExporter(
+    AnophelesCnvData,
+    AnophelesSnpData,
+):
+    """
+    Export per-sample read coverage to bedGraph, derived either from
+    CNV HMM data (windowed coverage, genome-wide) or from SNP calls
+    (per-site read depth, only at called SNP positions).
+
+    N.B., this does not reconstruct read alignments. It cannot
+    substitute for a BAM file, because the underlying Zarr arrays only
+    ever store windowed or per-site summary values (and copy number
+    calls derived from them) rather than individual reads. What this
+    class provides is a coverage-depth track that can be loaded into
+    IGV alongside (or instead of) an alignments track, as a fallback
+    for when the raw BAM file for a sample is not available, e.g.
+    because it is hosted externally and that host has become
+    unreachable.
+    """
+
+    def __init__(
+        self,
+        **kwargs,
+    ):
+        # N.B., this class is designed to work cooperatively, and
+        # so it's important that any remaining parameters are passed
+        # to the superclass constructor.
+        super().__init__(**kwargs)
+
+    def _lookup_sample_set(self, sample: str) -> str:
+        try:
+            sample_rec = self.sample_metadata().set_index("sample_id").loc[sample]
+        except KeyError as e:
+            raise ValueError(
+                f"No data found for sample {sample!r}. This sample might be "
+                "unavailable or irrelevant with respect to settings."
+            ) from e
+        return sample_rec["sample_set"]
+
+    @doc(
+        summary="""
+            Export per-sample CNV HMM coverage to bedGraph format.
+        """,
+        extended_summary="""
+            This function writes windowed read coverage for a single
+            sample, derived from CNV HMM data, to a bedGraph file. This
+            is not a substitute for a BAM file of aligned reads: it
+            contains only per-window summary coverage values (as stored
+            in the Zarr arrays), not individual reads. It is intended as
+            a fallback coverage track for IGV, for use when the aligned
+            reads (BAM) for a sample are not available, e.g. because the
+            file is hosted externally and unreachable. Coverage is
+            available genome-wide (in fixed-size windows), regardless of
+            whether any SNPs were called nearby. Data is written in
+            chunks to avoid loading the entire array into memory.
+            Supports optional gzip compression when the output path ends
+            with `.gz`.
+        """,
+        parameters=dict(
+            output_path="""
+                Path to write the bedGraph output file. Use a `.gz`
+                extension to enable gzip compression.
+            """,
+            sample="Sample identifier.",
+            field="""
+                Which coverage field to export. "NormCov" is coverage
+                normalised against a set of reference windows (comparable
+                between samples); "RawCov" is unnormalised read counts
+                per window.
+            """,
+        ),
+        returns="""
+        Path to the bedGraph output file.
+        """,
+    )
+    def cnv_hmm_coverage_to_bedgraph(
+        self,
+        output_path: str,
+        region: base_params.regions,
+        sample: str,
+        field: str = "NormCov",
+        max_coverage_variance: cnv_params.max_coverage_variance = None,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
+        chunks: base_params.chunks = base_params.native_chunks,
+        overwrite: plink_params.overwrite = False,
+    ) -> str:
+        if field not in _VALID_CNV_COVERAGE_FIELDS:
+            raise ValueError(
+                f"Unknown coverage field: {field!r}. "
+                f"Valid fields are: {sorted(_VALID_CNV_COVERAGE_FIELDS)}"
+            )
+
+        if os.path.exists(output_path) and not overwrite:
+            return output_path
+
+        # Look up which sample set this sample belongs to, so we only
+        # need to open the CNV HMM data for that one sample set.
+        sample_set = self._lookup_sample_set(sample)
+
+        ds = self.cnv_hmm(
+            region=region,
+            sample_sets=sample_set,
+            sample_query=f"sample_id == {sample!r}",
+            max_coverage_variance=max_coverage_variance,
+            inline_array=inline_array,
+            chunks=chunks,
+        )
+
+        if ds.sizes["samples"] == 0:
+            raise ValueError(
+                f"No CNV HMM data available for sample {sample!r}, this may be "
+                "because it was excluded by max_coverage_variance."
+            )
+
+        contigs = ds.attrs.get("contigs", self.contigs)
+        opener = _bedgraph_opener(output_path)
+
+        with opener(output_path, "wt") as f:
+            f.write(
+                f'track type=bedGraph name="{sample} {field}" '
+                f'description="CNV HMM {field} for {sample}"\n'
+            )
+
+            pos_data = ds["variant_position"].data
+            end_data = ds["variant_end"].data
+            contig_data = ds["variant_contig"].data
+            cov_data = ds[f"call_{field}"].data
+
+            chunk_sizes = pos_data.chunks[0]
+            offsets = np.cumsum((0,) + chunk_sizes)
+
+            with self._spinner(
+                f"Write bedGraph ({ds.sizes['variants']} coverage windows)"
+            ):
+                for ci in range(len(chunk_sizes)):
+                    start = offsets[ci]
+                    stop = offsets[ci + 1]
+                    pos_chunk = pos_data[start:stop].compute()
+                    end_chunk = end_data[start:stop].compute()
+                    contig_chunk = contig_data[start:stop].compute()
+                    # Select the single requested sample's coverage
+                    # column from the already-materialised chunk, rather
+                    # than indexing the dask/zarr array before compute,
+                    # which can trigger a less efficient (and, for
+                    # arrays with unwritten/fill-value chunks, buggy)
+                    # orthogonal-selection code path.
+                    cov_chunk = cov_data[start:stop].compute()[:, 0]
+
+                    lines: List[str] = []
+                    for j in range(pos_chunk.shape[0]):
+                        v = cov_chunk[j]
+                        if v < 0:
+                            # Masked/missing value, skip rather than
+                            # write a misleading zero.
+                            continue
+                        chrom = contigs[contig_chunk[j]]
+                        # bedGraph coordinates are 0-based, half-open;
+                        # variant_position is 1-based inclusive.
+                        bed_start = int(pos_chunk[j]) - 1
+                        bed_end = int(end_chunk[j])
+                        lines.append(f"{chrom}\t{bed_start}\t{bed_end}\t{v}\n")
+                    f.write("".join(lines))
+
+        return output_path
+
+    @doc(
+        summary="""
+            Export per-sample SNP read depth to bedGraph format.
+        """,
+        extended_summary="""
+            This function writes read depth at called SNP sites for a
+            single sample, derived from the allele depth (`AD`) field of
+            SNP calls, to a bedGraph file. Unlike
+            `cnv_hmm_coverage_to_bedgraph()`, this only has a value at
+            positions where a SNP was called, not genome-wide, but gives
+            higher-resolution, per-base depth in those locations rather
+            than a windowed summary. This is not a substitute for a BAM
+            file of aligned reads. It is intended as a fallback coverage
+            track for IGV, for use when the aligned reads (BAM) for a
+            sample are not available, e.g. because the file is hosted
+            externally and unreachable. Data is written in chunks to
+            avoid loading the entire array into memory. Supports
+            optional gzip compression when the output path ends with
+            `.gz`.
+        """,
+        parameters=dict(
+            output_path="""
+                Path to write the bedGraph output file. Use a `.gz`
+                extension to enable gzip compression.
+            """,
+            sample="Sample identifier.",
+        ),
+        returns="""
+        Path to the bedGraph output file.
+        """,
+    )
+    def snp_calls_coverage_to_bedgraph(
+        self,
+        output_path: str,
+        region: base_params.regions,
+        sample: str,
+        site_mask: Optional[base_params.site_mask] = None,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
+        chunks: base_params.chunks = base_params.native_chunks,
+        overwrite: plink_params.overwrite = False,
+    ) -> str:
+        if os.path.exists(output_path) and not overwrite:
+            return output_path
+
+        # Look up which sample set this sample belongs to, so we only
+        # need to open the SNP calls data for that one sample set.
+        sample_set = self._lookup_sample_set(sample)
+
+        ds = self.snp_calls(
+            region=region,
+            sample_sets=sample_set,
+            sample_query=f"sample_id == {sample!r}",
+            site_mask=site_mask,
+            inline_array=inline_array,
+            chunks=chunks,
+        )
+
+        if ds.sizes["samples"] == 0:
+            raise ValueError(f"No SNP calls data available for sample {sample!r}.")
+
+        contigs = ds.attrs.get("contigs", self.contigs)
+        opener = _bedgraph_opener(output_path)
+
+        with opener(output_path, "wt") as f:
+            f.write(
+                f'track type=bedGraph name="{sample} SNP depth" '
+                f'description="SNP read depth (sum of AD) for {sample}"\n'
+            )
+
+            pos_data = ds["variant_position"].data
+            contig_data = ds["variant_contig"].data
+            ad_data = ds["call_AD"].data
+
+            chunk_sizes = pos_data.chunks[0]
+            offsets = np.cumsum((0,) + chunk_sizes)
+
+            with self._spinner(f"Write bedGraph ({ds.sizes['variants']} SNP sites)"):
+                for ci in range(len(chunk_sizes)):
+                    start = offsets[ci]
+                    stop = offsets[ci + 1]
+                    pos_chunk = pos_data[start:stop].compute()
+                    contig_chunk = contig_data[start:stop].compute()
+                    # Select the single requested sample's allele depth
+                    # values from the already-materialised chunk, rather
+                    # than indexing the dask/zarr array before compute
+                    # (see the equivalent comment in
+                    # cnv_hmm_coverage_to_bedgraph).
+                    ad_chunk = ad_data[start:stop].compute()[:, 0, :]
+
+                    lines: List[str] = []
+                    for j in range(pos_chunk.shape[0]):
+                        ad_row = ad_chunk[j]
+                        if np.all(ad_row < 0):
+                            # No call for this sample at this site, skip
+                            # rather than write a misleading zero.
+                            continue
+                        depth = int(np.clip(ad_row, 0, None).sum())
+                        chrom = contigs[contig_chunk[j]]
+                        # bedGraph coordinates are 0-based, half-open;
+                        # variant_position is 1-based, and each SNP is a
+                        # single base position.
+                        bed_start = int(pos_chunk[j]) - 1
+                        bed_end = int(pos_chunk[j])
+                        lines.append(f"{chrom}\t{bed_start}\t{bed_end}\t{depth}\n")
+                    f.write("".join(lines))
+
+        return output_path
diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py
index b775dad1e..6d0cf6940 100644
--- a/malariagen_data/anopheles.py
+++ b/malariagen_data/anopheles.py
@@ -38,6 +38,7 @@
 from .anoph.ld import AnophelesLdAnalysis
 from .anoph.to_vcf import SnpVcfExporter
 from .anoph.to_vcf_cnv import CnvVcfExporter
+from .anoph.to_coverage import CoverageExporter
 from .anoph.g123 import AnophelesG123Analysis
 from .anoph.fst import AnophelesFstAnalysis
 from .anoph.h12 import AnophelesH12Analysis
@@ -95,6 +96,7 @@ class AnophelesDataResource(
     AnophelesLdAnalysis,
     SnpVcfExporter,
     CnvVcfExporter,
+    CoverageExporter,
     AnophelesIgv,
     AnophelesKaryotypeAnalysis,
     AnophelesAimData,
diff --git a/tests/anoph/conftest.py b/tests/anoph/conftest.py
index f94768ad3..d3cfd0174 100644
--- a/tests/anoph/conftest.py
+++ b/tests/anoph/conftest.py
@@ -444,20 +444,30 @@ def simulate_snp_genotypes(
         gt_chunks = (contig_n_sites // 5, n_samples // 3, None)
         calldata.create_dataset(name="GT", data=gt, chunks=gt_chunks)
 
-        # Create other arrays - these are never actually used currently
-        # so we'll create some empty arrays to avoid delaying the tests.
-        calldata.create_dataset(
-            name="GQ", shape=(contig_n_sites, n_samples), dtype="i1", fill_value=-1
-        )
-        calldata.create_dataset(
-            name="MQ", shape=(contig_n_sites, n_samples), dtype="f4", fill_value=-1
-        )
-        calldata.create_dataset(
-            name="AD",
-            shape=(contig_n_sites, n_samples, 4),
-            dtype="i2",
-            fill_value=-1,
-        )
+        # Simulate GQ, MQ and AD arrays with real (if arbitrary) values,
+        # reusing the missing call mask from GT above, rather than
+        # leaving them as constant fill-value arrays. A fill-value-only
+        # zarr array has no chunks actually written to the underlying
+        # store, and SafeStore (see malariagen_data/util.py) deliberately
+        # raises rather than silently substituting the fill value for an
+        # unwritten chunk, so code that fully computes these fields
+        # (e.g. VCF/coverage export) would otherwise hit a spurious
+        # FileNotFoundError against this fixture despite there being
+        # nothing wrong with the real data.
+        loc_missing_2d = loc_missing.reshape(contig_n_sites, n_samples)
+
+        gq = rng.integers(low=0, high=100, size=(contig_n_sites, n_samples), dtype="i1")
+        gq[loc_missing_2d] = -1
+        calldata.create_dataset(name="GQ", data=gq)
+
+        mq = rng.uniform(low=20, high=60, size=(contig_n_sites, n_samples)).astype("f4")
+        calldata.create_dataset(name="MQ", data=mq)
+
+        ad = rng.integers(
+            low=0, high=50, size=(contig_n_sites, n_samples, 4), dtype="i2"
+        )
+        ad[loc_missing_2d] = -1
+        calldata.create_dataset(name="AD", data=ad)
 
     zarr.consolidate_metadata(zarr_path)
 

From b2651bc2bcd58cf4117ee26f140d49d4b98bf40e Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 28 Sep 2026 16:21:08 +0100
Subject: [PATCH 03/38] don't allow None for sample_sets or sample_query in
 to_vcf

---
 malariagen_data/anoph/to_vcf.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 4a942fbb2..623539aba 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -51,8 +51,10 @@ def snp_calls_to_vcf(
         self,
         output_path: vcf_params.vcf_output_path,
         region: base_params.regions,
-        sample_sets: Optional[base_params.sample_sets] = None,
-        sample_query: Optional[base_params.sample_query] = None,
+        sample_sets: Optional[base_params.sample_sets],
+        sample_query: Optional[
+            base_params.sample_query
+        ],  # must be of form f"sample_id == '{sample_id}'"
         sample_query_options: Optional[base_params.sample_query_options] = None,
         sample_indices: Optional[base_params.sample_indices] = None,
         site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,

From 837260ded751e1364d7c615511d865d1ba21b361 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 28 Sep 2026 16:39:16 +0100
Subject: [PATCH 04/38] remove optional from sample_Sets and sample_query

---
 malariagen_data/anoph/to_vcf.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 623539aba..2d18c2840 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -51,10 +51,8 @@ def snp_calls_to_vcf(
         self,
         output_path: vcf_params.vcf_output_path,
         region: base_params.regions,
-        sample_sets: Optional[base_params.sample_sets],
-        sample_query: Optional[
-            base_params.sample_query
-        ],  # must be of form f"sample_id == '{sample_id}'"
+        sample_sets: base_params.sample_sets,
+        sample_query: base_params.sample_query,  # must be of form f"sample_id == '{sample_id}'"
         sample_query_options: Optional[base_params.sample_query_options] = None,
         sample_indices: Optional[base_params.sample_indices] = None,
         site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,

From 8d0d336836640da7653f702c94409968531bcfe9 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 28 Sep 2026 17:12:26 +0100
Subject: [PATCH 05/38] claude fixes for tests making sample_sets and
 sample_Wuery non-optional

---
 tests/anoph/test_vcf_exporter.py | 85 ++++++++++++++++++++++++++++++--
 1 file changed, 81 insertions(+), 4 deletions(-)

diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index 7635f536f..b78969329 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -64,16 +64,29 @@ def case_af1_sim(af1_sim_fixture, af1_sim_api):
     return af1_sim_fixture, af1_sim_api
 
 
+def _pick_single_sample_query(api: SnpVcfExporter, sample_sets):
+    """Pick one sample from the given sample sets and build a
+    `sample_query` that scopes a VCF export down to just that sample,
+    which is the only supported usage of `snp_calls_to_vcf()` (it is
+    used to generate a single-sample VCF for IGV)."""
+    df_samples = api.sample_metadata(sample_sets=sample_sets)
+    sample_id = str(df_samples["sample_id"].iloc[0])
+    sample_query = f"sample_id == '{sample_id}'"
+    return sample_id, sample_query
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter(fixture, api: SnpVcfExporter, tmp_path):
     region = random.choice(api.contigs)
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = random.sample(all_sample_sets, min(2, len(all_sample_sets)))
     site_mask = random.choice((None,) + api.site_mask_ids)
+    sample_id, sample_query = _pick_single_sample_query(api, sample_sets)
 
     data_params = dict(
         region=region,
         sample_sets=sample_sets,
+        sample_query=sample_query,
         site_mask=site_mask,
     )
 
@@ -81,6 +94,12 @@ def test_vcf_exporter(fixture, api: SnpVcfExporter, tmp_path):
     n_variants = ds.sizes["variants"]
     sample_ids = ds["sample_id"].values
 
+    # snp_calls_to_vcf() only supports exporting a single sample at a
+    # time (its only current use case is generating a per-sample VCF
+    # for IGV), so sample_query must narrow the dataset down to one
+    # sample.
+    assert list(sample_ids) == [sample_id]
+
     output_path = str(tmp_path / "test.vcf")
     api.snp_calls_to_vcf(output_path=output_path, **data_params)
 
@@ -119,29 +138,77 @@ def test_vcf_exporter(fixture, api: SnpVcfExporter, tmp_path):
         ), f"byte-string repr in REF/ALT: REF={ref!r} ALT={alt!r}"
 
 
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_requires_sample_sets_and_query(
+    fixture, api: SnpVcfExporter, tmp_path
+):
+    # sample_sets and sample_query are required: a VCF without an
+    # explicit cohort/sample basis for the calls it contains is not
+    # meaningful.
+    region = api.contigs[0]
+    output_path = str(tmp_path / "test_missing_args.vcf")
+
+    with pytest.raises(TypeError):
+        api.snp_calls_to_vcf(output_path=output_path, region=region)  # type: ignore[call-arg]
+
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    with pytest.raises(TypeError):
+        api.snp_calls_to_vcf(  # type: ignore[call-arg]
+            output_path=output_path, region=region, sample_sets=sample_sets
+        )
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_overwrite(fixture, api: SnpVcfExporter, tmp_path):
     region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
     output_path = str(tmp_path / "test.vcf")
 
-    api.snp_calls_to_vcf(output_path=output_path, region=region)
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+    )
     mtime_first = os.path.getmtime(output_path)
 
     # Without overwrite, should return early.
-    api.snp_calls_to_vcf(output_path=output_path, region=region)
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+    )
     assert os.path.getmtime(output_path) == mtime_first
 
     # With overwrite, file should be rewritten.
-    api.snp_calls_to_vcf(output_path=output_path, region=region, overwrite=True)
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+        overwrite=True,
+    )
     assert os.path.exists(output_path)
 
 
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_gzip(fixture, api: SnpVcfExporter, tmp_path):
     region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
     output_path = str(tmp_path / "test.vcf.gz")
 
-    api.snp_calls_to_vcf(output_path=output_path, region=region)
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+    )
     assert os.path.exists(output_path)
 
     # Verify it's valid gzip.
@@ -153,12 +220,17 @@ def test_vcf_exporter_gzip(fixture, api: SnpVcfExporter, tmp_path):
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_fields(fixture, api: SnpVcfExporter, tmp_path):
     region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
 
     # Test with additional FORMAT fields.
     output_path = str(tmp_path / "test_fields.vcf")
     api.snp_calls_to_vcf(
         output_path=output_path,
         region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
         fields=("GT", "GQ"),
     )
 
@@ -186,11 +258,16 @@ def test_vcf_exporter_fields(fixture, api: SnpVcfExporter, tmp_path):
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_fields_gt_required(fixture, api: SnpVcfExporter, tmp_path):
     region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
     output_path = str(tmp_path / "test_no_gt.vcf")
 
     with pytest.raises(ValueError, match="GT must be included"):
         api.snp_calls_to_vcf(
             output_path=output_path,
             region=region,
+            sample_sets=sample_sets,
+            sample_query=sample_query,
             fields=("GQ",),
         )

From a302a13be73513301bddaec77c72dad50ef6c515 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 28 Sep 2026 17:20:53 +0100
Subject: [PATCH 06/38] updated doctring re sample_sets and sample_query

---
 malariagen_data/anoph/to_vcf.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 2d18c2840..12a4cc79b 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -42,6 +42,15 @@ def __init__(
             in chunks to avoid loading the entire genotype matrix into
             memory. Supports optional gzip compression when the output
             path ends with `.gz`.
+
+            Sample query must be in a format that can be used against the
+            sample_metadata() dataframe. Sample set must be specified and
+            the query should return at least one sample for that sample set
+            As the current use case for this funcitonality, it is strongly
+            recommended that sample_query is in the format
+            f"sample_id == '\{sample_id\}'" - thus specifying a single
+            sample.
+
         """,
         returns="""
         Path to the VCF output file.
@@ -52,7 +61,7 @@ def snp_calls_to_vcf(
         output_path: vcf_params.vcf_output_path,
         region: base_params.regions,
         sample_sets: base_params.sample_sets,
-        sample_query: base_params.sample_query,  # must be of form f"sample_id == '{sample_id}'"
+        sample_query: base_params.sample_query,
         sample_query_options: Optional[base_params.sample_query_options] = None,
         sample_indices: Optional[base_params.sample_indices] = None,
         site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,

From bc181eab13d5f64bb42cac2e2af3673b8f246ddd Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 28 Sep 2026 17:26:36 +0100
Subject: [PATCH 07/38] claude draft input validation

---
 malariagen_data/anoph/to_vcf.py  | 62 +++++++++++++++++++++++++
 tests/anoph/test_vcf_exporter.py | 80 ++++++++++++++++++++++++++++++++
 2 files changed, 142 insertions(+)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 12a4cc79b..74f3ae91b 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -1,5 +1,6 @@
 import gzip
 import os
+import re
 from datetime import date
 from typing import Optional
 
@@ -20,6 +21,47 @@
     "MQ": '##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Mapping Quality">',
 }
 
+# snp_calls_to_vcf() only supports exporting a single sample at a time
+# (its current use case is generating a per-sample VCF for IGV), so
+# sample_query must be of the form "sample_id == '<sample_id>'".
+_SINGLE_SAMPLE_QUERY_PATTERN = re.compile(
+    r"""^\s*sample_id\s*==\s*(['"])[^'"]+\1\s*$"""
+)
+
+
+def _validate_single_sample_selection(
+    *,
+    sample_sets: base_params.sample_sets,
+    sample_query: base_params.sample_query,
+) -> None:
+    """
+    Validate that `sample_sets` and `sample_query` are provided and
+    together specify a single sample, which is the only usage that
+    `snp_calls_to_vcf()` currently supports. A VCF file is only
+    meaningful with respect to an explicit sample basis for its calls,
+    so both parameters are required; and because the only current use
+    case is generating a per-sample VCF for IGV, `sample_query` is
+    required to select exactly one sample.
+    """
+    if not sample_sets:
+        raise ValueError(
+            "sample_sets must be provided and non-empty: a VCF must be "
+            "generated against an explicit set of samples."
+        )
+    if not sample_query or not sample_query.strip():
+        raise ValueError(
+            "sample_query must be provided and non-empty, and must "
+            "select a single sample (see snp_calls_to_vcf() docs)."
+        )
+    if not _SINGLE_SAMPLE_QUERY_PATTERN.match(sample_query):
+        raise ValueError(
+            f"sample_query {sample_query!r} does not select a single "
+            "sample. snp_calls_to_vcf() only supports exporting a "
+            "single sample at a time (its current use case is "
+            "generating a per-sample VCF for IGV); sample_query must be "
+            "of the form \"sample_id == '<sample_id>'\"."
+        )
+
 
 class SnpVcfExporter(
     AnophelesSnpData,
@@ -73,6 +115,9 @@ def snp_calls_to_vcf(
         base_params._validate_sample_selection_params(
             sample_query=sample_query, sample_indices=sample_indices
         )
+        _validate_single_sample_selection(
+            sample_sets=sample_sets, sample_query=sample_query
+        )
 
         # Validate fields parameter.
         fields = tuple(fields)
@@ -99,6 +144,23 @@ def snp_calls_to_vcf(
             chunks=chunks,
         )
 
+        # sample_query is validated above to be of the single-sample
+        # form "sample_id == '<sample_id>'", but that only checks the
+        # shape of the query string. Confirm it actually resolved to
+        # exactly one sample within the given sample_sets — zero would
+        # mean the sample_id wasn't found (e.g. a typo, or the sample is
+        # not part of the given sample_sets); more than one should not
+        # be possible with an equality query on a unique identifier, but
+        # is checked defensively rather than silently written out as a
+        # multi-sample VCF.
+        n_samples_selected = ds.sizes["samples"]
+        if n_samples_selected != 1:
+            raise ValueError(
+                f"sample_query {sample_query!r} selected "
+                f"{n_samples_selected} samples from sample_sets "
+                f"{sample_sets!r}, expected exactly 1."
+            )
+
         sample_ids = ds["sample_id"].values
         contigs = ds.attrs.get("contigs", self.contigs)
         compress = output_path.endswith(".gz")
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index b78969329..7ea33a846 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -159,6 +159,86 @@ def test_vcf_exporter_requires_sample_sets_and_query(
         )
 
 
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_empty_sample_sets(fixture, api: SnpVcfExporter, tmp_path):
+    region = api.contigs[0]
+    output_path = str(tmp_path / "test_empty_sample_sets.vcf")
+
+    with pytest.raises(ValueError, match="sample_sets must be provided"):
+        api.snp_calls_to_vcf(
+            output_path=output_path,
+            region=region,
+            sample_sets=[],
+            sample_query="sample_id == 'anything'",
+        )
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_empty_sample_query(fixture, api: SnpVcfExporter, tmp_path):
+    region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    output_path = str(tmp_path / "test_empty_sample_query.vcf")
+
+    with pytest.raises(ValueError, match="sample_query must be provided"):
+        api.snp_calls_to_vcf(
+            output_path=output_path,
+            region=region,
+            sample_sets=sample_sets,
+            sample_query="",
+        )
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_multi_sample_query_rejected(
+    fixture, api: SnpVcfExporter, tmp_path
+):
+    # sample_query must select a single sample via equality on
+    # sample_id; a query that could match more than one sample (even a
+    # syntactically simple one like a country filter) is rejected
+    # up front, before touching any data.
+    region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    output_path = str(tmp_path / "test_multi_sample_query.vcf")
+
+    for bad_query in [
+        "country == 'Uganda'",
+        "sample_id in ['AB0085-C', 'AB0086-C']",
+        "sample_id != 'AB0085-C'",
+    ]:
+        with pytest.raises(ValueError, match="does not select a single sample"):
+            api.snp_calls_to_vcf(
+                output_path=output_path,
+                region=region,
+                sample_sets=sample_sets,
+                sample_query=bad_query,
+            )
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_sample_query_matches_zero_samples(
+    fixture, api: SnpVcfExporter, tmp_path
+):
+    # A query in the right shape but for a sample_id that isn't part of
+    # the given sample_sets should still be rejected, not silently
+    # produce a zero-sample VCF. In practice snp_calls() itself already
+    # raises for a query matching no samples, before our own post-hoc
+    # sample-count check ever runs; either way this must not succeed.
+    region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    output_path = str(tmp_path / "test_zero_sample_query.vcf")
+
+    with pytest.raises(ValueError):
+        api.snp_calls_to_vcf(
+            output_path=output_path,
+            region=region,
+            sample_sets=sample_sets,
+            sample_query="sample_id == 'not_a_real_sample_id'",
+        )
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_overwrite(fixture, api: SnpVcfExporter, tmp_path):
     region = api.contigs[0]

From 317c2b0326c339eec25f74c1c4ad8a9a11412219 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 28 Sep 2026 17:29:53 +0100
Subject: [PATCH 08/38] updated docstring to specify only one sample can be
 used- can revisit later if usage expands beyond IGV

---
 malariagen_data/anoph/to_vcf.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 74f3ae91b..e1c80a2a2 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -85,14 +85,14 @@ def __init__(
             memory. Supports optional gzip compression when the output
             path ends with `.gz`.
 
-            Sample query must be in a format that can be used against the
-            sample_metadata() dataframe. Sample set must be specified and
-            the query should return at least one sample for that sample set
-            As the current use case for this funcitonality, it is strongly
-            recommended that sample_query is in the format
-            f"sample_id == '\{sample_id\}'" - thus specifying a single
-            sample.
-
+            `sample_sets` and `sample_query` are both required: a VCF is
+            only meaningful with respect to an explicit sample basis for
+            its calls. The current use case for this functionality is
+            generating a single-sample VCF for IGV, so `sample_query` is
+            required to select exactly one sample, and must be of the
+            form `"sample_id == '<sample_id>'"`. Any other query (e.g.
+            selecting samples by cohort, or more than one sample_id) is
+            rejected.
         """,
         returns="""
         Path to the VCF output file.

From cf3e6b6e8fc0cc6da9c4e66531df51ba2b705c47 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 29 Sep 2026 09:49:19 +0100
Subject: [PATCH 09/38] claude suggested changes to batch call rather than
 separate for each chunk

---
 malariagen_data/anoph/to_vcf.py | 65 ++++++++++++++++++++++++---------
 1 file changed, 48 insertions(+), 17 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index e1c80a2a2..98d3580d9 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -4,6 +4,7 @@
 from datetime import date
 from typing import Optional
 
+import dask
 import numpy as np
 from numpydoc_decorator import doc  # type: ignore
 
@@ -223,33 +224,63 @@ def snp_calls_to_vcf(
             chunk_sizes = gt_data.chunks[0]
             offsets = np.cumsum((0,) + chunk_sizes)
 
+            # Which optional fields were requested, so we know what to
+            # fetch (and where to put the results) for each chunk below.
+            optional_names = []
+            optional_arrays = []
+            if gq_data is not None:
+                optional_names.append("GQ")
+                optional_arrays.append(gq_data)
+            if ad_data is not None:
+                optional_names.append("AD")
+                optional_arrays.append(ad_data)
+            if mq_data is not None:
+                optional_names.append("MQ")
+                optional_arrays.append(mq_data)
+
             # Write records in chunks.
             with self._spinner(f"Write VCF ({ds.sizes['variants']} variants)"):
                 for ci in range(len(chunk_sizes)):
                     start = offsets[ci]
                     stop = offsets[ci + 1]
-                    gt_chunk = gt_data[start:stop].compute()
-                    pos_chunk = pos_data[start:stop].compute()
-                    contig_chunk = contig_data[start:stop].compute()
-                    allele_chunk = allele_data[start:stop].compute()
 
-                    # Compute optional field chunks, handling missing data.
+                    # Fetch the required arrays for this chunk in a
+                    # single batched call, rather than one .compute()
+                    # call per array. Each separate .compute() call is
+                    # its own blocking round trip to the underlying
+                    # store (e.g. GCS); batching lets dask fetch all of
+                    # them concurrently instead of one at a time, which
+                    # matters a lot for a remote store and can be the
+                    # difference between a fast export and one that
+                    # takes hours longer than it needs to.
+                    gt_chunk, pos_chunk, contig_chunk, allele_chunk = dask.compute(
+                        gt_data[start:stop],
+                        pos_data[start:stop],
+                        contig_data[start:stop],
+                        allele_data[start:stop],
+                    )
+
+                    # Fetch any requested optional fields for this chunk,
+                    # again as a single batched call. If any of them
+                    # fail to load, fall back to "." for all requested
+                    # optional fields in this chunk (rather than only
+                    # the one that failed) — these arrays live in the
+                    # same region of the same store, so a failure
+                    # affecting one is likely to affect the others too,
+                    # and batching the fallback is the price of batching
+                    # the fetch.
                     gq_chunk = None
                     ad_chunk = None
                     mq_chunk = None
-                    if gq_data is not None:
-                        try:
-                            gq_chunk = gq_data[start:stop].compute()
-                        except (FileNotFoundError, KeyError):
-                            pass
-                    if ad_data is not None:
-                        try:
-                            ad_chunk = ad_data[start:stop].compute()
-                        except (FileNotFoundError, KeyError):
-                            pass
-                    if mq_data is not None:
+                    if optional_arrays:
                         try:
-                            mq_chunk = mq_data[start:stop].compute()
+                            computed = dask.compute(
+                                *(arr[start:stop] for arr in optional_arrays)
+                            )
+                            optional_chunks = dict(zip(optional_names, computed))
+                            gq_chunk = optional_chunks.get("GQ")
+                            ad_chunk = optional_chunks.get("AD")
+                            mq_chunk = optional_chunks.get("MQ")
                         except (FileNotFoundError, KeyError):
                             pass
 

From 50d620e2bf1d04852227b5aa199f69dc446e71d9 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 29 Sep 2026 10:50:58 +0100
Subject: [PATCH 10/38] removed the numpy array that is edited through a loop-
 i.e. not a vectorised implementation, noticed in diff igv.ipynb had changed
 due to me running it previously, restored to original state and added
 nbstripout to pre-commit hooks to prevent this happening in future

---
 .pre-commit-config.yaml         |   12 +
 malariagen_data/anoph/to_vcf.py |   44 +-
 notebooks/igv.ipynb             | 3764 +------------------------------
 3 files changed, 65 insertions(+), 3755 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 34d8c53c1..cb9d17692 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -16,3 +16,15 @@ repos:
           - "--fix"
       # Run the formatter.
       - id: ruff-format
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.9.1
+    hooks:
+      # Strip outputs, execution counts and volatile metadata (kernel
+      # display name, language version — these change depending on
+      # which local environment a notebook was last run under, not on
+      # any real edit) from notebooks before they're committed, so
+      # `git diff` only shows real cell-source changes.
+      - id: nbstripout
+        args:
+          - "--extra-keys"
+          - "metadata.kernelspec.display_name metadata.language_info.version"
diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 98d3580d9..132386520 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -145,15 +145,10 @@ def snp_calls_to_vcf(
             chunks=chunks,
         )
 
-        # sample_query is validated above to be of the single-sample
-        # form "sample_id == '<sample_id>'", but that only checks the
-        # shape of the query string. Confirm it actually resolved to
-        # exactly one sample within the given sample_sets — zero would
-        # mean the sample_id wasn't found (e.g. a typo, or the sample is
-        # not part of the given sample_sets); more than one should not
-        # be possible with an equality query on a unique identifier, but
-        # is checked defensively rather than silently written out as a
-        # multi-sample VCF.
+        # Confirm inputs actually resolved to exactly
+        # one sample within the given sample_sets
+        # checked defensively rather than silently written
+        # out as a multi-sample VCF.
         n_samples_selected = ds.sizes["samples"]
         if n_samples_selected != 1:
             raise ValueError(
@@ -249,10 +244,7 @@ def snp_calls_to_vcf(
                     # call per array. Each separate .compute() call is
                     # its own blocking round trip to the underlying
                     # store (e.g. GCS); batching lets dask fetch all of
-                    # them concurrently instead of one at a time, which
-                    # matters a lot for a remote store and can be the
-                    # difference between a fast export and one that
-                    # takes hours longer than it needs to.
+                    # them concurrently instead of one at a time
                     gt_chunk, pos_chunk, contig_chunk, allele_chunk = dask.compute(
                         gt_data[start:stop],
                         pos_data[start:stop],
@@ -260,15 +252,12 @@ def snp_calls_to_vcf(
                         allele_data[start:stop],
                     )
 
-                    # Fetch any requested optional fields for this chunk,
-                    # again as a single batched call. If any of them
-                    # fail to load, fall back to "." for all requested
-                    # optional fields in this chunk (rather than only
-                    # the one that failed) — these arrays live in the
-                    # same region of the same store, so a failure
+                    # Fetch requested optional fields for this chunk
+                    # as a single batched call. If any of them fail
+                    # to load, fall back to "." for all requested
+                    # optional fields in this chunk — these arrays live
+                    # in the same region of the same store, so a failure
                     # affecting one is likely to affect the others too,
-                    # and batching the fallback is the price of batching
-                    # the fetch.
                     gq_chunk = None
                     ad_chunk = None
                     mq_chunk = None
@@ -336,7 +325,16 @@ def snp_calls_to_vcf(
                             f"{chrom}\t{pos}\t.\t{ref}\t{alt}\t.\t.\t.\t{format_str}\t"
                         )
 
-                        sample_fields = np.empty(n_samples, dtype=object)
+                        # N.B., a plain Python list here, not a NumPy
+                        # array: this loop builds a handful of short
+                        # strings per variant via ordinary Python string
+                        # concatenation, not a numeric/vectorized
+                        # operation, so a `np.empty(..., dtype=object)`
+                        # array bought nothing but the overhead of a
+                        # NumPy allocation on every single variant row
+                        # (up to ~150 million times for a whole-genome
+                        # export).
+                        sample_fields = []
 
                         # Use pre-formatted GT strings and add other fields
                         for k in range(n_samples):
@@ -367,7 +365,7 @@ def snp_calls_to_vcf(
                                     parts.append("." if v < 0 else str(v))
                                 else:
                                     parts.append(".")
-                            sample_fields[k] = ":".join(parts)
+                            sample_fields.append(":".join(parts))
 
                         # Build and buffer the line
                         line = fixed_cols + "\t".join(sample_fields) + "\n"
diff --git a/notebooks/igv.ipynb b/notebooks/igv.ipynb
index dea51f0bb..104f217f0 100644
--- a/notebooks/igv.ipynb
+++ b/notebooks/igv.ipynb
@@ -2,8 +2,8 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "id": "07b16c04",
+   "execution_count": null,
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -12,420 +12,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
-   "id": "1c7ecf7a",
+   "execution_count": null,
+   "id": "1",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/javascript": [
-       "'use strict';\n",
-       "(function(root) {\n",
-       "  function now() {\n",
-       "    return new Date();\n",
-       "  }\n",
-       "\n",
-       "  const force = true;\n",
-       "\n",
-       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
-       "    root._bokeh_onload_callbacks = [];\n",
-       "    root._bokeh_is_loading = undefined;\n",
-       "  }\n",
-       "\n",
-       "const JS_MIME_TYPE = 'application/javascript';\n",
-       "  const HTML_MIME_TYPE = 'text/html';\n",
-       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
-       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
-       "\n",
-       "  /**\n",
-       "   * Render data to the DOM node\n",
-       "   */\n",
-       "  function render(props, node) {\n",
-       "    const script = document.createElement(\"script\");\n",
-       "    node.appendChild(script);\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when an output is cleared or removed\n",
-       "   */\n",
-       "  function handleClearOutput(event, handle) {\n",
-       "    function drop(id) {\n",
-       "      const view = Bokeh.index.get_by_id(id)\n",
-       "      if (view != null) {\n",
-       "        view.model.document.clear()\n",
-       "        Bokeh.index.delete(view)\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    const cell = handle.cell;\n",
-       "\n",
-       "    const id = cell.output_area._bokeh_element_id;\n",
-       "    const server_id = cell.output_area._bokeh_server_id;\n",
-       "\n",
-       "    // Clean up Bokeh references\n",
-       "    if (id != null) {\n",
-       "      drop(id)\n",
-       "    }\n",
-       "\n",
-       "    if (server_id !== undefined) {\n",
-       "      // Clean up Bokeh references\n",
-       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
-       "      cell.notebook.kernel.execute(cmd_clean, {\n",
-       "        iopub: {\n",
-       "          output: function(msg) {\n",
-       "            const id = msg.content.text.trim()\n",
-       "            drop(id)\n",
-       "          }\n",
-       "        }\n",
-       "      });\n",
-       "      // Destroy server and session\n",
-       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
-       "      cell.notebook.kernel.execute(cmd_destroy);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when a new output is added\n",
-       "   */\n",
-       "  function handleAddOutput(event, handle) {\n",
-       "    const output_area = handle.output_area;\n",
-       "    const output = handle.output;\n",
-       "\n",
-       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
-       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
-       "      return\n",
-       "    }\n",
-       "\n",
-       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
-       "\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
-       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
-       "      // store reference to embed id on output_area\n",
-       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
-       "    }\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
-       "      const bk_div = document.createElement(\"div\");\n",
-       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
-       "      const script_attrs = bk_div.children[0].attributes;\n",
-       "      for (let i = 0; i < script_attrs.length; i++) {\n",
-       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
-       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
-       "      }\n",
-       "      // store reference to server id on output_area\n",
-       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function register_renderer(events, OutputArea) {\n",
-       "\n",
-       "    function append_mime(data, metadata, element) {\n",
-       "      // create a DOM node to render to\n",
-       "      const toinsert = this.create_output_subarea(\n",
-       "        metadata,\n",
-       "        CLASS_NAME,\n",
-       "        EXEC_MIME_TYPE\n",
-       "      );\n",
-       "      this.keyboard_manager.register_events(toinsert);\n",
-       "      // Render to node\n",
-       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
-       "      render(props, toinsert[toinsert.length - 1]);\n",
-       "      element.append(toinsert);\n",
-       "      return toinsert\n",
-       "    }\n",
-       "\n",
-       "    /* Handle when an output is cleared or removed */\n",
-       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
-       "    events.on('delete.Cell', handleClearOutput);\n",
-       "\n",
-       "    /* Handle when a new output is added */\n",
-       "    events.on('output_added.OutputArea', handleAddOutput);\n",
-       "\n",
-       "    /**\n",
-       "     * Register the mime type and append_mime function with output_area\n",
-       "     */\n",
-       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
-       "      /* Is output safe? */\n",
-       "      safe: true,\n",
-       "      /* Index of renderer in `output_area.display_order` */\n",
-       "      index: 0\n",
-       "    });\n",
-       "  }\n",
-       "\n",
-       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
-       "  if (root.Jupyter !== undefined) {\n",
-       "    const events = require('base/js/events');\n",
-       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
-       "\n",
-       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
-       "      register_renderer(events, OutputArea);\n",
-       "    }\n",
-       "  }\n",
-       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
-       "    root._bokeh_timeout = Date.now() + 5000;\n",
-       "    root._bokeh_failed_load = false;\n",
-       "  }\n",
-       "\n",
-       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
-       "     \"<div style='background-color: #fdd'>\\n\"+\n",
-       "     \"<p>\\n\"+\n",
-       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
-       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
-       "     \"</p>\\n\"+\n",
-       "     \"<ul>\\n\"+\n",
-       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
-       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
-       "     \"</ul>\\n\"+\n",
-       "     \"<code>\\n\"+\n",
-       "     \"from bokeh.resources import INLINE\\n\"+\n",
-       "     \"output_notebook(resources=INLINE)\\n\"+\n",
-       "     \"</code>\\n\"+\n",
-       "     \"</div>\"}};\n",
-       "\n",
-       "  function display_loaded(error = null) {\n",
-       "    const el = document.getElementById(null);\n",
-       "    if (el != null) {\n",
-       "      const html = (() => {\n",
-       "        if (typeof root.Bokeh === \"undefined\") {\n",
-       "          if (error == null) {\n",
-       "            return \"BokehJS is loading ...\";\n",
-       "          } else {\n",
-       "            return \"BokehJS failed to load.\";\n",
-       "          }\n",
-       "        } else {\n",
-       "          const prefix = `BokehJS ${root.Bokeh.version}`;\n",
-       "          if (error == null) {\n",
-       "            return `${prefix} successfully loaded.`;\n",
-       "          } else {\n",
-       "            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n",
-       "          }\n",
-       "        }\n",
-       "      })();\n",
-       "      el.innerHTML = html;\n",
-       "\n",
-       "      if (error != null) {\n",
-       "        const wrapper = document.createElement(\"div\");\n",
-       "        wrapper.style.overflow = \"auto\";\n",
-       "        wrapper.style.height = \"5em\";\n",
-       "        wrapper.style.resize = \"vertical\";\n",
-       "        const content = document.createElement(\"div\");\n",
-       "        content.style.fontFamily = \"monospace\";\n",
-       "        content.style.whiteSpace = \"pre-wrap\";\n",
-       "        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n",
-       "        content.textContent = error.stack ?? error.toString();\n",
-       "        wrapper.append(content);\n",
-       "        el.append(wrapper);\n",
-       "      }\n",
-       "    } else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(() => display_loaded(error), 100);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function run_callbacks() {\n",
-       "    try {\n",
-       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
-       "        if (callback != null)\n",
-       "          callback();\n",
-       "      });\n",
-       "    } finally {\n",
-       "      delete root._bokeh_onload_callbacks\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
-       "  }\n",
-       "\n",
-       "  function load_libs(css_urls, js_urls, callback) {\n",
-       "    if (css_urls == null) css_urls = [];\n",
-       "    if (js_urls == null) js_urls = [];\n",
-       "\n",
-       "    root._bokeh_onload_callbacks.push(callback);\n",
-       "    if (root._bokeh_is_loading > 0) {\n",
-       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
-       "      return null;\n",
-       "    }\n",
-       "    if (js_urls == null || js_urls.length === 0) {\n",
-       "      run_callbacks();\n",
-       "      return null;\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
-       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
-       "\n",
-       "    function on_load() {\n",
-       "      root._bokeh_is_loading--;\n",
-       "      if (root._bokeh_is_loading === 0) {\n",
-       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
-       "        run_callbacks()\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    function on_error(url) {\n",
-       "      console.error(\"failed to load \" + url);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < css_urls.length; i++) {\n",
-       "      const url = css_urls[i];\n",
-       "      const element = document.createElement(\"link\");\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.rel = \"stylesheet\";\n",
-       "      element.type = \"text/css\";\n",
-       "      element.href = url;\n",
-       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
-       "      document.body.appendChild(element);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < js_urls.length; i++) {\n",
-       "      const url = js_urls[i];\n",
-       "      const element = document.createElement('script');\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.async = false;\n",
-       "      element.src = url;\n",
-       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
-       "      document.head.appendChild(element);\n",
-       "    }\n",
-       "  };\n",
-       "\n",
-       "  function inject_raw_css(css) {\n",
-       "    const element = document.createElement(\"style\");\n",
-       "    element.appendChild(document.createTextNode(css));\n",
-       "    document.body.appendChild(element);\n",
-       "  }\n",
-       "\n",
-       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.1.min.js\"];\n",
-       "  const css_urls = [];\n",
-       "\n",
-       "  const inline_js = [    function(Bokeh) {\n",
-       "      Bokeh.set_log_level(\"info\");\n",
-       "    },\n",
-       "function(Bokeh) {\n",
-       "    }\n",
-       "  ];\n",
-       "\n",
-       "  function run_inline_js() {\n",
-       "    if (root.Bokeh !== undefined || force === true) {\n",
-       "      try {\n",
-       "            for (let i = 0; i < inline_js.length; i++) {\n",
-       "      inline_js[i].call(root, root.Bokeh);\n",
-       "    }\n",
-       "\n",
-       "      } catch (error) {throw error;\n",
-       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(run_inline_js, 100);\n",
-       "    } else if (!root._bokeh_failed_load) {\n",
-       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
-       "      root._bokeh_failed_load = true;\n",
-       "    } else if (force !== true) {\n",
-       "      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
-       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  if (root._bokeh_is_loading === 0) {\n",
-       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
-       "    run_inline_js();\n",
-       "  } else {\n",
-       "    load_libs(css_urls, js_urls, function() {\n",
-       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
-       "      run_inline_js();\n",
-       "    });\n",
-       "  }\n",
-       "}(window));"
-      ],
-      "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded(error = null) {\n    const el = document.getElementById(null);\n    if (el != null) {\n      const html = (() => {\n        if (typeof root.Bokeh === \"undefined\") {\n          if (error == null) {\n            return \"BokehJS is loading ...\";\n          } else {\n            return \"BokehJS failed to load.\";\n          }\n        } else {\n          const prefix = `BokehJS ${root.Bokeh.version}`;\n          if (error == null) {\n            return `${prefix} successfully loaded.`;\n          } else {\n            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n          }\n        }\n      })();\n      el.innerHTML = html;\n\n      if (error != null) {\n        const wrapper = document.createElement(\"div\");\n        wrapper.style.overflow = \"auto\";\n        wrapper.style.height = \"5em\";\n        wrapper.style.resize = \"vertical\";\n        const content = document.createElement(\"div\");\n        content.style.fontFamily = \"monospace\";\n        content.style.whiteSpace = \"pre-wrap\";\n        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n        content.textContent = error.stack ?? error.toString();\n        wrapper.append(content);\n        el.append(wrapper);\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(() => display_loaded(error), 100);\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.1.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n      try {\n            for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n\n      } catch (error) {throw error;\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/html": [
-       "\n",
-       "            <table class=\"malariagen-ag3\">\n",
-       "                <thead>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\" colspan=\"2\">MalariaGEN Ag3 API client</th>\n",
-       "                    </tr>\n",
-       "                    <tr><td colspan=\"2\" style=\"text-align: left\">\n",
-       "                        Please note that data are subject to terms of use,\n",
-       "                        for more information see <a href=\"https://www.malariagen.net/data\">\n",
-       "                        the MalariaGEN website</a> or contact support@malariagen.net.\n",
-       "                        See also the <a href=\"https://malariagen.github.io/malariagen-data-python/v0.0.0/Ag3.html\">Ag3 API docs</a>.\n",
-       "                    </td></tr>\n",
-       "                </thead>\n",
-       "                <tbody>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Storage URL\n",
-       "                        </th>\n",
-       "                        <td>gs://vo_agam_release_master_us_central1/</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Data releases available\n",
-       "                        </th>\n",
-       "                        <td>3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 3.10, 3.11, 3.12, 3.13, 3.14</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Results cache\n",
-       "                        </th>\n",
-       "                        <td>None</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Cohorts analysis\n",
-       "                        </th>\n",
-       "                        <td>20250131</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            AIM analysis\n",
-       "                        </th>\n",
-       "                        <td>20220528</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Site filters analysis\n",
-       "                        </th>\n",
-       "                        <td>dt_20200416</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Software version\n",
-       "                        </th>\n",
-       "                        <td>malariagen_data 0.0.0</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Client location\n",
-       "                        </th>\n",
-       "                        <td>England, United Kingdom</td>\n",
-       "                    </tr>\n",
-       "                </tbody>\n",
-       "            </table>\n",
-       "        "
-      ],
-      "text/plain": [
-       "<MalariaGEN Ag3 API client>\n",
-       "Storage URL             : gs://vo_agam_release_master_us_central1/\n",
-       "Data releases available : 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 3.10, 3.11, 3.12, 3.13, 3.14\n",
-       "Results cache           : None\n",
-       "Cohorts analysis        : 20250131\n",
-       "AIM analysis            : 20220528\n",
-       "Site filters analysis   : dt_20200416\n",
-       "Software version        : malariagen_data 0.0.0\n",
-       "Client location         : England, United Kingdom\n",
-       "---\n",
-       "Please note that data are subject to terms of use,\n",
-       "for more information see https://www.malariagen.net/data\n",
-       "or contact support@malariagen.net. For API documentation see \n",
-       "https://malariagen.github.io/malariagen-data-python/v0.0.0/Ag3.html"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "ag3 = malariagen_data.Ag3()\n",
     "ag3"
@@ -433,1459 +23,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "id": "921aa6e4",
+   "execution_count": null,
+   "id": "2",
    "metadata": {},
-   "outputs": [
-    {
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r;for(hi(e,t-257,5),hi(e,i-1,5),hi(e,n-4,4),r=0;r<n;r++)hi(e,e.bl_tree[2*Yt[r]+1],3);yi(e,e.dyn_ltree,t-1),yi(e,e.dyn_dtree,i-1)})(e,e.l_desc.max_code+1,e.d_desc.max_code+1,o+1),bi(e,e.dyn_ltree,e.dyn_dtree)),pi(e),n&&gi(e)},ki={_tr_init:_i,_tr_stored_block:Ci,_tr_flush_block:xi,_tr_tally:(e,t,i)=>(e.pending_buf[e.sym_buf+e.sym_next++]=t,e.pending_buf[e.sym_buf+e.sym_next++]=t>>8,e.pending_buf[e.sym_buf+e.sym_next++]=i,0===t?e.dyn_ltree[2*i]++:(e.matches++,t--,e.dyn_ltree[2*(ei[i]+Qt+1)]++,e.dyn_dtree[2*ci(t)]++),e.sym_next===e.sym_end),_tr_align:e=>{hi(e,2,3),di(e,256,Xt),(e=>{16===e.bi_valid?(li(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=255&e.bi_buf,e.bi_buf>>=8,e.bi_valid-=8)})(e)}};var Ii=(e,t,i,n)=>{let r=65535&e,s=e>>>16&65535,o=0;for(;0!==i;){o=i>2e3?2e3:i,i-=o;do{r=r+t[n++]|0,s=s+r|0}while(--o);r%=65521,s%=65521}return r|s<<16};const Si=new Uint32Array((()=>{let e,t=[];for(var i=0;i<256;i++){e=i;for(var n=0;n<8;n++)e=1&e?3988292384^e>>>1:e>>>1;t[i]=e}return t})());var Ei=(e,t,i,n)=>{const r=Si,s=n+i;e^=-1;for(let i=n;i<s;i++)e=e>>>8^r[255&(e^t[i])];return~e},Ni={2:\"need dictionary\",1:\"stream end\",0:\"\",\"-1\":\"file error\",\"-2\":\"stream error\",\"-3\":\"data error\",\"-4\":\"insufficient memory\",\"-5\":\"buffer error\",\"-6\":\"incompatible version\"},Bi={Z_NO_FLUSH:0,Z_PARTIAL_FLUSH:1,Z_SYNC_FLUSH:2,Z_FULL_FLUSH:3,Z_FINISH:4,Z_BLOCK:5,Z_TREES:6,Z_OK:0,Z_STREAM_END:1,Z_NEED_DICT:2,Z_ERRNO:-1,Z_STREAM_ERROR:-2,Z_DATA_ERROR:-3,Z_MEM_ERROR:-4,Z_BUF_ERROR:-5,Z_NO_COMPRESSION:0,Z_BEST_SPEED:1,Z_BEST_COMPRESSION:9,Z_DEFAULT_COMPRESSION:-1,Z_FILTERED:1,Z_HUFFMAN_ONLY:2,Z_RLE:3,Z_FIXED:4,Z_DEFAULT_STRATEGY:0,Z_BINARY:0,Z_TEXT:1,Z_UNKNOWN:2,Z_DEFLATED:8};const{_tr_init:Mi,_tr_stored_block:Ri,_tr_flush_block:Di,_tr_tally:Ti,_tr_align:Li}=ki,{Z_NO_FLUSH:zi,Z_PARTIAL_FLUSH:Hi,Z_FULL_FLUSH:Pi,Z_FINISH:Oi,Z_BLOCK:Ui,Z_OK:qi,Z_STREAM_END:Qi,Z_STREAM_ERROR:Vi,Z_DATA_ERROR:ji,Z_BUF_ERROR:Wi,Z_DEFAULT_COMPRESSION:Gi,Z_FILTERED:$i,Z_HUFFMAN_ONLY:Ki,Z_RLE:Yi,Z_FIXED:Xi,Z_DEFAULT_STRATEGY:Zi,Z_UNKNOWN:Ji,Z_DEFLATED:en}=Bi,tn=258,nn=262,rn=42,sn=113,on=666,an=(e,t)=>(e.msg=Ni[t],t),cn=e=>2*e-(e>4?9:0),ln=e=>{let t=e.length;for(;--t>=0;)e[t]=0},hn=e=>{let t,i,n,r=e.w_size;t=e.hash_size,n=t;do{i=e.head[--n],e.head[n]=i>=r?i-r:0}while(--t);t=r,n=t;do{i=e.prev[--n],e.prev[n]=i>=r?i-r:0}while(--t)};let dn=(e,t,i)=>(t<<e.hash_shift^i)&e.hash_mask;const un=e=>{const t=e.state;let i=t.pending;i>e.avail_out&&(i=e.avail_out),0!==i&&(e.output.set(t.pending_buf.subarray(t.pending_out,t.pending_out+i),e.next_out),e.next_out+=i,t.pending_out+=i,e.total_out+=i,e.avail_out-=i,t.pending-=i,0===t.pending&&(t.pending_out=0))},fn=(e,t)=>{Di(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,un(e.strm)},pn=(e,t)=>{e.pending_buf[e.pending++]=t},gn=(e,t)=>{e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=255&t},mn=(e,t,i,n)=>{let r=e.avail_in;return r>n&&(r=n),0===r?0:(e.avail_in-=r,t.set(e.input.subarray(e.next_in,e.next_in+r),i),1===e.state.wrap?e.adler=Ii(e.adler,t,r,i):2===e.state.wrap&&(e.adler=Ei(e.adler,t,r,i)),e.next_in+=r,e.total_in+=r,r)},wn=(e,t)=>{let i,n,r=e.max_chain_length,s=e.strstart,o=e.prev_length,a=e.nice_match;const c=e.strstart>e.w_size-nn?e.strstart-(e.w_size-nn):0,l=e.window,h=e.w_mask,d=e.prev,u=e.strstart+tn;let f=l[s+o-1],p=l[s+o];e.prev_length>=e.good_match&&(r>>=2),a>e.lookahead&&(a=e.lookahead);do{if(i=t,l[i+o]===p&&l[i+o-1]===f&&l[i]===l[s]&&l[++i]===l[s+1]){s+=2,i++;do{}while(l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&s<u);if(n=tn-(u-s),s=u-tn,n>o){if(e.match_start=t,o=n,n>=a)break;f=l[s+o-1],p=l[s+o]}}}while((t=d[t&h])>c&&0!=--r);return o<=e.lookahead?o:e.lookahead},bn=e=>{const t=e.w_size;let i,n,r;do{if(n=e.window_size-e.lookahead-e.strstart,e.strstart>=t+(t-nn)&&(e.window.set(e.window.subarray(t,t+t-n),0),e.match_start-=t,e.strstart-=t,e.block_start-=t,e.insert>e.strstart&&(e.insert=e.strstart),hn(e),n+=t),0===e.strm.avail_in)break;if(i=mn(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=i,e.lookahead+e.insert>=3)for(r=e.strstart-e.insert,e.ins_h=e.window[r],e.ins_h=dn(e,e.ins_h,e.window[r+1]);e.insert&&(e.ins_h=dn(e,e.ins_h,e.window[r+3-1]),e.prev[r&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=r,r++,e.insert--,!(e.lookahead+e.insert<3)););}while(e.lookahead<nn&&0!==e.strm.avail_in)},Fn=(e,t)=>{let i,n,r,s=e.pending_buf_size-5>e.w_size?e.w_size:e.pending_buf_size-5,o=0,a=e.strm.avail_in;do{if(i=65535,r=e.bi_valid+42>>3,e.strm.avail_out<r)break;if(r=e.strm.avail_out-r,n=e.strstart-e.block_start,i>n+e.strm.avail_in&&(i=n+e.strm.avail_in),i>r&&(i=r),i<s&&(0===i&&t!==Oi||t===zi||i!==n+e.strm.avail_in))break;o=t===Oi&&i===n+e.strm.avail_in?1:0,Ri(e,0,0,o),e.pending_buf[e.pending-4]=i,e.pending_buf[e.pending-3]=i>>8,e.pending_buf[e.pending-2]=~i,e.pending_buf[e.pending-1]=~i>>8,un(e.strm),n&&(n>i&&(n=i),e.strm.output.set(e.window.subarray(e.block_start,e.block_start+n),e.strm.next_out),e.strm.next_out+=n,e.strm.avail_out-=n,e.strm.total_out+=n,e.block_start+=n,i-=n),i&&(mn(e.strm,e.strm.output,e.strm.next_out,i),e.strm.next_out+=i,e.strm.avail_out-=i,e.strm.total_out+=i)}while(0===o);return a-=e.strm.avail_in,a&&(a>=e.w_size?(e.matches=2,e.window.set(e.strm.input.subarray(e.strm.next_in-e.w_size,e.strm.next_in),0),e.strstart=e.w_size,e.insert=e.strstart):(e.window_size-e.strstart<=a&&(e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,e.insert>e.strstart&&(e.insert=e.strstart)),e.window.set(e.strm.input.subarray(e.strm.next_in-a,e.strm.next_in),e.strstart),e.strstart+=a,e.insert+=a>e.w_size-e.insert?e.w_size-e.insert:a),e.block_start=e.strstart),e.high_water<e.strstart&&(e.high_water=e.strstart),o?4:t!==zi&&t!==Oi&&0===e.strm.avail_in&&e.strstart===e.block_start?2:(r=e.window_size-e.strstart,e.strm.avail_in>r&&e.block_start>=e.w_size&&(e.block_start-=e.w_size,e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,r+=e.w_size,e.insert>e.strstart&&(e.insert=e.strstart)),r>e.strm.avail_in&&(r=e.strm.avail_in),r&&(mn(e.strm,e.window,e.strstart,r),e.strstart+=r,e.insert+=r>e.w_size-e.insert?e.w_size-e.insert:r),e.high_water<e.strstart&&(e.high_water=e.strstart),r=e.bi_valid+42>>3,r=e.pending_buf_size-r>65535?65535:e.pending_buf_size-r,s=r>e.w_size?e.w_size:r,n=e.strstart-e.block_start,(n>=s||(n||t===Oi)&&t!==zi&&0===e.strm.avail_in&&n<=r)&&(i=n>r?r:n,o=t===Oi&&0===e.strm.avail_in&&i===n?1:0,Ri(e,e.block_start,i,o),e.block_start+=i,un(e.strm)),o?3:1)},vn=(e,t)=>{let i,n;for(;;){if(e.lookahead<nn){if(bn(e),e.lookahead<nn&&t===zi)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),0!==i&&e.strstart-i<=e.w_size-nn&&(e.match_length=wn(e,i)),e.match_length>=3)if(n=Ti(e,e.strstart-e.match_start,e.match_length-3),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=3){e.match_length--;do{e.strstart++,e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart}while(0!=--e.match_length);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=dn(e,e.ins_h,e.window[e.strstart+1]);else n=Ti(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(fn(e,!1),0===e.strm.avail_out))return 1}return e.insert=e.strstart<2?e.strstart:2,t===Oi?(fn(e,!0),0===e.strm.avail_out?3:4):e.sym_next&&(fn(e,!1),0===e.strm.avail_out)?1:2},yn=(e,t)=>{let i,n,r;for(;;){if(e.lookahead<nn){if(bn(e),e.lookahead<nn&&t===zi)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),e.prev_length=e.match_length,e.prev_match=e.match_start,e.match_length=2,0!==i&&e.prev_length<e.max_lazy_match&&e.strstart-i<=e.w_size-nn&&(e.match_length=wn(e,i),e.match_length<=5&&(e.strategy===$i||3===e.match_length&&e.strstart-e.match_start>4096)&&(e.match_length=2)),e.prev_length>=3&&e.match_length<=e.prev_length){r=e.strstart+e.lookahead-3,n=Ti(e,e.strstart-1-e.prev_match,e.prev_length-3),e.lookahead-=e.prev_length-1,e.prev_length-=2;do{++e.strstart<=r&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart)}while(0!=--e.prev_length);if(e.match_available=0,e.match_length=2,e.strstart++,n&&(fn(e,!1),0===e.strm.avail_out))return 1}else if(e.match_available){if(n=Ti(e,0,e.window[e.strstart-1]),n&&fn(e,!1),e.strstart++,e.lookahead--,0===e.strm.avail_out)return 1}else e.match_available=1,e.strstart++,e.lookahead--}return e.match_available&&(n=Ti(e,0,e.window[e.strstart-1]),e.match_available=0),e.insert=e.strstart<2?e.strstart:2,t===Oi?(fn(e,!0),0===e.strm.avail_out?3:4):e.sym_next&&(fn(e,!1),0===e.strm.avail_out)?1:2};function An(e,t,i,n,r){this.good_length=e,this.max_lazy=t,this.nice_length=i,this.max_chain=n,this.func=r}const Cn=[new An(0,0,0,0,Fn),new An(4,4,8,4,vn),new An(4,5,16,8,vn),new An(4,6,32,32,vn),new An(4,4,16,16,yn),new An(8,16,32,32,yn),new An(8,16,128,128,yn),new An(8,32,128,256,yn),new An(32,128,258,1024,yn),new An(32,258,258,4096,yn)];function _n(){this.strm=null,this.status=0,this.pending_buf=null,this.pending_buf_size=0,this.pending_out=0,this.pending=0,this.wrap=0,this.gzhead=null,this.gzindex=0,this.method=en,this.last_flush=-1,this.w_size=0,this.w_bits=0,this.w_mask=0,this.window=null,this.window_size=0,this.prev=null,this.head=null,this.ins_h=0,this.hash_size=0,this.hash_bits=0,this.hash_mask=0,this.hash_shift=0,this.block_start=0,this.match_length=0,this.prev_match=0,this.match_available=0,this.strstart=0,this.match_start=0,this.lookahead=0,this.prev_length=0,this.max_chain_length=0,this.max_lazy_match=0,this.level=0,this.strategy=0,this.good_match=0,this.nice_match=0,this.dyn_ltree=new Uint16Array(1146),this.dyn_dtree=new Uint16Array(122),this.bl_tree=new Uint16Array(78),ln(this.dyn_ltree),ln(this.dyn_dtree),ln(this.bl_tree),this.l_desc=null,this.d_desc=null,this.bl_desc=null,this.bl_count=new Uint16Array(16),this.heap=new Uint16Array(573),ln(this.heap),this.heap_len=0,this.heap_max=0,this.depth=new Uint16Array(573),ln(this.depth),this.sym_buf=0,this.lit_bufsize=0,this.sym_next=0,this.sym_end=0,this.opt_len=0,this.static_len=0,this.matches=0,this.insert=0,this.bi_buf=0,this.bi_valid=0}const xn=e=>{if(!e)return 1;const t=e.state;return!t||t.strm!==e||t.status!==rn&&57!==t.status&&69!==t.status&&73!==t.status&&91!==t.status&&103!==t.status&&t.status!==sn&&t.status!==on?1:0},kn=e=>{if(xn(e))return an(e,Vi);e.total_in=e.total_out=0,e.data_type=Ji;const t=e.state;return t.pending=0,t.pending_out=0,t.wrap<0&&(t.wrap=-t.wrap),t.status=2===t.wrap?57:t.wrap?rn:sn,e.adler=2===t.wrap?0:1,t.last_flush=-2,Mi(t),qi},In=e=>{const t=kn(e);var i;return t===qi&&((i=e.state).window_size=2*i.w_size,ln(i.head),i.max_lazy_match=Cn[i.level].max_lazy,i.good_match=Cn[i.level].good_length,i.nice_match=Cn[i.level].nice_length,i.max_chain_length=Cn[i.level].max_chain,i.strstart=0,i.block_start=0,i.lookahead=0,i.insert=0,i.match_length=i.prev_length=2,i.match_available=0,i.ins_h=0),t},Sn=(e,t,i,n,r,s)=>{if(!e)return Vi;let o=1;if(t===Gi&&(t=6),n<0?(o=0,n=-n):n>15&&(o=2,n-=16),r<1||r>9||i!==en||n<8||n>15||t<0||t>9||s<0||s>Xi||8===n&&1!==o)return an(e,Vi);8===n&&(n=9);const a=new _n;return e.state=a,a.strm=e,a.status=rn,a.wrap=o,a.gzhead=null,a.w_bits=n,a.w_size=1<<a.w_bits,a.w_mask=a.w_size-1,a.hash_bits=r+7,a.hash_size=1<<a.hash_bits,a.hash_mask=a.hash_size-1,a.hash_shift=~~((a.hash_bits+3-1)/3),a.window=new Uint8Array(2*a.w_size),a.head=new Uint16Array(a.hash_size),a.prev=new Uint16Array(a.w_size),a.lit_bufsize=1<<r+6,a.pending_buf_size=4*a.lit_bufsize,a.pending_buf=new 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t}for(v=65535&b,F&=15,F&&(f<F&&(u+=_[i++]<<f,f+=8),v+=u&(1<<F)-1,u>>>=F,f-=F),f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=g[u&w];;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,16&F){if(y=65535&b,F&=15,f<F&&(u+=_[i++]<<f,f+=8,f<F&&(u+=_[i++]<<f,f+=8)),y+=u&(1<<F)-1,y>a){e.msg=\"invalid distance too far back\",k.mode=Zn;break e}if(u>>>=F,f-=F,F=r-s,y>F){if(F=y-F,F>l&&k.sane){e.msg=\"invalid distance too far back\",k.mode=Zn;break e}if(A=0,C=d,0===h){if(A+=c-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}else if(h<F){if(A+=c+h-F,F-=h,F<v){v-=F;do{x[r++]=d[A++]}while(--F);if(A=0,h<v){F=h,v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}}else if(A+=h-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}for(;v>2;)x[r++]=C[A++],x[r++]=C[A++],x[r++]=C[A++],v-=3;v&&(x[r++]=C[A++],v>1&&(x[r++]=C[A++]))}else{A=r-y;do{x[r++]=x[A++],x[r++]=x[A++],x[r++]=x[A++],v-=3}while(v>2);v&&(x[r++]=x[A++],v>1&&(x[r++]=x[A++]))}break}if(64&F){e.msg=\"invalid distance code\",k.mode=Zn;break e}b=g[(65535&b)+(u&(1<<F)-1)]}}break}}while(i<n&&r<o);v=f>>3,i-=v,f-=v<<3,u&=(1<<f)-1,e.next_in=i,e.next_out=r,e.avail_in=i<n?n-i+5:5-(i-n),e.avail_out=r<o?o-r+257:257-(r-o),k.hold=u,k.bits=f};const er=15,tr=new Uint16Array([3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0]),ir=new Uint8Array([16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78]),nr=new Uint16Array([1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0]),rr=new Uint8Array([16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64]);var sr=(e,t,i,n,r,s,o,a)=>{const c=a.bits;let l,h,d,u,f,p,g=0,m=0,w=0,b=0,F=0,v=0,y=0,A=0,C=0,_=0,x=null;const k=new Uint16Array(16),I=new Uint16Array(16);let S,E,N,B=null;for(g=0;g<=er;g++)k[g]=0;for(m=0;m<n;m++)k[t[i+m]]++;for(F=c,b=er;b>=1&&0===k[b];b--);if(F>b&&(F=b),0===b)return r[s++]=20971520,r[s++]=20971520,a.bits=1,0;for(w=1;w<b&&0===k[w];w++);for(F<w&&(F=w),A=1,g=1;g<=er;g++)if(A<<=1,A-=k[g],A<0)return-1;if(A>0&&(0===e||1!==b))return-1;for(I[1]=0,g=1;g<er;g++)I[g+1]=I[g]+k[g];for(m=0;m<n;m++)0!==t[i+m]&&(o[I[t[i+m]]++]=m);if(0===e?(x=B=o,p=20):1===e?(x=tr,B=ir,p=257):(x=nr,B=rr,p=0),_=0,m=0,g=w,f=s,v=F,y=0,d=-1,C=1<<F,u=C-1,1===e&&C>852||2===e&&C>592)return 1;for(;;){S=g-y,o[m]+1<p?(E=0,N=o[m]):o[m]>=p?(E=B[o[m]-p],N=x[o[m]-p]):(E=96,N=0),l=1<<g-y,h=1<<v,w=h;do{h-=l,r[f+(_>>y)+h]=S<<24|E<<16|N}while(0!==h);for(l=1<<g-1;_&l;)l>>=1;if(0!==l?(_&=l-1,_+=l):_=0,m++,0==--k[g]){if(g===b)break;g=t[i+o[m]]}if(g>F&&(_&u)!==d){for(0===y&&(y=F),f+=w,v=g-y,A=1<<v;v+y<b&&(A-=k[v+y],!(A<=0));)v++,A<<=1;if(C+=1<<v,1===e&&C>852||2===e&&C>592)return 1;d=_&u,r[d]=F<<24|v<<16|f-s}}return 0!==_&&(r[f+_]=g-y<<24|64<<16),a.bits=F,0};const{Z_FINISH:or,Z_BLOCK:ar,Z_TREES:cr,Z_OK:lr,Z_STREAM_END:hr,Z_NEED_DICT:dr,Z_STREAM_ERROR:ur,Z_DATA_ERROR:fr,Z_MEM_ERROR:pr,Z_BUF_ERROR:gr,Z_DEFLATED:mr}=Bi,wr=16180,br=16190,Fr=16191,vr=16192,yr=16194,Ar=16199,Cr=16200,_r=16206,xr=16209,kr=e=>(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24);function Ir(){this.strm=null,this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new Uint16Array(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}const Sr=e=>{if(!e)return 1;const t=e.state;return!t||t.strm!==e||t.mode<wr||t.mode>16211?1:0},Er=e=>{if(Sr(e))return ur;const t=e.state;return e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=wr,t.last=0,t.havedict=0,t.flags=-1,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new Int32Array(852),t.distcode=t.distdyn=new Int32Array(592),t.sane=1,t.back=-1,lr},Nr=e=>{if(Sr(e))return ur;const t=e.state;return t.wsize=0,t.whave=0,t.wnext=0,Er(e)},Br=(e,t)=>{let i;if(Sr(e))return ur;const n=e.state;return t<0?(i=0,t=-t):(i=5+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?ur:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,Nr(e))},Mr=(e,t)=>{if(!e)return ur;const i=new Ir;e.state=i,i.strm=e,i.window=null,i.mode=wr;const n=Br(e,t);return n!==lr&&(e.state=null),n};let Rr,Dr,Tr=!0;const Lr=e=>{if(Tr){Rr=new Int32Array(512),Dr=new Int32Array(32);let t=0;for(;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(sr(1,e.lens,0,288,Rr,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;sr(2,e.lens,0,32,Dr,0,e.work,{bits:5}),Tr=!1}e.lencode=Rr,e.lenbits=9,e.distcode=Dr,e.distbits=5},zr=(e,t,i,n)=>{let r;const s=e.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new Uint8Array(s.wsize)),n>=s.wsize?(s.window.set(t.subarray(i-s.wsize,i),0),s.wnext=0,s.whave=s.wsize):(r=s.wsize-s.wnext,r>n&&(r=n),s.window.set(t.subarray(i-n,i-n+r),s.wnext),(n-=r)?(s.window.set(t.subarray(i-n,i),0),s.wnext=n,s.whave=s.wsize):(s.wnext+=r,s.wnext===s.wsize&&(s.wnext=0),s.whave<s.wsize&&(s.whave+=r))),0};var Hr=(e,t)=>{let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_=0;const x=new Uint8Array(4);let k,I;const S=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(Sr(e)||!e.output||!e.input&&0!==e.avail_in)return ur;i=e.state,i.mode===Fr&&(i.mode=vr),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,d=a,u=c,C=lr;e:for(;;)switch(i.mode){case wr:if(0===i.wrap){i.mode=vr;break}for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(2&i.wrap&&35615===l){0===i.wbits&&(i.wbits=15),i.check=0,x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0),l=0,h=0,i.mode=16181;break}if(i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&l)<<8)+(l>>8))%31){e.msg=\"incorrect header check\",i.mode=xr;break}if((15&l)!==mr){e.msg=\"unknown compression method\",i.mode=xr;break}if(l>>>=4,h-=4,A=8+(15&l),0===i.wbits&&(i.wbits=A),A>15||A>i.wbits){e.msg=\"invalid window size\",i.mode=xr;break}i.dmax=1<<i.wbits,i.flags=0,e.adler=i.check=1,i.mode=512&l?16189:Fr,l=0,h=0;break;case 16181:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.flags=l,(255&i.flags)!==mr){e.msg=\"unknown compression method\",i.mode=xr;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=xr;break}i.head&&(i.head.text=l>>8&1),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0,i.mode=16182;case 16182:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.time=l),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,x[2]=l>>>16&255,x[3]=l>>>24&255,i.check=Ei(i.check,x,4,0)),l=0,h=0,i.mode=16183;case 16183:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.xflags=255&l,i.head.os=l>>8),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0,i.mode=16184;case 16184:if(1024&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length=l,i.head&&(i.head.extra_len=l),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0}else i.head&&(i.head.extra=null);i.mode=16185;case 16185:if(1024&i.flags&&(f=i.length,f>a&&(f=a),f&&(i.head&&(A=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Uint8Array(i.head.extra_len)),i.head.extra.set(n.subarray(s,s+f),A)),512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,i.length-=f),i.length))break e;i.length=0,i.mode=16186;case 16186:if(2048&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.name+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=16187;case 16187:if(4096&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.comment+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.comment=null);i.mode=16188;case 16188:if(512&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(4&i.wrap&&l!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=xr;break}l=0,h=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=Fr;break;case 16189:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}e.adler=i.check=kr(l),l=0,h=0,i.mode=br;case br:if(0===i.havedict)return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,dr;e.adler=i.check=1,i.mode=Fr;case Fr:if(t===ar||t===cr)break e;case vr:if(i.last){l>>>=7&h,h-=7&h,i.mode=_r;break}for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}switch(i.last=1&l,l>>>=1,h-=1,3&l){case 0:i.mode=16193;break;case 1:if(Lr(i),i.mode=Ar,t===cr){l>>>=2,h-=2;break e}break;case 2:i.mode=16196;break;case 3:e.msg=\"invalid block type\",i.mode=xr}l>>>=2,h-=2;break;case 16193:for(l>>>=7&h,h-=7&h;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if((65535&l)!=(l>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=xr;break}if(i.length=65535&l,l=0,h=0,i.mode=yr,t===cr)break e;case yr:i.mode=16195;case 16195:if(f=i.length,f){if(f>a&&(f=a),f>c&&(f=c),0===f)break e;r.set(n.subarray(s,s+f),o),a-=f,s+=f,c-=f,o+=f,i.length-=f;break}i.mode=Fr;break;case 16196:for(;h<14;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.nlen=257+(31&l),l>>>=5,h-=5,i.ndist=1+(31&l),l>>>=5,h-=5,i.ncode=4+(15&l),l>>>=4,h-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=xr;break}i.have=0,i.mode=16197;case 16197:for(;i.have<i.ncode;){for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.lens[S[i.have++]]=7&l,l>>>=3,h-=3}for(;i.have<19;)i.lens[S[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,k={bits:i.lenbits},C=sr(0,i.lens,0,19,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid code lengths set\",i.mode=xr;break}i.have=0,i.mode=16198;case 16198:for(;i.have<i.nlen+i.ndist;){for(;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(b<16)l>>>=m,h-=m,i.lens[i.have++]=b;else{if(16===b){for(I=m+2;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l>>>=m,h-=m,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=xr;break}A=i.lens[i.have-1],f=3+(3&l),l>>>=2,h-=2}else if(17===b){for(I=m+3;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=3+(7&l),l>>>=3,h-=3}else{for(I=m+7;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=11+(127&l),l>>>=7,h-=7}if(i.have+f>i.nlen+i.ndist){e.msg=\"invalid bit length repeat\",i.mode=xr;break}for(;f--;)i.lens[i.have++]=A}}if(i.mode===xr)break;if(0===i.lens[256]){e.msg=\"invalid code -- missing end-of-block\",i.mode=xr;break}if(i.lenbits=9,k={bits:i.lenbits},C=sr(1,i.lens,0,i.nlen,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid literal/lengths set\",i.mode=xr;break}if(i.distbits=6,i.distcode=i.distdyn,k={bits:i.distbits},C=sr(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,k),i.distbits=k.bits,C){e.msg=\"invalid distances set\",i.mode=xr;break}if(i.mode=Ar,t===cr)break e;case Ar:i.mode=Cr;case Cr:if(a>=6&&c>=258){e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,Jn(e,u),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,i.mode===Fr&&(i.back=-1);break}for(i.back=0;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(w&&!(240&w)){for(F=m,v=w,y=b;_=i.lencode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,i.length=b,0===w){i.mode=16205;break}if(32&w){i.back=-1,i.mode=Fr;break}if(64&w){e.msg=\"invalid literal/length code\",i.mode=xr;break}i.extra=15&w,i.mode=16201;case 16201:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=16202;case 16202:for(;_=i.distcode[l&(1<<i.distbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(!(240&w)){for(F=m,v=w,y=b;_=i.distcode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,64&w){e.msg=\"invalid distance code\",i.mode=xr;break}i.offset=b,i.extra=15&w,i.mode=16203;case 16203:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.offset+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=xr;break}i.mode=16204;case 16204:if(0===c)break e;if(f=u-c,i.offset>f){if(f=i.offset-f,f>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=xr;break}f>i.wnext?(f-=i.wnext,p=i.wsize-f):p=i.wnext-f,f>i.length&&(f=i.length),g=i.window}else g=r,p=o-i.offset,f=i.length;f>c&&(f=c),c-=f,i.length-=f;do{r[o++]=g[p++]}while(--f);0===i.length&&(i.mode=Cr);break;case 16205:if(0===c)break e;r[o++]=i.length,c--,i.mode=Cr;break;case _r:if(i.wrap){for(;h<32;){if(0===a)break e;a--,l|=n[s++]<<h,h+=8}if(u-=c,e.total_out+=u,i.total+=u,4&i.wrap&&u&&(e.adler=i.check=i.flags?Ei(i.check,r,u,o-u):Ii(i.check,r,u,o-u)),u=c,4&i.wrap&&(i.flags?l:kr(l))!==i.check){e.msg=\"incorrect data check\",i.mode=xr;break}l=0,h=0}i.mode=16207;case 16207:if(i.wrap&&i.flags){for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(4&i.wrap&&l!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=xr;break}l=0,h=0}i.mode=16208;case 16208:C=hr;break e;case xr:C=fr;break e;case 16210:return pr;default:return ur}return 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Object.values(this.allFeatures))for(let n of i)e(n)&&t.push(n);return t}queryFeatures(e,t,i){const n=this.treeMap[e];if(!n)return[];const r=n.findOverlapping(t,i);if(0===r.length)return[];{const n=[],s=this.allFeatures[e];if(s){for(let e of r){const r=e.value;for(let e=r.start;e<r.end;e++){let r=s[e];if(r.start>i)break;r.end>=t&&n.push(r)}}n.sort((function(e,t){return e.start-t.start}))}return n}}getAllFeatures(){return this.allFeatures}buildTreeMap(e,t){const i={},n=[];if(this.allFeatures={},e){for(let i of e){let e=i.chr;t&&(e=t.getChromosomeName(e));let r=this.allFeatures[e];r||(n.push(e),r=[],this.allFeatures[e]=r),r.push(i)}for(let e of n){const t=this.allFeatures[e];t.sort((function(e,t){return e.start===t.start?0:e.start>t.start?1:-1})),i[e]=Js(t)}}return i}}function Js(e){const t=new js,i=e.length,n=Math.max(10,Math.round(i/10));for(let r=0;r<i;r+=n){const s=Math.min(i,r+n),o=new eo(r,s),a=e[r].start;let c=a;for(let t=r;t<s;t++)c=Math.max(c,e[t].end);t.insert(a,c,o)}return t}class eo{constructor(e,t){this.start=e,this.end=t}}const to=function(e,t,i){if(e&&0!==e.length){const n=function(e){const t=new js,i=e.length,n=Math.max(10,Math.round(i/100));e.sort((function(e,t){return e.start===t.start?0:e.start>t.start?1:-1}));for(let r=0;r<i;r+=n){const s=Math.min(i,r+n),o=e.slice(r,s),a=o[0].start;let c=a;o.forEach((function(e){c=Math.max(c,e.end)})),t.insert(a,c,o)}return t}(e),r=n.findOverlapping(t,i);return 0===r.length?[]:(e=[],r.forEach((function(n){const r=n.value,s=r.length;for(let n=0;n<s;n++){const s=r[n];if(s.start>i)break;s.end>t&&e.push(s)}})),e.sort((function(e,t){return e.start-t.start})),e)}return[]};function io(e){if(3===(e=e.replace(/^#/,\"\")).length&&(e=e.split(\"\").map((e=>e+e)).join(\"\")),6!==e.length)throw new Error(\"Invalid HEX color.\");let t=parseInt(e,16);return`rgb(${t>>16&255}, ${t>>8&255}, ${255&t})`}const no={cantaloupe:{r:255,g:206,b:110},honeydew:{r:206,g:250,b:110},spindrift:{r:104,g:251,b:208},sky:{r:106,g:207,b:255},lavender:{r:210,g:120,b:255},carnation:{r:255,g:127,b:211},licorice:{r:0,g:0,b:0},snow:{r:255,g:255,b:255},salmon:{r:255,g:114,b:110},banana:{r:255,g:251,b:109},flora:{r:104,g:249,b:110},ice:{r:104,g:253,b:255},orchid:{r:110,g:118,b:255},bubblegum:{r:255,g:122,b:255},lead:{r:30,g:30,b:30},mercury:{r:232,g:232,b:232},tangerine:{r:255,g:136,b:2},lime:{r:131,g:249,b:2},sea_foam:{r:3,g:249,b:135},aqua:{r:0,g:140,b:255},grape:{r:137,g:49,b:255},strawberry:{r:255,g:41,b:135},tungsten:{r:58,g:58,b:58},silver:{r:208,g:208,b:208},maraschino:{r:255,g:33,b:1},lemon:{r:255,g:250,b:3},spring:{r:5,g:248,b:2},turquoise:{r:0,g:253,b:255},blueberry:{r:0,g:46,b:255},magenta:{r:255,g:57,b:255},iron:{r:84,g:84,b:83},magnesium:{r:184,g:184,b:184},mocha:{r:137,g:72,b:0},fern:{r:69,g:132,b:1},moss:{r:1,g:132,b:72},ocean:{r:0,g:74,b:136},eggplant:{r:73,g:26,b:136},maroon:{r:137,g:22,b:72},steel:{r:110,g:110,b:110},aluminum:{r:160,g:159,b:160},cayenne:{r:137,g:17,b:0},aspargus:{r:136,g:133,b:1},clover:{r:2,g:132,b:1},teal:{r:0,g:134,b:136},midnight:{r:0,g:24,b:136},plum:{r:137,g:30,b:136},tin:{r:135,g:134,b:135},nickel:{r:136,g:135,b:135}};function ro(e){const{r:t,g:i,b:n}=no[e];return`rgb(${t},${i},${n})`}const so={Set1:[\"rgb(228,26,28)\",\"rgb(55,126,184)\",\"rgb(77,175,74)\",\"rgb(166,86,40)\",\"rgb(152,78,163)\",\"rgb(255,127,0)\",\"rgb(247,129,191)\",\"rgb(153,153,153)\",\"rgb(255,255,51)\"],Dark2:[\"rgb(27,158,119)\",\"rgb(217,95,2)\",\"rgb(117,112,179)\",\"rgb(231,41,138)\",\"rgb(102,166,30)\",\"rgb(230,171,2)\",\"rgb(166,118,29)\",\"rgb(102,102,102)\"],Set2:[\"rgb(102, 194,165)\",\"rgb(252,141,98)\",\"rgb(141,160,203)\",\"rgb(231,138,195)\",\"rgb(166,216,84)\",\"rgb(255,217,47)\",\"rgb(229,196,148)\",\"rgb(179,179,179)\"],Set3:[\"rgb(141,211,199)\",\"rgb(255,255,179)\",\"rgb(190,186,218)\",\"rgb(251,128,114)\",\"rgb(128,177,211)\",\"rgb(253,180,98)\",\"rgb(179,222,105)\",\"rgb(252,205,229)\",\"rgb(217,217,217)\",\"rgb(188,128,189)\",\"rgb(204,235,197)\",\"rgb(255,237,111)\"],Pastel1:[\"rgb(251,180,174)\",\"rgb(179,205,227)\",\"rgb(204,235,197)\",\"rgb(222,203,228)\",\"rgb(254,217,166)\",\"rgb(255,255,204)\",\"rgb(229,216,189)\",\"rgb(253,218,236)\"],Pastel2:[\"rgb(173,226,207)\",\"rgb(253,205,172)\",\"rgb(203,213,232)\",\"rgb(244,202,228)\",\"rgb(230,245,201)\",\"rgb(255,242,174)\",\"rgb(243,225,206)\"],Accent:[\"rgb(127,201,127)\",\"rgb(190,174,212)\",\"rgb(253,192,134)\",\"rgb(255,255,153)\",\"rgb(56,108,176)\",\"rgb(240,2,127)\",\"rgb(191,91,23)\"]};class oo{constructor(e){this.colors=so[e],Array.isArray(this.colors)||(this.colors=[]),this.colorTable=new Map,this.nextIdx=0,this.colorGenerator=new co}getColor(e){return this.colorTable.has(e)||(this.nextIdx<this.colors.length?this.colorTable.set(e,this.colors[this.nextIdx]):this.colorTable.set(e,this.colorGenerator.get()),this.nextIdx++),this.colorTable.get(e)}}class ao{constructor(e){this.colorTable=e||{},this.nextIdx=0,this.colorGenerator=new co}getColor(e){if(!this.colorTable.hasOwnProperty(e)){if(this.colorTable.hasOwnProperty(\"*\"))return this.colorTable[\"*\"];this.colorTable[e]=this.colorGenerator.get()}return this.colorTable[e]}}function co(){this.hue=Math.random(),this.goldenRatio=.618033988749895,this.hexwidth=2}function lo(e,t,i,n){return`rgba(${e=ys.clamp(e,0,255)}, ${t=ys.clamp(t,0,255)}, ${i=ys.clamp(i,0,255)}, ${n=ys.clamp(n,0,1)})`}function ho(e,t){e=ys.clamp(e,0,255),t=ys.clamp(t,0,255);return`rgb(${Math.round(Math.random()*(t-e)+e).toString(10)},${Math.round(Math.random()*(t-e)+e).toString(10)},${Math.round(Math.random()*(t-e)+e).toString(10)})`}function uo(e){if(e.startsWith(\"rgb(\")){const[t,i]=e.split(\"(\"),[n]=i.split(\")\");return n.split(\",\").map((e=>parseInt(e)))}}co.prototype.hsvToRgb=function(e,t,i){var n=Math.floor(6*e),r=6*e-n,s=i*(1-t),o=i*(1-r*t),a=i*(1-(1-r)*t),c=255,l=255,h=255;switch(n){case 0:c=i,l=a,h=s;break;case 1:c=o,l=i,h=s;break;case 2:c=s,l=i,h=a;break;case 3:c=s,l=o,h=i;break;case 4:c=a,l=s,h=i;break;case 5:c=i,l=s,h=o}return[Math.floor(256*c),Math.floor(256*l),Math.floor(256*h)]},co.prototype.padHex=function(e){return e.length>this.hexwidth?e:new Array(this.hexwidth-e.length+1).join(\"0\")+e},co.prototype.get=function(e,t){this.hue+=this.goldenRatio,this.hue%=1,\"number\"!=typeof e&&(e=.5),\"number\"!=typeof t&&(t=.95);var i=this.hsvToRgb(this.hue,e,t);return\"#\"+this.padHex(i[0].toString(16))+this.padHex(i[1].toString(16))+this.padHex(i[2].toString(16))},new co;function fo(e,t,i){if(i<.005)return e;if(i>.995)return t;{let n,r,s,o,a,c;i<.5?(i/=.5,[n,r,s]=uo(e),[o,a,c]=uo(ro(\"snow\"))):(i=(i-.5)/.5,[n,r,s]=uo(ro(\"snow\")),[o,a,c]=uo(t));const[l,h,d]=[Math.floor(ys.lerp(n,o,i)),Math.floor(ys.lerp(r,a,i)),Math.floor(ys.lerp(s,c,i))];return function(e,t,i){return`rgb(${e=ys.clamp(e,0,255)}, ${t=ys.clamp(t,0,255)}, ${i=ys.clamp(i,0,255)})`}(l,h,d)}}const po=new Set([\"bedtype\",\"alignment\",\"annotation\",\"variant\",\"wig\",\"interact\",\"shoebox\"]),go=new Set([\"alignment\",\"annotation\",\"variant\",\"eqtl\",\"qtl\",\"snp\",\"shoebox\",\"wig\"]),mo=new Set([\"sequence\",\"ruler\",\"ideogram\"]),wo={};class bo{constructor(e){this.browser=e,this.initialize()}initialize(){const e=new c;e.add(\"...\");const t={parent:this.browser.root,content:e};this.dialog=new w(t),this.browser.root.appendChild(this.dialog.elem),i(this.dialog.elem)}trackMenuItemList(e){const t=[];return\"sequence\"!==e.track.config.type&&t.push(function(){const e=Bt(\"<div>\");function t(e){const t=()=>{const e=parseInt(this.browser.inputDialog.value,10);if(void 0!==e){const t=[];this.trackView.track.selected?t.push(...this.trackView.browser.getSelectedTrackViews().map((({track:e})=>e))):t.push(this);for(const i of t)i.trackView.autoHeight=!1,void 0!==i.minHeight&&i.minHeight>e&&(i.minHeight=e),void 0!==i.maxHeight&&i.maxHeight<e&&(i.minHeight=e),i.trackView.setTrackHeight(e,!0),i.trackView.checkContentHeight(),i.trackView.repaintViews()}},i={label:\"Track Height\",value:this.height,callback:t};this.browser.inputDialog.present(i,e)}return e.text(\"Set track height\"),{object:e,dialog:t}}()),!0===function(e){const t=e.browser.getSelectedTrackViews();return t&&t.length>1&&new Set(t).has(e)}(e)?t.push(...this.multiSelectMenuItems(e)):(\"sequence\"!==e.track.config.type&&t.push(function(){const e=Bt(\"<div>\");function t(e){const t=()=>{let e=this.browser.inputDialog.value;e=\"\"===e||void 0===e?\"untitled\":e.trim(),this.name=e},i={label:\"Track Name\",value:Ao(this)||\"unnamed\",callback:t};this.browser.inputDialog.present(i,e)}return e.text(\"Set track name\"),{object:e,click:t}}()),t.push(...this.defaultMenuItems(e))),!1!==e.track.removable&&(t.push(\"<hr/>\"),t.push(function(e){const t=e.track.selected?\"Remove tracks\":\"Remove track\",i=Bt(\"<div>\");function n(e){this.trackView.browser._removeTrack(this)}return i.text(t),{object:i,click:n,menuItemType:\"removeTrack\"}}(e))),t}defaultMenuItems(e){const t=[];return Co(e.track)&&(t.push(\"<hr/>\"),t.push(Fo({trackView:e,label:\"Set track color\",option:\"color\"})),t.push(vo({trackView:e,label:\"Unset track color\"})),\"wig\"!==e.track.config.type&&\"annotation\"!==e.track.config.type||(t.push(Fo({trackView:e,label:\"Set alt color\",option:\"altColor\"})),t.push(yo({trackView:e,label:\"Unset alt color\"})))),e.track.menuItemList&&t.push(...e.track.menuItemList()),function(e){const t=e.track;return t&&t.config&&void 0!==t.config.visibilityWindow||t&&go.has(t.type)}(e)&&(t.push(\"<hr/>\"),t.push(function(e){const t=Bt(\"<div>\");function i(t){const i=()=>{let e=this.browser.inputDialog.value;e=\"\"===e||void 0===e?-1:e.trim(),this.visibilityWindow=Number.parseInt(e),this.config.visibilityWindow=Number.parseInt(e),this.trackView.updateViews()},n={label:\"wig\"===e?\"Visibility window (bp). Enter 0 for whole chromosome, -1 for whole genome.\":\"Visibility window (bp). Enter 0 for whole chromosome.\",value:this.visibilityWindow,callback:i};this.browser.inputDialog.present(n,t)}return t.text(\"Set visibility window\"),{object:t,click:i}}(e.track.type))),t}multiSelectMenuItems(e){const t=[],i=e.browser.getSelectedTrackViews();var n;return!0===(n=i.map((({track:e})=>e.type)),1===[...new Set(n)].length)?(t.push(...this.defaultMenuItems(e)),\"wig\"===e.track.type&&(t.push(\"<hr/>\"),t.push(function(){const e=Bt(\"<div>\");function t(e){const t=so.Dark2,i=Math.floor(Math.random()*t.length),n=`auto-scale-group-${s()}`;wo[n]=t[i];const r=this.browser.getSelectedTrackViews();for(const{track:e}of r)e.autoscaleGroup=n;this.browser.updateViews()}return e.text(\"Group autoscale\"),{object:e,doAllMultiSelectedTracks:!0,click:t}}()))):Co(e.track)&&(t.push(\"<hr/>\"),t.push(Fo({trackView:e,label:\"Set track color\",option:\"color\"})),t.push(vo({trackView:e,label:\"Unset track color\"})),\"wig\"!==e.track.config.type&&\"annotation\"!==e.track.config.type||(t.push(Fo({trackView:e,label:\"Set alt color\",option:\"altColor\"})),t.push(yo({trackView:e,label:\"Unset alt color\"})))),t}}function Fo({trackView:e,label:t,option:i}){const n=Bt(\"<div>\");return n.text(t),{object:n,click:()=>e.presentColorPicker(i)}}function vo({trackView:e,label:t}){const i=Bt(\"<div>\");return i.text(t),{object:i,click:()=>{e.track.color=void 0,e.repaintViews()}}}function yo({trackView:e,label:t}){const i=Bt(\"<div>\");return i.text(t),{object:i,click:()=>{e.track.altColor=void 0,e.repaintViews()}}}function Ao(e){return e.name}function Co(e){return void 0===e.type||po.has(e.type)}class _o{constructor(e,t){this.browser=e,this.$container=Bt(\"<div>\",{class:\"igv-generic-dialog-container\"}),t.append(this.$container),this.$container.offset({left:0,top:0});const i=Bt(\"<div>\",{class:\"igv-generic-dialog-header\"});this.$container.append(i),u(i[0],(()=>{this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\"),this.$container.offset({left:0,top:0}),this.$container.hide()})),this.$minimum=Bt(\"<div>\",{class:\"igv-generic-dialog-label-input\"}),this.$container.append(this.$minimum);const n=Bt(\"<div>\");n.text(\"Minimum\"),this.$minimum.append(n),this.$minimum_input=Bt(\"<input>\"),this.$minimum.append(this.$minimum_input),this.$maximum=Bt(\"<div>\",{class:\"igv-generic-dialog-label-input\"}),this.$container.append(this.$maximum);const r=Bt(\"<div>\");r.text(\"Maximum\"),this.$maximum.append(r),this.$maximum_input=Bt(\"<input>\"),this.$maximum.append(this.$maximum_input);const s=Bt(\"<div>\",{class:\"igv-generic-dialog-ok-cancel\"});this.$container.append(s),this.$ok=Bt(\"<div>\"),s.append(this.$ok),this.$ok.text(\"OK\"),this.$cancel=Bt(\"<div>\"),s.append(this.$cancel),this.$cancel.text(\"Cancel\"),this.$cancel.on(\"click\",(()=>{this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\"),this.$container.offset({left:0,top:0}),this.$container.hide()})),p(this.$container.get(0),i.get(0)),this.$container.hide()}configure(e){let t;if(Array.isArray(e)){t={min:Number.MAX_SAFE_INTEGER,max:-Number.MAX_SAFE_INTEGER};for(const i of e)i.track.dataRange&&(t.min=Math.min(i.track.dataRange.min,t.min),t.max=Math.max(i.track.dataRange.max,t.max))}else t=e.track.dataRange;t&&(this.$minimum_input.val(t.min),this.$maximum_input.val(t.max)),this.$minimum_input.unbind(),this.$minimum_input.on(\"keyup\",(t=>{13===t.keyCode&&this.processResults(e),t.stopImmediatePropagation()})),this.$maximum_input.unbind(),this.$maximum_input.on(\"keyup\",(t=>{13===t.keyCode&&(t.stopImmediatePropagation(),this.processResults(e))})),this.$ok.unbind(),this.$ok.on(\"click\",(t=>{this.processResults(e)}))}processResults(e){if(\"\"!==this.$minimum_input.val()&&\"\"!==this.$maximum_input.val()){const t=Number(this.$minimum_input.val()),i=Number(this.$maximum_input.val());if(isNaN(t)||isNaN(i))this.browser.alert.present(new Error(\"Must input numeric values\"),void 0);else{const n=Array.isArray(e)?e:[e];for(const e of n)e.track.setDataRange({min:t,max:i})}this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\")}this.$container.offset({left:0,top:0}),this.$container.hide()}present(e){const t=e.offset().top,i=Bt(\"body\").scrollTop();this.$container.offset({left:e.width()-this.$container.width(),top:t+i}),this.$container.show()}}const xo={configureHighDPICanvas:function(e,t,i){const n=window.devicePixelRatio;e.canvas.style.width=`${t}px`,e.canvas.width=Math.floor(n*t),e.canvas.style.height=`${i}px`,e.canvas.height=Math.floor(n*i),e.scale(n,n)},setProperties:function(e,t){for(var i in t)if(t.hasOwnProperty(i)){var 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a=e=>{o.show(),i(n),e.preventDefault(),e.stopPropagation()};s.addEventListener(\"click\",a),s.addEventListener(\"touchend\",a),s.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}else s=e(),\"string\"==typeof t.label&&(s.innerHTML=t.label);if(t.click&&\"color\"!==t.type){function c(e){t.click(),i(n),e.preventDefault(),e.stopPropagation()}s.addEventListener(\"click\",c),s.addEventListener(\"touchend\",c),s.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}}return{object:s,init:t.init}}));return r}const rc=[[\"A\",\"T\"],[\"G\",\"C\"],[\"Y\",\"R\"],[\"W\",\"S\"],[\"K\",\"M\"],[\"D\",\"H\"],[\"B\",\"V\"]],sc=new Map;for(let _A of rc){const xA=_A[0],kA=_A[1];sc.set(xA,kA),sc.set(kA,xA),sc.set(xA.toLowerCase(),kA.toLowerCase()),sc.set(kA.toLowerCase(),xA.toLowerCase())}function oc(e){return sc.has(e)?sc.get(e):e}function ac(e){let t=\"\";for(let i of e)t+=sc.has(i)?sc.get(i):i;return t}function cc(e){let t=\"\",i=e.length;for(;i-- >0;){const n=e[i];t+=sc.has(n)?sc.get(n):n}return t}class lc{constructor(e,t,i,n){this.name=e,this.order=t,this.bpLength=i,this.altNames=n}getAltName(e){return this.altNames&&this.altNames.has(e)?this.altNames.get(e):this.name}}class hc{constructor(e,t,i,n){this.chr=e,this.start=t,this.end=i,this.features=n}contains(e,t,i){return this.chr===e&&this.start<=t&&this.end>=i}containsRange(e){return this.chr===e.chr&&this.start<=e.start&&this.end>=e.end}get locusString(){return`${this.chr}:${this.start+1}-${this.end}`}}class dc extends hc{constructor(e,t,i,n){super(e,t,i,n)}getSequence(e,t){if(e<this.start||t>this.end)return null;const i=e-this.start,n=t-e;return this.features?this.features.substring(i,i+n):null}hasSequence(e,t){return e>=this.start&&t<=this.end}}const uc=Dt,fc=new Set([\"fastaURL\",\"indexURL\",\"cytobandURL\",\"indexed\"]);class pc{#e;chromosomes=new Map;sequences=new Map;constructor(e){this.fastaURL=e.fastaURL,this.withCredentials=e.withCredentials;const t={};for(let i in e)e.hasOwnProperty(i)&&!fc.has(i)&&(t[i]=e[i]);this.config=t}async init(){return this.loadAll()}getSequenceRecord(e){return this.chromosomes.get(e)}get chromosomeNames(){return this.#e||(this.#e=Array.from(this.chromosomes.keys())),this.#e}getFirstChromosomeName(){return this.chromosomeNames[0]}async getSequence(e,t,i){if(0===this.sequences.size&&await this.loadAll(),!this.sequences.has(e))return;let n=this.sequences.get(e).find((e=>e.contains(t,i)));if(!n&&(n=this.sequences.get(e).find((e=>e.overlaps(t,i))),!n))return;t-=n.offset,i-=n.offset;let r=\"\";if(t<0)for(let e=t;e<Math.min(i,0);e++)r+=\"*\";if(i<=0)return r;const s=n.sequence,o=Math.min(i,s.length);return r+s.substring(t,o)}async loadAll(){let e;if(Ga(this.fastaURL)){let t=vs(this.fastaURL);e=\"\";for(let i of t)e+=String.fromCharCode(i)}else e=await Qs.load(this.fastaURL,Ua(this.config));const t=new Set,i=uc(e),n=i.length;let r,s=0,o=0,a={};for(;s<n;){if(r=i[s++].trim(),r.startsWith(\"#\")||0===r.length);else if(r.startsWith(\">\")){a&&a.seq&&c.call(this,a,o++);const e=r.substr(1).split(/\\s+/),t=e[0].split(\":\");if(a.chr=t[0],a.seq=\"\",a.offset=0,t.length>1&&t[1].indexOf(\"-\")>0){const i=t[1].split(\"-\");2===i.length&&/^[0-9]+$/.test(i[0])&&/^[0-9]+$/.test(i[1]);const n=Number.parseInt(i[0]);if(Number.parseInt(i[1])>n&&(a.offset=n-1),e.length>1&&e[1].startsWith(\"@len=\"))try{a.length=parseInt(e[1].trim().substring(5))}catch(e){a.length=void 0,console.error(`Error parsing sequence length for ${r}`)}else a.length=void 0}}else a.seq+=r;a&&a.seq&&c.call(this,a,o)}function c(e,i){const n=e.length||e.offset+e.seq.length;if(t.has(e.chr)){const t=this.chromosomes.get(e.chr);t.bpLength=Math.max(t.bpLength,n)}else this.sequences.set(e.chr,[]),this.chromosomes.set(e.chr,new lc(e.chr,i,n)),t.add(e.chr);this.sequences.get(e.chr).push(new gc(e.offset,e.seq))}}getSequenceInterval(e,t,i){const n=this.sequences.get(e);if(n)for(let r of n){const n=r.sequence,s=r.offset,o=s+n.length;if(s<=t&&o>=i)return new dc(e,s,o,n)}}}class gc{constructor(e,t){this.offset=e,this.sequence=t}contains(e,t){return this.offset<=e&&this.end>=t}overlaps(e,t){return this.offset<t&&this.end>e}get end(){return this.offset+this.sequence.length}}const mc=Dt,wc=new Set([\"fastaURL\",\"indexURL\",\"compressedIndexURL\",\"cytobandURL\",\"indexed\"]);class bc{#e;chromosomes=new Map;constructor(e){this.file=e.fastaURL,this.indexFile=e.indexURL,this.compressedIndexFile=e.compressedIndexURL,this.withCredentials=e.withCredentials;const t={};for(let i in e)e.hasOwnProperty(i)&&!wc.has(i)&&(t[i]=e[i]);this.config=t}getSequenceRecord(e){return this.chromosomes.get(e)}async init(){return this.getIndex()}get chromosomeNames(){return this.#e||(this.#e=Array.from(this.chromosomes.keys())),this.#e}getFirstChromosomeName(){return this.chromosomeNames[0]}async getIndex(){if(this.index)return this.index;{const e=await Qs.load(this.indexFile,Ua(this.config)),t=mc(e),i=t.length;let n=0,r=0;for(this.index={};n<i;){const e=t[n++].split(\"\\t\");if(5===e.length){const t=e[0],i=parseInt(e[1]),n={size:i,position:parseInt(e[2]),basesPerLine:parseInt(e[3]),bytesPerLine:parseInt(e[4])};this.index[t]=n,this.chromosomes.set(t,new lc(t,r++,i))}}return this.index}}async getCompressedIndex(){if(this.compressedIndex)return this.compressedIndex;if(!this.compressedIndexFile)return this.compressedIndex=[],this.compressedIndex;this.compressedIndex=[];const e=await Qs.loadArrayBuffer(this.compressedIndexFile,Ua(this.config)),t=e.byteLength;if(t<8)return console.log(\"Cannot parse GZI index file: length (\"+t+\" bytes) is insufficient to determine content of index.\"),this.compressedIndex;const i=e.slice(0,8),n=Number(new DataView(i).getBigUint64(0,!0)),r=8+2*n*8;if(t!=r)return console.log(\"Incorrect file size of reference genome index. Expected : \"+r+\". Received : \"+t),this.compressedIndex;this.compressedIndex.push([0,0]);for(let t=0;t<n;t++){const i=8+2*t*8,n=8+2*t*8+16,r=e.slice(i,n),s=new DataView(r),o=Number(s.getBigUint64(0,!0)),a=Number(s.getBigUint64(8,!0));this.compressedIndex.push([o,a])}return this.compressedIndex}async getRelevantCompressedBlockNumbers(e,t){if(e<0||t<0||t<e)return console.log(\"Incompatible query positions for reference-genome. Start:\"+e+\" | End:\"+t),[];await this.getCompressedIndex();let i=[];const n=this.compressedIndex.length-1;if(0==this.compressedIndex.length)return console.log(\"Compressed index does not contain any content\"),[];if(e>this.compressedIndex[n][1])return[n];let r=0,s=n,o=Math.floor(this.compressedIndex.length/2),a=this.compressedIndex.length+1,c=!1;for(let t=0;t<a;t++){const t=this.compressedIndex[o][1],i=o<this.compressedIndex.length-1?this.compressedIndex[o+1][1]:1/0;if(t<=e&&i>e){c=!0;break}t<e?r=o+1:s=o-1,o=Math.ceil((s-r)/2)+r}if(!c)return console.log(\"No blocks within compressed index found that correspond with query positions \"+e+\",\"+t),console.log(this.compressedIndex),[];i.push(o);for(let e=o+1;e<this.compressedIndex.length;e++){i.push(e);if(this.compressedIndex[e][1]>=t)break}const l=i[i.length-1];return l===this.compressedIndex.length-1&&this.compressedIndex[l][1]<t&&i.push(-1),i}async loadAndUncompressBlocks(e,t){if(await this.getCompressedIndex(),0==e.length)return\"\";let i=Array(e.length-1);for(let t=0;t<e.length-1;t++){const n=e[t],r=this.compressedIndex[n][0],s=e[t+1];let o=[];if(-1!=s){const e=this.compressedIndex[s][0]-r;o=await Qs.loadArrayBuffer(this.file,Ua(this.config,{range:{start:r,size:e}}))}else o=await Qs.loadArrayBuffer(this.file,Ua(this.config,{range:{start:r}}));const a=await gs(o);i[t]=a}let n=\"\";for(let e=0;e<i.length;e++)for(let t=0;t<i[e].length;t++){n+=String.fromCharCode(i[e][t])}const r=t-this.compressedIndex[e[0]][1];return n=n.substring(r),n}async readSequence(e,t,i){await this.getIndex(),await this.getCompressedIndex();const n=this.index[e];if(!n)return console.log(\"No index entry for chr: \"+e),this.index[e]=null,null;const r=Math.max(0,t),s=Math.min(n.size,i),o=n.bytesPerLine,a=n.basesPerLine,c=n.position,l=o-a,h=Math.floor(r/a),d=Math.floor(s/a),u=r-h*a,f=c+h*o+u,p=c+d*o+(s-d*a)-1,g=p-f+1;if(g<=0)return console.error(\"No sequence for \"+e+\":\"+t+\"-\"+i),null;let m;if(this.compressedIndexFile){let e=await this.getRelevantCompressedBlockNumbers(f,p);if(0===e.length)return console.log(\"No blocks in the compressed index that correspond with the requested byte positions (\"+f+\",\"+p+\")\"),null;m=await this.loadAndUncompressBlocks(e,f)}else m=await Qs.load(this.file,Ua(this.config,{range:{start:f,size:g}}));if(!m)return null;let w,b=\"\",F=0,v=m.length;for(u>0&&(w=Math.min(s-r,a-u),b+=m.substr(F,w),F+=w+l);F<v;)w=Math.min(a,v-F),b+=m.substr(F,w),F+=w+l;return b}}const Fc=Dt;class vc{#e;chromosomes=new Map;constructor(e){this.url=e}async init(){return this.loadAll()}getSequenceRecord(e){return this.chromosomes.get(e)}get chromosomeNames(){this.#e||(this.#e=Array.from(this.chromosomes.keys()))}async getSequence(e,t,i){return null}async loadAll(){let e;if(Ga(this.url)){let t=vs(this.fastaURL);e=\"\";for(let i of t)e+=String.fromCharCode(i)}else e=await Qs.load(this.url,{});const t=Fc(e);let i=0;for(let e of t){const t=e.split(\"\\t\");if(t.length>1){const e=Number.parseInt(t[1]),n=new lc(t[0],i++,e);this.chromosomes.set(t[0],n)}}}}class yc{constructor(e,t=!0){this.littleEndian=t,this.position=0,this.view=e,this.length=e.byteLength}dumpBytes(e=100){const t=this.position,i=[];for(let t=0;t<=e;t++)i.push(this.getByte());console.log(i.join(\" \")),this.setPosition(t)}setPosition(e){this.position=e}available(){return this.length-this.position}remLength(){return this.length-this.position}hasNext(){return this.position<this.length-1}getByte(){const e=this.view.getUint8(this.position,this.littleEndian);return this.position++,e}getShort(){const e=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,e}getUShort(){const e=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,e}getInt(){const e=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,e}getUInt(){const e=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,e}getLong(){var e=[];e[0]=this.view.getUint8(this.position),e[1]=this.view.getUint8(this.position+1),e[2]=this.view.getUint8(this.position+2),e[3]=this.view.getUint8(this.position+3),e[4]=this.view.getUint8(this.position+4),e[5]=this.view.getUint8(this.position+5),e[6]=this.view.getUint8(this.position+6),e[7]=this.view.getUint8(this.position+7);let t=0;if(this.littleEndian)for(let i=e.length-1;i>=0;i--)t=256*t+e[i];else for(let i=0;i<e.length;i++)t=256*t+e[i];return this.position+=8,t}getString(e){let t,i=\"\";for(;0!==(t=this.view.getUint8(this.position++))&&(i+=String.fromCharCode(t),!e||i.length!==e););return i}getFixedLengthString(e){let t=\"\";for(let i=0;i<e;i++){const e=this.view.getUint8(this.position++);e>0&&(t+=String.fromCharCode(e))}return t}getFloat(){var e=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,e}getDouble(){var e=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,e}skip(e){return this.position+=e,this.position}getVPointer(){var e=this.position,t=this.view.getUint8(e+1)<<8|this.view.getUint8(e),i=4294967296*(255&this.view.getUint8(e+6))+16777216*(255&this.view.getUint8(e+5))+65536*(255&this.view.getUint8(e+4))+256*(255&this.view.getUint8(e+3))+(255&this.view.getUint8(e+2));return this.position+=8,new Ac(i,t)}}class Ac{constructor(e,t){this.block=e,this.offset=t}isLessThan(e){return this.block<e.block||this.block===e.block&&this.offset<e.offset}isGreaterThan(e){return this.block>e.block||this.block===e.block&&this.offset>e.offset}isEqualTo(e){return this.block===e.block&&this.offset===e.offset}print(){return this.block+\":\"+this.offset}}class Cc{static magic=2026540177;littleEndian=!0;nodeCache=new Map;static async loadBpTree(e,t,i){return new Cc(e,t,i).init()}constructor(e,t,i){this.path=e,this.config=t,this.startOffset=i}async init(){const e=await this.#t(this.startOffset,32);let t=e.getInt();if(t!==Cc.magic&&(e.setPosition(0),this.littleEndian=!this.littleEndian,e.littleEndian=this.littleEndian,t=e.getInt(),t!==Cc.magic))throw Error(`Bad magic number ${t}`);const i=e.getInt(),n=e.getInt(),r=e.getInt(),s=e.getLong(),o=e.getLong(),a=this.startOffset+32;return this.header={magic:t,blockSize:i,keySize:n,valSize:r,itemCount:s,reserved:o,nodeOffset:a},this}async search(e){this.header||await this.init();const{keySize:t,valSize:i}=this.header;if(16!==i&&8!==i)throw Error(`Unexpected valSize ${i}`);const n=async e=>{if(this.nodeCache.has(e))return this.nodeCache.get(e);{let n=await this.#t(e,4);const r=n.getByte();n.getByte();const s=n.getUShort(),o=[];if(1===r){const r=s*(t+i);n=await this.#t(e+4,r);for(let e=0;e<s;e++){const e=n.getFixedLengthString(t),r=n.getLong();let s;if(16===i){const e=n.getInt();n.getInt(),s={offset:r,length:e}}else s={offset:r};o.push({key:e,value:s})}}else{const i=s*(t+8);n=await this.#t(e+4,i);for(let e=0;e<s;e++){const e=n.getFixedLengthString(t),i=n.getLong();o.push({key:e,offset:i})}}const a={type:r,count:s,items:o};return this.nodeCache.set(e,a),a}},r=async t=>{const i=await n(t);if(1!==i.type){let t=i.items[0].offset;for(let n=1;n<i.items.length;n++){const r=i.items[n].key;if(e.localeCompare(r)<0)break;t=i.items[n].offset}return r(t)}for(let t of i.items)if(e===t.key)return t.value};return r(this.header.nodeOffset)}async#t(e,t){const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:t}}));return new yc(new DataView(i),this.littleEndian)}}\n",
-       "/**\n",
-       "     * Note: Some portions of this code adapated from the GMOD two-bit.js project, @Copyright (c) 2017 Robert Buels\n",
-       "     * * https://github.com/GMOD/twobit-js/blob/master/src/twoBitFile.ts*\n",
-       "     */const _c=[\"T\",\"C\",\"A\",\"G\"],xc=[];for(let IA=0;IA<256;IA++)xc.push(_c[IA>>6&3]+_c[IA>>4&3]+_c[IA>>2&3]+_c[3&IA]);const kc=xc.map((e=>e.toLowerCase()));class Ic{littleEndian;metaIndex=new Map;constructor(e){this.url=e.twoBitURL||e.fastaURL,this.config=e,e.twoBitBptURL&&(this.bptURL=e.twoBitBptURL)}async init(){if(this.bptURL)this.index=await Cc.loadBpTree(this.bptURL,this.config,0);else{const e=await this._readIndex();this.index={search:async t=>e.has(t)?{offset:e.get(t)}:void 0}}}async readSequence(e,t,i){this.index||await this.init();const n=await this.getSequenceRecord(e);if(!n)return null;if(t<0)throw new TypeError(\"regionStart cannot be less than 0\");(void 0===i||i>n.dnaSize)&&(i=n.dnaSize);const r=this._getOverlappingBlocks(t,i,n.nBlocks),s=this._getOverlappingBlocks(t,i,n.maskBlocks),o=Math.floor(t/4),a=n.packedPos+o,c=Math.floor(i/4)-o+1,l=await Qs.loadArrayBuffer(this.url,{range:{start:a,size:c}}),h=new Uint8Array(l);let d=\"\";for(let e=t;e<i;e+=1){for(;s.length&&s[0].end<=e;)s.shift();const t=s[0]&&s[0].start<=e&&s[0].end>e;if(r[0]&&e>=r[0].start&&e<r[0].end){const t=r.shift();for(;e<t.end&&e<i;)d+=\"N\",e++;e--}else{const i=e%4,n=h[Math.floor(e/4)-o];d+=t?kc[n][i]:xc[n][i]}}return d}async _readIndex(){const e=new Map;let t=await Qs.loadArrayBuffer(this.url,{range:{start:0,size:64}}),i=new DataView(t),n=0;const r=i.getUint32(n,!0),s=i.getUint32(n,!1);n+=4;const o=440477507;if(r===o)this.littleEndian=!0;else{if(s!==o)throw Error(`Bad magic number ${o}`);this.littleEndian=!1}let a,c;this.version=i.getUint32(n,this.littleEndian),n+=4,this.sequenceCount=i.getUint32(n,this.littleEndian),n+=4,this.reserved=i.getUint32(n,this.littleEndian),n+=4;let l=20;for(let t=0;t<this.sequenceCount;t++){(!c||c.available()<1)&&(a=(this.sequenceCount-t)*l,c=await this._loadBinaryBuffer(n,a));const i=c.getByte();n+=1,c.available()<i+5&&(a=(this.sequenceCount-t)*l+100,c=await this._loadBinaryBuffer(n,a));const r=c.getString(i),s=c.getUInt();n+=i+4,e.set(r,s),l=Math.floor(l*(t/(t+1))+r.length/(t+1))}return e}async getSequenceRecord(e){if(!this.metaIndex.has(e)){if(!this.index)throw Error(\"TwobitSequence object must be initialized before accessing sequence\");let t=await this.index.search(e);if(!t)return;let i=t.offset,n=8,r=await this._loadBinaryBuffer(i,n);const s=r.getUInt(),o=r.getUInt();i+=n,n=8*o+4,r=await this._loadBinaryBuffer(i,n);const a=[];for(let e=0;e<o;e++)a.push(r.getUInt());const c=[];for(let e=0;e<o;e++)c.push(r.getUInt());const l=r.getUInt();i+=n,n=8*l+4,r=await this._loadBinaryBuffer(i,n);const h=[];for(let e=0;e<l;e++)h.push(r.getUInt());const d=[];for(let e=0;e<l;e++)d.push(r.getUInt());const u=[];for(let e=0;e<o;e++)u.push(new Sc(a[e],c[e]));const f=[];for(let e=0;e<l;e++)f.push(new Sc(h[e],d[e]));if(0!=r.getUInt())throw Error(\"Bad 2-bit file\");i+=n;const p={dnaSize:s,nBlocks:u,maskBlocks:f,packedPos:i,bpLength:s};this.metaIndex.set(e,p)}return this.metaIndex.get(e)}_getOverlappingBlocks(e,t,i){const n=[];for(let r of i){if(r.start>t)break;r.end<e||n.push(r)}return n}async _loadBinaryBuffer(e,t){const i=await Qs.loadArrayBuffer(this.url,{range:{start:e,size:t}});return new yc(new DataView(i),this.littleEndian)}}class Sc{constructor(e,t){this.start=e,this.size=t}get end(){return this.start+this.size}}class Ec{static#i=1e5;#n;#r=[];#s=10;constructor(e,t){this.sequenceReader=e,this.browser=t}get chromosomes(){return this.sequenceReader.chromosomes}async getSequenceRecord(e){return this.sequenceReader.getSequenceRecord(e)}async getSequence(e,t,i){let n=this.#r.find((n=>n.contains(e,t,i)));if(n||(n=await this.#o(e,t,i),this.#a(n),this.#r.push(n)),n){const e=t-n.start,r=i-t;return n.features?n.features.substring(e,e+r):null}}#a(e){this.#r=this.#r.filter((t=>!e.contains(t))),this.#r.length===this.#s&&this.#r.shift(),this.browser&&this.browser.referenceFrameList.length<100&&(this.#r=this.#r.filter((e=>void 0!==this.browser.referenceFrameList.find((t=>t.overlaps(e))))))}getSequenceInterval(e,t,i){return this.#r.find((n=>n.contains(e,t,i)))}async#o(e,t,i){let n=t,r=i;if(i-t<Ec.#i){const e=i-t,s=Math.round(t+e/2);n=Math.max(0,s-Ec.#i/2),r=n+Ec.#i}const s=new dc(e,n,r);if(this.#n&&this.#n[0].contains(e,t,i))return this.#n[1];{const t=new Promise((async(t,i)=>{s.features=await this.sequenceReader.readSequence(e,n,r),t(s)}));return this.#n=[s,t],t}}async init(){return this.sequenceReader.init()}get chromosomeNames(){return this.sequenceReader.chromosomeNames}getFirstChromosomeName(){return\"function\"==typeof this.sequenceReader.getFirstChromosomeName?this.sequenceReader.getFirstChromosomeName():void 0}#c(e){this.browser.referenceFrameList}}async function Nc(e,t){let i;return\"chromsizes\"===e.format?i=new vc(e.fastaURL||e.url):\"2bit\"===e.format||e.twoBitURL?i=new Ec(new Ic(e),t):Ga(e.fastaURL)||!e.indexURL?i=new pc(e):\"gbk\"===e.format||e.gbkURL||(i=new Ec(new bc(e),t)),await i.init(),i}const Bc={A:\"rgb(  0, 200,   0)\",C:\"rgb(  0,0,200)\",T:\"rgb(255,0,0)\",G:\"rgb(209,113,  5)\",N:\"rgb(80,80,80)\"};function Mc(e,t){if(e.length<6)return void console.log(\"Skipping line: \"+e.join(\" \"));var i={chr1:e[0],start1:Number.parseInt(e[1]),end1:Number.parseInt(e[2]),chr2:e[3],start2:Number.parseInt(e[4]),end2:Number.parseInt(e[5])};if(isNaN(i.start1)||isNaN(i.end1)||isNaN(i.start2)||isNaN(i.end2))return;t&&void 0===t.hiccups&&(t.hiccups=!!t.columnNames&&Dc(t.columnNames));const n=t&&t.hiccups,r=n?6:10;if(n||(e.length>6&&\".\"!==e[6]&&(i.name=e[6]),e.length>7&&\".\"!==e[7]&&(i.score=Number(e[7])),e.length>8&&\".\"!==e[8]&&(i.strand1=e[8]),e.length>9&&\".\"!==e[9]&&(i.strand2=e[9])),t){const n=t.colorColumn;n&&n<e.length&&(i.color=_s.createColorString(e[n]));const s=t.thicknessColumn;s&&s<e.length&&(i.thickness=e[s]),e.length>r&&t.columnNames&&t.columnNames.length===e.length&&(i.extras=e.slice(r))}return i.chr1===i.chr2&&(i.chr=i.chr1,i.start=Math.min(i.start1,i.start2),i.end=Math.max(i.end1,i.end2)),i}function Rc(e,t){if(!(e.length<8))return{chr:e[0],start:Number.parseInt(e[1]),end:Number.parseInt(e[2]),color:_s.createColorString(e[6]),value:Number(e[7])}}function Dc(e){return e&&(e.includes(\"fdrDonut\")||e.includes(\"fdr_donut\"))}function Tc(e,t){if(!(e.length<6))return{chr:e[0],start:Number.parseInt(e[1]),end:Number.parseInt(e[2]),chr1:e[8],start1:Number.parseInt(e[9]),end1:Number.parseInt(e[10]),chr2:e[13],start2:Number.parseInt(e[14]),end2:Number.parseInt(e[15]),name:e[3],score:Number(e[4]),value:Number(e[5]),color:\".\"===e[7]?void 0:\"0\"===e[7]?\"rgb(0,0,0)\":e[7]};console.log(\"Skipping line: \"+e.join(\" \"))}class Lc{constructor(e){this.message=e}}const zc=new Map([[\"%09\",\"\\t\"],[\"%0A\",\"\\n\"],[\"%0D\",\"\\r\"],[\"%25\",\"%\"],[\"%3B\",\";\"],[\"%3D\",\"=\"],[\"%26\",\"&\"],[\"%2C\",\",\"]]);function Hc(e){if(!e.includes(\"%\"))return e;let t=\"\";for(let i=0;i<e.length;i++)if(37===e.charCodeAt(i)&&i<e.length-2){const n=e.substring(i,i+3);zc.has(n)?t+=zc.get(n):t+=n,i+=2}else t+=e.charAt(i);return t}function Pc(e,t=\"=\"){const i=\"=\"===t;var n=[];for(let r of e.split(\";\")){r=r.trim();const e=r.indexOf(t);if(e>0&&e<r.length-1){let t=Hc(r.substring(0,e).trim()),s=Hc(r.substring(e+1).trim());i||(t=Oc(t),s=Oc(s)),n.push([t,s])}}return n}function Oc(e){return e.startsWith('\"')&&e.endsWith('\"')&&(e=e.substr(1,e.length-2)),e}function Uc(e,t,i=Number.MAX_SAFE_INTEGER){if(e.length<3)return;t&&t.gffTags;const n=e[0],r=parseInt(e[1]),s=e.length>2?parseInt(e[2]):r+1;if(isNaN(r)||isNaN(s))return new Lc(\"Unparsable bed record.\");const o=new nl({chr:n,start:r,end:s,score:1e3});let a=3;try{if(e.length>3&&a++<i){if(e[3].indexOf(\";\")>0&&e[3].indexOf(\"=\")>0){const i=Pc(e[3],\"=\");o.attributes={};for(let e of i)o.attributes[e[0]]=e[1],null!=t.nameField&&e[0]===t.nameField&&(o.name=e[1])}o.name||(o.name=\".\"===e[3]?\"\":e[3])}if(e.length>4&&a++<i&&(o.score=\".\"===e[4]?0:Number(e[4]),isNaN(o.score)))return o;if(e.length>5&&a++<i&&(o.strand=e[5],\".\"!==o.strand&&\"+\"!==o.strand&&\"-\"!==o.strand))return o;if(e.length>6&&a++<i&&(o.cdStart=parseInt(e[6]),isNaN(o.cdStart)))return o;if(e.length>7&&a++<i&&(o.cdEnd=parseInt(e[7]),isNaN(o.cdEnd)))return o;if(e.length>8&&a++<i&&\".\"!==e[8]&&\"0\"!==e[8]&&(o.color=_s.createColorString(e[8])),e.length>11&&a++<i){const t=parseInt(e[9]);if(t>1e3)return o;const i=e[10].replace(/,$/,\"\").split(\",\"),n=e[11].replace(/,$/,\"\").split(\",\");if(i.length!==n.length||t!==i.length)return o;const s=[];for(let e=0;e<t;e++){const t=r+parseInt(n[e]),o=t+parseInt(i[e]);s.push({start:t,end:o})}s.length>0&&(Yc(s,o.cdStart,o.cdEnd),o.exons=s)}if(t){let i=t.thicknessColumn,n=t.colorColumn;n&&n<e.length&&(o.color=_s.createColorString(e[n])),i&&i<e.length&&(o.thickness=e[i])}}catch(e){}return o}function qc(e,t){const i=Uc(e,t);return i&&e.length>14&&(i.signal=Number(e[12]),i.pValue=Number(e[13]),i.qValue=Number(e[14])),i}function Qc(e,t){const i=Uc(e,t,9);if(i){const t=[\"Coverage\",\"% Showing Methylation\",\"N-mod\",\"N-canonical\",\"N-other mod\",\"N-delete\",\"N-fail\",\"N-dff\",\"N-nocall\"];for(let n=9;n<e.length;n++){i[t[n-9]]=e[n]}}return i}function Vc(e,t){if(e.length<=15)return;return{swScore:Number.parseInt(e[1]),milliDiv:Number.parseInt(e[2]),milliDel:Number.parseInt(e[3]),milliIns:Number.parseInt(e[4]),chr:e[5],start:Number.parseInt(e[6]),end:Number.parseInt(e[7]),strand:e[9],repName:e[10],repClass:e[11],repFamily:e[12],repStart:Number.parseInt(e[13]),repEnd:Number.parseInt(e[14]),repLeft:Number.parseInt(e[15])}}function jc(e,t){var i=void 0===t.shift?0:1;if(e.length<=9+i)return;const n=parseInt(e[5+i]),r=parseInt(e[6+i]);var s={name:e[0+i],chr:e[1+i],strand:e[2+i],start:parseInt(e[3+i]),end:parseInt(e[4+i]),cdStart:n,cdEnd:r,id:e[0+i]};const o=Kc(parseInt(e[7+i]),e[8+i],e[9+i]);return Yc(o,n,r),s.exons=o,s}function Wc(e,t){var i=void 0===t.shift?0:1;if(e.length<=11+i)return;const n=parseInt(e[5+i]),r=parseInt(e[6+i]),s={name:e[11+i],chr:e[1+i],strand:e[2+i],start:parseInt(e[3+i]),end:parseInt(e[4+i]),cdStart:n,cdEnd:r,id:e[0+i]},o=Kc(parseInt(e[7+i]),e[8+i],e[9+i],e[14+i]);return Yc(o,n,r),s.exons=o,s}function Gc(e,t){var i=void 0===t.shift?0:1;if(e.length<=10+i)return;const n=parseInt(e[6+i]),r=parseInt(e[7+i]);var s={name:e[0+i],id:e[1+i],chr:e[2+i],strand:e[3+i],start:parseInt(e[4+i]),end:parseInt(e[5+i]),cdStart:n,cdEnd:r};const o=Kc(parseInt(e[8+i]),e[9+i],e[10+i]);return Yc(o,n,r),s.exons=o,s}function $c(e,t){if(e.length<21)return;const i=e[13],n=parseInt(e[15]),r=parseInt(e[16]),s=e[8].charAt(0),o=parseInt(e[17]),a=[],c=e[20].replace(/,$/,\"\").split(\",\"),l=e[18].replace(/,$/,\"\").split(\",\");for(let e=0;e<o;e++){const t=parseInt(c[e]),i=t+parseInt(l[e]);a.push({start:t,end:i})}return new rl({chr:i,start:n,end:r,strand:s,exons:a,tokens:e})}function Kc(e,t,i,n){const r=t.replace(/,$/,\"\").split(\",\"),s=i.replace(/,$/,\"\").split(\",\"),o=n?n.replace(/,$/,\"\").split(\",\"):void 0,a=[];for(let t=0;t<e;t++){const e={start:parseInt(r[t]),end:parseInt(s[t])};if(o){const i=parseInt(o[t]);-1!=i&&(e.readingFrame=i)}a.push(e)}return a}function Yc(e,t,i){for(let n of e){const e=n.end,r=n.start;e<t||r>i?n.utr=!0:(t>=r&&t<=e&&(n.cdStart=t),i>=r&&i<=e&&(n.cdEnd=i))}}function Xc(e,t){var i,n,r,s,o,a,c;if(!(e.length<9))return i=e[0],n=parseInt(e[1]),r=parseInt(e[2]),o=e[3],a=Number(e[4]),s=e[5].trim(),c=Number(e[6]),0===a&&(a=c),{chr:i,start:n,end:r,name:o,score:a,strand:s,signal:c,pValue:Number(e[7]),qValue:Number(e[8])}}function Zc(e,t){const i=Xc(e);return e.length>9&&(i.peak=Number(e[9])),i}function Jc(e,t){if(e.length<=3)return;const i={chr:e[0],start:parseInt(e[1]),end:parseInt(e[2]),value:Number(e[3])};if(t){let n=t.colorColumn;n&&n<e.length&&(i.color=_s.createColorString(e[n]))}return i}function el(e,t){const i=t.wig;if(i&&\"fixedStep\"===i.format){const t=i.index*i.step+i.start,n=t+i.span,r=Number(e[0]);return++i.index,isNaN(r)?null:{chr:i.chrom,start:t,end:n,value:r}}if(i&&\"variableStep\"===i.format){if(e.length<2)return null;const t=parseInt(e[0],10)-1,n=t+i.span,r=Number(e[1]);return isNaN(r)?null:{chr:i.chrom,start:t,end:n,value:r}}return Jc(e)}function tl(e,t){if(e.length<6)return;const i=[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"refNCBI\",\"refUCSC\",\"observed\",\"molType\",\"class\",\"valid\",\"avHet\",\"avHetSE\",\"func\",\"locType\",\"weight\",\"exceptions\",\"submitterCount\",\"submitters\",\"alleleFreqCount\",\"alleles\",\"alleleNs\",\"alleleFreqs\",\"bitfields\"],n={chr:e[1],start:Number.parseInt(e[2]),end:Number.parseInt(e[3]),name:e[4],score:Number.parseInt(e[5])},r=Math.min(e.length,i.length);for(let t=6;t<r;t++)n[i[t]]=e[t];return n}function il(e,t,i=Number.MAX_SAFE_INTEGER){if(e.length<4)return;const n=e[0],r=parseInt(e[1]),s=e.length>2?parseInt(e[2]):r+1;if(isNaN(r)||isNaN(s))return new Lc(\"Unparsable bed record.\");const o=new nl({chr:n,start:r,end:s,score:1e3}),a=[];for(let t=3;t<e.length;t++)a.push(Number.parseInt(e[t]));return o.values=a,o}class nl{constructor(e){Object.assign(this,e)}getAttributeValue(e){return this.hasOwnProperty(e)?this[e]:this.attributes?this.attributes[e]:void 0}}class rl{constructor(e){Object.assign(this,e)}get score(){const e=this.tokens,t=parseInt(e[0]),i=parseInt(e[2]),n=parseInt(e[1]),r=parseInt(e[4]),s=parseInt(e[6]),o=parseInt(e[10]);return Math.floor(1e3*(t+i-n-r-s)/o)}get matches(){return this.tokens[0]}get misMatches(){return this.tokens[1]}get repMatches(){return this.tokens[2]}get nCount(){return this.tokens[3]}get qNumInsert(){return this.tokens[4]}get qBaseInsert(){return this.tokens[5]}get tNumInsert(){return this.tokens[6]}get tBaseInsert(){return this.tokens[7]}popupData(){return[{name:\"chr\",value:this.chr},{name:\"start\",value:this.start+1},{name:\"end\",value:this.end},{name:\"strand\",value:this.strand},{name:\"score\",value:this.score},{name:\"match\",value:this.matches},{name:\"mis-match\",value:this.misMatches},{name:\"rep. match\",value:this.repMatches},{name:\"N's\",value:this.nCount},{name:\"Q gap count\",value:this.qNumInsert},{name:\"Q gap bases\",value:this.qBaseInsert},{name:\"T gap count\",value:this.tNumInsert},{name:\"T gap bases\",value:this.tBaseInsert}]}}const sl=new Set([\"transcript\",\"primary_transcript\",\"processed_transcript\",\"mRNA\",\"mrna\",\"lnc_RNA\",\"miRNA\",\"ncRNA\",\"rRNA\",\"scRNA\",\"snRNA\",\"snoRNA\",\"tRNA\"]),ol=new Set([\"CDS\",\"cds\"]),al=new Set([\"start_codon\",\"stop_codon\"]),cl=new Set([\"5UTR\",\"3UTR\",\"UTR\",\"five_prime_UTR\",\"three_prime_UTR\",\"3'-UTR\",\"5'-UTR\"]),ll=new Set([\"exon\",\"coding-exon\"]),hl=new Set;for(let SA of[ol,al,cl,ll])for(let EA of SA)hl.add(EA);function dl(e){return e.includes(\"intron\")}function ul(e){return ol.has(e)||al.has(e)}function fl(e){return cl.has(e)}function pl(e){return sl.has(e)||e.endsWith(\"RNA\")||e.endsWith(\"transcript\")}function gl(e){return hl.has(e)||e.endsWith(\"RNA\")||dl(e)}const ml=new Set([\"id\",\"parent\",\"name\"]);class wl{constructor(e){Object.assign(this,e),void 0!==e.phase&&\".\"!==e.phase&&(this.readingFrame=(3-parseInt(e.phase))%3)}popupData(e){const t=this.geneObject?this.geneObject.popupData():[];if(this.geneObject&&t.push(\"<hr/>\"),this.name&&t.push({name:\"Name\",value:this.name}),t.push({name:\"Type\",value:this.type}),t.push({name:\"Source\",value:this.source}),void 0!==this.score&&t.push({name:\"Score\",value:this.score}),t.push({name:\"Phase\",value:this.phase}),this.attributeString){const e=Pc(this.attributeString,this.delim);for(let[i,n]of e)void 0!==n&&n.length>0&&!ml.has(i.toLowerCase())&&t.push({name:i+\":\",value:n})}return t.push({name:\"Location\",value:`${this.chr}:${Rt(this.start+1)}-${Rt(this.end)}`}),t}getAttributeValue(e){if(this.hasOwnProperty(e))return this[e];if(this._attributeCache||(this._attributeCache=new Map),this._attributeCache.has(e))return this._attributeCache.get(e);{const t=Pc(this.attributeString,this.delim);let i;for(let[n,r]of t)if(n===e){i=r;break}return this._attributeCache.set(e,i),i}}}class bl extends wl{constructor(e){super(e),this.exons=[],this.parts=[]}addExon(e){this.exons.push(e),this.start=Math.min(this.start,e.start),this.end=Math.max(this.end,e.end)}addPart(e){this.parts.push(e)}assembleParts(){if(0===this.parts.length)return;this.parts.sort((function(e,t){return e.start-t.start}));let e=this.parts[0].start,t=this.parts[0].end;for(let i=1;i<this.parts.length;i++){const n=this.parts[i];if(!dl(n.type))if(n.start<=t)t=Math.max(t,n.end);else{this.findExonContaining({start:e,end:t})||this.exons.push({start:e,end:t,psuedo:!0}),e=n.start,t=n.end}}this.findExonContaining({start:e,end:t})||(this.exons.push({start:e,end:t,psuedo:!0}),this.start=Math.min(this.start,e),this.end=Math.max(this.end,t));for(let e of this.parts){const t=e.type;ul(t)?this.addCDS(e):fl(t)&&this.addUTR(e)}}findExonContaining({start:e,end:t}){for(let i of this.exons)if(i.end>=t&&i.start<=e)return i}addCDS(e){let t;const i=this.exons;for(let n of i)if(n.start<=e.start&&n.end>=e.end){t=n;break}t?(t.cdStart=t.cdStart?Math.min(e.start,t.cdStart):e.start,t.cdEnd=t.cdEnd?Math.max(e.end,t.cdEnd):e.end,t.readingFrame=e.readingFrame):console.error(\"No exon found spanning \"+e.start+\"-\"+e.end),this.cdStart=this.cdStart?Math.min(e.start,this.cdStart):e.start,this.cdEnd=this.cdEnd?Math.max(e.end,this.cdEnd):e.end}addUTR(e){let t;const i=this.exons;for(let n=0;n<i.length;n++)if(i[n].start<=e.start&&i[n].end>=e.end){t=i[n];break}t?e.start===t.start&&e.end===t.end?t.utr=!0:(e.end<t.end&&(t.cdStart=e.end),e.start>t.start&&(t.cdEnd=e.start)):console.error(\"No exon found spanning \"+cds.start+\"-\"+cds.end)}finish(){this.assembleParts();var e=this.cdStart,t=this.cdEnd;this.exons.sort((function(e,t){return e.start-t.start})),e&&this.exons.forEach((function(i){(i.end<e||i.start>t)&&(i.utr=!0)}))}popupData(e){const t=super.popupData(e);for(let i of this.exons)if(!i.pseudo&&e>=i.start&&e<i.end&&\"function\"==typeof i.popupData){t.push(\"<hr/>\");const n=i.popupData(e);for(let e of n)t.push(e)}for(let i of this.parts)if(e>=i.start&&e<i.end&&\"function\"==typeof i.popupData){t.push(\"<hr/>\");const n=i.popupData(e);for(let e of n)t.push(e)}return t}}function Fl(e,t){const i=t.format;if(e.length<9)return;const n=\"gff3\"===i?\"=\":\" \";return new wl({source:Hc(e[1]),type:e[2],chr:e[0],start:parseInt(e[3])-1,end:parseInt(e[4]),score:\".\"===e[5]?void 0:Number(e[5]),strand:e[6],phase:\".\"===e[7]?\".\":parseInt(e[7]),attributeString:e[8],delim:n})}function vl(e,t){const i=Fl(e,t);if(!i)return;const n=Pc(i.attributeString,i.delim);for(let[e,t]of n){const n=e.toLowerCase();\"color\"===n||\"colour\"===n?i.color=_s.createColorString(t):\"ID\"===e?i.id=t:\"Parent\"===e&&(i.parent=t)}return i}function yl(e,t){const i=Fl(e,t);if(!i)return;const n=Pc(i.attributeString,i.delim);let r,s;switch(i.type){case\"gene\":r=\"gene_id\";break;case\"transcript\":r=\"transcript_id\",s=\"gene_id\";break;default:s=\"transcript_id\"}for(let[e,t]of n){const n=e.toLowerCase();\"color\"===n||\"colour\"===n?i.color=_s.createColorString(t):e===r?i.id=t:e===s&&(i.parent=t)}return i}function Al(e,t){if(!(e.length<7)){var i=e[0],n=e[1],r=parseInt(e[2]),s=parseInt(e[3]),o=parseInt(e[4]),a=parseInt(e[5]),c=e[6],l={chr:i,name:n,junction_left:r,junction_right:s,num_junction_reads:o,num_spanning_frags:a,spanning_frag_coords:[],start:-1,end:-1},h=r,d=s;if(a>0)for(var u=c.split(\",\"),f=0;f<u.length;f++){var p=u[f].split(\"-\"),g=p[0],m=p[1];g<h&&(h=g),m>d&&(d=m),l.spanning_frag_coords.push({left:g,right:m})}return l.start=h,l.end=d,l}}function Cl(e,t){if(e.length<7)return null;const i={chr:e[0],start:parseInt(e[1])-1,end:parseInt(e[2]),\"Strongest SNP-risk allele\":e[3],\"Disease/Phenotype\":e[4],\"P-value\":e[5],\"Odds ratio or beta\":e[6]};return e.length>6&&(i.PUBMEDID=`<a target = \"blank\" href = \"https://www.ncbi.nlm.nih.gov/pubmed/${e[7]}\">${e[7]}</a>`),i}function _l(e,t){const i=t.customFormat;if(e.length<i.fields.length)return;const n=i.coords||0,r=e[i.chr],s=parseInt(e[i.start])-n,o={chr:r,start:s,end:void 0!==i.end?parseInt(e[i.end]):s+1};return i.fields&&i.fields.forEach((function(t,n){n!==i.chr&&n!==i.start&&n!==i.end&&(o[t]=e[n])})),o}function xl(e,t){const i=t.columnNames;if(!i)throw Error(\"Sample names are not defined.   Missing column headers?\");const n=i.length-3,r=e[0],s=parseInt(e[1]),o=parseInt(e[2]),a=e.slice(3).map(Number);return a.length==n?{chr:r,start:s,end:o,values:a}:void console.warn(`${r}:${s}-${o} row contains ${a.length} sample columns instead of the expected ${n} columns. Skipping...`)}const kl=[\"Name\",\"transcript_id\",\"gene_name\",\"gene\",\"gene_id\",\"alias\",\"locus\",\"name\"];class Il{constructor(e){this.format=e.format,this.nameField=e.nameField,this.filterTypes=void 0===e.filterTypes?new Set([\"chromosome\"]):new Set(e.filterTypes)}combineFeatures(e,t){let i;const n=this.filterTypes;if(e=e.filter((e=>void 0===n||!n.has(e.type))),\"gff3\"===this.format){const t=this.combineFeaturesById(e);i=this.combineFeaturesByType(t)}else i=this.combineFeaturesByType(e);return this.numberExons(i,t),this.nameFeatures(i),i}combineFeaturesById(e){const t=new Map,i=[];for(let n of e)if(gl(n.type)||pl(n.type)||!n.id)i.push(n);else{let e=t.get(n.chr);e||(e=new Map,t.set(n.chr,e));let i=e.get(n.id);i?i.push(n):e.set(n.id,[n])}for(let e of t.values())for(let t of e.values())if(t.length>1){const e=t[0];e.exons=[];for(let i of t)e.start=Math.min(e.start,i.start),e.end=Math.max(e.end,i.end),e.exons.push({start:i.start,end:i.end});i.push(e)}else i.push(t[0]);return i}combineFeaturesByType(e){const t=e.filter((e=>\"gene\"===e.type||e.type.endsWith(\"_gene\"))),i=Object.create(null);for(let e of t)i[e.id]=e;const n=Object.create(null),r=[],s=new Set,o=this.filterTypes;e=e.filter((e=>void 0===o||!o.has(e.type)));for(let t of e)if(pl(t.type)){const e=t.id;if(void 0!==e){const o=new bl(t);n[e]=o,r.push(o),s.add(t);const a=i[t.parent];a&&(o.geneObject=a,s.add(a))}}for(let t of e)if(gl(t.type)){const e=l(t);if(e)for(let i of e){let o=n[i];if(!o&&\"gtf\"===this.format){const e=Object.assign({},t);e.type=\"transcript\",o=new bl(e),n[i]=o,r.push(o)}if(void 0!==o){if(a=t.type,ll.has(a))if(e.length>1){const e=new wl(t);o.addExon(e)}else o.addExon(t);else o.addPart(t);s.add(t)}}}var a;r.forEach((function(e){\"function\"==typeof e.finish&&e.finish()}));const c=e.filter((e=>!s.has(e)));for(let e of c)r.push(e);return r;function l(e){return e.parent&&\"\"!==e.parent.trim()?e.parent.trim().split(\",\"):null}}numberExons(e,t){for(let i of e)if(i.exons&&(!t||i.end<=t.end&&i.start>t.start))for(let e=0;e<i.exons.length;e++){i.exons[e].number=\"-\"===i.strand?i.exons.length-e:e+1}}nameFeatures(e){for(let t of e)if(\"function\"==typeof t.getAttributeValue)if(this.nameField)t.name=t.getAttributeValue(this.nameField);else for(let e of kl){const i=t.getAttributeValue(e);if(i){t.name=i;break}}}}const Sl={gwascatalog:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"pubMedID\",\"author\",\"pubDate\",\"journal\",\"title\",\"trait\",\"initSample\",\"replSample\",\"region\",\"genes\",\"riskAllele\",\"riskAlFreq\",\"pValue\",\"pValueDesc\",\"orOrBeta\",\"ci95\",\"platform\",\"cnv\"]},wgrna:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"thickStart\",\"thickEnd\",\"type\"]},cpgislandext:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"length\",\"cpgNum\",\"gcNum\",\"perCpg\",\"perGc\",\"obsExp\"]},clinVarMain:{fields:[\"chr1\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"thickStart\",\"thickEnd\",\"reserved\",\"blockCount\",\"blockSizes\",\"chromStarts\",\"origName\",\"clinSign\",\"reviewStatus\",\"type\",\"geneId\",\"snpId\",\"nsvId\",\"rcvAcc\",\"testedInGtr\",\"phenotypeList\",\"phenotype\",\"origin\",\"assembly\",\"cytogenetic\",\"hgvsCod\",\"hgvsProt\",\"numSubmit\",\"lastEval\",\"guidelines\",\"otherIds\"]}};class El{constructor(e){this.config=e,this.header={},e.nameField&&(this.header.nameField=e.nameField),this.skipRows=0,e.decode?(this.decode=e.decode,this.delimiter=e.delimiter||\"\\t\"):e.format&&(this.header.format=e.format.toLowerCase(),this.setDecoder(this.header.format)),this.delimiter||(this.delimiter=\"\\t\")}async parseHeader(e){let t,i,n=this.header;for(;void 0!==(i=await e.nextLine());)if(i.startsWith(\"track\")||i.startsWith(\"#track\")){let e=Nl(i);Object.assign(n,e)}else if(i.startsWith(\"browser\"));else if(i.startsWith(\"#columns\")){let e=Bl(i);Object.assign(n,e)}else if(i.startsWith(\"##gff-version 3\"))n.format=\"gff3\";else if(i.startsWith(\"#gffTags\"))n.gffTags=!0;else{if(i.startsWith(\"fixedStep\")||i.startsWith(\"variableStep\"))break;if(i.startsWith(\"#\")){const e=i.split(this.delimiter||\"\\t\");e.length>1&&(t=e)}else{this.setDecoder(n.format);const e=i.split(this.delimiter||\"\\t\");try{const i=Object.assign({columnNames:t},n);if(this.decode(e,i))break;e.length>1&&(t=e)}catch(i){e.length>1&&(t=e)}}}if(t){n.columnNames=t;for(let e=0;e<t.length;e++)\"color\"===t[e]||\"colour\"===t[e]?n.colorColumn=e:\"thickness\"===t[e]&&(n.thicknessColumn=e)}return this.header=n,n}async parseFeatures(e){const t=[],i=this.decode,n=this.header.format,r=this.delimiter||\"\\t\";let s,o=0,a=0;for(;void 0!==(s=await e.nextLine());){if(o++,o<=this.skipRows)continue;if(!s||s.startsWith(\"track\")||s.startsWith(\"#\")||s.startsWith(\"browser\"))continue;if(\"wig\"===n&&s.startsWith(\"fixedStep\")){this.header.wig=Ml(s);continue}if(\"wig\"===n&&s.startsWith(\"variableStep\")){this.header.wig=Rl(s);continue}const e=s.split(r);if(e.length<1)continue;const c=i(e,this.header);c instanceof Lc?(a++,a>0&&console.error(`Error parsing line '${s}': ${c.message}`)):c&&t.push(c)}return i===Mc&&function(e){if(0==e.length)return;const t=e[0];if(void 0===t.score&&void 0!==t.name){for(let t of e)if(!Va(t.name)&&\".\"!==t.name)return;for(let t of e)t.score=Number(t.name),delete t.name}const i=e.filter((e=>e.chr1!==e.chr2));for(let t of i){const i=Object.assign({},t);i.dup=!0,e.push(i),t.chr=t.chr1,t.start=t.start1,t.end=t.end1,i.chr=i.chr2,i.start=i.start2,i.end=i.end2}}(t),\"gtf\"!==this.config.format&&\"gff3\"!==this.config.format&&\"gff\"!==this.config.format||!1===this.config.assembleGFF?t:new Il(this.config).combineFeatures(t)}setDecoder(e){switch(e){case\"broadpeak\":case\"regionpeak\":case\"peaks\":this.decode=Xc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"narrowpeak\":this.decode=Zc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedgraph\":this.decode=Jc,this.delimiter=/\\s+/;break;case\"wig\":this.decode=el,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gff3\":case\"gff\":this.decode=vl,this.delimiter=\"\\t\";break;case\"gtf\":this.decode=yl,this.delimiter=\"\\t\";break;case\"fusionjuncspan\":this.decode=Al,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gtexgwas\":this.skipRows=1,this.decode=Cl,this.delimiter=\"\\t\";break;case\"refflat\":this.decode=Gc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"genepred\":this.decode=jc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"genepredext\":this.decode=Wc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"ensgene\":this.decode=jc,this.header.shift=1,this.delimiter=this.config.delimiter||/\\s+/;break;case\"refgene\":this.decode=Wc,this.delimiter=this.config.delimiter||/\\s+/,this.header.shift=1;break;case\"bed\":this.decode=Uc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gappedpeak\":this.decode=qc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedmethyl\":this.decode=Qc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedpe\":case\"hiccups\":this.decode=Mc,this.delimiter=this.config.delimiter||\"\\t\";break;case\"bedpe-domain\":this.decode=Rc,this.headerLine=!0,this.delimiter=this.config.delimiter||\"\\t\";break;case\"bedpe-loop\":this.decode=Mc,this.delimiter=this.config.delimiter||\"\\t\",this.header={colorColumn:7};break;case\"interact\":this.decode=Tc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"snp\":this.decode=tl,this.delimiter=\"\\t\";break;case\"rmsk\":this.decode=Vc,this.delimiter=\"\\t\";break;case\"gcnv\":this.decode=xl,this.delimiter=\"\\t\";break;case\"shoebox\":this.decode=il,this.delimiter=\"\\t\";break;default:const t=function(e){return Sl&&Sl[e]?function(e){const t=e.fields,i=[\"chr\",\"start\",\"end\"];for(let n=0;n<t.length;n++)for(let r of i)r===t[n]&&(e[r]=n);return e}(Sl[e]):void 0}(e);void 0!==t?(this.decode=_l,this.header.customFormat=t,this.delimiter=t.delimiter||\"\\t\"):(this.decode=Uc,this.delimiter=this.config.delimiter||/\\s+/)}}}function Nl(e){const t={},i=e.split(/(?:\")([^\"]+)(?:\")|([^\\s\"]+)(?=\\s+|$)/g);let n;const r=[];for(let e of i)e&&0!==e.trim().length&&(e.endsWith(\"=\")?n=e:n?(r.push(n+e),n=void 0):r.push(e));for(let e of r){if(!e)return;var s=e.split(\"=\",2);if(2===s.length){const e=s[0].trim(),i=s[1].trim();if(t.hasOwnProperty(e)){let n=t[e];Array.isArray(n)?n.push(i):t[e]=[n,i]}else t[e]=i}}return\"interact\"==t.type?t.format=\"interact\":\"gcnv\"===t.type&&(t.format=\"gcnv\"),t}function Bl(e){let t={},i=e.split(/\\s+/);if(2===i.length){i[1].split(\";\").forEach((function(e){let i=e.split(\"=\");\"color\"===i[0]?t.colorColumn=Number.parseInt(i[1])-1:\"thickness\"===i[0]&&(t.thicknessColumn=Number.parseInt(i[1])-1)}))}return t}function Ml(e){const t=e.split(/\\s+/);return{format:\"fixedStep\",chrom:t[1].split(\"=\")[1],start:parseInt(t[2].split(\"=\")[1],10)-1,step:parseInt(t[3].split(\"=\")[1],10),span:t.length>4?parseInt(t[4].split(\"=\")[1],10):1,index:0}}function Rl(e){const t=e.split(/\\s+/);return{format:\"variableStep\",chrom:t[1].split(\"=\")[1],span:t.length>2?parseInt(t[2].split(\"=\")[1],10):1}}function Dl(t,i){const n=e({class:\"igv-menu-popup-check-container\"}),r=e();n.appendChild(r);const s=l(\"check\",!0===i?\"#444\":\"transparent\");r.appendChild(s);const o=e();return o.innerText=t,n.appendChild(o),n}function Tl(e,t){t=t||Number.MAX_SAFE_INTEGER;const i=[];e.sort((function(e,t){return e.start-t.start})),i.push(-1e3);for(let n of e){let e=0;const r=Math.min(i.length,t);for(e=0;e<r;e++)if(n.start>=i[e]){n.row=e,i[e]=n.end;break}n.row=e,i[e]=n.end}}async function Ll(e,t,i){const n=e=>{const i=Object.assign({},e);return i.chr=\"all\",i.start=t.getGenomeCoordinate(e.chr,e.start),i.end=t.getGenomeCoordinate(e.chr,e.end),i._f=e,i.exons&&delete i.exons,i},r=new Set(t.wgChromosomeNames),s=[];let o=0;for(let a of t.wgChromosomeNames){if(Array.isArray(e)){const i={};for(let n of e){const e=t.getChromosomeName(n.chr);i.hasOwnProperty(e)||(i[e]=[]),i[e].push(n)}e=i}const c=e[a];if(c){const e=i||1e4;for(let i of c){let a=t.getChromosomeName(i.chr);if(r.has(a))if(s.length<e)s.push(n(i));else{const t=e/(o+1);if(Math.random()<t){s[Math.floor(Math.random()*(e-1))]=n(i)}}o++}}}return s.sort((function(e,t){return e.start-t.start})),s}function zl(e,t){if(t=t||1e3,null==e||0===e.length)return;const i={},n=[];for(let t of e){const e=t.chr;let r=i[e];r||(r=[],i[e]=r,n.push(e)),r.push(t)}for(let e of n)Tl(i[e],t)}class Hl{static defaults={height:50,autoHeight:!1,visibilityWindow:void 0,color:void 0,altColor:void 0,supportHiDPI:!0,selected:!1};constructor(e,t){this.browser=t,this.init(e)}init(e){this.config=e,e.displayMode&&(e.displayMode=e.displayMode.toUpperCase());const t=Object.assign({},Hl.defaults);if(this.constructor.defaults)for(let e of Object.keys(this.constructor.defaults))t[e]=this.constructor.defaults[e];for(let n of Object.keys(t))this[n]=e.hasOwnProperty(n)?e[n]:t[n],\"color\"!==n&&\"altColor\"!==n||!this[n]||(this[n]=Mt(i=this[n])&&i.indexOf(\",\")>0&&!i.startsWith(\"rgb(\")&&!i.startsWith(\"rgba(\")?`rgb(${i})`:i);var i;e.name||e.label?this.name=e.name||e.label:Ht(e.url)?this.name=e.url.name:Mt(e.url)&&!e.url.startsWith(\"data:\")&&(this.name=zt(e.url)),this.url=e.url,this.config.type&&(this.type=this.config.type),this.id=void 0===this.config.id?this.name:this.config.id,this.order=e.order,this.autoscaleGroup=e.autoscaleGroup,this.removable=void 0===e.removable||e.removable,this.minHeight=e.minHeight||Math.min(25,this.height),this.maxHeight=e.maxHeight||Math.max(1e3,this.height),e.onclick&&(this.onclick=e.onclick,e.onclick=void 0),e.description&&(\"function\"==typeof e.description?this.description=e.description:this.description=()=>e.description),e.hoverTextFields?this.hoverText=Pl.bind(this):\"function\"==typeof this.config.hoverText&&(this.hoverText=this.config.hoverText)}get name(){return this._name}set name(e){this._name=e,this.trackView&&this.trackView.setTrackLabelName(e)}clearCachedFeatures(){this.trackView&&this.trackView.clearCachedFeatures()}updateViews(){this.trackView&&this.trackView.updateViews()}repaintViews(){this.trackView&&this.trackView.repaintViews()}getState(){const e={},t=Object.keys(this.config).filter((e=>{return!(void 0===(t=this.config[e])||\"function\"==typeof t||t instanceof Promise);var t}));for(const i of t)i.startsWith(\"_\")||(e[i]=this.config[i]);for(let t of Object.keys(e)){if(t.startsWith(\"_\"))continue;const i=this[t];void 0===i||!Oa(i)&&\"boolean\"!=typeof i&&\"metadata\"!==t||(e[t]=i)}const i=Object.assign({},Hl.defaults);if(this.constructor.defaults)for(let e of Object.keys(this.constructor.defaults))i[e]=this.constructor.defaults[e];for(let t of Object.keys(i))void 0!==this[t]&&i[t]!==this[t]&&(e[t]=this[t]);return!this.autoscale&&this.dataRange&&(e.min=this.dataRange.min,e.max=this.dataRange.max),this.autoscaleGroup&&(e.autoscaleGroup=this.autoscaleGroup),e}get supportsWholeGenome(){return!0===this.config.supportsWholeGenome}hasSamples(){return!1}getGenomeId(){return this.browser.genome?this.browser.genome.id:void 0}setTrackProperties(e){if(this.disposed)return;const t={};let i;for(let n of Object.keys(e))switch(n.toLowerCase()){case\"usescore\":t.useScore=1===e[n]||\"1\"===e[n]||\"on\"===e[n]||!0===e[n];break;case\"visibility\":switch(e[n]){case\"2\":case\"3\":case\"pack\":case\"full\":t.displayMode=\"EXPANDED\";break;case\"4\":case\"squish\":t.displayMode=\"SQUISHED\";break;case\"1\":case\"dense\":t.displayMode=\"COLLAPSED\"}break;case\"color\":case\"altcolor\":t[n]=e[n].startsWith(\"rgb(\")?e[n]:\"rgb(\"+e[n]+\")\";break;case\"featurevisiblitywindow\":case\"visibilitywindow\":t.visibilityWindow=Number.parseInt(e[n]);break;case\"maxheightpixels\":i=e[n].split(\":\"),3===i.length&&(t.minHeight=Number.parseInt(i[2]),t.height=Number.parseInt(i[1]),t.maxHeight=Number.parseInt(i[0]));break;case\"viewlimits\":if(!this.config.autoscale){i=e[n].split(\":\");let r,s=0;1==i.length?r=Number(i[0]):2==i.length&&(s=Number(i[0]),r=Number(i[1])),Number.isNaN(r)||Number.isNaN(s)?console.warn(`Unexpected viewLimits value in track line: ${e.viewLimits}`):(t.autoscale=!1,t.dataRange={min:s,max:r},this.viewLimitMin=s,this.viewLimitMax=r)}case\"name\":t[n]=e[n];break;case\"url\":t.infoURL=e[n];break;case\"type\":const r=e[n];Ol.has(r)?t[n]=Ol.get(r):t[n]=r;break;case\"graphtype\":t.graphType=e[n];break;default:t[n]=e[n]}for(let e of Object.keys(t))if(!this.config.hasOwnProperty(e)||\"name\"===e&&this.config._derivedName){let i=t[e];if(\"true\"===i&&(i=!0),\"false\"===i&&(i=!1),this[e]=i,\"height\"===e&&this.trackView)try{const e=Number.parseInt(i);this.trackView.setTrackHeight(e)}catch(e){console.error(e)}}}clickedFeatures(e){const t=e.viewport.cachedFeatures;if(!t||!Array.isArray(t)||0===t.length)return[];const i=e.genomicLocation,n=e.referenceFrame.bpPerPixel>.2?3*e.referenceFrame.bpPerPixel:.2;return to(t,i-n,i+n)}extractPopupData(e,t){const i=new Set([\"row\",\"color\",\"chr\",\"start\",\"end\",\"cdStart\",\"cdEnd\",\"strand\",\"alpha\"]),n=[];let r,s;for(let t in e)if(e.hasOwnProperty(t)&&!i.has(t)&&Oa(e[t])){let i=e[t];n.push({name:Lt(t),value:i}),\"alleles\"===t?r=e[t]:\"alleleFreqs\"===t&&(s=e[t])}if(r&&s){r.endsWith(\",\")&&(r=r.substr(0,r.length-1)),s.endsWith(\",\")&&(s=s.substr(0,s.length-1));let i=r.split(\",\"),o=s.split(\",\");if(o.length>1){let r=[];for(let e=0;e<o.length;e++)r.push({a:i[e],af:Number(o[e])});r.sort((function(e,t){return e.af-t.af}));let s=r[r.length-1].a;if(1===s.length)for(let i=r.length-2;i>=0;i--){let o=r[i].a;if(1===o.length){t||(t=this.getGenomeId());const i=Hl.getCravatLink(e.chr,e.start+1,s,o,t);console.log(i),i&&(n.push(\"<hr/>\"),n.push({html:i}),n.push(\"<hr/>\"))}}}}if(e.attributes)for(let t of Object.keys(e.attributes))n.push({name:t,value:e.attributes[t]});let o=`${e.chr}:${Rt(e.start+1)}-${Rt(e.end)}`;return e.strand&&(o+=` (${e.strand})`),n.push({name:\"Location\",value:o}),n}description(){const e=(e,t)=>`<div class=\"igv-track-label-popup-shim\"><b>${e}: </b>${t}</div>`;let t='<div class=\"igv-track-label-popup\">';if(this.url?Ht(this.url)?t+=e(\"Filename\",this.url.name):t+=e(\"URL\",this.url):t=this.name,this.config){if(this.config.metadata)for(let i of Object.keys(this.config.metadata)){t+=e(i,this.config.metadata[i])}for(let i of Object.keys(this.config)){if(i.startsWith(\"_\"))continue;let n=i.substr(0,1);if(n!==n.toLowerCase()){const n=this.config[i];n&&Oa(n)&&(t+=e(i,n))}}}return t+=\"</div>\",t}getColorForFeature(e){return\"function\"==typeof this.color?this.color(feature):this.color}numericDataMenuItems(){const e=[];e.push(\"<hr/>\");let t=Bt(\"<div>\");if(t.text(\"Set data range\"),e.push({object:t,dialog:function(){this.trackView.track.selected?this.browser.dataRangeDialog.configure(this.trackView.browser.getSelectedTrackViews()):this.browser.dataRangeDialog.configure(this.trackView),this.browser.dataRangeDialog.present(Bt(this.browser.columnContainer))}}),void 0!==this.logScale){function i(){this.logScale=!this.logScale,this.trackView.repaintViews()}t=Bt(Dl(\"Log scale\",this.logScale)),e.push({object:t,click:i})}return t=Bt(Dl(\"Autoscale\",this.autoscale)),e.push({object:t,click:function(){this.autoscaleGroup=void 0,this.autoscale=!this.autoscale,this.browser.updateViews()}}),e}setDataRange({min:e,max:t}){this.dataRange={min:e,max:t},this.autoscale=!1,this.autoscaleGroup=void 0,this.trackView.repaintViews()}async nextFeatureAfter(e,t,i){let n=this.trackView.viewports[0].cachedFeatures;if(n&&Array.isArray(n)&&n.length>0){if(this.browser.genome.getChromosomeName(n[0].chr)===e){const e=function(e,t,i=!0){const n=e=>(e.start+e.end)/2,r=i?(e,t)=>e.start-t.start+e.end-t.end:(e,t)=>t.start-e.start+t.end-e.end,s=Array.from(e);s.sort(r);let o=0,a=s.length;for(;o<a;){let e=Math.floor((o+a)/2);i?n(s[e])<=t?o=e+1:a=e:n(s[e])>=t?o=e+1:a=e}return s[o]}(n,t,i);if(e)return e}}if(\"function\"==typeof this.featureSource.nextFeature)return this.featureSource.nextFeature(e,t,i,this.visibilityWindow)}dispose(){this.disposed=!0;for(let e of Object.keys(this))this[e]=void 0}static getCravatLink(e,t,i,n,r){if(\"hg38\"===r||\"GRCh38\"===r){return`<a target=\"_blank\" href=\"https://run.opencravat.org/result/nocache/variant.html?chrom=${e.startsWith(\"chr\")?e:\"chr\"+e}&pos=${t}&ref_base=${i}&alt_base=${n}\"><b>Cravat ${i}->${n}</b></a>`}}static localFileInspection(e){const t=Object.assign({},e),i={url:\"file\",indexURL:\"indexFile\"};for(const e of[\"url\",\"indexURL\"])t[e]&&t[e]instanceof File&&(t[i[e]]=t[e].name,delete t[e]);return t}}function Pl(e){if(!this.hoverTextFields)return;const t=this.clickedFeatures(e);if(t&&t.length>0){let e=\"\";for(let i=0;i<t.length;i++){if(10===i){e+=\"; ...\";break}if(!t[i])continue;const n=t[i]._f||t[i];e.length>0&&(e+=\"\\n\"),e=\"\";for(let t of this.hoverTextFields)e.length>0&&(e+=\"\\n\"),n.hasOwnProperty(t)?e+=n[t]:\"function\"==typeof n.getAttribute&&(e+=n.getAttribute(t))}return e}}const Ol=new Map([[\"wiggle_0\",\"wig\"],[\"bed\",\"bed\"],[\"bigBed\",\"bigBed\"],[\"bigWig\",\"bigWig\"]]);class Ul{constructor(e){switch(this.type=e||\"seg\",this.type){case\"mut\":this.sampleColumn=3,this.chrColumn=0,this.startColumn=1,this.endColumn=2,this.dataColumn=4;break;case\"maf\":this.sampleColumn=15,this.chrColumn=4,this.startColumn=5,this.endColumn=6,this.dataColumn=8;break;default:this.sampleColumn=0,this.chrColumn=1,this.startColumn=2,this.endColumn=3}}async parseHeader(e){let t;for(;void 0!==(t=await e.nextLine());)if(!t.startsWith(\"#\")){const e=t.split(\"\\t\");this.header={headings:e};break}return this.header}async parseFeatures(e){const t=[];let i;this.header||(this.header=await this.parseHeader(e)),\"seg\"===this.type&&(this.dataColumn=this.header.headings.length-1),this.header.headings.length>5&&(i=this.extractExtraColumns(this.header.headings));const n=this.header.headings[this.dataColumn];let r;for(;void 0!==(r=await e.nextLine());){const e=r.split(\"\\t\"),s=\"seg\"===this.type?Number(e[this.dataColumn]):e[this.dataColumn];if(e.length>this.dataColumn){const r=new ql({sample:e[this.sampleColumn],chr:e[this.chrColumn],start:parseInt(e[this.startColumn])-1,end:parseInt(e[this.endColumn]),value:s,valueColumnName:n});if(i){const t=this.extractExtraColumns(e);r.setAttributes({names:i,values:t})}t.push(r)}}return t}extractExtraColumns(e){const t=[];for(let i=0;i<e.length;i++)i!==this.chrColumn&&i!==this.startColumn&&i!==this.endColumn&&i!==this.sampleColumn&&t.push(e[i]);return t}}class ql{constructor({sample:e,chr:t,start:i,end:n,value:r,valueColumnName:s}){this.sample=e,this.chr=t,this.start=i,this.end=n,this.value=r,this.valueColumnName=s}setAttributes({names:e,values:t}){this.attributeNames=e,this.attributeValues=t}getAttribute(e){if(this.attributeNames){const t=this.attributeNames.indexOf(e);if(t>=0)return this.attributeValues[t]}}popupData(e,t){const i=new Set([\"chr\",\"start\",\"end\",\"sample\",\"value\",\"row\",\"color\",\"sampleKey\",\"uniqueSampleKey\",\"sampleId\",\"chromosome\",\"uniquePatientKey\"]),n=this.chr+\":\"+Rt(this.start+1)+\"-\"+Rt(this.end),r=[{name:\"Sample\",value:this.sample},{name:\"Location\",value:n},{name:this.valueColumnName?Lt(this.valueColumnName):\"Value\",value:this.value}];if(\"mut\"===e&&\"hg38\"===t){const e=this.extractCravatLink(t);e&&(r.push(\"<hr/>\"),r.push({html:e}),r.push(\"<hr/>\"))}if(this.attributeNames&&this.attributeNames.length>0)for(let e=0;e<this.attributeNames.length;e++)!i.has(this.attributeNames[e])&this.valueColumnName!==this.attributeNames[e]&&r.push({name:Lt(this.attributeNames[e]),value:this.attributeValues[e]});return r}extractCravatLink(e){let t,i;if(this.attributeNames&&this.attributeNames.length>0)for(let n=0;n<this.attributeNames.length;n++)if(t||\"Reference_Allele\"!==this.attributeNames[n]||(t=this.attributeValues[n]),!i&&this.attributeNames[n].startsWith(\"Tumor_Seq_Allele\")&&this.attributeValues[n]!==t&&(i=this.attributeValues[n]),t&&i)return Hl.getCravatLink(this.chr,this.start+1,t,i,e)}}const Ql=new Map([[\"REF\",\"referenceBases\"],[\"ALT\",\"alternateBases\"],[\"QUAL\",\"quality\"],[\"FILTER\",\"filter\"]]);class Vl{constructor(e){this.chr=e[0],this.pos=parseInt(e[1]),this.names=e[2],this.referenceBases=e[3],this.alternateBases=e[4],this.quality=e[5],this.filter=e[6],this.info={};const t=e[7];if(t&&\".\"!==t)for(let e of t.split(\";\")){var i=e.split(\"=\");this.info[i[0]]=i[1]}this.init()}getAttributeValue(e){return Ql.has(e)&&(e=Ql.get(e)),this.hasOwnProperty(e)?this[e]:this.info[e]}init(){const e=this.referenceBases,t=this.alternateBases;if(this.info&&(this.info.VT?this.type=this.info.VT:this.info.SVTYPE?this.type=\"SV\":this.info.PERIOD&&(this.type=\"STR\")),void 0===this.type&&(this.type=function(e,t){const i=e.length;if(void 0===t)return\"UNKNOWN\";if(0===t.trim().length||\"<NON_REF>\"===t||\"<*>\"===t||\".\"===t)return\"NONVARIANT\";{const e=t.split(\",\").map((function(e){return 1===i&&1===e.length?\"SNP\":\"<NON_REF>\"===e?\"NONVARIANT\":e.length>i&&$l(e)?\"INSERTION\":e.length<i&&$l(e)?\"DELETION\":\"OTHER\"}));let n=e[0];for(let t of e)if(t!==n)return\"MIXED\";return n}}(e,t)),this.info.END)this.start=this.pos-1,this.info.CHR2&&this.info.CHR2!==this.chr?this.end=this.start+1:this.end=Number.parseInt(this.info.END);else if(\"NONVARIANT\"===this.type)this.start=this.pos-1,this.end=this.start+e.length;else{const i=t.split(\",\").filter((e=>e.length>0));this.alleles=[],this.start=void 0,this.end=void 0;for(let t of i)if(this.alleles.push(t),\"SV\"!==this.type&&$l(t)){let i=t.length,n=e.length;const r=Math.min(i,n);let s=0;for(;s<r&&e.charCodeAt(s)===t.charCodeAt(s);)s++,i--,n--;for(;i>0&&n>0;){const r=s+i-1,o=s+n-1;if(t.charCodeAt(r)!==e.charCodeAt(o))break;i--,n--}for(;i>0&&n>0;){const r=s,o=s;if(t.charCodeAt(r)!==e.charCodeAt(o))break;s++,i--,n--}const o=this.pos+s-1,a=o+n;this.start=void 0===this.start?o:Math.min(this.start,o),this.end=void 0===this.end?a:Math.max(this.end,a)}void 0===this.start&&(this.start=this.pos-1,this.end=this.pos),this.start===this.end&&(this.start-=.5,this.end+=.5)}}popupData(e,t){const i=`${Rt(this.pos)}`,n=this.start===this.end?`${Rt(this.start)} | ${Rt(this.start+1)}`:`${Rt(this.start+1)}-${Rt(this.end)}`,r=[{name:\"Chr\",value:this.chr},{name:\"Pos\",value:i},{name:\"Loc\",value:n},{name:\"ID\",value:this.names?this.names:\"\"},{name:\"Ref\",value:this.referenceBases},{name:\"Alt\",value:this.alternateBases.replace(\"<\",\"&lt;\")},{name:\"Qual\",value:this.quality},{name:\"Filter\",value:this.filter}];if(this.type&&r.push({name:\"Type\",value:this.type}),\"SNP\"===this.type){let e=this.referenceBases;if(1===e.length){let i=this.alternateBases.split(\",\");for(let n of i)if(1===n.length){let i=Hl.getCravatLink(this.chr,this.pos,e,n,t);i&&(r.push(\"<hr/>\"),r.push({html:i}))}}}const s=Object.keys(this.info);if(this.info&&s.length>0){r.push({html:'<hr style=\"border-top: dotted 1px;border-color: #c9c3ba\" />'});for(let e of s)r.push({name:e,value:Kl(decodeURIComponent(this.info[e]))})}return r}getInfo(e){return this.info?this.info[e]:void 0}isRefBlock(){return\"NONVARIANT\"===this.type}isFiltered(){return!(\".\"===this.filter||\"PASS\"===this.filter)}alleleFreq(){return this.info?this.info.AF:void 0}}class jl{constructor(e){this.mate=e,this.chr=e.info.CHR2,this.pos=Number.parseInt(e.info.END),this.start=this.pos-1,this.end=this.pos}get info(){return this.mate.info}get names(){return this.mate.names}get referenceBases(){return this.mate.referenceBases}get alternateBases(){return this.mate.alternateBases}get quality(){return this.mate.quality}get filter(){return this.mate.filter}get calls(){return this.mate.calls}getAttributeValue(e){return this.mate.getAttributeValue(e)}getInfo(e){this.mate.getInfo(e)}isFiltered(){return this.mate.isFiltered()}alleleFreq(){return this.mate.alleleFreq()}popupData(e,t){const i=[];return i.push(\"SV Breakpoint\"),i.push({name:\"Chr\",value:this.chr}),i.push({name:\"Pos\",value:`${Rt(this.pos)}`}),i.push({html:'<hr style=\"border-top: dotted 1px;border-color: #c9c3ba\" />'}),i.push(\"SV\"),i.push(...this.mate.popupData(e,t)),i}}class Wl{constructor({formatFields:e,sample:t,token:i}){this.info={},this.sample=t;const n=i.split(\":\");for(let t=0;t<n.length;t++){const i=n[t];if(t==e.genotypeIndex){this.genotype=[];for(let e of i.split(/[\\|\\/]/))this.genotype.push(\".\"===e?e:parseInt(e))}else this.info[e.fields[t]]=i}}get zygosity(){if(!this._zygosity)if(this.genotype){let e=!0,t=!0,i=!1;for(let n of this.genotype){if(\".\"===n){i=!0;break}0!==n&&(t=!1),0===n&&(e=!1)}this._zygosity=i?\"nocall\":t?\"homref\":e?\"homvar\":\"hetvar\"}else this._zygosity=\"unknown\";return this._zygosity}zygosityScore(){switch(this.zygosity){case\"homvar\":return 4;case\"hetvar\":return 3;case\"homref\":return 2;case\"nocall\":return 1;default:return 0}}#l(){switch(this.zygosity){case\"homref\":return\"Homozygous reference\";case\"homvar\":return\"Homozygous variant\";case\"hetvar\":return\"Heterozygous\";default:return\"\"}}popupData(e,t){const i=[];void 0!==this.sample&&i.push({name:\"Sample\",value:this.sample}),this.genotypeString&&i.push({name:\"Genotype\",value:this.genotypeString});const n=this.#l();n&&i.push({name:\"Zygosity\",value:n});var r=Object.keys(this.info);r.length&&i.push(\"<hr/>\");for(let e of r)i.push({name:e,value:decodeURIComponent(this.info[e])});return i}}const Gl=new Set([\"A\",\"C\",\"T\",\"G\"].map((e=>e.charCodeAt(0))));function $l(e){for(let t=0;t<e.length;t++)if(!Gl.has(e.charCodeAt(t)))return!1;return!0}function Kl(e,t){return void 0===t&&(t=\",\"),Array.isArray(e)?e.join(t):e}class Yl{construtor(){}async parseHeader(e,t){const i={};i.chrAliasTable=new Map;let n=await e.nextLine();if(!n.startsWith(\"##fileformat\"))throw new Error(\"Invalid VCF file: missing fileformat line\");for(i.version=n.substr(13);void 0!==(n=await e.nextLine())&&n.startsWith(\"#\");){let e;const s={};if(n.startsWith(\"##\")){if(n.startsWith(\"##INFO\")||n.startsWith(\"##FILTER\")||n.startsWith(\"##FORMAT\")){const t=n.indexOf(\"<\"),o=n.lastIndexOf(\">\");if(!(t>2&&o>0)){console.log(\"Malformed VCF header line: \"+n);continue}const a=n.substring(2,t-1);i[a]||(i[a]={});const c=Tt(n.substring(t+1,o-1),\",\");for(let t of c){var r=t.split(\"=\");r.length>1&&(\"ID\"===r[0]?e=r[1]:s[r[0]]=r[1])}e&&(i[a][e]=s)}else if(n.startsWith(\"##contig\")&&t){const e=n.indexOf(\"<ID=\");let r=n.indexOf(\",\",e);-1==r&&(r=n.indexOf(\">\",e));const s=n.substring(e+4,r),o=t.getChromosomeName(s);i.chrAliasTable.set(o,s)}}else if(n.startsWith(\"#CHROM\")){const e=n.split(\"\\t\");if(e.length>8){i.sampleNameMap=new Map;for(let t=9;t<e.length;t++)i.sampleNameMap.set(e[t],t-9)}}}return this.header=i,i}async parseFeatures(e){const t=[],i=this.header.sampleNameMap?Array.from(this.header.sampleNameMap.keys()):void 0,n=8+(i?i.length+1:0);let r;for(;void 0!==(r=await e.nextLine());)if(r&&!r.startsWith(\"#\")){const e=r.split(\"\\t\");if(e.length===n){const n=new Vl(e);if(n.header=this.header,t.push(n),e.length>9){const r=Xl(e[8].split(\":\"));n.calls=[];for(let t=9;t<e.length;t++){const s=i[t-9],o=e[t],a=new Wl({formatFields:r,sample:s,token:o});n.calls.push(a)}n.info&&n.info.CHR2&&n.info.END&&t.push(new jl(n))}}}return t}}function Xl(e){const t={genotypeIndex:-1,fields:e};for(let i=0;i<e.length;i++)\"GT\"===e[i]&&(t.genotypeIndex=i);return t}const Zl=Math.log10(Number.MIN_VALUE);class Jl{constructor(e){if(this.config=e,e.columns){if(void 0===e.columns.chromosome||void 0===e.columns.position||void 0===e.columns.value)throw Error(\"columns property must define chrCol, posCol, and valueCol\");this.posCol=e.columns.position-1,this.chrCol=e.columns.chromosome-1,this.valueCol=e.columns.value-1}else this.posCol=2,this.chrCol=1,this.valueCol=3}async parseHeader(e){const t=await e.nextLine();return this.parseHeaderLine(t)}parseHeaderLine(e){if(this.columns=e.split(/\\t/),!this.config.columns)for(let e=0;e<this.columns.length;e++){switch(this.columns[e].toLowerCase()){case\"chr\":case\"chromosome\":case\"chr_id\":this.chrCol=e;break;case\"bp\":case\"pos\":case\"position\":case\"chr_pos\":this.posCol=e;break;case\"p\":case\"pval\":case\"pvalue\":case\"p-value\":case\"p.value\":this.valueCol=e}}return this.columns}async parseFeatures(e){const t=[],i=e.nextLine();let n;this.columns||this.parseHeaderLine(i);const r=e=>{const t=e.indexOf(\"E\");if(t>0){if(Number.parseInt(e.substring(t+1))<Zl)return Number.MIN_VALUE}return Number(e)};for(;void 0!==(n=e.nextLine());){const e=n.split(/\\t/);if(e.length===this.columns.length){const i=e[this.posCol];if(i.indexOf(\";\")>0||0==i.length||i.indexOf(\"x\")>0)continue;const s=e[this.chrCol],o=r(e[this.valueCol]),a=parseInt(i)-1,c=a+1;t.push(new eh({chr:s,start:a,end:c,value:o,line:n,columns:this.columns}))}}return t}static isGWAS(e){const t=e.split(\"\\t\");if(t.length<5)return!1;const i=[[\"chr\",\"chromosome\",\"chr_id\",\"chrom\"],[\"bp\",\"pos\",\"position\",\"chr_pos\",\"chromEnd\"],[\"p\",\"pval\",\"p-value\",\"p.value\"]];for(let e of i)if(!t.some((t=>e.includes(t.toLowerCase()))))return!1;return!0}}class eh{constructor({chr:e,start:t,end:i,value:n,line:r,columns:s}){this.chr=e,this.start=t,this.end=i,this.value=n,this.line=r,this.columns=s}popupData(){const e=this.line.split(/\\t/);return this.columns.map((function(t,i){return{name:t,value:e[i]}}))}getAttribute(e){const t=this.line.split(/\\t/);for(let i=0;i<this.columns.length;i++)if(this.columns[i]===e)return t[i]}}var th=new RegExp(\"([^:]*)\\\\(([^)]*)\\\\)\"),ih=new RegExp(\"([^:]*):([^(]*)\\\\(([^)]*)\\\\)\");class nh{constructor(e){const t=e?e.decode:void 0;this.nameField=e?e.nameField:void 0,this.skipRows=0,this.decode=t||lh,this.delimiter=\"\\t\"}async parseHeader(e){let t,i;for(;(t=await e.nextLine())&&(t.startsWith(\"track\")||t.startsWith(\"#\")||t.startsWith(\"browser\"));)if(t.startsWith(\"track\")||t.startsWith(\"#track\")){let e=oh(t);i?Object.assign(i,e):i=e}else if(t.startsWith(\"#columns\")){let e=ah(t);i?Object.assign(i,e):i=e}else t.startsWith(\"##gff-version 3\")&&(this.format=\"gff3\",i||(i={}),i.format=\"gff3\");return this.header=i,i}async parseFeatures(e){const t=[],i=this.decode,n=this.delimiter||\"\\t\";let r,s=0;for(;void 0!==(r=e.nextLine());){if(s++,s<=this.skipRows||r.startsWith(\"track\")||r.startsWith(\"#\")||r.startsWith(\"browser\"))continue;let e=o();if(e.length<1)continue;if(!this.aed){this.aed=sh(e);continue}const n=i.call(this,e,undefined);n&&t.push(n)}return t;function o(){for(var e,t,i=[],s=\"\",o=!1;r||\"\"===r;){for(e=0;e<r.length;e++)(t=r.charAt(e))===n?o?s+=t:(i.push(s),s=\"\"):'\"'===t?e+1<r.length&&'\"'===r.charAt(e+1)?(o&&(s+='\"'),e++):o=!o:s+=t;if(!o)break;s+=\"\\n\",r=nextLine()}return i.push(s),i}}}function rh(e){var t=ih.exec(e);if(t)return{namespace:t[1],name:t[2],type:t[3]};if(t=th.exec(e))return{namespace:\"?\",name:t[1],type:t[2]};throw new Error(\"Error parsing the header row of AED file - column not in ns:name(ns:type) format\")}function sh(e){var t,i,n;for(t={columns:[],metadata:{}},i=0;i<e.length;i++)n=rh(e[i]),t.columns.push(n);return t}function oh(e){const t={},i=e.split(/(?:\")([^\"]+)(?:\")|([^\\s\"]+)(?=\\s+|$)/g);let n;const r=[];for(let e of i)e&&0!==e.trim().length&&(e.endsWith(\"=\")>0?n=e:n?(r.push(n+e),n=void 0):r.push(e));for(let e of r){if(!e)return;var s=e.split(\"=\",2);if(2===s.length){const e=s[0].trim(),i=s[1].trim();t[e]=i}}return t}function ah(e){let t={},i=e.split(/\\s+/);if(2===i.length){i[1].split(\";\").forEach((function(e){let i=e.split(\"=\");\"color\"===i[0]?t.colorColumn=Number.parseInt(i[1])-1:\"thickness\"===i[0]&&(t.thicknessColumn=Number.parseInt(i[1])-1)}))}return t}function ch(e,t){var i,n,r=e.columns;this.aed=e,this.allColumns=t,this.chr=null,this.start=null,this.end=null,this.score=1e3,this.strand=\".\",this.cdStart=null,this.cdEnd=null,this.name=null,this.color=null;for(let e=0;e<t.length;e++)if(i=t[e]){\"aed:Integer\"===(n=r[e]).type&&(i=parseInt(i));var s=[];if(n.namespace.length>0)for(let e=0;e<n.namespace.length;e++)s.push(n.namespace.charCodeAt(e));\"bio\"===n.namespace.trim()?\"sequence\"===n.name?this.chr=i:\"start\"===n.name?this.start=i:\"end\"===n.name?this.end=i:\"cdsMin\"===n.name?this.cdStart=i:\"cdsMax\"===n.name?this.cdEnd=i:\"strand\"===n.name&&(this.strand=i):\"aed\"===n.namespace?\"name\"===n.name&&(this.name=i):\"style\"===n.namespace&&\"color\"===n.name&&(this.color=_s.createColorString(i))}}function lh(e,t){var i,n,r,s,o,a,c=0,l=this.aed.columns;if(e.length===l.length){for(a=0;a<e.length;a++)s=l[a],\"\"!==(r=e[a])&&c++,\"name\"===s.name&&\"aed\"===s.namespace?i=r:\"value\"===s.name&&\"aed\"===s.namespace&&(n=r);if(2===c&&i&&n)return o=rh(i),this.aed.metadata[o.namespace]||(this.aed.metadata[o.namespace]={}),void(this.aed.metadata[o.namespace][o.name]||(this.aed.metadata[o.namespace][o.name]={type:o.type,value:n}));var h=new ch(this.aed,e);if(h.chr&&(h.start||0===h.start)&&h.end)return h;console.log(\"Cannot parse feature: \"+e.join(\",\"))}else console.log(\"Corrupted AED file row: \"+e.join(\",\"))}function hh(e,t){if(0===e.length)return e;if(e.sort((function(e,t){const i=e.minv.block-t.minv.block;return 0!==i?i:e.minv.offset-t.minv.offset})),e.length<=1)return e;t&&(e=e.filter((e=>e.maxv.isGreaterThan(t))));const i=[];let n;for(let t of e)n&&dh(n,t)?t.maxv.isGreaterThan(n.maxv)&&(n.maxv=t.maxv):(i.push(t),n=t);return i}function dh(e,t){const i=t.minv.block-e.maxv.block;return t.maxv.block-e.minv.block<5e6&&i<65e3}ch.prototype.popupData=function(){for(var e=[],t=this.aed,i=0;i<this.allColumns.length;i++){var n=this.allColumns[i],r=t.columns[i].name;\"sequence\"!==r&&\"color\"!==r&&n&&e.push({name:r,value:n})}return e};class uh{constructor(){this.tabix=!0}parse(e){const t=new yc(new DataView(e)),i=t.getInt();if(21582659!==i)throw 38359875===i?Error(\"CSI version 2 is not supported.  Please enter an issue at https://github.com/igvteam/igv.js\"):Error(\"Not a CSI index\");this.indices=[],this.blockMin=Number.MAX_SAFE_INTEGER,this.lastBlockPosition=[],this.sequenceIndexMap={},this.minShift=t.getInt(),this.depth=t.getInt();const n=[];let r=0;if(t.getInt()>=28){t.getInt(),t.getInt(),t.getInt(),t.getInt(),t.getInt(),t.getInt();const e=t.getInt(),i=t.position+e;let r=0;for(;t.position<i;){let e=t.getString();this.sequenceIndexMap[e]=r,n[r]=e,r++}}const s=this.bin_limit()+1,o=t.getInt();for(let e=0;e<o;e++){const i=[],n=[],o=t.getInt();for(let e=0;e<o;e++){const e=t.getInt();if(n[e]=t.getVPointer(),e>s)t.getInt(),t.getVPointer(),t.getVPointer(),t.getLong(),t.getLong();else{i[e]=[];const n=t.getInt();for(let s=0;s<n;s++){const n=t.getVPointer(),s=t.getVPointer();n&&s&&(n.block<this.blockMin&&(this.blockMin=n.block),s.block>r&&(r=s.block),i[e].push([n,s]))}}}o>0&&(this.indices[e]={binIndex:i,loffset:n})}this.lastBlockPosition=r}get sequenceNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(e,t,i){const n=this.indices[e];if(n){const e=this.reg2bins(t,i);if(0==e.length)return[];const r=[];for(let t of e)for(let e=t[0];e<=t[1];e++)if(n.binIndex[e]){const t=n.binIndex[e];for(let i of t){const t=i[0],n=i[1];r.push({minv:t,maxv:n,bin:e})}}let s=e[this.depth][0];do{if(n.binIndex[s])break;s>1+(this.getParentBin(s)<<3)?s--:s=this.getParentBin(s)}while(0!=s);return hh(r,n.loffset[s])}return[]}getParentBin(e){return 0==e?0:e-1>>3}reg2bins(e,t){(e-=1)<1&&(e=1),t>2**34&&(t=2**34),t-=1;let i=0,n=0,r=this.minShift+3*this.depth;const s=[];for(;i<=this.depth;r-=3,n+=1<<3*i,i+=1){const i=n+(e>>r),o=n+(t>>r);s.push([i,o])}return s}bin_limit(){return((1<<3*(this.depth+1))-1)/7}}class fh{constructor(){}async parse(e,t){const i=[];let n=Number.MAX_SAFE_INTEGER,r=0;const s=new yc(new DataView(e)),o=s.getInt(),a={};if(!(21578050===o||t&&21578324===o))throw new Error(indexURL+\" is not a \"+(t?\"tabix\":\"bai\")+\" file\");{const e=s.getInt();if(t){s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt();for(let t=0;t<e;t++){a[s.getString()]=t}}for(let t=0;t<e;t++){const e={},o=[],a=s.getInt();for(let t=0;t<a;t++){const t=s.getInt();if(37450===t)s.getInt(),s.getVPointer(),s.getVPointer(),s.getLong(),s.getLong();else{e[t]=[];const i=s.getInt();for(let o=0;o<i;o++){const i=s.getVPointer(),o=s.getVPointer();i&&o&&(i.block<n&&(n=i.block),o.block>r&&(r=o.block),e[t].push([i,o]))}}}const c=s.getInt();for(let e=0;e<c;e++){const e=s.getVPointer();o.push(e)}a>0&&(i[t]={binIndex:e,linearIndex:o})}this.firstBlockPosition=n,this.lastBlockPosition=r,this.indices=i,this.sequenceIndexMap=a,this.tabix=t}}get sequenceNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(e,t,i){const n=this.indices[e];if(n){const e=function(e,t){const i=[];t>=1<<29&&(t=1<<29);return--t,i.push([0,0]),i.push([1+(e>>26),1+(t>>26)]),i.push([9+(e>>23),9+(t>>23)]),i.push([73+(e>>20),73+(t>>20)]),i.push([585+(e>>17),585+(t>>17)]),i.push([4681+(e>>14),4681+(t>>14)]),i}(t,i),r=[];for(let t of e)for(let e=t[0];e<=t[1];e++)if(n.binIndex[e]){const t=n.binIndex[e];for(let e of t){const t=e[0],i=e[1];r.push({minv:t,maxv:i})}}const s=n.linearIndex.length;let o;const a=Math.min(t>>14,s-1),c=Math.min(i>>14,s-1);for(let e=a;e<=c;e++){const t=n.linearIndex[e];if(t){o=t;break}}return hh(r,o)}return[]}}class ph{constructor(){this.tribble=!0}async parse(e){let t=0;this.chrIndex={},this.lastBlockPosition=[];const i=new yc(new DataView(e));!function(e){e.getInt(),e.getInt();const t=e.getInt();if(e.getString(),e.getLong(),e.getLong(),e.getString(),e.getInt(),t>=3){let t=e.getInt();for(;t-- >0;)e.getString(),e.getString()}}(i);let n=i.getInt();for(;n-- >0;){let e=i.getString();const n=i.getInt(),r=i.getInt(),s=i.getInt();i.getInt(),i.getInt();let o=i.getLong();const a=[];for(let e=0;e<r;e++){const e=i.getLong();a.push({min:o,max:e}),o=e,e>t&&(t=e)}this.chrIndex[e]={chr:e,blocks:a,longestFeature:s,binWidth:n}}this.lastBlockPosition=t}get sequenceNames(){return Object.keys(this.chrIndex)}chunksForRange(e,t,i){const n=this.chrIndex[e];if(n){const e=n.blocks,r=n.longestFeature,s=n.binWidth,o=Math.max(t-r,0),a=Math.floor(o/s);if(a>=e.length)return[];{const t=Math.min(Math.floor((i-1)/s),e.length-1),n=e[a].min,r=e[t].max;if(0===r-n)return[];return[{minv:{block:n,offset:0},maxv:{block:r,offset:0}}]}}}}async function gh(e,t){let i=await Qs.loadArrayBuffer(e,Ua(t)),n=new DataView(i);if(31===n.getUint8(0)&&139===n.getUint8(1)){i=gs(i).buffer,n=new DataView(i)}switch(n.getInt32(0,!0)){case 21578050:return async function(e){const t=new fh;return await t.parse(e,!1),t}(i);case 21578324:return async function(e){const t=new fh;return await t.parse(e,!0),t}(i);case 21582659:return async function(e){const t=new uh;return t.parse(e),t}(i);case 1480870228:return async function(e){const t=new ph;return t.parse(e),t}(i);case 38359875:throw Error(\"CSI version 2 is not supported.\");default:throw Error(`Unrecognized index type: ${e}`)}}function mh(e){return\"string\"==typeof e||e instanceof String?new wh(e):new bh(e)}class wh{constructor(e){this.data=e,this.ptr=0}nextLine(){var e=this.ptr,t=this.data.indexOf(\"\\n\",e),i=this.data;if(t>0)return this.ptr=t+1,t>e&&\"\\r\"===i.charAt(t-1)?i.substring(e,t-1):i.substring(e,t);var n=i.length;return this.ptr=n,e>=n?void 0:i.substring(e)}}class bh{constructor(e){this.data=e,this.length=this.data.length,this.ptr=0}nextLine(){if(this.ptr>=this.data.length)return;let e=this.ptr;const t=this.data;let i=\"\",n=!1;for(;e<t.length;){var r=t[e],s=0,o=0;if(r<=127?(s=0,o=255&r):r<=223?(s=1,o=31&r):r<=239?(s=2,o=15&r):r<=244&&(s=3,o=7&r),t.length-e-s>0)for(var a=0;a<s;)o=o<<6|63&(r=t[e+a+1]),a+=1;else o=65533,s=t.length-e;e+=s+1;const c=String.fromCodePoint(o);if(\"\\r\"===c)n=!0;else{if(\"\\n\"===c)break;n&&(i+=\"\\r\",n=!1),i+=c}}return this.ptr=e,i}}class Fh{constructor(e){this.config=e,this.filePtr=0,this.bufferPtr=0,this.buffer}async nextLine(){let e;try{for(;;){const t=this.buffer?this.buffer.length:0;for(;this.bufferPtr<t;){const t=String.fromCharCode(this.buffer[this.bufferPtr++]);if(\"\\r\"!==t){if(\"\\n\"===t)return e;e=e?e+t:t}}if(this.eof)return e;await this.readNextBlock()}}catch(t){return console.warn(t),this.eof=!0,e}}async readNextBlock(){const e=Ua(this.config,{range:{start:this.filePtr,size:26}}),t=ms(await Qs.loadArrayBuffer(this.config.url,e));if(0===t)this.eof=!0,this.buffer=void 0;else{const e=Ua(this.config,{range:{start:this.filePtr,size:t}}),i=await Qs.loadArrayBuffer(this.config.url,e);i.byteLength<t&&(this.eof=!0),this.buffer=gs(i),0==this.buffer.byteLength&&(this.eof=!0),this.bufferPtr=0,this.filePtr+=i.byteLength}}}const vh=e=>{const t=ArrayBuffer.isView(e)?e:new Uint8Array(e);return 1+(t[17]<<8|t[16])};class yh{constructor(e){this.config=e,this.cacheBlocks=0!=e.cacheBlocks,this.cache=void 0}async getData(e,t){const i=e.block,n=t.block,r=0===t.offset,s=await this.getInflatedBlocks(i,n,r);if(1===s.length)return s[0];let o=0;for(const e of s)o+=e.byteLength;const a=new Uint8Array(o);let c=0;for(const e of s)a.set(e,c),c+=e.byteLength;return a}async getInflatedBlocks(e,t,i){if(this.cacheBlocks){const n=this.cache;if(n&&n.startBlock<=e&&(n.endBlock>=t||i&&n.nextEndBlock===t)){const i=e-n.startBlock,r=t-n.startBlock;return Ch(n.buffer,i,r)}{let r;if(!n||n.startBlock>t||n.endBlock<e)r=await this.loadBLockData(e,t,{skipEnd:i});else{const s=[];if(e<n.startBlock){const t=await this.loadBLockData(e,n.startBlock,{skipEnd:!0});s.push(t)}let o;if(e<=n.startBlock&&t>=n.endBlock)o=n.buffer;else{const i=Math.max(0,e-n.startBlock);let r;if(t>=n.endBlock)r=n.buffer.byteLength;else{const e=Ah(n.buffer);for(let i=0;i<e.length-1;i++)if(n.startBlock+e[i]===t){r=e[i+1];break}}o=n.buffer.slice(i,r)}if(s.push(o),t>n.endBlock){const e=await this.loadBLockData(n.endBlock,t,{skipStart:!0,skipEnd:i});s.push(e)}r=function(e){if(1===e.length)return e[0];let t=0;for(const i of e)t+=i.byteLength;const i=new Uint8Array(t);let n=0;for(const t of e)i.set(new Uint8Array(t),n),n+=t.byteLength;return i.buffer}(s)}let s=t;if(i){const e=Ah(r);t=e[e.length-1]}return this.cache={startBlock:e,endBlock:t,nextEndBlock:s,buffer:r},Ch(r)}}return Ch(await this.loadBLockData(e,t,{skipEnd:i}))}async loadBLockData(e,t,i){const n=this.config,r=i&&i.skipStart;let s=0;if(!(i&&i.skipEnd)){const e=Ua(n,{range:{start:t,size:26}}),i=await Qs.loadArrayBuffer(n.url,e);s=vh(i)}if(r){const t=Ua(n,{range:{start:e,size:26}}),i=await Qs.loadArrayBuffer(n.url,t);e+=vh(i)}const o=Ua(n,{range:{start:e,size:t+s-e}});return Qs.loadArrayBuffer(n.url,o)}}function Ah(e){const t=e.byteLength;let i=0;const n=[0];for(;i<t;){const r=new Uint8Array(e,i);i+=1+(r[17]<<8|r[16]),i<t&&n.push(i)}return n}function Ch(e,t,i){const n=[];let r=t=t||0;const s=e.byteLength-18;for(;r<s;)try{const t=new Uint8Array(e,r,18),s=t[11]<<8|t[10],o=t[17]<<8|t[16],a=12+s+r,c=e.byteLength-a,l=o-s-18;if(c<l||l<=0)break;const h=new Uint8Array(e,a,l),d=hs(h);if(n.push(d),i===r)break;r+=o+1}catch(e){console.error(e);break}return n}const _h=Math.log10(Number.MIN_VALUE);class xh{chrCol=-1;snpCol=-1;posCol=-1;pValueCol=-1;phenotypeColumn=-1;delimiter=\"\\t\";constructor(e){this.config=e}async parseHeader(e){const t=this.config;t.delimiter&&(this.delimiter=t.delimiter);const i=await e.nextLine(),n=this.parseHeaderLine(i);return t.chrColumn&&(this.chrColumn=t.chrColumn-1),t.snpColumn&&(this.snpColumn=t.snpColumn-1),t.posColumn&&(this.posColumn=t.posColumn-1),t.pValueColumn&&(this.pValueColumn=t.pValueColumn-1),t.phenotypeColumn&&(this.phenotypeColumn=t.phenotypeColumn-1),n}parseHeaderLine(e){this.columns=e.split(this.delimiter);for(let e=0;e<this.columns.length;e++){switch(this.columns[e].toLowerCase()){case\"chr\":case\"chromosome\":case\"chr_id\":case\"chrom\":this.chrColumn=e;break;case\"bp\":case\"pos\":case\"position\":case\"chr_pos\":case\"chromEnd\":this.posColumn=e;break;case\"p\":case\"pval\":case\"pvalue\":case\"p-value\":case\"p.value\":this.pValueColumn=e;break;case\"rsid\":case\"variant\":case\"snp\":this.snpColumn=e;break;case\"phenotype\":case\"gene\":case\"gene_id\":case\"molecular_trait_id\":this.phenotypeColumn=e}}return this.columns}async parseFeatures(e){const t=[],i=e.nextLine();let n;this.columns||this.parseHeaderLine(i);const r=e=>{const t=e.indexOf(\"E\");if(t>0){if(Number.parseInt(e.substring(t+1))<_h)return Number.MIN_VALUE}return Number(e)};for(;void 0!==(n=e.nextLine());){const e=n.split(this.delimiter);if(e.length===this.columns.length){const i=e[this.posColumn];if(i.indexOf(\";\")>0||0==i.length||i.indexOf(\"x\")>0)continue;const n=e[this.chrColumn],s=r(e[this.pValueColumn]),o=parseInt(i)-1,a=o+1,c=e[this.snpColumn],l=e[this.phenotypeColumn],h=new kh({chr:n,start:o,end:a,pValue:s,snp:c,phenotype:l},this.columns,e);t.push(h)}}return t}static isQTL(e){const t=e.split(\"\\t\");if(t.length<5)return!1;const i=[[\"chr\",\"chromosome\",\"chr_id\",\"chrom\"],[\"bp\",\"pos\",\"position\",\"chr_pos\",\"chromEnd\"],[\"p\",\"pval\",\"p-value\",\"p.value\"],[\"rsid\",\"variant\",\"snp\"],[\"phenotype\",\"gene\",\"gene_id\",\"molecular_trait_id\"]];for(let e of i)if(!t.some((t=>e.includes(t.toLowerCase()))))return!1;return!0}}class kh{constructor({chr:e,start:t,end:i,pValue:n,snp:r,phenotype:s},o,a){this.chr=e,this.start=t,this.end=i,this.pValue=n,this.snp=r,this.phenotype=s,this.headers=o,this.tokens=a}popupData(){const e=[];for(let t=0;t<this.headers.length;t++)e.push({name:this.headers[t],value:this.tokens[t]});return e}}class Ih{sequenceNames;constructor(e,t){if(this.config=e||{},this.genome=t,this.indexURL=e.indexURL,this.indexed=e.indexed||void 0!==this.indexURL,this.queryable=this.indexed,Ht(this.config.url))this.filename=this.config.url.name;else if(Ga(this.config.url))this.indexed=!1,this.dataURI=e.url;else{const t=Ot(this.config.url);this.filename=e.filename||t.file}this.parser=this.getParser(this.config),\"vcf\"!==this.config.format||this.config.indexURL||console.warn(\"Warning: index file not specified.  The entire vcf file will be loaded.\")}async defaultVisibilityWindow(){if(this.config.indexURL){const e=await this.getIndex();if(e&&e.lastBlockPosition){let t=0;const i=1e4;for(let i of e.sequenceNames){const e=this.genome.getChromosome(i);e&&(t+=e.bpLength)}return Math.round(t/e.lastBlockPosition*i)}}}async readFeatures(e,t,i){let n;this.dataURI||this.header||await this.readHeader();return await this.getIndex()?(this.indexed=!0,n=await this.loadFeaturesWithIndex(e,t,i)):this.dataURI?(this.indexed=!1,n=await this.loadFeaturesFromDataURI()):\"service\"===this.config.sourceType?n=await this.loadFeaturesFromService(e,t,i):(this.indexed=!1,n=await this.loadFeaturesNoIndex()),n.sort((function(e,t){return e.chr===t.chr?e.start-t.start:e.chr.localeCompare(t.chr)})),n}async readHeader(){if(this.dataURI)return await this.loadFeaturesFromDataURI(this.dataURI),this.header;if(this.config.indexURL){const e=await this.getIndex();if(!e)throw new Error(\"Unable to load index: \"+this.config.indexURL);let t;if(this.sequenceNames=new Set(e.sequenceNames),e.tabix)this._blockLoader=new yh(this.config),t=new Fh(this.config);else{const i=Object.values(e.chrIndex).flatMap((e=>e.blocks)).map((e=>e.max)).reduce(((e,t)=>Math.min(e,t)),Number.MAX_SAFE_INTEGER),n=Ua(this.config,{bgz:e.tabix,range:{start:0,size:i}});t=mh(await Qs.loadString(this.config.url,n))}return this.header=await this.parser.parseHeader(t),this.header}if(\"service\"!==this.config.sourceType){let e;if(this.config._filecontents)e=this.config._filecontents,delete this.config._filecontents;else{const t=Ua(this.config);e=await Qs.loadByteArray(this.config.url,t)}e.length<5e8&&(e=(new TextDecoder).decode(e));let t=mh(e);this.header=await this.parser.parseHeader(t),t=mh(e),this.features=await this.parser.parseFeatures(t),this.sequenceNames=new Set;for(let e of this.features)this.sequenceNames.add(e.chr);return this.header}if(this.config.seqnamesURL){const e=Ua(this.config,{}),t=await Qs.loadString(this.config.seqnamesURL,e);t&&(this.sequenceNames=new Set(t.split(\",\").map((e=>e.trim())).filter((e=>e))))}if(this.config.headerURL){const e=Ua(this.config,{}),t=mh(await Qs.loadString(this.config.headerURL,e));return this.header=await this.parser.parseHeader(t),this.header}}getParser(e){switch(e.format){case\"vcf\":return new Yl(e);case\"seg\":return new Ul(\"seg\");case\"mut\":return new Ul(\"mut\");case\"maf\":return new Ul(\"maf\");case\"gwas\":return new Jl(e);case\"qtl\":return new xh(e);case\"aed\":return new nh(e);default:return new El(e)}}async loadFeaturesNoIndex(){if(this.features){const e=this.features;return delete this.features,e}{const e=Ua(this.config),t=await Qs.loadByteArray(this.config.url,e);if(!this.header){const e=mh(t);this.header=await this.parser.parseHeader(e)}const i=mh(t),n=[];return await this._parse(n,i),n}}async loadFeaturesWithIndex(e,t,i){const n=this.config;this.parser;const r=this.index.tabix,s=r?this.index.sequenceIndexMap[e]:e;if(void 0===s)return[];const o=this.index.chunksForRange(s,t,i);if(o&&0!==o.length){const s=[];for(let a of o){let o;if(r)o=await this._blockLoader.getData(a.minv,a.maxv);else{const e=Ua(n,{range:{start:a.minv.block,size:a.maxv.block-a.minv.block+1}});o=await Qs.loadString(n.url,e)}const c=mh(a.minv.offset?o.slice(a.minv.offset):o);await this._parse(s,c,e,i,t)}return s}return[]}async loadFeaturesFromService(e,t,i){let n;n=\"function\"==typeof this.config.url?this.config.url({chr:e,start:t,end:i}):this.config.url.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i);const r=Ua(this.config),s=mh(await Qs.loadString(n,r)),o=[];return await this._parse(o,s),o}async _parse(e,t,i,n,r){let s=await this.parser.parseFeatures(t);if(s.sort((function(e,t){return e.chr===t.chr?e.start-t.start:e.chr.localeCompare(t.chr)})),void 0===i)for(let t of s)e.push(t);else{let t=!1;for(let o=0;o<s.length;o++){const a=s[o];if(a.chr===i){if(a.start>n){e.push(a);break}a.end>=r&&a.start<=n&&(t||(t=!0,o>0&&e.push(s[o-1])),e.push(a))}}}}async getIndex(){return this.index?this.index:this.config.indexURL?(this.index=await this.loadIndex(),this.index):void 0}async loadIndex(){return gh(this.config.indexURL,this.config)}async loadFeaturesFromDataURI(){if(this.features){const e=this.features;return delete this.features,e}{const e=vs(this.dataURI);let t=mh(e);this.header=await this.parser.parseHeader(t),this.header instanceof String&&this.header.startsWith(\"##gff-version 3\")&&(this.format=\"gff3\"),t=mh(e);const i=[];return await this._parse(i,t),i}}}const Sh=Mt;class Eh{constructor(e){this.config=e}async readFeatures(e,t,i){let n;n=\"function\"==typeof this.config.url?this.config.url({chr:e,start:t,end:i}):this.config.url.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i);let r,s=Object.assign({},this.config);void 0!==this.config.body&&(\"function\"==typeof this.config.body?s.body=this.config.body({chr:e,start:t,end:i}):s.body=this.config.body.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i));const o=await Qs.load(n,s);if(o&&(r=\"function\"==typeof this.config.parser?this.config.parser(o):Sh(o)?JSON.parse(o):o),this.config.mappings){let e=Object.keys(this.config.mappings);for(let t of r)for(let i of e)t[i]=t[this.config.mappings[i]]}return r}}const Nh=function(e,t){this.config=e,this.genome=t,this.expandQueryInterval=!1};Nh.prototype.readFeatures=function(e,t,i){const n=Math.max(0,Math.floor(t));let r=Math.ceil(i);if(this.genome){const t=this.genome.getChromosome(e);t&&r>t.bpLength&&(r=t.bpLength)}const s=this.config.url+\"?db=\"+this.config.db+\"&table=\"+this.config.tableName+\"&chr=\"+e+\"&start=\"+n+\"&end=\"+r;return Qs.loadJson(s,this.config).then((function(e){return e?(e.forEach((function(e){e.hasOwnProperty(\"exonStarts\")&&e.hasOwnProperty(\"exonEnds\")&&e.hasOwnProperty(\"exonCount\")&&e.hasOwnProperty(\"cdsStart\")&&e.hasOwnProperty(\"cdsEnd\")&&function(e){var t,i,n,r,s,o;t=e.exonCount,i=e.exonStarts.split(\",\"),n=e.exonEnds.split(\",\"),r=[];for(var a=0;a<t;a++){var c={start:s=parseInt(i[a]),end:o=parseInt(n[a])};(e.cdsStart>o||e.cdsEnd<e.cdsStart)&&(c.utr=!0),e.cdsStart>=s&&e.cdsStart<=o&&(c.cdStart=e.cdsStart),e.cdsEnd>=s&&e.cdsEnd<=o&&(c.cdEnd=e.cdsEnd),r.push(c)}e.exons=r}(e)})),e):null}))};class Bh{featureCaches=[];gtexChrs=new Set([\"chr1\",\"chr10\",\"chr11\",\"chr12\",\"chr13\",\"chr14\",\"chr15\",\"chr16\",\"chr17\",\"chr18\",\"chr19\",\"chr2\",\"chr20\",\"chr21\",\"chr22\",\"chr3\",\"chr4\",\"chr5\",\"chr6\",\"chr7\",\"chr8\",\"chr9\",\"chrM\",\"chrX\",\"chrY\"]);constructor(e){this.config=e,this.url=e.url,this.tissueId=e.tissueSiteDetailId,this.datasetId=e.datasetId||\"gtex_v8\"}async readFeatures(e,t,i){const n=e.startsWith(\"chr\")?e:\"MT\"===e?\"chrM\":\"chr\"+e;if(!this.gtexChrs.has(n))return[];const r=Math.floor(t),s=Math.ceil(i),o=this.datasetId,a=this.url+\"?chromosome=\"+n+\"&start=\"+r+\"&end=\"+s+\"&tissueSiteDetailId=\"+this.tissueId+\"&datasetId=\"+o,c=await Qs.loadJson(a,{withCredentials:this.config.withCredentials});return c&&c.singleTissueEqtl?c.singleTissueEqtl.map((e=>new Mh(e))):[]}}class Mh{constructor(e){this.chr=e.chromosome,this.start=e.pos-1,this.end=this.start+1,this.snp=e.snpId,this.phenotype=e.geneSymbol,this.pValue=e.pValue,this.json=e}popupData(){return Object.keys(this.json).map((e=>({name:e,value:this.json[e]})))}}class Rh{constructor(e,t){if(this.config=e,this.genome=t,!e.format)throw Error('Format is required, and must be either \"bam\" or \"cram\"');if(this.format=e.format.toUpperCase(),\"BAM\"!==this.format&&\"VCF\"!==this.format)throw Error(`htsget format ${e.format} is not supported`)}async readHeaderData(){const e=`${Dh(this.config)}?class=header&format=${this.format}`,t=await Qs.loadJson(e,Ua(this.config));return await this.loadUrls(t.htsget.urls)}async readData(e,t,i){const n=`${Dh(this.config)}?format=${this.format}&referenceName=${e}&start=${Math.floor(t)}&end=${Math.ceil(i)}`,r=await Qs.loadJson(n,Ua(this.config));return this.loadUrls(r.htsget.urls)}async loadUrls(e){const t=[];for(let i of e)if(i.url.startsWith(\"data:\"))t.push(Promise.resolve(Th(i.url)));else{const e=Ua(this.config||{});i.headers&&(e.headers=Object.assign(e.headers||{},i.headers)),t.push(Qs.loadArrayBuffer(i.url,e))}return function(e){let t=0;for(let i of e)t+=i.byteLength;let i=0;const n=new Uint8Array(t);for(let t of e){const e=new Uint8Array(t);n.set(e,i),i+=e.length}return n}(await Promise.all(t))}static async inferFormat(e){try{const t=Dh(e),i=`${t}${t.includes(\"?\")?\"&\":\"?\"}class=header`,n=await Qs.loadJson(i,Ua(e));if(n.htsget){const t=n.htsget.format;if(\"BAM\"!==t&&\"VCF\"!==t)throw Error(`htsget format ${t} is not supported`);e.format=t.toLowerCase(),e.sourceType=\"htsget\",e.name||(e.name=await ja(e.url))}}catch(e){}}}function Dh(e){if(e.url&&e.endpoint&&e.id)return e.url+e.endpoint+e.id;if(e.endpoint&&e.id)return e.endpoint+e.id;if(e.url)return e.url.startsWith(\"htsget://\")?e.url.replace(\"htsget://\",\"https://\"):e.url;throw Error(\"Must specify either 'url', or 'endpoint' and 'id\")}function Th(e){const t=e.split(\",\"),i=t[0].split(\":\")[1];let n=t[1];n=i.indexOf(\"base64\")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s<n.length;s++)r[s]=n.charCodeAt(s);return r}class Lh extends Rh{constructor(e,t){super(e,t),this.parser=new Yl}async readHeader(){if(!this.header){let e=await this.readHeaderData();fs(e)&&(e=ps(e));const t=mh(e);this.header=await this.parser.parseHeader(t,this.genome),this.chrAliasTable=this.header.chrAliasTable}return this.header}async readFeatures(e,t,i){if(this.config.format&&\"VCF\"!==this.config.format.toUpperCase())throw Error(`htsget format ${this.config.format} is not supported`);this.chrAliasTable||await this.readHeader();let n=this.chrAliasTable.has(e)?this.chrAliasTable.get(e):e,r=await this.readData(n,t,i);fs(r)&&(r=ps(r));const s=mh(r);return this.parser.parseFeatures(s)}}class zh{chrAliasTable=new Map;constructor(e,t){this.sequenceNames=new Set(e),this.genome=t}async getAliasName(e){if(!this.genome)return e;if(!this.chrAliasTable.has(e)){const t=await this.genome.getAliasRecord(e);if(t){let i;const n=Object.keys(t).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>t[e])).filter((e=>this.sequenceNames.has(e)));n.length>0&&(i=n[0]),this.chrAliasTable.set(e,i)}else this.chrAliasTable.set(e,void 0)}return this.chrAliasTable.get(e)}}class Hh{constructor(e){this.genome=e}async nextFeature(e,t,i,n){let r=this.genome.chromosomeNames||[e],s=r.indexOf(e);if(s<0)return;const o=Math.min(1e4,n||1e4);let a=i?t:Math.max(t-o,0);for(;s<r.length&&s>=0;){e=r[s];const c=this.genome.getChromosome(e).bpLength;for(;a<c&&a>=0;){let r=i?a+o:Math.min(t,a+o);const s=await this.getFeatures({chr:e,start:a,end:r,visibilityWindow:n});if(s){const e=(e,t)=>e.start-t.start+e.end-t.end,n=Array.from(s);n.sort(e);let r=i?0:n.length-1;for(;r>=0&&r<n.length;){const e=n[r],s=(e.start+e.end)/2;if(i){if(s>t)return e;r++}else{if(s<t)return e;r--}}}a=i?r:a-o}if(i)s++,a=0,t=0;else{if(s--,s<0)break;a=(t=this.genome.getChromosome(r[s]).bpLength)-o}}}async previousFeature(e,t,i,n){let r=this.genome.chromosomeNames||[e],s=r.indexOf(e);if(s<0)return;const o=Math.min(1e4,n||1e4);let a=i?t:Math.max(t-o,0);for(;s<r.length&&s>=0;){e=r[s];const c=this.genome.getChromosome(e).bpLength;for(;a<c&&a>=0;){let r=Math.min(t,a+o);const s=await this.getFeatures({chr:e,start:a,end:r,visibilityWindow:n});if(s){const e=(e,t)=>e.start-t.start+e.end-t.end,n=Array.from(s);n.sort(e);let r=i?0:n.length-1;for(;r>=0&&r<n.length;){const e=n[r],s=(e.start+e.end)/2;if(i){if(s>t)return e;r++}else{if(s<t)return e;r--}}}a=i?r:a-o}if(i)s++,a=0,t=0;else{if(s--,s<0)break;a=(t=this.genome.getChromosome(r[s]).bpLength)-o}}}}class Ph{constructor(e,t){this.config=e,this.genome=t,this.path=e.url,this.groupCache={},this.datasetCache={}}async readHeader(){if(void 0!==this.magic)return this;let e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:0,size:64e3}})),t=new yc(new DataView(e));if(this.magic=t.getInt(),this.version=t.getInt(),this.indexPos=t.getLong(),this.indexSize=t.getInt(),t.getInt(),this.version>=2){let e=t.getInt();for(this.windowFunctions=[];e-- >0;)this.windowFunctions.push(t.getString())}this.trackType=t.getString(),this.trackLine=t.getString();let i=t.getInt();for(this.trackNames=[];i-- >0;)this.trackNames.push(t.getString());this.genomeID=t.getString(),this.flags=t.getInt(),this.compressed=!!(1&this.flags),e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:this.indexPos,size:this.indexSize}})),t=new yc(new DataView(e)),this.datasetIndex={};let n=t.getInt();for(;n-- >0;){const e=t.getString(),i=t.getLong(),n=t.getInt();this.datasetIndex[e]={position:i,size:n}}for(this.groupIndex={},n=t.getInt();n-- >0;){const e=t.getString(),i=t.getLong(),n=t.getInt();this.groupIndex[e]={position:i,size:n}}return this}async readDataset(e,t,i){const n=e+\"_\"+t+\"_\"+i;if(this.datasetCache[n])return this.datasetCache[n];{await this.readHeader();const r=this.version<2?\"\":\"/\"+t,s=\"all\"===e.toLowerCase()||void 0===i?\"0\":i.toString();let o;o=\"raw\"===t?\"/\"+e+\"/raw\":\"/\"+e+\"/z\"+s+r;const a=this.datasetIndex[o];if(void 0===a)return;const c=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:a.position,size:a.size}}));if(!c)return;const l=new yc(new DataView(c));let h=l.getInt();const d={};for(;h-- >0;)d[l.getString()]=l.getString();const u=l.getString(),f=l.getFloat();let p=l.getInt();const g=[];for(;p-- >0;)g.push({position:l.getLong(),size:l.getInt()});const m={name:o,attributes:d,dataType:u,tileWidth:f,tiles:g};return this.datasetCache[n]=m,m}}async readRootGroup(){const e=this.genome,t=this.groupCache[\"/\"];if(t)return t;{const t=await this.readGroup(\"/\"),i=t.chromosomes,n=t.maxZoom;n&&(this.maxZoom=Number(n));const r=t.totalCount;r&&(t.totalCount=Number(r));const s={};return i&&i.split(\",\").forEach((function(t){const i=e.getChromosomeName(t);s[i]=t})),this.chrAliasTable=s,this.groupCache[\"/\"]=t,t}}async readGroup(e){const t=this.groupCache[e];if(t)return t;{await this.readHeader();const t=this.groupIndex[e];if(void 0===t)return;const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:t.position,size:t.size}}));if(!i)return;const n=new yc(new DataView(i)),r={name:e};let s=n.getInt();for(;s-- >0;){const e=n.getString(),t=n.getString();r[e]=t}return this.groupCache[e]=r,r}}async readTiles(e,t){if(e.sort((function(e,t){return e.position-t.position})),0===(e=e.filter((function(e){return e.size>0}))).length)return[];const i=[];for(let n of e){const e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:n.position,size:n.size}}));let r;try{r=this.compressed?ls(e).buffer:e}catch(e){console.error(e);continue}const s=new yc(new DataView(r)),o=s.getString();let a;switch(o){case\"fixedStep\":a=Oh(s,t);break;case\"variableStep\":a=Uh(s,t);break;case\"bed\":case\"bedWithName\":a=qh(s,t,o);break;default:throw\"Unknown tile type: \"+o}i.push(a)}return i}async readTile(e,t){let i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e.position,size:e.size}}));if(this.compressed){i=ls(i).buffer}const n=new yc(new DataView(i)),r=n.getString();switch(r){case\"fixedStep\":return Oh(n,t);case\"variableStep\":return Uh(n,t);case\"bed\":case\"bedWithName\":return qh(n,t,r);default:throw\"Unknown tile type: \"+r}}}function Oh(e,t){const i=e.getInt(),n=e.getInt(),r=e.getFloat(),s=[];let o=t;for(;o-- >0;){let t=i;const n=[];for(;t-- >0;)n.push(e.getFloat());s.push(n)}return{type:\"fixedStep\",start:n,span:r,data:s,nTracks:t,nPositions:i}}function Uh(e,t){const i=e.getInt(),n=e.getFloat(),r=e.getInt(),s=[];let o=r;for(;o-- >0;)s.push(e.getInt());e.getInt();const a=[];let c=t;for(;c-- >0;){o=r;const t=[];for(;o-- >0;)t.push(e.getFloat());a.push(t)}return{type:\"variableStep\",tileStart:i,span:n,start:s,data:a,nTracks:t,nPositions:r}}function qh(e,t,i){const n=e.getInt();let r=n;const s=[];for(;r-- >0;)s.push(e.getInt());r=n;const o=[];for(;r-- >0;)o.push(e.getInt());e.getInt();const a=[];let c=t;for(;c-- >0;){let t=n;const i=[];for(;t-- >0;)i.push(e.getFloat());a.push(i)}if(\"bedWithName\"===i){r=n;const t=[];for(;r-- >0;)t.push(e.getString())}return{type:i,start:s,end:o,data:a,nTracks:t,nPositions:n}}class Qh extends Hh{#h={};searchable=!1;constructor(e,t){super(t),this.genome=t,this.reader=new Ph(e,t),this.queryable=!0}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,windowFunction:r=\"mean\"}){return\"all\"===e.toLowerCase()?this.getWGValues(r,n):this._getFeatures(e,t,i,n,r)}async _getFeatures(e,t,i,n,r){const s=new hc(e,t,i),o=this.genome;if(!this.rootGroup&&(this.rootGroup=await this.reader.readRootGroup(),!this.normalizationFactor)){const e=this.rootGroup.totalCount;e&&(this.normalizationFactor=1e6/e)}s.bpPerPixel=n;const a=function(e,t,i){var n=i.getChromosome(e).bpLength;return Math.ceil(Math.log(Math.max(0,n/(700*t)))/Gh)}(e,n,o);let c=this.reader.chrAliasTable[e],l=this.reader.maxZoom;void 0===c&&(c=e),void 0===l&&(l=-1);const h=a>l?\"raw\":r,d=await this.reader.readDataset(c,h,a);if(null==d)return[];const u=d.tileWidth,f=Math.floor(t/u),p=Math.floor(i/u),g=await this.reader.readTiles(d.tiles.slice(f,p+1),1),m=[];for(let r of g)switch(r.type){case\"bed\":Vh(r,e,t,i,n,m);break;case\"variableStep\":jh(r,e,t,i,n,m);break;case\"fixedStep\":Wh(r,e,t,i,n,m);break;default:throw\"Unknown tile type: \"+r.type}return m.sort((function(e,t){return e.start-t.start})),m}get supportsWholeGenome(){return!0}get windowFunctions(){return this.reader.windowFunctions}async getWGValues(e,t){const i=this.#h[e];if(i&&i.bpPerPixel>.8*t&&i.bpPerPixel<1.2*t)return i.values;{const i=[],n=this.genome;if(this.genome.wgChromosomeNames)for(let r of n.wgChromosomeNames){const s=n.getChromosome(r).bpLength;t=s/1e3;const o=await this._getFeatures(r,0,s,t,e);if(o)for(let e of o){const t=Object.assign({},e);t.chr=\"all\",t.start=n.getGenomeCoordinate(e.chr,e.start),t.end=n.getGenomeCoordinate(e.chr,e.end),t._f=e,i.push(t)}}return this.#h[e]={values:i,bpPerPixel:t},i}}}function Vh(e,t,i,n,r,s){const o=e.nPositions,a=e.start,c=e.end,l=e.data[0];for(let e=0;e<o;e++){const r=a[e],o=c[e];if(!(o<i)){if(r>n)break;s.push({chr:t,start:r,end:o,value:l[e]})}}}function jh(e,t,i,n,r,s){const o=e.nPositions,a=e.start,c=e.span,l=e.data[0];for(let e=0;e<o;e++){const r=a[e],o=r+c;if(!(o<i)){if(r>n)break;s.push({chr:t,start:r,end:o,value:l[e]})}}}function Wh(e,t,i,n,r,s){const o=e.nPositions;let a=e.start;const c=e.span,l=e.data[0];for(let e=0;e<o;e++){const r=a+c;if(a>n)break;r>=i&&(Number.isNaN(l[e])||s.push({chr:t,start:a,end:r,value:l[e]})),a=r}}var Gh=Math.log(2);class $h{constructor(e,t,i,n){this.header=e,this.nameToId=t,this.idToName=i,this.sumLengths=n}static parseTree(e,t,i=!1){{const n=e.getInt(),r=e.getInt(),s=e.getInt(),o=e.getInt(),a=e.getLong(),c=e.getLong(),l={magic:n,blockSize:r,keySize:s,valSize:o,itemCount:a,reserved:c},h=new Map,d=[];let u=0;const f=n=>{n>=0&&(e.position=n);const r=e.getByte();e.getByte();const a=e.getUShort();if(1===r)for(let t=0;t<a;t++){let t,n=e.getFixedLengthString(s);if(8!==o)throw Error(`Unexpected \"valSize\" value in chromosome tree.  Expected 8, actual value is ${o}`);{t=e.getInt();const r=e.getInt();u+=r,i&&(n=i.getChromosomeName(n)),h.set(n,t),d[t]=n}}else for(let i=0;i<a;i++){e.getFixedLengthString(s);const i=e.getLong()-t,n=e.position;f(i),e.position=n}};return f(-1),new $h(l,h,d,u)}}}class Kh{static magic=610839776;littleEndian=!0;nodeCache=new Map;constructor(e,t,i){this.path=e,this.config=t,this.startOffset=i}async init(){const e=await this.#t(this.startOffset,48);let t=e.getInt();if(t!==Kh.magic&&(e.setPosition(0),this.littleEndian=!this.littleEndian,e.littleEndian=this.littleEndian,t=e.getInt(),t!==Kh.magic))throw Error(`Bad magic number ${t}`);const i=e.getUInt(),n=e.getLong(),r=e.getUInt(),s=e.getUInt(),o=e.getUInt(),a=e.getUInt(),c=e.getLong(),l=e.getUInt(),h=e.getUInt(),d=this.startOffset+48;return this.header={magic:t,blockSize:i,itemCount:n,startChromIx:r,startBase:s,endChromIx:o,endBase:a,endFileOffset:c,itemsPerSlot:l,reserved:h,rootNodeOffset:d},this}async#t(e,t){const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:t}}));return new yc(new DataView(i),this.littleEndian)}async findLeafItemsOverlapping(e,t,i,n){const r=[],s=async o=>{const a=await this.readNode(o);for(let o of a.items)Yh(o,e,t,i,n)&&(1===a.type?r.push(o):await s(o.childOffset))};return await s(this.header.rootNodeOffset),r}async readNode(e){const t=e;if(this.nodeCache.has(t))return this.nodeCache.get(t);let i=await this.#t(e,4);const n=i.getByte(),r=1===n;i.getByte();const s=i.getUShort();let o=s*(r?32:24);i=await this.#t(e+4,o);const a=[];for(let e=0;e<s;e++){let e={isLeaf:r,startChrom:i.getInt(),startBase:i.getInt(),endChrom:i.getInt(),endBase:i.getInt(),childOffset:i.getLong()};r&&(e.dataSize=i.getLong(),e.dataOffset=e.childOffset),a.push(e)}const c={type:n,items:a};return this.nodeCache.set(t,c),c}}function Yh(e,t,i,n,r){return e?(n>e.startChrom||n===e.startChrom&&r>=e.startBase)&&(t<e.endChrom||t===e.endChrom&&i<=e.endBase):(console.log(\"null item for \"+t+\" \"+i+\" \"+r),!1)}class Xh{ixFile;ixxFile;bufferCache=new Map;constructor(e,t){this.ixFile=t,this.ixxFile=e}async search(e,t){const i=e.split(\" \")[0].toLowerCase(),n=await this._getBuffer(i,t);if(!n)return;const r=n.slice(0,n.lastIndexOf(\"\\n\")).split(\"\\n\").filter((e=>!!e)),s=[];for(let e of r){const t=e.split(\" \")[0];if(t.startsWith(i)&&s.push(e),t.slice(0,i.length)>i)break}if(0!==s.length){const e=new Map;for(let t of s){const[i,...n]=t.split(\" \");e.set(i,n.map((e=>e.split(\",\")[0])))}return e}}async getIndex(e){return this.index||(this.index=await this._readIndex()),this.index}async _readIndex(e){return(await Qs.loadString(this.ixxFile)).split(\"\\n\").filter((e=>!!e)).map((e=>{const t=e.length-10,i=e.slice(0,t),n=e.slice(t);return[i,Number.parseInt(n,16)]}))}async _getBuffer(e,t){let i=0,n=65536;const r=await this.getIndex(t);for(let t=0;t<r.length;t++){const[s,o]=r[t],a=Math.min(s.length,e.length);s.slice(0,a)<e&&(i=o,n=o+65536)}const s=n-i;if(!(s<0)){if(this.bufferCache.has(i))return this.bufferCache.get(i);{const e=await Qs.loadString(this.ixFile,{range:{start:i,size:s}});return this.bufferCache.set(i,e),e}}}}class Zh{chrAliasTable=new Map;rpTreeCache=new Map;constructor(e,t){this.path=e.url,this.format=e.format||\"bigwig\",this.genome=t,this.config=e,this.bufferSize=512e3,this.loader=Ga(this.path)?new sd(vs(this.path).buffer):Qs;const i=e.trixURL||e.searchTrix;i&&(this._trix=new Xh(`${i}x`,i))}async preload(){const e=await Qs.loadArrayBuffer(this.path);this.loader=new sd(e)}async readWGFeatures(e,t){await this.loadHeader();const i=this.chromTree.idToName.length-1,n=this.chromTree.idToName[0],r=this.chromTree.idToName[i];return this.readFeatures(n,0,r,Number.MAX_VALUE,e,t)}async readFeatures(e,t,i,n,r,s=\"mean\"){t||(t=0),n||(n=Number.MAX_SAFE_INTEGER),await this.loadHeader();let o,a,c=await this.#d(e),l=await this.#d(i);if(void 0===c||void 0===l)return[];if(\"bigwig\"===this.type){const e=await this.getZoomHeaders();let t=r?function(e,t){let i;for(let n=0;n<t.length;n++){const r=t[n];if(r.reductionLevel<e){i=r;break}}return i}(r,e):void 0;t&&\"none\"!=s?(o=t.indexOffset,a=rd):(o=this.header.fullIndexOffset,a=id)}else o=this.header.fullIndexOffset,a=nd.call(this);const h=await this.loadRPTree(o),d=await h.findLeafItemsOverlapping(c,t,l,n);if(d&&0!==d.length){let e=Number.MAX_VALUE,i=0;for(let t of d)e=Math.min(e,t.dataOffset),i=Math.max(i,t.dataOffset+t.dataSize);const r=i-e,o=await this.loader.loadArrayBuffer(this.config.url,Ua(this.config,{range:{start:e,size:r}})),h=[];for(let i of d){const r=new Uint8Array(o,i.dataOffset-e,i.dataSize);let d;d=this.header.uncompressBuffSize>0?ls(r):r,a.call(this,new DataView(d.buffer),c,t,l,n,h,this.chromTree.idToName,s,this.littleEndian)}return h.sort((function(e,t){return e.start-t.start})),h}return[]}async#d(e){if(this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.chromTree.nameToId.get(e);if(void 0===t&&this.genome){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>this.chromTree.nameToId.has(e)));e.length>0&&(n=e[0],t=this.chromTree.nameToId.get(e[0]))}this.chrAliasTable.set(e,n)}return t}get searchable(){return\"bigbed\"===this.type}async search(e){if(this.header||await this.loadHeader(),!this.header||!this.header.extraIndexCount)return;const t=await this._searchForRegions(e);if(t){const i=await this._loadFeaturesForRange(t.offset,t.length);if(i){const t=i.filter((t=>{for(let i of Object.keys(t)){const n=t[i];if(Mt(n)&&n.toLowerCase()===e.toLowerCase())return!0}return!1}));return t.length>0?t.reduce(((e,t)=>e.end-e.start>t.end-t.start?e:t),i[0]):void 0}}}async _searchForRegions(e){const t=await this.#u();if(t){if(this._trix){const t=e.toLowerCase(),i=await this._trix.search(t);i&&i.has(t)&&(e=i.get(t)[0])}for(let i of t){const t=await i.search(e);if(t)return t}}}async#u(){if(void 0===this._searchTrees&&this.header.extraIndexOffsets&&this.header.extraIndexOffsets.length>0){this._searchTrees=[];for(let e of this.header.extraIndexOffsets){const t=await Cc.loadBpTree(this.path,this.config,e);this._searchTrees.push(t)}}return this._searchTrees}async getZoomHeaders(){return this.zoomLevelHeaders||await this.loadHeader(),this.zoomLevelHeaders}async loadHeader(){if(this.header)return this.header;{let e,t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:0,size:64}}));this.littleEndian=!0;const i=new yc(new DataView(t),this.littleEndian);let n=i.getUInt();if(2291137574===n)this.type=\"bigwig\";else if(2273964779===n)this.type=\"bigbed\";else{this.littleEndian=!1,i.littleEndian=!1,i.position=0;let e=i.getUInt();654085990===e?this.type=\"bigwig\":3958540679===e&&(this.type=\"bigbed\")}e={bwVersion:i.getUShort(),nZoomLevels:i.getUShort(),chromTreeOffset:i.getLong(),fullDataOffset:i.getLong(),fullIndexOffset:i.getLong(),fieldCount:i.getUShort(),definedFieldCount:i.getUShort(),autoSqlOffset:i.getLong(),totalSummaryOffset:i.getLong(),uncompressBuffSize:i.getInt(),extensionOffset:i.getLong()};const r=64;let s={start:r,size:e.totalSummaryOffset>0?e.totalSummaryOffset-r+40:Math.min(e.fullDataOffset,e.chromTreeOffset)-r};t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:s}));const o=new yc(new DataView(t),this.littleEndian),a=e.nZoomLevels;this.zoomLevelHeaders=[],this.firstZoomDataOffset=Number.MAX_SAFE_INTEGER;for(let e=1;e<=a;e++){const t=a-e,i=new Jh(t,o);this.firstZoomDataOffset=Math.min(i.dataOffset,this.firstZoomDataOffset),this.zoomLevelHeaders[t]=i}if(e.autoSqlOffset>0){o.position=e.autoSqlOffset-r;const t=o.getString();t&&(this.autoSql=function(e){let t;const i=[];let n=!1;const r=e.trim().split(/\\s*[\\r\\n]+\\s*/g);for(let e of r)if(e=e.trim(),e.length>0){if(e.startsWith(\"#\"))continue;if(e.startsWith(\"table\"))t=e.split(/\\s+/)[1].trim();else if(e.startsWith(\"(\"))n=!0;else if(e.startsWith(\")\"));else if(n){const t=e.indexOf(\";\");if(t>0){const n=e.substr(0,t).split(/\\s+/),r=e.substr(t+1).replace(/\"/g,\"\").trim();i.push({type:n[0],name:n[1],description:r})}}}return{table:t,fields:i}}(t))}e.totalSummaryOffset>0&&(o.position=e.totalSummaryOffset-r,this.totalSummary=new ed(o));const c=Math.min(2e5,Math.max(1e4,e.fullDataOffset-e.chromTreeOffset));if(this.chromTree=await this.#f(e.chromTreeOffset,c),this.chrNames=new Set(this.chromTree.idToName),\"bigbed\"===this.type){const t=await this.#p(e.fullDataOffset);this.featureDensity=t/this.chromTree.sumLengths}return this.header=e,e.extensionOffset>0&&await this.loadExtendedHeader(e.extensionOffset),this.header}}async#p(e){const t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:4}}));return new yc(new DataView(t),this.littleEndian).getInt()}async#f(e,t){let i=t;const n=async()=>{const t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:i}})),n=new yc(new DataView(t),this.littleEndian);return $h.parseTree(n,e,this.genome)};let r;for(;i<1e6;)try{return await n()}catch(e){r=e,i*=2}throw r}async loadExtendedHeader(e){let t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:64}})),i=new yc(new DataView(t),this.littleEndian);i.getUShort();const n=i.getUShort(),r=i.getLong();if(0===n)return;let s=56*n;t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:r,size:s}})),i=new yc(new DataView(t),this.littleEndian);const o=[],a=[],c=[];for(let e=0;e<n;e++){o.push(i.getUShort());const e=i.getUShort();c.push(i.getLong()),a.push(i.getInt());for(let t=0;t<e;t++)i.getUShort(),a.push(i.getUShort())}this.header.extraIndexCount=n,this.header.extraIndexOffsets=c}async loadRPTree(e){let t=this.rpTreeCache.get(e);return t||(t=new Kh(this.path,this.config,e),await t.init(),this.rpTreeCache.set(e,t),t)}async getType(){return await this.loadHeader(),this.type}async getTrackType(){return await this.loadHeader(),\"bigwig\"===this.type?\"wig\":this.autoSql&&\"chromatinInteract\"===this.autoSql.table?\"interact\":\"annotation\"}async _loadFeaturesForRange(e,t){const i=await this.loader.loadArrayBuffer(this.config.url,Ua(this.config,{range:{start:e,size:t}})),n=new Uint8Array(i),r=this.header.uncompressBuffSize>0?ls(n):n,s=[];return nd.call(this).call(this,new DataView(r.buffer),0,0,Number.MAX_SAFE_INTEGER,Number.MAX_SAFE_INTEGER,s,this.chromTree.idToName),s}}class Jh{constructor(e,t){this.index=e,this.reductionLevel=t.getInt(),this.reserved=t.getInt(),this.dataOffset=t.getLong(),this.indexOffset=t.getLong()}}class ed{constructor(e){e?(this.basesCovered=e.getLong(),this.minVal=e.getDouble(),this.maxVal=e.getDouble(),this.sumData=e.getDouble(),this.sumSquares=e.getDouble(),td.call(this)):(this.basesCovered=0,this.minVal=0,this.maxVal=0,this.sumData=0,this.sumSquares=0,this.mean=0,this.stddev=0)}}function td(){let e=this.basesCovered;if(e>0){this.mean=this.sumData/e,this.stddev=Math.sqrt(this.sumSquares/(e-1));let t=this.minVal<0?this.mean-2*this.stddev:0,i=this.maxVal>0?this.mean+2*this.stddev:0;this.defaultRange={min:t,max:i}}}function id(e,t,i,n,r,s,o,a,c){const l=new yc(e,c),h=l.getInt(),d=l.getInt();let u=d,f=l.getInt();const p=l.getInt(),g=l.getInt(),m=l.getByte();l.getByte();let w=l.getUShort();if(h>=t&&h<=n){let e=0;for(;w-- >0;){let a;switch(m){case 1:u=l.getInt(),f=l.getInt(),a=l.getFloat();break;case 2:u=l.getInt(),a=l.getFloat(),f=u+g;break;case 3:a=l.getFloat(),u=d+e*p,f=u+g,e++}if(!(h<t||h===t&&f<i)){if(h>n||h===n&&u>=r)break;if(Number.isFinite(a)){const e=o[h];s.push({chr:e,start:u,end:f,value:a})}}}}}function nd(){const e=function(e,t,i,n){if(\"biginteract\"===n||i&&(\"chromatinInteract\"===i.table||\"interact\"===i.table))return function(e,t){return e.chr1=t[5],e.start1=Number.parseInt(t[6]),e.end1=Number.parseInt(t[7]),e.chr2=t[10],e.start2=Number.parseInt(t[11]),e.end2=Number.parseInt(t[12]),e.name=t[0],e.score=Number(t[1]),e.value=Number(t[2]),e.color=\".\"===t[4]?void 0:\"0\"===t[4]?\"rgb(0,0,0)\":t[4],e};{const n=e-3;return function(r,s){if(n>0&&(r.name=s[0]),n>1&&(r.score=Number(s[1])),n>2&&(r.strand=s[2]),n>3&&(r.cdStart=parseInt(s[3])),n>4&&(r.cdEnd=parseInt(s[4])),n>5&&\".\"!==s[5]&&\"0\"!==s[5]&&\"-1\"!==s[5]){const e=_s.createColorString(s[5]);r.color=e.startsWith(\"rgb\")?e:void 0}if(n>8){const e=parseInt(s[6]),t=s[7].split(\",\"),i=s[8].split(\",\"),n=[];for(let s=0;s<e;s++){const e=r.start+parseInt(i[s]),o=e+parseInt(t[s]);n.push({start:e,end:o})}!function(e,t,i){for(let n of e){const e=n.end,r=n.start;e<t||r>i?n.utr=!0:(t>=r&&t<=e&&(n.cdStart=t),i>=r&&i<=e&&(n.cdEnd=i))}}(n,r.cdStart,r.cdEnd),r.exons=n}if(i)for(let n=e;n<t;n++)if(n<i.fields.length){const e=i.fields[n].name,t=s[n-3];r[e]=t}}}}(this.header.definedFieldCount,this.header.fieldCount,this.autoSql,this.format);return function(t,i,n,r,s,o,a,c,l){const h=new yc(t,l);for(;h.remLength()>=13;){const t=h.getInt(),c=a[t],l=h.getInt(),d=h.getInt(),u=h.getString();if(!(t<i||t===i&&d<n)){if(t>r||t===r&&l>=s)break;if(d>0){const t={chr:c,start:l,end:d};o.push(t);const i=u.split(\"\\t\");e(t,i)}}}}}function rd(e,t,i,n,r,s,o,a,c){const l=new yc(e,c);for(;l.remLength()>=32;){const e=l.getInt(),c=l.getInt(),h=l.getInt(),d=l.getInt(),u=l.getFloat(),f=l.getFloat(),p=l.getFloat();let g;switch(l.getFloat(),a){case\"min\":g=u;break;case\"max\":g=f;break;default:g=0===d?0:p/d}if(!(e<t||e===t&&h<i)){if(e>n||e===n&&c>=r)break;if(Number.isFinite(g)){const t=o[e];s.push({chr:t,start:c,end:h,value:g})}}}}class sd{constructor(e){this.data=e}loadArrayBuffer(e,t){const i=t.range;return i?this.data.slice(i.start,i.start+i.size):this.data}async dataViewForRange(e,t){const i=Math.min(this.data.byteLength-e.start,e.size);return t?new Uint8Array(this.data,e.start,i):new DataView(this.data,e.start,i)}}class od extends Hh{queryable=!0;#h={};windowFunctions=[\"mean\",\"min\",\"max\",\"none\"];constructor(e,t){super(t),this.reader=new Zh(e,t),this.genome=t,this.format=e.format||\"bigwig\"}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,windowFunction:r}){await this.reader.loadHeader();const s=\"bigwig\"===this.reader.type;let o;return o=\"all\"===e.toLowerCase()?s?await this.getWGValues(r,n):[]:await this.reader.readFeatures(e,t,e,i,n,r),s||Tl(o),o}async getHeader(){return this.reader.loadHeader()}async defaultVisibilityWindow(){return\"bigwig\"===this.reader.type?-1:this.reader.featureDensity?Math.floor(1e4/this.reader.featureDensity):-1}async getWGValues(e,t){const i=this.genome,n=this.#h[e];if(n&&n.bpPerPixel>.8*t&&n.bpPerPixel<1.2*t)return n.values;{const n=await this.reader.readWGFeatures(t,e);let r=[];for(let e of n){const t=e.chr,n=i.getCumulativeOffset(t);if(void 0===n)continue;const s=Object.assign({},e);s.chr=\"all\",s.start=n+e.start,s.end=n+e.end,s._f=e,r.push(s)}return r.sort(((e,t)=>e.start-t.start)),this.#h[e]={values:r,bpPerPixel:t},r}}supportsWholeGenome(){return\"bigwig\"===this.reader.type}async trackType(){return this.reader.getTrackType()}get searchable(){return this.reader.searchable}async search(e){return this.reader.search(e)}}const ad=.01;function cd(e,t,i,n){if(void 0===this.dataRange||void 0===this.dataRange.max||void 0===this.dataRange.min)return;xo.fillRect(e,0,0,t,i,{fillStyle:\"white\"}),n&&xo.fillRect(e,t-4-2,0,4,i,{fillStyle:n});const r=void 0!==this.flipAxis&&this.flipAxis,s=.95*t-8-5,o=.95*t-5,a={font:\"normal 10px Arial\",textAlign:\"right\",fillStyle:\"black\",strokeStyle:\"black\"};xo.strokeLine(e,s,ad*i,o,ad*i,a),xo.fillText(e,l(r?this.dataRange.min:this.dataRange.max),s+4,ad*i+12,a);const c=.99*i;function l(e){return 0===e?\"0\":Math.abs(e)>=10?e.toFixed():Math.abs(e)>=1?e.toFixed(1):Math.abs(e)>=.1?e.toFixed(2):e.toExponential(1)}xo.strokeLine(e,s,c,o,c,a),xo.fillText(e,l(r?this.dataRange.max:this.dataRange.min),s+4,c-4,a),xo.strokeLine(e,o,ad*i,o,c,a)}class ld extends Hl{static defaults={height:50,flipAxis:!1,logScale:!1,windowFunction:\"mean\",graphType:\"bar\",normalize:void 0,scaleFactor:void 0,overflowColor:\"rgb(255, 32, 255)\",baselineColor:\"lightGray\",summarize:!0,visibilityWindow:void 0};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"wig\",this.featureType=\"numeric\",this.resolutionAware=!0,this.paintAxis=cd;const t=e.format?e.format.toLowerCase():e.format;e.featureSource?(this.featureSource=e.featureSource,delete e.featureSource):this.featureSource=\"bigwig\"===t?new od(e,this.browser.genome):\"tdf\"===t?new Qh(e,this.browser.genome):Ad(e,this.browser.genome),void 0===e.max||!0===e.autoscale?this.autoscale=!0:this.dataRange={min:e.min||0,max:e.max}}async postInit(){const e=await this.getHeader();this.disposed||e&&this.setTrackProperties(e)}supportsWholeGenome(){return void 0===this.visibilityWindow||this.visibilityWindow<0}async getFeatures(e,t,i,n){const r=this.windowFunction,s=await this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow,windowFunction:r});if(this.normalize&&this.featureSource.normalizationFactor){const e=this.featureSource.normalizationFactor;for(let t of s)t.value*=e}if(this.scaleFactor){const e=this.scaleFactor;for(let t of s)t.value*=e}return!this.summarize||\"mean\"!==r&&\"min\"!==r&&\"max\"!==r?s:hd(s,t,n,r)}menuItemList(){const e=[];if(void 0!==this.flipAxis){function t(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}e.push(\"<hr>\"),e.push({label:\"Flip y-axis\",click:t})}return this.featureSource.windowFunctions&&e.push(...this.wigSummarizationItems()),e.push(...this.numericDataMenuItems()),e}wigSummarizationItems(){const e=this.featureSource.windowFunctions,t=[];t.push(\"<hr/>\"),t.push(\"<div>Windowing function</div>\");for(const i of e){const n=Bt(Dl(i,this.windowFunction===i));function r(){this.windowFunction=i,this.trackView.updateViews()}t.push({object:n,click:r})}return t}async getHeader(){return\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getScaleFactor(e,t,i,n){const r=!0===n?e<0?-Math.log10(Math.abs(e)+1):Math.log10(Math.abs(e)+1):e;return i/((!0===n?Math.log10(Math.abs(t)+1):t)-r)}computeYPixelValue(e,t){return(this.flipAxis?e-this.dataRange.min:this.dataRange.max-e)*t}computeYPixelValueInLogScale(e,t){let i=this.dataRange.max,n=this.dataRange.min;return n=n<0?-Math.log10(Math.abs(n)+1):Math.log10(Math.abs(n)+1),i=i<0?-Math.log10(Math.abs(i)+1):Math.log10(Math.abs(i)+1),e=e<0?-Math.log10(Math.abs(e)+1):Math.log10(e+1),(this.flipAxis?e-n:i-e)*t}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=e.pixelHeight-1,a=r+s*n+1,c=this.getScaleFactor(this.dataRange.min,this.dataRange.max,o,this.logScale),l=e=>this.logScale?this.computeYPixelValueInLogScale(e,c):this.computeYPixelValue(e,c);if(t&&t.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){let s,c=-1;const h=l(0);for(let d of t){if(d.end<r)continue;if(d.start>a)break;const t=(d.start-r)/n;if(isNaN(t))continue;let u=l(d.value);const f=(d.end-r)/n-t,p=e.alpha?_s.addAlpha(this.getColorForFeature(d),e.alpha):this.getColorForFeature(d);if(\"line\"===this.graphType)void 0!==s&&xo.strokeLine(i,c,s,t,u,{fillStyle:p,strokeStyle:p}),xo.strokeLine(i,t,u,t+f,u,{fillStyle:p,strokeStyle:p});else if(\"points\"===this.graphType){const e=this.config.pointSize||3,n=t+f/2;xo.fillCircle(i,n,u,e/2,{fillStyle:p,strokeStyle:p}),d.value>this.dataRange.max?xo.fillCircle(i,n,e/2,e/2,3,{fillStyle:this.overflowColor}):d.value<this.dataRange.min&&xo.fillCircle(i,n,o-e/2,e/2,3,{fillStyle:this.overflowColor})}else{const e=Math.min(o,u-h);xo.fillRect(i,t,h,f,e,{fillStyle:p}),d.value>this.dataRange.max?xo.fillRect(i,t,0,f,3,{fillStyle:this.overflowColor}):d.value<this.dataRange.min&&xo.fillRect(i,t,o-2,f,3,{fillStyle:this.overflowColor})}c=t+f,s=u}if(this.dataRange.min<0){let t=this.dataRange.max,n=this.dataRange.min;n=!0===this.logScale?n<0?-Math.log10(Math.abs(n)+1):Math.log10(Math.abs(n)+1):n,t=!0===this.logScale?t<0?-Math.log10(Math.abs(t)+1):Math.log10(Math.abs(t)+1):t;const r=t/(t-n),s=this.flipAxis?(1-r)*o:r*o;xo.strokeLine(i,0,s,e.pixelWidth,s,{strokeStyle:this.baselineColor})}}if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=l(t.y),n={strokeStyle:t.color,strokeWidth:2};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,n):xo.strokeLine(e.context,0,i,e.pixelWidth,i,n)}}popupData(e,t){if(void 0===t&&(t=this.clickedFeatures(e)),t&&t.length>0){const i=e.genomicLocation,n=[];t.sort((function(e,t){return Math.abs((e.start+e.end)/2-i)-Math.abs((t.start+t.end)/2-i)}));const r=t.length>10?t.slice(0,10):t;r.sort((function(e,t){return e.start-t.start}));for(let e of r)if(e){n.length>0&&n.push(\"<hr/>\");let t=e.end-e.start==1?Rt(Math.floor(e.start)+1):Rt(Math.floor(e.start)+1)+\"-\"+Rt(Math.floor(e.end));n.push({name:\"Position:\",value:t}),n.push({name:\"Value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\",value:Rt(e.value.toFixed(4))})}return r.length<t.length&&n.push(\"<hr/>...\"),n}return[]}get supportsWholeGenome(){return!this.config.indexURL&&!1!==this.config.supportsWholeGenome}getColorForFeature(e){let t=e.value<0&&this.altColor?this.altColor:this.color||\"rgb(150, 150, 150)\";return\"function\"==typeof t?t(e.value):t}dispose(){this.trackView=void 0}}function hd(e,t,i,n=\"mean\"){if(i<=1||!e||0===e.length)return e;const r=e[0].chr,s=i,o=[],a=e=>{const i=t+e.bin*s,a=i+s;let c;switch(n){case\"mean\":c=e.sumData/e.count;break;case\"max\":c=e.max;break;case\"min\":c=e.min;break;default:throw Error(`Unknown window function: ${n}`)}const l=`${n} of ${e.count} values`;o.push({chr:r,start:i,end:a,value:c,description:l})};let c;for(let i of e){let e=Math.floor((i.start-t)/s);const n=Math.floor((i.end-t)/s);if(c&&e===c.bin&&(c.add(i),e++),!c||n>c.bin){if(c&&a(c),n>e){const e=t+n*s;o.push({chr:r,start:i.start,end:e,value:i.value})}c=new dd(n,i)}}c&&a(c);const l=[];let h=o[0];for(let e of o)h.value===e.value&&e.start<=h.end?h.end=e.end:(l.push(h),h=e);return l.push(h),l}class dd{constructor(e,t){this.bin=e,this.sumData=t.value,this.count=1,this.min=t.value,this.max=t.value}add(e){this.sumData+=e.value,this.max=Math.max(e.value,this.max),this.min=Math.min(e.value,this.min),this.count++}get mean(){return this.sumData/this.count}}class ud extends Hh{constructor(e,t){super(t),this.config=e||{},this.genome=t,this.sourceType=void 0===e.sourceType?\"file\":e.sourceType,this.maxWGCount=e.maxWGCount||1e4,this.windowFunctions=[\"mean\",\"min\",\"max\",\"none\"];const i=new Set([\"bigwig\",\"bw\",\"bigbed\",\"bb\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\",\"tdf\"]);if(this.queryable=e.indexURL||!0===e.queryable,e.reader)this.reader=e.reader,this.queryable=!1!==e.queryable;else{if(\"ga4gh\"===e.sourceType)throw Error(\"Unsupported source type 'ga4gh'\");\"eqtl\"!==e.type&&\"qtl\"!==e.type||\"gtex-ws\"!==e.sourceType?\"htsget\"===e.sourceType?(this.reader=new Lh(e,t),this.queryable=!0):\"ucscservice\"===e.sourceType?(this.reader=new Nh(e.source),this.queryable=!0):\"custom\"===e.sourceType?(this.reader=new Eh(e.source),this.queryable=!1!==e.source.queryable):\"service\"===e.sourceType?(this.reader=new Ih(e,t),this.queryable=!0):(this.reader=new Ih(e,t),void 0!==e.queryable?this.queryable=e.queryable:(i.has(e.format)||this.reader.indexed)&&(this.queryable=!0)):(this.reader=new Bh(e),this.queryable=!0)}this.searchable=!1!==e.searchable}async defaultVisibilityWindow(){if(this.reader&&\"function\"==typeof this.reader.defaultVisibilityWindow)return this.reader.defaultVisibilityWindow()}async trackType(){const e=await this.getHeader();return e?e.type:void 0}async getHeader(){if(!this.header)if(this.reader&&\"function\"==typeof this.reader.readHeader){const e=await this.reader.readHeader();e?(this.header=e,e.format&&(this.config.format=e.format)):this.header={}}else this.header={};return this.header}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r,windowFunction:s}){const o=\"all\"===e.toLowerCase();if(t=t||0,i=i||Number.MAX_SAFE_INTEGER,(o&&!this.wgFeatures&&this.supportsWholeGenome()||this.config.disableCache||!this.featureCache||!this.featureCache.containsRange(new hc(e,t,i)))&&await this.loadFeatures(e,t,i,r),o){if(!this.wgFeatures)if(this.supportsWholeGenome())if(\"wig\"===this.config.type){const e=await Ll(this.featureCache.getAllFeatures(),this.genome,1e6);this.wgFeatures=hd(e,0,n,s)}else this.wgFeatures=await Ll(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount);else this.wgFeatures=[];return this.wgFeatures}return this.featureCache.queryFeatures(e,t,i)}async findFeatures(e){return this.featureCache?this.featureCache.findFeatures(e):[]}supportsWholeGenome(){return!this.queryable}getAllFeatures(){return this.queryable||!this.featureCache?[]:this.featureCache.getAllFeatures()}async loadFeatures(e,t,i,n){await this.getHeader();const r=this.reader;let s=t,o=i,a=e;if(!this.chrAliasManager&&this.reader&&this.reader.sequenceNames&&(this.chrAliasManager=new zh(this.reader.sequenceNames,this.genome)),this.chrAliasManager&&(a=await this.chrAliasManager.getAliasName(e)),(!n||n<=0)&&!1!==this.config.expandQuery){const e=this.genome?this.genome.getChromosome(a):void 0;s=0,o=Math.max(e?e.bpLength:Number.MAX_SAFE_INTEGER,i)}else if(n>i-t&&!1!==this.config.expandQuery){let e=Math.min(4.1*(i-t),n);this.config.minQuerySize&&e<this.config.minQuerySize&&(e=this.config.minQuerySize),s=Math.max(0,(t+i-e)/2),o=s+e}let c=await r.readFeatures(a,s,o);void 0===this.queryable&&(this.queryable=r.indexed);const l=this.queryable?new hc(e,s,o):void 0;if(c){if(\"wig\"!==this.config.format&&\"junctions\"!==this.config.type){zl(c,this.config.maxRows||Number.MAX_SAFE_INTEGER)}this.featureCache=new Zs(c,this.genome,l),this.searchable&&this.addFeaturesToDB(c,this.config)}else this.featureCache=new Zs([],l)}addFeaturesToDB(e,t){this.featureMap||(this.featureMap=new Map);const i=t.searchableFields||[\"name\",\"transcript_id\",\"gene_id\",\"gene_name\",\"id\"];for(let t of e)for(let e of i){let i;if(t.hasOwnProperty(e)?i=t[e]:\"function\"==typeof t.getAttributeValue&&(i=t.getAttributeValue(e)),i){if(i=i.replaceAll(\" \",\"+\").toUpperCase(),this.featureMap.has(i)){const e=this.featureMap.get(i);if(t.end-t.start<e.end-e.start)continue}this.featureMap.set(i,t)}}}search(e){if(this.featureMap)return this.featureMap.get(e.toUpperCase())}}class fd extends Hh{constructor(e,t){super(t),this.config=e,this.genome=t,this.queryable=!1,this.searchable=!1!==e.searchable,this.updateFeatures(e.features)}updateFeatures(e){zl(e=function(e,t){if(t)for(let i of e)i.chr=t.getChromosomeName(i.chr);return e}(e,this.genome)),this.config.mappings&&function(e,t){let i=Object.keys(t);e.forEach((function(e){i.forEach((function(i){e[i]=e[t[i]]}))}))}(e,this.config.mappings),this.featureCache=new Zs(e,this.genome),(this.searchable||this.config.searchableFields)&&this.addFeaturesToDB(e,this.config)}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome,o=s?s.getChromosomeName(e):e;return\"all\"===o.toLowerCase()?Ll(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.featureCache.queryFeatures(o,t,i)}getAllFeatures(){return this.featureCache.getAllFeatures()}supportsWholeGenome(){return!0}addFeaturesToDB(e,t){this.featureMap||(this.featureMap=new Map);const i=t.searchableFields||[\"name\"];for(let t of e)for(let e of i){let i;if(\"function\"==typeof t.getAttributeValue&&(i=t.getAttributeValue(e)),i||(i=t[e]),i){i=i.replaceAll(\" \",\"+\");const e=this.featureMap.get(i.toUpperCase());if(e&&e.end-e.start>t.end-t.start)continue;this.featureMap.set(i.toUpperCase(),t)}}}search(e){if(this.featureMap)return this.featureMap.get(e.toUpperCase())}}class pd{constructor({chr:e,locus:t,accession:i,aliases:n,features:r,sequence:s}){this.chr=e,this.locus=t,this.accession=i,this.aliases=n,this.features=r,this.sequence=s,this.bpLength=s.length}toJSON(){return{gbkURL:this.url}}getSequenceRecord(e){return{chr:this.chr,bpLength:this.bpLength}}get chromosomeNames(){return[this.chr]}getFirstChromosomeName(){return this.chr}get id(){return this.accession}get name(){return this.locus}get initialLocus(){return this.chr}get description(){return this.locus}get infoURL(){return this.url}showWholeGenomeView(){return!1}getHomeChromosomeName(){return this.chr}getChromosomeName(e){return e}getChromosomeDisplayName(e){return this.chr}getChromosome(e){if(e===this.chr)return{name:this.chr,bpLength:this.bpLength}}async loadChromosome(e){return this.getChromosome(e)}async getAliasRecord(e){}getCytobands(e){return[]}getChromosomes(){return[this.getChromosome(this.chr)]}get wgChromosomeNames(){}getGenomeCoordinate(e,t){if(e===this.chr)return t}getChromosomeCoordinate(e){return{chr:this.chr,position:e}}getCumulativeOffset(e){return 0}getGenomeLength(){return this.bpLength}async getSequence(e,t,i){return e===this.chr?this.sequence.substring(t,i):void 0}getSequenceInterval(e,t,i){return e===this.chr?new dc(this.chr,0,this.sequence.length,this.sequence):void 0}}const gd=/\\s+/,md=new Map;async function wd(e){let t=md.get(e);if(!t){t=function(e){if(!e)return null;const t=mh(e);let i=t.nextLine();const n=i.split(/\\s+/);if(\"LOCUS\"!==n[0].toUpperCase())throw Error(\"Expected `LOCUS` line.  Found: \"+i);const r=n[1].trim();let s,o;do{if(i=t.nextLine(),i.startsWith(\"ACCESSION\")){const e=i.split(gd);if(e.length<2)throw Error(\"Genbank file missing ACCESSION number.\");s=e[1].trim()}else if(i.startsWith(\"ALIASES\")){const e=i.split(gd);e.length>1&&(o=e[1].split(\",\"))}}while(i&&!i.startsWith(\"FEATURES\"));const a=s||r,c=function(e,t){const i=[];let n,r,s,o=0;for(;;)if(r=t.nextLine(),\"\"!==r){if(!r||r.startsWith(\"ORIGIN\"))break;if(r.length<6)o<10&&console(\"Unexpected line in genbank file (skipping): \"+r),o++;else if(\" \"!==r.charAt(5)){let t=r.substring(5,21).trim();s={chr:e,type:t,attributes:{},getAttributeValue:function(e){return this.attributes[e]}},n=r.substring(21),\"source\"!==t.toLowerCase()&&i.push(s)}else{let t=r.substring(21).trim();if(t.length>0)if(47===t.charCodeAt(0)){if(47===n.charCodeAt(0)){let e=n.split(\"=\",2);if(e.length>1){let t=e[0].length>1?e[0].substring(1):\"\",i=Fd(e[1]);s.attributes[t]=i}}else{const t=n.includes(\"complement\")?\"-\":\"+\";s.strand=t;let i=n.replace(\"join\",\"\").replace(\"order\",\"\").replace(\"complement\",\"\").replace(\"(\",\"\").replace(\")\",\"\");if(i.includes(\"..\")){i=i.replace(\"<\",\"\").replace(\">\",\"\");const n=bd(i,e,t),r=n[0];s.start=r.start;const o=n[n.length-1];s.end=o.end,n.length>1&&(s.exons=n)}else s.start=parseInt(i)-1,s.end=s.start+1}n=t}else n+=t}}return i}(a,t),l=function(e){let t,i=\"\";for(;(t=e.nextLine())&&!t.startsWith(\"//\");){t=t.trim();const e=t.split(/\\s+/);for(let t=1;t<e.length;t++)i+=e[t]}return i}(t);return new pd({chr:a,locus:r,accession:s,aliases:o,features:c,sequence:l})}(await Qs.loadString(e,{})),t.url=e,md.set(e,t)}return t}function bd(e,t,i){const n=e.split(\",\"),r=[];e.includes(\"complement\");for(const e of n){const n=e.split(\"..\");let s=0;try{s=parseInt(n[0])-1}catch(e){console.error(e)}let o=s+1;n.length>1&&(o=parseInt(n[1])),r.push({chr:t,start:s,end:o,strand:i})}return r.sort((function(e,t){return e.start-t.start})),r}function Fd(e){return e.startsWith('\"')&&e.endsWith('\"')&&(e=e.substring(1,e.length-2)),e}class vd extends Hh{constructor(e,t){super(t),this.config=e,this.searchable=!0}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){if(!this.featureSource){const e=await wd(this.config.url);this.featureSource=new fd({genome:this.config.genome,features:e.features,searchableFields:[\"gene\",\"db_xref\",\"locus_tag\",\"transcript_id\"]})}return this.featureSource.getFeatures({chr:e,start:t,end:i})}supportsWholeGenome(){return!1}search(e){return this.featureSource.search(e)}}const yd=new Set([\"bigwig\",\"bw\",\"bigbed\",\"bb\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\"]);function Ad(e,t){const i=e.format?e.format.toLowerCase():void 0;return e.features?new fd(e,t):yd.has(i)?new od(e,t):\"tdf\"===i?new Qh(e,t):\"gbk\"===i?new vd(e,t):new ud(e,t)}function Cd(e){return(3-e.readingFrame)%3}function _d(e){return e.cdStart||e.start}function xd(e){return e.cdEnd||e.end}const kd=.25;function Id(e,t,i){let n=(e.start-t)/i,r=(e.end-t)/i,s=r-n;return s<3&&(s=3,n-=1.5),{px:n,px1:r,pw:s}}function Sd(e,t,i,n,r,s){try{r.save(),r.fillStyle=this.color,r.strokeStyle=this.color;const n=this.getColorForFeature(e);let o,a;r.fillStyle=n,r.strokeStyle=n,\"SQUISHED\"===this.displayMode&&void 0!==e.row?(o=this.featureHeight/2,a=this.margin+this.squishedRowHeight*e.row):\"EXPANDED\"===this.displayMode&&void 0!==e.row?(o=this.featureHeight,a=this.margin+this.expandedRowHeight*e.row):(o=this.featureHeight,a=this.margin);const c=s.pixelWidth,l=a+o/2,h=o/2,d=l-h/2,u=e.exons?e.exons.length:0,f=Id(e,t,i),p=this.arrowSpacing,g=\"+\"===e.strand?1:\"-\"===e.strand?-1:0;if(0===u){const e=Math.max(0,f.px),t=Math.min(c,f.px1),i=t-e;if(r.fillRect(e,a,i,o),0!==g){r.fillStyle=\"white\",r.strokeStyle=\"white\";for(let i=e+p/2;i<t;i+=p)xo.strokeLine(r,i-2*g,l-2,i,l),xo.strokeLine(r,i-2*g,l+2,i,l);r.fillStyle=n,r.strokeStyle=n}}else{xo.strokeLine(r,f.px+1,l,f.px1-1,l);const u=Math.max(0,f.px)+p/2,m=Math.min(c,f.px1);for(let e=u;e<m;e+=p)xo.strokeLine(r,e-2*g,l-2,e,l),xo.strokeLine(r,e-2*g,l+2,e,l);for(let u=0;u<e.exons.length;u++){const f=e.exons[u];let m,w=Math.round((f.start-t)/i),b=Math.round((f.end-t)/i),F=Math.max(1,b-w);if(!(w+F<0)){if(w>c)break;if(f.utr)r.fillRect(w,d,F,h);else{if(f.cdStart&&(m=Math.round((f.cdStart-t)/i),r.fillRect(w,d,m-w,h),F-=m-w,w=m),f.cdEnd&&(m=Math.round((f.cdEnd-t)/i),r.fillRect(m,d,b-m,h),F-=b-m,b=m),F=Math.max(F,1),r.fillRect(w,a,F,o),void 0!==f.readingFrame&&s.bpPerPixel<kd&&s.sequenceInterval){const i=u>0&&void 0!==e.exons[u-1].readingFrame?e.exons[u-1]:void 0,n=u<e.exons.length-1&&void 0!==e.exons[u+1].readingFrame?e.exons[u+1]:void 0;Ed.call(this,r,e.strand,i,f,n,t,s.bpPerPixel,a,o,s.sequenceInterval)}if(F>p+5&&0!==g&&s.bpPerPixel>kd){r.fillStyle=\"white\",r.strokeStyle=\"white\";for(let e=w+p/2;e<b;e+=p)xo.strokeLine(r,e-2*g,l-2,e,l),xo.strokeLine(r,e-2*g,l+2,e,l);r.fillStyle=n,r.strokeStyle=n}}}}}s.drawLabel&&\"SQUISHED\"!==this.displayMode&&Nd.call(this,r,e,f.px,f.px1,a,s.referenceFrame,s)}finally{r.restore()}}function Ed(e,t,i,n,r,s,o,a,c,l){const h=[\"rgb(124,124,204)\",\"rgb(12, 12, 120)\"];e.save();const d=(t,i,n,r,d,u)=>{const f=Math.round((i-s)/o),p=Math.round((n-s)/o)-f;let g;if(void 0===r){if(l.hasSequence(i,n)){const e=l.getSequence(i,n);if(e&&3===e.length){const i=\"+\"===t?e:ac(e.split(\"\").reverse().join(\"\"));g=Gd[i]}}}else g=r;e.fillStyle=\"M\"===r||\"M\"===g&&0===u?\"#83f902\":\"STOP\"===g?\"#ff2101\":h[d],e.fillRect(f,a,p,c),g&&(e.save(),((t,i,n,r,s)=>{\"STOP\"===s&&(s=\"*\");const o=e.measureText(s).width;xo.fillText(e,s,n+(i-o)/2,r-4,{fillStyle:\"#ffffff\"})})(0,p,f,a+c,g),e.restore());const m=n-i;return m>0&&m<3?{start:i,end:n}:void 0},u=Cd(n);let f,p,g,m,w,b=_d(n),F=xd(n),v=1;if(\"+\"===t){for(u>0&&(b+=u),v=1,w=0,f=b;f<F;w++,f+=3)m=v%2,p=Math.min(F,f+3),g=d(t,f,p,void 0,v%2,w),++v;if(u>0||g){const e=u>0?Bd.call(this,t,u,b-u,b,g,i,n,r,l):Bd.call(this,t,void 0,void 0,void 0,g,i,n,r,l);if(e){const{left:i,rite:n}=e;i&&d(t,b-u,b,i.aminoAcidLetter,0,void 0),n&&d(t,g.start,g.end,n.aminoAcidLetter,m,void 0)}}}else{for(u>0&&(F-=u),v=1,w=0,w=0,p=F;p>b;w++,p-=3)m=v%2,f=Math.max(b,p-3),g=d(t,f,p,void 0,v%2,w),++v;if(u>0||g){const e=u>0?Bd.call(this,t,u,F,F+u,g,i,n,r,l):Bd.call(this,t,void 0,void 0,void 0,g,i,n,r,l);if(e){const{left:i,rite:n}=e;n&&d(t,F,F+u,n.aminoAcidLetter,0,void 0),i&&d(t,g.start,g.end,i.aminoAcidLetter,m,void 0)}}}e.restore()}function Nd(e,t,i,n,r,s,o){try{e.save();let s=t.name;if(void 0===s&&t.gene&&(s=t.gene.name),void 0===s&&(s=t.id||t.ID),!s||\".\"===s)return;let a=o.pixelXOffset||0;const c=Math.max(i,-a);let l,h=(c+Math.min(n,-a+o.viewportWidth))/2;\"COLLAPSED\"===this.displayMode&&\"SLANT\"===this.labelDisplayMode&&(l={rotate:{angle:45}});const d=function(e,t){return t?e+20:e+25}(r,l);let u=this.getColorForFeature(t),f=this.browser.qtlSelections.hasPhenotype(t.name);const p={textAlign:\"SLANT\"===this.labelDisplayMode?void 0:\"center\",fillStyle:u,strokeStyle:u},g=e.measureText(s),m=h-g.width/2,w=h+g.width/2,b=o.rowLastLabelX[t.row]||-Number.MAX_SAFE_INTEGER;(o.labelAllFeatures||m>b||f)&&(o.rowLastLabelX[t.row]=w,\"y\"===o.axis?(e.save(),xo.labelTransformWithContext(e,h),xo.fillText(e,s,h,d,p,l),e.restore()):(e.clearRect(h-g.width/2-1,d-g.actualBoundingBoxAscent-1,g.width+2,g.actualBoundingBoxAscent+g.actualBoundingBoxDescent+2),xo.fillText(e,s,h,d,p,l)))}finally{e.restore()}}function Bd(e,t,i,n,r,s,o,a,c){let l,h,d=\"\",u=\"\",f=\"\";const p={left:void 0,rite:void 0};if(\"+\"===e){if(t){if(u=c.getSequence(i,n),!u)return;if([l,h]=[xd(s)-(3-t),xd(s)],d=c.getSequence(l,h),!d)return;f=d+u,p.left={triplet:f,aminoAcidLetter:Gd[f]}}if(r){if(d=c.getSequence(r.start,r.end),!d)return;const e=Cd(a),t=_d(a);if(u=c.getSequence(t,t+e),!u)return;f=d+u,p.rite={triplet:f,aminoAcidLetter:Gd[f]}}}else{if(t){if(d=c.getSequence(i,n),void 0===d)return;if([l,h]=[_d(a),_d(a)+(3-t)],u=c.getSequence(l,h),void 0===u)return;f=d+u,f=ac(f.split(\"\").reverse().join(\"\")),p.rite={triplet:f,aminoAcidLetter:Gd[f]}}if(r){if(u=c.getSequence(r.start,r.end),void 0===u)return;const e=Cd(s),t=xd(s);if(d=c.getSequence(t-e,t),void 0===d)return;f=d+u,f=ac(f.split(\"\").reverse().join(\"\")),p.left={triplet:f,aminoAcidLetter:Gd[f]}}}return p}const Md=new Set([\"nonsense\",\"missense\",\"stop-loss\",\"frameshift\",\"cds-indel\"]),Rd=new Set([\"coding-synon\"]),Dd=new Set([\"splice-3\",\"splice-5\"]),Td=new Set([\"untranslated-5\",\"untranslated-3\"]);function Ld(e,t,i,n,r){var s,o,a,c,l,h,d=Id(e,t,i),u=this.margin,f=this.snpColors.length;switch(s=\"squished\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight,this.colorBy){case\"function\":c=e.func,h=c.split(\",\"),l=h.map((function(e){return Md.has(e)||Dd.has(e)?f-1:Rd.has(e)?f-2:Td.has(e)?f-3:0})),o=l.reduce((function(e,t){return Math.max(e,t)}));break;case\"class\":o=\"deletion\"===(a=e.class)?f-1:\"mnp\"===a?f-2:\"microsatellite\"===a||\"named\"===a?f-3:0}r.fillStyle=this.snpColors[o],r.fillRect(d.px,u,d.pw,s)}function zd(e,t,i,n,r){const s=\"EXPANDED\"===this.displayMode?this.expandedRowHeight:this.squishedRowHeight;let o=this.margin;\"COLLAPSED\"!==this.displayMode&&void 0!==e.row&&(o+=e.row*s);const a=o+.5*s,c=a-.5*s,l=a+.5*s,h=Math.round((e.junction_left-t)/i),d=Math.round((e.junction_right-t)/i);r.beginPath(),r.moveTo(h,a),r.bezierCurveTo(h,c,d,c,d,a),r.lineWidth=1+Math.log(e.num_junction_reads)/Math.log(2),r.strokeStyle=\"blue\",r.stroke();const u=e.spanning_frag_coords;for(let e=0;e<u.length;e++){const n=u[e],s=Math.round((n.left-t)/i),o=Math.round((n.right-t)/i);r.beginPath(),r.moveTo(s,a),r.bezierCurveTo(s,l,o,l,o,a),r.lineWidth=1,r.strokeStyle=\"purple\",r.stroke()}}class Hd extends Hl{static defaults={type:\"annotation\",maxRows:1e3,displayMode:\"EXPANDED\",margin:10,featureHeight:14,useScore:!1};constructor(e,t){super(e,t)}init(e){super.init(e),this.labelDisplayMode=e.labelDisplayMode,e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):\"blat\"!==e.type&&(this.featureSource=e.featureSource?e.featureSource:Ad(e,this.browser.genome)),\"FusionJuncSpan\"===e.type?(this.render=e.render||zd,this.squishedRowHeight=e.squishedRowHeight||50,this.expandedRowHeight=e.expandedRowHeight||50,this.height=e.height||this.margin+2*this.expandedRowHeight):\"snp\"===e.type?(this.render=e.render||Ld,this.snpColors=[\"rgb(0,0,0)\",\"rgb(0,0,255)\",\"rgb(0,255,0)\",\"rgb(255,0,0)\"],this.colorBy=\"function\",this.expandedRowHeight=e.expandedRowHeight||10,this.squishedRowHeight=e.squishedRowHeight||5,this.height=e.height||30):(this.render=e.render||Sd,this.arrowSpacing=30,function(e){e.browser.on&&(e.browser.on(\"trackdragend\",t),e.browser.on(\"trackremoved\",i));function t(){e.trackView&&\"SQUISHED\"!==e.displayMode&&e.trackView.repaintViews()}function i(n){e.browser.un&&e===n&&(e.browser.un(\"trackdragend\",t),e.browser.un(\"trackremoved\",i))}}(this),this.squishedRowHeight=e.squishedRowHeight||15,this.expandedRowHeight=e.expandedRowHeight||30,this.height=e.height||this.margin+2*this.expandedRowHeight,e.colorBy&&(e.colorBy.field&&(e.colorTable=e.colorBy.pallete||e.colorBy.palette,e.colorBy=e.colorBy.field),this.colorBy=e.colorBy,e.colorTable?this.colorTable=new ao(e.colorTable):this.colorTable=new oo(\"Set1\")))}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get searchable(){return this.featureSource.searchable}async search(e){return this.featureSource&&this.featureSource.searchable?this.featureSource.search(e):void 0}get supportsWholeGenome(){return void 0!==this.config.supportsWholeGenome?this.config.supportsWholeGenome:this.featureSource&&\"function\"==typeof this.featureSource.supportsWholeGenome?this.featureSource.supportsWholeGenome():!(void 0!==this.visibilityWindow||!1!==this.config.indexed&&this.config.indexURL)||void 0}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}computePixelHeight(e){if(\"COLLAPSED\"===this.displayMode)return this.margin+this.expandedRowHeight;{let t=0;if(e&&\"function\"==typeof e.forEach)for(let i of e)i.row&&i.row>t&&(t=i.row);return this.margin+(t+1)*(\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight)}}draw(e){const{features:t,context:i,bpPerPixel:n,bpStart:r,bpEnd:s,pixelWidth:o,pixelHeight:a,referenceFrame:c}=e;if(n<kd&&(e.sequenceInterval=this.browser.genome.getSequenceInterval(c.chr,r,s)),this.isMergedTrack||xo.fillRect(i,0,e.pixelTop,o,a,{fillStyle:\"rgb(255, 255, 255)\"}),t){const c=[];e.rowLastX=[],e.rowLastLabelX=[];for(let i of t)if(i.start>r&&i.end<s){const t=\"COLLAPSED\"===this.displayMode?0:i.row||0;c[t]?c[t]++:c[t]=1,e.rowLastX[t]=-Number.MAX_SAFE_INTEGER,e.rowLastLabelX[t]=-Number.MAX_SAFE_INTEGER}const l=o/Math.max(1,Math.max(...c.filter((e=>!isNaN(e)))));let h=[];const d=[];for(let o of t){if(o.end<r)continue;if(o.start>s)break;\"COLLAPSED\"===this.displayMode&&this.browser.qtlSelections.hasPhenotype(o.name)&&d.push(o);const t=\"COLLAPSED\"===this.displayMode?0:o.row;e.drawLabel=e.labelAllFeatures||l>10;const c=Math.ceil((o.end-r)/n),u=h[t];if(!u||c>u){this.render.call(this,o,r,n,a,i,e);const s=Math.floor((o.start-r)/n);u&&s-u<=0&&(i.globalAlpha=.5,xo.strokeLine(i,s,0,s,a,{strokeStyle:\"rgb(255, 255, 255)\"}),i.globalAlpha=1),h[t]=c}}for(let t of d)e.drawLabel=!0,this.render.call(this,t,r,n,a,i,e)}else console.log(\"No feature list\")}clickedFeatures(e){const t=e.y-this.margin,i=super.clickedFeatures(e);let n;switch(this.displayMode){case\"SQUISHED\":n=Math.floor(t/this.squishedRowHeight);break;case\"EXPANDED\":n=Math.floor(t/this.expandedRowHeight);break;default:n=void 0}return i.filter((function(e){return void 0===n||void 0===e.row||n===e.row}))}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=[];for(let e of t){const t=e._f||e,r=\"function\"==typeof t.popupData?t.popupData(i):this.extractPopupData(t);if(r){n.length>0&&n.push(\"<hr/><hr/>\");const s=this.infoURL||this.config.infoURL;for(let t of r)if(n.push(t),s&&t.name&&\"name\"===t.name.toLowerCase()&&t.value&&Mt(t.value)&&!t.value.startsWith(\"<\")){const i=s.replace(\"$$\",e.name);t.value=`<a target=_blank href=${i}>${t.value}</a>`}const o=\"gff\"===this.config.format||\"gff3\"===this.config.format||\"gtf\"===this.config.format;if(t.exons&&t.exons.length>1)for(let e=0;e<t.exons.length;e++){const r=t.exons[e];if(i>=r.start&&i<=r.end){const i=o?r.number:\"-\"===t.strand?t.exons.length-e:e+1;i&&(n.push(\"<hr/>\"),n.push({name:\"Exon Number\",value:i}));break}}}}return n}menuItemList(){const e=[];if(this.render===Ld){e.push(\"<hr/>\");for(const i of[\"function\",\"class\"]){const n=Bt(Dl(`Color by ${i}`,i===this.colorBy));function r(){this.colorBy=i,this.trackView.repaintViews()}e.push({object:n,click:r})}}e.push(\"<hr/>\");const t={COLLAPSED:\"Collapse\",SQUISHED:\"Squish\",EXPANDED:\"Expand\"};for(const s of[\"COLLAPSED\",\"SQUISHED\",\"EXPANDED\"]){const o=Bt(Dl(t[s],s===this.displayMode));function a(){this.displayMode=s,this.config.displayMode=s,this.trackView.checkContentHeight(),this.trackView.repaintViews()}e.push({object:o,click:a})}return e}contextMenuItemList(e){const t=this.clickedFeatures(e);if(void 0===t||0===t.length)return;t.length>1&&t.sort(((e,t)=>t.end-t.start-(e.end-e.start)));const i=t[0];if(i.end-i.start<=1e6){const e=[{label:\"View feature sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i.chr,i.start,i.end);e?\"-\"===i.strand&&(e=cc(e)):e=\"Unknown sequence\",this.browser.alert.present(e)}}];return Xa()&&void 0!==navigator.clipboard&&e.push({label:\"Copy feature sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i.chr,i.start,i.end);e?\"-\"===i.strand&&(e=cc(e)):e=\"Unknown sequence\";try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),e.push(\"<hr/>\"),e}}description(){if(Ld===this.render){let e=\"<html>\"+this.name+\"<hr/>\";return e+=\"<em>Color By Function:</em><br>\",e+='<span style=\"color:red\">Red</span>: Coding-Non-Synonymous, Splice Site<br>',e+='<span style=\"color:green\">Green</span>: Coding-Synonymous<br>',e+='<span style=\"color:blue\">Blue</span>: Untranslated<br>',e+='<span style=\"color:black\">Black</span>: Intron, Locus, Unknown<br><br>',e+=\"<em>Color By Class:</em><br>\",e+='<span style=\"color:red\">Red</span>: Deletion<br>',e+='<span style=\"color:green\">Green</span>: MNP<br>',e+='<span style=\"color:blue\">Blue</span>: Microsatellite, Named<br>',e+='<span style=\"color:black\">Black</span>: Indel, Insertion, SNP',e+=\"</html>\",e}return super.description()}getColorForFeature(e){const t=e._f||e;let i;if(e.name&&this.browser.qtlSelections.hasPhenotype(e.name))i=this.browser.qtlSelections.colorForGene(e.name);else if(this.altColor&&\"-\"===t.strand)i=\"function\"==typeof this.altColor?this.altColor(t):this.altColor;else if(this.color)i=\"function\"==typeof this.color?this.color(t):this.color;else if(this.colorBy){const e=t.getAttributeValue?t.getAttributeValue(this.colorBy):t[this.colorBy];i=this.colorTable.getColor(e)}else t.color&&(i=t.color);if(i||(i=\"rgb(0, 0, 150)\"),t.alpha&&1!==t.alpha)i=_s.addAlpha(i,t.alpha);else if(this.useScore&&t.score&&!Number.isNaN(t.score)){const e=function(e,t,i){const n=(t-e)/9,r=Math.floor((i-e)/n);return Math.min(1,.2+.8*r/9)}(this.config.min?this.config.min:this.viewLimitMin?this.viewLimitMin:0,this.config.max?this.config.max:this.viewLimitMax?this.viewLimitMax:1e3,t.score);t.alpha=e,i=_s.addAlpha(i,e)}return i}dispose(){this.trackView=void 0}}class Pd{constructor(t){if(this.config=t,this.browser=t.browser,this.columnFormat=t.columnFormat,this.tableRowSelectionList=[],this.tableDOM=e({class:\"igv-roi-table\"}),t.width){let[e]=t.width.split(\"px\");e=parseInt(e,10),this.tableDOM.style.width=`${Math.min(e,1600)}px`}t.parent.appendChild(this.tableDOM),this.headerDOM=t,this.tableColumnTitles=this.tableDOM,this.tableRowContainer=this.tableDOM,this.footerDOM=t.gotoButtonHandler}set headerDOM({browser:t,parent:i,headerTitle:n,dismissHandler:r}){const s=e();this.tableDOM.appendChild(s);const o=e();s.appendChild(o),o.innerHTML=n;const a=e();s.appendChild(a),a.appendChild(l(\"times\")),this.boundDismissHandler=function(e){e.stopPropagation(),r()}.bind(this),a.addEventListener(\"click\",this.boundDismissHandler);const{y:c}=t.root.getBoundingClientRect(),{y:h}=i.getBoundingClientRect(),d=-(h-c);p(this.tableDOM,s,{minX:0,minY:d}),this.tableDOM.style.display=\"none\",this._headerDOM=s}set tableColumnTitles(t){const i=e({class:\"igv-roi-table-column-titles\"});t.appendChild(i);for(const{label:t,width:n}of this.columnFormat){const r=e();i.appendChild(r),r.style.width=n,r.innerText=t}this._tableColumnTitlesDOM=i}get tableColumnTitles(){return this._tableColumnTitlesDOM}set tableRowContainer(t){const i=e({class:\"igv-roi-table-row-container\"});t.appendChild(i),this._tableRowContainerDOM=i}get tableRowContainer(){return this._tableRowContainerDOM}set footerDOM(t){const i=e();this.tableDOM.appendChild(i);const n=e({class:\"igv-roi-table-button\"});i.appendChild(n),n.id=\"igv-roi-table-view-button\",n.textContent=\"Go To\",n.style.pointerEvents=\"none\",this._footerDOM=i,this.gotoButton=n,this.boundGotoButtonHandler=t.bind(this),this.gotoButton.addEventListener(\"click\",this.boundGotoButtonHandler)}tableRowDOMHelper(e){e.addEventListener(\"mousedown\",(t=>{t.stopPropagation(),e.classList.toggle(\"igv-roi-table-row-selected\"),e.classList.contains(\"igv-roi-table-row-selected\")?e.classList.remove(\"igv-roi-table-row-hover\"):e.classList.add(\"igv-roi-table-row-hover\"),this.setTableRowSelectionState(e.classList.contains(\"igv-roi-table-row-selected\"))})),e.addEventListener(\"mouseover\",(t=>{e.classList.contains(\"igv-roi-table-row-selected\")?e.classList.remove(\"igv-roi-table-row-hover\"):e.classList.add(\"igv-roi-table-row-hover\")})),e.addEventListener(\"mouseout\",(t=>{e.classList.remove(\"igv-roi-table-row-hover\")}))}clearTable(){const e=this.tableRowContainer.querySelectorAll(\".igv-roi-table-row\");for(let t of e)t.remove()}setTableRowSelectionState(e){e?this.tableRowSelectionList.push(1):this.tableRowSelectionList.pop(),this.gotoButton.style.pointerEvents=this.tableRowSelectionList.length>0?\"auto\":\"none\"}present(){this.tableDOM.style.left=\"0px\";const{y:e}=this.browser.root.getBoundingClientRect(),{y:t}=this.config.parent.getBoundingClientRect();this.tableDOM.style.top=e-t+\"px\",this.tableDOM.style.display=\"flex\"}dismiss(){this.tableDOM.style.display=\"none\"}isVisible(){return\"none\"!==this.tableDOM.style.display}dispose(){this.tableDOM.innerHTML=\"\",this.tableDOM.remove();for(const e of Object.keys(this))this[e]=void 0;document.removeEventListener(\"click\",this.boundDismissHandler)}}class Od extends Pd{constructor(e){super(Object.assign({width:\"1024px\"},e)),this.descriptionDOM=e}set descriptionDOM(t){if(t.description){let i;i=e({class:\"igv-roi-table-description\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.style.height=\"auto\",i.innerHTML=\"BLAT result for query sequence:\",i=e({class:\"igv-roi-table-description\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.style.height=\"auto\",i.style.maxHeight=\"128px\",i.innerHTML=t.description,i=e({class:\"igv-roi-table-goto-explainer\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.innerHTML=\"Select one or more rows and click Go To to view the regions\"}}tableRowDOM(t){const i=e({class:\"igv-roi-table-row\"}),n=t.map((e=>isFinite(e)?Rt(e):e));for(let t=0;t<n.length;t++){const r=e();i.appendChild(r);const s=this.columnFormat[t];r.style.width=s.width||\"fit-content\",r.innerText=n[t]}return this.tableRowDOMHelper(i),i}renderTable(e){if(Array.from(this.tableRowContainer.querySelectorAll(\".igv-roi-table-row\")).forEach((e=>e.remove())),e.length>0)for(let t of e){const e=this.tableRowDOM(t);this.tableRowContainer.appendChild(e)}}static getColumnFormatConfiguration(){return[{label:\"chr\",width:\"7%\"},{label:\"start\",width:\"12%\"},{label:\"end\",width:\"12%\"},{label:\"strand\",width:\"5%\"},{label:\"score\",width:\"5%\"},{label:\"match\",width:\"5%\"},{label:\"mis-match\",width:\"7%\"},{label:\"rep. match\",width:\"7%\"},{label:\"N's\",width:\"3%\"},{label:\"Q gap count\",width:\"9%\"},{label:\"Q gap bases\",width:\"9%\"},{label:\"T gap count\",width:\"9%\"},{label:\"T gap bases\",width:\"9%\"}]}static gotoButtonHandler(e){e.stopPropagation();const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\"),i=[];for(const e of t){const t=[];e.querySelectorAll(\"div\").forEach((e=>t.push(e.innerText)));const[n,r,s]=t;i.push(`${n}:${r}-${s}`)}for(const e of this.tableDOM.querySelectorAll(\".igv-roi-table-row\"))e.classList.remove(\"igv-roi-table-row-selected\");this.setTableRowSelectionState(!1),this.browser.search(i.join(\" \"))}}const Ud=\"https://igv.org/services/blatUCSC.php\";async function qd({url:e,userSeq:t,db:i}){if(e=e||Ud,!i)throw Error(\"Blat database is not defined\");const n=await async function(e=\"\",t,i){const n=new URLSearchParams;n.append(\"userSeq\",t),n.append(\"db\",i);const r=await fetch(e,{method:\"post\",body:n});return r.json()}(e,t,i);n.fields;return n.blat.map($c)}const Qd=25e3;class Vd extends Hd{constructor(e,t){super(e,t),this.name||(this.name=\"Blat Results\"),this.sequence=e.sequence,this.table=void 0,e.features&&(this._features=e.features,this.featureSource=new fd({features:e.features},this.browser.genome),delete e.features)}async postInit(){if(!this.featureSource){const e=this.browser.genome.id,t=this.browser.config.blatServerURL,i=await qd({url:t,userSeq:this.sequence,db:e});this._features=i,this.featureSource=new fd({features:i},this.browser.genome)}}openTableView(){if(void 0===this.table){const e=this._features.map((e=>[e.chr,e.start+1,e.end,e.strand,e.score,e.matches,e.misMatches,e.repMatches,e.nCount,e.qNumInsert,e.qBaseInsert,e.tNumInsert,e.tBaseInsert])),t={browser:this.browser,parent:this.browser.columnContainer,headerTitle:this.config.title,description:this.sequence,dismissHandler:()=>{this.table.dismiss(),this.table.dispose(),this.table=void 0},columnFormat:Od.getColumnFormatConfiguration(),gotoButtonHandler:Od.gotoButtonHandler};this.table=new Od(t),this.table.renderTable(e)}this.table.present()}menuItemList(){const e=super.menuItemList();return e.push(\"<hr/>\"),e.push({label:\"Open table view\",click:function(){this.openTableView()}}),e}dispose(){super.dispose(),this.table&&this.table.popover.parentElement.removeChild(this.table.popover)}}async function jd({sequence:e,browser:t,name:i,title:n}){if(e.length>Qd)t.alert.present(`Sequence size exceeds maximum allowed length (${e.length} > 25000)`);else try{const r=t.genome.id,s=t.config.blatServerURL||\"https://igv.org/services/blatUCSC.php\",o={type:\"blat\",name:i||\"blat results\",title:n||\"blat results\",sequence:e,altColor:\"rgb(176, 176, 236)\",color:\"rgb(236, 176, 176)\",searchable:!1,features:await qd({url:s,userSeq:e,db:r})};(await t.loadTrack(o)).openTableView()}catch(e){t.alert.present(`Error performing blat search:  ${e}`)}}const Wd=Number.MIN_SAFE_INTEGER,Gd={TTT:\"F\",TTC:\"F\",TTA:\"L\",TTG:\"L\",CTT:\"L\",CTC:\"L\",CTA:\"L\",CTG:\"L\",ATT:\"I\",ATC:\"I\",ATA:\"I\",ATG:\"M\",GTT:\"V\",GTC:\"V\",GTA:\"V\",GTG:\"V\",TCT:\"S\",TCC:\"S\",TCA:\"S\",TCG:\"S\",CCT:\"P\",CCC:\"P\",CCA:\"P\",CCG:\"P\",ACT:\"T\",ACC:\"T\",ACA:\"T\",ACG:\"T\",GCT:\"A\",GCC:\"A\",GCA:\"A\",GCG:\"A\",TAT:\"Y\",TAC:\"Y\",TAA:\"STOP\",TAG:\"STOP\",CAT:\"H\",CAC:\"H\",CAA:\"Q\",CAG:\"Q\",AAT:\"N\",AAC:\"N\",AAA:\"K\",AAG:\"K\",GAT:\"D\",GAC:\"D\",GAA:\"E\",GAG:\"E\",TGT:\"C\",TGC:\"C\",TGA:\"STOP\",TGG:\"W\",CGT:\"R\",CGC:\"R\",CGA:\"R\",CGG:\"R\",AGT:\"S\",AGC:\"S\",AGA:\"R\",AGG:\"R\",GGT:\"G\",GGC:\"G\",GGA:\"G\",GGG:\"G\"},$d={},Kd=[\"A\",\"G\",\"C\",\"T\",\"Y\",\"R\",\"W\",\"S\",\"K\",\"M\",\"D\",\"V\",\"H\",\"B\",\"N\",\"X\"],Yd=[\"T\",\"C\",\"G\",\"A\",\"R\",\"Y\",\"W\",\"S\",\"M\",\"K\",\"H\",\"B\",\"D\",\"V\",\"N\",\"X\"];for(let NA=0;NA<Kd.length;NA++)$d[Kd[NA]]=Yd[NA],$d[Kd[NA].toLowerCase()]=Yd[NA].toLowerCase();const Xd=115;class Zd{constructor(e,t){this.config=e,this.browser=t,this.type=\"sequence\",this.removable=!0===e.removable,this.name=e.name,this.id=e.id,this.sequenceType=e.sequenceType||\"dna\",this.disableButtons=!1,this.order=e.order||Wd,this.ignoreTrackMenu=!1,this.reversed=!0===e.reversed,this.frameTranslate=!0===e.frameTranslate,this.height=this.frameTranslate?Xd:25,e.url&&(e.fastaURL=e.url),e.fastaURL||(this.id=e.id||\"sequence\")}menuItemList(){return[{name:this.reversed?\"Forward\":\"Reverse\",click:()=>{this.reversed=!this.reversed,this.trackView.repaintViews()}},{name:this.frameTranslate?\"Close Translation\":\"Three-frame Translate\",click:()=>{if(this.frameTranslate=!this.frameTranslate,this.frameTranslate){for(let e of this.trackView.viewports)e.setContentHeight(Xd);this.trackView.setTrackHeight(Xd)}else{for(let e of this.trackView.viewports)e.setContentHeight(25);this.trackView.setTrackHeight(25)}this.trackView.repaintViews()}}]}contextMenuItemList(e){const t=e.viewport;if(t.referenceFrame.bpPerPixel<=1){const e=t.getWidth()*t.referenceFrame.bpPerPixel,i=t.referenceFrame.chr,n=Math.floor(t.referenceFrame.start),r=Math.ceil(n+e),s=[{label:this.reversed?\"View visible sequence (reversed)...\":\"View visible sequence...\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);e?this.reversed&&(e=cc(e)):e=\"Unknown sequence\",this.browser.alert.present(e)}}];return Xa()&&s.push({label:\"Copy visible sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);e?this.reversed&&(e=cc(e)):e=\"Unknown sequence\";try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),s.push({label:\"BLAT read sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);if(e){this.reversed&&(e=cc(e));const t=`blat: ${i}:${n+1}-${r}`,s=`blat: ${i}:${n+1}-${r}`;jd({sequence:e,browser:this.browser,name:t,title:s})}}}),s.push(\"<hr/>\"),s}}translateSequence(e){const t=[[],[],[]];for(let i of[0,1,2]){let n=i;for(;e.length-n>=3;){let r=e.slice(n,n+3);this.reversed&&(r=r.split(\"\").reverse().join(\"\"));const s=Gd[r.toUpperCase()]||\"\";t[i].push({codons:r,aminoA:s}),n+=3}}return t}async getSequenceSource(){return this.config.fastaURL?(this.fasta||(this.fasta=new Jd(this.config,this.browser.genome),await this.fasta.init()),this.fasta):this.browser.genome}async getFeatures(e,t,i,n){if(t=Math.floor(t),i=Math.floor(i),n&&n>10)return null;{const n=await this.getSequenceSource();return{bpStart:t,sequence:await n.getSequence(e,t,i)}}}draw(e){const t=e.context;if(e.features){let i=e.features.sequence;if(!i)return;this.reversed&&(i=i.split(\"\").map((function(e){return $d[e]})).join(\"\"));const n=e.features.bpStart,r=1+e.bpStart+e.pixelWidth*e.bpPerPixel;for(let s=Math.floor(e.bpStart);s<=r;s++){const r=Math.floor(s-n);if(r>=0&&r<i.length){const n=(s-e.bpStart)/e.bpPerPixel,o=1/e.bpPerPixel,a=i[r],c=this.fillColor(a.toUpperCase());if(e.bpPerPixel>.1)xo.fillRect(t,n,5,o,10,{fillStyle:c});else{const i=n+.5*(o-t.measureText(a).width);\"y\"===e.axis?(t.save(),xo.labelTransformWithContext(t,i),xo.strokeText(t,a,i,15,{strokeStyle:c}),t.restore()):xo.strokeText(t,a,i,15,{strokeStyle:c})}}}if(this.frameTranslate){let r=25;const s=this.translateSequence(i);for(let i=0;i<s.length;i++){const o=s[i];for(let s=0;s<o.length;s++){let a=0==s%2?\"rgb(160,160,160)\":\"rgb(224,224,224)\";const c=o[s],l=n+i+3*s-e.bpStart,h=Math.floor(l/e.bpPerPixel),d=Math.floor((l+3)/e.bpPerPixel),u=Math.round((h+d)/2);if(d<0)continue;if(h>e.pixelWidth)break;let f=c.aminoA;c.aminoA.indexOf(\"STOP\")>-1?(a=\"rgb(255, 0, 0)\",f=\"STOP\"):\"M\"===c.aminoA&&(a=\"rgb(0, 153, 0)\",f=\"START\"),xo.fillRect(t,h,r,d-h,25,{fillStyle:a}),e.bpPerPixel<=.1&&xo.strokeText(t,f,u-t.measureText(f).width/2,r+15)}r+=30}}}}get supportsWholeGenome(){return!1}computePixelHeight(e){return this.height=this.frameTranslate?Xd:25,this.height}fillColor(e){return this.color?this.color:\"dna\"===this.sequenceType?this.browser.nucleotideColors[e]||\"gray\":\"rgb(0, 0, 150)\"}getState(){const e={type:\"sequence\"};return this.order!==Wd&&(e.order=this.order),this.reversed&&(e.revealed=!0),e}}class Jd{constructor(e,t){this.config=e,this.genome=t}async init(){this.fasta=await Nc(this.config),this.chrNameMap=new Map;for(let e of this.fasta.chromosomeNames)this.chrNameMap.set(this.genome.getChromosomeName(e),e)}async getSequence(e,t,i){const n=this.chrNameMap.has(e)?this.chrNameMap.get(e):e;return this.fasta.getSequence(n,t,i)}}class eu{constructor(e,t,i,n){this.guid=s(),this.trackView=e,this.referenceFrame=i,this.browser=e.browser,this.$viewport=Bt('<div class=\"igv-viewport\">'),t.appendChild(this.$viewport.get(0)),e.track.height&&(this.$viewport.get(0).style.height=`${e.track.height}px`),e.track instanceof Zd&&(this.alert=new Ta(this.$viewport.get(0))),this.contentTop=0,this.contentHeight=this.$viewport.height(),this.$viewport.width(n),this.initializationHelper()}initializationHelper(){}showMessage(e){this.messageDiv||(this.messageDiv=document.createElement(\"div\"),this.messageDiv.className=\"igv-viewport-message\",this.$viewport.append(Bt(this.messageDiv))),this.messageDiv.textContent=e,this.messageDiv.style.display=\"inline-block\"}hideMessage(e){this.messageDiv&&(this.messageDiv.style.display=\"none\")}setTrackLabel(e){}startSpinner(){}stopSpinner(){}checkZoomIn(){return!0}shift(){}setTop(e){this.contentTop=e,this.$viewport.height()}async loadFeatures(){}clearCache(){}repaint(){}draw(e,t,i){console.log(\"Viewport - draw(drawConfiguration, features, roiFeatures)\")}checkContentHeight(e){let t=this.trackView.track;if(e=e||this.cachedFeatures,\"FILL\"===t.displayMode)this.setContentHeight(this.$viewport.height());else if(\"function\"==typeof t.computePixelHeight&&e&&e.length>0){let i=t.computePixelHeight(e);i!==this.contentHeight&&this.setContentHeight(i)}}getContentHeight(){return this.contentHeight}setContentHeight(e){this.contentHeight=e}isLoading(){return!1}saveSVG(){}isVisible(){return this.$viewport.width()}setWidth(e){this.$viewport.width(e)}getWidth(){return this.$viewport.width()}getContentTop(){return this.contentTop}containsPosition(e,t){console.log(\"Viewport - containsPosition(chr, position)\")}addMouseHandlers(){}removeMouseHandlers(){}dispose(){this.$viewport.get(0).remove();for(let e of Object.keys(this))this[e]=void 0}}\n",
-       "/*!!\n",
-       "     *  Canvas 2 Svg v1.0.19\n",
-       "     *  A low level canvas to SVG converter. Uses a mock canvas context to build an SVG document.\n",
-       "     *\n",
-       "     *  Licensed under the MIT license:\n",
-       "     *  http://www.opensource.org/licenses/mit-license.php\n",
-       "     *\n",
-       "     *  Author:\n",
-       "     *  Kerry Liu\n",
-       "     *\n",
-       "     *  Copyright (c) 2014 Gliffy Inc.\n",
-       "     */function tu(e,t){var i,n=Object.keys(t);for(i=0;i<n.length;i++)e=e.replace(new RegExp(\"\\\\{\"+n[i]+\"\\\\}\",\"gi\"),t[n[i]]);return e}function iu(e){var t,i,n;if(!e)throw new Error(\"cannot create a random attribute name for an undefined object\");t=\"ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz\",i=\"\";do{for(i=\"\",n=0;n<12;n++)i+=t[Math.floor(51*Math.random())]}while(e[i]);return i}function nu(e){var t={alphabetic:\"alphabetic\",hanging:\"hanging\",top:\"text-before-edge\",bottom:\"text-after-edge\",middle:\"central\"};return t[e]||t.alphabetic}function ru(e){var t=Math.sqrt(e[0]*e[0]+e[1]*e[1]);return[e[0]/t,e[1]/t]}const su=function(e,t){var i,n,r,s={};for(e=e.split(\",\"),t=t||10,i=0;i<e.length;i+=2)n=\"&\"+e[i+1]+\";\",r=parseInt(e[i],t),s[n]=\"&#\"+r+\";\";return 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stroke\"},font:{canvas:\"10px sans-serif\"},shadowColor:{canvas:\"#000000\"},shadowOffsetX:{canvas:0},shadowOffsetY:{canvas:0},shadowBlur:{canvas:0},textAlign:{canvas:\"start\"},textBaseline:{canvas:\"alphabetic\"},lineDash:{svgAttr:\"stroke-dasharray\",canvas:[],svg:null,apply:\"stroke\"}};class au{constructor(e,t){this.__root=e,this.__ctx=t}addColorStop(e,t){var i,n=this.__ctx.__createElement(\"stop\");n.setAttribute(\"offset\",e),t&&-1!==t.indexOf(\"rgba\")?(i=/rgba\\(\\s*(\\d+)\\s*,\\s*(\\d+)\\s*,\\s*(\\d+)\\s*,\\s*(\\d?\\.?\\d*)\\s*\\)/gi.exec(t),n.setAttribute(\"stop-color\",tu(\"rgb({r},{g},{b})\",{r:i[1],g:i[2],b:i[3]})),n.setAttribute(\"stop-opacity\",i[4])):n.setAttribute(\"stop-color\",t),this.__root.appendChild(n)}}class cu{constructor(e,t){this.__root=e,this.__ctx=t}}class lu{constructor(e){if(!(this instanceof lu))return new 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e,t,i=Object.keys(ou);for(e=0;e<i.length;e++)this[t=i[e]]=ou[t].canvas}__applyStyleState(e){var t,i,n=Object.keys(e);for(t=0;t<n.length;t++)this[i=n[t]]=e[i]}__getStyleState(){var e,t,i={},n=Object.keys(ou);for(e=0;e<n.length;e++)i[t=n[e]]=this[t];return i}__applyStyleToCurrentElement(e){var t=this.__currentElement,i=this.__currentElementsToStyle;i&&(t.setAttribute(e,\"\"),t=i.element,i.children.forEach((function(t){t.setAttribute(e,\"\")})));var n,r,s,o,a,c=Object.keys(ou);for(n=0;n<c.length;n++)if(r=ou[c[n]],s=this[c[n]],r.apply)if(s instanceof cu){if(s.__ctx)for(;s.__ctx.__defs.childNodes.length;)o=s.__ctx.__defs.childNodes[0].getAttribute(\"id\"),this.__ids[o]=o,this.__defs.appendChild(s.__ctx.__defs.childNodes[0]);t.setAttribute(r.apply,tu(\"url(#{id})\",{id:s.__root.getAttribute(\"id\")}))}else if(s instanceof au)t.setAttribute(r.apply,tu(\"url(#{id})\",{id:s.__root.getAttribute(\"id\")}));else 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\"+w:w,l.setAttribute(\"transform\",b),o.appendChild(l)}}}else\"CANVAS\"!==p.nodeName&&\"IMG\"!==p.nodeName||((h=this.__createElement(\"image\")).setAttribute(\"width\",i),h.setAttribute(\"height\",n),h.setAttribute(\"preserveAspectRatio\",\"none\"),(g||m||r!==p.width||s!==p.height)&&((d=this.__document.createElement(\"canvas\")).width=i,d.height=n,d.getContext(\"2d\").drawImage(p,g,m,r,s,0,0,i,n),p=d),h.setAttribute(\"transform\",w),h.setAttributeNS(\"http://www.w3.org/1999/xlink\",\"xlink:href\",\"CANVAS\"===p.nodeName?p.toDataURL():p.getAttribute(\"src\")),o.appendChild(h))}createPattern(e,t){let i,n=this.__document.__createElement(\"pattern\"),r=iu(this.__ids);return n.setAttribute(\"id\",r),n.setAttribute(\"width\",e.width),n.setAttribute(\"height\",e.height),\"CANVAS\"===e.nodeName||\"IMG\"===e.nodeName?(i=this.__createElement(\"image\"),i.setAttribute(\"width\",e.width),i.setAttribute(\"height\",e.height),i.setAttributeNS(\"http://www.w3.org/1999/xlink\",\"xlink:href\",\"CANVAS\"===e.nodeName?e.toDataURL():e.getAttribute(\"src\")),n.appendChild(i),this.__defs.appendChild(n)):e instanceof lu&&(n.appendChild(e.__root.childNodes[1]),this.__defs.appendChild(n)),new cu(n,this)}setLineDash(e){e&&e.length>0?this.lineDash=e.join(\",\"):this.lineDash=null}drawFocusRing(){}createImageData(){}getImageData(){}putImageData(){}globalCompositeOperation(){}setTransform(){}}function hu(e){if(e.startsWith(\"GCF\")||e.startsWith(\"GCA\")&&e.length>=13){return\"https://hgdownload.soe.ucsc.edu/hubs/\"+e.substring(0,3)+\"/\"+e.substring(4,7)+\"/\"+e.substring(7,10)+\"/\"+e.substring(10,13)+\"/\"+e+\"/hub.txt\"}}class du{static supportedTypes=new Set([\"bigBed\",\"bigWig\",\"bigGenePred\",\"vcfTabix\"]);static filterTracks=new Set([\"cytoBandIdeo\",\"assembly\",\"gap\",\"gapOverlap\",\"allGaps\",\"cpgIslandExtUnmasked\",\"windowMasker\"]);static async loadHub(e){const t=e.lastIndexOf(\"/\"),i=e.substring(0,t+1),n=await pu(e);let r;if(\"genome\"===n[1].type){const e=n[1];if(e.hasProperty(\"groups\")){const t=i+e.getProperty(\"groups\");r=await pu(t)}if(e.hasProperty(\"chromSizes\")){const t=i+e.getProperty(\"chromSizes\"),n=await async function(e){try{const t=(await fetch(e,{method:\"HEAD\"})).headers;return t.has(\"content-length\")?t.get(\"content-length\"):null}catch(e){return null}}(t);null!==n&&Number.parseInt(n)<1e6&&e.setProperty(\"chromSizesURL\",t)}}return new du(e,n,r)}constructor(e,t,i){this.url=e;const n=e.lastIndexOf(\"/\");if(this.baseURL=e.substring(0,n+1),\"hub\"!==t[0].type)throw Error(\"Unexpected hub.txt file -- does the first line start with 'hub'?\");if(this.hubStanza=t[0],\"on\"!==this.hubStanza.getProperty(\"useOneFile\"))throw Error(\"Only 'useOneFile' hubs are currently supported\");if(t.length<2)throw Error(\"Expected at least 2 stanzas, hub and genome\");if(\"genome\"!==t[1].type)throw Error(`Unexpected hub file -- expected \"genome\" stanza but found \"${t[1].type}\"`);this.genomeStanza=t[1],this.trackStanzas=[];for(let e=2;e<t.length;e++)\"track\"===t[e].type&&this.trackStanzas.push(t[e]);if(i){this.groupStanzas=i,this.groupPriorityMap=new Map;for(let e of i)e.hasProperty(\"priority\")&&this.groupPriorityMap.set(e.getProperty(\"name\"),10*Number.parseInt(e.getProperty(\"priority\")))}}getDefaultPosition(){return this.genomeStanza.getProperty(\"defaultPos\")}getGenomeConfig(e={}){const t=this.genomeStanza.getProperty(\"genome\"),i=this.hubStanza.getProperty(\"shortLabel\")||this.genomeStanza.getProperty(\"scientificName\")||this.genomeStanza.getProperty(\"organism\")||this.genomeStanza.getProperty(\"description\"),n=i+(i?` (${t})`:` ${t}`),r={hubURL:this.url,id:t,name:n,twoBitURL:this.baseURL+this.genomeStanza.getProperty(\"twoBitPath\"),nameSet:\"ucsc\"};if(this.genomeStanza.hasProperty(\"chromSizesURL\")?r.chromSizesURL=this.genomeStanza.getProperty(\"chromSizesURL\"):(r.wholeGenomeView=!1,r.showChromosomeWidget=!1),this.genomeStanza.hasProperty(\"defaultPos\")){const e=this.genomeStanza.getProperty(\"defaultPos\");if(e){const t=e.lastIndexOf(\":\");r.locus=t>0?e.substring(0,t):e}}this.genomeStanza.hasProperty(\"blat\")&&(r.blat=this.baseURL+this.genomeStanza.getProperty(\"blat\")),this.genomeStanza.hasProperty(\"chromAliasBb\")&&(r.chromAliasBbURL=this.baseURL+this.genomeStanza.getProperty(\"chromAliasBb\")),this.genomeStanza.hasProperty(\"chromAlias\")&&(r.aliasURL=this.baseURL+this.genomeStanza.getProperty(\"chromAlias\")),this.genomeStanza.hasProperty(\"twoBitBptURL\")&&(r.twoBitBptURL=this.baseURL+this.genomeStanza.getProperty(\"twoBitBptURL\")),this.genomeStanza.hasProperty(\"twoBitBptUrl\")&&(r.twoBitBptURL=this.baseURL+this.genomeStanza.getProperty(\"twoBitBptUrl\")),e.includeChromSizes&&this.genomeStanza.hasProperty(\"chromSizes\")&&(r.chromSizesURL=this.baseURL+this.genomeStanza.getProperty(\"chromSizes\")),this.hubStanza.hasProperty(\"longLabel\")?r.description=this.hubStanza.getProperty(\"longLabel\").replace(\"/\",\"\\n\"):(r.description=r.id,this.genomeStanza.hasProperty(\"description\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"description\")}`),this.genomeStanza.hasProperty(\"organism\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"organism\")}`),this.genomeStanza.hasProperty(\"scientificName\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"scientificName\")}`),this.genomeStanza.hasProperty(\"htmlPath\")&&(r.infoURL=this.baseURL+this.genomeStanza.getProperty(\"htmlPath\")));const s=this.trackStanzas.filter((e=>\"cytoBandIdeo\"===e.name&&e.hasProperty(\"bigDataUrl\")));s.length>0&&(r.cytobandBbURL=this.baseURL+s[0].getProperty(\"bigDataUrl\"));return r.tracks=this.#g((e=>!du.filterTracks.has(e.name)&&\"hide\"!==e.getProperty(\"visibility\"))),r}getGroupedTrackConfigurations(){const e=new Map;for(let t of this.#g()){if(\"cytoBandIdeo\"===t.name)continue;const i=t.group||\"other\";e.has(i)?e.get(i).push(t):e.set(i,[t])}const t=this.groupStanzas?new Map(this.groupStanzas.map((e=>[e.getProperty(\"name\"),e]))):new Map;return Array.from(e.keys()).map((i=>({label:t.has(i)?t.get(i).getProperty(\"label\"):i,tracks:e.get(i)})))}#g(e){return this.trackStanzas.filter((t=>du.supportedTypes.has(t.format)&&t.hasProperty(\"bigDataUrl\")&&(!e||e(t)))).map((e=>this.#m(e)))}#m(e){const t=e.format,i={id:e.getProperty(\"track\"),name:e.getProperty(\"shortLabel\"),format:t,url:this.baseURL+e.getProperty(\"bigDataUrl\"),displayMode:e.displayMode};if(\"vcfTabix\"===t&&(i.indexURL=i.url+\".tbi\"),e.hasProperty(\"longLabel\")&&e.hasProperty(\"html\")?(i.description&&(i.description+=\"<br/>\"),i.description=`<a target=\"_blank\" href=\"${this.baseURL+e.getProperty(\"html\")}\">${e.getProperty(\"longLabel\")}</a>`):e.hasProperty(\"longLabel\")&&(i.description=e.getProperty(\"longLabel\")),e.hasProperty(\"autoScale\")&&(i.autoscale=\"on\"===e.getProperty(\"autoScale\").toLowerCase()),e.hasProperty(\"maxHeightPixels\")){const t=e.getProperty(\"maxHeightPixels\").split(\":\");i.maxHeight=Number.parseInt(t[0]),i.height=Number.parseInt(t[1]),i.minHeight=Number.parseInt(t[2])}if(e.hasProperty(\"color\")){const t=e.getProperty(\"color\");i.color=t.indexOf(\",\")>0?`rgb(${t})`:t}if(e.hasProperty(\"altColor\")){const t=e.getProperty(\"altColor\");i.altColor=t.indexOf(\",\")>0?`rgb(${t})`:t}if(e.hasProperty(\"viewLimits\")){const t=e.getProperty(\"viewLimits\").split(\":\");let n,r;t.length>1&&(n=Number.parseInt(t[0]),r=Number.parseInt(t[1])),Number.isNaN(r)||Number.isNaN(n)?console.warn(`Unexpected viewLimits value in track line: ${properties.viewLimits}`):(i.min=n,i.max=r)}if(e.hasProperty(\"itemRgb\"),\"hide\"===e.getProperty(\"visibility\")&&(i.visible=!1),e.hasProperty(\"url\")&&(i.infoURL=e.getProperty(\"url\")),e.hasProperty(\"searchIndex\")&&(i.searchIndex=e.getProperty(\"searchIndex\")),e.hasProperty(\"searchTrix\")&&(i.trixURL=this.baseURL+e.getProperty(\"searchTrix\")),e.hasProperty(\"group\")&&(i.group=e.getProperty(\"group\"),this.groupPriorityMap&&this.groupPriorityMap.has(i.group))){const e=this.groupPriorityMap.get(i.group)+1;i.order=e,this.groupPriorityMap.set(i.group,e)}return i}}function uu(e){const t=e.indexOf(\" \");return t>0?e.substring(0,t):e}class fu{properties=new Map;constructor(e,t){this.type=e,this.name=t}setProperty(e,t){this.properties.set(e,t)}getProperty(e){return this.properties.has(e)?this.properties.get(e):this.parent?this.parent.getProperty(e):void 0}hasProperty(e){return!!this.properties.has(e)||!!this.parent&&this.parent.hasProperty(e)}get format(){const e=this.getProperty(\"type\");if(e)return uu(e)}get displayMode(){let e=this.getProperty(\"visibility\");if(!e)return\"COLLAPSED\";switch(e=e.toLowerCase(),e){case\"dense\":default:return\"COLLAPSED\";case\"pack\":return\"EXPANDED\";case\"squish\":return\"SQUISHED\"}}}async function pu(e){const t=await fetch(e),i=(await t.text()).split(/\\n|\\r\\n|\\r/g),n=[];let r,s=!0;for(let e of i){const t=gu(e),i=e.indexOf(\" \",t);if(i<0)s=!0;else{const o=e.substring(t,i).trim();if(o.startsWith(\"#\"))continue;const a=e.substring(i+1).trim();if(s){const e=new fu(o,a);n.push(e),r=e,s=!1}r.setProperty(o,a)}}return function(e){const t=new Map;for(let i of e)t.set(i.name,i);for(let i of e)if(i.properties.has(\"parent\")){const e=uu(i.properties.get(\"parent\"));i.parent=t.get(e)}return e}(n)}function gu(e){let t=0;for(t=0;t<e.length;t++){const i=e.charAt(t);if(\" \"!==i&&\"\\t\"!==i)break}return t}const mu={initializeGenomes:async function(e){if(!mu.KNOWN_GENOMES){const t={};if(!1!==e.loadDefaultGenomes){const r=\"https://igv.org/genomes/genomes.json\";n(await Qs.loadJson(r,{timeout:5e3}))}const i=e.genomeList||e.genomes;if(i)if(\"string\"==typeof i){n(await Qs.loadJson(i,{}))}else n(i);function n(e){return e.forEach((function(e){t[e.id]=e})),t}mu.KNOWN_GENOMES=t}},isWholeGenomeView:function(e){return\"all\"===e.toLowerCase()},expandReference:async function(e,t){if(Mt(t)&&t.startsWith(\"{\"))try{t=JSON.parse(t)}catch(e){}let i;if(Mt(t)?i=t:t.genome?i=t.genome:void 0===t.id||t.fastaURL||t.twobitURL||(i=t.id),i){let t=mu.KNOWN_GENOMES[i];if(!t){if((i.startsWith(\"GCA_\")||i.startsWith(\"GCF_\"))&&i.length>=13)try{const e=hu(i);t=(await du.loadHub(e)).getGenomeConfig()}catch(e){console.error(e)}t||e.present(new Error(`Unknown genome id: ${i}`),void 0)}return t}return t}};let wu,bu,Fu=0,vu=0,yu=[];class Au extends eu{constructor(e,t,i,n){super(e,t,i,n)}initializationHelper(){this.$spinner=Bt(\"<div>\",{class:\"igv-loading-spinner-container\"}),this.$viewport.append(this.$spinner),this.$spinner.append(Bt(\"<div>\"));const e=this.trackView.track;\"sequence\"!==e.type&&(this.$zoomInNotice=this.createZoomInNotice(this.$viewport)),\"sequence\"!==e.id&&(this.$trackLabel=Bt('<div class=\"igv-track-label\">'),this.$viewport.append(this.$trackLabel),this.setTrackLabel(e.name||\"\"),!1===this.browser.doShowTrackLabels&&this.$trackLabel.hide()),this.stopSpinner(),this.addMouseHandlers()}setContentHeight(e){super.setContentHeight(e),this.featureCache&&(this.featureCache.redraw=!0)}setTrackLabel(e){this.$trackLabel.empty(),this.$trackLabel.html(e);const t=this.$trackLabel.text();this.$trackLabel.attr(\"title\",t)}startSpinner(){this.$spinner.show()}stopSpinner(){this.$spinner&&this.$spinner.hide()}checkZoomIn(){if(this.trackView.track&&\"sequence\"===this.trackView.track.type&&this.referenceFrame.bpPerPixel>10)return Bt(this.canvas).remove(),this.canvas=void 0,!1;if(!this.viewIsReady())return!1;if((()=>{if(\"all\"!==this.referenceFrame.chr.toLowerCase()||this.trackView.track.supportsWholeGenome){const e=this.trackView.track.visibilityWindow;return void 0!==e&&e>0&&this.referenceFrame.bpPerPixel*this.$viewport.width()>e}return!0})()){if(this.canvas&&(Bt(this.canvas).remove(),this.canvas=void 0),this.trackView.track.autoHeight){const e=this.trackView.minHeight||0;this.setContentHeight(e)}return this.$zoomInNotice&&this.$zoomInNotice.show(),!1}return this.$zoomInNotice&&this.$zoomInNotice.hide(),!0}shift(){const e=this.referenceFrame;this.canvas&&this.canvas._data&&this.canvas._data.referenceFrame.chr===this.referenceFrame.chr&&this.canvas._data.bpPerPixel===e.bpPerPixel&&(this.canvas._data.pixelShift=Math.round((this.canvas._data.bpStart-e.start)/e.bpPerPixel),this.canvas.style.left=this.canvas._data.pixelShift+\"px\")}genomicRange(){return{start:this.referenceFrame.start,end:this.referenceFrame.start+this.referenceFrame.bpPerPixel*this.$viewport.width()}}setTop(e){if(super.setTop(e),this.canvas){const t=this.$viewport.height(),i=e+this.canvas._data.pixelTop,n=i+this.canvas._data.pixelHeight;(i>0||n<t)&&this.repaint()}else this.repaint();if(this.canvas&&this.canvas._data){let t=e+this.canvas._data.pixelTop;this.canvas.style.top=`${t}px`}}async loadFeatures(){const e=this.referenceFrame,t=e.chr,i=await this.browser.genome.loadChromosome(t),n=i?i.bpLength:Number.MAX_SAFE_INTEGER,r=this.$viewport.width()*e.bpPerPixel,s=Math.floor(Math.max(0,e.start-r)),o=Math.ceil(Math.min(n,e.start+r+r));if(!this.loading||this.loading.start!==s||this.loading.end!==o){this.loading={start:s,end:o},this.startSpinner();try{const i=this.trackView.track,n=await this.getFeatures(i,t,s,o,e.bpPerPixel);if(n){let r=[];if(i.roiSets&&i.roiSets.length>0)for(let n of i.roiSets){const i=await n.getFeatures(t,s,o,e.bpPerPixel);r.push({track:n,features:i})}const a=i&&i.resolutionAware,c=this.windowFunction;return this.featureCache=new Cu(t,s,o,e.bpPerPixel,n,r,a,c),this.loading=!1,this.hideMessage(),this.stopSpinner(),this.featureCache}}catch(e){this.trackView&&!0!==this.trackView.disposed&&(this.showMessage(\"Error loading track data\"),this.browser.alert.present(e),console.error(e))}finally{this.loading=!1,this.stopSpinner()}}}get track(){return this.trackView.track}get windowFunction(){return this.track?this.track.windowFunction:void 0}repaintDimensions(){const e=mu.isWholeGenomeView(this.referenceFrame.chr),t=e?this.$viewport.width():3*this.$viewport.width(),i=this.referenceFrame.bpPerPixel;return{bpStart:this.referenceFrame.start-(e?0:this.$viewport.width()*i),bpEnd:e?Number.MAX_SAFE_INTEGER:this.referenceFrame.start+2*this.$viewport.width()*i+1,pixelWidth:t}}repaint(){if(void 0===this.featureCache)return;const{features:e,roiFeatures:t}=this.featureCache,{bpStart:i,bpEnd:n,pixelWidth:r}=this.repaintDimensions(),s=this.$viewport.height(),o=this.getContentHeight(),a=t?Math.max(o,s):o,c=Math.min(a,3*s);if(0===r||0===c)return void(this.canvas&&Bt(this.canvas).remove());const l=Math.max(0,-this.contentTop-Math.floor(c/3)),h=this.referenceFrame.bpPerPixel,d=Math.round((i-this.referenceFrame.start)/h),u=(this.contentTop||0)+l,f=document.createElement(\"canvas\");f.style.position=\"relative\",f.style.display=\"block\",f.style.width=r+\"px\",f.style.height=c+\"px\",f.style.left=d+\"px\",f.style.top=u+\"px\";const p=\"FILL\"===this.trackView.track.displayMode||!1!==this.trackView.track.supportHiDPI?window.devicePixelRatio:1;f.width=p*r,f.height=p*c;const g=f.getContext(\"2d\");g.scale(p,p),g.translate(0,-l);const m={context:g,pixelXOffset:d,pixelWidth:r,pixelHeight:c,pixelTop:l,bpStart:i,bpEnd:n,bpPerPixel:h,pixelShift:d,windowFunction:this.windowFunction,referenceFrame:this.referenceFrame,selection:this.selection,viewport:this,viewportWidth:this.$viewport.width()};this.draw(m,e,t),this.canvas&&Bt(this.canvas).remove(),f._data=m,this.canvas=f,this.$viewport.append(Bt(f))}refresh(){if(!this.canvas||!this.featureCache)return;const e=this.canvas._data;e.context.clearRect(0,0,this.canvas.width,this.canvas.height);const{features:t,roiFeatures:i}=this.featureCache;this.draw(e,t,i)}draw(e,t,i){if(t&&(e.features=t,this.trackView.track.draw(e)),i&&i.length>0)for(let t of i)e.features=t.features,t.track.draw(e)}containsPosition(e,t){return this.referenceFrame.chr===e&&t>=this.referenceFrame.start&&t<=this.referenceFrame.calculateEnd(this.getWidth())}isLoading(){return this.loading}savePNG(){if(!this.canvas)return;const e=this.canvas._data,t=e?e.pixelTop:0,i=window.devicePixelRatio,n=this.$viewport.width()*i,r=this.$viewport.height()*i,s=-Bt(this.canvas).position().left*i,o=(-this.contentTop-t)*i,a=this.canvas.getContext(\"2d\").getImageData(s,o,n,r),c=document.createElement(\"canvas\"),l=c.getContext(\"2d\");c.width=a.width,c.height=a.height,l.putImageData(a,0,0);Pt((this.$trackLabel.text()?this.$trackLabel.text():\"image\")+\".png\",c.toDataURL(\"image/png\"))}saveSVG(){let{width:e,height:t}=this.browser.columnContainer.getBoundingClientRect();const i=new lu({width:e,height:8e3,backdropColor:\"white\",multiLocusGap:0,viewbox:{x:0,y:0,width:e,height:8e3}}),n={deltaX:32,deltaY:32};this.renderSVGContext(i,n,!1),i.setHeight(t);const r=(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\"),o=this.browser.referenceFrameList.indexOf(this.referenceFrame),a=i.getSerializedSvg(!0),c=URL.createObjectURL(new Blob([a],{type:\"application/octet-stream\"}));Pt(`${`${r}_referenceFrame_${o}_guid_${s()}`}.svg`,c)}renderSVGContext(e,{deltaX:t,deltaY:i},n=!0){if(!(this.$zoomInNotice&&this.$zoomInNotice.is(\":visible\"))){const{width:n,height:r}=this.$viewport.get(0).getBoundingClientRect(),o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${s()}`,a=t,c=i+this.contentTop,l=-this.contentTop;e.saveWithTranslationAndClipRect(o,a,c,n,r,l);const{start:h,bpPerPixel:d}=this.referenceFrame,u=Math.round((h-this.referenceFrame.start)/d),f={context:e,viewport:this,referenceFrame:this.referenceFrame,top:l,pixelTop:l,pixelWidth:n,pixelHeight:r,pixelXOffset:u,pixelShift:u,bpStart:h,bpEnd:h+n*d,bpPerPixel:d,viewportWidth:n,selection:this.selection},p=this.featureCache?this.featureCache.features:void 0,g=this.featureCache?this.featureCache.roiFeatures:void 0;this.draw(f,p,g),e.restore()}if(n&&this.$trackLabel&&this.browser.doShowTrackLabels){const{x:n,y:r,width:s,height:o}=((e,t)=>{const{x:i,y:n,width:r,height:s}=e.getBoundingClientRect(),{x:o,y:a,width:c,height:l}=t.getBoundingClientRect();return{x:o-i,y:a-n,width:c,height:l}})(this.$viewport.get(0),this.$trackLabel.get(0));this.renderTrackLabelSVG(e,t+n,i+r,s,o)}}renderTrackLabelSVG(e,t,i,n,r){const o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_track_label_guid_${s()}`;e.saveWithTranslationAndClipRect(o,t,i,n,r,0),e.fillStyle=\"white\",e.fillRect(0,0,n,r),e.font=\"12px Arial\",e.fillStyle=\"rgb(68, 68, 68)\";const{width:a}=e.measureText(this.$trackLabel.text()),c=.25*(n-a),l=.7*(r-12);e.fillText(this.$trackLabel.text(),c,r-l),e.strokeStyle=\"rgb(68, 68, 68)\",e.strokeRect(0,0,n,r),e.restore()}get cachedFeatures(){return this.featureCache?this.featureCache.features:[]}clearCache(){this.featureCache=void 0,this.canvas&&(this.canvas._data=void 0)}async getFeatures(e,t,i,n,r){if(this.featureCache&&this.featureCache.containsRange(t,i,n,r,this.windowFunction))return this.featureCache.features;if(\"function\"==typeof e.getFeatures){const s=await e.getFeatures(t,i,n,r,this);return this.checkContentHeight(s),s}}needsRepaint(){if(!this.canvas)return!0;const e=this.canvas._data;return!e||this.referenceFrame.start<e.bpStart||this.referenceFrame.end>e.bpEnd||this.referenceFrame.chr!==e.referenceFrame.chr||this.referenceFrame.bpPerPixel!=e.bpPerPixel||this.windowFunction!=e.windowFunction}needsReload(){if(!this.featureCache)return!0;const{chr:e,bpPerPixel:t}=this.referenceFrame,{bpStart:i,bpEnd:n}=this.repaintDimensions();return!this.featureCache.containsRange(e,i,n,t,this.windowFunction)}createZoomInNotice(e){const t=Bt(\"<div>\",{class:\"igv-zoom-in-notice-container\"});e.append(t);const i=Bt(\"<div>\");return t.append(i),i.text(\"Zoom in to see features\"),t.hide(),t}viewIsReady(){return this.browser&&this.browser.referenceFrameList&&this.referenceFrame}addMouseHandlers(){const e=this.$viewport.get(0);this.addViewportContextMenuHandler(e);const t=e=>{this.enableClick=!0,this.browser.mouseDownOnViewport(e,this),r(e)};e.addEventListener(\"mousedown\",t),e.addEventListener(\"touchstart\",t);const i=e=>{this.browser.dragObject||this.browser.isScrolling?(this.browser.cancelTrackPan(),this.enableClick=!1):(this.browser.cancelTrackPan(),this.browser.endTrackDrag())};e.addEventListener(\"mouseup\",i),e.addEventListener(\"touchend\",i),\"function\"==typeof this.trackView.track.hoverText&&e.addEventListener(\"mousemove\",(e=>{if(0===e.buttons&&Date.now()-vu>100){vu=Date.now();const t=this.createClickState(e);if(t){const e=this.trackView.track.hoverText(t);e?this.$viewport[0].setAttribute(\"title\",e):this.$viewport[0].removeAttribute(\"title\")}}})),this.addViewportClickHandler(this.$viewport.get(0)),this.trackView.track.name&&\"sequence\"!==this.trackView.track.config.type&&this.addTrackLabelClickHandler(this.$trackLabel.get(0))}addViewportContextMenuHandler(e){e.addEventListener(\"contextmenu\",(e=>{if(this.browser.dragObject)return!1;const t=this.createClickState(e);if(void 0===t)return!1;e.preventDefault();let i=[];if(\"function\"==typeof this.trackView.track.contextMenuItemList){const e=this.trackView.track.contextMenuItemList(t);e&&(i=e)}i.length>0&&i.push({label:Bt(\"<HR>\")}),i.push({label:\"Save Image (PNG)\",click:()=>this.savePNG()}),i.push({label:\"Save Image (SVG)\",click:()=>this.saveSVG()}),this.browser.menuPopup.presentTrackContextMenu(e,i)}))}addViewportClickHandler(e){e.addEventListener(\"click\",(e=>{if(this.enableClick&&this.canvas){if(3===e.which||e.ctrlKey)return;if(this.browser.dragObject||this.browser.isScrolling)return;e.preventDefault();const t=a(e,this.$viewport.get(0)).x,i=a(e,this.canvas).x,n=this.referenceFrame;Math.floor(n.start+n.toBP(i));const r=Date.now();if(r-Fu<this.browser.constants.doubleClickDelay){wu&&(window.clearTimeout(wu),wu=void 0);const e=Math.round(n.start+n.toBP(t));let i;if(\"all\"===this.referenceFrame.chr.toLowerCase()){const t=this.browser.genome.getChromosomeCoordinate(e).chr;if(1===this.browser.referenceFrameList.length)i=t;else{const e=this.browser.referenceFrameList.map((({locusSearchString:e})=>e));e[this.browser.referenceFrameList.indexOf(this.referenceFrame)]=t,i=e.join(\" \")}this.browser.search(i)}else this.browser.zoomWithScaleFactor(.5,e,this.referenceFrame)}else\"function\"==typeof this.trackView.track.popupData&&(wu=setTimeout((()=>{const t=this.getPopupContent(e);if(t)if(!1===e.shiftKey){if(bu&&bu.dispose(),yu.length>0){for(const e of yu)e.dispose();yu.length=0}bu=new tc(this.$viewport.get(0).parentElement,!0,void 0,(()=>{bu.dispose()})),bu.presentContentWithEvent(e,t)}else{let i=new tc(this.$viewport.get(0).parentElement,!0,void 0,(()=>{const e=yu.indexOf(i);yu.splice(e,1),i.dispose()}));yu.push(i),i.presentContentWithEvent(e,t)}window.clearTimeout(wu),wu=void 0}),this.browser.constants.doubleClickDelay));Fu=r}}))}addTrackLabelClickHandler(e){e.addEventListener(\"click\",(e=>{e.stopPropagation();const{track:t}=this.trackView;let i;\"function\"==typeof t.description?i=t.description():t.description&&(i=`<div>${t.description}</div>`),i&&(void 0===this.popover&&(this.popover=new tc(this.browser.columnContainer,!0,t.name||\"\",void 0)),this.popover.presentContentWithEvent(e,i))}))}createClickState(e){if(!this.canvas)return;const t=this.referenceFrame,i=a(e,this.$viewport.get(0)),n=a(e,this.canvas),r=t.start+t.toBP(i.x);return{event:e,viewport:this,referenceFrame:t,genomicLocation:r,y:i.y-this.contentTop,canvasX:n.x,canvasY:n.y}}getPopupContent(e){const t=this.createClickState(e);if(void 0===t)return;let i=this.trackView.track;const n=i.popupData(t),r=this.browser.fireEvent(\"trackclick\",[i,n]);let s;return void 0===r||!0===r?n&&n.length>0&&(s=n.map((e=>{if(e.name){const t=`<span>${e.name}</span>&nbsp&nbsp&nbsp${e.value}`;return`<div title=\"${e.value}\">${t}</div>`}return\"<hr>\"===e?e:e.html?e.html:`<div title=\"${e}\">${e}</div>`})).join(\"\")):\"string\"==typeof r&&(s=r),s}dispose(){this.popover&&this.popover.dispose(),super.dispose()}}class Cu{constructor(e,t,i,n,r,s,o,a){this.chr=e,this.bpStart=t,this.bpEnd=i,this.bpPerPixel=n,this.features=r,this.roiFeatures=s,this.multiresolution=o,this.windowFunction=a}containsRange(e,t,i,n,r){if(r&&r!==this.windowFunction)return!1;const s=this.multiresolution?this.bpPerPixel/n:1;return t>=this.bpStart&&i<=this.bpEnd&&e===this.chr&&s>.5&&s<2}overlapsRange(e,t,i){return this.chr===e&&i>=this.bpStart&&t<=this.bpEnd}}const _u=function(e,t){const{r:i,g:n,b:r}=no[e];return`rgba(${i},${n},${r},${t})`}(\"nickel\",2/16),xu=_u;class ku{constructor(e,t){if(this.url=e.url,e.name&&(this.name=e.name),this.isUserDefined=e.isUserDefined,e.featureSource)this.featureSource=e.featureSource;else if(e.features)this.featureSource=new Su(e.features,t);else{if(!e.format)throw Error(\"ROI configuration must define either features or file format\");this.featureSource=Ad(e,t)}!0===this.isUserDefined?(this.color=e.color||xu,this.headerColor=\"rgba(155,185,129)\"):(this.color=e.color||_u,this.headerColor=\"rgb(190,190,190)\"),this.isVisible=void 0===e.isVisible||e.isVisible}async getFeatures(e,t,i){return this.featureSource.getFeatures({chr:e,start:t,end:i})}async getAllFeatures(){return\"function\"==typeof this.featureSource.getAllFeatures?await this.featureSource.getAllFeatures():{}}addFeature(e){this.featureSource.addFeature(e)}removeFeature(e){this.featureSource.removeFeature(e)}toJSON(){if(this.url)return{name:this.name,color:this.color,url:this.url,isUserDefined:this.isUserDefined,isVisible:this.isVisible};{const e=this.featureSource.getAllFeatures(),t=[];for(let i of Object.keys(e))for(let n of e[i])t.push(n);return{name:this.name,color:this.color,features:t,isUserDefined:this.isUserDefined,isVisible:this.isVisible}}}dispose(){for(let e of Object.keys(this))this[e]=void 0}}function Iu(e,t,i,n){let r=Math.round((e-i)/n);let s=Math.round((t-i)/n)-r;return s<3&&(s=3,r-=1),{x:r,width:s}}class Su{constructor(e,t){this.featureMap={},this.genome=t;for(let i of e){const e=t?t.getChromosomeName(i.chr):i.chr;let n=this.featureMap[e];n||(n=[],this.featureMap[e]=n),n.push(i)}for(let e of Object.keys(this.featureMap))this.featureMap[e].sort(((e,t)=>e.start-t.start))}async getFeatures({chr:e,start:t,end:i}){if(\"all\"===e.toLowerCase())return Ll(this.featureMap,this.genome);{const n=this.featureMap[e];return n?n.filter((e=>e.end>t&&e.start<i)):[]}}getAllFeatures(){return this.featureMap}supportsWholeGenome(){return!0}addFeature(e){let t=this.featureMap[e.chr];t||(t=[],this.featureMap[e.chr]=t),t.push(e),t.sort(((e,t)=>e.start-t.start))}removeFeature({chr:e,start:t,end:i}){if(this.featureMap[e]){const n=`${e}-${t}-${i}`;this.featureMap[e]=this.featureMap[e].filter((e=>n!==`${e.chr}-${e.start}-${e.end}`)),0===this.featureMap[e].length&&delete this.featureMap[e]}}}class Eu{constructor(t,i,n,r){this.rulerViewport=t,this.rulerSweeper=e({class:\"igv-ruler-sweeper\"}),i.appendChild(this.rulerSweeper),this.browser=n,this.referenceFrame=r,this.isMouseHandlers=void 0,this.addBrowserObserver()}addBrowserObserver(){this.boundObserverHandler=(()=>{this.referenceFrame&&(mu.isWholeGenomeView(this.referenceFrame.chr)?this.removeMouseHandlers():this.addMouseHandlers())}).bind(this),this.browser.on(\"locuschange\",this.boundObserverHandler)}removeBrowserObserver(){this.browser.off(\"locuschange\",this.boundObserverHandler)}addMouseHandlers(){if(!0===this.isMouseHandlers)return;let e,t,i,n,r,s;this.boundContentMouseDownHandler=function(s){e=!0,t=!0;const{x:o}=a(s,this.rulerViewport.contentDiv);n=i=o,r=1,this.rulerSweeper.style.display=\"block\",this.rulerSweeper.style.backgroundColor=!0===s.shiftKey?xu:\"rgba(68, 134, 247, 0.25)\",this.rulerSweeper.style.left=`${n}px`,this.rulerSweeper.style.width=`${r}px`}.bind(this),this.rulerViewport.contentDiv.addEventListener(\"mousedown\",this.boundContentMouseDownHandler),this.boundDocumentMouseMoveHandler=function(o){let c;if(e&&t){const{x:e}=a(o,this.rulerViewport.contentDiv);c=Math.max(Math.min(e,this.rulerViewport.contentDiv.clientWidth),0),s=c-i,r=Math.abs(s),this.rulerSweeper.style.width=`${r}px`,s<0&&(n=i+s,this.rulerSweeper.style.left=`${n}px`)}}.bind(this),document.addEventListener(\"mousemove\",this.boundDocumentMouseMoveHandler),this.boundDocumentMouseUpHandler=function(i){let s;if(!0===e&&!0===t&&(e=t=void 0,this.rulerSweeper.style.display=\"none\",r>1)){s={start:Math.floor(this.referenceFrame.calculateEnd(n)),end:Math.floor(this.referenceFrame.calculateEnd(n+r))};!0===i.shiftKey?this.browser.roiManager.updateUserDefinedROISet(Object.assign({chr:this.referenceFrame.chr},s)):(Qa(this.browser.genome.getChromosome(this.referenceFrame.chr).bpLength,s,this.browser.minimumBases()),function(e,t,i){e.start=Math.round(t.start),e.end=Math.round(t.end),e.bpPerPixel=(e.end-e.start)/i}(this.referenceFrame,s,this.rulerViewport.contentDiv.clientWidth),this.browser.updateViews(this.referenceFrame))}}.bind(this),document.addEventListener(\"mouseup\",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!0}removeMouseHandlers(){this.rulerViewport.contentDiv.removeEventListener(\"mousedown\",this.boundContentMouseDownHandler),document.removeEventListener(\"mousemove\",this.boundDocumentMouseMoveHandler),document.removeEventListener(\"mouseup\",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!1}dispose(){this.removeBrowserObserver(),this.removeMouseHandlers(),this.rulerSweeper.remove()}}function Nu(e){if(Bu[e])return Bu[e];if(Bu[\"chr\"+e]){const t=Bu[\"chr\"+e];return Bu[e]=t,t}{const t=_s.randomRGB(0,255);return Bu[e]=t,t}}const Bu={chrX:\"rgb(204, 153, 0)\",chrY:\"rgb(153, 204, 0)\",chrUn:\"rgb(50, 50, 50)\",chr1:\"rgb(80, 80, 255)\",chrI:\"rgb(139, 155, 187)\",chr2:\"rgb(206, 61, 50)\",chrII:\"rgb(206, 61, 50)\",chr2a:\"rgb(216, 71, 60)\",chr2b:\"rgb(226, 81, 70)\",chr3:\"rgb(116, 155, 88)\",chrIII:\"rgb(116, 155, 88)\",chr4:\"rgb(240, 230, 133)\",chrIV:\"rgb(240, 230, 133)\",chr5:\"rgb(70, 105, 131)\",chr6:\"rgb(186, 99, 56)\",chr7:\"rgb(93, 177, 221)\",chr8:\"rgb(128, 34, 104)\",chr9:\"rgb(107, 215, 107)\",chr10:\"rgb(213, 149, 167)\",chr11:\"rgb(146, 72, 34)\",chr12:\"rgb(131, 123, 141)\",chr13:\"rgb(199, 81, 39)\",chr14:\"rgb(213, 143, 92)\",chr15:\"rgb(122, 101, 165)\",chr16:\"rgb(228, 175, 105)\",chr17:\"rgb(59, 27, 83)\",chr18:\"rgb(205, 222, 183)\",chr19:\"rgb(97, 42, 121)\",chr20:\"rgb(174, 31, 99)\",chr21:\"rgb(231, 199, 111)\",chr22:\"rgb(90, 101, 94)\",chr23:\"rgb(204, 153, 0)\",chr24:\"rgb(153, 204, 0)\",chr25:\"rgb(51, 204, 0)\",chr26:\"rgb(0, 204, 51)\",chr27:\"rgb(0, 204, 153)\",chr28:\"rgb(0, 153, 204)\",chr29:\"rgb(10, 71, 255)\",chr30:\"rgb(71, 117, 255)\",chr31:\"rgb(255, 194, 10)\",chr32:\"rgb(255, 209, 71)\",chr33:\"rgb(153, 0, 51)\",chr34:\"rgb(153, 26, 0)\",chr35:\"rgb(153, 102, 0)\",chr36:\"rgb(128, 153, 0)\",chr37:\"rgb(51, 153, 0)\",chr38:\"rgb(0, 153, 26)\",chr39:\"rgb(0, 153, 102)\",chr40:\"rgb(0, 128, 153)\",chr41:\"rgb(0, 51, 153)\",chr42:\"rgb(26, 0, 153)\",chr43:\"rgb(102, 0, 153)\",chr44:\"rgb(153, 0, 128)\",chr45:\"rgb(214, 0, 71)\",chr46:\"rgb(255, 20, 99)\",chr47:\"rgb(0, 214, 143)\",chr48:\"rgb(20, 255, 177)\"};let Mu,Ru;class Du extends Au{constructor(e,t,i,n){super(e,t,i,n)}get contentDiv(){return this.$viewport.get(0)}initializationHelper(){let e;this.$multiLocusCloseButton=Bt(\"<div>\",{class:\"igv-multi-locus-close-button\"}),this.$viewport.append(this.$multiLocusCloseButton),this.$multiLocusCloseButton.get(0).appendChild(l(\"times-circle\")),this.$multiLocusCloseButton.click((()=>{this.browser.removeMultiLocusPanel(this.referenceFrame)})),this.$rulerLabel=Bt(\"<div>\",{class:\"igv-multi-locus-ruler-label\"}),this.$viewport.append(this.$rulerLabel),e=document.createElement(\"div\"),this.$rulerLabel.append(Bt(e)),this.$rulerLabel.get(0).addEventListener(\"click\",(async e=>{e.stopPropagation(),await this.browser.gotoMultilocusPanel(this.referenceFrame)})),this.$tooltip=Bt(\"<div>\",{class:\"igv-ruler-tooltip\"}),this.$tooltip.height(this.$viewport.height()),this.$viewport.append(this.$tooltip),this.$tooltipContent=Bt(\"<div>\"),this.$tooltip.append(this.$tooltipContent),this.rulerSweeper=new Eu(this,this.$viewport.get(0).parentElement,this.browser,this.referenceFrame),this.attachMouseHandlers(mu.isWholeGenomeView(this.referenceFrame.chr)),this.$tooltip.hide(),this.dismissLocusLabel()}presentLocusLabel(e){this.$multiLocusCloseButton.show(),this.$rulerLabel.show(),this.$rulerLabel.get(0).style.backgroundColor=Nu(this.referenceFrame.chr);const t=this.$rulerLabel.get(0).querySelector(\"div\"),{width:i}=this.$rulerLabel.get(0).getBoundingClientRect();t.innerHTML=`${this.referenceFrame.getMultiLocusLabel(e)}`;const{width:n}=t.getBoundingClientRect();n/i>.5&&(t.innerHTML=`${this.referenceFrame.getMultiLocusLabelBPLengthOnly(e)}`)}dismissLocusLabel(){this.$rulerLabel.hide(),this.$multiLocusCloseButton.hide()}attachMouseHandlers(e){if(this.namespace=`.ruler_track_viewport_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}`,this.$viewport.off(this.namespace),!0===e){const e=this.browser.referenceFrameList.indexOf(this.referenceFrame),t=`click${this.namespace}`;this.$viewport.on(t,(t=>{const{x:i}=a(t,this.$viewport.get(0)),n=Math.round(this.referenceFrame.start+this.referenceFrame.toBP(i));let r;const{chr:s}=this.browser.genome.getChromosomeCoordinate(n);if(1===this.browser.referenceFrameList.length)r=s;else{let t=this.browser.referenceFrameList.map((({locusSearchString:e})=>e));t[e]=s,r=t.join(\" \")}this.browser.search(r)})),this.$viewport.get(0).style.cursor=\"pointer\"}else this.$viewport.get(0).style.cursor=\"default\"}mouseMove(e){if(!0===this.browser.doShowCursorGuide){void 0===Ru?(Ru=this,this.$tooltip.show()):Ru.guid!==this.guid?(Ru.$tooltip&&Ru.$tooltip.hide(),this.$tooltip.show(),Ru=this):this.$tooltip.show();if(this.browser.isMultiLocusWholeGenomeView()||mu.isWholeGenomeView(this.referenceFrame.chr))return void this.$tooltip.hide();const{x:t}=a(e,this.$viewport.get(0)),{start:i,end:n,bpPerPixel:r}=this.referenceFrame,s=Math.round(.5+i+Math.max(0,t)*r);this.$tooltipContent.text(Rt(s));const{width:o}=this.$tooltipContent.get(0).getBoundingClientRect(),{width:c}=this.$viewport.get(0).getBoundingClientRect();return this.$tooltip.css({left:`${ys.clamp(t,0,c-o)}px`}),clearTimeout(Mu),Mu=setTimeout((()=>{this.$tooltip&&this.$tooltip.hide()}),1e4),{start:i,bp:s,end:n}}}startSpinner(){}stopSpinner(){}dispose(){this.rulerSweeper.dispose(),super.dispose()}}class Tu extends Au{featureCache=new Lu;constructor(e,t,i,n){super(e,t,i,n)}initializationHelper(){this.canvas=document.createElement(\"canvas\"),this.canvas.className=\"igv-ideogram-canvas\",this.$viewport.append(Bt(this.canvas)),this.ideogram_ctx=this.canvas.getContext(\"2d\"),this.addMouseHandlers()}async getFeatures(e,t,i,n){return this.featureCache.containsRange(e)?this.featureCache.get(e):this.loadFeatures()}async loadFeatures(){const e=this.referenceFrame.chr,t=await this.referenceFrame.genome.getCytobands(e);return this.featureCache.set(e,t),t}repaint(){if(void 0===this.featureCache)return;const{width:e,height:t}=this.$viewport[0].getBoundingClientRect();xo.configureHighDPICanvas(this.ideogram_ctx,e,t);const i=this.referenceFrame.chr,n=this.featureCache.get(i),r={context:this.ideogram_ctx,pixelWidth:e,pixelHeight:t,referenceFrame:this.referenceFrame,features:n};this.trackView.track.draw(r)}addMouseHandlers(){this.addViewportClickHandler(this.$viewport.get(0))}addViewportClickHandler(e){this.boundClickHandler=function(e){const{xNormalized:t,width:i}=a(e,this.ideogram_ctx.canvas),{bpLength:n}=this.browser.genome.getChromosome(this.referenceFrame.chr),r=this.referenceFrame.bpPerPixel*i/n;let s=t;s-r/2<0&&(s=r/2);s+r/2>1&&(s=1-r/2);const o=Math.round((s-r/2)*n),c=Math.round((s+r/2)*n);this.referenceFrame.start=o,this.referenceFrame.end=c,this.referenceFrame.bpPerPixel=(c-o)/i,this.browser.updateViews(this.referenceFrame,this.browser.trackViews,!0)}.bind(this),e.addEventListener(\"click\",this.boundClickHandler)}setWidth(e){this.$viewport.width(e)}renderSVGContext(e,{deltaX:t,deltaY:i},n=!0){const{width:r,height:o}=this.$viewport.get(0).getBoundingClientRect(),a=`ideogram_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${s()}`,c=t,l=i+this.contentTop,h=-this.contentTop;e.saveWithTranslationAndClipRect(a,c,l,r,o,h),this.trackView.track.draw({context:e,pixelWidth:r,pixelHeight:o,referenceFrame:this.referenceFrame,features:this.featureCache.get(this.referenceFrame.chr)}),e.restore()}startSpinner(){}stopSpinner(){}}class Lu{features=new Map;containsRange(e){return this.features.has(e)}set(e,t){this.features.set(e,t)}get(e){return this.features.get(e)}}function zu(e,t,i,n){if(\"ruler\"===e.track.type)return new Du(e,t,i,n);if(\"ideogram\"===e.track.id)return new Tu(e,t,i,n);{const r=new Au(e,t,i,n);return i.viewport=r,r}}const Hu=[\"rgb(255, 0, 0)\",\"rgb(0, 255, 0)\",\"rgb(0, 0, 255)\",\"rgb(255, 0, 255)\",\"rgb(0, 255, 255)\",\"rgb(128, 0, 128)\",\"rgb(255, 165, 0)\",\"rgb(255, 105, 180)\",\"rgb(255, 127, 80)\",\"rgb(220, 20, 60)\",\"rgb(255, 99, 71)\",\"rgb(173, 216, 230)\",\"rgb(144, 238, 144)\",\"rgb(224, 255, 255)\",\"rgb(250, 250, 210)\",\"rgb(152, 251, 152)\",\"rgb(70, 130, 180)\",\"rgb(102, 205, 170)\"].map((e=>{const[t,i,n]=e.split(\",\"),[r,s]=t.split(\"(\"),[o,a]=n.split(\")\");return[s,i,o]})),Pu=ro(\"magnesium\"),Ou=[\"#sampleTable\",\"#sampleMapping\",\"#colors\"];class Uu{static emptySpaceReplacement=\"|\";sampleDictionary={};attributeNames=[];sampleMappingDictionary={};colorDictionary={};attributeRangeLUT={};constructor(e){e.tracks.some((e=>\"function\"==typeof e.getSamples)).length>0&&e.sampleInfoControl.setButtonVisibility(!0),this.initialize()}initialize(){this.sampleInfoFiles=[],this.attributeNames=[],this.sampleDictionary={},this.sampleMappingDictionary={},this.colorDictionary={},this.attributeRangeLUT={},this.initialized=!1}get attributeCount(){return this.attributeNames?this.attributeNames.length:0}isInitialized(){return this.initialized}hasAttributes(){return this.attributeCount>0}getAttributes(e){const t=0===Object.keys(this.sampleMappingDictionary)?e:this.sampleMappingDictionary[e]||e;return this.sampleDictionary[t]}async loadSampleInfoFile(e){try{const t=await Qs.loadString(e);this.#w(t),this.sampleInfoFiles.push(e)}catch(e){console.error(e.message)}}#w(e){const t=function(e){const t={},i=e.split(/\\r?\\n|\\r/).map((e=>e.trim())).filter((e=>\"\"!==e));let n;Ou.includes(i[0])||(n=\"#sampleTable\",t[n]=[]);for(const e of i)Ou.includes(e)?(n=e,t[n]=[]):n&&!1===e.startsWith(\"#\")&&t[n].push(e);return t}(e);for(const[e,i]of Object.entries(t))switch(e){case\"#sampleTable\":this.#b(i);break;case\"#sampleMapping\":this.#F(i);break;case\"#colors\":this.#v(i)}this.initialized=!0}getAttributeColor(e,t){let i;if(\"-\"===t)i=ro(\"snow\");else if(\"string\"==typeof t&&this.colorDictionary[t])i=this.colorDictionary[t]();else if(this.colorDictionary[e])i=this.colorDictionary[e](t);else if(\"string\"==typeof t)i=\"NA\"===t?Pu:function(e){let t=0;for(let i=0;i<e.length;i++)t=e.charCodeAt(i)+((t<<5)-t);let i=[];for(let e=0;e<3;e++){const n=t>>8*e&255;i.push(n)}return`rgb(${i.join(\", \")})`}(t);else{const[n,r]=this.attributeRangeLUT[e],s=.2,o=Math.max((t-n)/(r-n),s),[a,c,l]=Hu[Object.keys(this.attributeRangeLUT).indexOf(e)];i=`rgba(${a},${c},${l},${o})`}return i}getSortedSampleKeysByAttribute(e,t,i){i=i||1;const n=e.filter((e=>\"number\"==typeof this.getAttributes(e)[t])),r=e.filter((e=>\"string\"==typeof this.getAttributes(e)[t])),s=(e,n)=>{const r=this.getAttributes(e)[t],s=this.getAttributes(n)[t];return\"string\"==typeof r&&\"string\"==typeof s?i*r.localeCompare(s):\"number\"==typeof r&&\"number\"==typeof s?i*(r-s):void 0};return n.sort(s),r.sort(s),-1===i?[...n,...r]:[...r,...n]}toJSON(){const e=[];for(const t of this.sampleInfoFiles){const i={url:t},n=Hl.localFileInspection(i);e.push(n)}return e}#b(e){const t=e.shift().split(\"\\t\").filter((e=>e.length>0));t.shift();const i=t.map((e=>e.split(\" \").join(Uu.emptySpaceReplacement))),n=e.filter((e=>e.length>0));let r;for(const e of n){const t=e.split(\"\\t\"),n=t.shift();void 0===r&&(r={}),r[n]={};for(let e=0;e<t.length;e++){const s={};\"\"===t[e]?s[i[e]]=\"-\":s[i[e]]=t[e],Object.assign(r[n],s)}}for(const[e,t]of Object.entries(r))r[e]=Qu(t);const s=function(e,t){const i={};for(const n of Object.values(t))for(const t of e){let e=n[t];void 0===i[t]&&(i[t]=[]),i[t].push(e)}const n=e=>\"number\"==typeof e,r=e=>\"string\"==typeof e;for(const e of Object.keys(i)){const t=i[e],s=new Set(t),o=Array.from(s);if(!0===o.some(r)&&!0===o.some(n)?i[e]=o.filter((e=>!r(e))):i[e]=o,!i[e].some(r)){const t=i[e].slice();i[e]=[Math.min(...t),Math.max(...t)]}}return i}(i,r);qu(this.attributeRangeLUT,s);const o=new Set(this.attributeNames);for(const e of i)o.has(e)||this.attributeNames.push(e);qu(this.sampleDictionary,r)}#F(e){for(const t of e){const[e,i]=t.split(\"\\t\");this.sampleMappingDictionary[e]=i}}#v(e){const t=(e,t,i)=>{let n;switch(t){case 0:n=e.split(\" \").join(Uu.emptySpaceReplacement);break;case 1:n=e.includes(\":\")?e.split(\":\").map((e=>parseFloat(e))):e;break;case 2:case 3:n=`rgb(${e})`}return n},i=e.map((e=>e.split(\"\\t\").map(t))),n=i.filter((e=>3===e.length&&!e.includes(\"*\"))).filter((([e,t,i])=>!Array.isArray(t))),r={};for(const e of n){const[t,i,n]=e;void 0===r[t]&&(r[t]={}),r[t][i.toUpperCase()]=n}for(const[e,t]of Object.entries(r)){const i=Object.assign({},t);this.colorDictionary[e]=e=>{const t=e.toUpperCase();return i[t]||ro(\"snow\")}}const s=i.filter((e=>Array.isArray(e[1])));for(const e of s){const[t,i]=e[1],n=e[0];if(3===e.length){const[r,s,o]=uo(e[2]);this.colorDictionary[n]=e=>{e=ys.clamp(e,t,i);return lo(r,s,o,(e-t)/(i-t))}}else if(4===e.length){const[t,i]=e[1],[n,r,s,o]=e;this.colorDictionary[n]=e=>{e=ys.clamp(e,t,i);return fo(s,o,(e-t)/(i-t))}}}const o=i.filter((e=>3===e.length&&e.includes(\"*\")));for(const e of o)if(\"*\"===e[1]){const[t,i,n]=e;this.colorDictionary[t]=e=>{if(\"NA\"===e)return Pu;{const[i,r]=this.attributeRangeLUT[t],s=(e-i)/(r-i),[o,a,c]=uo(n);return lo(o,a,c,s)}}}else if(\"*\"===e[0]){const[t,i,n]=e;this.colorDictionary[i]=()=>n}}}function qu(e,t){for(const[i,n]of Object.entries(t))i in e&&e[i]===n||(e[i]=n)}function Qu(e){const t=Object.assign({},e);for(const[e,i]of Object.entries(t))\"string\"!=typeof i||isNaN(i)||(t[e]=Number(i));return t}const Vu=16,ju=Rt;class Wu{constructor(e){this.browser=e,this.height=40,this.name=\"\",this.id=\"ruler\",this.disableButtons=!0,this.ignoreTrackMenu=!0,this.order=.01*Number.MIN_SAFE_INTEGER,this.removable=!1,this.type=\"ruler\"}async getFeatures(e,t,i){return[]}computePixelHeight(e){return this.height}draw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpPerPixel:r,bpStart:s}){mu.isWholeGenomeView(t.chr)?this.drawWholeGenome({context:e,pixelWidth:i,pixelHeight:n,bpPerPixel:r}):this.doDraw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpStart:s})}drawWholeGenome({context:e,pixelWidth:t,pixelHeight:i,bpPerPixel:n}){e.save(),xo.fillRect(e,0,0,t,i,{fillStyle:\"white\"});for(let t of this.browser.genome.wgChromosomeNames){let r=this.browser.genome.getCumulativeOffset(t),s=this.browser.genome.getChromosome(t).bpLength,o=Math.round(r/n),a=Math.round(s/n);this.renderChromosomeRect(e,o,0,a,i,t)}e.restore()}doDraw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpStart:r}){e.clearRect(0,0,i,n);const s=function(e,t){if(e<10)return new Gu(1,\"bp\",1);const i=Math.floor(Math.log10(e));let n=\"bp\",r=1;i>9?(n=\"gb\",r=1e9):i>6?(n=\"mb\",r=1e6):i>3&&(n=\"kb\",r=1e3);const s=Math.pow(10,i-1),o=e/s,a=75,c=Math.pow(10,i-1),l=Math.pow(10,i)/2;return new Gu(o<a&&!0!==t?c:l,n,r)}(Math.floor(t.toBP(i)),e.isSVG);let o=Math.floor(r/s.majorTick)-1;const{tickDelta:a,labelLength:c}=function(e,t,i,n,r){const s=l(t,c(1+n,r),i)-l(t,c(n,r),i),o=`${Rt(Math.floor(c(n,r)/r.unitMultiplier))} ${r.majorUnit}`,a=Math.floor(e.measureText(o).width);return{tickDelta:s,labelLength:a};function c(e,t){return Math.floor(e*t.majorTick)}function l(e,t,i){return Math.round(e.toPixels(t-1-i+.5))}}(e,t,r,o,s);let l,h;this.browser.referenceFrameList.indexOf(t);let d=a;const u=.25*c;do{h=Math.floor(o*s.majorTick);const i=`${Rt(Math.floor(h/s.unitMultiplier))} ${s.majorUnit}`;l=Math.round(t.toPixels(h-1-r+.5));const n=Math.round(l-e.measureText(i).width/2);n>0&&u+c<=d&&(xo.fillText(e,i,n,this.height-8),d=0),l>0&&xo.strokeLine(e,l,this.height-6,l,this.height-2),h=Math.floor((1+o)*s.majorTick);let f=l+(Math.round(t.toPixels(h-1-r+.5))-l)/2;f>0&&xo.strokeLine(e,f,this.height-6,f,this.height-2),++o,d+=a}while(l<i);xo.strokeLine(e,0,this.height-2,i,this.height-2)}renderChromosomeRect(e,t,i,n,r,s){e.textAlign=\"center\",e.textBaseline=\"middle\",e.font=\"12px sans-serif\",xo.strokeLine(e,t+n,i,t+n,i+r,{strokeStyle:_s.greyScale(191)});const o=(s=this.browser.genome.getChromosomeDisplayName(s)).startsWith(\"chr\")?s.substring(3):s;n>e.measureText(o).width&&xo.fillText(e,o,t+n/2,i+r/2,{fillStyle:_s.greyScale(68)})}get supportsWholeGenome(){return!0}dispose(){}}class Gu{constructor(e,t,i){this.majorTick=e,this.minorTick=e/10,this.majorUnit=t,this.unitMultiplier=i}description(e){console.log((e||\"\")+\" tick \"+ju(this.majorTick)+\" label width \"+ju(this.labelWidthBP)+\" multiplier \"+this.unitMultiplier)}}class $u{constructor(t,i,n){this.guid=s(),this.trackView=t,this.browser=t.browser,this.viewport=e({class:\"igv-viewport\"}),i.appendChild(this.viewport),this.viewport.style.height=`${t.track.height}px`,null===this.viewport.previousElementSibling&&(this.viewport.style.zIndex=16,this.viewport.style.overflow=\"visible\"),this.canvas=document.createElement(\"canvas\"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext(\"2d\"),this.ctx.font=\"10px verdana\",this.contentTop=0,this.hitList=void 0,this.sortDirection=1,this.setWidth(n),this.addMouseHandlers()}resizeCanvas(){const e=window.devicePixelRatio,t=this.browser.getSampleInfoViewportWidth();let i;if(this.browser.trackViews.length>1&&null===this.viewport.previousElementSibling){const[e,t]=[this.browser.ideogramTrackView.track,this.browser.rulerTrackView.track];i=e.height+t.height}else i=this.viewport.clientHeight;if(this.canvas.width!==t*e||this.canvas.height!==i*e){const n=this.canvas;n.width=t*e,n.height=i*e,n.style.width=`${t}px`,n.style.height=`${i}px`,this.ctx=this.canvas.getContext(\"2d\"),this.ctx.scale(e,e),null===this.viewport.previousElementSibling&&xo.fillRect(this.ctx,0,0,this.ctx.canvas.width,this.ctx.canvas.height,{fillStyle:ro(\"snow\")})}}setTop(e){\"function\"==typeof this.trackView.track.getSamples&&(this.contentTop=e,this.repaint())}setWidth(e){this.viewport.innerWidth=e,this.resizeCanvas()}setHeight(e){const t=this.browser.getSampleInfoViewportWidth();this.viewport.style.width=`${t}px`,this.viewport.style.height=`${e}px`;const i=window.devicePixelRatio;this.canvas.width=t*i,this.canvas.height=e*i,this.canvas.style.width=`${t}px`,this.canvas.style.height=`${e}px`,this.ctx=this.canvas.getContext(\"2d\"),this.ctx.scale(i,i),null===this.viewport.previousElementSibling&&xo.fillRect(this.ctx,0,0,this.ctx.canvas.width,this.ctx.canvas.height,{fillStyle:ro(\"snow\")})}async repaint(){if(this.resizeCanvas(),\"function\"==typeof this.trackView.track.getSamples){const e=this.trackView.track.getSamples();e.names&&e.names.length>0&&this.draw({context:this.ctx,samples:e})}else null===this.viewport.previousElementSibling&&(this.browser.rulerTrackView&&this.browser.rulerTrackView.setTrackHeight(!0===this.browser.sampleInfoControl.showSampleInfo?this.calculateSampleInfoColumnHeight():40,!0),this.renderSampleInfoColumns(this.ctx))}calculateSampleInfoColumnHeight(){const e=this.browser.sampleInfo.attributeNames.map((e=>this.ctx.measureText(e).width));return 4+Math.min(Math.max(...e),128)}draw({context:e,samples:t}){if(e.clearRect(0,0,e.canvas.width,e.canvas.height),e.fillStyle=ro(\"snow\"),e.fillRect(0,0,e.canvas.width,e.canvas.height),t&&t.names.length>0){const i=this.browser.sampleInfo.attributeNames,n=this.viewport.getBoundingClientRect().height;let r=1;const s=t.height;r=s-2*r<=1?0:1;let o=this.contentTop+t.yOffset;this.hitList={};for(const a of t.names){if(o>n)break;if(o+s>0){const t=this.browser.sampleInfo.getAttributes(a);if(t){const n=Object.entries(t);for(const t of n){const[n,a]=t;e.fillStyle=this.browser.sampleInfo.getAttributeColor(n,a);const c=8+i.indexOf(n)*Vu,l=o+r,h=s-2*r;e.fillRect(c,l,15,h);const d=`${Math.floor(c)}#${Math.floor(l)}#16#${Math.ceil(h)}`;this.hitList[d]=`${n}#${a}`}}}o+=s}}}renderSampleInfoColumns(e){const t=(e,t,i,n,r,s)=>{e.save(),e.font=\"10px verdana\",e.translate(i+r/2,n+s),e.rotate(-Math.PI/2),e.textAlign=\"left\",e.fillStyle=ro(\"lead\"),e.fillText(t,2,2),e.restore()},i=this.browser.sampleInfo.attributeNames;this.hitList={};for(let n=0;n<i.length;n++){const r=8+n*Vu,s=15,o=Math.round(e.canvas.height/window.devicePixelRatio);xo.fillRect(e,r,0,s,o,{fillStyle:ro(\"snow\")}),t(e,i[n],r,0,s,o);const a=`${Math.floor(r)}#0#${s}#${Math.ceil(o)}`;this.hitList[a]=`${i[n]}`}}renderSVGContext(e,{deltaX:t,deltaY:i}){if(\"function\"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:o,height:a}=this.viewport.getBoundingClientRect(),c=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_sample_names_guid_${s()}`;e.saveWithTranslationAndClipRect(c,t,i+r,o,a,-r),this.draw({context:e,samples:n}),e.restore()}}addMouseHandlers(){this.addMouseMoveHandler()}addMouseMoveHandler(){this.boundMouseMoveHandler=function(e){if(this.hitList){const t=Object.entries(this.hitList);if(null===this.viewport.previousElementSibling){const i=(t,i)=>{const{marginTop:n}=window.getComputedStyle(i),{x:r,y:s}=a(e,this.browser.columnContainer.querySelector(\".igv-sample-info-column\"));return{x:Math.floor(r),y:Math.floor(s-parseInt(n,10))}},n=this.browser.columnContainer.querySelector(\".igv-sample-info-column\"),{x:r,y:s}=i(n,this.viewport);n.setAttribute(\"title\",\"\");for(const[e,i]of t){const[t,o,a,c]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(r<t||r>t+a||s<o||s>o+c)){n.setAttribute(\"title\",`${i}`);break}}}else{const{x:i,y:n}=a(e,this.viewport);this.viewport.setAttribute(\"title\",\"\");for(const[e,r]of t){const[t,s,o,a]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(i<t||i>t+o||n<s||n>s+a)){const[e,t]=r.split(\"#\");this.viewport.setAttribute(\"title\",`${e.split(Uu.emptySpaceReplacement).join(\" \")}: ${\"-\"===t?\"\":t}`);break}}}}}.bind(this),this.viewport.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandlers(){this.viewport.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}show(){this.viewport.style.display=\"block\"}hide(){this.viewport.style.display=\"none\"}}class Ku{constructor(t,i,n,r){this.guid=s(),this.trackView=t,this.browser=t.browser,this.viewport=e({class:\"igv-viewport\"}),i.appendChild(this.viewport),t.track.height&&(this.viewport.style.height=`${t.track.height}px`),this.canvas=document.createElement(\"canvas\"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext(\"2d\"),this.trackScrollDelta=0,this.contentTop=0,this.hitList=void 0,this.sortDirection=1,this.setWidth(r),this.addMouseHandlers()}checkCanvas(){const e=this.browser.sampleNameViewportWidth||0;this.ctx.canvas.width=e*window.devicePixelRatio,this.ctx.canvas.style.width=`${e}px`,this.ctx.canvas.height=this.viewport.clientHeight*window.devicePixelRatio,this.ctx.canvas.style.height=`${this.viewport.clientHeight}px`,this.ctx.scale(window.devicePixelRatio,window.devicePixelRatio)}setTop(e){if(\"function\"==typeof this.trackView.track.getSamples){this.contentTop=e;const t=this.trackView.track.getSamples();this.repaint(t)}}setWidth(e){this.viewport.innerWidth=e,this.checkCanvas()}async repaint(e){if(e.names.length>0&&!0===this.browser.showSampleNames&&(this.checkCanvas(),this.draw({context:this.ctx,samples:e}),void 0===this.browser.sampleNameViewportWidth)){const t=e.names.map((e=>this.ctx.measureText(e).width));this.browser.sampleNameViewportWidth=Math.min(200,4+Math.ceil(Math.max(...t))),this.browser.layoutChange()}}draw({context:e,samples:t}){if(xo.fillRect(e,0,0,e.canvas.width,t.height,{fillStyle:ro(\"snow\")}),t&&t.names.length>0){const i=this.viewport.getBoundingClientRect().height,n=t.height,r=n-2<=1?0:1;let s=this.contentTop+t.yOffset;this.hitList={};for(const o of t.names){if(s>i)break;if(s+n>0){const t=n-2*r;Yu(e,o,0+2,s+r,e.canvas.width,t)}s+=n}}}renderSVGContext(e,{deltaX:t,deltaY:i}){if(\"function\"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:o,height:a}=this.viewport.getBoundingClientRect(),c=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_sample_names_guid_${s()}`;e.saveWithTranslationAndClipRect(c,t,i+r,o,a,-r),this.draw({context:e,samples:n}),e.restore()}}addMouseHandlers(){this.boundClickHandler=function(e){e.preventDefault();const t={label:\"Name Panel Width\",value:this.browser.sampleNameViewportWidth,callback:e=>{this.browser.sampleNameViewportWidth=parseInt(e),this.browser.layoutChange()}};this.browser.inputDialog.present(t,e)}.bind(this),this.viewport.addEventListener(\"contextmenu\",this.boundClickHandler),this.boundMouseMoveHandler=function(e){if(this.hitList){const t=Object.entries(this.hitList),{x:i,y:n}=a(e,this.viewport);this.viewport.setAttribute(\"title\",\"\");for(const[e,r]of t){const[t,s,o,a]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(i<t||i>t+o||n<s||n>s+a)){this.viewport.setAttribute(\"title\",`${r}`);break}}}}.bind(this),this.viewport.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandlers(){this.viewport.removeEventListener(\"contextmenu\",this.boundClickHandler),this.viewport.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}}function Yu(e,t,i,n,r,s){const o=Math.min(s,10);e.font=`${o}px sans-serif`,e.textAlign=\"start\",e.fillStyle=ro(\"lead\");const a=i,c=e.measureText(t),l=n+s/2+(c.actualBoundingBoxAscent+c.actualBoundingBoxDescent)/2;e.fillText(t,a,l)}class Xu{constructor(t){this.popover=e({class:\"igv-menu-popup\"}),t.appendChild(this.popover),this.parent=t;const i=e({class:\"igv-menu-popup-header\"});this.popover.appendChild(i),u(i,(()=>this.popover.style.display=\"none\")),this.popoverContent=e(),this.popover.appendChild(this.popoverContent),p(this.popover,i),i.addEventListener(\"click\",(e=>{e.stopPropagation(),e.preventDefault()})),this.popover.style.display=\"none\"}presentMenuList(e,t){if(Zu(this.parent),t.length>0){this.popoverContent.innerHTML=\"\";const i=this.parseMenuList(e,t);for(let e of i){e.init&&e.init();let t=e.object;0===i.indexOf(e)&&t.removeClass(\"igv-track-menu-border-top\"),t.hasClass(\"igv-track-menu-border-top\")||t.hasClass(\"igv-menu-popup-check-container\")||t.is(\"div\")&&t.addClass(\"igv-menu-popup-shim\"),this.popoverContent.appendChild(t.get(0))}this.popover.style.display=\"flex\";const{width:n}=this.popover.getBoundingClientRect();this.popover.style.left=-n+\"px\",this.popover.style.top=\"0px\"}}parseMenuList(e,t){return t.map(((t,i)=>{let n;if(t.name?(n=Bt(\"<div>\"),n.text(t.name)):t.object?n=t.object:\"string\"==typeof t.label?(n=Bt(\"<div>\"),n.html(t.label)):\"string\"==typeof t&&(n=t.startsWith(\"<\")?Bt(t):Bt(\"<div>\"+t+\"</div>\")),0===i&&n.addClass(\"igv-track-menu-border-top\"),t.click||t.dialog){const i=i=>{if(i.preventDefault(),i.stopPropagation(),t.click)if(e.track.selected){const n=e.browser.getSelectedTrackViews();if(!0===t.doAllMultiSelectedTracks)t.click.call(e.track,i);else if(\"removeTrack\"===t.menuItemType){const r=()=>{e.browser.overlayTrackButton.setVisibility(!1);for(const{track:e}of n)t.click.call(e,i)},s={html:`Are you sure you want to delete ${n.length} tracks?`,callback:r};e.browser.menuUtils.dialog.present(s,i)}else for(const{track:e}of n)t.click.call(e,i)}else t.click.call(e.track,i);else t.dialog&&t.dialog.call(e.track,i);this.popover.style.display=\"none\"};n.on(\"click\",i),n.on(\"touchend\",(e=>i(e))),n.on(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}return{object:n,init:t.init||void 0}}))}presentTrackContextMenu(t,n){this.popoverContent.innerHTML=\"\";const r=function(t,n){return t.map((t=>{let r;if(\"string\"==typeof t&&\"<hr/>\"===t)r=document.createElement(\"hr\");else if(\"string\"==typeof t)r=e({class:\"context-menu\"}),r.innerHTML=t;else if(\"Node\"==typeof t)r=t;else{if(\"function\"==typeof t.init&&t.init(),\"checkbox\"===t.type)r=Dl(\"Show all bases\",t.value);else if(\"color\"===t.type){const s=new Ra(n.parentElement);s.configure({color:\"grey\"}),r=e({class:\"context-menu\"}),\"string\"==typeof t.label&&(r.innerHTML=t.label);const o=e=>{s.show(),i(n),e.preventDefault(),e.stopPropagation()};r.addEventListener(\"click\",o),r.addEventListener(\"touchend\",o),r.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}else r=e({class:\"context-menu\"}),\"string\"==typeof t.label&&(r.innerHTML=t.label);if(t.click&&\"color\"!==t.type){function a(e){t.click(),i(n),e.preventDefault(),e.stopPropagation()}r.addEventListener(\"click\",a),r.addEventListener(\"touchend\",a),r.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}}return{el:r,init:t.init}}))}(n,this.popover);for(let{el:e}of r)this.popoverContent.appendChild(e);!function(e,t){t.style.display=\"flex\";const{x:i,y:n}=a(e,t.parentNode),{width:r}=t.getBoundingClientRect(),s=i+r,{width:o}=t.parentNode.getBoundingClientRect();t.style.left=`${s>o?i-(s-o):i}px`,t.style.top=`${n}px`}(t,this.popover)}hide(){this.popover.style.display=\"none\"}dispose(){this.popoverContent.innerHTML=\"\",this.popover.innerHTML=\"\",Object.keys(this).forEach((function(e){this[e]=void 0}))}}const Zu=e=>{const t=e.querySelectorAll(\".igv-menu-popup\");for(const e of t)e.style.display=\"none\"};class Ju{constructor(t,i,n,r,s,o,a){this.browser=i,this.button=e({class:\"igv-navbar-text-button\"}),t.appendChild(this.button),Array.isArray(n)?(this.textContent=n[0],this.title=n[1]):this.textContent=this.title=n,this.buttonLabel=r,this.imageDictionary={image:`url(\"data:image/svg+xml,${encodeURIComponent(s)}\")`,imageHover:`url(\"data:image/svg+xml,${encodeURIComponent(o)}\")`},this.responsiveKey=\"text\",this.configureButton(this.textContent,this.title),this.setState(a),i.on(\"navbar-resize\",(e=>{this.navbarResizeHandler(e)}))}navbarResizeHandler(e){const t=\"igv-navbar-icon-button\"===e?\"image\":\"text\";t!==this.responsiveKey&&(this.responsiveKey=t,this.configureButton(this.textContent,this.title),this.setState(void 0))}configureButton(e,t){this.groupElement=void 0,this.button.title=t,this.button.innerHTML=\"\",this.button.style.backgroundImage=\"none\",this.button.classList.remove(\"igv-navbar-icon-button\"),this.button.classList.remove(\"igv-navbar-text-button\"),\"text\"===this.responsiveKey?this.configureTextButton(e):this.configureIconButton()}configureTextButton(e){console.log(`text ${this.title}`),this.button.classList.add(\"igv-navbar-text-button\");const t=document.createElement(\"div\");t.innerHTML=this.buttonLabel;const i=t.firstChild;this.button.appendChild(i),this.groupElement=i.querySelector(\"#igv-navbar-button-group\");i.querySelector(\"#igv-navbar-button-label\").textContent=e}configureIconButton(){console.log(`icon ${this.title}`),this.button.classList.add(\"igv-navbar-icon-button\")}setState(e){void 0!==e&&(this.doHover=e),\"text\"===this.responsiveKey?this.setTextButtonState(this.doHover):this.setIconButtonState(this.doHover)}setTextButtonState(e){this.groupElement.classList.remove(...this.groupElement.classList);const t=!0===e?\"igv-navbar-text-button-svg-hover\":\"igv-navbar-text-button-svg-inactive\";this.groupElement.classList.add(t)}setIconButtonState(e){this.button.style.backgroundImage=!0===e?this.imageDictionary.imageHover:this.imageDictionary.image}show(){this.button.style.display=\"flex\"}hide(){this.button.style.display=\"none\"}setVisibility(e){!0===e?this.show():this.hide()}}const ef='<svg width=\"80px\" height=\"18px\" viewBox=\"0 0 80 18\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"igv-navbar-button-group\">\\n            <rect id=\"Rectangle\" x=\"0.5\" y=\"0.5\" width=\"79\" height=\"17\" rx=\"6\"></rect>\\n            <text id=\"igv-text-button-label\" x=\"50%\" y=\"50%\" dy=\".1em\" font-family=\"Helvetica\" font-size=\"12\" font-weight=\"normal\" letter-spacing=\"-0.372\">\\n                <tspan id=\"igv-navbar-button-label\"></tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>';class tf extends Hl{static defaults={autoscale:void 0,alpha:.5,height:50};constructor(e,t,i){super(e,t),this.type=\"merged\",this.paintAxis=cd,this.graphType=e.graphType,this.tracks=i||[]}async postInit(){if(this.config.tracks){for(let e of this.config.tracks){const t=await this.browser.createTrack(e);t?this.tracks.push(t):console.warn(\"Could not create track \"+e),\"function\"==typeof t.postInit&&await t.postInit()}this.config.tracks.every((e=>void 0!==e.autoscale||void 0!==e.max))||(this.config.autoscale=void 0===this.config.max)}for(let e of this.tracks)e.isMergedTrack=!0;if(this.config.autoscale?this.autoscale=this.config.autoscale:void 0!==this.config.max&&this.setDataRange({min:this.config.min||0,max:this.config.max}),void 0!==this.config.flipAxis)for(let e of this.tracks)e.flipAxis=this.config.flipAxis;if(void 0!==this.config.logScale)for(let e of this.tracks)e.logScale=this.config.logScale;this.resolutionAware=this.tracks.some((e=>e.resolutionAware))}set flipAxis(e){this.config.flipAxis=e;for(let t of rf(this.tracks))t.flipAxis=e}get flipAxis(){return rf(this.tracks).every((e=>e.flipAxis))}set logScale(e){this.config.logScale=e;for(let t of rf(this.tracks))t.logScale=e}get logScale(){return rf(this.tracks).every((e=>e.logScale))}get height(){return this._height}set height(e){if(this.config.height=e,this._height=e,this.tracks)for(let t of this.tracks)t.height=e,t.config.height=e}set autoscale(e){if(this._autoscale=e,!1===e&&this.tracks)for(let e of this.tracks)e.autoscale=!1}get autoscale(){return this._autoscale}set autoscaleGroup(e){if(this.tracks)for(let t of this.tracks)t.autoscaleGroup=e}get autoscaleGroup(){if(this.tracks&&this.tracks.length>0){const e=this.tracks[0].autoscaleGroup;return this.tracks.some((t=>e!==t.autoscaleGroup))?void 0:e}}setDataRange({min:e,max:t}){this.autoscale=!1;for(const i of rf(this.tracks))i.dataRange={min:e,max:t},i.autoscale=!1,i.autoscaleGroup=!1}set dataRange({min:e,max:t}){for(const i of rf(this.tracks))i.dataRange={min:e,max:t}}get dataRange(){if(this.tracks){const e=rf(this.tracks);if(e.length>0){const t=e[0].dataRange;if(e.every((e=>e.dataRange&&e.dataRange.min===t.min&&e.dataRange.max===t.max)))return t}}}menuItemList(){const e=[];return rf(this.tracks).length>0&&(void 0!==this.flipAxis&&e.push({label:\"Flip y-axis\",click:function(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),e.push(...this.numericDataMenuItems())),e.push(\"<hr/>\"),e.push(this.overlayTrackAlphaAdjustmentMenuItem()),e.push(this.trackSeparationMenuItem()),e}async getFeatures(e,t,i,n){const r=this.tracks.map((r=>r.getFeatures(e,t,i,n))),s=await Promise.all(r);if(s.every((e=>0===e.length)))return new nf([],[]);{const e=this.tracks.map((e=>e.name));return new nf(s,e)}}draw(e){const t=e.features;for(let i=0,n=this.tracks.length;i<n;i++){const n=Object.assign({},e);n.features=t.featureArrays[i],n.alpha=this.alpha,this.graphType&&(this.tracks[i].graphType=this.graphType),this.tracks[i].draw(n)}}popupData(e){const t=this.clickedFeatures(e);if(t&&t.length===this.tracks.length){const i=[];let n=!0;for(let r=0;r<t.length;r++)if(r>0&&i.push(\"<hr/>\"),i.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${t[r].trackName}</div>`),t[r].features.length>0){n=!1;const s=this.tracks[r].popupData(e,t[r].features);i.push(...s)}else i.push(\"Missing or 0 value(s)\");return!0===n?[]:i}}clickedFeatures(e){const t=e.viewport.cachedFeatures;if(!t||!t.featureArrays||!Array.isArray(t.featureArrays)||0===t.featureArrays.length)return[];const i=e.genomicLocation,n=[],r=e.referenceFrame.bpPerPixel>.2?3*e.referenceFrame.bpPerPixel:.2,s=i-r,o=i+r;for(let e=0;e<t.featureArrays.length;e++){const i=to(t.featureArrays[e],s,o);n.push({trackName:t.trackNames[e],features:i})}return n}get supportsWholeGenome(){return this.tracks.every((e=>e.supportsWholeGenome))}getState(){const e=super.getState(),t=[];for(let e of this.tracks)t.push(e.getState());return e.tracks=t,e}updateScales(e){let t;if(this.autoscale){t=!0;let i=[];for(let t of e){if(t.featureCache&&t.featureCache.features){const e=t.referenceFrame,n=e.start,r=n+e.toBP(t.getWidth()),s=t.featureCache.features;this.autoscale&&(i.push({value:s.getMax(n,r)}),i.push({value:s.getMin(n,r)}))}const e=qa(i);for(const t of rf(this.tracks))t.dataRange=e}}else{let i=-1;for(let n of this.tracks)if(++i,n.autoscale){t=!0;let r=[];for(let t of e)if(t.featureCache&&t.featureCache.features){const e=t.referenceFrame,n=e.start,s=n+e.toBP(t.getWidth()),o=t.featureCache.features.featureArrays[i];if(o)for(let e of o)if(!(e.end<n)){if(e.start>s)break;r.push(e)}}n.dataRange=qa(r)}}return t}overlayTrackAlphaAdjustmentMenuItem(){const t=e();return t.innerText=\"Set transparency\",{object:Bt(t),dialog:function(e){const t={label:\"Transparency\",value:this.alpha,min:0,max:1,scaleFactor:1e3,callback:e=>{this.alpha=Math.max(.001,e),this.repaintViews()}};this.browser.sliderDialog.present(t,e)}}}trackSeparationMenuItem(){const e=Bt(\"<div>\");return e.text(\"Separate tracks\"),{object:e,click:function(e){const t=this.autoscale,i=this.name,n=this.tracks,r=this.browser,s=this.order;r.removeTrack(this);for(let e of n)e.order=s,t&&(e.autoscaleGroup=i),e.isMergedTrack=!1,r.addTrack(e.config,e);r.updateViews()}}}}class nf{constructor(e,t){this.featureArrays=e,this.trackNames=t}getMax(e,t){let i=-Number.MAX_VALUE;for(let n of this.featureArrays)if(Array.isArray(n))for(let r of n)if(!(void 0===r.value||Number.isNaN(r.value)||r.end<e)){if(r.start>t)break;i=Math.max(i,r.value)}return i!==-Number.MAX_VALUE?i:100}getMin(e,t){let i=0;for(let n of this.featureArrays)if(Array.isArray(n))for(let r of n)if(void 0!==r.value&&!Number.isNaN(r.value)){if(r.end<e)continue;if(r.start>t)break;i=Math.min(i,r.value)}return i}}const rf=e=>e?e.filter((e=>void 0!==e.dataRange||void 0!==e.autoscale||void 0!==e.autoscaleGroup)):[];class sf extends Ju{constructor(e,t){super(e,t,\"Overlay Tracks\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>Overlay Tracks</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"Overlay-Tracks\">\\n            <rect id=\"backdrop\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"layer-group\" transform=\"translate(3, 127)\">\\n                <rect id=\"a\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#A1A1A1\" x=\"12\" y=\"12\" width=\"332\" height=\"139\"></rect>\\n                <rect id=\"a---hold-out\" fill=\"#A1A1A1\" x=\"9\" y=\"25\" width=\"324\" height=\"115\"></rect>\\n                <rect id=\"b\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#C9C9C9\" x=\"81\" y=\"103\" width=\"474\" height=\"139\"></rect>\\n                <rect id=\"c\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#ECECEC\" x=\"238\" y=\"214\" width=\"372\" height=\"139\"></rect>\\n                <rect id=\"c---hold-out\" fill=\"#ECECEC\" x=\"250\" y=\"226\" width=\"372\" height=\"115\"></rect>\\n            </g>\\n            <rect id=\"over-border\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>Overlay Tracks Hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"Overlay-Tracks-Hover\">\\n            <rect id=\"backdrop-copy\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"layer-group\" transform=\"translate(3, 127)\">\\n                <rect id=\"a\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#A1A1A1\" x=\"12\" y=\"12\" width=\"332\" height=\"139\"></rect>\\n                <rect id=\"a---hold-out\" fill=\"#A1A1A1\" x=\"9\" y=\"25\" width=\"324\" height=\"115\"></rect>\\n                <rect id=\"b\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#C9C9C9\" x=\"81\" y=\"103\" width=\"474\" height=\"139\"></rect>\\n                <rect id=\"c\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#ECECEC\" x=\"238\" y=\"214\" width=\"372\" height=\"139\"></rect>\\n                <rect id=\"c---hold-out\" fill=\"#ECECEC\" x=\"250\" y=\"226\" width=\"372\" height=\"115\"></rect>\\n            </g>\\n            <rect id=\"over-border-copy\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>',!1),this.button.addEventListener(\"mouseenter\",(()=>this.setState(!0))),this.button.addEventListener(\"mouseleave\",(()=>this.setState(!1)));this.boundMouseClickHandler=(()=>{this.setVisibility(!1),of.call(this)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(!0)}}function of(e){if(!0===af(this.browser)){const e=this.browser.getSelectedTrackViews().map((({track:e})=>e));for(const t of e)t.selected=!1;const t=[];for(let i of e)\"merged\"===i.type?t.push(...i.tracks):t.push(i);const i={name:\"Overlay\",type:\"merged\",autoscale:!1,alpha:.5,height:Math.max(...e.map((({height:e})=>e))),order:Math.min(...e.map((({order:e})=>e)))},n=new tf(i,this.browser,t);for(const t of e){const e=this.browser.trackViews.indexOf(t.trackView);this.browser.trackViews.splice(e,1),t.trackView.dispose()}this.browser.addTrack(i,n),n.trackView.updateViews()}}function af(e){const t=e.getSelectedTrackViews();if(t&&t.length>1){const e=new Set([\"wig\",\"merged\"]);return t.filter((({track:t})=>e.has(t.type))).length>1}return!1}const cf=new Set([\"sequence\",\"ruler\",\"ideogram\"]),lf=new Set([\"ruler\",\"sequence\",\"ideogram\"]);class hf{constructor(e,t,i){this.namespace=`trackview-${s()}`,this.browser=e,this.track=i,i.trackView=this,this.addDOMToColumnContainer(e,t,e.referenceFrameList)}startSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].startSpinner()}stopSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].stopSpinner()}addDOMToColumnContainer(e,t,i){this.axis=this.createAxis(e,this.track),this.createViewports(e,t,i),this.sampleInfoViewport=new $u(this,e.columnContainer.querySelector(\".igv-sample-info-column\"),e.getSampleInfoViewportWidth()),this.sampleNameViewport=new Ku(this,e.columnContainer.querySelector(\".igv-sample-name-column\"),void 0,e.getSampleNameViewportWidth()),this.createTrackScrollbar(e),this.createTrackDragHandle(e),this.createTrackGearPopup(e)}createViewports(e,t,i){this.viewports=[];const n=e.calculateViewportWidth(i.length),r=t.querySelectorAll(\".igv-column\");for(let e=0;e<r.length;e++){const t=zu(this,r[e],i[e],n);this.viewports.push(t)}}createAxis(t,i){const n=e();if(this.axis=n,t.columnContainer.querySelector(\".igv-axis-column\").appendChild(n),n.dataset.tracktype=i.type,n.style.height=`${i.height}px`,\"function\"==typeof i.paintAxis){const{width:e,height:t}=n.getBoundingClientRect();this.axisCanvas=document.createElement(\"canvas\"),this.axisCanvas.style.width=`${e}px`,this.axisCanvas.style.height=`${t}px`,n.appendChild(this.axisCanvas)}if(!1===mo.has(this.track.type)){this.trackSelectionContainer=e(),n.appendChild(this.trackSelectionContainer);const t='<input type=\"checkbox\" name=\"track-select\">',i=document.createRange().createContextualFragment(t).firstChild;this.trackSelectionContainer.appendChild(i),i.checked=this.track.selected||!1,i.addEventListener(\"change\",(e=>{e.preventDefault(),e.stopPropagation(),this.track.selected=e.target.checked,this.setDragHandleSelectionState(e.target.checked),this.browser.overlayTrackButton.setVisibility(af(this.browser))})),this.enableTrackSelection(!1)}return n}resizeAxisCanvas(e,t){this.axis.style.width=`${e}px`,this.axis.style.height=`${t}px`,\"function\"==typeof this.track.paintAxis&&(this.axisCanvas.style.width=`${e}px`,this.axisCanvas.style.height=`${t}px`)}renderSVGContext(e,{deltaX:t,deltaY:i}){!function(e,t,i,n,r){if(\"function\"==typeof t.paintAxis){const{y:o,width:a,height:c}=i.getBoundingClientRect(),l=`${(t.name||t.id).replace(/\\W/g,\"\")}_axis_guid_${s()}`;e.saveWithTranslationAndClipRect(l,n,o+r,a,c,0),t.paintAxis(e,a,c),e.restore()}}(e,this.track,this.axisCanvas,t,i);const{width:n}=this.axis.getBoundingClientRect(),{y:r}=this.viewports[0].$viewport.get(0).getBoundingClientRect();let o={deltaX:n+t,deltaY:r+i};for(let t of this.viewports){t.renderSVGContext(e,o);const{width:i}=t.$viewport.get(0).getBoundingClientRect();o.deltaX+=i}if(!0===this.browser.sampleInfo.isInitialized()&&!0===this.browser.sampleInfoControl.showSampleInfo){this.sampleInfoViewport.renderSVGContext(e,o);const{width:t}=this.sampleInfoViewport.viewport.getBoundingClientRect();o.deltaX+=t}!0===this.browser.showSampleNames&&this.sampleNameViewport.renderSVGContext(e,o)}presentColorPicker(e){if(!1===lf.has(this.track.type)){const t=[],i=this.track.color||this.track.defaultColor;Mt(i)&&t.push(i),this.track.altColor&&Mt(this.track.altColor)&&t.push(this.track.altColor);let n=t.map((e=>e.startsWith(\"#\")?e:e.startsWith(\"rgb(\")?_s.rgbToHex(e):_s.colorNameToHex(e))),r={color:e=>{this.track.color=io(e),this.repaintViews()},altColor:e=>{this.track.altColor=io(e),this.repaintViews()}};const s=this.browser.getSelectedTrackViews();s.length>0&&new Set(s).has(this)?(r={color:e=>{for(let t of s)t.track.color=e,t.repaintViews()}},this.browser.genericColorPicker.configure(n,r)):this.browser.genericColorPicker.configure(n,r),this.browser.genericColorPicker.setActiveColorHandler(e),this.browser.genericColorPicker.show()}}setTrackHeight(e,t){t||(this.track.minHeight&&(e=Math.max(this.track.minHeight,e)),this.track.maxHeight&&(e=Math.min(this.track.maxHeight,e))),this.track.height=e,this.resizeAxisCanvas(this.axis.clientWidth,this.track.height),\"function\"==typeof this.track.paintAxis&&this.paintAxis();for(let{$viewport:t}of this.viewports)t.height(e);if(this.sampleInfoViewport.setHeight(e),this.sampleNameViewport.viewport.style.height=`${e}px`,\"function\"!=typeof this.track.computePixelHeight)for(let t of this.viewports)t.setContentHeight(e);this.repaintViews(),this.updateScrollbar(),this.dragHandle.style.height=`${e}px`,this.gearContainer.style.height=`${e}px`}updateScrollbar(){const e=this.viewports[0].$viewport.height();if(this.outerScroll.style.height=`${e}px`,!1===cf.has(this.track.type)){const t=this.maxViewportContentHeight(),i=Math.round(e/t*e);t>e?(this.innerScroll.style.display=\"block\",this.innerScroll.style.height=`${i}px`):this.innerScroll.style.display=\"none\"}}moveScroller(e){const t=Bt(this.innerScroll).position().top+e,i=Math.min(Math.max(0,t),this.outerScroll.clientHeight-this.innerScroll.clientHeight);Bt(this.innerScroll).css(\"top\",`${i}px`);const n=this.maxViewportContentHeight(),r=-Math.round(i*(n/this.viewports[0].$viewport.height()));for(let e of this.viewports)e.setTop(r);this.sampleInfoViewport.setTop(r),this.sampleNameViewport.trackScrollDelta=e,this.sampleNameViewport.setTop(r)}isLoading(){for(let e of this.viewports)if(e.isLoading())return!0}repaintViews(){for(let e of this.viewports)e.isVisible()&&e.repaint();\"function\"==typeof this.track.paintAxis&&this.paintAxis(),this.repaintSampleInfo(),this.repaintSamples()}repaintSampleInfo(){this.sampleInfoViewport.repaint()}repaintSamples(){if(\"function\"==typeof this.track.getSamples){const e=this.track.getSamples();e.names&&e.names.length>0&&this.sampleNameViewport.repaint(e)}}setTrackLabelName(e){this.viewports.forEach((t=>t.setTrackLabel(e)))}resize(e){for(let t of this.viewports)t.setWidth(e)}async updateViews(){if(!this.browser||!this.browser.referenceFrameList)return;const e=this.viewports.filter((e=>e.isVisible()));if(e.forEach((e=>e.shift())),this.browser.dragObject)return;const t=e.filter((e=>e.needsRepaint())).filter((e=>e.checkZoomIn())),i=e.filter((e=>e.checkZoomIn())).filter((e=>e.needsReload()));for(let e of i)await e.loadFeatures();if(this.disposed)return;if(this.track&&\"function\"==typeof this.track.variantRowCount&&i.length>0){let e=0;for(let t of this.viewports)t.featureCache&&t.featureCache.features&&(e=Math.max(e,t.featureCache.features.reduce(((e,t)=>Math.max(e,t.row||0)),0)));if(this.track.nVariantRows!==e+1){this.track.variantRowCount(e+1);for(let e of this.viewports)e.checkContentHeight()}}let n;if(\"merged\"===this.track.type)n=this.track.updateScales(e);else if(this.track.autoscale){let t=[];for(let i of e){const e=i.referenceFrame,n=e.start,r=n+e.toBP(i.getWidth());if(i.featureCache&&i.featureCache.features)if(\"function\"==typeof i.featureCache.features.getMax){const e=i.featureCache.features.getMax(n,r);if(t.push({value:e}),\"function\"==typeof i.featureCache.features.getMin){const e=i.featureCache.features.getMin(n,r);t.push({value:e})}}else{const e=to(i.featureCache.features,n,r);for(let i of e)t.push(i)}}\"function\"==typeof this.track.doAutoscale?this.track.dataRange=this.track.doAutoscale(t):this.track.dataRange=qa(t)}const r=this.track.autoscale||this.track.autoscaleGroup||\"ruler\"===this.track.type||n||this.track.groupBy;for(let i of e)t.includes(i)?i.repaint():r&&i.refresh();this.adjustTrackHeight(),this.repaintSampleInfo(),this.repaintSamples(),this.updateRulerViewportLabels()}clearCachedFeatures(){for(let e of this.viewports)e.clearCache()}updateRulerViewportLabels(){const e=this.browser.calculateViewportWidth(this.viewports.length);for(let t of this.viewports)\"ruler\"===this.track.type&&(this.viewports.length>1?t.presentLocusLabel(e):t.dismissLocusLabel())}async getInViewFeatures(){if(!this.browser||!this.browser.referenceFrameList)return[];let e=[];const t=this.viewports.filter((e=>e.isVisible()));for(let i of t){const t=i.referenceFrame,{chr:n,start:r,bpPerPixel:s}=i.referenceFrame,o=r+t.toBP(i.getWidth());if((!i.featureCache||!i.featureCache.containsRange(n,r,o,s))&&await i.loadFeatures(),i.featureCache&&i.featureCache.features)if(\"function\"==typeof i.featureCache.features.getMax){const t=i.featureCache.features.getMax(r,o);e.push({value:t})}else{const t=\"function\"==typeof i.featureCache.queryFeatures?i.featureCache.queryFeatures(n,r,o):to(i.featureCache.features,r,o);e=e.concat(t)}}return e}checkContentHeight(){for(let e of this.viewports)e.checkContentHeight();this.adjustTrackHeight()}adjustTrackHeight(){var e=this.maxViewportContentHeight();if(this.track.autoHeight?this.setTrackHeight(e,!1):this.track.paintAxis&&this.paintAxis(),!1===cf.has(this.track.type)){const t=this.viewports[0].getContentTop(),i=this.viewports[0].$viewport.height(),n=Math.min(0,i-e);if(t<n)for(let e of this.viewports)e.setTop(n);this.updateScrollbar()}}viewportsToReload(e){return this.viewports.filter((t=>{if(!t.isVisible())return!1;if(t.checkZoomIn()){const i=t.referenceFrame,n=t.referenceFrame.chr,r=i.start,s=r+i.toBP(Bt(t.contentDiv).width()),o=i.bpPerPixel;return e||!t.tile||t.tile.invalidate||!t.tile.containsRange(n,r,s,o)}return!1}))}createTrackScrollbar(t){const i=e();if(t.columnContainer.querySelector(\".igv-scrollbar-column\").appendChild(i),i.style.height=`${this.track.height}px`,this.outerScroll=i,!1===cf.has(this.track.type)){const n=e();i.appendChild(n),this.innerScroll=n,this.addTrackScrollMouseHandlers(t)}}createTrackDragHandle(t){\"sequence\"!==this.track.type&&!0===mo.has(this.track.type)?this.dragHandle=e({class:\"igv-track-drag-shim\"}):(this.dragHandle=e({class:\"igv-track-drag-handle\"}),this.dragHandle.classList.add(\"igv-track-drag-handle-color\")),t.columnContainer.querySelector(\".igv-track-drag-column\").appendChild(this.dragHandle),this.dragHandle.style.height=`${this.track.height}px`,this.addTrackDragMouseHandlers(t)}createTrackGearPopup(t){if(this.gearContainer=e(),t.columnContainer.querySelector(\".igv-gear-menu-column\").appendChild(this.gearContainer),this.gearContainer.style.height=`${this.track.height}px`,!0===this.track.ignoreTrackMenu);else{function i(e){if(e.preventDefault(),e.stopPropagation(),\"none\"===this.trackGearPopup.popover.style.display){for(const e of t.trackViews.filter((e=>e!==this&&void 0!==e.trackGearPopup)))e.trackGearPopup.popover.style.display=\"none\";this.trackGearPopup.presentMenuList(this,t.menuUtils.trackMenuItemList(this))}else this.trackGearPopup.popover.style.display=\"none\"}this.gear=e(),this.gearContainer.appendChild(this.gear),this.gear.appendChild(l(\"cog\")),this.trackGearPopup=new Xu(this.gear),this.boundTrackGearClickHandler=i.bind(this),this.gear.addEventListener(\"click\",this.boundTrackGearClickHandler)}}addTrackScrollMouseHandlers(e){this.boundTrackScrollMouseDownHandler=function(t){t.stopPropagation();const{y:i}=r(t);Bt(this.innerScroll).data(\"yDown\",i.toString()),this.boundColumnContainerMouseMoveHandler=function(e){e.stopPropagation();const{y:t}=r(e);this.moveScroller(t-parseInt(Bt(this.innerScroll).data(\"yDown\"))),Bt(this.innerScroll).data(\"yDown\",t.toString())}.bind(this),e.columnContainer.addEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler)}.bind(this),this.innerScroll.addEventListener(\"mousedown\",this.boundTrackScrollMouseDownHandler),this.boundColumnContainerMouseUpHandler=function(t){e.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler)}.bind(this),e.columnContainer.addEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),e.columnContainer.addEventListener(\"mouseleave\",this.boundColumnContainerMouseUpHandler)}removeTrackScrollMouseHandlers(){!1===cf.has(this.track.type)&&(this.innerScroll.removeEventListener(\"mousedown\",this.boundTrackScrollMouseDownHandler),this.browser.columnContainer.removeEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.browser.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.browser.columnContainer.removeEventListener(\"mouseleave\",this.boundColumnContainerMouseMoveHandler))}addTrackDragMouseHandlers(e){if(\"sequence\"===this.track.type||!1===mo.has(this.track.type)){let t;function i(i){i.preventDefault(),t=i.target,!1===this.track.selected&&(t.classList.remove(\"igv-track-drag-handle-color\"),t.classList.add(\"igv-track-drag-handle-hover-color\")),e.startTrackDrag(this)}function n(i){e.endTrackDrag(),t&&i.target!==t&&!1===this.track.selected&&(t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.add(\"igv-track-drag-handle-color\")),t=void 0}function r(i){i.preventDefault(),void 0===t&&!1===this.track.selected&&(i.target.classList.remove(\"igv-track-drag-handle-color\"),i.target.classList.add(\"igv-track-drag-handle-hover-color\")),e.updateTrackDrag(this)}function s(e){e.preventDefault(),void 0===t&&!1===this.track.selected&&(e.target.classList.remove(\"igv-track-drag-handle-hover-color\"),e.target.classList.add(\"igv-track-drag-handle-color\"))}this.boundTrackDragMouseDownHandler=i.bind(this),this.dragHandle.addEventListener(\"mousedown\",this.boundTrackDragMouseDownHandler),this.boundDocumentTrackDragMouseUpHandler=n.bind(this),document.addEventListener(\"mouseup\",this.boundDocumentTrackDragMouseUpHandler),this.boundTrackDragMouseEnterHandler=r.bind(this),this.dragHandle.addEventListener(\"mouseenter\",this.boundTrackDragMouseEnterHandler),this.dragHandle.addEventListener(\"mouseout\",(e=>{e.preventDefault(),void 0===t&&!1===this.track.selected&&(e.target.classList.remove(\"igv-track-drag-handle-hover-color\"),e.target.classList.add(\"igv-track-drag-handle-color\"))})),this.boundTrackDragMouseOutHandler=s.bind(this),this.dragHandle.addEventListener(\"mouseout\",this.boundTrackDragMouseOutHandler)}}removeTrackDragMouseHandlers(){\"ideogram\"===this.track.type||\"ruler\"===this.track.type||(this.dragHandle.removeEventListener(\"mousedown\",this.boundTrackDragMouseDownHandler),document.removeEventListener(\"mouseup\",this.boundDocumentTrackDragMouseUpHandler),this.dragHandle.removeEventListener(\"mouseup\",this.boundTrackDragMouseEnterHandler),this.dragHandle.removeEventListener(\"mouseout\",this.boundTrackDragMouseOutHandler))}removeTrackGearMouseHandlers(){!0===this.track.ignoreTrackMenu||this.gear.removeEventListener(\"click\",this.boundTrackGearClickHandler)}removeDOMFromColumnContainer(){this.axis.remove(),this.removeViewportsFromColumnContainer(),this.sampleInfoViewport.dispose(),this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove()}removeViewportsFromColumnContainer(){for(let e of this.viewports)e.$viewport.remove()}dispose(){this.axis.remove();for(let e of this.viewports)e.dispose();this.sampleInfoViewport.dispose(),this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove(),\"function\"==typeof this.track.dispose&&this.track.dispose();for(let e of Object.keys(this))this[e]=void 0;this.alert&&this.alert.container.remove(),this.disposed=!0}paintAxis(){if(\"function\"==typeof this.track.paintAxis){const{width:e,height:t}=this.axisCanvas.getBoundingClientRect(),i=window.devicePixelRatio||1;this.axisCanvas.height=i*t,this.axisCanvas.width=i*e;const n=this.axisCanvas.getContext(\"2d\");if(n.scale(i,i),this.track.autoscaleGroup){if(void 0===wo[this.track.autoscaleGroup]){const e=so.Dark2,t=Math.floor(Math.random()*so.Dark2.length);wo[this.track.autoscaleGroup]=e[t]}const i=_s.addAlpha(wo[this.track.autoscaleGroup],.75);this.track.paintAxis(n,e,t,i)}else this.track.paintAxis(n,e,t,void 0)}}maxViewportContentHeight(){return Math.max(...this.viewports.map((e=>e.getContentHeight())))}enableTrackSelection(e){const t=this.trackSelectionContainer;if(t&&!mo.has(this.track.type))if(!1!==e)t.style.display=\"grid\";else{this.track.selected=!1;t.querySelector(\"[name=track-select]\").checked=this.track.selected,this.dragHandle&&this.setDragHandleSelectionState(!1),t.style.display=\"none\"}}setDragHandleSelectionState(e){const t=this.dragHandle;e?(t.classList.remove(\"igv-track-drag-handle-color\"),t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.add(\"igv-track-drag-handle-selected-color\")):(t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.remove(\"igv-track-drag-handle-selected-color\"),t.classList.add(\"igv-track-drag-handle-color\"))}}function df(e){this.thresholds=e.thresholds,this.colors=e.colors}function uf(e){this.scale=e,this.lowColor=\"rgb(\"+e.lowR+\",\"+e.lowG+\",\"+e.lowB+\")\",this.highColor=\"rgb(\"+e.highR+\",\"+e.highG+\",\"+e.highB+\")\",this.diff=e.high-e.low}df.prototype.getColor=function(e){for(let t of this.thresholds)if(e<t)return this.colors[this.thresholds.indexOf(t)];return this.colors[this.colors.length-1]},uf.prototype.getColor=function(e){var t,i=this.scale;return e<=i.low?this.lowColor:e>=i.high?this.highColor:(t=(e-i.low)/this.diff,\"rgb(\"+Math.floor(i.lowR+t*(i.highR-i.lowR))+\",\"+Math.floor(i.lowG+t*(i.highG-i.lowG))+\",\"+Math.floor(i.lowB+t*(i.highB-i.lowB))+\")\")};class ff{constructor(e){this.color=e}getColor(){return this.color}}const pf={threshold:2e3,r:0,g:0,b:255};class gf{constructor(e){e=e||pf,this.threshold=e.threshold,this.r=e.r,this.g=e.g,this.b=e.b,this.cache=[],this.nbins=2e3,this.binsize=this.threshold/this.nbins}setThreshold(e){this.threshold=e,this.cache=[],this.binsize=this.threshold/this.nbins}getThreshold(){return this.threshold}setColorComponents(e){this.r=e.r,this.g=e.g,this.b=e.b,this.cache=[]}getColorComponents(){return{r:this.r,g:this.g,b:this.b}}equals(e){return JSON.stringify(this)===JSON.stringify(e)}getColor(e){const t=Math.floor(Math.min(this.threshold,e)/this.binsize);if(void 0===this.cache[t]){const i=(ys.clamp(e,0,this.threshold)-0)/(this.threshold-0);this.cache[t]=`rgba(${this.r},${this.g},${this.b}, ${i})`}return this.cache[t]}stringify(){return this.threshold+\",\"+this.r+\",\"+this.g+\",\"+this.b}static parse(e){var t,i;return e.startsWith(\"R:\")?(t=e.substring(2).split(\":\"),(i=new RatioColorScale(Number.parseFloat(t[0]))).positiveScale=n(t[1]),i.negativeScale=n(t[2]),i):n(e);function n(e){var t,i;return t={threshold:(i=e.split(\",\"))[0],r:i[1],g:i[2],b:i[3]},new gf(t)}}}class mf{constructor(e){this.config=e,this.url=e.path||e.url}async read(e,t){const i={start:e,size:t};return Qs.loadArrayBuffer(this.url,{range:i})}}class wf{constructor(e){this.file=e}async read(e,t){const i=this.file;return void 0!==e?i.slice(e,e+t).arrayBuffer():i.arrayBuffer()}}class bf{constructor(e,t){this.file=e,this.rateLimiter=t}async read(e,t){const i=this.file,n=this.rateLimiter;return new Promise((function(r,s){n.limiter((async function(i){try{const n=await i.read(e,t);r(n)}catch(e){s(e)}}))(i)}))}}class Ff{constructor(e){this.file=e.file,this.size=e.size||64e3,this.position=0,this.bufferStart=0,this.bufferLength=0,this.buffer=void 0}async read(e,t){const i=e,n=e+t,r=this.bufferStart,s=this.bufferStart+this.bufferLength;if(t>this.size)return this.buffer=void 0,this.bufferStart=0,this.bufferLength=0,this.file.read(e,t);if(i>=r&&n<=s){const e=i-r,n=e+t;return this.buffer.slice(e,n)}if(i<r&&n>r){const n=r-i,s=await this.file.read(e,n),o=t-n;if(o>0){const e=this.buffer.slice(0,o);return vf(s,e)}return s}if(!(i<s&&n>s))return this.buffer=await this.file.read(e,this.size),this.bufferStart=e,this.bufferLength=this.buffer.byteLength,this.buffer.slice(0,t);{const e=s-i,n=this.bufferLength-e,r=this.buffer.slice(n,this.bufferLength),o=t-e;if(!(o>0))return r;try{this.buffer=await this.file.read(s,this.size),this.bufferStart=s,this.bufferLength=this.buffer.byteLength;const e=this.buffer.slice(0,o);return vf(r,e)}catch(e){if(e.code&&416===e.code)return r;throw e}}}}var vf=function(e,t){var i=new Uint8Array(e.byteLength+t.byteLength);return i.set(new Uint8Array(e),0),i.set(new Uint8Array(t),e.byteLength),i.buffer};const yf=function(e,t){this.littleEndian=void 0===t||t,this.position=0,this.view=e,this.length=e.byteLength};function Af(e,t){this.block=e,this.offset=t}yf.prototype.available=function(){return this.length-this.position},yf.prototype.remLength=function(){return this.length-this.position},yf.prototype.hasNext=function(){return this.position<this.length-1},yf.prototype.getByte=function(){var e=this.view.getUint8(this.position,this.littleEndian);return this.position++,e},yf.prototype.getShort=function(){var e=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,e},yf.prototype.getUShort=function(){var e=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,e},yf.prototype.getInt=function(){var e=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getUInt=function(){var e=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getLong=function(){var e=[];e[0]=this.view.getUint8(this.position),e[1]=this.view.getUint8(this.position+1),e[2]=this.view.getUint8(this.position+2),e[3]=this.view.getUint8(this.position+3),e[4]=this.view.getUint8(this.position+4),e[5]=this.view.getUint8(this.position+5),e[6]=this.view.getUint8(this.position+6),e[7]=this.view.getUint8(this.position+7);var t=0;if(this.littleEndian)for(var i=e.length-1;i>=0;i--)t=256*t+e[i];else for(i=0;i<e.length;i++)t=256*t+e[i];return this.position+=8,t},yf.prototype.getString=function(e){for(var t,i=\"\";0!=(t=this.view.getUint8(this.position++))&&(i+=String.fromCharCode(t),!e||i.length!=e););return i},yf.prototype.getFixedLengthString=function(e){var t,i,n=\"\";for(t=0;t<e;t++)(i=this.view.getUint8(this.position++))>0&&(n+=String.fromCharCode(i));return n},yf.prototype.getFixedLengthTrimmedString=function(e){var t,i,n=\"\";for(t=0;t<e;t++)(i=this.view.getUint8(this.position++))>32&&(n+=String.fromCharCode(i));return n},yf.prototype.getFloat=function(){var e=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getDouble=function(){var e=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,e},yf.prototype.skip=function(e){return this.position+=e,this.position},yf.prototype.getVPointer=function(){var e=this.position,t=this.view.getUint8(e+1)<<8|this.view.getUint8(e),i=4294967296*(255&this.view.getUint8(e+6))+16777216*(255&this.view.getUint8(e+5))+65536*(255&this.view.getUint8(e+4))+256*(255&this.view.getUint8(e+3))+(255&this.view.getUint8(e+2));return this.position+=8,new Af(i,t)},Af.prototype.isLessThan=function(e){return this.block<e.block||this.block===e.block&&this.offset<e.offset},Af.prototype.isGreaterThan=function(e){return this.block>e.block||this.block===e.block&&this.offset>e.offset},Af.prototype.print=function(){return this.block+\":\"+this.offset};class Cf{constructor(e,t){this.chr1=e,this.chr2=t}getKey(){return this.chr1.name+\"_\"+this.chr2.name+\"_\"+this.zoom.unit+\"_\"+this.zoom.binSize}getBlockNumbers(e,t,i){if(e.chr==this.chr2&&t.chr===this.chr1){const i=e;e=t,t=i}const n=this.chr1===this.chr2,r=this.zoom.binSize,s=this.blockBinCount,o=this.blockColumnCount;return i<9||!n?function(){const i=e.start/r,a=e.end/r,c=t.start/r,l=t.end/r,h=Math.floor(i/s),d=Math.floor((a-1)/s),u=Math.floor(c/s),f=Math.floor((l-1)/s),p=[];for(let e=u;e<=f;e++)for(let t=h;t<=d;t++){let i;i=n&&e<t?t*o+e:e*o+t,p.includes(i)||p.push(i)}return p}():function(){const i=e.start/r,n=e.end/r,a=t.start/r,c=t.end/r,l=Math.floor((i+a)/2/s),h=Math.floor((n+c)/2/s),d=Math.floor(Math.log2(1+Math.abs(i-c)/Math.sqrt(2)/s)),u=Math.floor(Math.log2(1+Math.abs(n-a)/Math.sqrt(2)/s)),f=(n-a)*(i-c)<0?0:Math.min(d,u),p=Math.max(d,u),g=[];for(let e=f;e<=p;e++)for(let t=l;t<=h;t++){const i=e*o+t;g.push(i)}return g}()}static parseMatrixZoomData(e,t,i){const n=new Cf(e,t),r=i.getString(),s=i.getInt(),o=i.getFloat(),a=i.getFloat(),c=i.getFloat(),l=i.getFloat(),h=i.getInt();n.blockBinCount=i.getInt(),n.blockColumnCount=i.getInt();const d=i.getInt();n.zoom={index:s,unit:r,binSize:h},n.blockIndex=new _f(d,i);const u=o/(e.size/h)/(t.size/h);return n.averageCount=u,n.sumCounts=o,n.stdDev=c,n.occupiedCellCount=a,n.percent95=l,n}}class _f{constructor(e,t){for(this.blockIndex={};e-- >0;){const e=t.getInt(),i=t.getLong(),n=t.getInt();this.blockIndex[e]={filePosition:i,size:n}}}getBlockIndexEntry(e){return this.blockIndex[e]}}class xf{constructor(e,t,i){this.chr1=e,this.chr2=t,this.bpZoomData=[],this.fragZoomData=[];for(let e of i)\"BP\"===e.zoom.unit?this.bpZoomData.push(e):this.fragZoomData.push(e)}findZoomForResolution(e,t){const i=\"FRAG\"===t?this.fragZoomData:this.bpZoomData;for(let t=1;t<i.length;t++){if(i[t].zoom.binSize<e)return t-1}return i.length-1}getZoomData(e,t){const i=\"BP\"===(t=t||\"BP\")?this.bpZoomData:this.fragZoomData;for(let t=0;t<i.length;t++){var n=i[t];if(e===n.zoom.binSize)return n}}getZoomDataByIndex(e,t){return(\"FRAG\"===t?this.fragZoomData:this.bpZoomData)[e]}static getKey(e,t){if(e>t){const i=e;e=t,t=i}return`${e}_${t}`}static parseMatrix(e,t){const i=new yf(new DataView(e)),n=i.getInt(),r=i.getInt(),s=t[n],o=t[r];let a=i.getInt();const c=[];for(;a-- >0;){const e=Cf.parseMatrixZoomData(s,o,i);c.push(e)}return new xf(n,r,c)}}class kf{constructor(e,t,i){this.bin1=e,this.bin2=t,this.counts=i}getKey(){return this.bin1+\"_\"+this.bin2}}class If{constructor(e=10){this.max=e,this.map=new Map}get(e){let t=this.map.get(e);return t&&(this.map.delete(e),this.map.set(e,t)),t}set(e,t){this.map.has(e)?this.map.delete(e):this.map.size===this.max&&this.map.delete(this.first()),this.map.set(e,t)}has(e){return this.map.has(e)}clear(){this.map.clear()}first(){return this.map.keys().next().value}}class Sf{constructor(e,t,i,n){this.file=e,this.filePosition=t,this.nValues=i,this.dataType=n,this.cache=void 0}async getValues(e,t){if(!this.cache||e<this.cache.start||t>this.cache.end){const i=Math.max(0,e-1e3),n=Math.min(this.nValues,t+1e3),r=this.filePosition+i*this.dataType,s=n-i,o=s*this.dataType,a=await this.file.read(r,o);if(!a)return;const c=new yf(new DataView(a)),l=[];for(let e=0;e<s;e++)l[e]=8===this.dataType?c.getDouble():c.getFloat();this.cache={start:i,end:n,values:l}}const i=e-this.cache.start,n=i+(t-e);return this.cache.values.slice(i,n)}getKey(){return Sf.getKey(this.type,this.chrIdx,this.unit,this.resolution)}static getNormalizationVectorKey(e,t,i,n){return e+\"_\"+t+\"_\"+i+\"_\"+n}}var 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mf(e);(t=this.url).indexOf(\"drive.google.com\")>=0||t.indexOf(\"www.googleapis.com/drive\")>0?this.file=new bf(i,Bf):this.file=i}}var t}async init(){this.initialized||(await this.readHeaderAndFooter(),this.initialized=!0)}async getVersion(){if(void 0===this.version){const e=await this.file.read(0,128);if(!e)return;const t=new yf(new DataView(e));return this.magic=t.getString(),this.version=t.getInt(),this.version}return this.version}async getMetaData(){return await this.init(),this.meta}async readHeaderAndFooter(){let e=await this.file.read(0,16);if(!e||0===e.byteLength)throw Error(\"File content is empty\");let t=new yf(new DataView(e));if(this.magic=t.getString(),this.version=t.getInt(),this.version<5)throw Error(\"Unsupported hic version: \"+this.version);this.footerPosition=t.getLong(),await this.readFooter();const i=Object.values(this.masterIndex).reduce(((e,t)=>Math.min(e,t.start)),Number.MAX_VALUE)-16;e=await this.file.read(16,i),t=new yf(new DataView(e)),this.genomeId=t.getString(),this.version>=9&&(this.normVectorIndexPosition=t.getLong(),this.normVectorIndexSize=t.getLong()),this.attributes={};let n=t.getInt();for(;n-- >0;)this.attributes[t.getString()]=t.getString();this.chromosomes=[],this.chromosomeIndexMap={};let r=t.getInt(),s=0;for(;r-- >0;){const e={index:s,name:t.getString(),size:this.version<9?t.getInt():t.getLong()};\"all\"===e.name.toLowerCase()&&(this.wholeGenomeChromosome=e,this.wholeGenomeResolution=Math.round(2*e.size)),this.chromosomes.push(e),this.chromosomeIndexMap[e.name]=e.index,s++}this.bpResolutions=[];let o=t.getInt();for(;o-- >0;)this.bpResolutions.push(t.getInt());if(this.loadFragData){this.fragResolutions=[];let e=t.getInt();if(e>0)for(;e-- >0;)this.fragResolutions.push(t.getInt())}this.chrAliasTable={};for(let e of Object.keys(this.chromosomeIndexMap))e.startsWith(\"chr\")?this.chrAliasTable[e.substr(3)]=e:\"MT\"===e?this.chrAliasTable.chrM=e:this.chrAliasTable[\"chr\"+e]=e;this.meta={version:this.version,genome:this.genomeId,chromosomes:this.chromosomes,resolutions:this.bpResolutions}}async readFooter(){const e=this.version<9?8:12;let t=await this.file.read(this.footerPosition,e);if(!t)return null;let i=new yf(new DataView(t));const n=this.version<9?i.getInt():i.getLong();let r=i.getInt();const s=196*r;for(t=await this.file.read(this.footerPosition+e,Math.min(s,n)),i=new yf(new DataView(t)),this.masterIndex={};r-- >0;){const e=i.getString(),t=i.getLong(),n=i.getInt();this.masterIndex[e]={start:t,size:n}}if(this.expectedValueVectors={},this.version>5){const e=this.version<9?4:8;this.normExpectedValueVectorsPosition=this.footerPosition+e+n}return this}async printIndexStats(){let e,t=0,i=0;await await this.init();for(let n of Object.keys(this.masterIndex)){const r=this.masterIndex[n];t+=r.size,r.size>i&&(i=r.size,e=n)}console.log(`${i}  ${e}  ${this.config.url}`)}async getMatrix(e,t){const i=xf.getKey(e,t);if(this.matrixCache.has(i))return this.matrixCache.get(i);{const n=await this.readMatrix(e,t);return this.matrixCache.set(i,n),n}}async readMatrix(e,t){if(await this.init(),e>t){const i=e;e=t,t=i}const i=xf.getKey(e,t),n=this.masterIndex[i];if(!n)return;const r=await this.file.read(n.start,n.size);return r?xf.parseMatrix(r,this.chromosomes):void 0}async getContactRecords(e,t,i,n,r,s=!1){await this.init();const o=this.chromosomeIndexMap[this.getFileChrName(t.chr)],a=this.chromosomeIndexMap[this.getFileChrName(i.chr)];if(o>a||o===a&&t.start>=i.end){const e=t;t=i,i=e}const c=await this.getBlocks(t,i,n,r);if(!c||0===c.length)return[];const l=[],h=t.start/r,d=t.end/r,u=i.start/r,f=i.end/r,p=Math.floor(h),g=Math.ceil(d),m=Math.floor(u),w=Math.ceil(f);for(let o of c)if(o){let a,c,b=e&&\"NONE\"!==e;const F=this.getFileChrName(t.chr),v=this.getFileChrName(i.chr);if(b){const t=await this.getNormalizationVector(e,F,n,r),i=F===v?t:await this.getNormalizationVector(e,v,n,r);t&&i?(a=await t.getValues(p,g),c=await i.getValues(m,w)):b=!1}for(let e of o.records)if(s||e.bin1>=h&&e.bin1<d&&e.bin2>=u&&e.bin2<f)if(b){const t=e.bin1,i=e.bin2,n=a[t-p]*c[i-m];if(0!==n&&!isNaN(n)){const r=e.counts/n;l.push(new kf(t,i,r))}}else l.push(e);void 0===this.percentile95&&o.records.length>10&&(this.percentile95=Lf(o.records,95))}return l}async getBlocks(e,t,i,n){const r=(e,t)=>`${t.getKey()}_${e}`;await this.init();const s=this.getFileChrName(e.chr),o=this.getFileChrName(t.chr),a=this.chromosomeIndexMap[s],c=this.chromosomeIndexMap[o];if(void 0===a)return console.log(\"No chromosome named: \"+e.chr),[];if(void 0===c)return console.log(\"No chromosome named: \"+t.chr),[];const l=await this.getMatrix(a,c);if(!l)return console.log(\"No matrix for \"+e.chr+\"-\"+t.chr),[];const h=l.getZoomData(n,i);if(!h){let i=`No data avalailble for resolution: ${n}  for map ${e.chr}-${t.chr}`;throw new Error(i)}const d=h.getBlockNumbers(e,t,this.version),u=[],f=[];for(let e of d){const t=r(e,h);this.blockCache.has(n,t)?u.push(this.blockCache.get(n,t)):f.push(e)}const p=f.map((e=>this.readBlock(e,h))),g=await Promise.all(p);for(let e of g)e&&this.blockCache.set(n,r(e.blockNumber,h),e);return u.concat(g)}async readBlock(e,t){const i=await t.blockIndex.getBlockIndexEntry(e);if(i){let n=await this.file.read(i.filePosition,i.size);if(!n)return;n=new ls(new Uint8Array(n)).buffer;const r=new yf(new DataView(n)),s=r.getInt(),o=[];if(this.version<7)for(let e=0;e<s;e++){const e=r.getInt(),t=r.getInt(),i=r.getFloat();o.push(new kf(e,t,i))}else{const e=r.getInt(),t=r.getInt(),i=1===r.getByte(),n=!(this.version<9)&&1==r.getByte(),s=!(this.version<9)&&1==r.getByte(),a=r.getByte();if(1===a){const a=s?r.getInt():r.getShort();for(let c=0;c<a;c++){const a=t+(s?r.getInt():r.getShort()),c=n?r.getInt():r.getShort();for(let t=0;t<c;t++){const t=e+(n?r.getInt():r.getShort()),s=i?r.getFloat():r.getShort();o.push(new kf(t,a,s))}}}else{if(2!=a)throw new Error(\"Unknown block type: \"+a);{const n=r.getInt(),s=r.getShort();for(let a=0;a<n;a++){const n=Math.floor(a/s),c=e+(a-n*s),l=t+n;if(i){const e=r.getFloat();isNaN(e)||o.push(new kf(c,l,e))}else{const e=r.getShort();-32768!=e&&o.push(new kf(c,l,e))}}}}}return new Df(e,t,o,i)}}async hasNormalizationVector(e,t,i,n){let r;if(await this.init(),Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}const s=Rf(e,r,i.toString(),n),o=await this.getNormVectorIndex();return o&&o[s]}async isNormalizationValueAvailableAtResolution(e,t,i,n){let r;if(Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}return void 0!==(await this.getNormVectorIndex())[Rf(e,r,i.toString(),n)]}async getNormalizationVector(e,t,i,n){let r;if(await this.init(),Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}const s=Rf(e,r,i.toString(),n);if(this.normVectorCache.has(s))return this.normVectorCache.get(s);const o=await this.getNormVectorIndex();if(!o)return void console.log(\"Normalization vectors not present in this file\");if(!1===await this.isNormalizationValueAvailableAtResolution(e,t,i,n)){const t=`Normalization option ${e} not available at resolution ${n}. Will use NONE.`;return console.log(t),void(this.alert&&this.alert(t))}const a=o[s],c=await this.file.read(a.filePosition,8);if(!c)return;const l=new yf(new DataView(c)),h=this.version<9?l.getInt():l.getLong(),d=this.version<9?8:4,u=this.version<9?a.filePosition+4:a.filePosition+8,f=new Sf(this.file,u,h,d);return this.normVectorCache.set(s,f),f}async getNormVectorIndex(){if(!(this.version<6)){if(!this.normVectorIndex){if(!this.config.nvi&&this.remote&&this.url){const e=new URL(this.url),t=encodeURIComponent(e.hostname+e.pathname);Ef.hasOwnProperty(t)&&(this.config.nvi=Ef[t])}if(this.config.nvi){const e=decodeURIComponent(this.config.nvi).split(\",\"),t={start:parseInt(e[0]),size:parseInt(e[1])};return this.readNormVectorIndex(t)}try{return await this.readNormExpectedValuesAndNormVectorIndex(),this.normVectorIndex}catch(e){\"416\"===e.code||416===e.code?this.normExpectedValueVectorsPosition=void 0:console.error(e)}}return this.normVectorIndex}}async getNormalizationOptions(){return await this.getNormVectorIndex(),this.normalizationTypes}async readNormVectorIndex(e){await this.init(),this.normalizationVectorIndexRange=e;const t=await this.file.read(e.start,e.size),i=new yf(new DataView(t));this.normVectorIndex={};let n=i.getInt();for(;n-- >0;)this.parseNormVectorEntry(i);return this.normVectorIndex}async readNormExpectedValuesAndNormVectorIndex(){if(await this.init(),void 0===this.normExpectedValueVectorsPosition)return;const e=await this.skipExpectedValues(this.normExpectedValueVectorsPosition);let t=4,i=await this.file.read(e,4);if(0===i.byteLength)return;const n=new yf(new DataView(i)).getInt(),r={start:e+t,size:30*n};i=await this.file.read(r.start,r.size),this.normalizedExpectedValueVectors={},this.normVectorIndex={},await async function i(n,r){const s=new yf(new DataView(r));for(;n-- >0;){if(s.available()<100){n++,t+=s.position;const r=Math.max(1e3,30*n),o={start:e+t,size:r},a=await this.file.read(o.start,o.size);return i.call(this,n,a)}this.parseNormVectorEntry(s)}t+=s.position}.call(this,n,i),this.config.nvi=e.toString()+\",\"+t}async skipExpectedValues(e){const t=this.version,i=new Ff({file:this.file,size:256e3}),n={start:e,size:4},r=await i.read(n.start,n.size),s=new yf(new DataView(r)).getInt();return 0===s?e+4:async function e(n,r){let s={start:n,size:500},o=0,a=n,c=await i.read(s.start,s.size),l=new yf(new DataView(c));l.getString(),l.getString(),l.getInt();const h=t<9?l.getInt():l.getLong();o+=l.position+h*(t<9?8:4),s={start:n+o,size:4},c=await i.read(s.start,s.size),l=new yf(new DataView(c));const d=l.getInt();return o+=4+d*(4+(t<9?8:4)),r--,0===r?a+o:e(a+o,r)}(e+4,s)}getZoomIndexForBinSize(e,t){let i;if(\"BP\"===(t=t||\"BP\"))i=this.bpResolutions;else{if(\"FRAG\"!==t)throw new Error(\"Invalid unit: \"+t);i=this.fragResolutions}for(let t=0;t<i.length;t++)if(i[t]===e)return t;return-1}parseNormVectorEntry(e){const t=e.getString(),i=e.getInt(),n=e.getString(),r=e.getInt(),s=e.getLong(),o=this.version<9?e.getInt():e.getLong(),a=t+\"_\"+i+\"_\"+n+\"_\"+r;this.normalizationTypes.includes(t)||this.normalizationTypes.push(t),this.normVectorIndex[a]={filePosition:s,size:o}}getFileChrName(e){return this.chrAliasTable.hasOwnProperty(e)?this.chrAliasTable[e]:e}}function Rf(e,t,i,n){return e+\"_\"+t+\"_\"+i+\"_\"+n}class Df{constructor(e,t,i,n){this.blockNumber=e,this.zoomData=t,this.records=i,this.idx=n}}class Tf{constructor(){this.resolution=void 0,this.map=new If(6)}set(e,t,i){this.resolution!==e&&this.map.clear(),this.resolution=e,this.map.set(t,i)}get(e,t){return this.resolution===e?this.map.get(t):void 0}has(e,t){return this.resolution===e&&this.map.has(t)}}function Lf(e,t){const i=e.map((e=>e.counts));i.sort((function(e,t){return e-t}));return i[Math.floor(t/100*e.length)]}class zf{constructor(e,t){this.config=e,this.genome=t,this.hicFile=e._hicFile?e._hicFile:new Mf(e),e._hicFile=void 0}async getHeader(){return await this.hicFile.init(),this.hicFile}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){this.hicFile.initialized||await this.hicFile.init();const s=this.hicFile.bpResolutions,o=s[s.length-1];return(await this.hicFile.getContactRecords(void 0,{chr:e,start:t,end:i},{chr:\"celltype\",start:0,end:1e8},\"BP\",o)).map((t=>{const i=t.bin1*o;return{chr:e,start:i,end:i+o,value:t.counts,sample:t.bin2.toString()}}))}supportsWholeGenome(){return!1}}function Hf(e,t){const i=new Set(e.attributeNames),n=t[0];if(void 0===e.getAttributes(n))return!1;{const t=Object.keys(e.getAttributes(n));for(const e of t)if(!1===i.has(e))return!1}return!0}class Pf extends Hl{#y=new Map;constructor(e,t){super(e,t)}init(e){if(super.init(e),this.type=e.type||\"seg\",\"maf\"===this.type&&(this.type=\"mut\"),this.isLog=e.isLog,this.displayMode=e.displayMode||\"EXPANDED\",this.height=e.height||300,this.maxHeight=e.maxHeight||500,this.squishedRowHeight=e.sampleSquishHeight||e.squishedRowHeight||2,this.expandedRowHeight=e.sampleExpandHeight||e.expandedRowHeight||13,this.sampleHeight=this.squishedRowHeight,this.sampleKeys=[],e.samples){for(let t of e.samples)this.sampleKeys.push(t);this.explicitSamples=!0}if(e.color)this.color=e.color;else if(e.colorTable)this.colorTable=new ao(e.colorTable);else switch(this.type){case\"mut\":this.colorTable=new ao(qf);break;case\"shoebox\":e.colorScale&&(this.sbColorScale=gf.parse(e.colorScale));break;default:this.posColorScale=new uf(e.posColorScale||Of),this.negColorScale=new uf(e.negColorScale||Uf)}const t=Object.assign({},this.config);t.maxWGCount=t.maxWGCount||Number.MAX_SAFE_INTEGER,\"shoebox\"===this.type?(this.featureSource=new zf(t,this.browser.genome),this.height=e.height||500,this.maxHeight=e.maxHeight||800,this.isLog=!1,this.squishedRowHeight=e.squishedRowHeight||1,this.displayMode=e.displayMode||\"SQUISHED\",this.visibilityWindow=void 0===e.visibilityWindow?1e6:e.visibilityWindow):this.featureSource=Ad(t,this.browser.genome),this.initialSort=e.sort}async postInit(){\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader(),this.disposed)||this.header&&this.setTrackProperties(this.header)}menuItemList(){const e=[];if(!0===Hf(this.browser.sampleInfo,this.sampleKeys)){e.push(\"<hr/>\"),e.push(\"Sort by attribute:\");for(const n of this.browser.sampleInfo.attributeNames){if(this.sampleKeys.some((e=>{const t=this.browser.sampleInfo.getAttributes(e);return t&&t[n]}))){const r=Bt(\"<div>\");function s(){const e=this.#y.get(n)||1;this.sortByAttribute(n,e),this.#y.set(n,-1*e),this.config.sort={option:\"ATTRIBUTE\",attribute:n,direction:1===e?\"ASC\":\"DESC\"}}r.html(`&nbsp;&nbsp;${n.split(Uu.emptySpaceReplacement).join(\" \")}`),e.push({object:r,click:s})}}}const t={SQUISHED:\"Squish\",EXPANDED:\"Expand\",FILL:\"Fill\"};if(\"shoebox\"===this.type&&this.sbColorScale){function o(e){this.browser.inputDialog.present({label:\"Color Scale Threshold\",value:this.sbColorScale.threshold,callback:()=>{const e=Number(this.browser.inputDialog.value,10);e&&(this.sbColorScale.setThreshold(e),this.trackView.repaintViews())}},e)}e.push(\"<hr/>\"),e.push({object:Bt(\"<div>Set color scale threshold</div>\"),dialog:o})}e.push(\"<hr/>\"),e.push(\"DisplayMode:\");const i=\"seg\"===this.type||\"shoebox\"===this.type?[\"SQUISHED\",\"EXPANDED\",\"FILL\"]:[\"SQUISHED\",\"EXPANDED\"];for(let a of i){const c=Dl(t[a],a===this.displayMode);e.push({object:Bt(c),click:function(){this.displayMode=a,this.config.displayMode=a,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)}})}return e}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys,height:this.sampleHeight,yOffset:0}}async getFeatures(e,t,i){const n=await this.featureSource.getFeatures({chr:e,start:t,end:i});if(this.updateSampleKeys(n),this.initialSort){const e=this.initialSort;if(void 0===e.option||\"VALUE\"===e.option.toUpperCase())this.sortByValue(e,n);else if(\"ATTRIBUTE\"===e.option.toUpperCase()&&e.attribute){const t=\"DESC\"===e.direction?1:-1;this.sortByAttribute(e.attribute,t)}this.initialSort=void 0}return n}draw({context:e,pixelTop:t,pixelWidth:i,pixelHeight:n,features:r,bpPerPixel:s,bpStart:o}){if(xo.fillRect(e,0,t,i,n,{fillStyle:\"rgb(255, 255, 255)\"}),r&&r.length>0){if(this.checkForLog(r),\"shoebox\"===this.type&&!this.sbColorScale){const e=this.featureSource.hicFile.percentile95||2e3;this.sbColorScale=new gf({threshold:e,r:0,g:0,b:255})}const a={};let c;switch(this.sampleKeys.forEach((function(e,t){a[e]=t})),this.displayMode){case\"FILL\":this.sampleHeight=n/this.sampleKeys.length,c=0;break;case\"SQUISHED\":this.sampleHeight=this.squishedRowHeight,c=0;break;default:this.sampleHeight=this.expandedRowHeight,c=1}const l=this.sampleHeight;for(let e of r)e.pixelRect=void 0;const h=t+n,d=o+i*s+1,u=s;this.sampleYStart=void 0;for(let i of r){if(i.end<o||i.start>d)continue;const n=i.sampleKey||i.sample;i.row=a[n];const r=i.row*l+c;void 0===this.sampleYStart&&(this.sampleYStart=r);if(r+l<t||r>h)continue;const s=Math.max(i.start,o);let f=Math.round((s-o)/u);const p=Math.min(i.end,d),g=Math.round((p-o)/u);let m,w,b=Math.max(1,g-f);if(this.color?m=\"function\"==typeof this.color?this.color(i):this.color:this.colorTable&&(m=this.colorTable.getColor(i.value.toLowerCase())),\"mut\"===this.type)w=l-2*c,b<3&&(b=3,f-=1);else if(\"shoebox\"===this.type){m=this.sbColorScale.getColor(i.value);let e=l;if(l<.25){const t=.1+2*Math.abs(t.value);e=Math.min(1,t*l)}w=e-2*c}else{let e=i.value;this.isLog||(e=ys.log2(e/2)),m=e<-.1?this.negColorScale.getColor(e):e>.1?this.posColorScale.getColor(e):\"white\";let t=l;if(l<.25){const i=.1+2*Math.abs(e);t=Math.min(1,i*l)}w=t-2*c}i.pixelRect={x:f,y:r,w:b,h:w},e.fillStyle=m,e.fillRect(f,r,b,w)}}}checkForLog(e){if(void 0===this.isLog){this.isLog=!1;for(let t of e)if(t.value<0)return void(this.isLog=!0)}}computePixelHeight(e){if(!e)return 0;const t=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight;return this.updateSampleKeys(e),this.sampleKeys.length*t}async sortByValue(e,t){const i=e.chr;let n,r;if(e.position?(n=e.position-1,r=n+1):(n=e.start,r=e.end),t||(t=await this.featureSource.getFeatures({chr:i,start:n,end:r})),!t)return;this.updateSampleKeys(t);const s={},o=\"ASC\"===e.direction?1:-1,a=()=>{const e=r-n+1;for(let i of t){if(i.end<n)continue;if(i.start>r)break;const t=Math.max(n,i.start),o=(Math.min(r,i.end)-t)/e,a=i.sampleKey||i.sample,c=s[a]||0;s[a]=c+o*i.value}this.sampleKeys.sort((function(e,t){let i=s[e],n=s[t];return i||(i=o*Number.MAX_VALUE),n||(n=o*Number.MAX_VALUE),i===n?0:i>n?o:-1*o}))},c=()=>{for(let e of t){if(e.end<n)continue;if(e.start>r)break;const t=e.sampleKey||e.sample;(!s.hasOwnProperty(t)||e.value.localeCompare(s[t])>0)&&(s[t]=e.value)}this.sampleKeys.sort((function(e,t){let i=s[e]||\"\",n=s[t]||\"\";return o*i.localeCompare(n)}))};\"mut\"===this.type?c():a(),this.trackView.repaintViews()}sortByAttribute(e,t){this.sampleKeys=this.browser.sampleInfo.getSortedSampleKeysByAttribute(this.sampleKeys,e,t),this.trackView.repaintViews()}clickedFeatures(e){const t=super.clickedFeatures(e),i=e.y;return t.filter((function(e){const t=e.pixelRect;return t&&i>=t.y&&i<=t.y+t.h}))}hoverText(e){const t=this.clickedFeatures(e);if(t&&t.length>0)return`${t[0].sample}: ${t[0].value}`}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){i.length>0&&(i.push(\"<hr/>\"),i.push(\"<hr/>\"));const t=e._f||e,n=\"function\"==typeof t.popupData?t.popupData(this.type,this.browser.genome.id):this.extractPopupData(t);Array.prototype.push.apply(i,n)}return i}contextMenuItemList(e){const t=e.genomicLocation,i=t=>{const i=e.viewport.cachedFeatures;this.sortByValue(t,i)},n=e.referenceFrame.toBP(2.5);return[\"DESC\",\"ASC\"].map((r=>{const s=\"DESC\"===r?\"descending\":\"ascending\";return{label:\"seg\"===this.type||\"shoebox\"===this.type?`Sort by value (${s})`:`Sort by type (${s})`,click:()=>{const s={option:\"VALUE\",direction:r,chr:e.referenceFrame.chr,start:Math.floor(t-n),end:Math.floor(t+n)};i(s),this.config.sort=s}}}))}get supportsWholeGenome(){return(!1===this.config.indexed||!this.config.indexURL)&&!1!==this.config.supportsWholeGenome}updateSampleKeys(e){if(this.explicitSamples)return;const t=new Set(this.sampleKeys);for(let i of e){const e=i.sampleKey||i.sample;t.has(e)||(this.sampleKeys.push(e),t.add(e))}}}const Of={low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0},Uf={low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255},qf={indel:\"rgb(0,200,0)\",\"targeted region\":\"rgb(236,155,43)\",truncating:\"rgb(\\t150,0,0)\",\"non-coding transcript\":\"rgb(0,0,150)\",synonymous:\"rgb(109,165,95)\",silent:\"rgb(109,135,80)\",missense_mutation:\"rgb(72,130,187)\",missense:\"rgb(72,130,187)\",\"splice site\":\"rgb(143,83,155)\",splice_region:\"rgb(143,83,155)\",nonsense:\"rgb(216, 57,81)\",nonsense_mutation:\"rgb(216, 57,81)\",frame_shift_del:\"rgb(226,135,65)\",frame_shift_ins:\"rgb(226,135,65)\",in_frame_del:\"rgb(247,235,94)\",in_frame_ins:\"rgb(247,235,94)\",\"*other*\":\"rgb(159,91,50)\"};class Qf{constructor(e){this.paired=!0,this.firstAlignment=e,this.chr=e.chr,this.readName=e.readName,e.start<e.mate.position?(this.start=e.start,this.scStart=e.scStart,this.connectingStart=e.start+e.lengthOnRef,this.connectingEnd=e.mate.position):(this.start=e.mate.position,this.scStart=this.start,this.connectingStart=e.mate.position,this.connectingEnd=e.start),this.end=Math.max(e.mate.position,e.start+e.lengthOnRef),this.lengthOnRef=this.end-this.start;let t=Math.max(this.end,e.scStart+e.scLengthOnRef);this.scLengthOnRef=t-this.scStart}setSecondAlignment(e){this.secondAlignment=e;const t=this.firstAlignment;e.start>t.start?this.connectingEnd=e.start:this.connectingStart=e.start+e.lengthOnRef,this.start=Math.min(t.start,e.start),this.end=Math.max(t.start+t.lengthOnRef,e.start+e.lengthOnRef),this.lengthOnRef=this.end-this.start,this.scStart=Math.min(t.scStart,e.scStart);const i=Math.max(t.scStart+t.scLengthOnRef,e.scStart+e.scLengthOnRef);this.scLengthOnRef=i-this.scStart}containsLocation(e,t){const i=t?this.scStart:this.start,n=t?this.scLengthOnRef:this.lengthOnRef;return e>=i&&e<=i+n}alignmentContaining(e,t){return this.firstAlignment.containsLocation(e,t)?this.firstAlignment:this.secondAlignment&&this.secondAlignment.containsLocation(e,t)?this.secondAlignment:void 0}popupData(e){let t=this.firstAlignment.popupData(e);return this.secondAlignment&&(t.push(\"-------------------------------\"),t=t.concat(this.secondAlignment.popupData(e))),t}isPaired(){return!0}isMateMapped(){return!0}isProperPair(){return this.firstAlignment.isProperPair()}get fragmentLength(){return Math.abs(this.firstAlignment.fragmentLength)}get firstOfPairStrand(){return this.firstAlignment.firstOfPairStrand}get pairOrientation(){return this.firstAlignment.pairOrientation}hasTag(e){return this.firstAlignment.hasTag(e)||this.secondAlignment&&this.secondAlignment.hasTag(e)}getGroupValue({option:e,tag:t}){switch(e){case\"strand\":return this.isNegativeStrand()?\"-\":\"+\";case\"FIRST_IN_PAIR_STRAND\":return this.isPaired()?this.isFirstOfPair()?this.isNegativeStrand()?\"-\":\"+\":this.isSecondOfPair()?this.isNegativeStrand()?\"+\":\"-\":void 0:void 0;case\"START\":return this.start;case\"INSERT_SIZE\":return this.fragmentLength;case\"MATE_CHR\":return this.mate?this.mate.chr:void 0;case\"MQ\":return this.mq;case\"ALIGNED_READ_LENGTH\":return this.lengthOnRef;case\"TAG\":return this.tags()[t];case\"PHASE\":return this.tags().HP;case\"READ_ORDER\":return this.isPaired()&&this.isFirstOfPair()?\"FIRST\":this.isPaired()&&this.isSecondOfPair()?\"SECOND\":\"\";default:return}}}class Vf{static instances=new Map;static getKey(e,t,i){const n=\"\"+e+t+i;return Vf.instances.has(n)||Vf.instances.set(n,new Vf(e,t,i)),Vf.instances.get(n)}constructor(e,t,i){this.base=e,this.strand=t,this.modification=i,this.canonicalBase=\"+\"===this.strand?this.base:oc(this.base)}getCanonicalBase(){}toString(){return\"\"+this.base+this.strand+this.modification}static compare(e,t){const i=e.modification,n=t.modification;return i===n?e.strand.charAt(0)-t.strand.charAt(0):jf.has(i)&jf.has(n)?jf.get(i)-jf.get(n):jf.has(i)?1:jf.has(n)?-1:i>n?1:-1}}const jf=new Map([\"NONE_C\",\"NONE_T\",\"NONE_G\",\"NONE_A\",\"m\",\"h\",\"f\",\"c\",\"C\",\"g\",\"e\",\"b\",\"T\",\"U\",\"a\",\"A\",\"o\",\"G\",\"n\",\"N\"].map(((e,t)=>[e,t])));class Wf{constructor(e,t,i,n){this.base=e,this.modification=i,this.strand=t,this.likelihoods=n,this.canonicalBase=\"+\"==this.strand?this.base:oc(this.base),this.key=Vf.getKey(e,t,i)}containsPosition(e){return this.likelihoods.has(e)}is5mC(){return this.modification.equals(\"m\")&&(\"C\"===this.base&&\"+\"===this.strand||\"G\"===this.base&&\"-\"===this.strand)}fullName(){return Gf.get(this.modification)||this.modification}}const Gf=new Map;Gf.set(\"m\",\"5mC\"),Gf.set(\"h\",\"5hmC\"),Gf.set(\"f\",\"5fC\"),Gf.set(\"c\",\"5caC\"),Gf.set(\"g\",\"5hmU\"),Gf.set(\"e\",\"5fU\"),Gf.set(\"b\",\"5caU\"),Gf.set(\"a\",\"6mA\"),Gf.set(\"o\",\"8xoG\"),Gf.set(\"n\",\"Xao\"),Gf.set(\"C\",\"Unknown C\"),Gf.set(\"T\",\"Unknown T\"),Gf.set(\"A\",\"Unknown A\"),Gf.set(\"G\",\"Unknown G\"),Gf.set(\"N\",\"Unknown\");const $f=new Map([[\"m\",\"5mC\"],[\"h\",\"5hmC\"],[\"f\",\"5fC\"],[\"c\",\"5caC\"],[\"g\",\"5hmU\"],[\"e\",\"5fU\"],[\"b\",\"5caU\"],[\"a\",\"6mA\"],[\"o\",\"8xoG\"],[\"n\",\"Xao\"],[\"C\",\"Unknown C\"],[\"T\",\"Unknown T\"],[\"A\",\"Unknown A\"],[\"G\",\"Unknown G\"],[\"N\",\"Unknown\"]]);function Kf(e){return $f.has(e)?$f.get(e):\"Uknown\"}function Yf(e){if(!e)return!1;const t=e.length;if(0==t)return!1;for(let i=0;i<t;i++){const t=e.charAt(i);if(t<\"0\"||t>\"9\")return!1}return!0}function Xf(e){return e<0?e+256:e}class Zf{allModifications=new Set;simplexModifications=new Set;maxLikelihoods=new Map;nomodLikelihoods=new Map;lastThreshold;incrementCounts(e){if(!e.blocks)return;const t=e.getBaseModificationSets();if(t)for(let i of e.blocks)if(\"S\"!==i.type)for(let e=0;e<i.len;e++){let n,r=e+i.seqOffset,s=0,o=-1,a=255;for(let e of t){const t=Vf.getKey(e.base,e.strand,e.modification);this.allModifications.add(t);const i=e.likelihoods;if(e.containsPosition(r)){const c=Xf(i.get(r));a-=c,c>o&&(s=e.canonicalBase,o=c,n=t)}}if(0!=s){const t=i.start+e,r=Vf.getKey(s,\"+\",\"NONE_\"+s);this.allModifications.add(r);const c=(e,t,i,n)=>{let r=n.get(i);r||(r=new Map,n.set(i,r));let s=r.get(e);s||(s=[],r.set(e,s)),s.push(t)};c(t,o,n,this.maxLikelihoods),a>o?c(t,a,r,this.nomodLikelihoods):c(t,o,n,this.nomodLikelihoods)}}}getCount(e,t,i,n){this.lastThreshold=i;const r=255*i,s=n?this.nomodLikelihoods.get(t):this.maxLikelihoods.get(t);if(!s)return 0;const o=s.get(e);if(o){let e=0;for(let t of o){Xf(t)>=r&&e++}return e}return 0}getLikelihoodSum(e,t,i,n){this.lastThreshold=i;const r=255*i,s=(n?this.nomodLikelihoods.get(t):this.maxLikelihoods.get(t)).get(e);if(s){let e=0;for(let t of s){const i=Xf(t);i>=r&&(e+=i)}return e}return 0}popupData(e,t){const i=[];i.push(\"<b>Modifications with likelihood > \"+100*this.lastThreshold+\"%</b>\");for(let n of this.maxLikelihoods.keys()){if(this.maxLikelihoods.get(n).has(e)){let r=\"basemod2\"===t;const s=this.getCount(e,n,this.lastThreshold,r);if(s>0){const t=this.getLikelihoodSum(e,n,this.lastThreshold,r)/s*.3921568,o=Kf(n.modification);i.push(o+\" (\"+n.base+n.strand+\"): \"+s+\"  @ average likelihood \"+Math.round(t)+\"%\")}}}return i}computeSimplex(){const e=new Set(Array.from(this.allModifications).filter((e=>\"-\"===e.strand)).map((e=>e.modification)));for(let t of this.allModifications)\"+\"!==t.strand||e.has(t.modification)||(this.simplexModifications.add(t.modification),this.simplexModifications.add(\"NONE_\"+t.getCanonicalBase()))}}class Jf{constructor(){this.alignments=[],this.score=void 0}findAlignment(e,t=!1){const i=(e,i)=>i>=e.start&&i<e.start+(t?e.fragmentLength:e.lengthOnRef);let n;for(let r=0;r<this.alignments.length;r++){const s=this.alignments[r];if(e>=s.start&&e<s.start+(t?s.fragmentLength:s.lengthOnRef)){s.paired?s.firstAlignment&&i(s.firstAlignment,e)?n=s.firstAlignment:s.secondAlignment&&i(s.secondAlignment,e)&&(n=s.secondAlignment):n=s;break}}return n}getSortValue({position:e,option:t,tag:i,sortAsPairs:n},r){t||(t=\"BASE\");const s=this.findAlignment(e,n);if(void 0===s)return Number.MAX_VALUE;switch(t){case\"NUCLEOTIDE\":case\"BASE\":return function(e,t,i){let n;const r=Math.floor(i)-t.start;r<t.sequence.length&&(n=t.sequence.charAt(r));if(!n)return 0;const s=e.readBaseAt(i),o=e.readBaseQualityAt(i),a=t.coverageMap,c=Math.floor(i-a.bpStart),l=a.coverage[c];let h=0;if(e.insertions)for(let t of e.insertions)t.start===i&&(h=-l.ins);if(s)if(n=n.toUpperCase(),\"N\"===s&&0===h)h=2;else if(n!==s&&\"=\"!==s||0!==h){if(\"X\"===s||n!==s){h-=l[\"pos\"+s]+l[\"neg\"+s]+o/1e3}}else h=4-o/1e3;else{const e=l.del;e>0?h-=e:0===h&&(h=1)}return h}(s,r,e);case\"strand\":return s.strand?1:-1;case\"START\":return s.start;case\"TAG\":return s.tags()[i];case\"READ_NAME\":return s.readName;case\"INSERT_SIZE\":return-Math.abs(s.fragmentLength);case\"GAP_SIZE\":return-s.gapSizeAt(e);case\"MATE_CHR\":return s.mate?s.mate.chr:Number.MAX_VALUE;case\"MQ\":return void 0===s.mq?Number.MAX_VALUE:-s.mq;case\"ALIGNED_READ_LENGTH\":return-s.lengthOnRef;default:return Number.MAX_VALUE}}}var ep={fr:{F1R2:\"LR\",F2R1:\"LR\",F1F2:\"LL\",F2F1:\"LL\",R1R2:\"RR\",R2R1:\"RR\",R1F2:\"RL\",R2F1:\"RL\"},rf:{R1F2:\"LR\",R2F1:\"LR\",R1R2:\"LL\",R2R1:\"LL\",F1F2:\"RR\",F2F1:\"RR\",F1R2:\"RL\",F2R1:\"RL\"},ff:{F2F1:\"LR\",R1R2:\"LR\",F2R1:\"LL\",R1F2:\"LL\",R2F1:\"RR\",F1R2:\"RR\",R2R1:\"RL\",F1F2:\"RL\"}};class tp{#A=[];baseModificationKeys=new Set;constructor(e,t,i,{samplingWindowSize:n,samplingDepth:r,alleleFreqThreshold:s,colorBy:o}){this.alleleFreqThreshold=void 0===s?.2:s,this.samplingWindowSize=n||100,this.samplingDepth=r||1e3,this.chr=e,this.start=Math.floor(t),this.end=Math.ceil(i),this.length=i-t,this.coverageMap=new np(e,t,i,this.alleleFreqThreshold),this.downsampledIntervals=[],o&&o.startsWith(\"basemod\")&&(this.baseModCounts=new Zf),this.alignments=[],this.pairsCache=new Map,this.downsampledReads=new Set,this.currentBucket=new ip(this.start,this.start+this.samplingWindowSize,this),this.hasPairs=!1}pack({viewAsPairs:e,showSoftClips:t,expectedPairOrientation:i,groupBy:n,displayMode:r}){let s=this.allAlignments();s=e?function(e){const t=new Map,i=e.map((e=>{if(ap(e)){let i=t.get(e.readName);return i?(i.setSecondAlignment(e),t.delete(e.readName),i):(i=new Qf(e),t.set(e.readName,i),i)}return e}));return i}(s):function(e){return e.flatMap((e=>e instanceof Qf?[e.firstAlignment,e.secondAlignment].filter(Boolean):[e]))}(s),this.packAlignmentRows(s,t,i,n,r),this.alignments&&delete this.alignments}packAlignmentRows(e,t,i,n,r){this.#A=[];const s=(e,i)=>{e.sort((function(e,i){return t?e.scStart-i.scStart:e.start-i.start}));const n=new op(i);let r,s=0,o=0;const a=new Set,c=()=>{r=new Jf,n.push(r),s=0,o=0,a.clear()};for(c();e.length>0;)if(o>=0&&o<e.length){const i=e[o];a.add(i),r.alignments.push(i),s=t?i.scStart+i.scLengthOnRef+2:i.start+i.lengthOnRef+2,o=cp(e,(e=>(t?e.scStart:e.start)>s),o)}else e=e.filter((e=>!a.has(e))),c();return n},o=(e,t)=>{e.sort((function(e,t){return e.start-t.start}));const i=new op(t),{start:n,end:r}=this.viewport.genomicRange();for(let t of e)if(t.end<n||t.start>r)this.#A.push(t);else{const e=new Jf;e.alignments.push(t),i.push(e)}return i};if(!e||0===e.length)return new Map;{const t=new Map;if(n)for(let r of e){const e=lp(r,n,i)||\"\";t.has(e)||t.set(e,[]),t.get(e).push(r)}else t.set(\"\",e);const a=new Map,c=Array.from(t.keys()).sort(function(e,t){switch(e){case\"pairOrientation\":return function(e){const t=[\"LL\",\"RR\",\"RL\",\"LR\",\"\"];return(e,i)=>t.indexOf(e)-t.indexOf(i)}();case\"strand\":case\"firstOfPairStrand\":return up;default:return e&&e.startsWith(\"base:\")?dp:fp}}(n));for(let e of c){const i=t.get(e),n=\"FULL\"===r?o(i,e):s(i,e);a.set(e,n)}this.packedGroups=a}}push(e){this.hasPairs=this.hasPairs||e.isPaired(),this.coverageMap.incCounts(e);const t=e.getBaseModificationSets();if(t)for(let e of t)this.baseModificationKeys.add(e.key);this.baseModCounts&&this.baseModCounts.incrementCounts(e),this.downsampledReads.has(e.readName)?this.currentBucket.downsampledCount++:(e.start>=this.currentBucket.end&&(this.finishBucket(),this.currentBucket=new ip(e.start,e.start+this.samplingWindowSize,this)),this.currentBucket.addAlignment(e))}finish(){void 0!==this.currentBucket&&this.finishBucket(),this.hasAlignments=this.alignments.length>0,this.alignments.sort((function(e,t){return e.start-t.start})),this.baseModCounts&&this.baseModCounts.computeSimplex(),delete this.currentBucket,delete this.pairsCache,delete this.downsampledReads}contains(e,t,i){return this.chr===e&&this.start<=t&&this.end>=i}hasDownsampledIntervals(){return this.downsampledIntervals&&this.downsampledIntervals.length>0}finishBucket(){this.alignments=this.alignments.concat(this.currentBucket.alignments),this.currentBucket.downsampledCount>0&&this.downsampledIntervals.push(new sp(this.currentBucket.start,this.currentBucket.end,this.currentBucket.downsampledCount))}allAlignments(){if(this.alignments)return this.alignments;if(this.packedGroups){const e=Array.from(this.packedGroups.values()).flatMap((e=>e.rows.flatMap((e=>e.alignments))));if(this.#A&&this.#A.length>0)for(let t of this.#A)e.push(t);return e}return[]}getMax(e,t){return this.coverageMap.getMax(e,t)}sortRows(e){if(this.packedGroups)for(let t of this.packedGroups.values())t.sortRows(e,this)}}class ip{constructor(e,t,{samplingDepth:i,downsampledReads:n,pairsCache:r}){this.start=e,this.end=t,this.alignments=[],this.downsampledCount=0,this.samplingDepth=i,this.downsampledReads=n,this.pairsCache=r,this.hasPairs=!1}addAlignment(e){this.hasPairs=this.hasPairs||e.isPaired();const t=this.hasPairs?Math.ceil(this.samplingDepth/2):this.samplingDepth;if(ap(e)){const t=this.pairsCache.get(e.readName);if(t)return t.setSecondAlignment(e),void this.pairsCache.delete(e.readName)}if(this.alignments.length<t)if(ap(e)){const t=new Qf(e);this.pairsCache.set(e.readName,t),this.alignments.push(t)}else this.alignments.push(e);else{const i=Math.floor(Math.random()*(t+this.downsampledCount-1));if(i<t){const t=this.alignments[i];if(this.pairsCache.has(t.readName)&&this.pairsCache.delete(t.readName),ap(e)){const t=new Qf(e);this.pairsCache.set(e.readName,t),this.alignments[i]=t}else this.alignments[i]=e;this.downsampledReads.add(t.readName)}else this.downsampledReads.add(e.readName);this.downsampledCount++}}}class np{constructor(e,t,i,n){this.chr=e,this.bpStart=t,this.length=i-t,this.coverage=new Array(this.length),this.maximum=0,this.threshold=n,this.qualityWeight=!0}getMax(e,t){let i=0;const n=this.coverage.length;for(let r=0;r<n;r++){const n=this.bpStart+r;if(n>t)break;const s=this.coverage[r];n>=e&&s&&(i=Math.max(i,s.total))}return i}incCounts(e){var t=this;if(void 0===e.blocks?i(e):e.blocks.forEach((function(e){i(e)})),e.gaps)for(let i of e.gaps)if(\"D\"===i.type){const e=i.start-t.bpStart;for(let n=e;n<e+i.len;n++)n<0||(this.coverage[n]||(this.coverage[n]=new rp(t.threshold)),this.coverage[n].del++)}if(e.insertions)for(let i of e.insertions){const e=i.start-this.bpStart;e<0||(this.coverage[e]||(this.coverage[e]=new rp(t.threshold)),this.coverage[e].ins++)}function i(i){if(\"S\"===i.type)return;const n=e.seq,r=e.qual,s=i.seqOffset;for(let o=i.start-t.bpStart,a=0;a<i.len;o++,a++){t.coverage[o]||(t.coverage[o]=new rp(t.threshold));const i=null==n?\"N\":n.charAt(s+a),c=e.strand?\"pos\"+i:\"neg\"+i,l=r&&s+a<r.length?r[s+a]:30;t.coverage[o][c]+=1,t.coverage[o][\"qual\"+i]+=l,t.coverage[o].total+=1,t.coverage[o].qual+=l,t.maximum=Math.max(t.coverage[o].total,t.maximum)}}}getPosCount(e,t){const i=e-this.bpStart;if(i<0||i>=this.coverage.length)return 0;const n=this.coverage[i];switch(t){case\"A\":case\"a\":return n.posA;case\"C\":case\"c\":return n.posC;case\"T\":case\"t\":return n.posT;case\"G\":case\"g\":return n.posG;case\"N\":case\"n\":return n.posN;default:return 0}}getNegCount(e,t){const i=e-this.bpStart;if(i<0||i>=this.coverage.length)return 0;const n=this.coverage[i];switch(t){case\"A\":case\"a\":return n.negA;case\"C\":case\"c\":return n.negC;case\"T\":case\"t\":return n.negT;case\"G\":case\"g\":return n.negG;case\"N\":case\"n\":return n.negN;default:return 0}}getCount(e,t){return this.getPosCount(e,t)+this.getNegCount(e,t)}getTotalCount(e){const t=e-this.bpStart;return t>=0&&t<this.coverage.length?this.coverage[t].total:0}}class rp{constructor(e){this.qualityWeight=!0,this.posA=0,this.negA=0,this.posT=0,this.negT=0,this.posC=0,this.negC=0,this.posG=0,this.negG=0,this.posN=0,this.negN=0,this.pos=0,this.neg=0,this.qualA=0,this.qualT=0,this.qualC=0,this.qualG=0,this.qualN=0,this.qual=0,this.total=0,this.del=0,this.ins=0,this.threshold=e}hoverText(){const e=this.posA+this.posT+this.posC+this.posG+this.posN,t=this.negA+this.negT+this.negC+this.negG+this.negN;return`${this.total} (${e}+, ${t}-)`}isMismatch(e){const t=this.threshold*(this.qualityWeight&&this.qual?this.qual:this.total);let i=0;for(let t of[\"A\",\"T\",\"C\",\"G\"])t!==e&&(i+=this.qualityWeight&&this.qual?this[\"qual\"+t]:this[\"pos\"+t]+this[\"neg\"+t]);return i>=t}}class sp{constructor(e,t,i){this.start=e,this.end=t,this.counts=i}popupData(e){return[{name:\"start\",value:Math.floor(this.start+1)},{name:\"end\",value:this.end},{name:\"# downsampled:\",value:this.counts}]}}class op{pixelTop=0;pixelBottom=0;rows=[];constructor(e){this.name=this.name}push(e){this.rows.push(e)}get length(){return this.rows.length}sortRows(e,t){const i=[],n=[];for(let t of this.rows){void 0!==t.findAlignment(e.position,e.sortAsPairs)?i.push(t):n.push(t)}i.sort(((i,n)=>{const r=e.direction,s=i.getSortValue(e,t),o=n.getSortValue(e,t);if(void 0===o&&void 0!==o)return 1;if(void 0!==s&&void 0===o)return-1;const a=s>o?1:s<o?-1:0;return!0===r?a:-a}));for(let e of n)i.push(e);this.rows=i}}function ap(e){return e.isPaired()&&e.mate&&e.isMateMapped()&&e.chr===e.mate.chr&&(e.isFirstOfPair()||e.isSecondOfPair())&&!(e.isSecondary()||e.isSupplementary())}function cp(e,t,i){let n=i-1,r=e.length;for(;1+n<r;){const i=n+(r-n>>1);t(e[i])?r=i:n=i}return r}function lp(e,t,i){let n,r,s;if(t.startsWith(\"tag:\"))n=t.substring(4),t=\"tag\";else if(t.startsWith(\"base:\")){const e=t.split(\":\");3===e.length&&(t=\"base\",r=e[1],s=Number.parseInt(e[2].replaceAll(\",\",\"\"))-1)}switch(t){case\"strand\":return e.strand?\"+\":\"-\";case\"firstOfPairStrand\":const t=e.firstOfPairStrand;return void 0===t?\"\":t?\"+\":\"-\";case\"mateChr\":return e.mate&&e.isMateMapped()?e.mate.chr:\"\";case\"pairOrientation\":return ep[i][e.pairOrientation]||\"\";case\"chimeric\":return e.tags().SA?\"chimeric\":\"\";case\"supplementary\":return e.isSupplementary?\"supplementary\":\"\";case\"readOrder\":return e.isPaired()&&e.isFirstOfPair()?\"first\":e.isPaired()&&e.isSecondOfPair()?\"second\":\"\";case\"phase\":return e.tags().HP||\"\";case\"tag\":return e.tags()[n]||\"\";case\"base\":if(e.chr===r&&e.start<=s&&e.end>s){const t=e.readBaseAt(s);return t||\"GAP\"}return\"\";default:return}}const hp=new Map([[\"A\",1],[\"T\",2],[\"C\",3],[\"G\",4],[\"N\",5],[\"GAP\",5],[\"\",7]]);function dp(e,t){return hp.has(e)&&hp.has(t)?hp.get(e)-hp.get(t):e.localeCompare(t,void 0,{sensitivity:\"base\"})}function up(e,t){return e===t?0:e&&t?-e.localeCompare(t):e?1:-1}function fp(e,t){if(e||t){if(e){if(t){if(e===t)return 0;if(Va(e)&&(Va(t),1))return Number.parseFloat(e)-Number.parseFloat(t);{let i=e.toString(),n=t.toString();return i.localeCompare(n,void 0,{sensitivity:\"base\"})}}return-1}return 1}return 0}class pp{constructor(e){const t=e.split(\",\");this.chr=t[0],this.start=parseInt(t[1]),this.strand=t[2].charAt(0),this.mapQ=parseInt(t[4]),this.numMismatches=parseInt(t[5]),this.lenOnRef=function(e){let t=0,i=\"\";for(let n=0;n<e.length;n++){const r=e.charCodeAt(n);if(r>47&&r<58)i+=e.charAt(n);else{switch(r){case 78:case 68:case 77:case 61:case 88:t+=parseInt(i.toString())}i=\"\"}}return t}(t[3])}printString(){return this.chr+\":\"+Rt(this.start)+\"-\"+Rt(this.start+this.lenOnRef)+\" (\"+this.strand+\") = \"+Rt(this.lenOnRef)+\"bp @MAPQ: \"+this.mapQ+\" NM: \"+this.numMismatches}}function gp(e){return e.split(\";\").filter((e=>e.length>0)).map((e=>new pp(e)))}const mp={c:1,C:1,s:2,S:2,i:4,I:4,f:4};class wp{constructor(){this.hidden=!1}isMapped(){return!(4&this.flags)}isPaired(){return!!(1&this.flags)}isProperPair(){return!!(2&this.flags)}isFirstOfPair(){return!!(64&this.flags)}isSecondOfPair(){return!!(128&this.flags)}isSecondary(){return!!(256&this.flags)}isSupplementary(){return!!(2048&this.flags)}isFailsVendorQualityCheck(){return!!(512&this.flags)}isDuplicate(){return!!(1024&this.flags)}isMateMapped(){return!(8&this.flags)}isNegativeStrand(){return!!(16&this.flags)}isMateNegativeStrand(){return!!(32&this.flags)}hasTag(e){const t=this.tagDict||function(e){let t=0;const i=e.length,n={};for(;t<i;){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const s=String.fromCharCode(e[t++]);let o;if(\"A\"===s)o=String.fromCharCode(e[t]),t++;else if(\"i\"===s||\"I\"===s)o=vp(e,t),t+=4;else if(\"c\"===s)o=Cp(e,t),t++;else if(\"C\"===s)o=_p(e,t),t++;else if(\"s\"===s||\"S\"===s)o=yp(e,t),t+=2;else if(\"f\"===s)o=Ap(e,t),t+=4;else if(\"Z\"===s)for(o=\"\";;){var r=e[t++];if(0===r)break;o+=String.fromCharCode(r)}else{if(\"B\"!==s){o=\"Error unknown type: \"+s,n[i]=o;break}{const r=String.fromCharCode(e[t++]);let s=mp[r];if(void 0===s){n[i]=`Error: unknown element type '${r}'`;break}const a=vp(e,t);t+=4;const c=t+a*s;o=[];const l=new DataView(e.buffer);for(;t<c;){switch(r){case\"c\":o.push(l.getInt8(t));break;case\"C\":o.push(l.getUint8(t));break;case\"s\":o.push(l.getInt16(t));break;case\"S\":o.push(l.getUint16(t));break;case\"i\":o.push(l.getInt32(t));break;case\"I\":o.push(l.getUint32(t));break;case\"f\":o.push(l.getFloat32(t))}t+=s}}}n[i]=o}return n}(this.tagBA);return t.hasOwnProperty(e)}tags(){return this.tagDict}getTag(e){return this.tags()[e]}get firstOfPairStrand(){if(this.isPaired()){if(this.isFirstOfPair())return this.strand;if(this.isMateMapped())return this.mate.strand}}containsLocation(e,t){const i=t?this.scStart:this.start,n=t?this.scLengthOnRef:this.lengthOnRef;return e>=i&&e<=i+n}popupData(e){const t=[];if(e=Math.floor(e),this.insertions){const n=this.seq;for(let r of this.insertions){var i=r.start;if(e===i||e===i-1)return t.push({name:\"Insertion\",value:n.substr(r.seqOffset,r.len)}),t.push({name:\"Location\",value:i}),t}}t.push({name:\"Read Name\",value:this.readName}),t.push(\"<hr/>\"),t.push({name:\"Alignment Start\",value:Rt(1+this.start),borderTop:!0}),t.push({name:\"Read Strand\",value:!0===this.strand?\"(+)\":\"(-)\",borderTop:!0});let n=this.cigar;if(n&&n.length>50){const e=25;n=`${n.substring(0,e-2)} ... ${n.substring(n.length-e+2)}`}t.push({name:\"Cigar\",value:n}),t.push({name:\"Mapping Quality\",value:this.mq}),t.push({name:\"Secondary\",value:a(this.isSecondary())}),t.push({name:\"Supplementary\",value:a(this.isSupplementary())}),t.push({name:\"Duplicate\",value:a(this.isDuplicate())}),t.push({name:\"Failed QC\",value:a(this.isFailsVendorQualityCheck())}),this.isPaired()&&(t.push(\"<hr/>\"),t.push({name:\"First in Pair\",value:!this.isSecondOfPair(),borderTop:!0}),t.push({name:\"Mate is Mapped\",value:a(this.isMateMapped())}),this.pairOrientation&&t.push({name:\"Pair Orientation\",value:this.pairOrientation}),this.isMateMapped()&&(t.push({name:\"Mate Chromosome\",value:this.mate.chr}),t.push({name:\"Mate Start\",value:this.mate.position+1}),t.push({name:\"Mate Strand\",value:!0===this.mate.strand?\"(+)\":\"(-)\"}),t.push({name:\"Insert Size\",value:this.fragmentLength})));const r=this.tags();if(r.hasOwnProperty(\"SA\")){t.push(\"<hr/>\"),t.push({name:\"Supplementary Alignments\",value:\"\"});const e=gp(r.SA);if(e){t.push(\"<ul>\");for(let i of e)t.push(`<li>${i.printString()}</li>`);t.push(\"</ul>\")}}const s=new Set([\"SA\",\"MD\"]);t.push(\"<hr/>\");for(let e in r)s.has(e)||t.push({name:e,value:r[e]});t.push({name:\"Hidden Tags\",value:\"SA, MD\"}),t.push(\"<hr/>\"),t.push({name:\"Genomic Location: \",value:Rt(1+e)}),t.push({name:\"Read Base:\",value:this.readBaseAt(e)}),t.push({name:\"Base Quality:\",value:this.readBaseQualityAt(e)});const o=this.getBaseModificationSets();if(o){const i=this.positionToReadIndex(e);if(void 0!==i){let e=!1;for(let n of o)if(n.containsPosition(i)){e||(t.push(\"<hr/>\"),t.push(\"<b>Base modifications:</b>\"),e=!0);const r=Math.round(100/255*Xf(n.likelihoods.get(i)));t.push(`${n.fullName()} @ likelihood =  ${r}%`)}}}return t;function a(e){return e?\"Yes\":\"No\"}}readBaseAt(e){const t=Fp(this.blocks,e);if(t){if(\"*\"===this.seq)return\"*\";{const i=t.seqIndexAt(e);return this.seq[i]}}}readBaseQualityAt(e){const t=Fp(this.blocks,e);if(t){if(\"*\"===this.qual)return 30;{const i=t.seqIndexAt(e);return i>=0&&this.qual&&i<this.qual.length?this.qual[i]:30}}}gapSizeAt(e){if(this.gaps)for(let t of this.gaps)if(e>=t.start&&e<t.start+t.len)return t.len;return 0}softClippedBlocks(){let e,t,i;for(let n of this.blocks)\"S\"===n.type?i?t=n:e=n:\"H\"!==n.type&&(i=!0);return{left:e,right:t}}getBaseModificationSets(){if(!this.baseModificationSets&&(this.tagDict.MM||this.tagDict.Mm)){const e=this.tagDict.MM||this.tagDict.Mm,t=this.tagDict.ML||this.tagDict.Ml;!Mt(e)||t&&!Array.isArray(t)||(0===e.length?this.baseModificationSets=bp:this.baseModificationSets=function(e,t,i,n){n&&(i=cc(i));const r=[],s=e.split(\";\");let o=0;for(let e of s){const s=e.split(\",\"),a=s[0].charAt(0),c=s[0].charAt(1),l=s[0].endsWith(\".\");if(1==s.length);else{const e=s[0].endsWith(\".\")||s[0].endsWith(\"?\")?s[0].substring(2,s[0].length-1):s[0].substring(2);let h=[];if(e.length>1)if(Yf(e))h.push(e);else for(let t=0;t<e.length;t++)h.push(e.substring(t,t+1));else h.push(e);const d=new Map;for(let e of h)d.set(e,new Map);let u=1,f=Number.parseInt(s[u++]),p=0,g=0;for(;p<i.length;){if(\"N\"===a||i[p]===a){const e=n?i.length-1-p:p;if(g===f){for(let i of h){const n=t?t[o++]:255;d.get(i).set(e,n)}if(u<s.length)f=Number.parseInt(s[u++]),g=0;else{if(!l)break;f=-1}}else{if(l)for(let t of h)d.get(t).set(e,0);g++}}p++}for(let e of h)r.push(new Wf(a,c,e,d.get(e)))}}return r}(e,t,this.seq,this.isNegativeStrand()))}return this.baseModificationSets}getGroupValue(e,t,i){const n=this;switch(e){case\"strand\":return n.strand?\"+\":\"-\";case\"firstOfPairStrand\":const e=n.firstOfPairStrand;return void 0===e?\"\":e?\"+\":\"-\";case\"mateChr\":return n.mate&&n.isMateMapped()?n.mate.chr:\"\";case\"pairOrientation\":return ep[i][n.pairOrientation]||\"\";case\"chimeric\":return n.tags().SA?\"chimeric\":\"\";case\"supplementary\":return n.isSupplementary?\"supplementary\":\"\";case\"readOrder\":return n.isPaired()&&n.isFirstOfPair()?\"first\":n.isPaired()&&n.isSecondOfPair()?\"second\":\"\";case\"phase\":return n.tags().HP||\"\";case\"tag\":return n.tags()[t]||\"\";default:return}}positionToReadIndex(e){const t=Fp(this.blocks,e);return t?e-t.start+t.seqOffset:void 0}}const bp=new Set;function Fp(e,t){for(let i=0;i<e.length;i++){const n=e[i];if(t>=n.start&&t<n.start+n.len)return n}}function vp(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function yp(e,t){return e[t+1]<<8|e[t]}function Ap(e,t){return new DataView(e.buffer).getFloat32(t)}function Cp(e,t){return new DataView(e.buffer).getInt8(t)}function _p(e,t){return new DataView(e.buffer).getUint8(t)}class xp{constructor(e){e&&Object.assign(this,e)}seqIndexAt(e){return Math.floor(e)-this.start+this.seqOffset}}class kp{constructor(e){e||(e={}),this.vendorFailed=e.vendorFailed=!1!==e.vendorFailed,this.duplicate=e.duplicate=!1!==e.duplicate,this.secondary=e.secondary||!1,this.supplementary=e.supplementary||!1,this.mq=e.mq||0,e.readgroups&&(this.readgroups=new Set(e.readgroups))}pass(e){if(!e.isMapped())return!1;if(this.vendorFailed&&e.isFailsVendorQualityCheck())return!1;if(this.duplicate&&e.isDuplicate())return!1;if(this.secondary&&e.isSecondary())return!1;if(this.supplementary&&e.isSupplementary())return!1;if(e.mq<this.mq)return!1;if(this.readgroups){const t=e.tags().RG;return this.readgroups.has(t)}return!0}}const Ip=Dp(new Uint8Array([66,65,77,1]),0),Sp=[\"=\",\"A\",\"C\",\"M\",\"G\",\"R\",\"S\",\"V\",\"T\",\"W\",\"Y\",\"H\",\"K\",\"D\",\"B\",\"N\"],Ep=[\"M\",\"I\",\"D\",\"N\",\"S\",\"H\",\"P\",\"=\",\"X\",\"?\",\"?\",\"?\",\"?\",\"?\",\"?\",\"?\"],Np={c:1,C:1,s:2,S:2,i:4,I:4,f:4},Bp=1e4,Mp={readHeader:async function(e,t,i){const n=gs(await Qs.loadArrayBuffer(e,t));return Mp.decodeBamHeader(n,i)},decodeBamHeader:function(e){const t=Dp(e,0);if(t!==Ip)throw new Error(\"BAM header errror: bad magic number.  This could be caused by either a corrupt or missing file.\");const i=Dp(e,4);let n=\"\";for(var r=0;r<i;++r)n+=String.fromCharCode(e[r+8]);const s=Dp(e,i+8);let o=i+12;const a={},c=[];for(r=0;r<s;++r){const t=Dp(e,o);let i=\"\";for(var l=0;l<t-1;++l)i+=String.fromCharCode(e[o+4+l]);a[i]=r,c[r]=i,o=o+8+t}return{magicNumber:t,size:o,chrNames:c,chrToIndex:a}},bam_tag2cigar:function(e,t,i,n,r,s){function o(e){return\"C\"===e||\"c\"===e||\"A\"===e?1:\"S\"===e||\"s\"===e?2:\"I\"===e||\"i\"===e||\"f\"===e?4:0}if(1!==s.length||r.start<0)return!1;for(var a=i+(n+1>>1)+n;a+4<t;){if(\"CG\"===String.fromCharCode(e[a])+String.fromCharCode(e[a+1]))break;var c=String.fromCharCode(e[a+2]);if(\"B\"===c)a+=8+o(c=String.fromCharCode(e[a+3]))*Dp(e,a+4);else if(\"Z\"===c||\"H\"===c)for(a+=3;0!==e[a++];);else a+=3+o(c)}if(a>=t)return!1;if(\"B\"!==String.fromCharCode(e[a+2])||\"I\"!==String.fromCharCode(e[a+3]))return!1;var l=Dp(e,a+4),h=a+8;if(h+4*l>t)return!1;var d=\"\",u=0;s.length=0,a=h;for(var f=0;f<l;++f,a+=4){var p=Dp(e,a),g=p>>4,m=Ep[15&p];\"M\"!==m&&\"EQ\"!==m&&\"X\"!==m&&\"D\"!==m&&\"N\"!==m&&\"=\"!==m||(u+=g),d=d+g+m,s.push({len:g,ltr:m})}return r.cigar=d,r.lengthOnRef=u,!0},decodeBamRecords:function(e,t,i,n,r,s,o,a){for(;t<e.length;){const u=t+Dp(e,t)+4,f=new wp,p=Dp(e,t+4),g=Dp(e,t+8);if(u>e.length)return;if(p<0){t=u;continue}if(void 0!==r&&(p>r||g>o))return!0;if(void 0!==r&&p<r){t=u;continue}const m=Dp(e,t+12),w=(65280&m)>>8,b=255&m,F=Dp(e,t+16),v=(4294901760&F)>>16,y=65535&F,A=Dp(e,t+20),C=Dp(e,t+24),_=Dp(e,t+28),x=Dp(e,t+32);let k=[];for(let i=0;i<b-1;++i)k.push(String.fromCharCode(e[t+36+i]));k=k.join(\"\");let I=0,S=\"\",E=t+36+b;const N=[];let B;for(let t=0;t<y;++t){var c=Dp(e,E),l=c>>4,h=Ep[15&c];\"M\"!==h&&\"EQ\"!==h&&\"X\"!==h&&\"D\"!==h&&\"N\"!==h&&\"=\"!==h||(I+=l),S=S+l+h,E+=4,B={len:l,ltr:h},N.push(B)}if(f.chr=n[p],f.start=g,f.flags=v,f.strand=!(16&v),f.readName=k,f.cigar=S,f.lengthOnRef=I,f.fragmentLength=x,f.mq=w,Mp.bam_tag2cigar(e,u,E,A,f,N),f.end=f.start+f.lengthOnRef,f.end<s){t=u;continue}let M=[];const R=A+1>>1;for(let t=0;t<R;++t){var d=e[E+t];M.push(Sp[(240&d)>>4]),M.push(Sp[15&d])}M=M.slice(0,A).join(\"\"),E+=R;const D=[];for(let t=0;t<A;++t)D.push(e[E+t]);E+=A,C>=0&&(f.mate={chr:n[C],position:_,strand:!(32&v)}),f.seq=M,f.qual=D;const T=new Uint8Array(e.buffer.slice(E,u));f.tagDict=zp(T),this.setPairOrientation(f),(void 0===a||a.pass(f))&&(Rp(f,N),i.push(f)),t=u}},decodeSamRecords:function(e,t,i,n,r,s){var o,a,c,l,h,d,u,f,p,g;for(l=(o=Dt(e)).length,!1,a=0;a<l;a++)if(h=o[a].split(\"\\t\"),(p=new wp).chr=h[2],p.start=Number.parseInt(h[3])-1,p.flags=Number.parseInt(h[1]),p.readName=h[0],p.strand=!(16&p.flags),p.mq=Number.parseInt(h[4]),p.cigar=h[5],p.fragmentLength=Number.parseInt(h[8]),p.seq=h[9],\"*\"!==p.chr&&p.isMapped()&&p.chr===i){if(p.start>r)break;if(f=0,(g=Tp(p.cigar)).forEach((function(e){var t=e.len,i=e.ltr;\"M\"!==i&&\"EQ\"!==i&&\"X\"!==i&&\"D\"!==i&&\"N\"!==i&&\"=\"!==i||(f+=t)})),p.lengthOnRef=f,!(p.start+f<n)){for(d=h[10],p.qual=[],c=0;c<d.length;c++)p.qual[c]=d.charCodeAt(c)-33;p.tagDict=h.length<11?{}:Lp(h.slice(11)),p.isMateMapped()&&(u=h[6],p.mate={chr:\"=\"===u?p.chr:u,position:Number.parseInt(h[7]),strand:!(32&p.flags)}),this.setPairOrientation(p),(void 0===s||s.pass(p))&&(Rp(p,g),t.push(p))}}},setReaderDefaults:function(e,t){e.filter=\"function\"==typeof t.filter?{pass:t.filter}:new kp(t.filter),t.readgroup&&(e.filter.readgroups=new Set([t.readgroup])),e.alleleFreqThreshold=void 0===t.alleleFreqThreshold?.2:t.alleleFreqThreshold,e.samplingWindowSize=void 0===t.samplingWindowSize?100:t.samplingWindowSize,e.samplingDepth=void 0===t.samplingDepth?500:t.samplingDepth,e.samplingDepth>Bp&&(console.log(\"Warning: attempt to set sampling depth > maximum value of \"+Bp),e.samplingDepth=Bp)},setPairOrientation:function(e){if(e.isMapped()&&e.mate&&e.isMateMapped()&&e.mate.chr===e.chr){var t=e.strand?\"F\":\"R\",i=e.mate,n=i.strand?\"F\":\"R\",r=\" \",s=\" \";e.isFirstOfPair()?(r=\"1\",s=\"2\"):e.isSecondOfPair()&&(r=\"2\",s=\"1\");var o=[],a=e.fragmentLength,c=e.end-e.start;if(0===a)a=(e.start<i.position?i.position+c:i.position-c)-e.start;a>0?(o[0]=t,o[1]=r,o[2]=n,o[3]=s):(o[2]=t,o[3]=r,o[0]=n,o[1]=s),e.pairOrientation=o.join(\"\")}}};function Rp(e,t){const i=[];let n,r,s=0,o=e.start;e.scStart=e.start,e.scLengthOnRef=e.lengthOnRef;for(let a of t){let t;switch(a.ltr){case\"H\":case\"P\":break;case\"S\":t=o,e.scLengthOnRef+=a.len,0===i.length&&(e.scStart-=a.len,t-=a.len),i.push(new xp({start:t,seqOffset:s,len:a.len,type:\"S\"})),s+=a.len;break;case\"N\":case\"D\":void 0===r&&(r=[]),r.push({start:o,len:a.len,type:a.ltr}),o+=a.len;break;case\"I\":void 0===n&&(n=[]),n.push(new xp({start:o,len:a.len,seqOffset:s,type:\"I\"})),s+=a.len;break;case\"M\":case\"EQ\":case\"=\":case\"X\":i.push(new xp({start:o,seqOffset:s,len:a.len,type:\"M\"})),s+=a.len,o+=a.len;break;default:console.log(\"Error processing cigar element: \"+a.len+a.ltr)}}e.blocks=i,e.insertions=n,e.gaps=r}function Dp(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function Tp(e){var t,i,n,r,s,o,a,c,l;for(t=[],i=[],s=null,r=e.length,n=0;n<r;n++)o=e.charAt(n),l=void 0,(l=o.charCodeAt(0))>=48&&l<=57?i.push(o):(a=o,c=Number.parseInt(i.join(\"\")),i=[],null!==s&&s.ltr===a?s.len+=c:(s={len:c,ltr:a},t.push(s)));return t}function Lp(e){var t={};return e.forEach((function(e){var i=e.split(\":\");t[i[0]]=i[2]})),t}function zp(e){let t=0;const i=e.length,n={},r=new DataView(e.buffer);for(;t<i;){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const o=String.fromCharCode(e[t++]);let a;if(\"A\"===o)a=String.fromCharCode(e[t]),t++;else if(\"i\"===o||\"I\"===o)a=r.getInt32(t,!0),t+=4;else if(\"c\"===o)a=r.getInt8(t,!0),t++;else if(\"C\"===o)a=r.getUint8(t,!0),t++;else if(\"s\"===o||\"S\"===o)a=r.getInt16(t,!0),t+=2;else if(\"f\"===o)a=r.getFloat32(t,!0),t+=4;else if(\"Z\"===o)for(a=\"\";;){var s=e[t++];if(0===s)break;a+=String.fromCharCode(s)}else{if(\"B\"!==o){a=\"Error unknown type: \"+o,n[i]=a;break}{const s=String.fromCharCode(e[t++]);let o=Np[s];if(void 0===o){n[i]=`Error: unknown element type '${s}'`;break}const c=r.getInt32(t,!0);t+=4;const l=t+c*o;for(a=[];t<l;){switch(s){case\"c\":a.push(r.getInt8(t,!0));break;case\"C\":a.push(r.getUint8(t,!0));break;case\"s\":a.push(r.getInt16(t,!0));break;case\"S\":a.push(r.getUint16(t,!0));break;case\"i\":a.push(r.getInt32(t,!0));break;case\"I\":a.push(r.getUint32(t,!0));break;case\"f\":a.push(r.getFloat32(t,!0))}t+=o}}}n[i]=a}return n}class Hp{chrAliasTable=new Map;constructor(e,t){this.config=e,this.genome=t,this.bamPath=e.url,this.isDataUri=Ga(e.url),Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(!this.alignmentCache){let e;if(this.isDataUri){const t=function(e){const t=e.split(\",\"),i=t[0].split(\":\")[1];let n=t[1];n=i.indexOf(\"base64\")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s<n.length;s++)r[s]=n.charCodeAt(s);return r}(this.bamPath);e=gs(t.buffer)}else{e=gs(await Qs.loadArrayBuffer(this.bamPath,Ua(this.config)))}this.alignmentCache=this.#C(e)}const n=await this.#_(e),r=this.alignmentCache.queryFeatures(n,t,i),s=new tp(e,t,i,this.config);for(let e of r)s.push(e);return s.finish(),s}#C(e){const t=[];return this.header=Mp.decodeBamHeader(e),Mp.decodeBamRecords(e,this.header.size,t,this.header.chrNames,void 0,0,Number.MAX_SAFE_INTEGER,this.filter),new Zs(t,this.genome)}async#_(e){const t=new Set(this.header.chrNames);if(t.has(e))return e;if(this.chrAliasTable.has(e))return this.chrAliasTable.get(e);if(this.genome){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>t.has(e)));e.length>0&&(n=e[0])}return this.chrAliasTable.set(e,n),n}return e}}class Pp{chrAliasTable=new Map;constructor(e,t){this.config=e,this.genome=t,this.bamPath=e.url,this.baiPath=e.indexURL,Mp.setReaderDefaults(this,e),this._blockLoader=new yh(e)}async readAlignments(e,t,i){const n=await this.#x(e),r=new tp(e,t,i,this.config);if(void 0===n)return r;{const e=(await this.getIndex()).chunksForRange(n,t,i);if(!e||0===e.length)return r;for(let s of e){const e=await this._blockLoader.getData(s.minv,s.maxv);if(Mp.decodeBamRecords(e,s.minv.offset,r,this.header.chrNames,n,t,i,this.filter))break}return r.finish(),r}}async#x(e){if(await this.getHeader(),this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.header.chrToIndex[e];if(void 0===t){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>void 0!==this.header.chrToIndex[e]));e.length>0&&(n=e[0],t=this.header.chrToIndex[e[0]])}this.chrAliasTable.set(e,n)}return t}async getHeader(){if(!this.header){const e=this.genome,t=await this.getIndex();let i;if(t.firstBlockPosition){const e=Ua(this.config,{range:{start:t.firstBlockPosition,size:26}}),n=ms(await Qs.loadArrayBuffer(this.bamPath,e));i=t.firstBlockPosition+n}else i=64e3;const n=Ua(this.config,{range:{start:0,size:i}});this.header=await Mp.readHeader(this.bamPath,n,e)}return this.header}async getIndex(){return this.index||(this.index=await gh(this.baiPath,this.config)),this.index}async getChrIndex(){if(this.chrToIndex)return this.chrToIndex;{const e=await this.getHeader();return this.chrToIndex=e.chrToIndex,this.indexToChr=e.chrNames,this.chrNames=new Set(e.chrNames),this.chrToIndex}}}class Op{constructor(e,t){this.config=e,this.genome=t;const i={};e.sources.sequences.forEach((function(n){const r=t?t.getChromosomeName(n):n;i[r]=function(e,t,i){const n={url:e.sources.url.replace(\"$CHR\",i)};e.sources.indexURL&&(n.indexURL=e.sources.indexURL.replace(\"$CHR\",i));const r=Object.assign(e,n);return new Pp(r,t)}(e,t,n)})),this.bamReaders=i,Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(this.bamReaders.hasOwnProperty(e)){let n=this.bamReaders[e];return await n.readAlignments(e,t,i)}return new tp(e,t,i,this.config)}}const Up=function(e,t){this.config=e,this.genome=t,Mp.setReaderDefaults(this,e)};function qp(){const e=this,t=this.genome;if(this.header)return Promise.resolve(this.header);{const i=this.config.url+\"?file=\"+this.config.alignmentFile+\"&options=-b,-H\",n=Ua(this.config);return Mp.readHeader(i,n,t).then((function(t){return e.header=t,t}))}}Up.prototype.readAlignments=function(e,t,i){var n=this;return qp.call(n).then((function(r){var s,o;return s=r.chrAliasTable.hasOwnProperty(e)?r.chrAliasTable[e]:e,o=n.config.url+\"?reference=\"+n.config.referenceFile+\"&file=\"+n.config.alignmentFile+\"&region=\"+s+\":\"+t+\"-\"+i,Qs.loadString(o,Ua(n.config)).then((function(o){var a;return r.chrToIndex[s],a=new tp(e,t,i,n.config),Mp.decodeSamRecords(o,a,s,t,i,n.filter),a}))}))};class Qp extends Rh{constructor(e,t){super(e,t),Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(!this.header){const e=gs((await this.readHeaderData()).buffer);this.header=Mp.decodeBamHeader(e,this.genome),this.chrAliasTable=new Map;for(let e of this.header.chrNames)this.chrAliasTable.set(e,this.genome.getChromosomeName(e))}let n=this.chrAliasTable.has(e)?this.chrAliasTable.get(e):e;const r=gs((await this.readData(n,t,i)).buffer);this.header=Mp.decodeBamHeader(r,this.genome);const s=this.header.chrToIndex[e],o=new tp(e,t,i,this.config);return Mp.decodeBamRecords(r,this.header.size,o,this.header.chrNames,s,t,i,this.filter),o.finish(),o}}\n",
-       "/*! For license information please see cram-bundle.js.LICENSE.txt */for(var Vp=(()=>{var e={4923:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(8712),s=i(5931),o=i(9747);function a(e,t){const[i,n,r,s,o,a]=t,c=i;e[c]||(e[c]=[]),e[c].push({start:n,span:r,containerStart:s,sliceStart:o,sliceBytes:a})}t.default=class{constructor(e){this.filehandle=(0,s.open)(e.url,e.path,e.filehandle)}parseIndex(){return n(this,void 0,void 0,(function*(){const e={},t=31===(i=yield this.filehandle.readFile())[0]&&139===i[1]?(0,r.unzip)(i):i;var i;if(t.length>4&&21578050===t.readUInt32LE(0))throw new o.CramMalformedError(\"invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support\");let n=[],s=\"\";for(const i of t)if(i>=48&&i<=57||!s&&45===i)s+=String.fromCharCode(i);else if(9===i)n.push(Number.parseInt(s,10)),s=\"\";else if(10===i)n.push(Number.parseInt(s,10)),s=\"\",a(e,n),n=[];else if(13!==i&&32!==i)throw new o.CramMalformedError(\"invalid .crai index file\");return s&&n.push(Number.parseInt(s,10)),6===n.length&&a(e,n),Object.entries(e).forEach((([t,i])=>{const n=i;e[t]=n.sort(((e,t)=>e.start-t.start||e.span-t.span))})),e}))}getIndex(){return this.parseIndexP||(this.parseIndexP=this.parseIndex().catch((e=>{throw this.parseIndexP=void 0,e}))),this.parseIndexP}hasDataForReferenceSequence(e){return n(this,void 0,void 0,(function*(){return!!(yield this.getIndex())[e]}))}getEntriesForRange(e,t,i){return n(this,void 0,void 0,(function*(){const n=(yield this.getIndex())[e];if(!n)return[];const r=e=>{const n=e.start,r=e.start+e.span;return n>i?-1:r<=t?1:0},s=[];for(const e of n)0===r(e)&&s.push(e);return s}))}}},9508:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=class{constructor(e,t){this.parameters=e,this.dataType=t}}},368:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`)}decode(e,t,i,n){return(0,o.getBits)(t.content,n.coreBlock,this.parameters.length)-this.parameters.offset}}t.default=a},8635:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=n(i(9508)),s=i(400);class o extends r.default{constructor(e,t,i){super(e,t),this.instantiateCodec=i}decode(e,t,i,n){const r=this._getLengthCodec().decode(e,t,i,n),s=this._getDataCodec(),o=new Uint8Array(r);for(let a=0;a<r;a+=1)o[a]=s.decode(e,t,i,n);return o}_getLengthCodec(){const e=this.parameters.lengthsEncoding;return this.instantiateCodec(e,\"int\")}_getDataCodec(){const e=this.parameters.valuesEncoding;return this.instantiateCodec(e,\"byte\")}}t.default=o,\"_getLengthCodec _getDataCodec\".split(\" \").forEach((e=>{(0,s.tinyMemoize)(o,e)}))},4839:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{decode(e,t,i,n){const{blockContentId:s}=this.parameters,o=i[s];if(!o)throw new r.CramMalformedError(`no block found with content ID ${s}`);const a=n.externalBlocks.getCursor(s);return this._decodeByteArray(o,a)}_decodeByteArray(e,t){const i=e.content,{stopByte:n}=this.parameters,r=t.bytePosition;let s=t.bytePosition;for(;i[s]!==n&&s<i.length;){if(s===i.length)throw new o.CramBufferOverrunError(\"byteArrayStop reading beyond length of data buffer?\");s+=1}return t.bytePosition=s+1,i.subarray(r,s)}}t.default=a},8153:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(400),a=i(612);class c extends s.default{constructor(e,t){if(super(e,t),\"int\"===this.dataType)this._decodeData=this._decodeInt;else{if(\"byte\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by EXTERNAL codec`);this._decodeData=this._decodeByte}}decode(e,t,i,n){const{blockContentId:s}=this.parameters,o=i[s];if(!o)throw new r.CramMalformedError(`no block found with content ID ${s}}`);const a=n.externalBlocks.getCursor(s);return this._decodeData(o,a)}_decodeInt(e,t){const[i,n]=(0,o.parseItf8)(e.content,t.bytePosition);return t.bytePosition=t.bytePosition+n,i}_decodeByte(e,t){if(t.bytePosition>=e.content.length)throw new a.CramBufferOverrunError(\"attempted to read beyond end of block. this file seems truncated.\");return e.content[t.bytePosition++]}}t.default=c},8185:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`)}decode(e,t,i,n){let r=1;for(;0===(0,o.getBits)(t.content,n.coreBlock,1);)r+=1;return((0,o.getBits)(t.content,n.coreBlock,r-1)|1<<r-1)-this.parameters.offset}}t.default=a},612:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.CramBufferOverrunError=void 0,t.getBits=function(e,t,n){let r=0;if(t.bytePosition+(7-t.bitPosition+n)/8>e.length)throw new i(\"read error during 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t=0;t<this.parameters.numCodes;t++)e[t]={symbol:this.parameters.symbols[t],bitLength:this.parameters.bitLengths[t]};e=e.sort(((e,t)=>e.bitLength-t.bitLength||e.symbol-t.symbol)),this.codeBook={},e.forEach((e=>{this.codeBook[e.bitLength]||(this.codeBook[e.bitLength]=[]),this.codeBook[e.bitLength].push(e.symbol)}))}buildCodes(){this.codes={};let e=0,t=-1;Object.entries(this.codeBook).forEach((([i,n])=>{const s=Number.parseInt(i,10);n.forEach((i=>{const n={bitLength:s,value:i,bitCode:0};t+=1;const o=s-e;if(t<<=o,n.bitCode=t,e+=o,function(e){let t=e-(e>>1)&1431655765;return t=(858993459&t)+(t>>2&858993459),16843009*(t+(t>>4)&252645135)>>24}(t)>s)throw new r.CramMalformedError(\"Symbol out of range\");this.codes[i]=n}))}))}buildCaches(){this.sortedCodes=Object.values(this.codes).sort(((e,t)=>e.bitLength-t.bitLength||e.bitCode-t.bitCode)),this.sortedValuesByBitCode=this.sortedCodes.map((e=>e.value)),this.sortedBitCodes=this.sortedCodes.map((e=>e.bitCode)),this.sortedBitLengthsByBitCode=this.sortedCodes.map((e=>e.bitLength));const e=Math.max(...this.sortedBitCodes);this.bitCodeToValue=new Array(e+1).fill(-1);for(let e=0;e<this.sortedBitCodes.length;e+=1)this.bitCodeToValue[this.sortedCodes[e].bitCode]=e}decode(e,t,i,n){return this._decode(e,t,n.coreBlock)}_decodeZeroLengthCode(){return this.sortedCodes[0].value}_decode(e,t,i){const n=t.content;let s=0,a=0;for(let e=0;e<this.sortedCodes.length;e+=1){const t=this.sortedCodes[e].bitLength;a<<=t-s,a|=(0,o.getBits)(n,i,t-s),s=t;{const i=this.bitCodeToValue[a];if(i>-1&&this.sortedBitLengthsByBitCode[i]===t)return this.sortedValuesByBitCode[i];for(let i=e;this.sortedCodes[i+1].bitLength===t&&i<this.sortedCodes.length;i+=1)e+=1}}throw new r.CramMalformedError(\"Huffman symbol not found.\")}}t.default=a},6524:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.instantiateCodec=function e(t,i){const n=(s=\"ignore\"===i?0:t.codecId,u[s]);var s;if(!n)throw new r.CramUnimplementedError(`no codec implemented for codec ID ${t.codecId}`);return new n(t.parameters,i,e)};const r=i(9747),s=n(i(4341)),o=n(i(8153)),a=n(i(4839)),c=n(i(8635)),l=n(i(368)),h=n(i(8185)),d=n(i(99)),u={1:o.default,3:s.default,4:c.default,5:a.default,6:l.default,7:d.default,9:h.default}},99:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new 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0===a?(r=this.parameters.K,s=(0,o.getBits)(t.content,n.coreBlock,r)):(r=a+this.parameters.K-1,s=1<<r|(0,o.getBits)(t.content,n.coreBlock,r)),s-this.parameters.offset}}t.default=a},7295:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default={CRAM_FLAG_PRESERVE_QUAL_SCORES:1,CRAM_FLAG_DETACHED:2,CRAM_FLAG_MATE_DOWNSTREAM:4,CRAM_FLAG_NO_SEQ:8,CRAM_FLAG_MASK:15,CRAM_M_REVERSE:1,CRAM_M_UNMAP:2,BAM_FPAIRED:1,BAM_FPROPER_PAIR:2,BAM_FUNMAP:4,BAM_FMUNMAP:8,BAM_FREVERSE:16,BAM_FMREVERSE:32,BAM_FREAD1:64,BAM_FREAD2:128,BAM_FSECONDARY:256,BAM_FQCFAIL:512,BAM_FDUP:1024,BAM_FSUPPLEMENTARY:2048,BAM_CMATCH:0,BAM_CINS:1,BAM_CDEL:2,BAM_CREF_SKIP:3,BAM_CSOFT_CLIP:4,BAM_CHARD_CLIP:5,BAM_CPAD:6,BAM_CEQUAL:7,BAM_CDIFF:8,BAM_CBACK:9,BAM_CIGAR_STR:\"MIDNSHP:XB\",BAM_CIGAR_SHIFT:4,BAM_CIGAR_MASK:15,BAM_CIGAR_TYPE:246183}},7219:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0});const 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t[0][e[0]>>6&3]=\"C\",t[0][e[0]>>4&3]=\"G\",t[0][e[0]>>2&3]=\"T\",t[0][3&e[0]]=\"N\",t[1][e[1]>>6&3]=\"A\",t[1][e[1]>>4&3]=\"G\",t[1][e[1]>>2&3]=\"T\",t[1][3&e[1]]=\"N\",t[2][e[2]>>6&3]=\"A\",t[2][e[2]>>4&3]=\"C\",t[2][e[2]>>2&3]=\"T\",t[2][3&e[2]]=\"N\",t[3][e[3]>>6&3]=\"A\",t[3][e[3]>>4&3]=\"C\",t[3][e[3]>>2&3]=\"G\",t[3][3&e[3]]=\"N\",t[4][e[4]>>6&3]=\"A\",t[4][e[4]>>4&3]=\"C\",t[4][e[4]>>2&3]=\"G\",t[4][3&e[4]]=\"T\",t}(e.preservation.SM),this.dataSeriesEncoding=e.dataSeriesEncoding,this.tagEncoding=e.tagEncoding}getCodecForTag(e){const t=this.tagCodecCache[e];if(t)return t;{const t=this.tagEncoding[e];if(!t)throw new Error(\"Error, no tag encoding\");const i=(0,n.instantiateCodec)(t,\"byteArray\");return this.tagCodecCache[e]=i,i}}getTagNames(e){return this.tagIdsDictionary[e]}getCodecForDataSeries(e){let t=this.dataSeriesCodecCache[e];if(void 0===t){const i=this.dataSeriesEncoding[e];if(i){const o=s[e];if(!o)throw new r.CramMalformedError(`data series name ${e} not defined in 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0:e.numRecords))return null;const{majorVersion:t}=yield this.file.getDefinition(),i=(0,h.getSectionParsers)(t),n=yield this.getFirstBlock();if(void 0===n)return;if(\"COMPRESSION_HEADER\"!==n.contentType)throw new o.CramMalformedError(`invalid content type ${n.contentType} in compression header block`);const r=(0,a.parseItem)(n.content,i.cramCompressionHeader.parser,0,n.contentPosition);return Object.assign(Object.assign({},n),{parsedContent:r})}))}getFirstBlock(){return n(this,void 0,void 0,(function*(){const e=yield this.getHeader();if(e)return this.file.readBlock(e._endPosition)}))}getCompressionScheme(){return n(this,void 0,void 0,(function*(){const e=yield this.getCompressionHeaderBlock();if(e)return new l.default(e.parsedContent)}))}getSlice(e,t){return new c.default(this,e,t)}_readContainerHeader(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield 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\").forEach((e=>{(0,a.tinyMemoize)(d,e)}))},6794:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(8287),o=r(i(928)),a=r(i(7392)),c=r(i(6960)),l=r(i(235)),h=i(1307),d=i(9747),u=i(8712),f=r(i(9989)),p=i(3165),g=r(i(78)),m=i(5931),w=i(400),b=i(5417);class F{constructor(e){var t;if(this.file=(0,m.open)(e.url,e.path,e.filehandle),this.validateChecksums=!0,this.fetchReferenceSequenceCallback=e.seqFetch,this.options={checkSequenceMD5:e.checkSequenceMD5,cacheSize:null!==(t=e.cacheSize)&&void 0!==t?t:2e4},this.featureCache=new a.default({maxSize:this.options.cacheSize}),function(){const e=new Uint32Array([287454020]),t=new Uint8Array(e.buffer);return 68===t[0]?0:17===t[0]?1:2}()>0)throw new Error(\"Detected big-endian machine, may be unable to run\")}read(e,t,i,n){return this.file.read(e,t,i,n)}stat(){return this.file.stat()}getDefinition(){return n(this,void 0,void 0,(function*(){const{maxLength:e,parser:t}=(0,p.cramFileDefinition)(),i=s.Buffer.allocUnsafe(e);yield this.file.read(i,0,e,0);const n=t(i).value;if(2!==n.majorVersion&&3!==n.majorVersion)throw new d.CramUnimplementedError(`CRAM version ${n.majorVersion} not supported`);return n}))}getSamHeader(){return n(this,void 0,void 0,(function*(){const e=yield this.getContainerById(0);if(!e)throw new d.CramMalformedError(\"file contains no containers\");const t=yield e.getFirstBlock();if(void 0===t)return(0,b.parseHeaderText)(\"\");const i=t.content,n=i.readInt32LE(0),r=i.toString(\"utf8\",4,4+n);return this.header=r,(0,b.parseHeaderText)(r)}))}getHeaderText(){return n(this,void 0,void 0,(function*(){return yield this.getSamHeader(),this.header}))}getContainerById(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t);let n=i.cramFileDefinition.maxLength;const{size:r}=yield this.file.stat(),{cramContainerHeader1:s}=i;let o;for(let t=0;t<=e;t++){if(n+s.maxLength+8>=r)return;o=this.getContainerAtPosition(n);const i=yield o.getHeader();if(!i)throw new d.CramMalformedError(`container ${e} not found in file`);if(0===t){n=i._endPosition;for(let e=0;e<i.numBlocks;e++){const e=yield this.readBlock(n);if(void 0===e)return;n=e._endPosition}}else n+=i._size+i.length}return o}))}checkCrc32(e,t,i,r){return n(this,void 0,void 0,(function*(){const n=s.Buffer.allocUnsafe(t);yield this.file.read(n,0,t,e);const a=o.default.unsigned(n);if(a!==i)throw new d.CramMalformedError(`crc mismatch in ${r}: recorded CRC32 = ${i}, but calculated CRC32 = ${a}`)}))}containerCount(){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.getDefinition(),t=(0,p.getSectionParsers)(e),{size:i}=yield this.file.stat(),{cramContainerHeader1:n}=t;let r=0,s=t.cramFileDefinition.maxLength;for(;s+n.maxLength+8<i;){const e=yield this.getContainerAtPosition(s).getHeader();if(!e)break;if(0===r){s=e._endPosition;for(let t=0;t<e.numBlocks;t++){const e=yield this.readBlock(s);if(void 0===e)return;s=e._endPosition}}else s+=e._size+e.length;r+=1}return r}))}getContainerAtPosition(e){return new g.default(this,e)}readBlockHeader(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t),{cramBlockHeader:n}=i,{size:r}=yield this.file.stat();if(e+n.maxLength>=r)return;const o=s.Buffer.allocUnsafe(n.maxLength);return yield this.file.read(o,0,n.maxLength,e),(0,w.parseItem)(o,n.parser,0,e)}))}_parseSection(e,t){return n(this,arguments,void 0,(function*(e,t,i=e.maxLength,n){let r;if(n)r=n;else{const{size:e}=yield this.file.stat();if(t+i>=e)return;r=s.Buffer.allocUnsafe(i),yield this.file.read(r,0,i,t)}const o=(0,w.parseItem)(r,e.parser,0,t);if(o._size!==i)throw new d.CramMalformedError(`section read error: requested size ${i} does not equal parsed size ${o._size}`);return o}))}_uncompress(e,t,i){return n(this,void 0,void 0,(function*(){if(\"gzip\"===e)(0,u.unzip)(t).copy(i);else if(\"bzip2\"===e){const e=l.default.array(t);let n,r=l.default.header(e),o=0;do{n=l.default.decompress(e,r),-1!==n&&(s.Buffer.from(n).copy(i,o),o+=n.length,r-=n.length)}while(-1!==n)}else if(\"lzma\"===e){const e=new Response(new h.XzReadableStream((n=t,new ReadableStream({start(e){e.enqueue(n),e.close()}}))));s.Buffer.from(yield e.arrayBuffer()).copy(i)}else if(\"rans\"===e)(0,f.default)(t,i);else if(\"rans4x16\"===e)c.default.r4x16_uncompress(t,i);else if(\"arith\"===e)c.default.arith_uncompress(t,i);else if(\"fqzcomp\"===e)c.default.fqzcomp_uncompress(t,i);else{if(\"tok3\"!==e)throw new d.CramUnimplementedError(`${e} decompression not yet implemented`);c.default.tok3_uncompress(t,i)}var n}))}readBlock(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t),n=yield this.readBlockHeader(e);if(void 0===n)return;const r=n._endPosition,o=s.Buffer.allocUnsafe(n.uncompressedSize),a=Object.assign(Object.assign({},n),{_endPosition:r,contentPosition:r,content:o});if(\"raw\"!==n.compressionMethod){const e=s.Buffer.allocUnsafe(n.compressedSize);yield this.read(e,0,n.compressedSize,r),yield this._uncompress(n.compressionMethod,e,o)}else yield this.read(o,0,n.uncompressedSize,r);if(t>=3){const t=yield this._parseSection(i.cramBlockCrc32,r+n.compressedSize);if(void 0===t)return;a.crc32=t.crc32,this.validateChecksums&&(yield this.checkCrc32(e,n._size+n.compressedSize,t.crc32,\"block data\")),a._endPosition=t._endPosition,a._size=a.compressedSize+i.cramBlockCrc32.maxLength}else a._endPosition=r+a.compressedSize,a._size=a.compressedSize;return a}))}}t.default=F,\"getDefinition getSectionParsers getSamHeader\".split(\" \").forEach((e=>{(0,w.tinyMemoize)(F,e)}))},7390:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=t.CramRecord=void 0;var r=i(8401);Object.defineProperty(t,\"CramRecord\",{enumerable:!0,get:function(){return n(r).default}});var s=i(6794);Object.defineProperty(t,\"default\",{enumerable:!0,get:function(){return n(s).default}})},8401:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.MateFlagsDecoder=t.CramFlagsDecoder=t.BamFlagsDecoder=t.MateFlags=t.CramFlags=t.BamFlags=void 0;const r=n(i(7295)),s={a:0,A:0,c:1,C:1,g:2,G:2,t:3,T:3,n:4,N:4};function o(e){const t={};for(const[i,n]of e)t[`is${n}`]=e=>!!(e&i),t[`set${n}`]=e=>e|i;return t}t.BamFlags=[[1,\"Paired\"],[2,\"ProperlyPaired\"],[4,\"SegmentUnmapped\"],[8,\"MateUnmapped\"],[16,\"ReverseComplemented\"],[32,\"MateReverseComplemented\"],[64,\"Read1\"],[128,\"Read2\"],[256,\"Secondary\"],[512,\"FailedQc\"],[1024,\"Duplicate\"],[2048,\"Supplementary\"]],t.CramFlags=[[1,\"PreservingQualityScores\"],[2,\"Detached\"],[4,\"WithMateDownstream\"],[8,\"DecodeSequenceAsStar\"]],t.MateFlags=[[1,\"OnNegativeStrand\"],[2,\"Unmapped\"]],t.BamFlagsDecoder=o(t.BamFlags),t.CramFlagsDecoder=o(t.CramFlags),t.MateFlagsDecoder=o(t.MateFlags),t.default=class{constructor({flags:e,cramFlags:t,readLength:i,mappingQuality:n,lengthOnRef:r,qualityScores:s,mateRecordNumber:o,readBases:a,readFeatures:c,mateToUse:l,readGroupId:h,readName:d,sequenceId:u,uniqueId:f,templateSize:p,alignmentStart:g,tags:m}){this.flags=e,this.cramFlags=t,this.readLength=i,this.mappingQuality=n,this.lengthOnRef=r,this.qualityScores=s,a&&(this.readBases=a),this.readGroupId=h,this.readName=d,this.sequenceId=u,this.uniqueId=f,this.templateSize=p,this.alignmentStart=g,this.tags=m,c&&(this.readFeatures=c),l&&(this.mate={flags:l.mateFlags,readName:l.mateReadName,sequenceId:l.mateSequenceId,alignmentStart:l.mateAlignmentStart}),o&&(this.mateRecordNumber=o)}isPaired(){return!!(this.flags&r.default.BAM_FPAIRED)}isProperlyPaired(){return!!(this.flags&r.default.BAM_FPROPER_PAIR)}isSegmentUnmapped(){return!!(this.flags&r.default.BAM_FUNMAP)}isMateUnmapped(){return!!(this.flags&r.default.BAM_FMUNMAP)}isReverseComplemented(){return!!(this.flags&r.default.BAM_FREVERSE)}isMateReverseComplemented(){return!!(this.flags&r.default.BAM_FMREVERSE)}isRead1(){return!!(this.flags&r.default.BAM_FREAD1)}isRead2(){return!!(this.flags&r.default.BAM_FREAD2)}isSecondary(){return!!(this.flags&r.default.BAM_FSECONDARY)}isFailedQc(){return!!(this.flags&r.default.BAM_FQCFAIL)}isDuplicate(){return!!(this.flags&r.default.BAM_FDUP)}isSupplementary(){return!!(this.flags&r.default.BAM_FSUPPLEMENTARY)}isDetached(){return!!(this.cramFlags&r.default.CRAM_FLAG_DETACHED)}hasMateDownStream(){return!!(this.cramFlags&r.default.CRAM_FLAG_MATE_DOWNSTREAM)}isPreservingQualityScores(){return!!(this.cramFlags&r.default.CRAM_FLAG_PRESERVE_QUAL_SCORES)}isUnknownBases(){return!!(this.cramFlags&r.default.CRAM_FLAG_NO_SEQ)}getReadBases(){if(!this.readBases&&this._refRegion){const e=function(e,t){if(!e.lengthOnRef&&!e.readLength)return null;if(e.isUnknownBases())return null;const i=e.alignmentStart-t.start;if(!e.readFeatures)return t.seq.slice(i,i+(e.lengthOnRef||0)).toUpperCase();let n=\"\",r=i,s=0;for(;n.length<e.readLength;)if(s<e.readFeatures.length){const i=e.readFeatures[s];if(\"Q\"===i.code||\"q\"===i.code)s+=1;else if(i.pos===n.length+1)if(s+=1,\"b\"===i.code){const e=i.data;n+=e,r+=e.length}else\"B\"===i.code?(n+=i.data[0],r+=1):\"X\"===i.code?(n+=i.sub,r+=1):\"I\"===i.code?n+=i.data:\"D\"===i.code?r+=i.data:\"i\"===i.code?n+=i.data:\"N\"===i.code?r+=i.data:\"S\"===i.code?n+=i.data:\"P\"===i.code||i.code;else if(s<e.readFeatures.length){const e=t.seq.slice(r,r+i.pos-n.length-1);n+=e,r+=e.length}}else{const i=t.seq.slice(r,r+e.readLength-n.length);n+=i,r+=i.length}return n.toUpperCase()}(this,this._refRegion);e&&(this.readBases=e)}return this.readBases}getPairOrientation(){if(!this.isSegmentUnmapped()&&this.isPaired()&&!this.isMateUnmapped()&&this.mate&&this.sequenceId===this.mate.sequenceId){const e=this.isReverseComplemented()?\"R\":\"F\",t=this.isMateReverseComplemented()?\"R\":\"F\";let i=\" \",n=\" \";this.isRead1()?(i=\"1\",n=\"2\"):this.isRead2()&&(i=\"2\",n=\"1\");const r=[];let s=this.templateLength||this.templateSize;if(void 0===s)throw new Error(\"One of templateSize and templateLength must be set\");return this.alignmentStart>this.mate.alignmentStart&&s>0&&(s=-s),s>0?(r[0]=e,r[1]=i,r[2]=t,r[3]=n):(r[2]=e,r[3]=i,r[0]=t,r[1]=n),r.join(\"\")}return null}addReferenceSequence(e,t){this.readFeatures&&this.readFeatures.forEach((i=>{\"X\"===i.code&&function(e,t,i,n){const r=n.refPos-t.start,o=t.seq.charAt(r);o&&(n.ref=o);let a=s[o];void 0===a&&(a=4);const c=i.substitutionMatrix[a][n.data];c&&(n.sub=c)}(0,e,t,i)})),!this.readBases&&e.start<=this.alignmentStart&&e.end>=this.alignmentStart+(this.lengthOnRef||this.readLength)-1&&(this._refRegion=e)}toJSON(){const e={};return Object.keys(this).forEach((t=>{t.startsWith(\"_\")||(e[t]=this[t])})),e.readBases=this.getReadBases(),e}}},3165:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.cramFileDefinition=r,t.cramBlockHeader=s,t.cramBlockCrc32=o,t.cramTagDictionary=c,t.cramPreservationMap=l,t.isMappedSliceHeader=function(e){return\"number\"==typeof e.refSeqId},t.getSectionParsers=function(e){return{cramFileDefinition:r(),cramBlockHeader:s(),cramBlockCrc32:o(),cramDataSeriesEncodingMap:p(),cramTagEncodingMap:g(),cramCompressionHeader:{parser:(e,t)=>{const{value:i,offset:n}=l().parser(e,t);t=n;const{value:r,offset:s}=p().parser(e,t);t=s;const{value:o,offset:a}=g().parser(e,t);return t=a,{value:{dataSeriesEncoding:h(r),preservation:h(i),tagEncoding:h(o)},offset:t}}},cramEncoding:{parser:(e,t)=>f(e,t)},cramUnmappedSliceHeader:d(e),cramMappedSliceHeader:u(e),cramContainerHeader1:m(e),cramContainerHeader2:w(e)}};const n=i(400);function r(){return{parser:(e,t=0)=>{const i=e,n=new DataView(i.buffer,i.byteOffset,i.length);let r=0;const s=e.subarray(r,r+4).toString();r+=4;const o=n.getUint8(r);r+=1;const a=n.getUint8(r);r+=1;const c=i.subarray(r,r+20).toString().replaceAll(\"\\0\",\"\");return r+=20,{value:{magic:s,majorVersion:o,minorVersion:a,fileId:c},offset:r}},maxLength:26}}function s(){return{parser:(e,t=0)=>{const i=e,r=new DataView(i.buffer,i.byteOffset,i.length);let s=0;const o=r.getUint8(s),a=[\"raw\",\"gzip\",\"bzip2\",\"lzma\",\"rans\",\"rans4x16\",\"arith\",\"fqzcomp\",\"tok3\"][o];if(!a)throw new Error(`compression method number ${o} not implemented`);s+=1;const c=r.getUint8(s),l=[\"FILE_HEADER\",\"COMPRESSION_HEADER\",\"MAPPED_SLICE_HEADER\",\"UNMAPPED_SLICE_HEADER\",\"EXTERNAL_DATA\",\"CORE_DATA\"][c];if(!l)throw new Error(`invalid block content type id ${c}`);s+=1;const[h,d]=(0,n.parseItf8)(e,s);s+=d;const[u,f]=(0,n.parseItf8)(e,s);s+=f;const[p,g]=(0,n.parseItf8)(e,s);return s+=g,{offset:s,value:{uncompressedSize:p,compressedSize:u,contentId:h,contentType:l,compressionMethod:a}}},maxLength:17}}function o(){return{parser:(e,t)=>{const i=e,n=new DataView(i.buffer,i.byteOffset,i.length).getUint32(t,!0);return{offset:t+=4,value:{crc32:n}}},maxLength:4}}function a(e,t,i){const n=e.toString(\"utf8\",t,i),r=[];for(let e=0;e<n.length;e+=3)r.push(n.slice(e,e+3));return r}function c(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const s=e.subarray(t,t+i);t+=i;const o=[];let c=0,l=0;for(;l<s.length;l++)s[l]||(o.push(a(s,c,l)),c=l+1);return l>c&&o.push(a(s,c,l)),{value:{size:i,ents:o},offset:t}}}}function l(){return{parser:(e,t)=>{const i=e,r=new DataView(i.buffer,i.byteOffset,i.length),[s,o]=(0,n.parseItf8)(e,t);t+=o;const[a,l]=(0,n.parseItf8)(e,t);t+=l;const h=[];for(let i=0;i<a;i++){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);if(t+=2,\"MI\"===i||\"UI\"===i||\"PI\"===i||\"RN\"===i||\"AP\"===i||\"RR\"===i)h.push({key:i,value:!!r.getUint8(t)}),t+=1;else if(\"SM\"===i)h.push({key:i,value:[r.getUint8(t),r.getUint8(t+1),r.getUint8(t+2),r.getUint8(t+3),r.getUint8(t+4)]}),t+=5;else{if(\"TD\"!==i)throw new Error(`unknown key ${i}`);{const{offset:n,value:r}=c().parser(e,t);h.push({key:i,value:r.ents}),t=n}}}return{value:{mapSize:s,mapCount:a,ents:h},offset:t}}}}function h(e){const t={};for(const{key:i,value:n}of e.ents)t[i]&&console.warn(`duplicate key ${i} in map`),t[i]=n;return t}function d(e){return{parser:(t,i)=>{const[r,s]=(0,n.parseItf8)(t,i);i+=s;let o=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);i+=r,o=e}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);i+=r,o=e}else console.warn(\"recordCounter=0\");const[a,c]=(0,n.parseItf8)(t,i);i+=c;const[l,h]=(0,n.parseItf8)(t,i);i+=h;const d=[];for(let e=0;e<l;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,d.push(e)}let u;return e>=2&&(u=[...t.subarray(i,i+16)],i+=16),{value:{recordCounter:o,md5:u,contentIds:d,numContentIds:l,numBlocks:a,numRecords:r},offset:i}},maxLength:e=>40+5*e}}function u(e){return{parser:(t,i)=>{const[r,s]=(0,n.parseItf8)(t,i);i+=s;const[o,a]=(0,n.parseItf8)(t,i);i+=a;const[c,l]=(0,n.parseItf8)(t,i);i+=l;const[h,d]=(0,n.parseItf8)(t,i);i+=d;let u=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);i+=r,u=e}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);i+=r,u=e}else console.warn(\"majorVersion is <2, recordCounter set to 0\");const[f,p]=(0,n.parseItf8)(t,i);i+=p;const[g,m]=(0,n.parseItf8)(t,i);i+=m;const w=[];for(let e=0;e<g;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,w.push(e)}const[b,F]=(0,n.parseItf8)(t,i);let v;return i+=F,e>=2&&(v=[...t.subarray(i,i+16)],i+=16),{value:{md5:v,numBlocks:f,numRecords:h,numContentIds:g,refSeqSpan:c,refSeqId:r,refSeqStart:o,recordCounter:u,refBaseBlockId:b,contentIds:w},offset:i}},maxLength:e=>60+5*e}}function f(e,t){const i=e,r=new DataView(i.buffer,i.byteOffset,i.length),[s,o]=(0,n.parseItf8)(e,t);t+=o;const[a,c]=(0,n.parseItf8)(e,t);t+=c;const l={};if(0===s);else if(1===s){const[i,r]=(0,n.parseItf8)(e,t);l.blockContentId=i,t+=r}else if(2===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.M=s,t+=o}else if(3===s){const i=(0,n.parseItf8)(e,t),r=i[0];t+=i[1];const s=[];for(let i=0;i<r;i++){const i=(0,n.parseItf8)(e,t);s.push(i[0]),t+=i[1]}l.symbols=s;const o=(0,n.parseItf8)(e,t),a=i[0];l.numLengths=a,l.numCodes=r,l.numLengths=a,t+=o[1];const c=[];for(let i=0;i<a;i++){const i=(0,n.parseItf8)(e,t);t+=i[1],c.push(i[0])}l.bitLengths=c}else if(4===s){const{value:i,offset:n}=f(e,t);l.lengthsEncoding=i,t=n;const{value:r,offset:s}=f(e,t);l.valuesEncoding=r,t=s}else if(5===s){l.stopByte=r.getUint8(t),t+=1;const[i,s]=(0,n.parseItf8)(e,t);l.blockContentId=i,t+=s}else if(6===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.length=s,t+=o}else if(7===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.K=s,t+=o}else if(8===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.log2m=s,t+=o}else{if(9!==s)throw new Error(`unknown codecId ${s}`);{const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r}}return{value:{codecId:s,parametersBytes:a,parameters:l},offset:t}}function p(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const[s,o]=(0,n.parseItf8)(e,t);t+=o;const a=[];for(let i=0;i<s;i++){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const{value:n,offset:r}=f(e,t);t=r,a.push({key:i,value:n})}return{value:{mapSize:i,ents:a,mapCount:s},offset:t}}}}function g(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const[s,o]=(0,n.parseItf8)(e,t);t+=o;const a=[];for(let i=0;i<s;i++){const[i,r]=(0,n.parseItf8)(e,t);t+=r;const s=String.fromCharCode(i>>16&255)+String.fromCharCode(i>>8&255)+String.fromCharCode(255&i),{value:o,offset:c}=f(e,t);t=c,a.push({key:s,value:o})}return{value:{mapSize:i,ents:a,mapCount:s},offset:t}}}}function m(e){return{maxLength:52,parser:(t,i)=>{const r=t,s=new DataView(r.buffer,r.byteOffset,r.length).getInt32(i,!0);i+=4;const[o,a]=(0,n.parseItf8)(t,i);i+=a;const[c,l]=(0,n.parseItf8)(t,i);i+=l;const[h,d]=(0,n.parseItf8)(t,i);i+=d;const[u,f]=(0,n.parseItf8)(t,i);i+=f;let p,g=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);g=e,i+=r}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);g=e,i+=r}else console.warn(\"setting recordCounter=0\");if(e>1){const[e,r]=(0,n.parseLtf8)(t,i);p=e,i+=r}const[m,w]=(0,n.parseItf8)(t,i);i+=w;const[b,F]=(0,n.parseItf8)(t,i);return{value:{length:s,refSeqId:o,refSeqStart:c,alignmentSpan:h,numBlocks:m,numLandmarks:b,numBases:p,recordCounter:g,numRecords:u},offset:i+=F}}}}function w(e){return{parser:(t,i)=>{const r=t,s=new DataView(r.buffer,r.byteOffset,r.length),[o,a]=(0,n.parseItf8)(t,i);i+=a;const c=[];for(let e=0;e<o;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,c.push(e)}let l;return e>=3&&(l=s.getUint32(i,!0),i+=4),{value:Object.assign(Object.assign({},void 0===l?{}:{crc32:l}),{numLandmarks:o,landmarks:c}),offset:i}},maxLength:e=>5+5*e+4}}},6484:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,c,l,h,d,u,f){let p=t(\"BF\");const g=t(\"CF\");if(!(0,s.isMappedSliceHeader)(c.parsedContent))throw new Error(\"slice header not mapped\");const m=u>1&&-2===c.parsedContent.refSeqId?t(\"RI\"):c.parsedContent.refSeqId,w=t(\"RL\");let b=t(\"AP\");i.APdelta&&(b+=d.lastAlignmentStart),d.lastAlignmentStart=b;const F=t(\"RG\");let v,y,A,C;if(i.readNamesIncluded&&(v=o(t(\"RN\"))),r.CramFlagsDecoder.isDetached(g)){const e=t(\"MF\");let n;i.readNamesIncluded||(n=o(t(\"RN\")),v=n);const s=t(\"NS\"),a=t(\"NP\");(e||s>-1)&&(y={mateFlags:e,mateSequenceId:s,mateAlignmentStart:a,mateReadName:n}),A=t(\"TS\"),r.MateFlagsDecoder.isUnmapped(e)&&(p=r.BamFlagsDecoder.setMateUnmapped(p)),r.MateFlagsDecoder.isOnNegativeStrand(e)&&(p=r.BamFlagsDecoder.setMateReverseComplemented(p))}else r.CramFlagsDecoder.isWithMateDownstream(g)&&(C=t(\"NF\")+f+1);const _=t(\"TL\");if(_<0)throw new n.CramMalformedError(\"invalid TL index\");const x={},k=i.getTagNames(_),I=k.length;for(let t=0;t<I;t+=1){const n=k[t],r=n.slice(0,2),s=n.slice(2,3),o=i.getCodecForTag(n).decode(e,l,h,d);x[r]=\"number\"==typeof o?o:a(s,o)}let S,E,N,B,M;if(r.BamFlagsDecoder.isSegmentUnmapped(p))if(r.CramFlagsDecoder.isDecodeSequenceAsStar(g))M=null,B=null;else{const e=new Array(w);for(let i=0;i<e.length;i+=1)e[i]=t(\"BA\");if(M=String.fromCharCode(...e),r.CramFlagsDecoder.isPreservingQualityScores(g)){B=new Array(w);for(let i=0;i<e.length;i+=1)B[i]=t(\"QS\")}}else{const e=t(\"FN\");if(e&&(S=function(e,t,i,r,s){let o=0,a=e-1;const c=new Array(t);function l([e,t]){const n=i(t);if(\"character\"===e)return String.fromCharCode(n);if(\"string\"===e){let e=\"\";for(let t=0;t<n.byteLength;t++)e+=String.fromCharCode(n[t]);return e}return\"numArray\"===e?n.toArray():n}for(let e=0;e<t;e+=1){const t=String.fromCharCode(i(\"FC\")),r=i(\"FP\"),h={B:[\"character\",\"BA\"],S:[\"string\",s>1?\"SC\":\"IN\"],X:[\"number\",\"BS\"],D:[\"number\",\"DL\"],I:[\"string\",\"IN\"],i:[\"character\",\"BA\"],b:[\"string\",\"BB\"],q:[\"numArray\",\"QQ\"],Q:[\"number\",\"QS\"],H:[\"number\",\"HC\"],P:[\"number\",\"PD\"],N:[\"number\",\"RS\"]}[t];if(!h)throw new n.CramMalformedError(`invalid read feature code \"${t}\"`);let d=l(h);const u={B:[\"number\",\"QS\"]}[t];u&&(d=[d,l(u)]),o+=r;const f=o;a+=r;const p=a;\"D\"===t||\"N\"===t?a+=d:\"I\"===t||\"S\"===t?a-=d.length:\"i\"===t&&(a-=1),c[e]={code:t,pos:f,refPos:p,data:d}}return c}(b,e,t,0,u)),E=w,S)for(const{code:e,data:t}of S)\"D\"===e||\"N\"===e?E+=t:\"I\"===e||\"S\"===e?E-=t.length:\"i\"===e&&(E-=1);if(Number.isNaN(E)&&(console.warn(`${v||`${m}:${b}`} record has invalid read features`),E=w),N=t(\"MQ\"),r.CramFlagsDecoder.isPreservingQualityScores(g)){B=new Array(w);for(let e=0;e<B.length;e++)B[e]=t(\"QS\")}}return{readLength:w,sequenceId:m,cramFlags:g,flags:p,alignmentStart:b,readGroupId:F,readName:v,mateToUse:y,templateSize:A,mateRecordNumber:C,readFeatures:S,lengthOnRef:E,mappingQuality:N,qualityScores:B,readBases:M,tags:x}};const n=i(9747),r=i(8401),s=i(3165);function o(e){let t=\"\";for(let i=0;i<e.length&&0!==e[i];i++)t+=String.fromCharCode(e[i]);return t}function a(e,t){if(\"Z\"===e)return o(t);if(\"A\"===e)return String.fromCharCode(t[0]);if(\"I\"===e)return new Uint32Array(t.buffer)[0];if(\"i\"===e)return new Int32Array(t.buffer)[0];if(\"s\"===e)return new Int16Array(t.buffer)[0];if(\"S\"===e)return new Uint16Array(t.buffer)[0];if(\"c\"===e)return new Int8Array(t.buffer)[0];if(\"C\"===e)return t[0];if(\"f\"===e)return new Float32Array(t.buffer)[0];if(\"H\"===e)return Number.parseInt(o(t).replace(/^0x/,\"\"),16);if(\"B\"===e)return function(e){const t=String.fromCharCode(e[0]),i=new DataView(e.buffer).getUint32(1,!0),n=new Array(i);if(e=e.slice(5),\"c\"===t){const t=new Int8Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"C\"===t){const t=new Uint8Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"s\"===t){const t=new Int16Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"S\"===t){const t=new Uint16Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"i\"===t){const t=new Int32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"I\"===t){const t=new Uint32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else{if(\"f\"!==t)throw new Error(`unknown type: ${t}`);{const t=new Float32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}}return n}(t);throw new n.CramMalformedError(`Unrecognized tag type ${e}`)}},6771:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(9747),o=i(400),a=r(i(7295)),c=r(i(6484)),l=r(i(8401)),h=i(3165),d=i(612);function u(e,t,i,n){const r=!!(n.mate||void 0!==n.mateRecordNumber&&n.mateRecordNumber!==t);i.readName||(i.readName=String(i.uniqueId),n.readName=i.readName),i.mate={sequenceId:n.sequenceId,alignmentStart:n.alignmentStart,uniqueId:n.uniqueId},n.readName&&(i.mate.readName=n.readName),n.mate||void 0!==n.mateRecordNumber||(n.mate={sequenceId:i.sequenceId,alignmentStart:i.alignmentStart,uniqueId:i.uniqueId},i.readName&&(n.mate.readName=i.readName)),i.flags|=a.default.BAM_FPAIRED,n.flags&a.default.BAM_FUNMAP&&(i.flags|=a.default.BAM_FMUNMAP),i.flags&a.default.BAM_FUNMAP&&(n.flags|=a.default.BAM_FMUNMAP),n.flags&a.default.BAM_FREVERSE&&(i.flags|=a.default.BAM_FMREVERSE),i.flags&a.default.BAM_FREVERSE&&(n.flags|=a.default.BAM_FMREVERSE),void 0===i.templateLength&&(r?function(e,t,i){const n=function t(i){const n=[i];if(void 0!==i.mateRecordNumber&&i.mateRecordNumber>=0){const r=e[i.mateRecordNumber];if(!r)throw new s.CramMalformedError(\"intra-slice mate record not found, this file seems malformed\");n.push(...t(r))}return n}(i),r=n.map((e=>e.alignmentStart)),o=n.map((e=>e.alignmentStart+e.readLength-1)),a=Math.max(...o)-Math.min(...r)+1;a>=0&&n.forEach((e=>{if(void 0!==e.templateLength)throw new s.CramMalformedError(\"mate pair group has some members that have template lengths already, this file seems malformed\");e.templateLength=a}))}(e,0,i):function(e,t){const i=Math.min(e.alignmentStart,t.alignmentStart),n=Math.max(e.alignmentStart+e.readLength-1,t.alignmentStart+t.readLength-1)-i+1;e.templateLength=n,t.templateLength=n}(i,n)),i.mateRecordNumber=void 0}class f{constructor(e,t,i){this.container=e,this.containerPosition=t,this.sliceSize=i,this.file=e.file}getHeader(){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.file.getDefinition(),t=(0,h.getSectionParsers)(e),i=yield this.container.getHeader();if(!i)throw new Error(\"no container header detected\");const n=yield this.file.readBlock(i._endPosition+this.containerPosition);if(void 0===n)throw new Error(\"block header undefined\");if(\"MAPPED_SLICE_HEADER\"===n.contentType){const e=(0,o.parseItem)(n.content,t.cramMappedSliceHeader.parser,0,i._endPosition);return Object.assign(Object.assign({},n),{parsedContent:e})}if(\"UNMAPPED_SLICE_HEADER\"===n.contentType){const e=(0,o.parseItem)(n.content,t.cramUnmappedSliceHeader.parser,0,i._endPosition);return Object.assign(Object.assign({},n),{parsedContent:e})}throw new s.CramMalformedError(`error reading slice header block, invalid content type ${n.contentType}`)}))}getBlocks(){return n(this,void 0,void 0,(function*(){const e=yield this.getHeader();let t=e._endPosition;const i=new Array(e.parsedContent.numBlocks);for(let e=0;e<i.length;e++){const n=yield this.file.readBlock(t);if(void 0===n)throw new Error(\"block undefined\");i[e]=n,t=i[e]._endPosition}return i}))}getCoreDataBlock(){return n(this,void 0,void 0,(function*(){return(yield this.getBlocks())[0]}))}_getBlocksContentIdIndex(){return n(this,void 0,void 0,(function*(){const e=yield this.getBlocks(),t={};return e.forEach((e=>{\"EXTERNAL_DATA\"===e.contentType&&(t[e.contentId]=e)})),t}))}getBlockByContentId(e){return n(this,void 0,void 0,(function*(){return(yield this._getBlocksContentIdIndex())[e]}))}getReferenceRegion(){return n(this,void 0,void 0,(function*(){const e=(yield this.getHeader()).parsedContent;if(!(0,h.isMappedSliceHeader)(e))throw new Error(\"slice header not mapped\");if(e.refSeqId<0)return;const t=yield this.container.getCompressionScheme();if(void 0===t)throw new Error(\"compression scheme undefined\");if(e.refBaseBlockId>=0){const t=yield this.getBlockByContentId(e.refBaseBlockId);if(!t)throw new s.CramMalformedError(\"embedded reference specified, but reference block does not exist\");return{seq:t.data.toString(\"utf8\"),start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan}}if(t.referenceRequired||this.file.fetchReferenceSequenceCallback){if(!this.file.fetchReferenceSequenceCallback)throw new Error(\"reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence\");const t=yield this.file.fetchReferenceSequenceCallback(e.refSeqId,e.refSeqStart,e.refSeqStart+e.refSeqSpan-1);if(t.length!==e.refSeqSpan)throw new s.CramArgumentError(\"seqFetch callback returned a reference sequence of the wrong length\");return{seq:t,start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan}}}))}getAllRecords(){return this.getRecords((()=>!0))}_fetchRecords(){return n(this,void 0,void 0,(function*(){var e,t;const{majorVersion:i}=yield this.file.getDefinition(),n=yield this.container.getCompressionScheme();if(void 0===n)throw new Error(\"compression scheme undefined\");const r=yield this.getHeader(),a=yield this._getBlocksContentIdIndex();if(i>1&&this.file.options.checkSequenceMD5&&(0,h.isMappedSliceHeader)(r.parsedContent)&&r.parsedContent.refSeqId>=0&&\"0000000000000000\"!==(null===(e=r.parsedContent.md5)||void 0===e?void 0:e.join(\"\"))){const e=yield this.getReferenceRegion();if(e){const{seq:i,start:n,end:a}=e,c=(0,o.sequenceMD5)(i),l=null===(t=r.parsedContent.md5)||void 0===t?void 0:t.map((e=>(e<16?\"0\":\"\")+e.toString(16))).join(\"\");if(c!==l)throw new s.CramMalformedError(`MD5 checksum reference mismatch for ref ${r.parsedContent.refSeqId} pos ${n}..${a}. recorded MD5: ${l}, calculated MD5: ${c}`)}}const f=yield this.getCoreDataBlock(),p={lastAlignmentStart:(0,h.isMappedSliceHeader)(r.parsedContent)?r.parsedContent.refSeqStart:0,coreBlock:{bitPosition:7,bytePosition:0},externalBlocks:{map:new Map,getCursor(e){let t=this.map.get(e);return void 0===t&&(t={bitPosition:7,bytePosition:0},this.map.set(e,t)),t}}},g=e=>{const t=n.getCodecForDataSeries(e);if(!t)throw new s.CramMalformedError(`no codec defined for ${e} data series`);return t.decode(this,f,a,p)},m=new Array(r.parsedContent.numRecords);for(let t=0;t<m.length;t+=1)try{const e=(0,c.default)(this,g,n,r,f,a,p,i,t);m[t]=new l.default(Object.assign(Object.assign({},e),{uniqueId:r.contentPosition+r.parsedContent.recordCounter+t+1}))}catch(e){if(e instanceof d.CramBufferOverrunError){console.warn(\"read attempted beyond end of buffer, file seems truncated.\");break}throw e}for(let e=0;e<m.length;e+=1){const{mateRecordNumber:t}=m[e];void 0!==t&&t>=0&&u(m,e,m[e],m[t])}return m}))}getRecords(e){return n(this,void 0,void 0,(function*(){const t=this.container.filePosition+this.containerPosition;let i=this.file.featureCache.get(t.toString());i||(i=this._fetchRecords(),this.file.featureCache.set(t.toString(),i));const r=(yield i).filter(e);if(r.length&&this.file.fetchReferenceSequenceCallback){const e=yield this.getHeader();if((0,h.isMappedSliceHeader)(e.parsedContent)&&(e.parsedContent.refSeqId>=0||-2===e.parsedContent.refSeqId)){const t=e.parsedContent.refSeqId>=0?e.parsedContent.refSeqId:void 0,i=yield this.container.getCompressionScheme();if(void 0===i)throw new Error(\"compression scheme undefined\");const s={};for(const e of r){const i=void 0!==t?t:e.sequenceId;let n=s[i];n||(n={id:i,start:e.alignmentStart,end:Number.NEGATIVE_INFINITY,seq:null},s[i]=n);const r=e.alignmentStart+(e.lengthOnRef||e.readLength)-1;r>n.end&&(n.end=r),e.alignmentStart<n.start&&(n.start=e.alignmentStart)}yield Promise.all(Object.values(s).map((e=>n(this,void 0,void 0,(function*(){-1!==e.id&&e.start<=e.end&&this.file.fetchReferenceSequenceCallback&&(e.seq=yield this.file.fetchReferenceSequenceCallback(e.id,e.start,e.end))})))));for(const e of r){const n=s[void 0!==t?t:e.sequenceId];if(null==n?void 0:n.seq){const t=n.seq;e.addReferenceSequence(Object.assign(Object.assign({},n),{seq:t}),i)}}}}return r}))}}t.default=f,\"getHeader getBlocks _getBlocksContentIdIndex\".split(\" \").forEach((e=>{(0,o.tinyMemoize)(f,e)}))},400:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.itf8Size=function(e){return-128&e?-16384&e?-2097152&e?-268435456&e?5:4:3:2:1},t.parseItf8=function(e,t){let i=t;const n=e[i];let r;if(n<128?(r=n,i+=1):n<192?(r=16383&(n<<8|e[i+1]),i+=2):n<224?(r=2097151&(n<<16|e[i+1]<<8|e[i+2]),i+=3):n<240?(r=268435455&(n<<24|e[i+1]<<16|e[i+2]<<8|e[i+3]),i+=4):(r=(15&n)<<28|e[i+1]<<20|e[i+2]<<12|e[i+3]<<4|15&e[i+4],i+=5),i>e.length)throw new o.CramBufferOverrunError(\"Attempted to read beyond end of buffer; this file seems truncated.\");return[r,i-t]},t.parseLtf8=function(e,t){let i=t;const n=e[i];let r;if(n<128)r=n,i+=1;else if(n<192)r=16383&(e[i]<<8|e[i+1]),i+=2;else if(n<224)r=2097151&(e[i]<<16|e[i+1]<<8|e[i+2]),r=(63&n)<<16|e.readUInt16LE(i+1),i+=3;else if(n<240)r=268435455&(e[i]<<24|e[i+1]<<16|e[i+2]<<8|e[i+3]),i+=4;else if(n<248)r=(15&e[i])*Math.pow(2,32)+(e[i+1]<<24)|e[i+2]<<16|e[i+3]<<8|e[i+4],i+=5;else if(n<252)r=((7&e[i])<<8|e[i+1])*Math.pow(2,32)+(e[i+2]<<24)|e[i+3]<<16|e[i+4]<<8|e[i+5],i+=6;else if(n<254)r=((3&e[i])<<16|e[i+1]<<8|e[i+2])*Math.pow(2,32)+(e[i+3]<<24)|e[i+4]<<16|e[i+5]<<8|e[i+6],i+=7;else if(n<255){if(r=s.default.fromBytesBE(e.slice(i+1,i+8)),r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new Error(\"integer overflow\");r=r.toNumber(),i+=8}else{if(r=s.default.fromBytesBE(e.slice(i+1,i+9)),r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new Error(\"integer overflow\");r=r.toNumber(),i+=9}return[r,i-t]},t.parseItem=function(e,t,i=0,n=0){const{offset:r,value:s}=t(e,i);return Object.assign(Object.assign({},s),{_endPosition:r+n,_size:r-i})},t.tinyMemoize=function(e,t){const i=e.prototype[t],n=`_memo_${t}`;e.prototype[t]=function(){if(!(n in this)){const e=i.call(this);this[n]=e,Promise.resolve(e).catch((()=>{delete this[n]}))}return this[n]}},t.sequenceMD5=function(e){return(0,r.default)(e.toUpperCase().replaceAll(/[^\\u0021-\\u007e]/g,\"\"))};const r=n(i(3503)),s=n(i(8570)),o=i(612)},9747:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.CramArgumentError=t.CramSizeLimitError=t.CramMalformedError=t.CramUnimplementedError=t.CramError=void 0;class i extends Error{}t.CramError=i;class n extends Error{}t.CramUnimplementedError=n,t.CramMalformedError=class extends i{},t.CramSizeLimitError=class extends i{},t.CramArgumentError=class extends i{}},7806:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.IndexedCramFile=t.CraiIndex=t.CramRecord=t.CramFile=void 0;var r=i(7390);Object.defineProperty(t,\"CramFile\",{enumerable:!0,get:function(){return n(r).default}}),Object.defineProperty(t,\"CramRecord\",{enumerable:!0,get:function(){return r.CramRecord}});var s=i(4923);Object.defineProperty(t,\"CraiIndex\",{enumerable:!0,get:function(){return n(s).default}});var o=i(6014);Object.defineProperty(t,\"IndexedCramFile\",{enumerable:!0,get:function(){return n(o).default}})},6014:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(9747),o=r(i(7390));t.default=class{constructor(e){var t;if(this.cram=null!==(t=e.cram)&&void 0!==t?t:new o.default({url:e.cramUrl,path:e.cramPath,filehandle:e.cramFilehandle,seqFetch:e.seqFetch,checkSequenceMD5:e.checkSequenceMD5,cacheSize:e.cacheSize}),!(this.cram instanceof o.default))throw new Error(\"invalid arguments: no cramfile\");this.index=e.index}getRecordsForRange(e,t,i){return n(this,arguments,void 0,(function*(e,t,i,n={}){if(n.viewAsPairs=n.viewAsPairs||!1,n.pairAcrossChr=n.pairAcrossChr||!1,n.maxInsertSize=n.maxInsertSize||2e5,\"string\"==typeof e)throw new s.CramUnimplementedError(\"string sequence names not yet supported\");const r=e,o=yield this.index.getEntriesForRange(r,t,i),a=n=>n.sequenceId===e&&n.alignmentStart<=i&&void 0!==n.lengthOnRef&&n.alignmentStart+n.lengthOnRef-1>=t,c=yield Promise.all(o.map((e=>this.getRecordsInSlice(e,a))));let l=Array.prototype.concat(...c);if(n.viewAsPairs){const e={},t={};for(const i of l){const n=i.readName;if(void 0===n)throw new Error(\"readName undefined\");const r=i.uniqueId;e[n]||(e[n]=0),e[n]+=1,t[r]=1}const i={};Object.entries(e).forEach((([e,t])=>{1===t&&(i[e]=!0)}));const s=[];for(const e of l){const t=e.readName;if(void 0===t)throw new Error(\"readName undefined\");if(i[t]&&e.mate&&(e.mate.sequenceId===r||n.pairAcrossChr)&&Math.abs(e.alignmentStart-e.mate.alignmentStart)<n.maxInsertSize){const t=this.index.getEntriesForRange(e.mate.sequenceId,e.mate.alignmentStart,e.mate.alignmentStart+1);s.push(t)}}const o=yield Promise.all(s);let a=[];for(const e of o)a.push(...e);a=a.sort(((e,t)=>e.toString().localeCompare(t.toString()))).filter(((e,t,i)=>!t||e.toString()!==i[t-1].toString()));const c=[];for(const e of a){let n=this.cram.featureCache.get(e.toString());n||(n=this.getRecordsInSlice(e,(()=>!0)),this.cram.featureCache.set(e.toString(),n));const r=n.then((e=>{const n=[];for(const r of e){if(void 0===r.readName)throw new Error(\"readName undefined\");i[r.readName]&&!t[r.uniqueId]&&n.push(r)}return n}));c.push(r)}const h=yield Promise.all(c);if(h.length){const e=h.reduce(((e,t)=>e.concat(t)));l=l.concat(e)}}return l}))}getRecordsInSlice({containerStart:e,sliceStart:t,sliceBytes:i},n){return this.cram.getContainerAtPosition(e).getSlice(t,i).getRecords(n)}hasDataForReferenceSequence(e){return this.index.hasDataForReferenceSequence(e)}}},5931:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.RemoteFile=t.LocalFile=void 0,t.open=function(e,t,i){if(i)return i;if(e)return new n.RemoteFile(e);if(t)return new n.LocalFile(t);throw new Error(\"no url, path, or filehandle provided, cannot open\")};const n=i(1113);var r=i(1113);Object.defineProperty(t,\"LocalFile\",{enumerable:!0,get:function(){return r.LocalFile}}),Object.defineProperty(t,\"RemoteFile\",{enumerable:!0,get:function(){return r.RemoteFile}})},6476:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.RANS_BYTE_L=t.TOTFREQ=t.TF_SHIFT=void 0,t.TF_SHIFT=12,t.TOTFREQ=4096,t.RANS_BYTE_L=1<<23},997:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,n){let a=e.getInt(),c=e.getInt(),l=e.getInt(),h=e.getInt();const d=n.remaining(),u=-4&d;for(let r=0;r<u;r+=4){const d=t.R[o.default.get(a,s.TF_SHIFT)],u=t.R[o.default.get(c,s.TF_SHIFT)],f=t.R[o.default.get(l,s.TF_SHIFT)],p=t.R[o.default.get(h,s.TF_SHIFT)];n.putAt(r,d),n.putAt(r+1,u),n.putAt(r+2,f),n.putAt(r+3,p),a=o.default.advanceSymbolStep(a,i[255&d],s.TF_SHIFT),c=o.default.advanceSymbolStep(c,i[255&u],s.TF_SHIFT),l=o.default.advanceSymbolStep(l,i[255&f],s.TF_SHIFT),h=o.default.advanceSymbolStep(h,i[255&p],s.TF_SHIFT),a=o.default.renormalize(a,e),c=o.default.renormalize(c,e),l=o.default.renormalize(l,e),h=o.default.renormalize(h,e)}let f;switch(n.setPosition(u),3&d){case 0:break;case 1:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f);break;case 2:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(c,s.TF_SHIFT)],o.default.advanceSymbol(c,e,i[255&f],s.TF_SHIFT),n.put(f);break;case 3:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(c,s.TF_SHIFT)],o.default.advanceSymbol(c,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(l,s.TF_SHIFT)],o.default.advanceSymbol(l,e,i[255&f],s.TF_SHIFT),n.put(f);break;default:throw new r.CramMalformedError(\"invalid output size encountered during rANS decoding\")}n.setPosition(0)};const r=i(9747),s=i(6476),o=n(i(488))},7960:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,n){const o=t.remaining();let a=e.getInt(),c=e.getInt(),l=e.getInt(),h=e.getInt();const d=o>>2;let u=0,f=d,p=2*d,g=3*d,m=0,w=0,b=0,F=0;for(;u<d;u+=1,f+=1,p+=1,g+=1){const o=255&i[m].R[s.default.get(a,r.TF_SHIFT)],d=255&i[w].R[s.default.get(c,r.TF_SHIFT)],v=255&i[b].R[s.default.get(l,r.TF_SHIFT)],y=255&i[F].R[s.default.get(h,r.TF_SHIFT)];t.putAt(u,o),t.putAt(f,d),t.putAt(p,v),t.putAt(g,y),a=s.default.advanceSymbolStep(a,n[m][o],r.TF_SHIFT),c=s.default.advanceSymbolStep(c,n[w][d],r.TF_SHIFT),l=s.default.advanceSymbolStep(l,n[b][v],r.TF_SHIFT),h=s.default.advanceSymbolStep(h,n[F][y],r.TF_SHIFT),a=s.default.renormalize(a,e),c=s.default.renormalize(c,e),l=s.default.renormalize(l,e),h=s.default.renormalize(h,e),m=o,w=d,b=v,F=y}for(;g<o;g+=1){const o=255&i[F].R[s.default.get(h,r.TF_SHIFT)];t.putAt(g,o),h=s.default.advanceSymbol(h,e,n[F][o],r.TF_SHIFT),F=o}};const r=i(6476),s=n(i(488))},488:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0});const n=i(9747),r=i(6476);class s{constructor(){this.F=void 0,this.C=void 0}}function o(e,t,i,n){return i*(e>>n)+(e&(1<<n)-1)-t}t.default={FC:s,AriDecoder:class{constructor(){this.fc=new Array(256);for(let e=0;e<this.fc.length;e+=1)this.fc[e]=new s;this.R=null}},DecodingSymbol:class{constructor(){this.start=void 0,this.freq=void 0}},symbolInit:function(e,t,i){if(!(t<=65536))throw new n.CramMalformedError(\"assertion failed: start <= 1<<16\");if(!(i<=65536-t))throw new n.CramMalformedError(\"assertion failed: freq <= 1<<16\");e.start=t,e.freq=i},advanceStep:o,advanceSymbolStep:function(e,t,i){return o(e,t.start,t.freq,i)},get:function(e,t){return e&(1<<t)-1},advanceSymbol:function(e,t,i,n){return function(e,t,i,n,s){if((e=n*(e>>s)+(e&(1<<s)-1)-i)<r.RANS_BYTE_L)do{e=e<<8|255&t.get()}while(e<r.RANS_BYTE_L);return e}(e,t,i.start,i.freq,n)},renormalize:function(e,t){if(e<r.RANS_BYTE_L)do{e=e<<8|255&t.get()}while(e<r.RANS_BYTE_L);return e}}},1971:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.readStatsO0=function(e,t,i){let n=0,r=0,c=255&e.get();do{null==t.fc[c]&&(t.fc[c]=new o.default.FC),t.fc[c].F=255&e.get(),t.fc[c].F>=128&&(t.fc[c].F&=-129,t.fc[c].F=(127&t.fc[c].F)<<8|255&e.get()),t.fc[c].C=r,o.default.symbolInit(i[c],t.fc[c].C,t.fc[c].F),t.R||(t.R=new Array(s.TOTFREQ)),t.R.fill(c,r,r+t.fc[c].F),r+=t.fc[c].F,0===n&&c+1===(255&e.getByteAt(e.position()))?(c=255&e.get(),n=255&e.get()):0!==n?(n-=1,c+=1):c=255&e.get()}while(0!==c);a(r<s.TOTFREQ)},t.readStatsO1=function(e,t,i){let n=0,r=255&e.get();do{let c=0,l=0,h=255&e.get();null==t[r]&&(t[r]=new o.default.AriDecoder);do{null==t[r].fc[h]&&(t[r].fc[h]=new o.default.FC),t[r].fc[h].F=255&e.get(),t[r].fc[h].F>=128&&(t[r].fc[h].F&=-129,t[r].fc[h].F=(127&t[r].fc[h].F)<<8|255&e.get()),t[r].fc[h].C=l,0===t[r].fc[h].F&&(t[r].fc[h].F=s.TOTFREQ),null==i[r][h]&&(i[r][h]=new o.default.RansDecSymbol),o.default.symbolInit(i[r][h],t[r].fc[h].C,t[r].fc[h].F),null==t[r].R&&(t[r].R=new Array(s.TOTFREQ)),t[r].R.fill(h,l,l+t[r].fc[h].F),l+=t[r].fc[h].F,a(l<=s.TOTFREQ),0===c&&h+1===(255&e.getByteAt(e.position()))?(h=255&e.get(),c=255&e.get()):0!==c?(c-=1,h+=1):h=255&e.get()}while(0!==h);0===n&&r+1===(255&e.getByteAt(e.position()))?(r=255&e.get(),n=255&e.get()):0!==n?(n-=1,r+=1):r=255&e.get()}while(0!==r)};const r=i(9747),s=i(6476),o=n(i(488));function a(e){if(!e)throw new r.CramMalformedError(\"assertion failed\")}},9989:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i=0){if(0===e.length)return t.fill(0),t;const n=new d(e,i),u=n.get();if(0!==u&&1!==u)throw new s.CramMalformedError(`Invalid rANS order ${u}`);if(n.getInt()!==n.remaining()-h)throw new s.CramMalformedError(\"Incorrect input length.\");const f=n.getInt(),p=new d(t||r.Buffer.allocUnsafe(f));if(p.length<f)throw new s.CramMalformedError(`Output buffer too small to fit ${f} bytes.`);switch(u){case 0:return function(e,t){const i=new o.default.AriDecoder,n=new Array(256);for(let e=0;e<n.length;e+=1)n[e]=new o.default.DecodingSymbol;return(0,a.readStatsO0)(e,i,n),(0,c.default)(e,i,n,t),t}(n,p);case 1:return function(e,t){const i=new Array(256);for(let e=0;e<i.length;e+=1)i[e]=new o.default.AriDecoder;const n=new Array(256);for(let e=0;e<n.length;e+=1){n[e]=new Array(256);for(let t=0;t<n[e].length;t+=1)n[e][t]=new o.default.DecodingSymbol}return(0,a.readStatsO1)(e,i,n),(0,l.default)(e,t,i,n),t}(n,p);default:throw new s.CramMalformedError(`Invalid rANS order: ${u}`)}};const r=i(8287),s=i(9747),o=n(i(488)),a=i(1971),c=n(i(997)),l=n(i(7960)),h=4;class d{constructor(e,t=0){this._buffer=e,this._position=t,this.length=e.length}get(){const e=this._buffer[this._position];return this._position+=1,e}getByte(){return this.get()}getByteAt(e){return this._buffer[e]}position(){return this._position}put(e){return this._buffer[this._position]=e,this._position+=1,e}putAt(e,t){return this._buffer[e]=t,t}setPosition(e){return this._position=e,e}getInt(){const e=this._buffer.readInt32LE(this._position);return this._position+=4,e}remaining(){return this._buffer.length-this._position}}},5417:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.parseHeaderText=function(e){const t=e.split(/\\r?\\n/),i=[];for(const e of t){const[t,...n]=e.split(/\\t/);t&&i.push({tag:t.slice(1),data:n.map((e=>{const t=e.indexOf(\":\");return-1!==t?{tag:e.slice(0,t),value:e.slice(t+1)}:{tag:e,value:\"\"}}))})}return i}},8712:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.unzip=function(e){return r.Buffer.from((0,n.inflate)(e))};const n=i(1668),r=i(8287)},635:(e,t,i)=>{var n=i(8287).Buffer;const r=i(4646),s=i(8706),o=i(9614),a=i(235),c=128;e.exports=class{decode(e){return this.stream=new s(e),this.decodeStream(this.stream)}decodeStream(e,t=0){var i=this.stream.ReadByte();16&i||(t=this.stream.ReadUint7());var n,r=t,s=1&i;if(8&i)return this.decodeStripe(this.stream,t);if(i&c&&([n,r]=this.decodePackMeta(this.stream)),32&i)var o=this.decodeCat(this.stream,r);else o=4&i?this.decodeExt(this.stream,r):64&i?s?this.decodeRLE1(this.stream,r):this.decodeRLE0(this.stream,r):s?this.decode1(this.stream,r):this.decode0(this.stream,r);return i&c&&(o=this.decodePack(o,n,t)),o}encode(e,t){if(this.stream=new s(\"\",0,1.1*e.length+100),this.stream.WriteByte(t),16&t||this.stream.WriteUint7(e.length),8&t)return n.concat([this.stream.buf.slice(0,this.stream.pos),this.encodeStripe(this.stream,e,t>>8)]);var i,r=1&t,o=e.length;return t&c&&([i,e,o]=this.encodePack(e)),t&c&&this.stream.WriteStream(i),64&t?r?this.encodeRLE1(e,o,this.stream):this.encodeRLE0(e,o,this.stream):r?this.encode1(e,o,this.stream):this.encode0(e,o,this.stream)}decode0(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);var a=new o(s),c=new r(e);c.RangeStartDecode(e);for(var l=0;l<t;l++)i[l]=a.ModelDecode(e,c);return i}encode0(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new o(n);i.WriteByte(n);var c=new r(i);for(s=0;s<t;s++)a.ModelEncode(i,c,e[s]);return c.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decode1(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new Array(s),c=0;c<s;c++)a[c]=new o(s);var l=new r(e);l.RangeStartDecode(e);var h=0;for(c=0;c<t;c++)i[c]=a[h].ModelDecode(e,l),h=i[c];return i}encode1(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new Array(n);for(s=0;s<n;s++)a[s]=new o(n);i.WriteByte(n);var c=new r(i),l=0;for(s=0;s<t;s++)a[l].ModelEncode(i,c,e[s]),l=e[s];return c.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeExt(e,t){var i=new n.allocUnsafe(t),r=a.array(e.buf.slice(e.pos)),s=a.header(r),o=0;do{var c=a.decompress(r,s);-1!=c&&(n.from(c).copy(i,o),o+=c.length,s-=c.length)}while(-1!=c);return i}encodeExt(e,t){}decodeRLE0(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new o(s),c=new Array(258),l=0;l<=257;l++)c[l]=new o(4);var h=new r(e);for(h.RangeStartDecode(e),l=0;l<t;){i[l]=a.ModelDecode(e,h);for(var d=c[i[l]].ModelDecode(e,h),u=d,f=256;3==d;)d=c[f].ModelDecode(e,h),f=257,u+=d;for(var p=1;p<=u;p++)i[l+p]=i[l];l+=u+1}return i}encodeRLE0(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new o(n),c=new Array(258);for(s=0;s<=257;s++)c[s]=new o(4);i.WriteByte(n);var l=new r(i);for(s=0;s<t;){a.ModelEncode(i,l,e[s]);for(var h=1;s+h<t&&e[s+h]==e[s];)h++;h--;var d=e[s];e[s],s+=h+1;var u=h>=3?3:h;for(c[d].ModelEncode(i,l,u),h-=u,d=256;3==u;)u=h>=3?3:h,c[d].ModelEncode(i,l,u),d=257,h-=u}return l.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeRLE1(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new Array(s),c=0;c<s;c++)a[c]=new o(s);var l=new Array(258);for(c=0;c<=257;c++)l[c]=new o(4);var h=new r(e);h.RangeStartDecode(e);var d=0;for(c=0;c<t;){i[c]=a[d].ModelDecode(e,h),d=i[c];for(var u=l[i[c]].ModelDecode(e,h),f=u,p=256;3==u;)u=l[p].ModelDecode(e,h),p=257,f+=u;for(var g=1;g<=f;g++)i[c+g]=i[c];c+=f+1}return i}encodeRLE1(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new Array(n);for(s=0;s<n;s++)a[s]=new o(n);var c=new Array(258);for(s=0;s<=257;s++)c[s]=new o(4);i.WriteByte(n);for(var l=new r(i),h=(s=0,0);s<t;){a[h].ModelEncode(i,l,e[s]);for(var d=1;s+d<t&&e[s+d]==e[s];)d++;d--;var u=e[s];h=e[s],s+=d+1;var f=d>=3?3:d;for(c[u].ModelEncode(i,l,f),d-=f,u=256;3==f;)f=d>=3?3:d,c[u].ModelEncode(i,l,f),u=257,d-=f}return l.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodePackMeta(e){this.nsym=e.ReadByte();for(var t=new Array(this.nsym),i=0;i<this.nsym;i++)t[i]=e.ReadByte();return[t,e.ReadUint7()]}decodePack(e,t,i){var r=new n.allocUnsafe(i);if(this.nsym<=1)for(var s=0;s<i;s++)r[s]=t[0];else if(this.nsym<=2){s=0;for(var o=0;s<i;s++){if(s%8==0)var a=e[o++];r[s]=t[1&a],a>>=1}}else if(this.nsym<=4)for(s=0,o=0;s<i;s++)s%4==0&&(a=e[o++]),r[s]=t[3&a],a>>=2;else{if(!(this.nsym<=16))return e;for(s=0,o=0;s<i;s++)s%2==0&&(a=e[o++]),r[s]=t[15&a],a>>=4}return r}packMeta(e){for(var t=new s(\"\",0,1024),i=new Array(256),n=0;n<e.length;n++)i[e[n]]=1;var r=0;for(n=0;n<256;n++)i[n]&&(i[n]=++r);for(t.WriteByte(r),n=0;n<256;n++)i[n]&&(t.WriteByte(n),i[n]--);return[t,i,r]}encodePack(e){var t,i,r;[t,i,r]=this.packMeta(e);var s=e.length,o=0;if(r<=1)return t.WriteUint7(0),[t,new n.allocUnsafe(0),0];if(r<=2){for(var a=new n.allocUnsafe(Math.floor((s+7)/8)),c=(o=0,0);o<(-8&s);o+=8,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<1)+(i[e[o+2]]<<2)+(i[e[o+3]]<<3)+(i[e[o+4]]<<4)+(i[e[o+5]]<<5)+(i[e[o+6]]<<6)+(i[e[o+7]]<<7);if(o<s){a[c]=0;for(var l=0;o<s;)a[c]|=i[e[o++]]<<l,l++;c++}return t.WriteUint7(c),[t,a,a.length]}if(r<=4){for(a=new n.allocUnsafe(Math.floor((s+3)/4)),o=0,c=0;o<(-4&s);o+=4,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<2)+(i[e[o+2]]<<4)+(i[e[o+3]]<<6);if(o<s){for(a[c]=0,l=0;o<s;)a[c]|=i[e[o++]]<<l,l+=2;c++}return t.WriteUint7(c),[t,a,a.length]}if(r<=16){for(a=new n.allocUnsafe(Math.floor((s+1)/2)),o=0,c=0;o<(-2&s);o+=2,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<4);return o<s&&(a[c++]=i[e[o++]]),t.WriteUint7(c),[t,a,a.length]}return t.WriteUint7(e.length),[t,e,e.length]}encodeStripe(e,t,i){0==i&&(i=4);for(var n=new Array(i),r=new Array(i),o=0;o<i;o++)r[o]=Math.floor(t.length/i)+(t.length%i>o),n[o]=new Array(r[o]);for(var a=0,c=0;c<t.length;c+=i,a++)for(var l=0;l<i;l++)a<n[l].length&&(n[l][a]=t[c+l]);var h=new Array(i),d=0;for(o=0;o<i;o++){var u=this.encode(n[o],0),f=this.encode(n[o],1);h[o]=f.length<u.length?f:u,d+=h[o].length}var p=new s(\"\",0,d+5*i+1);for(p.WriteByte(i),o=0;o<i;o++)p.WriteUint7(h[o].length);for(o=0;o<i;o++)p.WriteData(h[o],h[o].length);return p.buf.slice(0,p.buf.pos)}decodeStripe(e,t){for(var i=e.ReadByte(),r=new Array(i),s=new Array(i),o=0;o<i;o++)r[o]=e.ReadUint7();var a=new Array(i);for(o=0;o<i;o++)s[o]=Math.floor(t/i)+(t%i>o),a[o]=this.decodeStream(e,s[o]);var c=new n.allocUnsafe(t);for(o=0;o<i;o++)for(var l=0;l<s[o];l++)c[l*i+o]=a[o][l];return c}decodeCat(e,t){for(var i=new n.allocUnsafe(t),r=0;r<t;r++)i[r]=e.ReadByte();return i}}},4646:e=>{e.exports=class{constructor(e){this.low=0,this.range=4294967295,this.code=0,this.FFnum=0,this.carry=0,this.cache=0}RangeStartDecode(e){for(var t=0;t<5;t++)this.code=(this.code<<8)+e.ReadByte();this.code&=4294967295,this.code>>>=0}RangeGetFrequency(e){return this.range=Math.floor(this.range/e),Math.floor(this.code/this.range)}RangeDecode(e,t,i,n){for(this.code-=t*this.range,this.range*=i;this.range<1<<24;)this.range*=256,this.code=256*this.code+e.ReadByte()}RangeShiftLow(e){if(this.low<4278190080|this.carry){for(e.WriteByte(this.cache+this.carry);this.FFnum;)e.WriteByte(this.carry-1),this.FFnum--;this.cache=this.low>>>24,this.carry=0}else this.FFnum++;this.low<<=8,this.low>>>=0}RangeEncode(e,t,i,n){var r=this.low;for(this.range=Math.floor(this.range/n),this.low+=t*this.range,this.low>>>=0,this.range*=i,this.low<r&&(0!=this.carry&&console.log(\"ERROR: Multiple carry\"),this.carry=1);this.range<1<<24;)this.range*=256,this.RangeShiftLow(e)}RangeFinishEncode(e){for(var t=0;t<5;t++)this.RangeShiftLow(e)}}},9614:e=>{e.exports=class{constructor(e=256){this.total_freq=e,this.max_sym=e-1,this.S=new Array,this.F=new Array;for(var t=0;t<=this.max_sym;t++)this.S[t]=t,this.F[t]=1}ModelDecode(e,t){for(var i=t.RangeGetFrequency(this.total_freq),n=0,r=0;n+this.F[r]<=i;)n+=this.F[r++];t.RangeDecode(e,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise();var s=this.S[r];if(r>0&&this.F[r]>this.F[r-1]){var o=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=o,o=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=o}return s}ModelRenormalise(){this.total_freq=0;for(var e=0;e<=this.max_sym;e++)this.F[e]-=Math.floor(this.F[e]/2),this.total_freq+=this.F[e]}ModelEncode(e,t,i){for(var n=0,r=0;this.S[r]!=i;r++)n+=this.F[r];if(t.RangeEncode(e,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise(),i=this.S[r],r>0&&this.F[r]>this.F[r-1]){var s=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=s,s=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=s}}}},6038:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706),s=i(9614),o=i(4646);function a(e,t,i){for(var n=0,r=0,s=-1,o=new Array(1024);r<i;){var a=e.ReadByte();if(o[n++]=a,r+=a,a==s){var c=e.ReadByte();for(r+=a*c;c--;)o[n++]=a}s=a}var l=0;for(n=0,r=0;r<i;){var h=0;do{var d=o[n++];h+=d}while(255==d);for(;h--;)t[r++]=l;l++}}function c(e,t,i){var n=e.context;return t.qctx=(t.qctx<<e.qshift)+e.qtab[i],n+=(t.qctx&(1<<e.qbits)-1)<<e.qloc,e.do_pos&&(n+=e.ptab[Math.min(t.p,1023)]<<e.ploc),e.do_delta&&(n+=e.dtab[Math.min(t.delta,255)]<<e.dloc,t.delta+=t.prevq!=i?1:0,t.prevq=i),e.do_sel&&(n+=t.s<<e.sloc),t.p--,65535&n}function l(e){var t={};t.context=e.ReadUint16(),t.pflags=e.ReadByte(),t.do_dedup=2&t.pflags,t.fixed_len=4&t.pflags,t.do_sel=8&t.pflags,t.do_qmap=16&t.pflags,t.do_pos=32&t.pflags,t.do_delta=64&t.pflags,t.do_qtab=128&t.pflags,t.max_sym=e.ReadByte();var i=e.ReadByte();if(t.qbits=i>>4,t.qshift=15&i,i=e.ReadByte(),t.qloc=i>>4,t.sloc=15&i,i=e.ReadByte(),t.ploc=i>>4,t.dloc=15&i,t.qmap=new Array(256),16&t.pflags)for(var n=0;n<t.max_sym;n++)t.qmap[n]=e.ReadByte();else for(n=0;n<256;n++)t.qmap[n]=n;if(t.qtab=new Array(1024),t.qbits>0&&128&t.pflags)a(e,t.qtab,256);else for(n=0;n<256;n++)t.qtab[n]=n;return t.ptab=new Array(1024),32&t.pflags&&a(e,t.ptab,1024),t.dtab=new Array(256),64&t.pflags&&a(e,t.dtab,256),t}function h(e,t,i,n,r,s){i.max_sel>0?r.s=n.sel.ModelDecode(e,t):r.s=0,r.x=i.stab[r.s];var o=i.params[r.x];if(o.fixed_len>=0){var a=n.len[0].ModelDecode(e,t);a|=n.len[1].ModelDecode(e,t)<<8,a|=n.len[2].ModelDecode(e,t)<<16,a|=n.len[3].ModelDecode(e,t)<<24,o.fixed_len>0&&(o.fixed_len=-a)}else a=-o.fixed_len;r.len=a,i.do_rev&&(s[r.rec]=n.rev.ModelDecode(e,t)),r.is_dup=0,2&o.pflags&&n.dup.ModelDecode(e,t)&&(r.is_dup=1),r.p=a,r.delta=0,r.qctx=0,r.prevq=0,r.rec++}function d(e,t,i){for(var n=0,r=0,s=new Array(2*i),o=0;n<i;){for(var a=n;n<i&&t[n]==r;)n++;var c=n-a;do{var l=Math.min(255,c);s[o++]=l,c-=l}while(255==l);r++}var h=-1,d=new Array(2*i),u=0;for(n=0;n<o;){var f=s[n++];if(d[u++]=f,f==h){for(a=n;n<o&&s[n]==h&&n-a<255;)n++;d[u++]=n-a}else h=f}e.WriteData(d,u)}e.exports={decode:function(e,t){return function(e,t){var i=e.ReadUint7(),r=function(e){var t={max_sym:0};if(5==e.ReadByte()){var i=e.ReadByte(),n=1&i?e.ReadByte():1,r=i.nparam>1?i.nparam-1:0,s=new Array(256);if(2&i)r=e.ReadByte(),a(e,s,256);else{for(var o=0;o<n;o++)s[o]=o;for(;o<256;o++)s[o]=n-1}t.do_rev=4&i,t.stab=s,t.max_sel=r,t.params=new Array(t.nparam);for(var c=0;c<n;c++)t.params[c]=l(e),t.max_sym<t.params[c].max_sym&&(t.max_sym=t.params[c].max_sym);return t}console.error(\"Invalid FQZComp version number\")}(e);if(r){var d=r.params,u=new Array(t.length),f=function(e){var t={};t.qual=new Array(65536);for(var i=0;i<65536;i++)t.qual[i]=new s(e.max_sym+1);for(t.len=new Array(4),i=0;i<4;i++)t.len[i]=new s(256);return t.rev=new s(2),t.dup=new s(2),e.max_sel>0&&(t.sel=new s(e.max_sel+1)),t}(r),p=new o(e);p.RangeStartDecode(e);for(var g=new n.allocUnsafe(i),m={qctx:0,prevq:0,delta:0,p:0,s:0,x:0,len:0,is_dup:0,rec:0},w=0;w<i;){if(0==m.p){if(h(e,p,r,f,m,u),m.is_dup>0&&f.dup.ModelDecode(e,p)){for(var b=0;b<len;b++)g[w+b]=g[w+b-m.len];w+=m.len,m.p=0;continue}t.push(m.len);var F=(d=r.params[m.x]).context}var v=f.qual[F].ModelDecode(e,p);g[w++]=d.qmap[v],F=c(d,m,v)}return r.do_rev&&function(e,t,i,n){for(var r=0,s=0;s<t;){if(i[r])for(var o=0,a=n[r]-1;o<a;){var c=e[s+o];e[s+o]=e[s+a],e[s+a]=c,o++,a--}s+=n[r++]}}(g,i,u,t),g}}(new r(e),t)},encode:function(e,t,i){for(var n=new Array(2),a=new Array(2),c=new Array(2),l=new Array(2),h=new Array(256),u=0;u<2;u++)n[u]=new Array(256),a[u]=new Array(256),c[u]=new Array(1024),l[u]=new Array(256);(p=new r(\"\",0,1.1*e.length+100)).WriteUint7(e.length);var f=function(e,t,i,n){for(var r=i[0],s=0;s<i.length&&i[s]==r;s++);var o=s==i.length?1:0,a=0,c=0;for(s=0;s<256;s++)n[0][s]=0;var l=0,h=0;for(s=0;s<e.length;s++)0==h&&(h=t[l<t.length-1?l++:l]),n[0][e[s]]++,h--;for(s=0;s<256;s++)n[0][s]&&(c<s&&(c=s),a++);var d=5,u=0;return a<=16&&(u=1,d=a<=2?1:a<=4?2:a<=8?3:4),[{qbits:8+(d>4),qshift:d,qloc:7,pbits:7,pshift:t[0]>128?1:0,ploc:0,dbits:d>4?0:1,dshift:3,dloc:15,sbits:0,sloc:15,do_stab:0,context:0,max_sym:c,nsym:a,do_qmap:u,do_dedup:0,fixed_len:1==t.length?1:0,do_sel:0,do_rev:0,do_pos:1,do_delta:d<=4?1:0,do_qtab:0,qbits:8+(d>4)-(0==o),sbits:1,sloc:15-(d<=4),do_stab:1,do_sel:1}]}(e,t,i,n),p=function(e,t,i,n,r,s,o){for(var a=[0,1,1,1,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7],c=0;c<t.length;c++)o[c]=c;for(;c<256;c++)o[c]=t.length-1;e.WriteByte(5);var l=(t.length>1?1:0)|(t[0].do_stab?2:0);if(e.WriteByte(l),1&l&&e.WriteByte(t.length),2&l){var h=1<<t[0].sbits;h>0&&h--,e.WriteByte(h),d(e,o,256)}for(var u=0;u<t.length;u++){if(e.WriteUint16(t[u].context),e.WriteByte((t[u].do_qtab?128:0)|(t[u].do_delta?64:0)|(t[u].do_pos?32:0)|(t[u].do_qmap?16:0)|(t[u].do_sel?8:0)|(t[u].fixed_len?4:0)|(t[u].do_dedup?2:0)),t[u].do_qmap?e.WriteByte(t[u].nsym):e.WriteByte(t[u].max_sym),e.WriteByte(t[u].qbits<<4|t[u].qshift),e.WriteByte(t[u].qloc<<4|t[u].sloc),e.WriteByte(t[u].ploc<<4|t[u].dloc),t[u].do_qmap){t[u].max_sym=t[u].nsym;var f=0;for(c=0;c<256;c++)i[u][c]&&(e.WriteByte(c),i[u][c]=f++);for(;f<t[u].nsym;f++)e.WriteByte(0)}else for(c=0;c<256;c++)i[u][c]=c;if(t[u].qbits>0){for(c=0;c<256;c++)n[u][c]=c;t[u].do_qtab&&d(e,n[u],256)}if(t[u].pbits>0){for(c=0;c<1024;c++)r[u][c]=Math.min((1<<t[u].pbits)-1,c>>t[u].pshift);d(e,r[u],1024)}if(t[u].dbits>0){for(c=0;c<256;c++)a[c]>(1<<t[u].dbits)-1&&(a[c]=(1<<t[u].dbits)-1);for(c=0;c<256;c++)s[u][c]=a[Math.min(a.length-1,c>>t[u].dshift)];d(e,s[u],256)}}return e}(p,f,n,a,c,l,h);return function(e,t,i,n,r,a,c,l,h,d){var u=1<<r[0].sbits;u>0&&u--;for(var f=t.length,p=0,g=0;g<r.length;g++)p<r[g].max_sym&&(p=r[g].max_sym);for(var m=new Array(65536),w=0;w<65536;w++)m[w]=new s(p+1);var b=new Array(4);for(w=0;w<4;w++)b[w]=new s(256);new s(2),new s(2);for(var F=new s(u+1),v=new o(t),y=(g=0,w=0,0);w<f;){if(0==g){var A=n[y];r[0].sbits>0&&F.ModelEncode(e,v,A);var C=d[A],_=i[Math.min(i.length-1,y++)];r[C].fixed_len?r[C].fixed_len>0&&(b[0].ModelEncode(e,v,255&_),b[1].ModelEncode(e,v,_>>8&255),b[2].ModelEncode(e,v,_>>16&255),b[3].ModelEncode(e,v,_>>24&255),r[C].fixed_len=-1):(b[0].ModelEncode(e,v,255&_),b[1].ModelEncode(e,v,_>>8&255),b[2].ModelEncode(e,v,_>>16&255),b[3].ModelEncode(e,v,_>>24&255)),r[C].do_dedup&&process.exit(1),g=_;var x=0,k=r[C].context,I=0,S=0}var E=t[w++],N=a[C][E];m[k].ModelEncode(e,v,N),I=(I<<r[C].qshift)+c[C][N],k=r[C].context,k+=(I&(1<<r[C].qbits)-1)<<r[C].qloc,r[C].pbits>0&&(k+=l[C][Math.min(g,1023)]<<r[C].ploc),r[C].dbits>0&&(k+=h[C][Math.min(x,255)]<<r[C].dloc,x+=S!=N?1:0,S=N),r[C].do_sel&&(k+=A<<r[C].sloc),k&=65535,g--}return v.RangeFinishEncode(e),e.buf.slice(0,e.pos)}(p,e,t,i,f,n,a,c,l,h)}}},6960:(e,t,i)=>{var n=i(8287).Buffer,r=i(5460),s=i(8223),o=i(635),a=i(6038),c=i(5997);e.exports={r4x8_uncompress:function(e,t){r.decode(e).copy(t,0,0)},r4x16_uncompress:function(e,t){s.decode(e).copy(t,0,0)},arith_uncompress:function(e,t){o.decode(e).copy(t,0,0)},fqzcomp_uncompress:function(e,t){var i=new Array;a.decode(e,i).copy(t,0,0)},tok3_uncompress:function(e,t){var i=c.decode(e,0,\"\\0\");n.from(i,\"binary\").copy(t,0,0)}}},8706:(e,t,i)=>{var n=i(8287).Buffer;e.exports=class{constructor(e,t=0,i=0){0!=i?(this.buf=n.allocUnsafe(i),this.length=i):(this.buf=e,this.length=e.length),this.pos=t}EOF(){return this.pos>=this.length}ReadData(e){var t=this.buf.slice(this.pos,this.pos+e);return this.pos+=e,t}ReadByte(){const e=this.buf[this.pos];return this.pos++,e}ReadChar(){const e=this.buf[this.pos];return this.pos++,String.fromCharCode(e)}ReadUint16(){return this.ReadByte()|this.ReadByte()<<8}ReadUint32(){const e=this.buf.readInt32LE(this.pos);return this.pos+=4,e}ReadString(){var e=\"\";do{var t=this.buf[this.pos++];t&&(e+=String.fromCharCode(t))}while(t);return e}ReadUint7(){var e=0;do{var t=this.ReadByte();e=e<<7|127&t}while(128&t);return e}ReadITF8(){var e=this.buf[this.pos];return this.pos++,e>=240?(e=(15&e)<<28,e+=(this.buf[this.pos+0]<<20)+(this.buf[this.pos+1]<<12)+(this.buf[this.pos+2]<<4)+(this.buf[this.pos+3]>>4),this.pos+=4):e>=224?(e=(15&e)<<24,e+=(this.buf[this.pos+0]<<16)+(this.buf[this.pos+1]<<8)+(0|this.buf[this.pos+2]),this.pos+=3):e>=192?(e=(31&e)<<16,e+=(this.buf[this.pos+0]<<8)+(0|this.buf[this.pos+1]),this.pos+=2):e>=128&&(e=(63&e)<<8,e+=this.buf[this.pos],this.pos++),e}WriteByte(e){this.buf[this.pos++]=e}WriteChar(e){this.buf[this.pos++]=e.charCodeAt(0)}WriteString(e){for(var t=0;t<e.length;t++)this.buf[this.pos++]=e.charCodeAt(t);this.buf[this.pos++]=0}WriteData(e,t){for(var i=0;i<t;i++)this.buf[this.pos++]=e[i]}WriteStream(e){this.WriteData(e.buf,e.pos)}WriteUint16(e){this.WriteByte(255&e),this.WriteByte(e>>8&255)}WriteUint32(e){this.buf.writeInt32LE(e,this.pos),this.pos+=4}WriteUint7(e){var t=0,i=e;do{t+=7,i>>=7}while(i>0);do{t-=7,this.WriteByte((e>>t&127)+((t>0)<<7))}while(t>0)}WriteITF8(e){e<0&&(e=1+e),e<=127?this.buf[this.pos++]=e:e<=16383?(this.buf[this.pos++]=128|Math.floor(e/256),this.buf[this.pos++]=255&e):e<131071?(this.buf[this.pos++]=192|Math.floor(e/65536),this.buf[this.pos++]=255&Math.floor(e/256),this.buf[this.pos++]=255&e):e<268435455?(this.buf[this.pos++]=224|Math.floor(e/16777216),this.buf[this.pos++]=255&Math.floor(e/65536),this.buf[this.pos++]=255&Math.floor(e/256),this.buf[this.pos++]=255&e):(this.buf[this.pos++]=240|Math.floor(e/268435456),this.buf[this.pos++]=255&Math.floor(e/1048576),this.buf[this.pos++]=255&Math.floor(e/4096),this.buf[this.pos++]=255&Math.floor(e/4),this.buf[this.pos++]=15&e)}WriteByteNeg(e){this.buf[--this.pos]=e}}},5460:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706);function s(e){return 4095&e}function o(e,t){for(var i=0;t>=e[i+1];)i++;return i}function a(e){for(var t=new 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o=0,a=0,c=0;for(i=0,n=0;n<256;n++)0!=e[n]&&(o<e[n]&&(o=e[n],a=n),e[n]=Math.floor(e[n]*s),0==e[n]&&(e[n]=1),i+=e[n]);i<r?e[a]+=r-i:i-r<e[a]/2&&e[a]>2?e[a]-=i-r:i!=r&&(s=r/i,c=1)}while(c)}function b(e,t){for(var i=0,n=0;n<256;n++)i+=e[n];if(0!=i&&i!=1<<t){for(var r=0;i<1<<t;)i*=2,r++;for(n=0;n<256;n++)e[n]<<=r}}function F(e,t){for(var i=0,n=0;n<256;n++)if(t[n])if(i>0)i--;else if(e.WriteByte(n),n>0&&t[n-1]>0){for(i=n+1;i<256&&t[i];i++);i-=n+1,e.WriteByte(i)}e.WriteByte(0)}function v(e){const t=e.length;var i=new r(\"\",0,780),s=new Array(256);!function(e,t){for(var i=0;i<256;i++)t[i]=0;for(i=0;i<e.length;i++)t[e[i]]++}(e,s);var o=Math.ceil(Math.log2(t));o>12&&(o=12),w(s,o),function(e,t){F(e,t);for(var i=0;i<256;i++)t[i]&&e.WriteUint7(t[i])}(i,s),w(s,12);var a=new Array(256);a[0]=0;for(var c=1;c<256;c++)a[c]=a[c-1]+s[c-1];var l=new Array(4);for(c=0;c<4;c++)l[c]=32768;var u=new r(\"\",1.05*t+100|0,1.05*t+100|0);for(c=t-1;c>=0;c--)l[c%4]=d(l[c%4],u,a[e[c]],s[e[c]],12);for(c=3;c>=0;c--)h(l[c],u);return n.concat([i.buf.slice(0,i.pos),u.buf.slice(u.pos,u.length)],i.pos+u.length-u.pos)}e.exports={decode:function(e){return f(new r(e),0)},encode:p}},5997:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706),s=i(8223);var o=new(i(635));function a(e,t){for(var i=e+\"\";i.length<t;)i=\"0\"+i;return i}function c(e,t,i,n){var r=e[0][0].ReadByte(),s=n-e[0][r].ReadUint32();if(5==r)return t[n]=t[s],i[n]=i[s],t[n];var o=1;t[n]=\"\",i[n]=new Array(256);do{switch(r=e[o][0].ReadByte()){case 2:i[n][o]=e[o][2].ReadChar();break;case 1:i[n][o]=e[o][1].ReadString();break;case 7:i[n][o]=e[o][7].ReadUint32();break;case 3:var c=e[o][3].ReadUint32(),l=e[o][4].ReadByte();i[n][o]=a(c,l);break;case 8:i[n][o]=(0|i[s][o])+e[o][8].ReadByte();break;case 9:c=(0|i[s][o])+e[o][9].ReadByte(),l=i[s][o].length,i[n][o]=a(c,l);break;case 10:i[n][o]=i[s][o];break;default:i[n][o]=\"\"}t[n]+=i[n][o++]}while(12!=r);return t[n]}function l(e,t,i,n,r,s){for(var o=0;o<n.length;o++)if(!(i>0&&5==t[o][0].type)&&t[o][i])switch(e[0].WriteByte(t[o][i].type),t[o][i].type){case 6:e[6].WriteUint32(t[o][i].val);break;case 5:e[5].WriteUint32(t[o][i].val);break;case 1:e[1].WriteString(t[o][i].val);break;case 2:e[2].WriteChar(t[o][i].val);break;case 7:e[7].WriteUint32(t[o][i].val);break;case 3:e[3].WriteUint32(t[o][i].val),e[4].WriteByte(t[o][i].val.length);break;case 8:case 9:e[t[o][i].type].WriteByte(t[o][i].val)}}function h(e,t,i,n){for(var r=0;r<=12;r++)if(!(e[r].pos<=0)){n.WriteByte(r+(0==r?128:0)),e[r]=e[r].buf.slice(0,e[r].pos);var s=d(e[r],i);n.WriteUint7(s.length),n.WriteData(s,s.length)}}function d(e,t){var i,n=1<<30,r=[0,1,64,65,128,129,201];for(var a in r){var c=r[a];if(!(1&c&&e.length<100||8&c&&e.length%4!=0)){try{var l=t?o.encode(e,c):s.encode(e,c)}catch(e){l=0}l&&n>l.length&&(n=l.length,i=l)}}return i}function u(e,t,i,n,r){var s=0,o=r-1;e[r]=new Array(256),t[n]?e[r][0]={type:5,val:r-t[n]}:e[r][0]={type:6,val:0==r?0:1},t[n]=r;for(var a=n.match(/([a-zA-Z0-9]{1,9})|([^a-zA-Z0-9]+)/g),c=0;c<a.length;c++){var l=c+1,h=1,d=a[c];if(a[c].match(/^0+[0-9]*$/g)?h=3:a[c].match(/^[0-9]+$/g)?h=7:1==a[c].length&&(h=2),o>=0&&e[o][l])if(e[o][l].str==a[c])h=10,d=\"\";else if(7==e[o][l].type||8==e[o][l].type){var u=d-e[o][l].str;i[l]++,u>=0&&u<256&&i[l]>r/2&&(h=8,d=u)}else 3!=e[o][l].type&&9!=e[o][l].type||e[o][l].str.length!=d.length||(u=d-e[o][l].str,i[l]++,u>=0&&u<256&&i[l]>r/2&&(h=9,d=u));e[r][l]={str:a[c],val:d,type:h},s<e[r][l].val.length+3&&(s=e[r][l].val.length+3)}return e[r][++l]={type:12},[l+1,s]}e.exports={encode:function(e,t){var i=e.toString();\"\\n\"==i[i.length-1]&&(i=i.substring(0,i.length-1));var n=i.split(\"\\n\"),s=new r(\"\",0,2*i.length+1e4);s.WriteUint32(i.length),s.WriteUint32(n.length),s.WriteByte(t);for(var o=new Array(n.length),a={},c=new Array(256).fill(0),d=0,f=0,p=0;p<n.length;p++){var[g,m]=u(o,a,c,n[p],p);d<g&&(d=g),f<m&&(f=m)}for(var w=0;w<d;w++){for(var b=new Array(13),F=0;F<=12;F++)b[F]=new r(\"\",0,n.length*f);l(b,o,w,n),h(b,0,t,s)}return s.buf.slice(0,s.pos)},decode:function(e,t,i){(e=new r(e)).ReadUint32();var a=e.ReadUint32(),l=e.ReadByte(),h=function(e,t,i,a){for(var c=-1,l=new Array(256);!e.EOF();){var h=e.ReadByte(),d=128&h,u=64&h,f=63&h;if(d&&(l[++c]=new Array(13)),0!=f&&d){var p=new Array(a-1).fill(10);l[c][0]=new r(n.from([f].concat(p)))}if(u){var g=e.ReadByte(),m=e.ReadByte();l[c][f]=new r(l[g][m].buf)}else{var w=e.ReadUint7(),b=e.ReadData(w);l[c][f]=i?o.decode(b):s.decode(b),l[c][f]=new r(l[c][f])}}return l}(e,0,l,a),d=new Array(a),u=new Array(a),f=\"\";void 0===i&&(i=\"\\n\");for(var p=0;p<a;p++)f+=c(h,d,u,p)+i;return f}}},7526:(e,t)=>{t.byteLength=function(e){var t=a(e),i=t[0],n=t[1];return 3*(i+n)/4-n},t.toByteArray=function(e){var t,i,s=a(e),o=s[0],c=s[1],l=new r(function(e,t,i){return 3*(t+i)/4-i}(0,o,c)),h=0,d=c>0?o-4:o;for(i=0;i<d;i+=4)t=n[e.charCodeAt(i)]<<18|n[e.charCodeAt(i+1)]<<12|n[e.charCodeAt(i+2)]<<6|n[e.charCodeAt(i+3)],l[h++]=t>>16&255,l[h++]=t>>8&255,l[h++]=255&t;return 2===c&&(t=n[e.charCodeAt(i)]<<2|n[e.charCodeAt(i+1)]>>4,l[h++]=255&t),1===c&&(t=n[e.charCodeAt(i)]<<10|n[e.charCodeAt(i+1)]<<4|n[e.charCodeAt(i+2)]>>2,l[h++]=t>>8&255,l[h++]=255&t),l},t.fromByteArray=function(e){for(var t,n=e.length,r=n%3,s=[],o=16383,a=0,l=n-r;a<l;a+=o)s.push(c(e,a,a+o>l?l:a+o));return 1===r?(t=e[n-1],s.push(i[t>>2]+i[t<<4&63]+\"==\")):2===r&&(t=(e[n-2]<<8)+e[n-1],s.push(i[t>>10]+i[t>>4&63]+i[t<<2&63]+\"=\")),s.join(\"\")};for(var i=[],n=[],r=\"undefined\"!=typeof Uint8Array?Uint8Array:Array,s=\"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/\",o=0;o<64;++o)i[o]=s[o],n[s.charCodeAt(o)]=o;function a(e){var t=e.length;if(t%4>0)throw new Error(\"Invalid string. 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Received type number');return d(e)}return l(e,t,i)}function l(e,t,i){if(\"string\"==typeof e)return function(e,t){if(\"string\"==typeof t&&\"\"!==t||(t=\"utf8\"),!c.isEncoding(t))throw new TypeError(\"Unknown encoding: \"+t);const i=0|g(e,t);let n=a(i);const r=n.write(e,t);return r!==i&&(n=n.slice(0,r)),n}(e,t);if(ArrayBuffer.isView(e))return function(e){if(K(e,Uint8Array)){const t=new Uint8Array(e);return f(t.buffer,t.byteOffset,t.byteLength)}return u(e)}(e);if(null==e)throw new TypeError(\"The first argument must be one of type string, Buffer, ArrayBuffer, Array, or Array-like Object. Received type \"+typeof e);if(K(e,ArrayBuffer)||e&&K(e.buffer,ArrayBuffer))return f(e,t,i);if(\"undefined\"!=typeof SharedArrayBuffer&&(K(e,SharedArrayBuffer)||e&&K(e.buffer,SharedArrayBuffer)))return f(e,t,i);if(\"number\"==typeof e)throw new TypeError('The \"value\" argument must not be of type number. Received type number');const n=e.valueOf&&e.valueOf();if(null!=n&&n!==e)return c.from(n,t,i);const r=function(e){if(c.isBuffer(e)){const t=0|p(e.length),i=a(t);return 0===i.length||e.copy(i,0,0,t),i}return void 0!==e.length?\"number\"!=typeof e.length||Y(e.length)?a(0):u(e):\"Buffer\"===e.type&&Array.isArray(e.data)?u(e.data):void 0}(e);if(r)return r;if(\"undefined\"!=typeof Symbol&&null!=Symbol.toPrimitive&&\"function\"==typeof e[Symbol.toPrimitive])return c.from(e[Symbol.toPrimitive](\"string\"),t,i);throw new TypeError(\"The first argument must be one of type string, Buffer, ArrayBuffer, Array, or Array-like Object. 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reading blob\"))},t.onabort=()=>{n(new Error(\"blob reading was aborted\"))},t.onload=()=>{t.result&&\"string\"!=typeof t.result?i(t.result):n(new Error(\"unknown error reading blob\"))},t.readAsArrayBuffer(e)}))}class l{constructor(e){this.blob=e,this.size=e.size}async read(e,t=0,i,n=0){if(!i)return{bytesRead:0,buffer:e};const r=n,o=r+i,a=await c(this.blob.slice(r,o)),l=s.Buffer.from(a);return{bytesRead:l.copy(e,t),buffer:l}}async readFile(e){const t=\"string\"==typeof e?e:null==e?void 0:e.encoding;if(\"utf8\"===t)return function(e){const t=new FileReader;return new Promise(((i,n)=>{t.onerror=()=>{t.abort(),n(new Error(\"problem reading blob\"))},t.onabort=()=>{n(new Error(\"blob reading was aborted\"))},t.onload=()=>{t.result&&\"string\"==typeof t.result?i(t.result):n(new Error(\"unknown error reading blob\"))},t.readAsText(e)}))}(this.blob);if(t)throw new Error(`unsupported encoding: ${t}`);const i=await c(this.blob);return s.Buffer.from(i)}async stat(){return{size:this.size}}async close(){}}function h(e,t={}){return new a(e,t)}function d(e,t,i,n={}){if(void 0!==i)return i;if(void 0!==e)return h(e,n);if(void 0!==t)return new(r())(t,n);throw new Error(\"no url, path, or filehandle provided, cannot open\")}},251:(e,t)=>{t.read=function(e,t,i,n,r){var s,o,a=8*r-n-1,c=(1<<a)-1,l=c>>1,h=-7,d=i?r-1:0,u=i?-1:1,f=e[t+d];for(d+=u,s=f&(1<<-h)-1,f>>=-h,h+=a;h>0;s=256*s+e[t+d],d+=u,h-=8);for(o=s&(1<<-h)-1,s>>=-h,h+=n;h>0;o=256*o+e[t+d],d+=u,h-=8);if(0===s)s=1-l;else{if(s===c)return o?NaN:1/0*(f?-1:1);o+=Math.pow(2,n),s-=l}return(f?-1:1)*o*Math.pow(2,s-n)},t.write=function(e,t,i,n,r,s){var o,a,c,l=8*s-r-1,h=(1<<l)-1,d=h>>1,u=23===r?Math.pow(2,-24)-Math.pow(2,-77):0,f=n?0:s-1,p=n?1:-1,g=t<0||0===t&&1/t<0?1:0;for(t=Math.abs(t),isNaN(t)||t===1/0?(a=isNaN(t)?1:0,o=h):(o=Math.floor(Math.log(t)/Math.LN2),t*(c=Math.pow(2,-o))<1&&(o--,c*=2),(t+=o+d>=1?u/c:u*Math.pow(2,1-d))*c>=2&&(o++,c/=2),o+d>=h?(a=0,o=h):o+d>=1?(a=(t*c-1)*Math.pow(2,r),o+=d):(a=t*Math.pow(2,d-1)*Math.pow(2,r),o=0));r>=8;e[i+f]=255&a,f+=p,a/=256,r-=8);for(o=o<<r|a,l+=r;l>0;e[i+f]=255&o,f+=p,o/=256,l-=8);e[i+f-p]|=128*g}},8570:e=>{e.exports=i;var t=null;try{t=new WebAssembly.Instance(new WebAssembly.Module(new Uint8Array([0,97,115,109,1,0,0,0,1,13,2,96,0,1,127,96,4,127,127,127,127,1,127,3,7,6,0,1,1,1,1,1,6,6,1,127,1,65,0,11,7,50,6,3,109,117,108,0,1,5,100,105,118,95,115,0,2,5,100,105,118,95,117,0,3,5,114,101,109,95,115,0,4,5,114,101,109,95,117,0,5,8,103,101,116,95,104,105,103,104,0,0,10,191,1,6,4,0,35,0,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,126,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,127,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,128,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,129,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,130,34,4,66,32,135,167,36,0,32,4,167,11])),{}).exports}catch(e){}function i(e,t,i){this.low=0|e,this.high=0|t,this.unsigned=!!i}function n(e){return!0===(e&&e.__isLong__)}i.prototype.__isLong__,Object.defineProperty(i.prototype,\"__isLong__\",{value:!0}),i.isLong=n;var r={},s={};function o(e,t){var i,n,o;return t?(o=0<=(e>>>=0)&&e<256)&&(n=s[e])?n:(i=c(e,(0|e)<0?-1:0,!0),o&&(s[e]=i),i):(o=-128<=(e|=0)&&e<128)&&(n=r[e])?n:(i=c(e,e<0?-1:0,!1),o&&(r[e]=i),i)}function a(e,t){if(isNaN(e))return t?w:m;if(t){if(e<0)return w;if(e>=f)return A}else{if(e<=-p)return C;if(e+1>=p)return y}return e<0?a(-e,t).neg():c(e%u|0,e/u|0,t)}function c(e,t,n){return new i(e,t,n)}i.fromInt=o,i.fromNumber=a,i.fromBits=c;var l=Math.pow;function h(e,t,i){if(0===e.length)throw Error(\"empty string\");if(\"NaN\"===e||\"Infinity\"===e||\"+Infinity\"===e||\"-Infinity\"===e)return m;if(\"number\"==typeof t?(i=t,t=!1):t=!!t,(i=i||10)<2||36<i)throw RangeError(\"radix\");var n;if((n=e.indexOf(\"-\"))>0)throw Error(\"interior hyphen\");if(0===n)return h(e.substring(1),t,i).neg();for(var r=a(l(i,8)),s=m,o=0;o<e.length;o+=8){var c=Math.min(8,e.length-o),d=parseInt(e.substring(o,o+c),i);if(c<8){var u=a(l(i,c));s=s.mul(u).add(a(d))}else s=(s=s.mul(r)).add(a(d))}return s.unsigned=t,s}function d(e,t){return\"number\"==typeof e?a(e,t):\"string\"==typeof e?h(e,t):c(e.low,e.high,\"boolean\"==typeof t?t:e.unsigned)}i.fromString=h,i.fromValue=d;var u=4294967296,f=u*u,p=f/2,g=o(1<<24),m=o(0);i.ZERO=m;var w=o(0,!0);i.UZERO=w;var b=o(1);i.ONE=b;var F=o(1,!0);i.UONE=F;var v=o(-1);i.NEG_ONE=v;var y=c(-1,2147483647,!1);i.MAX_VALUE=y;var A=c(-1,-1,!0);i.MAX_UNSIGNED_VALUE=A;var C=c(0,-2147483648,!1);i.MIN_VALUE=C;var _=i.prototype;_.toInt=function(){return this.unsigned?this.low>>>0:this.low},_.toNumber=function(){return this.unsigned?(this.high>>>0)*u+(this.low>>>0):this.high*u+(this.low>>>0)},_.toString=function(e){if((e=e||10)<2||36<e)throw RangeError(\"radix\");if(this.isZero())return\"0\";if(this.isNegative()){if(this.eq(C)){var t=a(e),i=this.div(t),n=i.mul(t).sub(this);return i.toString(e)+n.toInt().toString(e)}return\"-\"+this.neg().toString(e)}for(var r=a(l(e,6),this.unsigned),s=this,o=\"\";;){var c=s.div(r),h=(s.sub(c.mul(r)).toInt()>>>0).toString(e);if((s=c).isZero())return h+o;for(;h.length<6;)h=\"0\"+h;o=\"\"+h+o}},_.getHighBits=function(){return this.high},_.getHighBitsUnsigned=function(){return this.high>>>0},_.getLowBits=function(){return this.low},_.getLowBitsUnsigned=function(){return this.low>>>0},_.getNumBitsAbs=function(){if(this.isNegative())return this.eq(C)?64:this.neg().getNumBitsAbs();for(var e=0!=this.high?this.high:this.low,t=31;t>0&&!(e&1<<t);t--);return 0!=this.high?t+33:t+1},_.isZero=function(){return 0===this.high&&0===this.low},_.eqz=_.isZero,_.isNegative=function(){return!this.unsigned&&this.high<0},_.isPositive=function(){return this.unsigned||this.high>=0},_.isOdd=function(){return!(1&~this.low)},_.isEven=function(){return!(1&this.low)},_.equals=function(e){return n(e)||(e=d(e)),(this.unsigned===e.unsigned||this.high>>>31!=1||e.high>>>31!=1)&&this.high===e.high&&this.low===e.low},_.eq=_.equals,_.notEquals=function(e){return!this.eq(e)},_.neq=_.notEquals,_.ne=_.notEquals,_.lessThan=function(e){return this.comp(e)<0},_.lt=_.lessThan,_.lessThanOrEqual=function(e){return this.comp(e)<=0},_.lte=_.lessThanOrEqual,_.le=_.lessThanOrEqual,_.greaterThan=function(e){return this.comp(e)>0},_.gt=_.greaterThan,_.greaterThanOrEqual=function(e){return this.comp(e)>=0},_.gte=_.greaterThanOrEqual,_.ge=_.greaterThanOrEqual,_.compare=function(e){if(n(e)||(e=d(e)),this.eq(e))return 0;var t=this.isNegative(),i=e.isNegative();return t&&!i?-1:!t&&i?1:this.unsigned?e.high>>>0>this.high>>>0||e.high===this.high&&e.low>>>0>this.low>>>0?-1:1:this.sub(e).isNegative()?-1:1},_.comp=_.compare,_.negate=function(){return!this.unsigned&&this.eq(C)?C:this.not().add(b)},_.neg=_.negate,_.add=function(e){n(e)||(e=d(e));var t=this.high>>>16,i=65535&this.high,r=this.low>>>16,s=65535&this.low,o=e.high>>>16,a=65535&e.high,l=e.low>>>16,h=0,u=0,f=0,p=0;return f+=(p+=s+(65535&e.low))>>>16,u+=(f+=r+l)>>>16,h+=(u+=i+a)>>>16,h+=t+o,c((f&=65535)<<16|(p&=65535),(h&=65535)<<16|(u&=65535),this.unsigned)},_.subtract=function(e){return n(e)||(e=d(e)),this.add(e.neg())},_.sub=_.subtract,_.multiply=function(e){if(this.isZero())return m;if(n(e)||(e=d(e)),t)return c(t.mul(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned);if(e.isZero())return m;if(this.eq(C))return e.isOdd()?C:m;if(e.eq(C))return this.isOdd()?C:m;if(this.isNegative())return e.isNegative()?this.neg().mul(e.neg()):this.neg().mul(e).neg();if(e.isNegative())return this.mul(e.neg()).neg();if(this.lt(g)&&e.lt(g))return a(this.toNumber()*e.toNumber(),this.unsigned);var i=this.high>>>16,r=65535&this.high,s=this.low>>>16,o=65535&this.low,l=e.high>>>16,h=65535&e.high,u=e.low>>>16,f=65535&e.low,p=0,w=0,b=0,F=0;return b+=(F+=o*f)>>>16,w+=(b+=s*f)>>>16,b&=65535,w+=(b+=o*u)>>>16,p+=(w+=r*f)>>>16,w&=65535,p+=(w+=s*u)>>>16,w&=65535,p+=(w+=o*h)>>>16,p+=i*f+r*u+s*h+o*l,c((b&=65535)<<16|(F&=65535),(p&=65535)<<16|(w&=65535),this.unsigned)},_.mul=_.multiply,_.divide=function(e){if(n(e)||(e=d(e)),e.isZero())throw Error(\"division by zero\");var i,r,s;if(t)return this.unsigned||-2147483648!==this.high||-1!==e.low||-1!==e.high?c((this.unsigned?t.div_u:t.div_s)(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned):this;if(this.isZero())return this.unsigned?w:m;if(this.unsigned){if(e.unsigned||(e=e.toUnsigned()),e.gt(this))return w;if(e.gt(this.shru(1)))return F;s=w}else{if(this.eq(C))return e.eq(b)||e.eq(v)?C:e.eq(C)?b:(i=this.shr(1).div(e).shl(1)).eq(m)?e.isNegative()?b:v:(r=this.sub(e.mul(i)),s=i.add(r.div(e)));if(e.eq(C))return this.unsigned?w:m;if(this.isNegative())return e.isNegative()?this.neg().div(e.neg()):this.neg().div(e).neg();if(e.isNegative())return this.div(e.neg()).neg();s=m}for(r=this;r.gte(e);){i=Math.max(1,Math.floor(r.toNumber()/e.toNumber()));for(var o=Math.ceil(Math.log(i)/Math.LN2),h=o<=48?1:l(2,o-48),u=a(i),f=u.mul(e);f.isNegative()||f.gt(r);)f=(u=a(i-=h,this.unsigned)).mul(e);u.isZero()&&(u=b),s=s.add(u),r=r.sub(f)}return s},_.div=_.divide,_.modulo=function(e){return n(e)||(e=d(e)),t?c((this.unsigned?t.rem_u:t.rem_s)(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned):this.sub(this.div(e).mul(e))},_.mod=_.modulo,_.rem=_.modulo,_.not=function(){return c(~this.low,~this.high,this.unsigned)},_.and=function(e){return n(e)||(e=d(e)),c(this.low&e.low,this.high&e.high,this.unsigned)},_.or=function(e){return n(e)||(e=d(e)),c(this.low|e.low,this.high|e.high,this.unsigned)},_.xor=function(e){return n(e)||(e=d(e)),c(this.low^e.low,this.high^e.high,this.unsigned)},_.shiftLeft=function(e){return 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e=this.high,t=this.low;return[e>>>24,e>>>16&255,e>>>8&255,255&e,t>>>24,t>>>16&255,t>>>8&255,255&t]},i.fromBytes=function(e,t,n){return n?i.fromBytesLE(e,t):i.fromBytesBE(e,t)},i.fromBytesLE=function(e,t){return new i(e[0]|e[1]<<8|e[2]<<16|e[3]<<24,e[4]|e[5]<<8|e[6]<<16|e[7]<<24,t)},i.fromBytesBE=function(e,t){return new i(e[4]<<24|e[5]<<16|e[6]<<8|e[7],e[0]<<24|e[1]<<16|e[2]<<8|e[3],t)}},3503:(e,t,i)=>{var n,r,s,o,a;n=i(3939),r=i(2151).utf8,s=i(652),o=i(2151).bin,(a=function(e,t){e.constructor==String?e=t&&\"binary\"===t.encoding?o.stringToBytes(e):r.stringToBytes(e):s(e)?e=Array.prototype.slice.call(e,0):Array.isArray(e)||e.constructor===Uint8Array||(e=e.toString());for(var i=n.bytesToWords(e),c=8*e.length,l=1732584193,h=-271733879,d=-1732584194,u=271733878,f=0;f<i.length;f++)i[f]=16711935&(i[f]<<8|i[f]>>>24)|4278255360&(i[f]<<24|i[f]>>>8);i[c>>>5]|=128<<c%32,i[14+(c+64>>>9<<4)]=c;var p=a._ff,g=a._gg,m=a._hh,w=a._ii;for(f=0;f<i.length;f+=16){var 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e.state=c,c.strm=e,c.wrap=a,c.gzhead=null,c.w_bits=n,c.w_size=1<<c.w_bits,c.w_mask=c.w_size-1,c.hash_bits=s+7,c.hash_size=1<<c.hash_bits,c.hash_mask=c.hash_size-1,c.hash_shift=~~((c.hash_bits+F-1)/F),c.window=new r.Buf8(2*c.w_size),c.head=new r.Buf16(c.hash_size),c.prev=new r.Buf16(c.w_size),c.lit_bufsize=1<<s+6,c.pending_buf_size=4*c.lit_bufsize,c.pending_buf=new r.Buf8(c.pending_buf_size),c.d_buf=1*c.lit_bufsize,c.l_buf=3*c.lit_bufsize,c.level=t,c.strategy=o,c.method=i,U(e)}n=[new H(0,0,0,0,(function(e,t){var i=65535;for(i>e.pending_buf_size-5&&(i=e.pending_buf_size-5);;){if(e.lookahead<=1){if(T(e),0===e.lookahead&&t===l)return 1;if(0===e.lookahead)break}e.strstart+=e.lookahead,e.lookahead=0;var n=e.block_start+i;if((0===e.strstart||e.strstart>=n)&&(e.lookahead=e.strstart-n,e.strstart=n,N(e,!1),0===e.strm.avail_out))return 1;if(e.strstart-e.block_start>=e.w_size-y&&(N(e,!1),0===e.strm.avail_out))return 1}return 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1;if(0===e.lookahead)break}if(e.match_length=0,e.lookahead>=F&&e.strstart>0&&(n=a[r=e.strstart-1])===a[++r]&&n===a[++r]&&n===a[++r]){o=e.strstart+v;do{}while(n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&r<o);e.match_length=v-(o-r),e.match_length>e.lookahead&&(e.match_length=e.lookahead)}if(e.match_length>=F?(i=s._tr_tally(e,1,e.match_length-F),e.lookahead-=e.match_length,e.strstart+=e.match_length,e.match_length=0):(i=s._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++),i&&(N(e,!1),0===e.strm.avail_out))return 1}return e.insert=0,4===t?(N(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(N(e,!1),0===e.strm.avail_out)?1:2}(r,t):n[r.level].func(r,t);if(3!==p&&4!==p||(r.status=x),1===p||3===p)return 0===e.avail_out&&(r.last_flush=-1),h;if(2===p&&(1===t?s._tr_align(r):5!==t&&(s._tr_stored_block(r,0,0,!1),3===t&&(S(r.head),0===r.lookahead&&(r.strstart=0,r.block_start=0,r.insert=0))),E(e),0===e.avail_out))return r.last_flush=-1,h}return 4!==t?h:r.wrap<=0?1:(2===r.wrap?(B(r,255&e.adler),B(r,e.adler>>8&255),B(r,e.adler>>16&255),B(r,e.adler>>24&255),B(r,255&e.total_in),B(r,e.total_in>>8&255),B(r,e.total_in>>16&255),B(r,e.total_in>>24&255)):(M(r,e.adler>>>16),M(r,65535&e.adler)),E(e),r.wrap>0&&(r.wrap=-r.wrap),0!==r.pending?h:1)},t.deflateEnd=function(e){var t;return e&&e.state?(t=e.state.status)!==A&&69!==t&&73!==t&&91!==t&&t!==C&&t!==_&&t!==x?k(e,d):(e.state=null,t===_?k(e,-3):h):d},t.deflateSetDictionary=function(e,t){var i,n,s,a,c,l,u,f,p=t.length;if(!e||!e.state)return d;if(2===(a=(i=e.state).wrap)||1===a&&i.status!==A||i.lookahead)return d;for(1===a&&(e.adler=o(e.adler,t,p,0)),i.wrap=0,p>=i.w_size&&(0===a&&(S(i.head),i.strstart=0,i.block_start=0,i.insert=0),f=new r.Buf8(i.w_size),r.arraySet(f,t,p-i.w_size,i.w_size,0),t=f,p=i.w_size),c=e.avail_in,l=e.next_in,u=e.input,e.avail_in=p,e.next_in=0,e.input=t,T(i);i.lookahead>=F;){n=i.strstart,s=i.lookahead-(F-1);do{i.ins_h=(i.ins_h<<i.hash_shift^i.window[n+F-1])&i.hash_mask,i.prev[n&i.w_mask]=i.head[i.ins_h],i.head[i.ins_h]=n,n++}while(--s);i.strstart=n,i.lookahead=F-1,T(i)}return i.strstart+=i.lookahead,i.block_start=i.strstart,i.insert=i.lookahead,i.lookahead=0,i.match_length=i.prev_length=F-1,i.match_available=0,e.next_in=l,e.input=u,e.avail_in=c,i.wrap=a,h},t.deflateInfo=\"pako deflate (from Nodeca project)\"},7414:e=>{e.exports=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name=\"\",this.comment=\"\",this.hcrc=0,this.done=!1}},7293:e=>{e.exports=function(e,t){var i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_,x,k;i=e.state,n=e.next_in,x=e.input,r=n+(e.avail_in-5),s=e.next_out,k=e.output,o=s-(t-e.avail_out),a=s+(e.avail_out-257),c=i.dmax,l=i.wsize,h=i.whave,d=i.wnext,u=i.window,f=i.hold,p=i.bits,g=i.lencode,m=i.distcode,w=(1<<i.lenbits)-1,b=(1<<i.distbits)-1;e:do{p<15&&(f+=x[n++]<<p,p+=8,f+=x[n++]<<p,p+=8),F=g[f&w];t:for(;;){if(f>>>=v=F>>>24,p-=v,0==(v=F>>>16&255))k[s++]=65535&F;else{if(!(16&v)){if(64&v){if(32&v){i.mode=12;break e}e.msg=\"invalid literal/length code\",i.mode=30;break e}F=g[(65535&F)+(f&(1<<v)-1)];continue t}for(y=65535&F,(v&=15)&&(p<v&&(f+=x[n++]<<p,p+=8),y+=f&(1<<v)-1,f>>>=v,p-=v),p<15&&(f+=x[n++]<<p,p+=8,f+=x[n++]<<p,p+=8),F=m[f&b];;){if(f>>>=v=F>>>24,p-=v,16&(v=F>>>16&255)){if(A=65535&F,p<(v&=15)&&(f+=x[n++]<<p,(p+=8)<v&&(f+=x[n++]<<p,p+=8)),(A+=f&(1<<v)-1)>c){e.msg=\"invalid distance too far back\",i.mode=30;break e}if(f>>>=v,p-=v,A>(v=s-o)){if((v=A-v)>h&&i.sane){e.msg=\"invalid distance too far back\",i.mode=30;break e}if(C=0,_=u,0===d){if(C+=l-v,v<y){y-=v;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}}else if(d<v){if(C+=l+d-v,(v-=d)<y){y-=v;do{k[s++]=u[C++]}while(--v);if(C=0,d<y){y-=v=d;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}}}else if(C+=d-v,v<y){y-=v;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}for(;y>2;)k[s++]=_[C++],k[s++]=_[C++],k[s++]=_[C++],y-=3;y&&(k[s++]=_[C++],y>1&&(k[s++]=_[C++]))}else{C=s-A;do{k[s++]=k[C++],k[s++]=k[C++],k[s++]=k[C++],y-=3}while(y>2);y&&(k[s++]=k[C++],y>1&&(k[s++]=k[C++]))}break}if(64&v){e.msg=\"invalid distance code\",i.mode=30;break e}F=m[(65535&F)+(f&(1<<v)-1)]}}break}}while(n<r&&s<a);n-=y=p>>3,f&=(1<<(p-=y<<3))-1,e.next_in=n,e.next_out=s,e.avail_in=n<r?r-n+5:5-(n-r),e.avail_out=s<a?a-s+257:257-(s-a),i.hold=f,i.bits=p}},1447:(e,t,i)=>{var n=i(9805),r=i(3269),s=i(4823),o=i(7293),a=i(1998),c=0,l=-2,h=1,d=12,u=30,f=852,p=592;function g(e){return(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24)}function m(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new n.Buf16(320),this.work=new n.Buf16(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}function w(e){var t;return e&&e.state?(t=e.state,e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=h,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new n.Buf32(f),t.distcode=t.distdyn=new n.Buf32(p),t.sane=1,t.back=-1,c):l}function b(e){var t;return e&&e.state?((t=e.state).wsize=0,t.whave=0,t.wnext=0,w(e)):l}function F(e,t){var i,n;return e&&e.state?(n=e.state,t<0?(i=0,t=-t):(i=1+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?l:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,b(e))):l}function v(e,t){var i,n;return e?(n=new m,e.state=n,n.window=null,(i=F(e,t))!==c&&(e.state=null),i):l}var y,A,C=!0;function _(e){if(C){var t;for(y=new n.Buf32(512),A=new n.Buf32(32),t=0;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(a(1,e.lens,0,288,y,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;a(2,e.lens,0,32,A,0,e.work,{bits:5}),C=!1}e.lencode=y,e.lenbits=9,e.distcode=A,e.distbits=5}function x(e,t,i,r){var s,o=e.state;return null===o.window&&(o.wsize=1<<o.wbits,o.wnext=0,o.whave=0,o.window=new n.Buf8(o.wsize)),r>=o.wsize?(n.arraySet(o.window,t,i-o.wsize,o.wsize,0),o.wnext=0,o.whave=o.wsize):((s=o.wsize-o.wnext)>r&&(s=r),n.arraySet(o.window,t,i-r,s,o.wnext),(r-=s)?(n.arraySet(o.window,t,i-r,r,0),o.wnext=r,o.whave=o.wsize):(o.wnext+=s,o.wnext===o.wsize&&(o.wnext=0),o.whave<o.wsize&&(o.whave+=s))),0}t.inflateReset=b,t.inflateReset2=F,t.inflateResetKeep=w,t.inflateInit=function(e){return v(e,15)},t.inflateInit2=v,t.inflate=function(e,t){var i,f,p,m,w,b,F,v,y,A,C,k,I,S,E,N,B,M,R,D,T,L,z,H,P=0,O=new n.Buf8(4),U=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];if(!e||!e.state||!e.output||!e.input&&0!==e.avail_in)return l;(i=e.state).mode===d&&(i.mode=13),w=e.next_out,p=e.output,F=e.avail_out,m=e.next_in,f=e.input,b=e.avail_in,v=i.hold,y=i.bits,A=b,C=F,L=c;e:for(;;)switch(i.mode){case h:if(0===i.wrap){i.mode=13;break}for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(2&i.wrap&&35615===v){i.check=0,O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0),v=0,y=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&v)<<8)+(v>>8))%31){e.msg=\"incorrect header check\",i.mode=u;break}if(8!=(15&v)){e.msg=\"unknown compression method\",i.mode=u;break}if(y-=4,T=8+(15&(v>>>=4)),0===i.wbits)i.wbits=T;else if(T>i.wbits){e.msg=\"invalid window size\",i.mode=u;break}i.dmax=1<<T,e.adler=i.check=1,i.mode=512&v?10:d,v=0,y=0;break;case 2:for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(i.flags=v,8!=(255&i.flags)){e.msg=\"unknown compression method\",i.mode=u;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=u;break}i.head&&(i.head.text=v>>8&1),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0,i.mode=3;case 3:for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.head&&(i.head.time=v),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,O[2]=v>>>16&255,O[3]=v>>>24&255,i.check=s(i.check,O,4,0)),v=0,y=0,i.mode=4;case 4:for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.head&&(i.head.xflags=255&v,i.head.os=v>>8),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0,i.mode=5;case 5:if(1024&i.flags){for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.length=v,i.head&&(i.head.extra_len=v),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&((k=i.length)>b&&(k=b),k&&(i.head&&(T=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Array(i.head.extra_len)),n.arraySet(i.head.extra,f,m,k,T)),512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,i.length-=k),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===b)break e;k=0;do{T=f[m+k++],i.head&&T&&i.length<65536&&(i.head.name+=String.fromCharCode(T))}while(T&&k<b);if(512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,T)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===b)break e;k=0;do{T=f[m+k++],i.head&&T&&i.length<65536&&(i.head.comment+=String.fromCharCode(T))}while(T&&k<b);if(512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,T)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=u;break}v=0,y=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=d;break;case 10:for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}e.adler=i.check=g(v),v=0,y=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=w,e.avail_out=F,e.next_in=m,e.avail_in=b,i.hold=v,i.bits=y,2;e.adler=i.check=1,i.mode=d;case d:if(5===t||6===t)break e;case 13:if(i.last){v>>>=7&y,y-=7&y,i.mode=27;break}for(;y<3;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}switch(i.last=1&v,y-=1,3&(v>>>=1)){case 0:i.mode=14;break;case 1:if(_(i),i.mode=20,6===t){v>>>=2,y-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg=\"invalid block type\",i.mode=u}v>>>=2,y-=2;break;case 14:for(v>>>=7&y,y-=7&y;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if((65535&v)!=(v>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=u;break}if(i.length=65535&v,v=0,y=0,i.mode=15,6===t)break e;case 15:i.mode=16;case 16:if(k=i.length){if(k>b&&(k=b),k>F&&(k=F),0===k)break e;n.arraySet(p,f,m,k,w),b-=k,m+=k,F-=k,w+=k,i.length-=k;break}i.mode=d;break;case 17:for(;y<14;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(i.nlen=257+(31&v),v>>>=5,y-=5,i.ndist=1+(31&v),v>>>=5,y-=5,i.ncode=4+(15&v),v>>>=4,y-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=u;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;y<3;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.lens[U[i.have++]]=7&v,v>>>=3,y-=3}for(;i.have<19;)i.lens[U[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,z={bits:i.lenbits},L=a(0,i.lens,0,19,i.lencode,0,i.work,z),i.lenbits=z.bits,L){e.msg=\"invalid code lengths set\",i.mode=u;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;N=(P=i.lencode[v&(1<<i.lenbits)-1])>>>16&255,B=65535&P,!((E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(B<16)v>>>=E,y-=E,i.lens[i.have++]=B;else{if(16===B){for(H=E+2;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v>>>=E,y-=E,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=u;break}T=i.lens[i.have-1],k=3+(3&v),v>>>=2,y-=2}else if(17===B){for(H=E+3;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}y-=E,T=0,k=3+(7&(v>>>=E)),v>>>=3,y-=3}else{for(H=E+7;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}y-=E,T=0,k=11+(127&(v>>>=E)),v>>>=7,y-=7}if(i.have+k>i.nlen+i.ndist){e.msg=\"invalid bit length 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e;b--,v+=f[m++]<<y,y+=8}if(N&&!(240&N)){for(M=E,R=N,D=B;N=(P=i.lencode[D+((v&(1<<M+R)-1)>>M)])>>>16&255,B=65535&P,!(M+(E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}v>>>=M,y-=M,i.back+=M}if(v>>>=E,y-=E,i.back+=E,i.length=B,0===N){i.mode=26;break}if(32&N){i.back=-1,i.mode=d;break}if(64&N){e.msg=\"invalid literal/length code\",i.mode=u;break}i.extra=15&N,i.mode=22;case 22:if(i.extra){for(H=i.extra;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.length+=v&(1<<i.extra)-1,v>>>=i.extra,y-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;N=(P=i.distcode[v&(1<<i.distbits)-1])>>>16&255,B=65535&P,!((E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(!(240&N)){for(M=E,R=N,D=B;N=(P=i.distcode[D+((v&(1<<M+R)-1)>>M)])>>>16&255,B=65535&P,!(M+(E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}v>>>=M,y-=M,i.back+=M}if(v>>>=E,y-=E,i.back+=E,64&N){e.msg=\"invalid distance code\",i.mode=u;break}i.offset=B,i.extra=15&N,i.mode=24;case 24:if(i.extra){for(H=i.extra;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.offset+=v&(1<<i.extra)-1,v>>>=i.extra,y-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=u;break}i.mode=25;case 25:if(0===F)break e;if(k=C-F,i.offset>k){if((k=i.offset-k)>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=u;break}k>i.wnext?(k-=i.wnext,I=i.wsize-k):I=i.wnext-k,k>i.length&&(k=i.length),S=i.window}else S=p,I=w-i.offset,k=i.length;k>F&&(k=F),F-=k,i.length-=k;do{p[w++]=S[I++]}while(--k);0===i.length&&(i.mode=21);break;case 26:if(0===F)break e;p[w++]=i.length,F--,i.mode=21;break;case 27:if(i.wrap){for(;y<32;){if(0===b)break e;b--,v|=f[m++]<<y,y+=8}if(C-=F,e.total_out+=C,i.total+=C,C&&(e.adler=i.check=i.flags?s(i.check,p,C,w-C):r(i.check,p,C,w-C)),C=F,(i.flags?v:g(v))!==i.check){e.msg=\"incorrect data check\",i.mode=u;break}v=0,y=0}i.mode=28;case 28:if(i.wrap&&i.flags){for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=u;break}v=0,y=0}i.mode=29;case 29:L=1;break e;case u:L=-3;break e;case 31:return-4;default:return l}return e.next_out=w,e.avail_out=F,e.next_in=m,e.avail_in=b,i.hold=v,i.bits=y,(i.wsize||C!==e.avail_out&&i.mode<u&&(i.mode<27||4!==t))&&x(e,e.output,e.next_out,C-e.avail_out)?(i.mode=31,-4):(A-=e.avail_in,C-=e.avail_out,e.total_in+=A,e.total_out+=C,i.total+=C,i.wrap&&C&&(e.adler=i.check=i.flags?s(i.check,p,C,e.next_out-C):r(i.check,p,C,e.next_out-C)),e.data_type=i.bits+(i.last?64:0)+(i.mode===d?128:0)+(20===i.mode||15===i.mode?256:0),(0===A&&0===C||4===t)&&L===c&&(L=-5),L)},t.inflateEnd=function(e){if(!e||!e.state)return l;var t=e.state;return t.window&&(t.window=null),e.state=null,c},t.inflateGetHeader=function(e,t){var i;return e&&e.state&&2&(i=e.state).wrap?(i.head=t,t.done=!1,c):l},t.inflateSetDictionary=function(e,t){var i,n=t.length;return e&&e.state?0!==(i=e.state).wrap&&11!==i.mode?l:11===i.mode&&r(1,t,n,0)!==i.check?-3:x(e,t,n,n)?(i.mode=31,-4):(i.havedict=1,c):l},t.inflateInfo=\"pako inflate (from Nodeca project)\"},1998:(e,t,i)=>{var n=i(9805),r=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],s=[16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78],o=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0],a=[16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64];e.exports=function(e,t,i,c,l,h,d,u){var f,p,g,m,w,b,F,v,y,A=u.bits,C=0,_=0,x=0,k=0,I=0,S=0,E=0,N=0,B=0,M=0,R=null,D=0,T=new n.Buf16(16),L=new n.Buf16(16),z=null,H=0;for(C=0;C<=15;C++)T[C]=0;for(_=0;_<c;_++)T[t[i+_]]++;for(I=A,k=15;k>=1&&0===T[k];k--);if(I>k&&(I=k),0===k)return l[h++]=20971520,l[h++]=20971520,u.bits=1,0;for(x=1;x<k&&0===T[x];x++);for(I<x&&(I=x),N=1,C=1;C<=15;C++)if(N<<=1,(N-=T[C])<0)return-1;if(N>0&&(0===e||1!==k))return-1;for(L[1]=0,C=1;C<15;C++)L[C+1]=L[C]+T[C];for(_=0;_<c;_++)0!==t[i+_]&&(d[L[t[i+_]]++]=_);if(0===e?(R=z=d,b=19):1===e?(R=r,D-=257,z=s,H-=257,b=256):(R=o,z=a,b=-1),M=0,_=0,C=x,w=h,S=I,E=0,g=-1,m=(B=1<<I)-1,1===e&&B>852||2===e&&B>592)return 1;for(;;){F=C-E,d[_]<b?(v=0,y=d[_]):d[_]>b?(v=z[H+d[_]],y=R[D+d[_]]):(v=96,y=0),f=1<<C-E,x=p=1<<S;do{l[w+(M>>E)+(p-=f)]=F<<24|v<<16|y}while(0!==p);for(f=1<<C-1;M&f;)f>>=1;if(0!==f?(M&=f-1,M+=f):M=0,_++,0==--T[C]){if(C===k)break;C=t[i+d[_]]}if(C>I&&(M&m)!==g){for(0===E&&(E=I),w+=x,N=1<<(S=C-E);S+E<k&&!((N-=T[S+E])<=0);)S++,N<<=1;if(B+=1<<S,1===e&&B>852||2===e&&B>592)return 1;l[g=M&m]=I<<24|S<<16|w-h}}return 0!==M&&(l[w+M]=C-E<<24|64<<16),u.bits=I,0}},4674:e=>{e.exports={2:\"need dictionary\",1:\"stream end\",0:\"\",\"-1\":\"file error\",\"-2\":\"stream error\",\"-3\":\"data error\",\"-4\":\"insufficient memory\",\"-5\":\"buffer error\",\"-6\":\"incompatible version\"}},3665:(e,t,i)=>{var n=i(9805);function r(e){for(var t=e.length;--t>=0;)e[t]=0}var s=15,o=16,a=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0],c=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13],l=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7],h=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],d=new Array(576);r(d);var u=new Array(60);r(u);var f=new Array(512);r(f);var p=new Array(256);r(p);var g=new Array(29);r(g);var m,w,b,F=new Array(30);function v(e,t,i,n,r){this.static_tree=e,this.extra_bits=t,this.extra_base=i,this.elems=n,this.max_length=r,this.has_stree=e&&e.length}function y(e,t){this.dyn_tree=e,this.max_code=0,this.stat_desc=t}function A(e){return e<256?f[e]:f[256+(e>>>7)]}function C(e,t){e.pending_buf[e.pending++]=255&t,e.pending_buf[e.pending++]=t>>>8&255}function 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M(e,t,i){var n,r,s,o,l=0;if(0!==e.last_lit)do{n=e.pending_buf[e.d_buf+2*l]<<8|e.pending_buf[e.d_buf+2*l+1],r=e.pending_buf[e.l_buf+l],l++,0===n?x(e,r,t):(x(e,(s=p[r])+256+1,t),0!==(o=a[s])&&_(e,r-=g[s],o),x(e,s=A(--n),i),0!==(o=c[s])&&_(e,n-=F[s],o))}while(l<e.last_lit);x(e,256,t)}function R(e,t){var i,n,r,o=t.dyn_tree,a=t.stat_desc.static_tree,c=t.stat_desc.has_stree,l=t.stat_desc.elems,h=-1;for(e.heap_len=0,e.heap_max=573,i=0;i<l;i++)0!==o[2*i]?(e.heap[++e.heap_len]=h=i,e.depth[i]=0):o[2*i+1]=0;for(;e.heap_len<2;)o[2*(r=e.heap[++e.heap_len]=h<2?++h:0)]=1,e.depth[r]=0,e.opt_len--,c&&(e.static_len-=a[2*r+1]);for(t.max_code=h,i=e.heap_len>>1;i>=1;i--)B(e,o,i);r=l;do{i=e.heap[1],e.heap[1]=e.heap[e.heap_len--],B(e,o,1),n=e.heap[1],e.heap[--e.heap_max]=i,e.heap[--e.heap_max]=n,o[2*r]=o[2*i]+o[2*n],e.depth[r]=(e.depth[i]>=e.depth[n]?e.depth[i]:e.depth[n])+1,o[2*i+1]=o[2*n+1]=r,e.heap[1]=r++,B(e,o,1)}while(e.heap_len>=2);e.heap[--e.heap_max]=e.heap[1],function(e,t){var i,n,r,o,a,c,l=t.dyn_tree,h=t.max_code,d=t.stat_desc.static_tree,u=t.stat_desc.has_stree,f=t.stat_desc.extra_bits,p=t.stat_desc.extra_base,g=t.stat_desc.max_length,m=0;for(o=0;o<=s;o++)e.bl_count[o]=0;for(l[2*e.heap[e.heap_max]+1]=0,i=e.heap_max+1;i<573;i++)(o=l[2*l[2*(n=e.heap[i])+1]+1]+1)>g&&(o=g,m++),l[2*n+1]=o,n>h||(e.bl_count[o]++,a=0,n>=p&&(a=f[n-p]),c=l[2*n],e.opt_len+=c*(o+a),u&&(e.static_len+=c*(d[2*n+1]+a)));if(0!==m){do{for(o=g-1;0===e.bl_count[o];)o--;e.bl_count[o]--,e.bl_count[o+1]+=2,e.bl_count[g]--,m-=2}while(m>0);for(o=g;0!==o;o--)for(n=e.bl_count[o];0!==n;)(r=e.heap[--i])>h||(l[2*r+1]!==o&&(e.opt_len+=(o-l[2*r+1])*l[2*r],l[2*r+1]=o),n--)}}(e,t),I(o,h,e.bl_count)}function D(e,t,i){var n,r,s=-1,o=t[1],a=0,c=7,l=4;for(0===o&&(c=138,l=3),t[2*(i+1)+1]=65535,n=0;n<=i;n++)r=o,o=t[2*(n+1)+1],++a<c&&r===o||(a<l?e.bl_tree[2*r]+=a:0!==r?(r!==s&&e.bl_tree[2*r]++,e.bl_tree[32]++):a<=10?e.bl_tree[34]++:e.bl_tree[36]++,a=0,s=r,0===o?(c=138,l=3):r===o?(c=6,l=3):(c=7,l=4))}function 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v(d,a,257,286,s),w=new v(u,c,0,30,s),b=new v(new Array(0),l,0,19,7)}(),L=!0),e.l_desc=new y(e.dyn_ltree,m),e.d_desc=new y(e.dyn_dtree,w),e.bl_desc=new y(e.bl_tree,b),e.bi_buf=0,e.bi_valid=0,S(e)},t._tr_stored_block=z,t._tr_flush_block=function(e,t,i,n){var r,s,o=0;e.level>0?(2===e.strm.data_type&&(e.strm.data_type=function(e){var t,i=4093624447;for(t=0;t<=31;t++,i>>>=1)if(1&i&&0!==e.dyn_ltree[2*t])return 0;if(0!==e.dyn_ltree[18]||0!==e.dyn_ltree[20]||0!==e.dyn_ltree[26])return 1;for(t=32;t<256;t++)if(0!==e.dyn_ltree[2*t])return 1;return 0}(e)),R(e,e.l_desc),R(e,e.d_desc),o=function(e){var t;for(D(e,e.dyn_ltree,e.l_desc.max_code),D(e,e.dyn_dtree,e.d_desc.max_code),R(e,e.bl_desc),t=18;t>=3&&0===e.bl_tree[2*h[t]+1];t--);return e.opt_len+=3*(t+1)+5+5+4,t}(e),r=e.opt_len+3+7>>>3,(s=e.static_len+3+7>>>3)<=r&&(r=s)):r=s=i+5,i+4<=r&&-1!==t?z(e,t,i,n):4===e.strategy||s===r?(_(e,2+(n?1:0),3),M(e,d,u)):(_(e,4+(n?1:0),3),function(e,t,i,n){var r;for(_(e,t-257,5),_(e,i-1,5),_(e,n-4,4),r=0;r<n;r++)_(e,e.bl_tree[2*h[r]+1],3);T(e,e.dyn_ltree,t-1),T(e,e.dyn_dtree,i-1)}(e,e.l_desc.max_code+1,e.d_desc.max_code+1,o+1),M(e,e.dyn_ltree,e.dyn_dtree)),S(e),n&&E(e)},t._tr_tally=function(e,t,i){return e.pending_buf[e.d_buf+2*e.last_lit]=t>>>8&255,e.pending_buf[e.d_buf+2*e.last_lit+1]=255&t,e.pending_buf[e.l_buf+e.last_lit]=255&i,e.last_lit++,0===t?e.dyn_ltree[2*i]++:(e.matches++,t--,e.dyn_ltree[2*(p[i]+256+1)]++,e.dyn_dtree[2*A(t)]++),e.last_lit===e.lit_bufsize-1},t._tr_align=function(e){_(e,2,3),x(e,256,d),function(e){16===e.bi_valid?(C(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=255&e.bi_buf,e.bi_buf>>=8,e.bi_valid-=8)}(e)}},4442:e=>{e.exports=function(){this.input=null,this.next_in=0,this.avail_in=0,this.total_in=0,this.output=null,this.next_out=0,this.avail_out=0,this.total_out=0,this.msg=\"\",this.state=null,this.data_type=2,this.adler=0}},7392:e=>{class t{constructor(e={}){if(!(e.maxSize&&e.maxSize>0))throw new TypeError(\"`maxSize` must be a number greater than 0\");this.maxSize=e.maxSize,this.cache=new Map,this.oldCache=new Map,this._size=0}_set(e,t){this.cache.set(e,t),this._size++,this._size>=this.maxSize&&(this._size=0,this.oldCache=this.cache,this.cache=new Map)}get(e){if(this.cache.has(e))return this.cache.get(e);if(this.oldCache.has(e)){const t=this.oldCache.get(e);return this.oldCache.delete(e),this._set(e,t),t}}set(e,t){return this.cache.has(e)?this.cache.set(e,t):this._set(e,t),this}has(e){return this.cache.has(e)||this.oldCache.has(e)}peek(e){return this.cache.has(e)?this.cache.get(e):this.oldCache.has(e)?this.oldCache.get(e):void 0}delete(e){const t=this.cache.delete(e);return t&&this._size--,this.oldCache.delete(e)||t}clear(){this.cache.clear(),this.oldCache.clear(),this._size=0}*keys(){for(const[e]of this)yield e}*values(){for(const[,e]of this)yield e}*[Symbol.iterator](){for(const e of this.cache)yield e;for(const e of this.oldCache){const[t]=e;this.cache.has(t)||(yield e)}}get size(){let e=0;for(const t of this.oldCache.keys())this.cache.has(t)||e++;return this._size+e}}e.exports=t},1307:function(e,t,i){var n;n=e=>(()=>{var 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\"},t=>{t.exports=e}],i={};function 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-       "/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */var Jp={read:function(e,t,i,n,r){var s,o,a=8*r-n-1,c=(1<<a)-1,l=c>>1,h=-7,d=i?r-1:0,u=i?-1:1,f=e[t+d];for(d+=u,s=f&(1<<-h)-1,f>>=-h,h+=a;h>0;s=256*s+e[t+d],d+=u,h-=8);for(o=s&(1<<-h)-1,s>>=-h,h+=n;h>0;o=256*o+e[t+d],d+=u,h-=8);if(0===s)s=1-l;else{if(s===c)return o?NaN:1/0*(f?-1:1);o+=Math.pow(2,n),s-=l}return(f?-1:1)*o*Math.pow(2,s-n)},write:function(e,t,i,n,r,s){var o,a,c,l=8*s-r-1,h=(1<<l)-1,d=h>>1,u=23===r?Math.pow(2,-24)-Math.pow(2,-77):0,f=n?0:s-1,p=n?1:-1,g=t<0||0===t&&1/t<0?1:0;for(t=Math.abs(t),isNaN(t)||t===1/0?(a=isNaN(t)?1:0,o=h):(o=Math.floor(Math.log(t)/Math.LN2),t*(c=Math.pow(2,-o))<1&&(o--,c*=2),(t+=o+d>=1?u/c:u*Math.pow(2,1-d))*c>=2&&(o++,c/=2),o+d>=h?(a=0,o=h):o+d>=1?(a=(t*c-1)*Math.pow(2,r),o+=d):(a=t*Math.pow(2,d-1)*Math.pow(2,r),o=0));r>=8;e[i+f]=255&a,f+=p,a/=256,r-=8);for(o=o<<r|a,l+=r;l>0;e[i+f]=255&o,f+=p,o/=256,l-=8);e[i+f-p]|=128*g}};\n",
-       "/*!\n",
-       "     * The buffer module from node.js, for the browser.\n",
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-       "     * @author   Feross Aboukhadijeh <https://feross.org>\n",
-       "     * @license  MIT\n",
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e>>>=0,t||Ig(e,4,this.length),Jp.read(this,e,!1,23,4)},ng.prototype.readDoubleLE=function(e,t){return e>>>=0,t||Ig(e,8,this.length),Jp.read(this,e,!0,52,8)},ng.prototype.readDoubleBE=function(e,t){return e>>>=0,t||Ig(e,8,this.length),Jp.read(this,e,!1,52,8)},ng.prototype.writeUintLE=ng.prototype.writeUIntLE=function(e,t,i,n){if(e=+e,t>>>=0,i>>>=0,!n){Sg(this,e,t,i,Math.pow(2,8*i)-1,0)}let r=1,s=0;for(this[t]=255&e;++s<i&&(r*=256);)this[t+s]=e/r&255;return t+i},ng.prototype.writeUintBE=ng.prototype.writeUIntBE=function(e,t,i,n){if(e=+e,t>>>=0,i>>>=0,!n){Sg(this,e,t,i,Math.pow(2,8*i)-1,0)}let r=i-1,s=1;for(this[t+r]=255&e;--r>=0&&(s*=256);)this[t+r]=e/s&255;return t+i},ng.prototype.writeUint8=ng.prototype.writeUInt8=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,1,255,0),this[t]=255&e,t+1},ng.prototype.writeUint16LE=ng.prototype.writeUInt16LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,65535,0),this[t]=255&e,this[t+1]=e>>>8,t+2},ng.prototype.writeUint16BE=ng.prototype.writeUInt16BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,65535,0),this[t]=e>>>8,this[t+1]=255&e,t+2},ng.prototype.writeUint32LE=ng.prototype.writeUInt32LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,4294967295,0),this[t+3]=e>>>24,this[t+2]=e>>>16,this[t+1]=e>>>8,this[t]=255&e,t+4},ng.prototype.writeUint32BE=ng.prototype.writeUInt32BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,4294967295,0),this[t]=e>>>24,this[t+1]=e>>>16,this[t+2]=e>>>8,this[t+3]=255&e,t+4},ng.prototype.writeBigUInt64LE=Gg((function(e,t=0){return Eg(this,e,t,BigInt(0),BigInt(\"0xffffffffffffffff\"))})),ng.prototype.writeBigUInt64BE=Gg((function(e,t=0){return Ng(this,e,t,BigInt(0),BigInt(\"0xffffffffffffffff\"))})),ng.prototype.writeIntLE=function(e,t,i,n){if(e=+e,t>>>=0,!n){const n=Math.pow(2,8*i-1);Sg(this,e,t,i,n-1,-n)}let r=0,s=1,o=0;for(this[t]=255&e;++r<i&&(s*=256);)e<0&&0===o&&0!==this[t+r-1]&&(o=1),this[t+r]=(e/s|0)-o&255;return t+i},ng.prototype.writeIntBE=function(e,t,i,n){if(e=+e,t>>>=0,!n){const n=Math.pow(2,8*i-1);Sg(this,e,t,i,n-1,-n)}let r=i-1,s=1,o=0;for(this[t+r]=255&e;--r>=0&&(s*=256);)e<0&&0===o&&0!==this[t+r+1]&&(o=1),this[t+r]=(e/s|0)-o&255;return t+i},ng.prototype.writeInt8=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,1,127,-128),e<0&&(e=255+e+1),this[t]=255&e,t+1},ng.prototype.writeInt16LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,32767,-32768),this[t]=255&e,this[t+1]=e>>>8,t+2},ng.prototype.writeInt16BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,32767,-32768),this[t]=e>>>8,this[t+1]=255&e,t+2},ng.prototype.writeInt32LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,2147483647,-2147483648),this[t]=255&e,this[t+1]=e>>>8,this[t+2]=e>>>16,this[t+3]=e>>>24,t+4},ng.prototype.writeInt32BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,2147483647,-2147483648),e<0&&(e=4294967295+e+1),this[t]=e>>>24,this[t+1]=e>>>16,this[t+2]=e>>>8,this[t+3]=255&e,t+4},ng.prototype.writeBigInt64LE=Gg((function(e,t=0){return Eg(this,e,t,-BigInt(\"0x8000000000000000\"),BigInt(\"0x7fffffffffffffff\"))})),ng.prototype.writeBigInt64BE=Gg((function(e,t=0){return Ng(this,e,t,-BigInt(\"0x8000000000000000\"),BigInt(\"0x7fffffffffffffff\"))})),ng.prototype.writeFloatLE=function(e,t,i){return Mg(this,e,t,!0,i)},ng.prototype.writeFloatBE=function(e,t,i){return Mg(this,e,t,!1,i)},ng.prototype.writeDoubleLE=function(e,t,i){return Rg(this,e,t,!0,i)},ng.prototype.writeDoubleBE=function(e,t,i){return Rg(this,e,t,!1,i)},ng.prototype.copy=function(e,t,i,n){if(!ng.isBuffer(e))throw new TypeError(\"argument should be a Buffer\");if(i||(i=0),n||0===n||(n=this.length),t>=e.length&&(t=e.length),t||(t=0),n>0&&n<i&&(n=i),n===i)return 0;if(0===e.length||0===this.length)return 0;if(t<0)throw new RangeError(\"targetStart out of bounds\");if(i<0||i>=this.length)throw new RangeError(\"Index out of range\");if(n<0)throw new RangeError(\"sourceEnd out of bounds\");n>this.length&&(n=this.length),e.length-t<n-i&&(n=e.length-t+i);const r=n-i;return this===e&&\"function\"==typeof Uint8Array.prototype.copyWithin?this.copyWithin(t,i,n):Uint8Array.prototype.set.call(e,this.subarray(i,n),t),r},ng.prototype.fill=function(e,t,i,n){if(\"string\"==typeof e){if(\"string\"==typeof t?(n=t,t=0,i=this.length):\"string\"==typeof i&&(n=i,i=this.length),void 0!==n&&\"string\"!=typeof n)throw new TypeError(\"encoding must be a string\");if(\"string\"==typeof n&&!ng.isEncoding(n))throw new TypeError(\"Unknown encoding: \"+n);if(1===e.length){const t=e.charCodeAt(0);(\"utf8\"===n&&t<128||\"latin1\"===n)&&(e=t)}}else\"number\"==typeof e?e&=255:\"boolean\"==typeof e&&(e=Number(e));if(t<0||this.length<t||this.length<i)throw new RangeError(\"Out of range index\");if(i<=t)return this;let r;if(t>>>=0,i=void 0===i?this.length:i>>>0,e||(e=0),\"number\"==typeof e)for(r=t;r<i;++r)this[r]=e;else{const s=ng.isBuffer(e)?e:ng.from(e,n),o=s.length;if(0===o)throw new TypeError('The value \"'+e+'\" is invalid for argument \"value\"');for(r=0;r<i-t;++r)this[r+t]=s[r%o]}return this};const Dg={};function Tg(e,t,i){Dg[e]=class extends i{constructor(){super(),Object.defineProperty(this,\"message\",{value:t.apply(this,arguments),writable:!0,configurable:!0}),this.name=`${this.name} [${e}]`,this.stack,delete this.name}get code(){return e}set code(e){Object.defineProperty(this,\"code\",{configurable:!0,enumerable:!0,value:e,writable:!0})}toString(){return`${this.name} [${e}]: ${this.message}`}}}function Lg(e){let t=\"\",i=e.length;const n=\"-\"===e[0]?1:0;for(;i>=n+4;i-=3)t=`_${e.slice(i-3,i)}${t}`;return`${e.slice(0,i)}${t}`}function zg(e,t,i,n,r,s){if(e>i||e<t){const n=\"bigint\"==typeof t?\"n\":\"\";let r;throw r=s>3?0===t||t===BigInt(0)?`>= 0${n} and < 2${n} ** ${8*(s+1)}${n}`:`>= -(2${n} ** 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Received ${r}`,n}),RangeError);const Og=/[^+/0-9A-Za-z-_]/g;function Ug(e,t){let i;t=t||1/0;const n=e.length;let r=null;const s=[];for(let o=0;o<n;++o){if(i=e.charCodeAt(o),i>55295&&i<57344){if(!r){if(i>56319){(t-=3)>-1&&s.push(239,191,189);continue}if(o+1===n){(t-=3)>-1&&s.push(239,191,189);continue}r=i;continue}if(i<56320){(t-=3)>-1&&s.push(239,191,189),r=i;continue}i=65536+(r-55296<<10|i-56320)}else r&&(t-=3)>-1&&s.push(239,191,189);if(r=null,i<128){if((t-=1)<0)break;s.push(i)}else if(i<2048){if((t-=2)<0)break;s.push(i>>6|192,63&i|128)}else if(i<65536){if((t-=3)<0)break;s.push(i>>12|224,i>>6&63|128,63&i|128)}else{if(!(i<1114112))throw new Error(\"Invalid code point\");if((t-=4)<0)break;s.push(i>>18|240,i>>12&63|128,i>>6&63|128,63&i|128)}}return s}function qg(e){return Zp.toByteArray(function(e){if((e=(e=e.split(\"=\")[0]).trim().replace(Og,\"\")).length<2)return\"\";for(;e.length%4!=0;)e+=\"=\";return e}(e))}function Qg(e,t,i,n){let r;for(r=0;r<n&&!(r+i>=t.length||r>=e.length);++r)t[r+i]=e[r];return r}function Vg(e,t){return e instanceof t||null!=e&&null!=e.constructor&&null!=e.constructor.name&&e.constructor.name===t.name}function jg(e){return e!=e}const Wg=function(){const e=\"0123456789abcdef\",t=new Array(256);for(let i=0;i<16;++i){const n=16*i;for(let r=0;r<16;++r)t[n+r]=e[i]+e[r]}return t}();function Gg(e){return\"undefined\"==typeof BigInt?$g:e}function $g(){throw new Error(\"BigInt not supported\")}class Kg{constructor(e,t){this.position=0,this.url=e,this.config=t,Ht(e)||!1===t.cacheFetches?this.useCache=!1:(this.useCache=!0,this.cache=new Yg({fetch:(e,t)=>this._fetch(e,t),fetchSize:t.fetchSize||1e4}))}async _fetch(e,t){const i={start:e,size:t};this._stat={size:void 0};const n=await Qs.loadArrayBuffer(this.url,Ua(this.config,{range:i}));return ng.from(n)}async read(e,t=0,i=1/0,n=0){if(this.useCache)await this.cache.get(e,t,n,i);else{(await this._fetch(n,i)).copy(e,t)}return{bytesRead:i,buffer:e}}async readFile(){const e=await Qs.loadArrayBuffer(this.url,Ua(this.config));return ng.from(e)}async stat(){if(!this._stat){const e=ng.allocUnsafe(10);if(await this.read(e,0,10,0),!this._stat)throw new Error(`unable to determine size of file at ${this.url}`)}return this._stat}}class Yg{constructor({fetch:e,fetchSize:t=3e4}){this.fetch=e,this.position=0,this.buffer=ng.allocUnsafe(0),this.fetchSize=t}async get(e,t,i,n){if(e.length<t+n)throw new Error(\"output buffer not big enough for request\");if(i>=this.position&&i+n<=this.position+this.buffer.length);else{const e=Math.max(n,this.fetchSize);this.buffer=await this.fetch(i,e),this.position=i}const r=t,s=i-this.position,o=s+n;this.buffer.copy(e,r,s,o)}}class Xg{chrAliasTable=new Map;constructor(e,t,i){this.config=e,this.browser=i,this.genome=t,this.cramFile=new Vp.CramFile({filehandle:e.fileHandle?e.fileHandle:new Kg(e.url,e),seqFetch:e.seqFetch||async function(e,t,i){const n=this.genome,r=await this.getHeader(),s=n.getChromosomeName(r.indexToChr[e]);return this.genome.getSequence(s,t-1,i)}.bind(this),checkSequenceMD5:void 0===e.checkSequenceMD5||e.checkSequenceMD5});const n=e.indexFileHandle?e.indexFileHandle:new Kg(e.indexURL,e);this.indexedCramFile=new Vp.IndexedCramFile({cram:this.cramFile,index:new Vp.CraiIndex({filehandle:n}),fetchSizeLimit:e.fetchSizeLimit||1e9}),Mp.setReaderDefaults(this,e)}async getHeader(){if(!this.header){const e=await this.cramFile.getSamHeader(),t={},i=[],n=[];for(let r of e)if(\"SQ\"===r.tag){for(let e of r.data)if(\"SN\"===e.tag){const n=e.value;t[n]=i.length,i.push(n);break}}else\"RG\"===r.tag&&n.push(r.data);this.header={indexToChr:i,chrToIndex:t,chrNames:Object.keys(t),readGroups:n}}return this.header}async#x(e){if(await this.getHeader(),this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.header.chrToIndex[e];if(void 0===t){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>void 0!==this.header.chrToIndex[e]));e.length>0&&(n=e[0],t=this.header.chrToIndex[e[0]])}this.chrAliasTable.set(e,n)}return t}async readAlignments(e,t,i){const n=await this.getHeader(),r=await this.#x(e),s=new tp(e,t,i,this.config);if(void 0===r)return s;try{const e=await this.indexedCramFile.getRecordsForRange(r,t,i);for(let a of e){const e=a.sequenceId,c=a.alignmentStart,l=c+a.lengthOnRef;if(e<0)continue;if(e>r||c>i)return;if(e<r)continue;if(l<t)continue;const h=o(a,n.chrNames);this.filter.pass(h)&&s.push(h)}return s.finish(),s}catch(e){let t=e.message;throw t&&t.indexOf(\"MD5\")>=0&&(t=\"Sequence mismatch. Is this the correct genome for the loaded CRAM?\"),this.browser.alert.present(new Error(t)),e}function o(e,t){const i=new wp;if(i.chr=t[e.sequenceId],i.start=e.alignmentStart-1,i.lengthOnRef=e.lengthOnRef,i.flags=e.flags,i.strand=!(16&e.flags),i.fragmentLength=e.templateLength||e.templateSize,i.mq=e.mappingQuality,i.end=e.alignmentStart+e.lengthOnRef,i.readGroupId=e.readGroupId,e.mate&&void 0!==e.mate.sequenceId){const n=void 0!==e.mate.flags?!(1&e.mate.flags):!(32&e.flags);i.mate={chr:t[e.mate.sequenceId],position:e.mate.alignmentStart,strand:n}}return i.seq=e.getReadBases(),i.qual=e.qualityScores,i.tagDict=e.tags,i.readName=e.readName,function(e,t){const i=[];let n,r,s=0,o=\"\";if(t.scStart=t.start,t.scLengthOnRef=t.lengthOnRef,e.readFeatures)for(let a of e.readFeatures){const e=a.code,c=a.data,l=a.pos-1,h=a.refPos-1;switch(e){case\"S\":case\"I\":case\"i\":case\"N\":case\"D\":if(l>s){const e=l-s;i.push(new xp({start:h-e,seqOffset:s,len:e,type:\"M\"})),s+=e,o+=e+\"M\"}if(\"S\"===e){let n=h;t.scLengthOnRef+=c.length,0===l&&(t.scStart-=c.length,n-=c.length);const r=c.length;i.push(new xp({start:n,seqOffset:s,len:r,type:\"S\"})),s+=r,o+=r+e}else if(\"I\"===e||\"i\"===e){void 0===n&&(n=[]);const t=\"i\"===e?1:c.length;n.push(new xp({start:h,len:t,seqOffset:s,type:\"I\"})),s+=t,o+=t+e}else\"D\"!==e&&\"N\"!==e||(r||(r=[]),r.push({start:h,len:c,type:e}),o+=c+e);break;case\"H\":case\"P\":o+=c+e}}const a=e.readLength-s;a>0&&(i.push(new xp({start:e.alignmentStart+e.lengthOnRef-a-1,seqOffset:s,len:a,type:\"M\"})),o+=a+\"M\");t.blocks=i,t.insertions=n,t.gaps=r,t.cigar=o}(e,i),i.mate&&i.start>i.mate.position&&i.fragmentLength>0&&(i.fragmentLength=-i.fragmentLength),Mp.setPairOrientation(i),i}}}const Zg=2291137574,Jg=2273964779,em=[84,68,70,52],tm=new Uint8Array([66,65,77,1]),im=[67,82,65,77],nm=[31,139],rm=4,sm=new Set([\"narrowpeak\",\"broadpeak\",\"regionpeak\",\"peaks\",\"bedgraph\",\"wig\",\"gff3\",\"gff\",\"gtf\",\"fusionjuncspan\",\"refflat\",\"seg\",\"aed\",\"bed\",\"bedMethyl\",\"vcf\",\"bb\",\"bigbed\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\",\"bw\",\"bigwig\",\"bam\",\"tdf\",\"refgene\",\"genepred\",\"genepredext\",\"bedpe\",\"bp\",\"snp\",\"rmsk\",\"cram\",\"gwas\",\"maf\",\"mut\",\"hiccups\",\"fasta\",\"fa\",\"fna\",\"pytor\",\"hic\",\"qtl\"]);function om(e,t){const i=Math.min(e.length,t.length);if(0==i)return!1;for(let n=0;n<i;n++)if(e[n]!==t[n])return!1;return!0}async function am(e){let t;const i=e.filename||await ja(e.url);return i&&(t=await function(e){if(!e)return;if((e=e.toLowerCase()).endsWith(\"refgene.txt.gz\")||e.endsWith(\"refgene.txt.bgz\")||e.endsWith(\"refgene.txt\")||e.endsWith(\"refgene.sorted.txt.gz\")||e.endsWith(\"refgene.sorted.txt.bgz\"))return\"refgene\";e.endsWith(\".gz\")&&(e=e.substring(0,e.length-3));e.endsWith(\".bgz\")&&(e=e.substring(0,e.length-4));(e.endsWith(\".txt\")||e.endsWith(\".tab\")||e.endsWith(\".tsv\"))&&(e=e.substring(0,e.length-4));const t=e.lastIndexOf(\".\"),i=t<0?e:e.substring(t+1);switch(i){case\"bw\":return\"bigwig\";case\"bb\":return\"bigbed\";case\"fasta\":case\"fa\":case\"fna\":return\"fasta\";default:return sm.has(i)?i:void 0}}(i)),t||(t=await async function(e){const t=e.url;let i=Ua(e,{range:{start:0,size:1e3}}),n=await Qs.loadArrayBuffer(t,i),r=new Uint8Array(n);if(om(r,nm)){if(0!==(r[3]&rm)&&66===r[12]&&67===r[13]){i=Ua(e,{range:{start:0,size:ms(n)}}),n=await Qs.loadArrayBuffer(t,i),r=gs(n)}else i=Ua(e,{}),n=await Qs.loadArrayBuffer(t,i),r=ps(n),e._filecontents=r}if(om(r,tm))return\"bam\";if(om(r,im))return\"cram\";const s=!0;let o=new yc(new DataView(n),s).getUInt();if(o===Zg)return\"bigwig\";if(o===Jg)return\"bigbed\";if(om(r,em))return\"tdf\";const a=new TextDecoder(\"utf-8\").decode(r),c=a.split(/\\r?\\n/)[0];if(c.startsWith(\"##fileformat=VCF\"))return\"vcf\";if(c.startsWith(\"##gff-version 3\"))return\"gff3\";if(c.startsWith(\"##gff-version\"))return\"gff\";if(c.startsWith(\"##fileformat=\"))return c.substring(13).toLowerCase();if(xh.isQTL(c))return\"qtl\";if(Jl.isGWAS(c))return\"gwas\";if(Dc(c.split(\"\\t\")))return\"hiccups\";return null}(e)),t}class cm{constructor(e,t){const i=t.genome;if(this.config=e,this.genome=i,Ga(e.url)&&(this.config.indexed=!1),\"ga4gh\"===e.sourceType)throw Error(\"Unsupported source type 'ga4gh'\");if(\"pysam\"===e.sourceType)this.bamReader=new Up(e,i);else if(\"htsget\"===e.sourceType)this.bamReader=new Qp(e,i);else if(\"shardedBam\"===e.sourceType)this.bamReader=new Op(e,i);else if(\"cram\"===e.format)this.bamReader=new Xg(e,i,t);else{if(!this.config.indexURL&&!1!==e.indexed)if(Mt(this.config.url)){const e=function(e,t){if(Mt(e)){if(e.includes(\"?\")){const i=e.indexOf(\"?\");return e.substring(0,i)+\".\"+t+e.substring(i)}return e+\".\"+t}}(this.config.url,\"bai\");e?(console.warn(`Warning: no indexURL specified for ${this.config.url}.  Guessing ${e}`),this.config.indexURL=e):(console.warning(`Warning: no indexURL specified for ${this.config.url}.`),this.config.indexed=!1)}else console.warning(`Warning: no indexURL specified for ${this.config.name}.`),this.config.indexed=!1;!1!==this.config.indexed?this.bamReader=new Pp(e,i):this.bamReader=new Hp(e,i)}}async getAlignments(e,t,i){const n=this.genome,r=await this.bamReader.readAlignments(e,t,i);if(r.hasAlignments){const t=await n.getSequence(e,r.start,r.end);if(t)return r.coverageMap.refSeq=t,r.sequence=t,r;console.error(\"No sequence for: \"+e+\":\"+r.start+\"-\"+r.end)}return r}}class lm{constructor({chr:e,start:t,end:i}){this.chr=e,this.start=t,this.end=i}contains(e){return e.chr===this.chr&&e.start>=this.start&&e.end<=this.end}overlaps(e){return e.chr===this.chr&&!(e.end<this.start||e.start>this.end)}extend(e){e.chr===this.chr&&(this.start=Math.min(e.start,this.start),this.end=Math.max(e.end,this.end))}getLocusString(){if(\"all\"===this.chr)return\"all\";{const e=Rt(Math.floor(this.start)+1),t=Rt(Math.round(this.end));return`${this.chr}:${e}-${t}`}}static fromLocusString(e){if(\"all\"===e)return new lm({chr:\"all\"});const t=e.split(\":\"),i=t[0],n=t[1].split(\"-\"),r=Number.parseInt(n[0].replace(/,/g,\"\"))-1,s=Number.parseInt(n[1].replace(/,/g,\"\"));return new lm({chr:i,start:r,end:s})}}\n",
-       "/*!\n",
-       "     * vanilla-picker v2.12.1\n",
-       "     * https://vanilla-picker.js.org\n",
-       "     *\n",
-       "     * Copyright 2017-2021 Andreas Borgen (https://github.com/Sphinxxxx), Adam Brooks (https://github.com/dissimulate)\n",
-       "     * Released under the ISC license.\n",
-       "     */var hm=function(e,t){if(!(e instanceof t))throw new TypeError(\"Cannot call a class as a function\")},dm=function(){function e(e,t){for(var i=0;i<t.length;i++){var n=t[i];n.enumerable=n.enumerable||!1,n.configurable=!0,\"value\"in n&&(n.writable=!0),Object.defineProperty(e,n.key,n)}}return function(t,i,n){return i&&e(t.prototype,i),n&&e(t,n),t}}(),um=function(e,t){if(Array.isArray(e))return e;if(Symbol.iterator in Object(e))return function(e,t){var i=[],n=!0,r=!1,s=void 0;try{for(var o,a=e[Symbol.iterator]();!(n=(o=a.next()).done)&&(i.push(o.value),!t||i.length!==t);n=!0);}catch(e){r=!0,s=e}finally{try{!n&&a.return&&a.return()}finally{if(r)throw s}}return i}(e,t);throw new TypeError(\"Invalid attempt to destructure non-iterable instance\")};String.prototype.startsWith=String.prototype.startsWith||function(e){return 0===this.indexOf(e)},String.prototype.padStart=String.prototype.padStart||function(e,t){for(var i=this;i.length<e;)i=t+i;return i};var fm={cb:\"0f8ff\",tqw:\"aebd7\",q:\"-ffff\",qmrn:\"7fffd4\",zr:\"0ffff\",bg:\"5f5dc\",bsq:\"e4c4\",bck:\"---\",nch:\"ebcd\",b:\"--ff\",bvt:\"8a2be2\",brwn:\"a52a2a\",brw:\"deb887\",ctb:\"5f9ea0\",hrt:\"7fff-\",chcT:\"d2691e\",cr:\"7f50\",rnw:\"6495ed\",crns:\"8dc\",crms:\"dc143c\",cn:\"-ffff\",Db:\"--8b\",Dcn:\"-8b8b\",Dgnr:\"b8860b\",Dgr:\"a9a9a9\",Dgrn:\"-64-\",Dkhk:\"bdb76b\",Dmgn:\"8b-8b\",Dvgr:\"556b2f\",Drng:\"8c-\",Drch:\"9932cc\",Dr:\"8b--\",Dsmn:\"e9967a\",Dsgr:\"8fbc8f\",DsTb:\"483d8b\",DsTg:\"2f4f4f\",Dtrq:\"-ced1\",Dvt:\"94-d3\",ppnk:\"1493\",pskb:\"-bfff\",mgr:\"696969\",grb:\"1e90ff\",rbrc:\"b22222\",rwht:\"af0\",stg:\"228b22\",chs:\"-ff\",gnsb:\"dcdcdc\",st:\"8f8ff\",g:\"d7-\",gnr:\"daa520\",gr:\"808080\",grn:\"-8-0\",grnw:\"adff2f\",hnw:\"0fff0\",htpn:\"69b4\",nnr:\"cd5c5c\",ng:\"4b-82\",vr:\"0\",khk:\"0e68c\",vnr:\"e6e6fa\",nrb:\"0f5\",wngr:\"7cfc-\",mnch:\"acd\",Lb:\"add8e6\",Lcr:\"08080\",Lcn:\"e0ffff\",Lgnr:\"afad2\",Lgr:\"d3d3d3\",Lgrn:\"90ee90\",Lpnk:\"b6c1\",Lsmn:\"a07a\",Lsgr:\"20b2aa\",Lskb:\"87cefa\",LsTg:\"778899\",Lstb:\"b0c4de\",Lw:\"e0\",m:\"-ff-\",mgrn:\"32cd32\",nn:\"af0e6\",mgnt:\"-ff\",mrn:\"8--0\",mqm:\"66cdaa\",mmb:\"--cd\",mmrc:\"ba55d3\",mmpr:\"9370db\",msg:\"3cb371\",mmsT:\"7b68ee\",\"\":\"-fa9a\",mtr:\"48d1cc\",mmvt:\"c71585\",mnLb:\"191970\",ntc:\"5fffa\",mstr:\"e4e1\",mccs:\"e4b5\",vjw:\"dead\",nv:\"--80\",c:\"df5e6\",v:\"808-0\",vrb:\"6b8e23\",rng:\"a5-\",rngr:\"45-\",rch:\"da70d6\",pgnr:\"eee8aa\",pgrn:\"98fb98\",ptrq:\"afeeee\",pvtr:\"db7093\",ppwh:\"efd5\",pchp:\"dab9\",pr:\"cd853f\",pnk:\"c0cb\",pm:\"dda0dd\",pwrb:\"b0e0e6\",prp:\"8-080\",cc:\"663399\",r:\"--\",sbr:\"bc8f8f\",rb:\"4169e1\",sbrw:\"8b4513\",smn:\"a8072\",nbr:\"4a460\",sgrn:\"2e8b57\",ssh:\"5ee\",snn:\"a0522d\",svr:\"c0c0c0\",skb:\"87ceeb\",sTb:\"6a5acd\",sTgr:\"708090\",snw:\"afa\",n:\"-ff7f\",stb:\"4682b4\",tn:\"d2b48c\",t:\"-8080\",thst:\"d8bfd8\",tmT:\"6347\",trqs:\"40e0d0\",vt:\"ee82ee\",whT:\"5deb3\",wht:\"\",hts:\"5f5f5\",w:\"-\",wgrn:\"9acd32\"};function pm(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:1;return(t>0?e.toFixed(t).replace(/0+$/,\"\").replace(/\\.$/,\"\"):e.toString())||\"0\"}var gm=function(){function e(t,i,n,r){hm(this,e);var s=this;if(void 0===t);else if(Array.isArray(t))this.rgba=t;else if(void 0===n){var o=t&&\"\"+t;o&&function(t){if(t.startsWith(\"hsl\")){var i=t.match(/([\\-\\d\\.e]+)/g).map(Number),n=um(i,4),r=n[0],o=n[1],a=n[2],c=n[3];void 0===c&&(c=1),r/=360,o/=100,a/=100,s.hsla=[r,o,a,c]}else if(t.startsWith(\"rgb\")){var l=t.match(/([\\-\\d\\.e]+)/g).map(Number),h=um(l,4),d=h[0],u=h[1],f=h[2],p=h[3];void 0===p&&(p=1),s.rgba=[d,u,f,p]}else t.startsWith(\"#\")?s.rgba=e.hexToRgb(t):s.rgba=e.nameToRgb(t)||e.hexToRgb(t)}(o.toLowerCase())}else this.rgba=[t,i,n,void 0===r?1:r]}return dm(e,[{key:\"printRGB\",value:function(e){var t=(e?this.rgba:this.rgba.slice(0,3)).map((function(e,t){return pm(e,3===t?3:0)}));return e?\"rgba(\"+t+\")\":\"rgb(\"+t+\")\"}},{key:\"printHSL\",value:function(e){var t=[360,100,100,1],i=[\"\",\"%\",\"%\",\"\"],n=(e?this.hsla:this.hsla.slice(0,3)).map((function(e,n){return pm(e*t[n],3===n?3:1)+i[n]}));return e?\"hsla(\"+n+\")\":\"hsl(\"+n+\")\"}},{key:\"printHex\",value:function(e){var t=this.hex;return e?t:t.substring(0,7)}},{key:\"rgba\",get:function(){if(this._rgba)return this._rgba;if(!this._hsla)throw new Error(\"No color is set\");return this._rgba=e.hslToRgb(this._hsla)},set:function(e){3===e.length&&(e[3]=1),this._rgba=e,this._hsla=null}},{key:\"rgbString\",get:function(){return this.printRGB()}},{key:\"rgbaString\",get:function(){return this.printRGB(!0)}},{key:\"hsla\",get:function(){if(this._hsla)return this._hsla;if(!this._rgba)throw new Error(\"No color is set\");return this._hsla=e.rgbToHsl(this._rgba)},set:function(e){3===e.length&&(e[3]=1),this._hsla=e,this._rgba=null}},{key:\"hslString\",get:function(){return this.printHSL()}},{key:\"hslaString\",get:function(){return this.printHSL(!0)}},{key:\"hex\",get:function(){var e=this.rgba.map((function(e,t){return t<3?e.toString(16):Math.round(255*e).toString(16)}));return\"#\"+e.map((function(e){return e.padStart(2,\"0\")})).join(\"\")},set:function(t){this.rgba=e.hexToRgb(t)}}],[{key:\"hexToRgb\",value:function(e){var t=(e.startsWith(\"#\")?e.slice(1):e).replace(/^(\\w{3})$/,\"$1F\").replace(/^(\\w)(\\w)(\\w)(\\w)$/,\"$1$1$2$2$3$3$4$4\").replace(/^(\\w{6})$/,\"$1FF\");if(!t.match(/^([0-9a-fA-F]{8})$/))throw new Error(\"Unknown hex color; \"+e);var i=t.match(/^(\\w\\w)(\\w\\w)(\\w\\w)(\\w\\w)$/).slice(1).map((function(e){return parseInt(e,16)}));return i[3]=i[3]/255,i}},{key:\"nameToRgb\",value:function(t){var i=t.toLowerCase().replace(\"at\",\"T\").replace(/[aeiouyldf]/g,\"\").replace(\"ght\",\"L\").replace(\"rk\",\"D\").slice(-5,4),n=fm[i];return void 0===n?n:e.hexToRgb(n.replace(/\\-/g,\"00\").padStart(6,\"f\"))}},{key:\"rgbToHsl\",value:function(e){var t=um(e,4),i=t[0],n=t[1],r=t[2],s=t[3];i/=255,n/=255,r/=255;var o=Math.max(i,n,r),a=Math.min(i,n,r),c=void 0,l=void 0,h=(o+a)/2;if(o===a)c=l=0;else{var d=o-a;switch(l=h>.5?d/(2-o-a):d/(o+a),o){case i:c=(n-r)/d+(n<r?6:0);break;case n:c=(r-i)/d+2;break;case r:c=(i-n)/d+4}c/=6}return[c,l,h,s]}},{key:\"hslToRgb\",value:function(e){var t=um(e,4),i=t[0],n=t[1],r=t[2],s=t[3],o=void 0,a=void 0,c=void 0;if(0===n)o=a=c=r;else{var l=function(e,t,i){return i<0&&(i+=1),i>1&&(i-=1),i<1/6?e+6*(t-e)*i:i<.5?t:i<2/3?e+(t-e)*(2/3-i)*6:e},h=r<.5?r*(1+n):r+n-r*n,d=2*r-h;o=l(d,h,i+1/3),a=l(d,h,i),c=l(d,h,i-1/3)}var u=[255*o,255*a,255*c].map(Math.round);return u[3]=s,u}}]),e}(),mm=function(){function e(){hm(this,e),this._events=[]}return dm(e,[{key:\"add\",value:function(e,t,i){e.addEventListener(t,i,!1),this._events.push({target:e,type:t,handler:i})}},{key:\"remove\",value:function(t,i,n){this._events=this._events.filter((function(r){var s=!0;return t&&t!==r.target&&(s=!1),i&&i!==r.type&&(s=!1),n&&n!==r.handler&&(s=!1),s&&e._doRemove(r.target,r.type,r.handler),!s}))}},{key:\"destroy\",value:function(){this._events.forEach((function(t){return e._doRemove(t.target,t.type,t.handler)})),this._events=[]}}],[{key:\"_doRemove\",value:function(e,t,i){e.removeEventListener(t,i,!1)}}]),e}();function wm(e,t,i){var n=!1;function r(e,t,i){return Math.max(t,Math.min(e,i))}function s(e,s,o){if(o&&(n=!0),n){e.preventDefault();var a=t.getBoundingClientRect(),c=a.width,l=a.height,h=s.clientX,d=s.clientY,u=r(h-a.left,0,c),f=r(d-a.top,0,l);i(u/c,f/l)}}function o(e,t){1===(void 0===e.buttons?e.which:e.buttons)?s(e,e,t):n=!1}function a(e,t){1===e.touches.length?s(e,e.touches[0],t):n=!1}e.add(t,\"mousedown\",(function(e){o(e,!0)})),e.add(t,\"touchstart\",(function(e){a(e,!0)})),e.add(window,\"mousemove\",o),e.add(t,\"touchmove\",a),e.add(window,\"mouseup\",(function(e){n=!1})),e.add(t,\"touchend\",(function(e){n=!1})),e.add(t,\"touchcancel\",(function(e){n=!1}))}var bm=\"keydown\",Fm=\"mousedown\",vm=\"focusin\";function ym(e,t){return(t||document).querySelector(e)}function Am(e){e.preventDefault(),e.stopPropagation()}function Cm(e,t,i,n,r){e.add(t,bm,(function(e){i.indexOf(e.key)>=0&&(r&&Am(e),n(e))}))}var _m=function(){function e(t){hm(this,e),this.settings={popup:\"right\",layout:\"default\",alpha:!0,editor:!0,editorFormat:\"hex\",cancelButton:!1,defaultColor:\"#0cf\"},this._events=new mm,this.onChange=null,this.onDone=null,this.onOpen=null,this.onClose=null,this.setOptions(t)}return dm(e,[{key:\"setOptions\",value:function(e){var t=this;if(e){var i=this.settings;if(e instanceof HTMLElement)i.parent=e;else{i.parent&&e.parent&&i.parent!==e.parent&&(this._events.remove(i.parent),this._popupInited=!1),function(e,t,i){for(var n in e)i&&i.indexOf(n)>=0||(t[n]=e[n])}(e,i),e.onChange&&(this.onChange=e.onChange),e.onDone&&(this.onDone=e.onDone),e.onOpen&&(this.onOpen=e.onOpen),e.onClose&&(this.onClose=e.onClose);var n=e.color||e.colour;n&&this._setColor(n)}var r=i.parent;if(r&&i.popup&&!this._popupInited){var s=function(e){return t.openHandler(e)};this._events.add(r,\"click\",s),Cm(this._events,r,[\" \",\"Spacebar\",\"Enter\"],s),this._popupInited=!0}else e.parent&&!i.popup&&this.show()}}},{key:\"openHandler\",value:function(e){if(this.show()){e&&e.preventDefault(),this.settings.parent.style.pointerEvents=\"none\";var t=e&&e.type===bm?this._domEdit:this.domElement;setTimeout((function(){return t.focus()}),100),this.onOpen&&this.onOpen(this.colour)}}},{key:\"closeHandler\",value:function(e){var t=e&&e.type,i=!1;if(e)if(t===Fm||t===vm){var n=(this.__containedEvent||0)+100;e.timeStamp>n&&(i=!0)}else Am(e),i=!0;else i=!0;i&&this.hide()&&(this.settings.parent.style.pointerEvents=\"\",t!==Fm&&this.settings.parent.focus(),this.onClose&&this.onClose(this.colour))}},{key:\"movePopup\",value:function(e,t){this.closeHandler(),this.setOptions(e),t&&this.openHandler()}},{key:\"setColor\",value:function(e,t){this._setColor(e,{silent:t})}},{key:\"_setColor\",value:function(e,t){if(\"string\"==typeof e&&(e=e.trim()),e){t=t||{};var i=void 0;try{i=new gm(e)}catch(e){if(t.failSilently)return;throw e}if(!this.settings.alpha){var n=i.hsla;n[3]=1,i.hsla=n}this.colour=this.color=i,this._setHSLA(null,null,null,null,t)}}},{key:\"setColour\",value:function(e,t){this.setColor(e,t)}},{key:\"show\",value:function(){if(!this.settings.parent)return!1;if(this.domElement){var e=this._toggleDOM(!0);return this._setPosition(),e}var t=function(e){var t=document.createElement(\"div\");return t.innerHTML=e,t.firstElementChild}(this.settings.template||'<div class=\"picker_wrapper\" tabindex=\"-1\"><div class=\"picker_arrow\"></div><div class=\"picker_hue picker_slider\"><div class=\"picker_selector\"></div></div><div class=\"picker_sl\"><div class=\"picker_selector\"></div></div><div class=\"picker_alpha picker_slider\"><div class=\"picker_selector\"></div></div><div class=\"picker_editor\"><input aria-label=\"Type a color name or hex value\"/></div><div class=\"picker_sample\"></div><div class=\"picker_done\"><button>Ok</button></div><div class=\"picker_cancel\"><button>Cancel</button></div></div>');return this.domElement=t,this._domH=ym(\".picker_hue\",t),this._domSL=ym(\".picker_sl\",t),this._domA=ym(\".picker_alpha\",t),this._domEdit=ym(\".picker_editor input\",t),this._domSample=ym(\".picker_sample\",t),this._domOkay=ym(\".picker_done button\",t),this._domCancel=ym(\".picker_cancel button\",t),t.classList.add(\"layout_\"+this.settings.layout),this.settings.alpha||t.classList.add(\"no_alpha\"),this.settings.editor||t.classList.add(\"no_editor\"),this.settings.cancelButton||t.classList.add(\"no_cancel\"),this._ifPopup((function(){return t.classList.add(\"popup\")})),this._setPosition(),this.colour?this._updateUI():this._setColor(this.settings.defaultColor),this._bindEvents(),!0}},{key:\"hide\",value:function(){return this._toggleDOM(!1)}},{key:\"destroy\",value:function(){this._events.destroy(),this.domElement&&this.settings.parent.removeChild(this.domElement)}},{key:\"_bindEvents\",value:function(){var e=this,t=this,i=this.domElement,n=this._events;function r(e,t,i){n.add(e,t,i)}r(i,\"click\",(function(e){return e.preventDefault()})),wm(n,this._domH,(function(e,i){return t._setHSLA(e)})),wm(n,this._domSL,(function(e,i){return t._setHSLA(null,e,1-i)})),this.settings.alpha&&wm(n,this._domA,(function(e,i){return t._setHSLA(null,null,null,1-i)}));var s=this._domEdit;r(s,\"input\",(function(e){t._setColor(this.value,{fromEditor:!0,failSilently:!0})})),r(s,\"focus\",(function(e){var t=this;t.selectionStart===t.selectionEnd&&t.select()})),this._ifPopup((function(){var t=function(t){return e.closeHandler(t)};r(window,Fm,t),r(window,vm,t),Cm(n,i,[\"Esc\",\"Escape\"],t);var s=function(t){e.__containedEvent=t.timeStamp};r(i,Fm,s),r(i,vm,s),r(e._domCancel,\"click\",t)}));var o=function(t){e._ifPopup((function(){return e.closeHandler(t)})),e.onDone&&e.onDone(e.colour)};r(this._domOkay,\"click\",o),Cm(n,i,[\"Enter\"],o)}},{key:\"_setPosition\",value:function(){var e=this.settings.parent,t=this.domElement;e!==t.parentNode&&e.appendChild(t),this._ifPopup((function(i){\"static\"===getComputedStyle(e).position&&(e.style.position=\"relative\");var n=!0===i?\"popup_right\":\"popup_\"+i;[\"popup_top\",\"popup_bottom\",\"popup_left\",\"popup_right\"].forEach((function(e){e===n?t.classList.add(e):t.classList.remove(e)})),t.classList.add(n)}))}},{key:\"_setHSLA\",value:function(e,t,i,n,r){r=r||{};var s=this.colour,o=s.hsla;[e,t,i,n].forEach((function(e,t){(e||0===e)&&(o[t]=e)})),s.hsla=o,this._updateUI(r),this.onChange&&!r.silent&&this.onChange(s)}},{key:\"_updateUI\",value:function(e){if(this.domElement){e=e||{};var t=this.colour,i=t.hsla,n=\"hsl(\"+360*i[0]+\", 100%, 50%)\",r=t.hslString,s=t.hslaString,o=this._domH,a=this._domSL,c=this._domA,l=ym(\".picker_selector\",o),h=ym(\".picker_selector\",a),d=ym(\".picker_selector\",c);b(0,l,i[0]),this._domSL.style.backgroundColor=this._domH.style.color=n,b(0,h,i[1]),F(0,h,1-i[2]),a.style.color=r,F(0,d,1-i[3]);var u=r,f=u.replace(\"hsl\",\"hsla\").replace(\")\",\", 0)\"),p=\"linear-gradient(\"+[u,f]+\")\";if(this._domA.style.background=p+\", linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0 / 2em 2em,\\n                   linear-gradient(45deg, lightgrey 25%,       white 25%,       white 75%, lightgrey 75%) 1em 1em / 2em 2em\",!e.fromEditor){var g=this.settings.editorFormat,m=this.settings.alpha,w=void 0;switch(g){case\"rgb\":w=t.printRGB(m);break;case\"hsl\":w=t.printHSL(m);break;default:w=t.printHex(m)}this._domEdit.value=w}this._domSample.style.color=s}function b(e,t,i){t.style.left=100*i+\"%\"}function F(e,t,i){t.style.top=100*i+\"%\"}}},{key:\"_ifPopup\",value:function(e,t){this.settings.parent&&this.settings.popup?e&&e(this.settings.popup):t&&t()}},{key:\"_toggleDOM\",value:function(e){var t=this.domElement;if(!t)return!1;var i=e?\"\":\"none\",n=t.style.display!==i;return n&&(t.style.display=i),n}}]),e}(),xm=document.createElement(\"style\");function km(e){if(Im[e])return Im[e];if(Im[\"chr\"+e]){const t=Im[\"chr\"+e];return Im[e]=t,t}{const r=(t=Math.round(255*Math.random()).toString(10),i=Math.round(255*Math.random()).toString(10),n=Math.round(255*Math.random()).toString(10),\"rgb(\"+t+\",\"+i+\",\"+n+\")\");return Im[e]=r,r}var t,i,n}xm.textContent='.picker_wrapper.no_alpha .picker_alpha{display:none}.picker_wrapper.no_editor .picker_editor{position:absolute;z-index:-1;opacity:0}.picker_wrapper.no_cancel .picker_cancel{display:none}.layout_default.picker_wrapper{display:flex;flex-flow:row wrap;justify-content:space-between;align-items:stretch;font-size:10px;width:25em;padding:.5em}.layout_default.picker_wrapper input,.layout_default.picker_wrapper button{font-size:1rem}.layout_default.picker_wrapper>*{margin:.5em}.layout_default.picker_wrapper::before{content:\"\";display:block;width:100%;height:0;order:1}.layout_default .picker_slider,.layout_default .picker_selector{padding:1em}.layout_default .picker_hue{width:100%}.layout_default .picker_sl{flex:1 1 auto}.layout_default .picker_sl::before{content:\"\";display:block;padding-bottom:100%}.layout_default .picker_editor{order:1;width:6.5rem}.layout_default .picker_editor input{width:100%;height:100%}.layout_default .picker_sample{order:1;flex:1 1 auto}.layout_default .picker_done,.layout_default .picker_cancel{order:1}.picker_wrapper{box-sizing:border-box;background:#f2f2f2;box-shadow:0 0 0 1px silver;cursor:default;font-family:sans-serif;color:#444;pointer-events:auto}.picker_wrapper:focus{outline:none}.picker_wrapper button,.picker_wrapper input{box-sizing:border-box;border:none;box-shadow:0 0 0 1px silver;outline:none}.picker_wrapper button:focus,.picker_wrapper button:active,.picker_wrapper input:focus,.picker_wrapper input:active{box-shadow:0 0 2px 1px #1e90ff}.picker_wrapper button{padding:.4em .6em;cursor:pointer;background-color:#f5f5f5;background-image:linear-gradient(0deg, gainsboro, transparent)}.picker_wrapper button:active{background-image:linear-gradient(0deg, transparent, gainsboro)}.picker_wrapper button:hover{background-color:#fff}.picker_selector{position:absolute;z-index:1;display:block;-webkit-transform:translate(-50%, -50%);transform:translate(-50%, -50%);border:2px solid #fff;border-radius:100%;box-shadow:0 0 3px 1px #67b9ff;background:currentColor;cursor:pointer}.picker_slider .picker_selector{border-radius:2px}.picker_hue{position:relative;background-image:linear-gradient(90deg, red, yellow, lime, cyan, blue, magenta, red);box-shadow:0 0 0 1px silver}.picker_sl{position:relative;box-shadow:0 0 0 1px silver;background-image:linear-gradient(180deg, white, rgba(255, 255, 255, 0) 50%),linear-gradient(0deg, black, rgba(0, 0, 0, 0) 50%),linear-gradient(90deg, #808080, rgba(128, 128, 128, 0))}.picker_alpha,.picker_sample{position:relative;background:linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0/2em 2em,linear-gradient(45deg, lightgrey 25%, white 25%, white 75%, lightgrey 75%) 1em 1em/2em 2em;box-shadow:0 0 0 1px silver}.picker_alpha .picker_selector,.picker_sample .picker_selector{background:none}.picker_editor input{font-family:monospace;padding:.2em .4em}.picker_sample::before{content:\"\";position:absolute;display:block;width:100%;height:100%;background:currentColor}.picker_arrow{position:absolute;z-index:-1}.picker_wrapper.popup{position:absolute;z-index:2;margin:1.5em}.picker_wrapper.popup,.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{background:#f2f2f2;box-shadow:0 0 10px 1px rgba(0,0,0,.4)}.picker_wrapper.popup .picker_arrow{width:3em;height:3em;margin:0}.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{content:\"\";display:block;position:absolute;top:0;left:0;z-index:-99}.picker_wrapper.popup .picker_arrow::before{width:100%;height:100%;-webkit-transform:skew(45deg);transform:skew(45deg);-webkit-transform-origin:0 100%;transform-origin:0 100%}.picker_wrapper.popup .picker_arrow::after{width:150%;height:150%;box-shadow:none}.popup.popup_top{bottom:100%;left:0}.popup.popup_top .picker_arrow{bottom:0;left:0;-webkit-transform:rotate(-90deg);transform:rotate(-90deg)}.popup.popup_bottom{top:100%;left:0}.popup.popup_bottom .picker_arrow{top:0;left:0;-webkit-transform:rotate(90deg) scale(1, -1);transform:rotate(90deg) scale(1, -1)}.popup.popup_left{top:0;right:100%}.popup.popup_left .picker_arrow{top:0;right:0;-webkit-transform:scale(-1, 1);transform:scale(-1, 1)}.popup.popup_right{top:0;left:100%}.popup.popup_right .picker_arrow{top:0;left:0}',document.documentElement.firstElementChild.appendChild(xm),_m.StyleElement=xm;const Im={chrX:\"rgb(204, 153, 0)\",chrY:\"rgb(153, 204, 0\",chrUn:\"rgb(50, 50, 50)\",chr1:\"rgb(80, 80, 255)\",chrI:\"rgb(139, 155, 187)\",chr2:\"rgb(206, 61, 50)\",chrII:\"rgb(206, 61, 50)\",chr2a:\"rgb(216, 71, 60)\",chr2b:\"rgb(226, 81, 70)\",chr3:\"rgb(116, 155, 88)\",chrIII:\"rgb(116, 155, 88)\",chr4:\"rgb(240, 230, 133)\",chrIV:\"rgb(240, 230, 133)\",chr5:\"rgb(70, 105, 131)\",chr6:\"rgb(186, 99, 56)\",chr7:\"rgb(93, 177, 221)\",chr8:\"rgb(128, 34, 104)\",chr9:\"rgb(107, 215, 107)\",chr10:\"rgb(213, 149, 167)\",chr11:\"rgb(146, 72, 34)\",chr12:\"rgb(131, 123, 141)\",chr13:\"rgb(199, 81, 39)\",chr14:\"rgb(213, 143, 92)\",chr15:\"rgb(122, 101, 165)\",chr16:\"rgb(228, 175, 105)\",chr17:\"rgb(59, 27, 83)\",chr18:\"rgb(205, 222, 183)\",chr19:\"rgb(97, 42, 121)\",chr20:\"rgb(174, 31, 99)\",chr21:\"rgb(231, 199, 111)\",chr22:\"rgb(90, 101, 94)\",chr23:\"rgb(204, 153, 0)\",chr24:\"rgb(153, 204, 0)\",chr25:\"rgb(51, 204, 0)\",chr26:\"rgb(0, 204, 51)\",chr27:\"rgb(0, 204, 153)\",chr28:\"rgb(0, 153, 204)\",chr29:\"rgb(10, 71, 255)\",chr30:\"rgb(71, 117, 255)\",chr31:\"rgb(255, 194, 10)\",chr32:\"rgb(255, 209, 71)\",chr33:\"rgb(153, 0, 51)\",chr34:\"rgb(153, 26, 0)\",chr35:\"rgb(153, 102, 0)\",chr36:\"rgb(128, 153, 0)\",chr37:\"rgb(51, 153, 0)\",chr38:\"rgb(0, 153, 26)\",chr39:\"rgb(0, 153, 102)\",chr40:\"rgb(0, 128, 153)\",chr41:\"rgb(0, 51, 153)\",chr42:\"rgb(26, 0, 153)\",chr43:\"rgb(102, 0, 153)\",chr44:\"rgb(153, 0, 128)\",chr45:\"rgb(214, 0, 71)\",chr46:\"rgb(255, 20, 99)\",chr47:\"rgb(0, 214, 143)\",chr48:\"rgb(20, 255, 177)\"};class Sm{constructor(e){this.tracks=[],this.chordSets=[]}addChordSet(e){this.chordSets=this.chordSets.filter((t=>t.name!==e.name)),this.chordSets.push(e);let t=this.tracks.find((t=>e.trackName===t.name));t&&(t.chordSets=t.chordSets.filter((t=>t.name!==e.name)),t.chordSets.push(e)),t||(t=new Em(e),this.tracks.push(t))}clearChords(){this.tracks=[],this.chordSets=[]}getTrack(e){return this.tracks.find((t=>e===t.name))}getChordSet(e){return this.chordSets.find((t=>e===t.name))}}class Em{constructor(e){this.name=e.trackName,this.color=e.trackColor,this.visible=!0,this.chordSets=[e],this.id=(\"0000\"+(Math.random()*Math.pow(36,4)|0).toString(36)).slice(-4)}get chords(){if(1===this.chordSets.length)return this.chordSets[0].chords;const e=[];for(let t of this.chordSets)for(let i of t.chords)e.push(i);return e}}const Nm=Math.exp(5);class Bm{static isInstalled(){return void 0!==window.JBrowseReactCircularGenomeView&&void 0!==window.React&&void 0!==window.ReactDOM}constructor(e,t){if(t=t||{},this.config=t,Bm.isInstalled()){this.parent=e,this.groupByTrack=!0===t.groupByTrack,this.chordManager=new Sm(t);const i=document.createElement(\"div\");i.className=\"igv-circview-container\",e.appendChild(i),this.createControls(i),this.resetControlPanel();const n=document.createElement(\"div\");n.className=\"igv-circview-circular-genome-view\",i.appendChild(n),this.container=n,t.assembly&&this.setAssembly(t.assembly),this.width=t.width||500,this.height=t.height||500,this.setSize(this.width,this.height)}else console.error(\"JBrowse circular view is not installed\")}createControls(e){const t=document.createElement(\"div\");t.className=\"igv-circview-toolbar\",e.appendChild(t),this.toolbar=t;const i=document.createElement(\"div\");i.className=\"igv-circview-track-panel\",e.appendChild(i),this.controlPanel=i,this.controlPanel.style.display=\"none\";const n=document.createElement(\"div\");n.className=\"igv-circview-toolbar-button-container\",this.toolbar.appendChild(n),this.showControlsButton=document.createElement(\"div\"),this.showControlsButton.className=\"igv-circview-button\",n.appendChild(this.showControlsButton),this.showControlsButton.innerText=\"none\"===this.controlPanel.style.display?\"Show Controls\":\"Hide Controls\",this.showControlsButton.addEventListener(\"click\",(e=>{this.controlPanel.querySelectorAll(\"div\").length>0&&(\"none\"===this.controlPanel.style.display?(this.controlPanel.style.display=\"flex\",e.target.innerText=\"Hide Controls\"):(this.controlPanel.style.display=\"none\",e.target.innerText=\"Show Controls\"))}));let r=document.createElement(\"div\");r.className=\"igv-circview-button\",n.appendChild(r),r.innerText=\"Clear All\",r.addEventListener(\"click\",(()=>{this.clearChords()})),!1!==this.config.showCloseButton&&(r=document.createElement(\"div\"),r.className=\"igv-circview-button\",n.appendChild(r),r.innerText=\"Close\",r.addEventListener(\"click\",(()=>{this.visible=!1})))}resetControlPanel(){this.controlPanel.innerHTML=\"\",this.controlPanel.appendChild(this.createGroupByCB());const e=this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets;for(let t of e)this.addToControlPanel(t)}createGroupByCB(){const e=document.createElement(\"input\");e.type=\"checkbox\",e.id=\"groupByCB\",e.style.width=\"1.4em\",e.style.height=\"1.4em\",e.checked=this.groupByTrack,e.onclick=e=>{this.groupByTrack=e.target.checked,this.resetControlPanel(),this.render()};const t=document.createElement(\"label\");t.for=\"groupByCB\",t.innerText=\"Group by track\",t.style.color=\"black\",t.style.paddingLeft=\"10px\";const i=document.createElement(\"div\");return i.style.width=\"100%\",i.style.paddingTop=\"5px\",i.style.paddingBottom=\"5px\",i.style.background=\"rgb(216, 230, 234)\",i.appendChild(e),i.appendChild(t),i}addToControlPanel(e){const t=document.createElement(\"div\");this.controlPanel.appendChild(t);const i=document.createElement(\"div\");i.className=\"igv-circview-button\",t.appendChild(i),i.innerText=!0===e.visible?\"Hide\":\"Show\",i.addEventListener(\"click\",(t=>{!0===e.visible?(this.hideChordSet(e.name),t.target.innerText=\"Show\"):(this.showChordSet(e.name),t.target.innerText=\"Hide\")}));const n=document.createElement(\"input\"),r=e=>200*Math.log(e*Nm),s=document.createElement(\"div\");s.className=\"igv-circview-button\",s.innerHTML=\"&nbsp;&nbsp;&nbsp;&nbsp;\",t.appendChild(s),s.style.backgroundColor=Mm(e.color,1);const o={parent:s,popup:\"right\",editorFormat:\"rgb\",color:e.color,onChange:({rgbaString:t})=>{s.style.backgroundColor=Mm(t,1),this.setColor(e.name,t),n.value=r(Rm(e.color))}},a=new _m(o);n.setAttribute(\"title\",\"Adjust transparency of arcs\"),n.type=\"range\",n.style.width=\"100px\",n.style.marginRight=\"10px\",n.setAttribute(\"class\",\"range\"),n.setAttribute(\"min\",\"0\"),n.setAttribute(\"max\",\"1000\"),n.value=r(Rm(e.color)),n.oninput=()=>{const t=(i=n.value,Math.exp(i/200)/Nm);var i;this.setColor(e.name,Mm(e.color,t)),a.setColor(e.color)},t.appendChild(n);const c=document.createElement(\"div\");c.style.color=\"black\",t.appendChild(c),c.innerText=c.title=e.name}setAssembly(e){const t=this.genomeId||Lm();if(this.genomeId===t)return;this.chordManager.clearChords(),this.genomeId=t,this.chrNames=new Set(e.chromosomes.map((e=>Dm(e.name))));const i=[],n=[];for(let t of e.chromosomes){const e=Dm(t.name);n.push(t.color||km(e)),i.push({refName:e,uniqueId:e,start:0,end:t.bpLength})}this.assembly={name:e.name,sequence:{trackId:t,type:\"ReferenceSequenceTrack\",adapter:{type:\"FromConfigSequenceAdapter\",features:i}},refNameColors:n},this.render()}addChords(e,t={}){const i=t.name||t.track||\"*\",n=i.split(\" \")[0].replaceAll(\"%20\",\" \"),r={name:i.replaceAll(\"%20\",\" \"),trackName:n,chords:e,color:t.color||\"black\",trackColor:t.trackColor||t.color||\"black\",visible:!0,id:t.id||Lm()};this.chordManager.addChordSet(r),this.resetControlPanel(),this.render()}setSize(e,t){if(t=t||e,this.width=e,this.height=t,this.viewState){const i=this.viewState.session.view;i.setWidth(e),i.setHeight(t),i.setBpPerPx(i.minBpPerPx)}}getSize(){return Math.min(this.width,this.height)}clearChords(){this.chordManager.clearChords(),this.resetControlPanel(),this.render()}clearSelection(){this.viewState.pluginManager.rootModel.session.clearSelection()}show(){this.parent.style.display=\"block\"}hide(){this.parent.style.display=\"none\"}get visible(){return\"none\"!==this.parent.style.display}set visible(e){this.parent.style.display=e?\"block\":\"none\"}hideChordSet(e){let t=this.getChordSet(e);t?(t.visible=!1,this.render()):console.warn(`No track with name: ${name}`)}showChordSet(e){let t=this.getChordSet(e);t?(t.visible=!0,this.render()):console.warn(`No track with name: ${e}`)}deleteTrack(e){let t=this.tracks.findIndex((t=>e===t.name));t>=0&&this.tracks.splice(t,1),this.render()}getChordSet(e){return this.groupByTrack?this.chordManager.getTrack(e):this.chordManager.getChordSet(e)}setColor(e,t){const i=this.getChordSet(e);if(i){i.color=t;const e=i.id;for(let i of this.viewState.config.tracks)if(e===i.trackId){i.displays[0].renderer.strokeColor.set(t);break}}}render(){const{createViewState:e,JBrowseCircularGenomeView:t}=JBrowseReactCircularGenomeView;ReactDOM.unmountComponentAtNode(this.container);const i=(this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets).filter((e=>e.visible)),n=[],r=[];for(let e of i)n.push({trackId:e.id,name:e.name,assemblyNames:[\"forIGV\"],type:\"VariantTrack\",adapter:{type:\"FromConfigAdapter\",features:e.chords}}),r.push(e.color);this.viewState=e({assembly:this.assembly,tracks:n});for(let e=0;e<i.length;e++)this.viewState.config.tracks[e].displays[0].renderer.strokeColor.set(r[e]);this.element=React.createElement(t,{viewState:this.viewState}),this.setSize(this.width,this.height),ReactDOM.render(this.element,this.container);const s=this.config.onChordClick||Tm;for(let e=0;e<i.length;e++)this.viewState.session.view.showTrack(this.viewState.config.tracks[e].trackId),s&&(this.viewState.pluginManager.jexl.addFunction(\"onChordClick\",s),this.viewState.config.tracks[e].displays[0].onChordClick.set(\"jexl:onChordClick(feature, track, pluginManager)\"))}}function Mm(e,t){const[i,n,r,s]=e.split(\",\");return`${i},${n},${r},${t})`}function Rm(e){return e.startsWith(\"rgba(\")?Number(e.split(\",\")[3].replace(\")\",\"\")):1}function Dm(e){return e.startsWith(\"chr\")?e.substring(3):e}function Tm(e,t,i){console.log(e)}function Lm(){return(\"0000\"+(Math.random()*Math.pow(36,4)|0).toString(36)).slice(-4)}if(\"undefined\"!=typeof document){function BA(e){for(let t of document.styleSheets)if(t=t.href?t.href.replace(/^.*[\\\\\\/]/,\"\"):\"\",t===e)return!0;return!1}BA(\"circular-view.css\")||function(){const e=document.createElement(\"style\");e.setAttribute(\"type\",\"text/css\"),e.innerHTML='.igv-circview-container {\\n  width: fit-content;\\n  height: fit-content;\\n  box-sizing: content-box;\\n  color: dimgray;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  background-color: white;\\n  border-color: dimgray;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-circview-toolbar {\\n  position: relative;\\n  width: 100%;\\n  height: 32px;\\n  background-color: lightgrey;\\n  border-bottom-style: solid;\\n  border-bottom-color: dimgray;\\n  border-bottom-width: thin;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n\\n.igv-circview-toolbar-button-container {\\n  height: 100%;\\n  width: fit-content;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-circview-toolbar-button-container > div {\\n  margin: 4px;\\n}\\n\\n.igv-circview-track-panel {\\n  z-index: 1024;\\n  position: absolute;\\n  top: 33px;\\n  left: 0;\\n  width: 100%;\\n  height: fit-content;\\n  border-bottom-style: solid;\\n  border-bottom-color: dimgray;\\n  border-bottom-width: thin;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n.igv-circview-track-panel > div {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-circview-track-panel > div > div {\\n  margin: 4px;\\n}\\n\\n.igv-circview-swatch-button {\\n  cursor: pointer;\\n  padding: 5px;\\n  width: 8px;\\n  height: 8px;\\n  border: 1px solid #8d8b8b;\\n  border-radius: 16px;\\n}\\n\\n.igv-circview-button {\\n  cursor: pointer;\\n  padding: 5px;\\n  color: #444;\\n  vertical-align: middle;\\n  text-align: center;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  border: 1px solid #8d8b8b;\\n  border-radius: 4px;\\n  background: #efefef;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.2);\\n}\\n\\n.igv-circview-button:hover {\\n  background: #efefef;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\\n}\\n\\n.igv-circview-button:active {\\n  color: #007bff;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\\n}\\n\\n/*# sourceMappingURL=circular-view.css.map */\\n',document.head.insertBefore(e,document.head.childNodes[document.head.childNodes.length-1])}()}const zm=e=>e.startsWith(\"chr\")?e.substring(3):e;function Hm(e){const t=[],i=[];if(e.wgChromosomeNames)for(let n of e.wgChromosomeNames){const r=e.getChromosome(n);i.push(Nu(r.name)),t.push({name:r.name,bpLength:r.bpLength})}return t}function Pm(e,t,i,n){const r=t.color||\"rgb(0,0,255)\",s=_s.addAlpha(\"all\"===i.chr?r:Nu(i.chr),n),o=_s.addAlpha(r,n),a=t.name.replaceAll(\" \",\"%20\"),c=\"all\"===i.chr?a:`${a}  ${i.chr}:${i.start}-${i.end}`;t.browser.circularView.addChords(e,{track:c,color:s,trackColor:o}),t.browser.circularViewVisible||(t.browser.circularViewVisible=!0)}class Om{constructor(e,{minTLENPercentile:t,maxTLENPercentile:i}){this.totalCount=0,this.frCount=0,this.rfCount=0,this.ffCount=0,this.sumF=0,this.sumF2=0,this.lp=void 0===t?.1:t,this.up=void 0===i?99.5:i,this.isizes=[],this.compute(e)}compute(e){for(let n of e)if(n.isProperPair()){var t=Math.abs(n.fragmentLength);this.sumF+=t,this.sumF2+=t*t,this.isizes.push(t);var i=n.pairOrientation;if(\"string\"==typeof i&&4===i.length)switch(\"\"+i.charAt(0)+i.charAt(2)){case\"FF\":case\"RR\":this.ffCount++;break;case\"FR\":this.frCount++;break;case\"RF\":this.rfCount++}this.totalCount++}this.ffCount/this.totalCount>.9?this.orienation=\"ff\":this.frCount/this.totalCount>.9?this.orienation=\"fr\":this.rfCount/this.totalCount>.9&&(this.orienation=\"rf\"),this.minTLEN=0===this.lp?0:Um(this.isizes,this.lp),this.maxTLEN=Um(this.isizes,this.up)}}function Um(e,t){if(0!==e.length){var i=Math.floor(e.length*(t/100));return e.sort((function(e,t){return e-t})),e[i]}}const qm=\"rgb(255,0,255)\",Qm=\"rgb(0,0,255)\",Vm=\"rgb(132, 178, 158)\",jm=new Map;jm.set(\"m\",\"rgb(255,0,0)\"),jm.set(\"h\",qm),jm.set(\"o\",\"rgb(111, 78, 129)\"),jm.set(\"f\",\"rgb(246, 200, 95)\"),jm.set(\"c\",\"rgb(157, 216, 102)\"),jm.set(\"g\",\"rgb(255, 160, 86)\"),jm.set(\"e\",\"rgb(141, 221, 208)\"),jm.set(\"b\",\"rgb(202, 71, 47)\"),jm.set(\"h\",qm),jm.set(\"a\",\"rgb(51,0,111)\"),jm.set(\"NONE_A\",Qm),jm.set(\"NONE_C\",Qm),jm.set(\"NONE_T\",Qm),jm.set(\"NONE_G\",Qm),jm.set(\"NONE_N\",Qm);const Wm=new Map;function Gm(e,t,i){let n=function(e,t){return jm.has(e)?jm.get(e):Vm}(e),r=Xf(t);if(r>255)return n;const s=e+r+i;if(r<0&&(r=0),!Wm.has(s)){const e=\"basemod2\"===i?Math.max(20,Math.min(255,r*r/50-4*r+200+20)):Math.max(20,Math.min(255,.006127*r*r)),[t,o,a]=_s.rgbComponents(n);Wm.set(s,`rgba(${t},${o},${a},${e/255})`)}return Wm.get(s)}class $m{constructor(e){this.alignmentTrack=e}updateContext(e){this.context=e}drawModifications(e,t,i,n,r,s){const{ctx:o,pixelEnd:a,bpStart:c,bpPerPixel:l}=n,h=e.getBaseModificationSets();if(h){let n;const d=r.split(\":\");2==d.length&&(r=d[0],n=d[1]);for(let d of e.blocks){if(\"S\"===d.type)continue;const e=t,u=i;let f=Math.max(1,1/l);for(let t=d.seqOffset;t<d.seqOffset+d.len;t++){let i=(d.start+(t-d.seqOffset)-c)/l;if(i>a)break;if(i+f<0)continue;let p,g=-1,m=255,w=0;for(let e of h)if((!n||e.modification===n)&&e.containsPosition(t)){const i=Xf(e.likelihoods.get(t));m-=i,(!p||i>g)&&(p=e.modification,w=e.canonicalBase,g=i)}if(p){const t=255*s;let n;m>g&&\"basemod2\"===r&&m>=t?n=Gm(\"NONE_\"+w,m,r):g>=t&&(n=Gm(p,g,r)),o.fillStyle=n,f<3&&(f=3,i--),o.fillRect(i,e,f,Math.max(1,u-2))}}}}}}const Km=new Set([\"firstOfPairStrand\"]);class Ym extends Hl{static defaults={viewAsPairs:!1,showSoftClips:!1,showAllBases:!1,showInsertions:!0,showMismatches:!0,colorBy:void 0,groupBy:void 0,displayMode:\"EXPANDED\",alignmentRowHeight:14,squishedRowHeight:3,negStrandColor:\"rgba(150, 150, 230, 0.75)\",posStrandColor:\"rgba(230, 150, 150, 0.75)\",baseModPosStrandColor:\"rgb(195, 195, 195)\",baseModNegStrandColor:\"rgb(195, 210, 195)\",insertionColor:\"rgb(138, 94, 161)\",insertionTextColor:\"white\",showInsertionText:!1,deletionColor:\"black\",deletionTextColor:\"black\",showDeletionText:!1,skippedColor:\"rgb(150, 170, 170)\",pairConnectorColor:void 0,smallTLENColor:\"rgb(0, 0, 150)\",largeTLENColor:\"rgb(200, 0, 0)\",expectedPairOrientation:\"fr\",rlColor:\"rgb(0, 150, 0)\",rrColor:\"rgb(20, 50, 200)\",llColor:\"rgb(0, 150, 150)\",bamColorTag:\"YC\",hideSmallIndels:!1,indelSizeThreshold:1,highlightColor:void 0,minTLEN:void 0,maxTLEN:void 0,tagColorPallete:\"Set1\"};_colorTables=new Map;_baseModifications=new Set;constructor(e,t){super(e,t),(e.colorTable||e.tagColorTable)&&(this.colorTable=new ao(e.tagColorTable)),e.largeFragmentLengthColor&&(this.largeTLENColor=e.largeFragmentLengthColor),e.pairOrienation&&(this.expectedPairOrientation=e.pairOrientation),e.smallFragmentLengthColor&&(this.smallTLENColor=e.smallFragmentLengthColor),e.largeFragmentLengthColor&&(this.largeTLENColor=e.largeFragmentLengthColor),e.minFragmentLength&&(this.minTLEN=e.minFragmentLength),e.maxFragmentLength&&(this.maxTLEN=e.maxFragmentLength),e.displayMode&&(this.displayMode=e.displayMode.toUpperCase()),e.colorBy&&e.colorByTag&&(this.colorBy=e.colorBy+\":\"+e.colorByTag),this.featureSource=this.parent.featureSource,this.top=0===e.coverageTrackHeight?0:e.coverageTrackHeight+5,this.pairColors={RL:this.rlColor,RR:this.rrColor,LL:this.llColor},e.highlightedReads&&this.setHighlightedReads(e.highlightedReads),this.hasPairs=!1,this.hasSupplemental=!1,this._groupByTags=[],this._groupByPositions=[],e.groupBy&&(this.groupBy=e.groupBy,e.groupBy.startsWith(\"base:\")&&this._groupByPositions.push(e.groupBy.substring(5)),e.groupBy.startsWith(\"tag:\")&&this._groupByTags.push(e.groupBy.substring(4))),this._locusChange=Zm.bind(this),this.browser.on(\"locuschange\",this._locusChange)}init(e){this.parent=e.parent,delete e.parent,super.init(e)}dispose(){this.browser.off(\"locuschage\",this._locusChange)}get baseModRenderer(){return this._baseModRenderer||(this._baseModRenderer=new $m(this)),this._baseModRenderer}get baseModificationThreshold(){return this.parent.baseModificationThreshold}setTop(e,t){this.top=0===e.height||!1===t?0:5+e.height}setHighlightedReads(e,t){if(!Array.isArray(e)||!e.every((e=>\"string\"==typeof e)))throw new Error(\"AlignmentTrack.setHighlightedReads() only accept array of strings\");t&&(this.highlightColor=t),this.highlightedReads=new Set(e)}computePixelHeight(e){if(e.packedGroups){let t=e.hasDownsampledIntervals()?15:0;const i=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;for(let n of e.packedGroups.values())t+=i*n.length+10;return t+5}return 0}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=r+s*n+1,a=this.showSoftClips,c=this.showAllBases,l=this.browser.nucleotideColors;i.save();for(let e of t.baseModificationKeys)this._baseModifications.add(e.modification);let h=t.sequence;h&&(h=h.toUpperCase());let d=0;this.colorBy||(this.colorBy=this.hasPairs?\"unexpectedPair\":\"none\");let u=e.pixelTop;this.top&&i.translate(0,this.top);const f=u+e.pixelHeight;t.hasDownsampledIntervals()?(d=15,t.downsampledIntervals.forEach((function(e){var t=(e.start-r)/n,s=(e.end-r)/n;s-t>5&&(t+=1,s-=1),xo.fillRect(i,t,2,s-t,8,{fillStyle:\"black\"})}))):d=0,this.alignmentsYOffset=d;const p=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight,g=t.packedGroups;if(g){let t=d;for(let n of g.keys()){const a=g.get(n),c=a.rows,l=c.length;a.pixelTop=t;for(let e=0;e<l;e++){const i=c[e],n=p<=4?p:p-2;if(t>f)break;if(t+n<u)t+=p;else{for(let e of i.alignments)if(this.browser.circularView&&(this.hasSupplemental=this.hasSupplemental||e.hasTag(\"SA\")),!(e.start+e.lengthOnRef<r)){if(e.start>o)break;!0!==e.hidden&&(e instanceof Qf?(m.call(this,e,t,n),w.call(this,e.firstAlignment,t,n),e.secondAlignment&&w.call(this,e.secondAlignment,t,n)):w.call(this,e,t,n))}t+=p}}if(a.pixelBottom=t,this.groupBy&&n){i.save(),i.font=\"400 12px sans-serif\";const r=i.measureText(n),o=r.width+10,c=-e.pixelShift+e.viewportWidth-o-10,l=r.actualBoundingBoxAscent+r.actualBoundingBoxDescent+10,h=Math.min(a.pixelTop+l-1,a.pixelBottom);i.textAlign=\"center\",i.fillStyle=\"white\",i.strokeStyle=\"lightGray\",xo.roundRect(i,c,h-r.actualBoundingBoxAscent-5,o,l,2,1,1),i.fillStyle=\"black\",i.fillText(n,c+o/2,h),xo.dashedLine(i,0,t,s,t),i.restore(),t+=10}}}function m(e,t,s){var a=this.getConnectorColor(e.firstAlignment),c=(e.connectingStart-r)/n,l=(e.connectingEnd-r)/n,h=t+s/2;e.connectingEnd<r||e.connectingStart>o||(e.mq<=0&&(a=_s.addAlpha(a,.15)),xo.setProperties(i,{fillStyle:a,strokeStyle:a}),xo.strokeLine(i,c,h,l,h))}function w(e,d,u){if(e.start+e.lengthOnRef<r||e.start>o)return;const f=a?e.blocks:e.blocks.filter((e=>\"S\"!==e.type));let g=this.getAlignmentColor(e);const m=g;e.mq<=0&&(g=_s.addAlpha(g,.15)),xo.setProperties(i,{fillStyle:g,strokeStyle:m});const w=[];for(let e=0;e<f.length;e++){const t=f[e];if(!(e!==f.length-1&&f[e+1].start<r)&&(w.push(...b.call(this,t,e)),t.start+t.len>o))break}if(e.gaps){const t=d+u/2;for(let s of e.gaps){const e=(s.start-r)/n,o=(s.start+s.len-r)/n,a=o-e,c=s.len.toString(),l=6*c.length,h=e+a/2,u=\"D\"===s.type?this.deletionColor:this.skippedColor;if(xo.strokeLine(i,e,t,o,t,{strokeStyle:u,lineWidth:2}),this.showDeletionText&&s.len>1&&a>=l+8){const e=h-l/2;xo.fillRect(i,e-1,d-1,l+2,12,{fillStyle:\"white\"}),xo.fillText(i,c,e,d+10,{font:\"normal 10px monospace\",fillStyle:this.deletionTextColor})}}}if(e.insertions&&this.showInsertions){let t=-1;for(let s of e.insertions){if(this.hideSmallIndels&&s.len<=this.indelSizeThreshold)continue;if(s.start<r)continue;if(s.start>o)break;const e=s.start-r,a=s.len.toString(),c=2+6*a.length,l=this.showInsertionText&&1!==s.len?Math.round(s.len/n):2,h=Math.max(Math.min(c,l),2),f=e/n-h/2;if(f-t>2){const e={fillStyle:this.insertionColor};xo.fillRect(i,f-2,d,h+4,2,e),xo.fillRect(i,f,d+2,h,u-4,e),xo.fillRect(i,f-2,d+u-2,h+4,2,e),this.showInsertionText&&s.len>1&&l>c&&xo.fillText(i,a,f+1,d+10,{font:\"normal 10px monospace\",fillStyle:this.insertionTextColor}),t=f}}}for(let{bbox:e,baseColor:t,readChar:r}of w){if(n<=.1&&e.height>=8){const n=Math.min(10,e.height);i.font=n+\"px sans-serif\";const s=e.x+e.width/2;xo.strokeText(i,r,s-i.measureText(r).width/2,n-1+e.y,{strokeStyle:t})}else xo.fillRect(i,e.x,e.y,e.width,e.height,{fillStyle:t})}if(this.colorBy&&this.colorBy.startsWith(\"basemod\")){const t={ctx:i,bpPerPixel:n,bpStart:r,bpEnd:o,pixelEnd:s};this.baseModRenderer.drawModifications(e,d,u,t,this.colorBy,this.baseModificationThreshold)}function b(o,a){const w=[],b=o.start-t.start,F=(o.start-r)/n,v=(o.start+o.len-r)/n,y=Math.max(1,v-F),A=100/n,C=Math.min(p/2,A/6),_=\"S\"===o.type,x=e.mq<=0||this.selectedReadName===e.readName||_||this.highlightedReads&&this.highlightedReads.has(e.readName);let k=m;this.selectedReadName===e.readName?k=\"red\":_?k=\"rgb(50,50,50)\":this.highlightedReads&&this.highlightedReads.has(e.readName)&&(k=this.highlightColor||\"#00ff00\");const I=!0===e.strand&&a===f.length-1,S=!1===e.strand&&0===a;if(I|S){let e,t;I?(e=[F,v,v+C,v,F,F],t=[d,d,d+u/2,d+u,d+u,d]):S&&(e=[v,F,F-C,F,v,v],t=[d,d,d+u/2,d+u,d+u,d]),xo.fillPolygon(i,e,t,{fillStyle:g}),x&&xo.strokePolygon(i,e,t,{strokeStyle:k})}else xo.fillRect(i,F,d,y,u,{fillStyle:g}),x&&(i.save(),i.strokeStyle=k,i.strokeRect(F,d,y,u),i.restore());if(_||c||this.showMismatches&&h&&e.seq&&\"*\"!==e.seq){const t=e.seq?e.seq.toUpperCase():void 0,i=e.qual,a=o.seqOffset,f=Math.max(1,1/n);for(let e=0,p=o.len;e<p;e++){const p=(o.start+e-r)/n;if(p+f<0)continue;if(p>s)break;let g=t?t.charAt(a+e):\"\";const m=b+e>=0?h.charAt(b+e):\"\";if(\"=\"===g&&(g=m),\"X\"===g||m!==g||_||c){let t=l[g]||\"rgb(0,0,0)\";if(!_&&void 0!==i&&i.length>a+e){t=Xm(i[a+e],t)}w.push({bbox:{x:p,y:d,width:f,height:u},baseColor:t,readChar:g})}}}return w}}i.restore()}popupData(e){const t=this.getClickedObject(e);return t?t.popupData(e.genomicLocation):void 0}menuItemList(){let e=[];e.push(\"<hr/>\");const t=Bt('<div class=\"igv-track-menu-category\">');t.text(\"Color by:\"),e.push({name:void 0,object:t,click:void 0,init:void 0});const i=[];i.push({key:\"none\",label:\"none\"}),i.push({key:\"strand\",label:\"read strand\"}),this.hasPairs&&(i.push({key:\"firstOfPairStrand\",label:\"first-of-pair strand\"}),i.push({key:\"pairOrientation\",label:\"pair orientation\"}),i.push({key:\"tlen\",label:\"insert size (TLEN)\"}),i.push({key:\"unexpectedPair\",label:\"pair orientation & insert size (TLEN)\"})),i.push({key:\"tag\",label:\"tag\"});for(let t of i){const i=void 0===this.colorBy&&\"none\"===t.key||this.colorBy===t.key;e.push(this.colorByCB(t,i))}const n=this._baseModifications.size;if(n>0){e.push('<hr style=\"border-top:1px dotted;border-bottom: none;\">');let t=1===n?\"base modification\":\"base modification (all)\";if(e.push(this.basemodColorByCB({key:\"basemod\",label:t})),n>1)for(let t of this._baseModifications)e.push(this.basemodColorByCB({key:\"basemod:\"+t,label:`base modification (${Kf(t)})`}));if(e.push('<hr style=\"border-top:1px dotted;border-bottom: none;\">'),t=1===n?\"base modification 2-color\":\"base modification 2-color (all)\",e.push(this.basemodColorByCB({key:\"basemod2\",label:t})),n>1)for(let t of this._baseModifications)e.push(this.basemodColorByCB({key:\"basemod2:\"+t,label:`base modification 2-color (${Kf(t)})`}))}e.push(\"<hr/>\");const r=Bt('<div class=\"igv-track-menu-category\">');r.text(\"Group by:\"),e.push({name:void 0,object:r,click:void 0,init:void 0});const s=[];s.push({key:\"none\",label:\"none\"}),s.push({key:\"strand\",label:\"read strand\"}),this.hasPairs&&(s.push({key:\"firstOfPairStrand\",label:\"first-of-pair strand\"}),s.push({key:\"pairOrientation\",label:\"pair orientation\"}),s.push({key:\"mateChr\",label:\"chromosome of mate\"})),s.push({key:\"chimeric\",label:\"chimeric\"}),s.push({key:\"supplementary\",label:\"supplementary flag\"}),s.push({key:\"readOrder\",label:\"read order\"});for(let e of this._groupByTags)s.push({key:`tag:${e}`,label:`tag:${e}`});for(let e of this._groupByPositions)s.push({key:`base:${e}`,label:`base:${e}`});s.push({key:\"tag\",label:\"tag...\"});for(let t of s){const i=void 0===this.groupBy&&\"none\"===t.key||this.groupBy===t.key;e.push(this.groupByCB(t,i))}e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"Show all bases\",this.showAllBases)),click:function(){this.alignmentTrack.showAllBases=!this.alignmentTrack.showAllBases,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show mismatches\",this.showMismatches)),click:function(){this.alignmentTrack.showMismatches=!this.alignmentTrack.showMismatches,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show insertions\",this.showInsertions)),click:function(){this.alignmentTrack.showInsertions=!this.alignmentTrack.showInsertions,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show soft clips\",this.showSoftClips)),click:function(){this.alignmentTrack.showSoftClips=!this.alignmentTrack.showSoftClips;const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this);this.trackView.repaintViews()}}),this.hasPairs&&(e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"View as pairs\",this.viewAsPairs)),click:function(){const e=!this.alignmentTrack.viewAsPairs;if(e&&this.groupBy&&!Km.has(this.groupBy))return void this.browser.alert.present(`'View as Pairs' is incompatible with 'Group By ${this.groupBy}'`);this.alignmentTrack.viewAsPairs=e;const t=this.getCachedAlignmentContainers();for(let e of t)e.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(e.push(\"<hr/>\"),this.hasPairs&&e.push({label:\"Add discordant pairs to circular view\",click:function(){for(let e of this.trackView.viewports)this.addPairedChordsForViewport(e)}}),this.hasSupplemental&&e.push({label:\"Add split reads to circular view\",click:function(){for(let e of this.trackView.viewports)this.addSplitChordsForViewport(e)}})),e.push(\"<hr/>\");const o=Bt('<div class=\"igv-track-menu-category\">');o.text(\"Display mode:\"),e.push({name:void 0,object:o,click:void 0,init:void 0});for(let t of[\"EXPANDED\",\"SQUISHED\",\"FULL\"])e.push({object:Bt(Dl(t.toLowerCase(),this.displayMode===t)),click:function(){this.alignmentTrack.setDisplayMode(t)}});return e}setDisplayMode(e){const t=\"FULL\"===this.displayMode||\"FULL\"===e;if(this.displayMode=e,t){const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this)}this.trackView.checkContentHeight(),this.trackView.repaintViews()}colorByCB(e,t){const i=Bt(Dl(e.label,t));if(\"tag\"!==e.key){function n(){this.alignmentTrack.colorBy=e.key,this.trackView.repaintViews()}return{name:void 0,object:i,click:n,init:void 0}}{function r(e){const t=this.alignmentTrack.colorBy.startsWith(\"tag:\")?this.alignmentTrack.colorBy.substring(4):\"\";this.browser.inputDialog.present({label:\"Tag Name\",value:t,callback:e=>{const t=this.alignmentTrack;e?(t.colorBy=\"tag:\"+e,t.colorTable||(t.colorTable=new oo(\"Set1\"))):t.colorBy=void 0,this.trackView.repaintViews()}},e)}return{name:void 0,object:i,dialog:r,init:void 0}}}basemodColorByCB(e){const t=this.colorBy===e.key;return{name:void 0,object:Bt(Dl(e.label,t)),click:function(){this.alignmentTrack.colorBy=e.key,this.trackView.repaintViews()},init:void 0}}groupByCB(e,t){return{name:void 0,object:Bt(Dl(e.label,t)),dialog:function(t){const i=()=>this.alignmentTrack.repackAlignments();if(\"tag\"===e.key){let e=\"\";this.alignmentTrack.groupBy&&this.alignmentTrack.groupBy.startsWith(\"tag:\")&&(e=this.alignmentTrack.groupBy.substring(4)),this.browser.inputDialog.present({label:\"Tag Name\",value:e,callback:e=>{e&&(this.alignmentTrack.groupBy=\"tag:\"+e,this.alignmentTrack._groupByTags.push(e),i())}},t)}else\"none\"===e.key?this.alignmentTrack.groupBy=void 0:this.alignmentTrack.groupBy=e.key,i()},init:void 0}}repackAlignments(){const e=this.getCachedAlignmentContainers();for(let t of e)\"function\"==typeof t.pack&&t.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}contextMenuItemList(e){const t=e.viewport,i=[],n=i=>{const n=this.sortObject,r=!n||n.position!==Math.floor(e.genomicLocation)||!n.direction,s={chr:t.referenceFrame.chr,position:Math.floor(e.genomicLocation),option:i,direction:r,sortAsPairs:t.trackView.track.viewAsPairs};this.sortObject=s,t.cachedFeatures.sortRows(s),t.repaint()};i.push(\"<b>Sort by...</b>\"),i.push({label:\"&nbsp; base\",click:()=>n(\"BASE\")}),i.push({label:\"&nbsp; read strand\",click:()=>n(\"strand\")}),i.push({label:\"&nbsp; start location\",click:()=>n(\"START\")}),i.push({label:\"&nbsp; insert size\",click:()=>n(\"INSERT_SIZE\")}),i.push({label:\"&nbsp; gap size\",click:()=>n(\"GAP_SIZE\")}),i.push({label:\"&nbsp; chromosome of mate\",click:()=>n(\"MATE_CHR\")}),i.push({label:\"&nbsp; mapping quality\",click:()=>n(\"MQ\")}),i.push({label:\"&nbsp; read name\",click:()=>n(\"READ_NAME\")}),i.push({label:\"&nbsp; aligned read length\",click:()=>n(\"ALIGNED_READ_LENGTH\")}),i.push({label:\"&nbsp; tag\",click:()=>{const i=this.sortObject,n=!i||i.position!==Math.floor(e.genomicLocation)||!i.direction,r={label:\"Tag Name\",value:this.sortByTag?this.sortByTag:\"\",callback:i=>{if(i){const r={chr:t.referenceFrame.chr,position:Math.floor(e.genomicLocation),option:\"TAG\",tag:i,direction:n};this.sortByTag=i,this.sortObject=r,t.cachedFeatures.sortRows(r),t.repaint()}}};this.browser.inputDialog.present(r,e.event)}}),i.push(\"<hr/>\");const r=`${t.referenceFrame.chr}:${Rt(Math.floor(e.genomicLocation)+1)}`;i.push({label:`Group by base @${r}`,click:()=>{this._groupByPositions.push(r),this.groupBy=`base:${r}`;const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),i.push(\"<hr/>\");const s=this.getClickedObject(e);if(s){const t=this.showSoftClips,n=\"function\"==typeof s.alignmentContaining?s.alignmentContaining(e.genomicLocation,t):s;if(n){n.isPaired()&&n.isMateMapped()&&i.push({label:\"View mate in split screen\",click:()=>{if(n.mate){const t=e.viewport.referenceFrame,i=this.browser.genome.getChromosome(n.mate.chr);if(i){this.selectedReadName=n.readName;const r=t.bpPerPixel*e.viewport.getWidth(),s=n.mate.position-r/2,o=n.mate.position+r/2;this.browser.addMultiLocusPanel(i.name,s,o,t)}else this.browser.alert.present(`Reference does not contain chromosome: ${n.mate.chr}`)}},init:void 0}),i.push({label:\"View read sequence\",click:()=>{const e=n.seq;e&&\"*\"!==e?this.browser.alert.present(e):this.browser.alert.present(\"Read sequence: *\")}}),Xa()&&i.push({label:\"Copy read sequence\",click:async()=>{const e=n.seq;try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}});const t=n.seq;if(t&&\"*\"!==t){t.length<Qd&&i.push({label:\"BLAT read sequence\",click:()=>{const e=n.isNegativeStrand()?cc(t):t,i=`${n.readName} - blat`,r=`${this.name} - ${i}`;jd({sequence:e,browser:this.browser,name:i,title:r})}});const e=n.softClippedBlocks();e.left&&e.left.len>20&&e.left.len<Qd&&i.push({label:\"BLAT left soft-clipped sequence\",click:()=>{const i=t.substr(e.left.seqOffset,e.left.len),r=n.isNegativeStrand()?cc(i):i,s=`${n.readName} - blat left clip`,o=`${this.name} - ${s}`;jd({sequence:r,browser:this.browser,name:s,title:o})}}),e.right&&e.right.len>20&&e.right.len<Qd&&i.push({label:\"BLAT right soft-clipped sequence\",click:()=>{const i=t.substr(e.right.seqOffset,e.right.len),r=n.isNegativeStrand()?cc(i):i,s=`${n.readName} - blat right clip`,o=`${this.name} - ${s}`;jd({sequence:r,browser:this.browser,name:s,title:o})}})}i.push(\"<hr/>\")}}return this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(this.hasPairs&&i.push({label:\"Add discordant pairs to circular view\",click:()=>{this.addPairedChordsForViewport(t)}}),this.hasSupplemental&&i.push({label:\"Add split reads to circular view\",click:()=>{this.addSplitChordsForViewport(t)}}),i.push(\"<hr/>\")),i}getClickedObject(e){let t=e.viewport.cachedFeatures;if(!t)return;const i=e.y-this.top,n=e.genomicLocation;if(t.packedGroups){let e=Number.MAX_VALUE;for(let r of t.packedGroups.values())if(e=Math.min(e,r.pixelTop),i>r.pixelTop&&i<=r.pixelBottom){const e=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;let t=Math.floor((i-r.pixelTop)/e);if(t>=0&&t<r.length){const e=r.rows[t].alignments.filter((e=>e.containsLocation(n,this.showSoftClips)));if(e.length>0)return e[0]}}}if(i<minGroupY&&t.downsampledIntervals)for(const e of t.downsampledIntervals)if(e.start<=n&&e.end>=n)return e}getConnectorColor(e){if(this.pairConnectorColor)return this.pairConnectorColor;let t=this.colorBy;switch(t&&t.startsWith(\"tag:\")&&(t.substring(4),t=\"tag\"),t){case\"strand\":case\"firstOfPairStrand\":case\"pairOrientation\":case\"tag\":return this.color?\"function\"==typeof this.color?this.color(e):this.color:\"rgb(200, 200, 200)\";default:return this.getAlignmentColor(e)}}getAlignmentColor(e){let t;t=this.color?\"function\"==typeof this.color?this.color(e):this.color:\"rgb(185, 185, 185)\";let i,n=this.colorBy;switch(n&&n.startsWith(\"tag:\")&&(i=n.substring(4),n=\"tag\"),n){case\"basemod\":case\"basemod2\":t=e.strand?this.baseModPosStrandColor:this.baseModNegStrandColor;break;case\"strand\":t=e.strand?this.posStrandColor:this.negStrandColor;break;case\"firstOfPairStrand\":const r=e.firstOfPairStrand;void 0!==r&&(t=r?this.posStrandColor:this.negStrandColor);break;case\"unexpectedPair\":case\"pairOrientation\":if(e.pairOrientation){const i=ep[this.expectedPairOrientation];if(i){const n=this.pairColors[i[e.pairOrientation]];if(n){t=n;break}}}if(\"pairOrientation\"===n)break;case\"tlen\":case\"fragmentLength\":e.mate&&e.isMateMapped()&&(e.mate.chr!==e.chr?t=Nu(e.mate.chr):this.minTemplateLength&&Math.abs(e.fragmentLength)<this.minTemplateLength?t=this.smallTLENColor:this.maxTemplateLength&&Math.abs(e.fragmentLength)>this.maxTemplateLength&&(t=this.largeTLENColor));break;case\"tag\":const s=e.tags()[i];void 0!==s&&(this.bamColorTag===i&&(t=_s.createColorStringSafe(s)),this.colorTable||(this.colorTable=new oo(this.tagColorPallete)),t=this.colorTable.getColor(s))}return t}get nucleotideColors(){return this.browser.nucleotideColors}get minTemplateLength(){return void 0!==this.minTLEN?this.minTLEN:this.parent._pairedEndStats?this.parent._pairedEndStats.minTLEN:0}get maxTemplateLength(){return void 0!==this.maxTLEN?this.maxTLEN:this.parent._pairedEndStats?this.parent._pairedEndStats.maxTLEN:1e3}getState(){const e=super.getState();return this.highlightedReads&&(e.highlightedReads=Array.from(this.highlightedReads)),e}get name(){return this.parent.name}set name(e){this.parent.name=e}get color(){return this.parent.color}set color(e){this.parent.color=e}get trackView(){return this.parent.trackView}get getCachedAlignmentContainers(){return this.parent.getCachedAlignmentContainers}get sortObject(){return this.parent.sortObject}set sortObject(e){this.parent.sortObject=e}addPairedChordsForViewport(e){return this.parent.addPairedChordsForViewport(e)}addSplitChordsForViewport(e){return this.parent.addSplitChordsForViewport(e)}}function Xm(e,t){let i;return i=e<5?.1:Math.max(.1,Math.min(1,.1+.9*(e-5)/15)),i=Math.round(10*i)/10,i<1&&(t=_s.addAlpha(t,i)),t}function Zm(){\"FULL\"!==this.displayMode||this.browser.isTrackPanning()||this.repackAlignments()}function Jm(e,t,i,n,r,s,o,a,c){const l=o.baseModCounts,h=o.coverageMap;if(l){let o;const d=a.split(\":\");2==d.length&&(a=d[0],o=d[1]);const u=Array.from(l.allModifications);u.sort(Vf.compare);const f=h.getTotalCount(s);if(!u.filter((e=>o?o===e.modification:!e.modification.startsWith(\"NONE_\"))).find((e=>l.getCount(s,e,0,!1)>0)))return;for(let d of u){if(d.modification.startsWith(\"NONE_\")&&\"basemod2\"!==a)continue;if(o&&o!==d.modification&&!d.modification.startsWith(\"NONE_\"))continue;const u=d.base,p=oc(u),g=h.getCount(s,u)+h.getCount(s,p),m=l.simplexModifications.has(d.modification)?h.getPosCount(s,u)+h.getNegCount(s,p):g;if(0==m)continue;const w=\"basemod2\"===a,b=l.getCount(s,d,c,w);if(0==b)continue;const F=g/f*(b/m),v=Math.round(F*r),y=l.getLikelihoodSum(s,d,c,w)/b,A=i-v,C=Gm(d.modification,y,a);e.fillStyle=C,e.fillRect(t,A,n,v),i=A}}}class ew{constructor(e,t){this.featureType=\"numeric\",this.parent=t,this.featureSource=t.featureSource,this.paintAxis=cd,this.top=0,this.autoscale=e.autoscale||void 0===e.max,e.coverageColor&&(this.color=e.coverageColor),this.autoscale||(this.dataRange={min:e.min||0,max:e.max})}get height(){return this.parent.coverageTrackHeight}draw(e){const t=e.pixelTop;e.pixelHeight;const i=this.parent.browser.nucleotideColors;if(t>this.height)return;const n=e.context,r=e.features,s=r.coverageMap;let o;s.refSeq&&(o=s.refSeq.toUpperCase());const a=e.bpPerPixel,c=e.bpStart,l=c+e.pixelWidth*a+1;let h;h=this.color?this.color:this.parent.color&&\"function\"!=typeof this.parent.color?_s.darkenLighten(this.parent.color,-35):\"rgb(150, 150, 150)\",xo.setProperties(n,{fillStyle:h,strokeStyle:h});const d=Math.max(1,1/a);for(let e=0,t=s.coverage.length;e<t;e++){const t=s.bpStart+e;if(t<c)continue;if(t>l)break;const i=s.coverage[e];if(!i)continue;const r=i.total/this.dataRange.max*this.height,o=this.height-r,h=(t-c)/a;xo.fillRect(n,h,o,d,r)}if(o)for(let e=0,t=s.coverage.length;e<t;e++){const t=s.bpStart+e;if(t<c)continue;if(t>l)break;const h=s.coverage[e];if(!h)continue;const u=h.total/this.dataRange.max*this.height;let f=this.height-u;const p=Math.floor((t-c)/a),g=o[e];if(this.parent.colorBy&&this.parent.colorBy.startsWith(\"basemod\"))Jm(n,p,this.height,d,u,t,r,this.parent.colorBy,this.parent.baseModificationThreshold);else if(h.isMismatch(g)){xo.setProperties(n,{fillStyle:i[g]}),xo.fillRect(n,p,f,d,u);let e=0;for(let t of[\"A\",\"C\",\"T\",\"G\"]){const r=(h[\"pos\"+t]+h[\"neg\"+t])/this.dataRange.max*this.height;f=this.height-r-e,e+=r,xo.setProperties(n,{fillStyle:i[t]}),xo.fillRect(n,p,f,d,r)}}}}getClickedObject(e){let t=e.viewport.cachedFeatures;if(!t||0===t.length)return;const i=Math.floor(e.genomicLocation),n=t.coverageMap,r=Math.floor(i-n.bpStart),s=n.coverage[r];return s?{coverage:s,baseModCounts:t.baseModCounts,hoverText:()=>n.coverage[r].hoverText()}:void 0}popupData(e){const t=[],{coverage:i,baseModCounts:n}=this.getClickedObject(e);if(i){const r=Math.floor(e.genomicLocation),s=e.viewport.referenceFrame;t.push(s.chr+\":\"+Rt(1+r)),t.push({name:\"Total Count\",value:i.total});let o=i.posA+i.negA;o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posA+\"+, \"+i.negA+\"- )\"),t.push({name:\"A\",value:o}),o=i.posC+i.negC,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posC+\"+, \"+i.negC+\"- )\"),t.push({name:\"C\",value:o}),o=i.posG+i.negG,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posG+\"+, \"+i.negG+\"- )\"),t.push({name:\"G\",value:o}),o=i.posT+i.negT,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posT+\"+, \"+i.negT+\"- )\"),t.push({name:\"T\",value:o}),o=i.posN+i.negN,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posN+\"+, \"+i.negN+\"- )\"),t.push({name:\"N\",value:o}),t.push(\"<HR/>\"),t.push({name:\"DEL\",value:i.del.toString()}),t.push({name:\"INS\",value:i.ins.toString()}),n&&(t.push(\"<hr/>\"),t.push(...n.popupData(r,this.parent.colorBy)))}return t}}class tw extends Hl{static defaults={alleleFreqThreshold:.2,visibilityWindow:3e4,showCoverage:!0,showAlignments:!0,height:300,coverageTrackHeight:50,baseModificationThreshold:0};constructor(e,t){super(e,t)}init(e){this.type=\"alignment\",this.featureSource=new cm(e,this.browser);const t=Object.assign({parent:this},e);this.coverageTrack=new ew(t,this);const i=Object.assign({parent:this},e);this.alignmentTrack=new Ym(i,this.browser),super.init(e),this.showAlignments||(this._height=this.coverageTrackHeight),e.sort&&(Array.isArray(e.sort)?this.assignSort(e.sort[0]):this.assignSort(e.sort))}dispose(){this.alignmentTrack.dispose()}setHighlightedReads(e,t){this.alignmentTrack.setHighlightedReads(e,t),this.updateViews()}get expectedPairOrientation(){return this.alignmentTrack.expectedPairOrientation}get viewAsPairs(){return this.alignmentTrack.viewAsPairs}get colorBy(){return this.alignmentTrack.colorBy}set height(e){this._height=e,this.showAlignments&&(this.alignmentTrack.height=this.showCoverage?e-this.coverageTrackHeight:e)}get height(){return this._height}sort(e){e=this.assignSort(e);for(let t of this.trackView.viewports)if(t.containsPosition(e.chr,e.position)){const i=t.cachedFeatures;i&&(i.sortRows(e),t.repaint())}}assignSort(e){if(e.locus){const t=function(e){const t=e.split(\":\"),i=t[1].split(\"-\"),n={chr:t[0],start:Number.parseInt(i[0].replace(/,/g,\"\"))-1};return i.length>1?n.end=Number.parseInt(i[1].replace(/,/g,\"\")):n.end=n.start+1,n}(e.locus);e.chr=t.chr,e.position=t.start}else e.position--;return e.direction=\"ASC\"===e.direction||!0===e.direction,e.chr=this.browser.genome.getChromosomeName(e.chr),this.sortObject=e,this.sortObject}async getFeatures(e,t,i,n,r){const s=await this.featureSource.getAlignments(e,t,i);if(s.viewport=r,s.hasPairs&&!this._pairedEndStats&&!this.config.maxFragmentLength){const e=new Om(s.allAlignments(),this.config);e.totalCount>99&&(this._pairedEndStats=e)}s.pack(this.alignmentTrack);const o=this.sortObject;return o&&o.chr===e&&o.position>=t&&o.position<=i&&s.sortRows(o),this.alignmentTrack.hasPairs=this.alignmentTrack.hasPairs||s.hasPairs,s}computePixelHeight(e){return(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.computePixelHeight(e):0)}draw(e){xo.fillRect(e.context,0,e.pixelTop,e.pixelWidth,e.pixelHeight,{fillStyle:\"rgb(255, 255, 255)\"}),!0===this.showCoverage&&this.coverageTrackHeight>0?(this.trackView.axisCanvas.style.display=\"block\",this.coverageTrack.draw(e)):this.trackView.axisCanvas.style.display=\"none\",!0===this.showAlignments&&(this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.alignmentTrack.draw(e))}paintAxis(e,t,i){this.coverageTrack.paintAxis(e,t,this.coverageTrackHeight)}contextMenuItemList(e){return this.alignmentTrack.contextMenuItemList(e)}popupData(e){return!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight?this.coverageTrack.popupData(e):this.alignmentTrack.popupData(e)}clickedFeatures(e){let t;return t=!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight?this.coverageTrack.getClickedObject(e):this.alignmentTrack.getClickedObject(e),t?[t]:void 0}hoverText(e){if(!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight){const t=this.coverageTrack.getClickedObject(e);if(t)return t.hoverText()}}menuItemList(){let e=[];e=e.concat(this.numericDataMenuItems()),e=e.concat(this.alignmentTrack.menuItemList());const t=()=>{if(!this.autoHeight){const e=(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.height:0);this.trackView.setTrackHeight(e)}};return e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"Show Coverage\",this.showCoverage)),click:function(){this.showCoverage=!this.showCoverage,t(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show Alignments\",this.showAlignments)),click:function(){this.showAlignments=!this.showAlignments,t(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),e}getState(){const e=super.getState();return this.sortObject&&(e.sort={chr:this.sortObject.chr,position:this.sortObject.position+1,option:this.sortObject.option,direction:this.sortObject.direction?\"ASC\":\"DESC\"}),Object.assign(e,this.alignmentTrack.getState()),e}getCachedAlignmentContainers(){return this.trackView.viewports.map((e=>e.cachedFeatures))}get dataRange(){return this.coverageTrack.dataRange}set dataRange(e){this.coverageTrack.dataRange=e}get logScale(){return this.coverageTrack.logScale}set logScale(e){this.coverageTrack.logScale=e}get autoscale(){return this.coverageTrack.autoscale}set autoscale(e){this.coverageTrack.autoscale=e}addPairedChordsForViewport(e){const t=this.maxTemplateLength,i=[],n=e.referenceFrame;for(let r of e.cachedFeatures.allAlignments())r.end>=n.start&&r.start<=n.end&&(r.paired?r.end-r.start>t&&i.push(r):r.mate&&r.mate.chr&&(r.mate.chr!==r.chr||Math.max(r.fragmentLength)>t)&&i.push(r));Pm((e=>{const t=[];for(let i of e)if(i.paired)i.firstAlignment&&i.secondAlignment&&t.push({uniqueId:i.readName,refName:zm(i.firstAlignment.chr),start:i.firstAlignment.start,end:i.firstAlignment.end,mate:{refName:zm(i.secondAlignment.chr),start:i.secondAlignment.start,end:i.secondAlignment.end}});else{const e=i.mate;e&&e.chr&&e.position&&t.push({uniqueId:i.readName,refName:zm(i.chr),start:i.start,end:i.end,mate:{refName:zm(e.chr),start:e.position-1,end:e.position}})}return t})(i),this,n,.02)}addSplitChordsForViewport(e){const t=[],i=e.referenceFrame;for(let n of e.cachedFeatures.allAlignments()){const e=n.hasTag(\"SA\");n.end>=i.start&&n.start<=i.end&&e&&t.push(n)}Pm((e=>{const t=e=>{const t=gp(e.tags().SA);let n=0;for(let r of t)r.start!==e.start&&i.push({uniqueId:`${e.readName}_${n++}`,refName:zm(e.chr),start:e.start,end:e.end,mate:{refName:zm(r.chr),start:r.start,end:r.start+r.lenOnRef}})},i=[];for(let i of e)i.paired?(t(i.firstAlignment),i.secondAlignment&&t(i.secondAlignment)):t(i);return i})(t),this,i,.02)}}class iw extends Hl{static defaults={height:250,theta:Math.PI/4,arcOrientation:\"UP\",showBlocks:!0,blockHeight:3,thickness:1,color:\"rgb(180,25,137)\",alpha:.02,logScale:!0};constructor(e,t){super(e,t)}init(e){super.init(e),!1===e.arcOrientation?this.arcOrientation=\"DOWN\":!0===e.arcOrientation?this.arcOrientation=\"UP\":e.arcOrientation?this.arcOrientation=e.arcOrientation.toUpperCase():this.arcOrientation=\"UP\",this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta),this.arcType=function(e){if(!e.arcType)return\"nested\";switch(e.arcType){case\"chiapet\":return\"inView\";case\"chiapetoutbound\":return\"partialInView\";default:return e.arcType}}(e),this.painter={flipAxis:\"DOWN\"===this.arcOrientation,dataRange:this.dataRange,paintAxis:cd},e.valueColumn?(this.valueColumn=e.valueColumn,this.hasValue=!0):e.useScore&&(this.hasValue=!0,this.valueColumn=\"score\"),e.max?(this.dataRange={min:e.min||0,max:e.max},this.autoscale=!1):this.autoscale=!0,e.featureSource?(this.featureSource=e.featureSource,delete e._featureSource):(this.featureSource=Ad(e,this.browser.genome),this.featureSource.getWGFeatures=aw)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow(),this.featureSource.visibilityWindow=this.visibilityWindow),this}get supportsWholeGenome(){return!0}async getFeatures(e,t,i){const n=this.visibilityWindow,r=await this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n});return void 0===this.hasValue&&r&&r.length>0&&(this.hasValue=void 0!==r[0].score),r}draw(e){\"proportional\"===this.arcType||\"inView\"===this.arcType||\"partialInView\"===this.arcType?this.drawProportional(e):this.drawNested(e)}drawNested(e){const t=e.context,i=e.pixelWidth,n=e.pixelHeight,r=e.viewportWidth,s=e.bpPerPixel,o=e.bpStart,a=s;xo.fillRect(t,0,e.pixelTop,i,n,{fillStyle:\"rgb(255, 255, 255)\"});const c=e.features;if(c){(function(){let e=0;for(let t of c){let n=(t.start-o)/a,r=(t.end-o)/a;n>=0&&r<=i&&(e=Math.max(e,r-n))}let t=Math.min(r,e)/2;if(e>0){let e=(n-10)/t;this.theta=function(e){let t,i=[.01570925532366355,.15838444032453644,.3249196962329063,.5095254494944288,.7265425280053609,.9999999999999999],n=[.031415926535897934,.3141592653589793,.6283185307179586,.9424777960769379,1.2566370614359172,1.5707963267948966];for(t=0;t<i.length&&!(i[t]>e);t++);let r=0===t?0:i[t-1],s=t<i.length?i[t]:1,o=(e-r)/(s-r),a=0===t?0:n[t-1],c=t<n.length?n[t]:Math.PI/2;return Math.min(Math.PI/2,a+o*(c-a))}(e),this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta)}}).call(this);const s=\"UP\"===this.arcOrientation,h=s?e.pixelHeight:0;t.font=\"8px sans-serif\",t.textAlign=\"center\";for(let e of c){let n;if(e.drawState=void 0,\"function\"==typeof this.color?n=this.color(e):(n=this.color||e.color||\"rgb(180,25,137)\",n&&this.config.useScore&&(n=ow(n,(l=e.score,Math.min(1,.11+l/779*.89).toString())))),t.lineWidth=e.thickness||this.thickness||1,e.chr1===e.chr2||\"all\"===e.chr){const{m1:c,m2:l}=nw(e,this.browser.genome);let d=Math.round((c-o)/a),u=Math.round((l-o)/a);if(u<0||d>i)continue;let f=u-d;f<3&&(f=3,d--);const p=f/2,g=p/this.sinTheta,m=this.cosTheta*g,w=d+p;let b,F,v;if(s?(b=this.height+m,F=Math.PI+Math.PI/2-this.theta,v=Math.PI+Math.PI/2+this.theta):(b=-m,F=Math.PI/2-this.theta,v=Math.PI/2+this.theta),this.showBlocks&&\"all\"!==e.chr){const i=(e.start1-o)/a,n=(e.end1-o)/a,r=(e.start2-o)/a,c=(e.end2-o)/a,l=s?-this.blockHeight:this.blockHeight;t.fillRect(i,h,n-i,l),t.fillRect(r,h,c-r,l)}n&&!this.config.useScore&&f>r&&(n=ow(n,this.alpha)),t.strokeStyle=n,t.fillStyle=n,t.beginPath(),t.arc(w,b,g,F,v,!1),t.stroke(),e.drawState={xc:w,yc:b,r:g}}else{let r=Math.round((e.start-o)/a),c=Math.round((e.end-o)/a);if(c<0||r>i)continue;let l=c-r;l<3&&(l=3,r--);const h=e.chr===e.chr1?e.chr2:e.chr1;t.strokeStyle=n,t.fillStyle=ow(Nu(h),.5),s?(t.fillRect(r,this.height/2,l,this.height/2),t.fillText(h,r+l/2,this.height/2-5),e.drawState={x:r,y:this.height/2,w:l,h:this.height/2}):(t.fillRect(r,0,l,this.height/2),t.fillText(h,r+l/2,this.height/2+13),e.drawState={x:r,y:0,w:l,h:this.height/2})}}}var l}getScaleFactor(e,t,i,n){return n?i/(Math.log10(t+1)-(e<=0?0:Math.log10(e+1))):i/(t-e)}drawProportional(e){const t=e.context,i=e.pixelWidth,n=e.pixelHeight,r=e.bpPerPixel,s=e.bpStart,o=r,a=e.referenceFrame.start,c=e.referenceFrame.end,l=\"UP\"===this.arcOrientation;xo.fillRect(t,0,e.pixelTop,i,n,{fillStyle:\"rgb(255, 255, 255)\"});const h=e.features;if(h&&h.length>0){const n=0,r=this.getScaleFactor(n,this.dataRange.max,e.pixelHeight-1,this.logScale),d=l?e.pixelHeight:0;for(let e of h){e.drawState=void 0;const n=this.valueColumn?e[this.valueColumn]:e.score;if(void 0===n||Number.isNaN(n))continue;const h=Math.round((this.logScale?Math.log10(n+1):n)*r);if(e.chr1===e.chr2||\"all\"===e.chr){const{m1:i,m2:r}=nw(e,this.browser.genome);let u=Math.round((i-s)/o),f=Math.round((r-s)/o)-u;if(f<3&&(f=3,u--),n<this.dataRange.min||n>this.dataRange.max)continue;if(\"proportional\"!==this.arcType){const e=\"partialInView\"===this.arcType,t=i>=a&&r<=c;let n=!1,s=!1;if(!t&&e&&(n=a<=i&&i<=c,n||(s=a<=r&&r<=c)),!(t||n||s))continue}const p=f/2,g=u+f/2;e.drawState={xc:g,yc:d,radiusX:p,radiusY:h};const m=l,w=e.color||this.color;if(t.strokeStyle=w,t.lineWidth=e.thickness||this.thickness||1,!0===t.isSVG?t.strokeEllipse(g,d,p,h,0,0,Math.PI,m):(t.beginPath(),t.ellipse(g,d,p,h,0,0,Math.PI,m),t.stroke()),this.alpha&&(t.fillStyle=ow(w,this.alpha),!0===t.isSVG?t.fillEllipse(g,d,p,h,0,0,Math.PI,m):t.fill()),this.showBlocks&&\"all\"!==e.chr){t.fillStyle=w;const i=(e.start1-s)/o,n=(e.end1-s)/o,r=(e.start2-s)/o,a=(e.end2-s)/o,c=l?-this.blockHeight:this.blockHeight;t.fillRect(i,d,n-i,c),t.fillRect(r,d,a-r,c)}}else{let r=Math.round((e.start-s)/o),a=Math.round((e.end-s)/o);if(a<0||r>i||n<this.dataRange.min||n>this.dataRange.max)continue;const c=Math.min(h,this.height-13);let d=a-r;d<3&&(d=3,r--);const u=e.chr===e.chr1?e.chr2:e.chr1;if(t.font=\"8px sans-serif\",t.textAlign=\"center\",t.fillStyle=ow(Nu(u),.5),l){const i=this.height-c;t.fillRect(r,i,d,c),t.fillText(u,r+d/2,i-5),e.drawState={x:r,y:i,w:d,h:c}}else t.fillRect(r,0,d,c),t.fillText(u,r+d/2,c+13),e.drawState={x:r,y:0,w:d,h:c}}}}}clearAxis(e,t,i){xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"})}paintAxis(e,t,i){const n={min:0,max:this.dataRange.max};\"proportional\"===this.arcType||\"inView\"===this.arcType||\"partialInView\"===this.arcType?(this.painter.flipAxis=\"DOWN\"===this.arcOrientation,this.painter.dataRange=n,this.painter.paintAxis(e,t,i)):this.clearAxis(e,t,i)}menuItemList(){let e=[];if(this.hasValue){e.push(\"<hr/>\");const t={nested:\"Nested\",proportional:\"Proportional - All\",inView:\"Proportional - Both Ends in View\",partialInView:\"Proportional - One End in View\"};e.push(\"<b>Arc Type</b>\");for(let i of[\"nested\",\"proportional\",\"inView\",\"partialInView\"])e.push({object:Bt(Dl(t[i],i===this.arcType)),click:function(){this.arcType=i,this.trackView.repaintViews()}})}return e.push(\"<hr/>\"),e.push({name:\"Toggle arc direction\",click:function(){this.arcOrientation=\"UP\"===this.arcOrientation?\"DOWN\":\"UP\",this.trackView.repaintViews()}}),e.push({name:this.showBlocks?\"Hide Blocks\":\"Show Blocks\",click:function(){this.showBlocks=!this.showBlocks,this.trackView.repaintViews()}}),\"proportional\"!==this.arcType&&\"inView\"!==this.arcType&&\"partialInView\"!==this.arcType||(e=e.concat(this.numericDataMenuItems())),this.browser.circularView&&(e.push(\"<hr/>\"),e.push({label:\"Add interactions to circular view\",click:function(){for(let e of this.trackView.viewports)this.addChordsForViewport(e.referenceFrame)}})),e}contextMenuItemList(e){if(this.browser.circularView){const t=e.viewport,i=[];return i.push({label:\"Add interactions to circular view\",click:()=>{const e=t.referenceFrame;this.addChordsForViewport(e)}}),i.push(\"<hr/>\"),i}}addChordsForViewport(e){let t;if(\"all\"===e.chr)t=Object.values(this.featureSource.getAllFeatures()).flat();else{t=this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end).filter((e=>e.drawState))}if(0===t.length)return;Pm(t.map((e=>{const t=e._f||e;return{uniqueId:`${t.chr1}:${t.start1}-${t.end1}_${t.chr2}:${t.start2}-${t.end2}`,refName:zm(t.chr1),start:t.start1,end:t.end1,mate:{refName:zm(t.chr2),start:t.start2,end:t.end2}}})),this,e,.5)}doAutoscale(e){let t=0;if(e)for(let i of e){const e=this.valueColumn?i[this.valueColumn]:i.score;Number.isNaN(e)||(t=Math.max(t,e))}return{min:0,max:t}}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){const t=e._||e;if(i.push({name:\"Region 1\",value:rw(t.chr1,t.start1,t.end1,t.strand1)}),i.push({name:\"Region 2\",value:rw(t.chr2,t.start2,t.end2,t.strand2)}),t.name&&i.push({name:\"Name\",value:t.name}),void 0!==t.value&&i.push({name:\"Value\",value:t.value}),void 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i})(s,r)},utf8border:(e,t)=>{(t=t||e.length)>e.length&&(t=e.length);let i=t-1;for(;i>=0&&128==(192&e[i]);)i--;return i<0||0===i?t:i+Kw[e[i]]>t?i:t}};var Xw=function(){this.input=null,this.next_in=0,this.avail_in=0,this.total_in=0,this.output=null,this.next_out=0,this.avail_out=0,this.total_out=0,this.msg=\"\",this.state=null,this.data_type=2,this.adler=0},Zw=function(e,t){let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_,x;const k=e.state;i=e.next_in,_=e.input,n=i+(e.avail_in-5),r=e.next_out,x=e.output,s=r-(t-e.avail_out),o=r+(e.avail_out-257),a=k.dmax,c=k.wsize,l=k.whave,h=k.wnext,d=k.window,u=k.hold,f=k.bits,p=k.lencode,g=k.distcode,m=(1<<k.lenbits)-1,w=(1<<k.distbits)-1;e:do{f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=p[u&m];t:for(;;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,0===F)x[r++]=65535&b;else{if(!(16&F)){if(64&F){if(32&F){k.mode=12;break e}e.msg=\"invalid literal/length code\",k.mode=30;break e}b=p[(65535&b)+(u&(1<<F)-1)];continue t}for(v=65535&b,F&=15,F&&(f<F&&(u+=_[i++]<<f,f+=8),v+=u&(1<<F)-1,u>>>=F,f-=F),f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=g[u&w];;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,16&F){if(y=65535&b,F&=15,f<F&&(u+=_[i++]<<f,f+=8,f<F&&(u+=_[i++]<<f,f+=8)),y+=u&(1<<F)-1,y>a){e.msg=\"invalid distance too far back\",k.mode=30;break e}if(u>>>=F,f-=F,F=r-s,y>F){if(F=y-F,F>l&&k.sane){e.msg=\"invalid distance too far back\",k.mode=30;break e}if(A=0,C=d,0===h){if(A+=c-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}else if(h<F){if(A+=c+h-F,F-=h,F<v){v-=F;do{x[r++]=d[A++]}while(--F);if(A=0,h<v){F=h,v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}}else if(A+=h-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}for(;v>2;)x[r++]=C[A++],x[r++]=C[A++],x[r++]=C[A++],v-=3;v&&(x[r++]=C[A++],v>1&&(x[r++]=C[A++]))}else{A=r-y;do{x[r++]=x[A++],x[r++]=x[A++],x[r++]=x[A++],v-=3}while(v>2);v&&(x[r++]=x[A++],v>1&&(x[r++]=x[A++]))}break}if(64&F){e.msg=\"invalid distance code\",k.mode=30;break 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0!==_&&(r[f+_]=g-y<<24|64<<16),a.bits=F,0},{Z_FINISH:sb,Z_BLOCK:ob,Z_TREES:ab,Z_OK:cb,Z_STREAM_END:lb,Z_NEED_DICT:hb,Z_STREAM_ERROR:db,Z_DATA_ERROR:ub,Z_MEM_ERROR:fb,Z_BUF_ERROR:pb,Z_DEFLATED:gb}=jw,mb=12,wb=30,bb=e=>(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24);function Fb(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new Uint16Array(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}var vb,yb,Ab=e=>{if(!e||!e.state)return db;const t=e.state;return e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=1,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new Int32Array(852),t.distcode=t.distdyn=new Int32Array(592),t.sane=1,t.back=-1,cb},Cb=e=>{if(!e||!e.state)return db;const t=e.state;return t.wsize=0,t.whave=0,t.wnext=0,Ab(e)},_b=(e,t)=>{let i;if(!e||!e.state)return db;const n=e.state;return t<0?(i=0,t=-t):(i=1+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?db:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,Cb(e))},xb=(e,t)=>{if(!e)return db;const i=new Fb;e.state=i,i.window=null;const n=_b(e,t);return n!==cb&&(e.state=null),n},kb=!0,Ib=e=>{if(kb){vb=new Int32Array(512),yb=new Int32Array(32);let t=0;for(;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(rb(1,e.lens,0,288,vb,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;rb(2,e.lens,0,32,yb,0,e.work,{bits:5}),kb=!1}e.lencode=vb,e.lenbits=9,e.distcode=yb,e.distbits=5},Sb=(e,t,i,n)=>{let r;const s=e.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new Uint8Array(s.wsize)),n>=s.wsize?(s.window.set(t.subarray(i-s.wsize,i),0),s.wnext=0,s.whave=s.wsize):(r=s.wsize-s.wnext,r>n&&(r=n),s.window.set(t.subarray(i-n,i-n+r),s.wnext),(n-=r)?(s.window.set(t.subarray(i-n,i),0),s.wnext=n,s.whave=s.wsize):(s.wnext+=r,s.wnext===s.wsize&&(s.wnext=0),s.whave<s.wsize&&(s.whave+=r))),0},Eb=(e,t)=>{let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_=0;const x=new Uint8Array(4);let k,I;const S=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(!e||!e.state||!e.output||!e.input&&0!==e.avail_in)return db;i=e.state,i.mode===mb&&(i.mode=13),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,d=a,u=c,C=cb;e:for(;;)switch(i.mode){case 1:if(0===i.wrap){i.mode=13;break}for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(2&i.wrap&&35615===l){i.check=0,x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0),l=0,h=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&l)<<8)+(l>>8))%31){e.msg=\"incorrect header check\",i.mode=wb;break}if((15&l)!==gb){e.msg=\"unknown compression method\",i.mode=wb;break}if(l>>>=4,h-=4,A=8+(15&l),0===i.wbits)i.wbits=A;else if(A>i.wbits){e.msg=\"invalid window size\",i.mode=wb;break}i.dmax=1<<i.wbits,e.adler=i.check=1,i.mode=512&l?10:mb,l=0,h=0;break;case 2:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.flags=l,(255&i.flags)!==gb){e.msg=\"unknown compression method\",i.mode=wb;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=wb;break}i.head&&(i.head.text=l>>8&1),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0,i.mode=3;case 3:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.time=l),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,x[2]=l>>>16&255,x[3]=l>>>24&255,i.check=Qw(i.check,x,4,0)),l=0,h=0,i.mode=4;case 4:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.xflags=255&l,i.head.os=l>>8),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0,i.mode=5;case 5:if(1024&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length=l,i.head&&(i.head.extra_len=l),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&(f=i.length,f>a&&(f=a),f&&(i.head&&(A=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Uint8Array(i.head.extra_len)),i.head.extra.set(n.subarray(s,s+f),A)),512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,i.length-=f),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.name+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.comment+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=wb;break}l=0,h=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=mb;break;case 10:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}e.adler=i.check=bb(l),l=0,h=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,hb;e.adler=i.check=1,i.mode=mb;case mb:if(t===ob||t===ab)break e;case 13:if(i.last){l>>>=7&h,h-=7&h,i.mode=27;break}for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}switch(i.last=1&l,l>>>=1,h-=1,3&l){case 0:i.mode=14;break;case 1:if(Ib(i),i.mode=20,t===ab){l>>>=2,h-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg=\"invalid block type\",i.mode=wb}l>>>=2,h-=2;break;case 14:for(l>>>=7&h,h-=7&h;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if((65535&l)!=(l>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=wb;break}if(i.length=65535&l,l=0,h=0,i.mode=15,t===ab)break e;case 15:i.mode=16;case 16:if(f=i.length,f){if(f>a&&(f=a),f>c&&(f=c),0===f)break e;r.set(n.subarray(s,s+f),o),a-=f,s+=f,c-=f,o+=f,i.length-=f;break}i.mode=mb;break;case 17:for(;h<14;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.nlen=257+(31&l),l>>>=5,h-=5,i.ndist=1+(31&l),l>>>=5,h-=5,i.ncode=4+(15&l),l>>>=4,h-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=wb;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.lens[S[i.have++]]=7&l,l>>>=3,h-=3}for(;i.have<19;)i.lens[S[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,k={bits:i.lenbits},C=rb(0,i.lens,0,19,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid code lengths set\",i.mode=wb;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(b<16)l>>>=m,h-=m,i.lens[i.have++]=b;else{if(16===b){for(I=m+2;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l>>>=m,h-=m,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=wb;break}A=i.lens[i.have-1],f=3+(3&l),l>>>=2,h-=2}else if(17===b){for(I=m+3;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=3+(7&l),l>>>=3,h-=3}else{for(I=m+7;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=11+(127&l),l>>>=7,h-=7}if(i.have+f>i.nlen+i.ndist){e.msg=\"invalid bit length repeat\",i.mode=wb;break}for(;f--;)i.lens[i.have++]=A}}if(i.mode===wb)break;if(0===i.lens[256]){e.msg=\"invalid code -- missing end-of-block\",i.mode=wb;break}if(i.lenbits=9,k={bits:i.lenbits},C=rb(1,i.lens,0,i.nlen,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid literal/lengths set\",i.mode=wb;break}if(i.distbits=6,i.distcode=i.distdyn,k={bits:i.distbits},C=rb(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,k),i.distbits=k.bits,C){e.msg=\"invalid distances set\",i.mode=wb;break}if(i.mode=20,t===ab)break e;case 20:i.mode=21;case 21:if(a>=6&&c>=258){e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,Zw(e,u),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,i.mode===mb&&(i.back=-1);break}for(i.back=0;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(w&&!(240&w)){for(F=m,v=w,y=b;_=i.lencode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,i.length=b,0===w){i.mode=26;break}if(32&w){i.back=-1,i.mode=mb;break}if(64&w){e.msg=\"invalid literal/length code\",i.mode=wb;break}i.extra=15&w,i.mode=22;case 22:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;_=i.distcode[l&(1<<i.distbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(!(240&w)){for(F=m,v=w,y=b;_=i.distcode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,64&w){e.msg=\"invalid distance code\",i.mode=wb;break}i.offset=b,i.extra=15&w,i.mode=24;case 24:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.offset+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=wb;break}i.mode=25;case 25:if(0===c)break e;if(f=u-c,i.offset>f){if(f=i.offset-f,f>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=wb;break}f>i.wnext?(f-=i.wnext,p=i.wsize-f):p=i.wnext-f,f>i.length&&(f=i.length),g=i.window}else g=r,p=o-i.offset,f=i.length;f>c&&(f=c),c-=f,i.length-=f;do{r[o++]=g[p++]}while(--f);0===i.length&&(i.mode=21);break;case 26:if(0===c)break e;r[o++]=i.length,c--,i.mode=21;break;case 27:if(i.wrap){for(;h<32;){if(0===a)break e;a--,l|=n[s++]<<h,h+=8}if(u-=c,e.total_out+=u,i.total+=u,u&&(e.adler=i.check=i.flags?Qw(i.check,r,u,o-u):Uw(i.check,r,u,o-u)),u=c,(i.flags?l:bb(l))!==i.check){e.msg=\"incorrect data check\",i.mode=wb;break}l=0,h=0}i.mode=28;case 28:if(i.wrap&&i.flags){for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=wb;break}l=0,h=0}i.mode=29;case 29:C=lb;break e;case wb:C=ub;break e;case 31:return fb;default:return db}return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,(i.wsize||u!==e.avail_out&&i.mode<wb&&(i.mode<27||t!==sb))&&Sb(e,e.output,e.next_out,u-e.avail_out),d-=e.avail_in,u-=e.avail_out,e.total_in+=d,e.total_out+=u,i.total+=u,i.wrap&&u&&(e.adler=i.check=i.flags?Qw(i.check,r,u,e.next_out-u):Uw(i.check,r,u,e.next_out-u)),e.data_type=i.bits+(i.last?64:0)+(i.mode===mb?128:0)+(20===i.mode||15===i.mode?256:0),(0===d&&0===u||t===sb)&&C===cb&&(C=pb),C},Nb={inflateReset:Cb,inflateReset2:_b,inflateResetKeep:Ab,inflateInit:e=>xb(e,15),inflateInit2:xb,inflate:Eb,inflateEnd:e=>{if(!e||!e.state)return db;let t=e.state;return t.window&&(t.window=null),e.state=null,cb},inflateGetHeader:(e,t)=>{if(!e||!e.state)return db;const i=e.state;return 2&i.wrap?(i.head=t,t.done=!1,cb):db},inflateSetDictionary:(e,t)=>{const i=t.length;let n,r,s;return e&&e.state?(n=e.state,0!==n.wrap&&11!==n.mode?db:11===n.mode&&(r=1,r=Uw(r,t,i,0),r!==n.check)?ub:(s=Sb(e,t,i,i),s?(n.mode=31,fb):(n.havedict=1,cb))):db},inflateInfo:\"pako inflate (from Nodeca project)\"};var Bb=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name=\"\",this.comment=\"\",this.hcrc=0,this.done=!1},Mb=Object.prototype.toString,{Z_NO_FLUSH:Rb,Z_FINISH:Db,Z_OK:Tb,Z_STREAM_END:Lb,Z_NEED_DICT:zb,Z_STREAM_ERROR:Hb,Z_DATA_ERROR:Pb,Z_MEM_ERROR:Ob}=jw;function Ub(e){this.options=Gw.assign({chunkSize:65536,windowBits:15,to:\"\"},e||{});const t=this.options;t.raw&&t.windowBits>=0&&t.windowBits<16&&(t.windowBits=-t.windowBits,0===t.windowBits&&(t.windowBits=-15)),!(t.windowBits>=0&&t.windowBits<16)||e&&e.windowBits||(t.windowBits+=32),t.windowBits>15&&t.windowBits<48&&(15&t.windowBits||(t.windowBits|=15)),this.err=0,this.msg=\"\",this.ended=!1,this.chunks=[],this.strm=new Xw,this.strm.avail_out=0;let i=Nb.inflateInit2(this.strm,t.windowBits);if(i!==Tb)throw new Error(Vw[i]);if(this.header=new Bb,Nb.inflateGetHeader(this.strm,this.header),t.dictionary&&(\"string\"==typeof t.dictionary?t.dictionary=Yw.string2buf(t.dictionary):\"[object ArrayBuffer]\"===Mb.call(t.dictionary)&&(t.dictionary=new Uint8Array(t.dictionary)),t.raw&&(i=Nb.inflateSetDictionary(this.strm,t.dictionary),i!==Tb)))throw new Error(Vw[i])}function qb(e,t){const i=new Ub(t);if(i.push(e),i.err)throw i.msg||Vw[i.err];return i.result}Ub.prototype.push=function(e,t){const i=this.strm,n=this.options.chunkSize,r=this.options.dictionary;let s,o,a;if(this.ended)return!1;for(o=t===~~t?t:!0===t?Db:Rb,\"[object ArrayBuffer]\"===Mb.call(e)?i.input=new Uint8Array(e):i.input=e,i.next_in=0,i.avail_in=i.input.length;;){for(0===i.avail_out&&(i.output=new Uint8Array(n),i.next_out=0,i.avail_out=n),s=Nb.inflate(i,o),s===zb&&r&&(s=Nb.inflateSetDictionary(i,r),s===Tb?s=Nb.inflate(i,o):s===Pb&&(s=zb));i.avail_in>0&&s===Lb&&i.state.wrap>0&&0!==e[i.next_in];)Nb.inflateReset(i),s=Nb.inflate(i,o);switch(s){case Hb:case Pb:case zb:case Ob:return this.onEnd(s),this.ended=!0,!1}if(a=i.avail_out,i.next_out&&(0===i.avail_out||s===Lb))if(\"string\"===this.options.to){let e=Yw.utf8border(i.output,i.next_out),t=i.next_out-e,r=Yw.buf2string(i.output,e);i.next_out=t,i.avail_out=n-t,t&&i.output.set(i.output.subarray(e,e+t),0),this.onData(r)}else this.onData(i.output.length===i.next_out?i.output:i.output.subarray(0,i.next_out));if(s!==Tb||0!==a){if(s===Lb)return s=Nb.inflateEnd(this.strm),this.onEnd(s),this.ended=!0,!0;if(0===i.avail_in)break}}return!0},Ub.prototype.onData=function(e){this.chunks.push(e)},Ub.prototype.onEnd=function(e){e===Tb&&(\"string\"===this.options.to?this.result=this.chunks.join(\"\"):this.result=Gw.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg};var Qb=function(e,t){return(t=t||{}).raw=!0,qb(e,t)},Vb={Inflate:Ub,inflate:qb,inflateRaw:Qb,ungzip:qb,constants:jw},{Inflate:jb,inflate:Wb,inflateRaw:Gb,ungzip:$b}=Vb,Kb=Wb,Yb=$b;var Xb=new Map([[1,function(e,t){let i=new Uint8Array(e);return Kb(i).buffer}],[2,function(e,t){let i=e.byteLength,n=new Uint8Array(i),r=Math.floor(i/t),s=new DataView(e);for(var o=0;o<t;o++)for(var a=0;a<r;a++)n[o+a*t]=s.getUint8(o*r+a);return n.buffer}],[3,function(e,t){return function(e){for(var t=e.byteLength%2!=0,i=e.byteLength-4,n=new DataView(e),r=0,s=0,o=0;o<i-1;o+=2){s=(s+(r=(r+n.getUint16(o,!0))%65535))%65535}if(t){s=(s+(r=(r+n.getUint8(i-1))%65535))%65535}var[a,c]=Aw.unpack_from(\">HH\",e,i);if(c%=65535,r!=(a%=65535)||s!=c)throw'ValueError(\"fletcher32 checksum invalid\")'}(e),e.slice(0,-4)}]]),Zb=class{constructor(e,t){this.fh=e,this.offset=t,this.depth=null}async init(){this.all_nodes=new Map,await this._read_root_node(),await this._read_children()}async _read_children(){let e=this.depth;for(;e>0;){for(var t of this.all_nodes.get(e))for(var i of t.get(\"addresses\"))this._add_node(await this._read_node(i,e-1));e--}}async _read_root_node(){let e=await this._read_node(this.offset,null);this._add_node(e),this.depth=e.get(\"node_level\")}_add_node(e){let t=e.get(\"node_level\");this.all_nodes.has(t)?this.all_nodes.get(t).push(e):this.all_nodes.set(t,[e])}async _read_node(e,t){let i=await this._read_node_header(e,t);return i.set(\"keys\",[]),i.set(\"addresses\",[]),i}async _read_node_header(e){throw\"NotImplementedError: must define _read_node_header in implementation class\"}},Jb=class extends Zb{constructor(){super(...arguments),pw(this,\"B_LINK_NODE\",new Map([[\"signature\",\"4s\"],[\"node_type\",\"B\"],[\"node_level\",\"B\"],[\"entries_used\",\"H\"],[\"left_sibling\",\"Q\"],[\"right_sibling\",\"Q\"]]))}async _read_node_header(e,t){let i=await gw(this.B_LINK_NODE,this.fh,e);if(null!=t&&i.get(\"node_level\")!=t)throw\"node level does not match\";return i}},eF=class extends Jb{constructor(e,t){super(e,t),pw(this,\"NODE_TYPE\",0),this.ready=this.init()}async _read_node(e,t){let i=await this._read_node_header(e,t);e+=bw(this.B_LINK_NODE);let n=[],r=[],s=i.get(\"entries_used\");for(var o=0;o<s;o++){let t=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8;let i=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8,n.push(t),r.push(i)}return n.push((await Aw.unpack_from_async(\"<Q\",this.fh,e))[0]),i.set(\"keys\",n),i.set(\"addresses\",r),i}symbol_table_addresses(){var e=[],t=this.all_nodes.get(0);for(var i of t)e=e.concat(i.get(\"addresses\"));return e}},tF=class extends Jb{constructor(e,t,i){super(e,t),pw(this,\"NODE_TYPE\",1),this.dims=i,this.ready=this.init()}async _read_node(e,t){let i=await this._read_node_header(e,t);e+=bw(this.B_LINK_NODE);var n=[],r=[];let s=i.get(\"entries_used\");for(var o=0;o<s;o++){let[t,i]=await Aw.unpack_from_async(\"<II\",this.fh,e);e+=8;let s=\"<\"+this.dims.toFixed()+\"Q\",o=Aw.calcsize(s),a=await Aw.unpack_from_async(s,this.fh,e);e+=o;let c=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8,n.push(new Map([[\"chunk_size\",t],[\"filter_mask\",i],[\"chunk_offset\",a]])),r.push(c)}return i.set(\"keys\",n),i.set(\"addresses\",r),i}async construct_data_from_chunks(e,t,i,n){var r,s,o;if(i instanceof Array){let e=i[0];if(\"REFERENCE\"==e){if(8!=i[1])throw\"NotImplementedError('Unsupported Reference type')\";i=\"<u8\",r=\"getUint64\",s=!1,o=8}else{if(\"VLEN_STRING\"!=e&&\"VLEN_SEQUENCE\"!=e)throw\"NotImplementedError('datatype not implemented')\";r=\"getVLENStruct\",s=!1,o=16}}else[r,s,o]=yw(i);var a=t.reduce((function(e,t){return e*t}),1),c=e.reduce((function(e,t){return e*t}),1);let l=t.length;var h=1;e.slice().map((function(e){let t=h;return h*=e,t}));h=1;var d=t.slice().reverse().map((function(e){let t=h;return h*=e,t})).reverse(),u=new Array(a);let f=c*o;for(var p of this.all_nodes.get(0)){let i=p.get(\"keys\"),a=p.get(\"addresses\"),h=i.length;for(var g=0;g<h;g++){let h=i[g],p=a[g];var m;if(null==n)m=await this.fh.slice(p,p+f);else{m=await this.fh.slice(p,p+h.get(\"chunk_size\"));let e=h.get(\"filter_mask\");m=this._filter_chunk(m,e,n,o)}for(var w=h.get(\"chunk_offset\").slice(),b=w.slice(),F=b.map((function(){return 0})),v=new Cw(m),y=0;y<c;y++){for(var A=l-1;A>=0&&F[A]>=e[A];A--)F[A]=0,b[A]=w[A],A>0&&(F[A-1]+=1,b[A-1]+=1);if(b.slice(0,-1).every((function(e,i){return e<t[i]}))){let e=y*o,t=v[r](e,!s,o),i=b.slice(0,-1).reduce((function(e,t,i){return t*d[i]+e}),0);u[i]=t}F[l-1]+=1,b[l-1]+=1}}}return u}_filter_chunk(e,t,i,n){let r=i.length,s=e.slice();for(var o=r-1;o>=0;o--){if(t&1<<o)continue;let e=i[o],r=e.get(\"filter_id\"),a=e.get(\"client_data\");if(!Xb.has(r))throw'NotImplementedError(\"Filter with id:'+r.toFixed()+' not supported\")';s=Xb.get(r)(s,n,a)}return s}},iF=class extends Zb{constructor(e,t){super(e,t),pw(this,\"B_TREE_HEADER\",new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"node_type\",\"B\"],[\"node_size\",\"I\"],[\"record_size\",\"H\"],[\"depth\",\"H\"],[\"split_percent\",\"B\"],[\"merge_percent\",\"B\"],[\"root_address\",\"Q\"],[\"root_nrecords\",\"H\"],[\"total_nrecords\",\"Q\"]])),pw(this,\"B_LINK_NODE\",new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"node_type\",\"B\"]])),this.ready=this.init()}async _read_root_node(){let e=await this._read_tree_header(this.offset);this.address_formats=this._calculate_address_formats(e),this.header=e,this.depth=e.get(\"depth\");let t=[e.get(\"root_address\"),e.get(\"root_nrecords\"),e.get(\"total_nrecords\")],i=await this._read_node(t,this.depth);this._add_node(i)}async _read_tree_header(e){return await gw(this.B_TREE_HEADER,this.fh,this.offset)}_calculate_address_formats(e){let t=e.get(\"node_size\"),i=e.get(\"record_size\"),n=0,r=0,s=new Map,o=e.get(\"depth\");for(var a=0;a<=o;a++){let e,c,l,h=\"\",d=\"\",u=\"\";if(0==a?(e=0,c=0,l=0):1==a?(e=8,h=\"<Q\",c=this._required_bytes(n),d=this._int_format(c),l=0):(e=8,h=\"<Q\",c=this._required_bytes(n),d=this._int_format(c),l=this._required_bytes(r),u=this._int_format(l)),s.set(a,[e,c,l,h,d,u]),a<o){let s=e+c+l;n=this._nrecords_max(t,i,s),r>0?r*=n:r=n}}return s}_nrecords_max(e,t,i){return Math.floor((e-10-i)/(t+i))}_required_bytes(e){return Math.ceil(_w(e)/8)}_int_format(e){return[\"<B\",\"<H\",\"<I\",\"<Q\"][e-1]}async _read_node(e,t){let[i,n,r]=e,s=this._read_node_header(i,t);i+=bw(this.B_LINK_NODE);let o=this.header.get(\"record_size\"),a=[];for(let e=0;e<n;e++){let e=await this._parse_record(this.fh,i,o);i+=o,a.push(e)}let c=[],l=this.address_formats.get(t);if(0!=t){let[e,t,r,s,o,a]=l;for(let l=0;l<=n;l++){let n=(await Aw.unpack_from_async(s,this.fh,i))[0];i+=e;let l=(await Aw.unpack_from_async(o,this.fh,i))[0];i+=t;let h=l;r>0&&(h=(await Aw.unpack_from_async(a,this.fh,i))[0],i+=r),c.push([n,l,h])}}return s.set(\"keys\",a),s.set(\"addresses\",c),s}async _read_node_header(e,t){let i=await gw(this.B_LINK_NODE,this.fh,e);return i.set(\"node_level\",t),i}*iter_records(){for(let e of this.all_nodes.values())for(let t of e)for(let e of t.get(\"keys\"))yield e}_parse_record(e){throw\"NotImplementedError\"}},nF=class extends iF{constructor(){super(...arguments),pw(this,\"NODE_TYPE\",5)}async _parse_record(e,t,i){let n=(await Aw.unpack_from_async(\"<I\",e,t))[0];t+=4;const r=await e.slice(t,t+7);return new Map([[\"namehash\",n],[\"heapid\",r]])}},rF=class extends iF{constructor(){super(...arguments),pw(this,\"NODE_TYPE\",6)}async _parse_record(e,t,i){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];t+=8;const r=await e.slice(t,t+7);return new Map([[\"creationorder\",n],[\"heapid\",r]])}},sF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await Aw.unpack_from_async(\"<B\",e,t+8);var n;if(0==i)n=await gw(uF,e,t),this._end_of_sblock=t+fF;else{if(2!=i&&3!=i)throw\"unsupported superblock version: \"+i.toFixed();n=await gw(pF,e,t),this._end_of_sblock=t+gF}if(n.get(\"format_signature\")!=hF)throw\"Incorrect file signature: \"+n.get(\"format_signature\");if(8!=n.get(\"offset_size\")||8!=n.get(\"length_size\"))throw\"File uses non-64-bit addressing\";this.version=n.get(\"superblock_version\"),this._contents=n,this._root_symbol_table=null,this._fh=e}async get_offset_to_dataobjects(){if(0==this.version){var e=new aF(this._fh,this._end_of_sblock,!0);return await e.ready,this._root_symbol_table=e,e.group_offset}if(2==this.version||3==this.version)return this._contents.get(\"root_group_address\");throw\"Not implemented version = \"+this.version.toFixed()}},oF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await gw(vF,e,t);ww(\"HEAP\"==i.get(\"signature\")),ww(0==i.get(\"version\"));let n=i.get(\"address_of_data_segment\"),r=await e.slice(n,n+i.get(\"data_segment_size\"));i.set(\"heap_data\",r),this._contents=i,this.data=r}get_object_name(e){let t=new Uint8Array(this.data).indexOf(0,e)-e;return Aw.unpack_from(\"<\"+t.toFixed()+\"s\",this.data,e)[0]}},aF=class{constructor(e,t,i=!1){this.ready=this.init(e,t,i)}async init(e,t,i){var n;if(i)n=new Map([[\"symbols\",1]]);else{if(\"SNOD\"!=(n=await gw(bF,e,t)).get(\"signature\"))throw\"incorrect node type\";t+=FF}for(var r=[],s=n.get(\"symbols\"),o=0;o<s;o++)r.push(await gw(mF,e,t)),t+=wF;return i&&(this.group_offset=r[0].get(\"object_header_address\")),this.entries=r,this._contents=n,this}assign_name(e){this.entries.forEach((function(t){let i=t.get(\"link_name_offset\"),n=e.get_object_name(i);t.set(\"link_name\",n)}))}get_links(e){var t={};return this.entries.forEach((function(i){let n=i.get(\"cache_type\"),r=i.get(\"link_name\");if(0==n||1==n)t[r]=i.get(\"object_header_address\");else if(2==n){let n=i.get(\"scratch\"),o=new ArrayBuffer(4),a=new Uint8Array(o);for(var s=0;s<4;s++)a[s]=n.charCodeAt(s);let c=Aw.unpack_from(\"<I\",o,0)[0];t[r]=e.get_object_name(c)}})),t}},cF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await gw(yF,e,t);t+=AF;let n=i.get(\"collection_size\")-AF,r=await e.slice(t,t+n);this.heap_data=r,this._header=i,this._objects=null}get objects(){if(null==this._objects){this._objects=new Map;for(var e=0;e<=this.heap_data.byteLength-_F;){let t=mw(CF,this.heap_data,e);if(0==t.get(\"object_index\"))break;e+=_F;let i=this.heap_data.slice(e,e+t.get(\"object_size\"));this._objects.set(t.get(\"object_index\"),i),e+=Fw(t.get(\"object_size\"))}}return this._objects}},lF=class{constructor(e,t){this.fh=e,this.ready=this.init(t)}async init(e){let t=await gw(xF,this.fh,e);if(e+=bw(xF),ww(\"FRHP\"==t.get(\"signature\")),ww(0==t.get(\"version\")),t.get(\"filter_info_size\")>0)throw\"Filter info size not supported on FractalHeap\";if(t.get(\"btree_address_huge_objects\")!=dF)throw\"Huge objects not implemented in FractalHeap\";t.set(\"btree_address_huge_objects\",null),t.get(\"root_block_address\")==dF&&t.set(\"root_block_address\",null);let i=t.get(\"log2_maximum_heap_size\"),n=this._min_size_nbits(i),r=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"heap_header_adddress\",\"Q\"],[\"block_offset\",`${n}B`]]);this.indirect_block_header=new Map(r),this.indirect_block_header_size=bw(r),2&~t.get(\"flags\")||r.set(\"checksum\",\"I\"),this.direct_block_header=r,this.direct_block_header_size=bw(r);let s=t.get(\"maximum_direct_block_size\");this._managed_object_offset_size=this._min_size_nbits(i);let o=Math.min(s,t.get(\"max_managed_object_size\"));this._managed_object_length_size=this._min_size_integer(o);let a=t.get(\"starting_block_size\"),c=t.get(\"table_width\");if(!(a>0))throw\"Starting block size == 0 not implemented\";let l=Number(Math.floor(Math.log2(s)));ww(1n<<BigInt(l)==s);let h=Number(Math.floor(Math.log2(a)));ww(1n<<BigInt(h)==a),this._max_direct_nrows=l-h+2;let d=Math.floor(Math.log2(c));ww(1<<d==c),this._indirect_nrows_sub=d+h-1,this.header=t,this.nobjects=t.get(\"managed_object_count\")+t.get(\"huge_object_count\")+t.get(\"tiny_object_count\");let u=[],f=t.get(\"root_block_address\"),p=0;if(null!=f&&(p=t.get(\"indirect_current_rows_count\")),p>0)for await(let e of this._iter_indirect_block(this.fh,f,p))u.push(e);else{let e=await this._read_direct_block(this.fh,f,a);u.push(e)}let g=u.reduce(((e,t)=>e+t.byteLength),0),m=new Uint8Array(g),w=0;u.forEach((e=>{m.set(new Uint8Array(e),w),w+=e.byteLength})),this.managed=m.buffer}async _read_direct_block(e,t,i){let n=await e.slice(t,t+i);return ww(\"FHDB\"==mw(this.direct_block_header,n).get(\"signature\")),n}get_data(e){let t=Aw.unpack_from(\"<B\",e,0)[0],i=t>>4&3,n=1;if(0==i){ww(0==t>>6);let i=this._managed_object_offset_size,r=xw(i,e,n);n+=i,i=this._managed_object_length_size;let s=xw(i,e,n);return this.managed.slice(r,r+s)}throw 1==i?\"tiny objectID not supported in FractalHeap\":2==i?\"huge objectID not supported in FractalHeap\":\"unknown objectID type in FractalHeap\"}_min_size_integer(e){return this._min_size_nbits(_w(e))}_min_size_nbits(e){return Math.ceil(e/8)}async*_iter_indirect_block(e,t,i){let n=await gw(this.indirect_block_header,e,t);t+=this.indirect_block_header_size,ww(\"FHIB\"==n.get(\"signature\"));let r=n.get(\"block_offset\").reduce(((e,t,i)=>e+(t<<8*i)),0);n.set(\"block_offset\",r);let[s,o]=this._indirect_info(i),a=[];for(let i=0;i<s;i++){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];if(t+=8,n==dF)break;let r=this._calc_block_size(i);a.push([n,r])}let c=[];for(let i=s;i<s+o;i++){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];if(t+=8,n==dF)break;let r=this._calc_block_size(i),s=this._iblock_nrows_from_block_size(r);c.push([n,s])}for(let[t,i]of a){let n=await this._read_direct_block(e,t,i);yield n}for(let[t,i]of c)for await(let n of this._iter_indirect_block(e,t,i))yield n}_calc_block_size(e){let t=Math.floor(e/this.header.get(\"table_width\"));return 2**Math.max(t-1,0)*this.header.get(\"starting_block_size\")}_iblock_nrows_from_block_size(e){let t=Math.floor(Math.log2(e));return ww(2**t==e),t-this._indirect_nrows_sub}_indirect_info(e){let t,i,n=this.header.get(\"table_width\"),r=e*n,s=this._max_direct_nrows*n;return e<=s?(t=r,i=0):(t=s,i=r-s),[t,i]}_int_format(e){return[\"B\",\"H\",\"I\",\"Q\"][e-1]}},hF=Aw.unpack_from(\"8s\",new Uint8Array([137,72,68,70,13,10,26,10]).buffer)[0],dF=Aw.unpack_from(\"<Q\",new Uint8Array([255,255,255,255,255,255,255,255]).buffer)[0],uF=new Map([[\"format_signature\",\"8s\"],[\"superblock_version\",\"B\"],[\"free_storage_version\",\"B\"],[\"root_group_version\",\"B\"],[\"reserved_0\",\"B\"],[\"shared_header_version\",\"B\"],[\"offset_size\",\"B\"],[\"length_size\",\"B\"],[\"reserved_1\",\"B\"],[\"group_leaf_node_k\",\"H\"],[\"group_internal_node_k\",\"H\"],[\"file_consistency_flags\",\"L\"],[\"base_address_lower\",\"Q\"],[\"free_space_address\",\"Q\"],[\"end_of_file_address\",\"Q\"],[\"driver_information_address\",\"Q\"]]),fF=bw(uF),pF=new Map([[\"format_signature\",\"8s\"],[\"superblock_version\",\"B\"],[\"offset_size\",\"B\"],[\"length_size\",\"B\"],[\"file_consistency_flags\",\"B\"],[\"base_address\",\"Q\"],[\"superblock_extension_address\",\"Q\"],[\"end_of_file_address\",\"Q\"],[\"root_group_address\",\"Q\"],[\"superblock_checksum\",\"I\"]]),gF=bw(pF),mF=new Map([[\"link_name_offset\",\"Q\"],[\"object_header_address\",\"Q\"],[\"cache_type\",\"I\"],[\"reserved\",\"I\"],[\"scratch\",\"16s\"]]),wF=bw(mF),bF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved_0\",\"B\"],[\"symbols\",\"H\"]]),FF=bw(bF),vF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved\",\"3s\"],[\"data_segment_size\",\"Q\"],[\"offset_to_free_list\",\"Q\"],[\"address_of_data_segment\",\"Q\"]]),yF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved\",\"3s\"],[\"collection_size\",\"Q\"]]),AF=bw(yF),CF=new Map([[\"object_index\",\"H\"],[\"reference_count\",\"H\"],[\"reserved\",\"I\"],[\"object_size\",\"Q\"]]),_F=bw(CF),xF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"object_index_size\",\"H\"],[\"filter_info_size\",\"H\"],[\"flags\",\"B\"],[\"max_managed_object_size\",\"I\"],[\"next_huge_object_index\",\"Q\"],[\"btree_address_huge_objects\",\"Q\"],[\"managed_freespace_size\",\"Q\"],[\"freespace_manager_address\",\"Q\"],[\"managed_space_size\",\"Q\"],[\"managed_alloc_size\",\"Q\"],[\"next_directblock_iterator_address\",\"Q\"],[\"managed_object_count\",\"Q\"],[\"huge_objects_total_size\",\"Q\"],[\"huge_object_count\",\"Q\"],[\"tiny_objects_total_size\",\"Q\"],[\"tiny_object_count\",\"Q\"],[\"table_width\",\"H\"],[\"starting_block_size\",\"Q\"],[\"maximum_direct_block_size\",\"Q\"],[\"log2_maximum_heap_size\",\"H\"],[\"indirect_starting_rows_count\",\"H\"],[\"root_block_address\",\"Q\"],[\"indirect_current_rows_count\",\"H\"]]),kF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];if(1==i)var[n,r,s]=await this._parse_v1_objects(e,t);else{if(i!=\"O\".charCodeAt(0))throw\"InvalidHDF5File('unknown Data Object Header')\";var[n,r,s]=await this._parse_v2_objects(e,t)}this.fh=e,this.msgs=n,this.msg_data=r,this.offset=t,this._global_heaps={},this._header=s,this._filter_pipeline=null,this._chunk_params_set=!1,this._chunks=null,this._chunk_dims=null,this._chunk_address=null}get dtype(){let e=this.find_msg_type(ev)[0].get(\"offset_to_message\");return new kw(this.fh,e).dtype}get chunks(){return this._get_chunk_params().then((()=>this._chunks))}get shape(){let e=this.find_msg_type(ZF)[0].get(\"offset_to_message\");return async function(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];var n;if(1==i)ww(1==(n=await gw(TF,e,t)).get(\"version\")),t+=LF;else{if(2!=i)throw\"InvalidHDF5File('unknown dataspace message version')\";ww(2==(n=await gw(zF,e,t)).get(\"version\")),t+=HF}let r=n.get(\"dimensionality\");return(await Aw.unpack_from_async(\"<\"+(2*r).toFixed()+\"I\",e,t)).filter((function(e,t){return t%2==0}))}(this.fh,e)}async get_filter_pipeline(){if(null!=this._filter_pipeline)return this._filter_pipeline;let e=this.find_msg_type(rv);if(!e.length)return this._filter_pipeline=null,this._filter_pipeline;var t=e[0].get(\"offset_to_message\");let[i,n]=await Aw.unpack_from_async(\"<BB\",this.fh,t);t+=Aw.calcsize(\"<BB\");var r=[];if(1==i){await Aw.unpack_from_async(\"<HI\",this.fh,t),t+=Aw.calcsize(\"<HI\");for(var s=0;s<n;s++){let e=await gw(YF,this.fh,t);t+=XF;let i=Fw(e.get(\"name_length\"),8),n=\"<\"+i.toFixed()+\"s\",s=(await Aw.unpack_from_async(n,this.fh,t))[0];e.set(\"filter_name\",s),t+=i,n=\"<\"+e.get(\"client_data_values\").toFixed()+\"I\";let o=await Aw.unpack_from_async(n,this.fh,t);e.set(\"client_data\",o),t+=4*e.get(\"client_data_values\"),e.get(\"client_data_values\")%2&&(t+=4),r.push(e)}}else{if(2!=i)throw`version ${i} is not supported`;for(let e=0;e<n;e++){let e=new Map,i=this.fh,n=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2,e.set(\"filter_id\",n);let s=0;n>255&&(s=(await Aw.unpack_from_async(\"<H\",i,t))[0],t+=2);let o=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2;let a=(1&o)>0;e.set(\"optional\",a);let c,l=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2,s>0&&(c=(await Aw.unpack_from_async(`${s}s`,i,t))[0],t+=s),e.set(\"name\",c);let h=await Aw.unpack_from_async(`<${l}i`,i,t);t+=4*l,e.set(\"client_data_values\",h),r.push(e)}}return this._filter_pipeline=r,this._filter_pipeline}find_msg_type(e){return this.msgs.filter((function(t){return t.get(\"type\")==e}))}async get_attributes(){let e={},t=this.find_msg_type(sv);for(let i of t){let t=i.get(\"offset_to_message\"),[n,r]=await this.unpack_attribute(t);e[n]=r}return e}async get_fillvalue(){var e,t=this.find_msg_type(tv)[0].get(\"offset_to_message\");let i=(await Aw.unpack_from_async(\"<B\",this.fh,t))[0];var n,r,s;if(1==i||2==i)n=await gw(WF,this.fh,t),t+=GF,e=n.get(\"fillvalue_defined\");else{if(3!=i)throw'InvalidHDF5File(\"Unknown fillvalue msg version: \"'+String(i);n=await gw($F,this.fh,t),t+=KF,e=32&n.get(\"flags\")}if(e?(r=(await Aw.unpack_from_async(\"<I\",this.fh,t))[0],t+=4):r=0,r){let[e,i,n]=yw(await this.dtype);s=new Cw(await this.fh.slice(t,t+n))[e](t,!i,n)}else s=0;return s}async unpack_attribute(e){let t=(await Aw.unpack_from_async(\"<B\",this.fh,e))[0];var i,n;if(1==t)ww(1==(i=await gw(EF,this.fh,e)).get(\"version\")),e+=NF,n=8;else{if(3!=t)throw\"unsupported attribute message version: \"+t;ww(3==(i=await gw(BF,this.fh,e)).get(\"version\")),e+=MF,n=1}let r=i.get(\"name_size\"),s=(await Aw.unpack_from_async(\"<\"+r.toFixed()+\"s\",this.fh,e))[0];var o;s=s.replace(/\\x00$/,\"\"),e+=Fw(r,n);try{o=await new kw(this.fh,e).dtype}catch(e){return console.warn(\"Attribute \"+s+\" type not implemented, set to null.\"),[s,null]}e+=Fw(i.get(\"datatype_size\"),n);let a=await this.determine_data_shape(this.fh,e),c=a.reduce((function(e,t){return e*t}),1);if(e+=Fw(i.get(\"dataspace_size\"),n),5===o.datatype_class)l=await this.fh.slice(e,e+o.size);else{var l=await this._attr_value(o,this.fh,c,e);0==a.length&&(l=l[0])}return[s,l]}async determine_data_shape(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];var n;if(1==i)ww(1==(n=await gw(TF,e,t)).get(\"version\")),t+=LF;else{if(2!=i)throw\"unknown dataspace message version\";ww(2==(n=await gw(zF,e,t)).get(\"version\")),t+=HF}let r=n.get(\"dimensionality\");return await Aw.unpack_from_async(\"<\"+r.toFixed()+\"Q\",e,t)}async _attr_value(e,t,i,n){var r=new Array(i);if(e instanceof Array){let l=e[0];for(var s=0;s<i;s++)if(\"VLEN_STRING\"==l){let i=e[2];var[o,a]=await this._vlen_size_and_data(t,n);const c=new TextDecoder(0==i?\"ascii\":\"utf-8\");r[s]=c.decode(a),n+=16}else if(\"REFERENCE\"==l){var c=await Aw.unpack_from_async(\"<Q\",t,n);r[s]=c,n+=8}else{if(\"VLEN_SEQUENCE\"!=l)throw\"NotImplementedError\";{let i=e[1];var[o,a]=this._vlen_size_and_data(t,n);r[s]=this._attr_value(i,a,o,0),n+=16}}}else{let[o,a,c]=yw(e);const l=await t.slice(n,n+i*c);let h=new Cw(l,0),d=0;for(s=0;s<i;s++)r[s]=h[o](d,!a,c),d+=c}return r}async _vlen_size_and_data(e,t){let i=(await Aw.unpack_from_async(\"<I\",e,t))[0],n=await gw(SF,e,t+4),r=n.get(\"collection_address\");var s;return ww(n.get(\"collection_address\")<Number.MAX_SAFE_INTEGER),r in this._global_heaps||(s=new cF(this.fh,r),await s.ready,this._global_heaps[r]=s),[i,(s=this._global_heaps[r]).objects.get(n.get(\"object_index\"))]}async _parse_v1_objects(e,t){let i=await gw(RF,e,t);ww(1==i.get(\"version\"));let n=i.get(\"total_header_messages\");for(var r=i.get(\"object_header_size\"),s=t+bw(RF),o=await e.slice(s,s+r),a=[[s,r]],c=0,l=0,h=new Array(n),d=0;d<n;d++){l>=r&&([s,r]=a[++c],l=0);let t=await gw(PF,e,s+l),i=s+l+OF;if(t.set(\"offset_to_message\",i),t.get(\"type\")==ov){var[u,f]=await Aw.unpack_from_async(\"<QQ\",e,i);a.push([u,f])}l+=OF+t.get(\"size\"),h[d]=t}return[h,o,i]}async _parse_v2_objects(e,t){var[i,n,r]=await this._parse_v2_header(e,t);t=r;for(var s=[],o=i.get(\"size_of_chunk_0\"),a=e.slice(t,t+=o),c=[[r,o]],l=0,h=0;;){if(h>=o-qF){let e=c[++l];if(null==e)break;[r,o]=e,h=0}let t=await gw(UF,e,r+h),i=r+h+qF+n;if(t.set(\"offset_to_message\",i),t.get(\"type\")==ov){var[d,u]=await Aw.unpack_from_async(\"<QQ\",e,i);c.push([d+4,u-4])}h+=qF+t.get(\"size\")+n,s.push(t)}return[s,a,i]}async _parse_v2_header(e,t){let i=await gw(DF,e,t);var n;if(t+=bw(DF),ww(2==i.get(\"version\")),n=4&i.get(\"flags\")?2:0,ww(!(16&i.get(\"flags\"))),32&i.get(\"flags\")){let n=await Aw.unpack_from_async(\"<4I\",e,t);t+=16,i.set(\"access_time\",n[0]),i.set(\"modification_time\",n[1]),i.set(\"change_time\",n[2]),i.set(\"birth_time\",n[3])}let r=[\"<B\",\"<H\",\"<I\",\"<Q\"][3&i.get(\"flags\")];return i.set(\"size_of_chunk_0\",(await Aw.unpack_from_async(r,e,t))[0]),[i,n,t+=Aw.calcsize(r)]}async find_link(e){if(this._links){for(link of this._links)if(e===link[0])return link}else{const t=[];for await(const i of this.iter_links()){if(e===i[0])return i;t.push(i)}this._links=t}}async get_links(){const e=[];for await(const t of this.iter_links())e.push(t);return Object.fromEntries(e)}async*iter_links(){for(let e of this.msgs)e.get(\"type\")==av?yield*this._iter_links_from_symbol_tables(e):e.get(\"type\")==iv?yield this._get_link_from_link_msg(e):e.get(\"type\")==JF&&(yield*this._iter_link_from_link_info_msg(e))}async*_iter_links_from_symbol_tables(e){ww(16==e.get(\"size\"));let t=await gw(QF,this.fh,e.get(\"offset_to_message\"));yield*this._iter_links_btree_v1(t.get(\"btree_address\"),t.get(\"heap_address\"))}async*_iter_links_btree_v1(e,t){let i=new eF(this.fh,e);await i.ready;let n=new oF(this.fh,t);await n.ready;for(let e of 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t=e.get(\"offset_to_message\"),i=await this._decode_link_info_msg(this.fh,t),n=i.get(\"heap_address\"),r=i.get(\"name_btree_address\"),s=i.get(\"order_btree_address\");null!=r&&(yield*this._iter_links_btree_v2(r,s,n))}async*_iter_links_btree_v2(e,t,i){let n,r=new lF(this.fh,i);await r.ready;const s=null!=t;s?(n=new rF(this.fh,t),await n.ready):(n=new nF(this.fh,e),await n.ready);let o=new Map;for(let e of n.iter_records()){let t=r.get_data(e.get(\"heapid\")),[i,n]=await this._decode_link_msg(t,0);const a=s?i:n[0];o.set(a,n)}let a=Array.from(o.keys()).sort();for(let e of a)yield o.get(e)}async _decode_link_info_msg(e,t){let[i,n]=await Aw.unpack_from_async(\"<BB\",e,t);ww(0==i),t+=2,(1&n)>0&&(t+=8);let r=(2&n)>0?jF:VF,s=await gw(r,e,t),o=new Map;for(let[e,t]of s.entries())o.set(e,t==IF?null:t);return o}get is_dataset(){return this.find_msg_type(ZF).length>0}async get_data(){let e=this.find_msg_type(nv)[0].get(\"offset_to_message\");var[t,i,n,r]=await 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wv(this.pytor_keys),n=i.get_rd_bins(),r=i.get_snp_bins();this.available_bins=[...new Set(n,r)],this.available_bins.includes(e)||(e=this.available_bins.at(-1));const s=await t.get(\"rd_chromosomes\");await s.dtype;let o=await s.value,a=await this.rd_stat(e);var c=[],l=[],h=[],d=[],u=[],f=[];for(let t of o){let i=new gv(t,e);var p=i.signals.raw_RD;let n=await this.get_chr_signal(t,e,p,a);c=c.concat(n);var g=i.signals.gc_RD;let r=await this.get_chr_signal(t,e,g,a);l=l.concat(r);let s=i.signals.gc_partition,o=await this.get_chr_signal(t,e,s,a);h=h.concat(o);let m=await this.rd_call_combined(t,e,a,i);d=d.concat(m);let w=i.signals.baf_i1,b=await this.get_baf_signals_v2(t,e,w);u=u.concat(b[0]),f=f.concat(b[1])}this.callers=[],0!=d.length&&this.callers.push(\"ReadDepth\"),0!=d.length&&this.callers.push(\"2D\");var m={},w={RD_Raw:c,RD_Raw_gc_coor:l,ReadDepth:h,\"2D\":d,BAF1:u,BAF2:f};return m[e]=w,m}decode_segments(e){let t=[],i=[];for(let n of e)4294967295==n?(t.push(i),i=[]):i.push(n);return t}async rd_call_combined(e,t,i,n){let r,s=[],o=n.signals.Mosaic_segments;if(this.pytor_keys.includes(o)){const e=await this.h5_obj.get(o);let t=await e.value;r=this.decode_segments(t)}let a=n.signals.Mosaic_calls;if(this.pytor_keys.includes(a)){const n=await this.h5_obj.get(a);let o=await n.to_array();r.forEach(((n,r)=>{n.forEach(((n,a)=>{s.push({chr:e,start:n*t,end:(n+1)*t,value:o[0][r]/i[4]*2})}))}))}return s}async rd_stat(e){let t,i=`rd_stat_${e}_auto`;if(this.pytor_keys.includes(i)){const e=await this.h5_obj.get(i);t=await e.value}return t}async get_chr_signal(e,t,i,n){let r=[];if(this.pytor_keys.includes(i)){const s=await this.h5_obj.get(i);(await s.value).forEach(((i,s)=>{r.push({chr:e,start:s*t,end:(s+1)*t,value:i/n[4]*2})}))}return r}async get_baf_signals(e,t,i,n=-1){let r=[],s=[];if(this.pytor_keys.includes(i)){let o=await this.h5_obj.get(i);(await o.to_array()).forEach(((i,o)=>{let a=Math.max(...i);const c=i.indexOf(a);let l=Math.max(c/200,1-c/200);r.push({chr:e,start:o*t,end:(o+1)*t,value:n*l}),.5!=l&&s.push({chr:e,start:o*t,end:(o+1)*t,value:n*(1-l)})}))}return[r,s]}async get_baf_signals_v2(e,t,i,n=-1){let r=[],s=[];if(this.pytor_keys.includes(i)){let o=await this.h5_obj.get(i);(await o.to_array()).forEach(((i,o)=>{isNaN(i)||(r.push({chr:e,start:o*t,end:(o+1)*t,value:n*(.5-i)}),.5!=i&&s.push({chr:e,start:o*t,end:(o+1)*t,value:n*(.5+i)}))}))}return[r,s]}}class wv{constructor(e){this.signals=e}get_rd_bins(){let e=[];this.signals.forEach((t=>{let i=t.match(/^his_rd_p_(.*)_(\\d+)$/);i&&e.push({chr:i[1],bin_size:i[2]})}));return[...new Set(e.map((e=>Number(e.bin_size))))]}get_snp_bins(){let e=[];this.signals.forEach((t=>{let i=t.match(/^snp_likelihood_(.*)_(\\d+)_mask$/);i&&e.push({chr:i[1],bin_size:i[2]})}));return[...new Set(e.map((e=>Number(e.bin_size))))]}}function bv(e){let t=function(e){if(e.length<4)return e;let t,i,n,r,s,o;return t=e.slice().sort(((e,t)=>e-t)),t.length/4%1==0?(i=.5*(t[t.length/4]+t[t.length/4+1]),n=.5*(t[t.length*(3/4)]+t[t.length*(3/4)+1])):(i=t[Math.floor(t.length/4+1)],n=t[Math.ceil(t.length*(3/4)+1)]),r=n-i,s=n+1.5*r,o=i-1.5*r,t.filter((e=>e>=o&&e<=s))}(e);const i=t.length,n=t.reduce(((e,t)=>e+t))/i,r=Math.sqrt(t.map((e=>Math.pow(e-n,2))).reduce(((e,t)=>e+t))/i);return[n,r]}var Fv={range_function:function(e,t,i){return Array(Math.ceil((t-e)/i)).fill(e).map(((e,t)=>e+t*i))},getDistParams:bv,linspace:function(e,t,i){if(void 0===i&&(i=Math.max(Math.round(t-e)+1,1)),i<2)return 1===i?[e]:[];var n=Array(i);for(let r=--i;r>=0;r--)n[r]=(r*t+(i-r)*e)/i;return n},GetFit:class{constructor(e){this.allBins=e}getValues(){return Object.values(this.allBins).reduce(((e,t)=>e.concat(t.filter((e=>e.binScore>0)).map((e=>e.binScore)))),[])}getMean(e){return e.reduce((function(e,t){return e+t}))/e.length}fit_data(){return bv(this.getValues())}histogram(e,t){const i=t[1]-t[0],n=[];e.forEach(((e,r)=>{t.forEach(((t,r)=>{if(n[t]||(n[t]={count:0}),t<=e&&e<t+i)return n[t].count++,!1}))}));const r=[];return n.forEach(((e,t)=>{r.push(e.count)})),r}}};function vv(e,t){return isNaN(e)||isNaN(t)||t<=0?NaN:0===e?.5:.5+.5*(yv(.5*t,.5,1)-yv(.5*t,.5,t/(t+e*e)))*Math.sign(e)}function yv(e,t,i){if(0==i)return 0;if(1==i)return 1;{let n=xv(e+t)-xv(e)-xv(t)+e*Math.log(i)+t*Math.log(1-i);return i<(e+1)/(e+t+2)?Math.exp(n)*Av(e,t,i)/e:1-Math.exp(n)*Av(t,e,1-i)/t}}function Av(e,t,i,n=1e3){let r=1,s=1,o=1,a=e+t,c=e+1,l=e-1,h=1-a*i/c;for(let d=0;d<=n;d++){let n=parseFloat(d+1),u=n+n,f=n*(t-n)*i/((l+u)*(e+u)),p=r+f*s,g=h+f*o;f=-(e+n)*(a+n)*i/((c+u)*(e+u));let m=g+f*h,w=r;if(s=p/m,o=g/m,r=(p+f*r)/m,h=1,Math.abs(r-w)<3e-7*Math.abs(r))return r}}function Cv(e){if(0==e||1==e)return 1;return e*Cv(e-1)}function _v(e){let t;var i=[75122.633153,80916.6278952,36308.2951477,8687.24529705,1168.92649479,83.8676043424,2.50662827511],n=0,r=1;if(0==e)t=1e99;else if(e%1==0)t=Cv(e-1);else{for(let t=0;t<i.length;t++)n+=i[t]*Math.pow(e,t),r*=e+t;t=n*Math.pow(e+5.5,e+.5)*Math.exp(-(e+5.5))/r}return t}function xv(e){return Math.log(_v(e))}var kv={TdistributionCDF:vv,gamma:_v,t_test_1_sample:function(e,t,i,n){0==i&&(i=1);var r=(e-t)/i*Math.sqrt(n);return 1-vv(Math.abs(r),n-1)},t_test_2_samples:function(e,t,i,n,r,s){0==t&&(t=1),0==r&&(r=1);var o=(e-n)/Math.sqrt(t**2/i+r**2/s),a=(t**2/i+r**2/s)**2*(i-1)*(s-1)/(t**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-vv(Math.abs(o),parseInt(a+.5))}};function Iv(e){return e.reduce((function(e,t){return e>t?e:t}))}function Sv(e,t,i,n){return t*Math.exp(-1*(e-i)**2/(2*n**2))/Math.sqrt(2*Math.PI)/n}function Ev(e,t,i,n){return Math.exp(-1*(e-i)**2/(t**2+n**2))}function Nv(e,t){let i;try{i=e.reduce(((e,i,n)=>e+Math.min(i,t[n])))}catch{return console.log(\"Failed to find likelihood overlap: \",e,t),0}return i}function Bv(e,t,i,n){return 0==t&&0==n?{nl:.5*(e+i),ne:0}:{nl:(e*n*n+i*t*t)/(t*t+n*n),ne:Math.sqrt(t*t*n*n/(t*t+n*n))}}function Mv(e,t){let i=parseInt(t*(e.length-1)),n=t*(e.length-1)-i;return i<e.length-1?e[i]*(1-n)+e[i+1]*n:e[i]}function Rv(e){const t=e.length,i=Math.max(...e);let n=e.indexOf(i);n>Math.floor(t/2)&&(n=t-1-n);const r=(t/2-n)/(t+1),s=Math.floor((t/2+n)/2),o=t-1-s;let a=e.slice(s,o+1).reduce(((e,t)=>e+t),0)/e.reduce(((e,t)=>e+t),0);return n===Math.floor(t/2)&&(a=1),{mean:r,p:a}}var Dv=class{constructor(e,t){this.wigFeatures=e,this.binSize=t}get_fit(){var e=new Fv.GetFit(this.wigFeatures),[t,i]=e.fit_data();return{globalMean:t,globalStd:i}}async call_2d(e=null,t=null,i=\"both\",n=.1,r=0,s=10,o=0){let a=this.get_fit();this.globalMean=a.globalMean,this.globalStd=a.globalStd;let c=null==e?.05*this.binSize/3e9:e,l=null==t?parseInt(this.binSize/1e4):t,h=[],d=[],u=[],f=[],p=[],g=[];for(const[e,t]of Object.entries(this.wigFeatures)){let e=[],i=[],s=[];t.forEach(((t,n)=>{t.hets_count>4&&t.dp_count>l&&(e.push([n]),i.push(t.binScore),s.push(t.likelihood_score),delete t.likelihood_score)}));let o=[];for(let e=1;e<i.length;e++)o.push(Math.abs(i[e]-i[e-1]));let a=[0];for(let e=1;e<o.length;e++)a.push(Math.min(o[e-1],o[e]));a.push(0);let g=i.map(((e,t)=>Math.sqrt(Math.sqrt(e)**2+this.globalStd**2+Math.pow(a[t]/2,2)))),m=[];for(let t=0;t<e.length-1;t++){let n=0;try{n=Nv(s[t],s[t+1])}catch{console.log(\"Overlap failed: \",t,s[t],e[t+1],s[t+1])}let r=Ev(i[t],g[t],i[t+1],g[t+1]);m.push(r*n)}for(;m.length>0;){m=m.filter((e=>\"number\"==typeof e));let t=Iv(m);if(isNaN(t)&&console.log(\"NaN value\",m),t<c)break;let n,r,o=m.indexOf(t),a=Bv(i[o],g[o],i[o+1],g[o+1]);try{n=s[o].map(((e,t)=>e*s[o+1][t])),r=n.reduce(((e,t)=>e+t))}catch{console.log(s),console.log(\"max_overlap:\",t,o,m.length),console.log(\"likelihood: \",o,s[o],s[o+1]),console.log(\"nlh: \",r)}if(i[o]=a.nl,g[o]=a.ne,s[o]=n.map((function(e){return e/r})),e[o].push(...e[o+1]),i.splice(o+1,1),g.splice(o+1,1),e.splice(o+1,1),s.splice(o+1,1),m.splice(o,1),o<m.length){let e=Ev(i[o],g[o],i[o+1],g[o+1])*Nv(s[o],s[o+1]);m[o]=e}if(o>0){let e=Ev(i[o-1],g[o-1],i[o],g[o])*Nv(s[o-1],s[o]);m[o-1]=e}}let w=-1;for(;;){m=[];for(let t=0;t<i.length;t++)for(let r=t;r<i.length;r++)e[r][0]-e[t].at(-1)<n*(e[t].length+e[r].length)&&m.push(Ev(i[t],g[t],i[r],g[r])*Nv(s[t],s[r]));if(0==m.length)break;let t=Iv(m);if(t<c)break;let r=0,o=1;for(;r<e.length-1;){let a=Ev(i[r],g[r],i[o],g[o])*Nv(s[r],s[o]);if(e[o][0]-e[r].at(-1)<n*(e[r].length+e[o].length)&&a==t){let t=Bv(i[r],g[r],i[r+1],g[r+1]);i[r]=t.nl,g[r]=t.ne;let n=s[r].map(((e,t)=>e*s[r+1][t])),a=n.reduce(((e,t)=>e+t));s[r]=n.map((function(e){return e/a})),e[r].push(...e[r+1]),e[r]=e[r].sort(((e,t)=>e-t)),i.splice(o,1),g.splice(o,1),e.splice(o,1),s.splice(o,1),o>=e.length&&(r+=1,o=r+1)}else o+=1,o>=e.length&&(r+=1,o=r+1)}if(w==e.length)break;w=e.length}e.forEach(((e,n)=>{let o=Rv(s[n]);e.length>1&&(e.forEach(((e,s)=>{d.push(t[e]),o.mean<=r&&h.push(t[e]),t[e].segment_score=i[n]})),u.push(i[n]),f.push(g[n]),p.push(s[n]))}))}let m=parseInt(1e3*(1-o));0==m&&(m=1);let w=Fv.linspace(o,1,m),b={},F={};for(let e=10;e>-1;e--)for(let t=0;t<e/2+1;t++){let n,r,s=e-t,o=w.map(((t,i)=>1-t+t*e/2)),a=e/2;e>0?(n=.5-t/(t+s),r=w.map(((e,i)=>.5-(1-e+e*t)/(2-2*e+(t+s)*e)))):(n=0,r=w.map(((e,t)=>0*e)));for(let i=0;i<u.length;i++){let c=Sv(a*this.globalMean,1,u[i],f[i])*Mv(p[i],.5+n);i in F?F[i].push([e,t,s,c,1]):F[i]=[e,t,s,c,1];let l=0,h=0,d=0;o.forEach(((e,t)=>{if(!isNaN(r[t])){let n=Sv(e*this.globalMean,1,u[i],f[i])*Mv(p[i],.5+r[t]);l+=n,n>h&&(h=n,d=w[t])}})),i in b?b[i].push([e,t,s,l/w.length,d]):b[i]=[e,t,s,l/w.length,d]}for(let e=0;e<u.length;e++)if(\"germline\"==i)b[e].sort(((e,t)=>e[3]-t[3]));else if(b[e].sort(((e,t)=>e[3]-t[3])),\"both\"==i&&(F[e].sort(((e,t)=>e[3]-t[3])),F[e][0][3]>b[e][0][3])){let t=b[e].filter((t=>t[0]!=F[e][0][0]&&t[1]<=F[e][0][1]));b[e]=[F[e][0]].push(...t)}for(let e=0;e<u.length;e++)b[e][0][0],b[e][0][0],u[e],this.globalMean,kv.t_test_1_sample(this.globalMean,u[e],f[e],g[e])}return{binScore:this.formatDataStructure(this.wigFeatures,\"binScore\",this.globalMean),segment_score:this.formatDataStructure(this.wigFeatures,\"segment_score\",this.globalMean)}}formatDataStructure(e,t,i=1){const n=[];for(const[r,s]of Object.entries(e))s.forEach((e=>{var r={...e};1!=i&&(r.value=e[t]/i*2),n.push(r)}));return n}formatDataStructure_BAF(e,t=-1){const i=[],n=[];for(const[r,s]of Object.entries(this.wigFeatures))s.forEach((r=>{var s={...r},o={...r};let a=r[e];.5!=a&&(o.value=t*(1-a),n.push(o)),s.value=t*a,i.push(s)}));return[i,n]}};const Tv=2871e6;function Lv(e){for(var t=1,i=1,n=1*e,r=1;r<50;r++)t*=r,n+=(i*=-1)*Math.pow(e,2*r+1)/(t*(2*r+1));return 2*n/Math.sqrt(3.14159265358979)}function zv(e,t,i,n,r){var s=new Ov(i.slice(n,r));return 0==s.std&&(s.std=t>0?t*s.mean/e:1),Uv(e,s.mean,s.std,r-n)/(r-n)}function Hv(e,t,i,n,r){var s=new Ov(i.slice(n,r));if(s.mean<e){var o=(s.max-s.mean)/(t*Math.sqrt(2));return Math.pow(.5*(1+Lv(o)),r-n)}o=(s.min-s.mean)/(t*Math.sqrt(2));return Math.pow(.5*(1-Lv(o)),r-n)}function Pv(e,t,i,n,r,s,o=1e3){for(var a=zv(e,t,i,n,r),c=0,l=!1;a>s&!l&c<o;){l=!0,c+=1;var[h,d,u,f]=[1e10,1e10,1e10,1e10];if(n>0&&(h=zv(e,t,i,n-1,r)),r-n>2)var d=zv(e,t,i,n+1,r),u=zv(e,t,i,n,r-1);if(r<i.length)var f=zv(e,t,i,n,r+1);Math.min[f]<a&&(l=!1,h==Math.min[f]&&(n-=1,a=h),elif(d==Math.min[f]),n+=1,a=d,elif(u==Math.min[f]),r-=1,a=u,elif(f==Math.min[f]),r+=1,a=f)}return a<=s?r:0}class Ov{constructor(e){this.data=e,this.mean=e.reduce(((e,t)=>e+t))/e.length,this.std=Math.sqrt(e.reduce(((e,t)=>(t-this.mean)**2))/e.length)}}function Uv(e,t,i,n){0==i&&(i=1);var r=(e-t)/i*Math.sqrt(n);return 1-kv.TdistributionCDF(Math.abs(r),n-1)}function qv(e,t,i,n,r,s){0==t&&(t=1),0==r&&(r=1);var o=(e-n)/Math.sqrt(t**2/i+r**2/s),a=(t**2/i+r**2/s)**2*(i-1)*(s-1)/(t**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-kv.TdistributionCDF(Math.abs(o),parseInt(a+.5))}var Qv=class{constructor(e,t,i){this.rd=e,this.mean=t,this.std=i,this.bin_bands=[2,3,4,5,6,7,8,10,12,14,16,20,24,28,32,40,48,56,64,80,96,112,128]}get_rd_signal_bandwidth(e){var t=[];return e.forEach(((e,i)=>{var n=0;n=e>this.mean/4?this.mean/(this.std**2*e):4/this.std**2,t.push(n)})),t}meanShiftCaller(e,t=3){var i={};return Object.entries(this.rd).forEach((([e,n])=>{var r=new Array(n.length).fill(!1),s=new Array(n.length);for(let e=0;e<n.length;e++)r[e]||(s[e]=n[e]);this.bin_bands.forEach(((e,i)=>{var o=r.map(((e,t)=>!e)),a=[];Object.entries(n).forEach((([e,t])=>{a.push(t.binScore)}));var c=[0],l=0;for(let e=0;e<r.length;e++)r[e]?l>0&&(c.push(c[c.length-1]+l-1),l=0):l+=1;c.shift();for(let i=0;i<t;i++){var h=this.get_rd_signal_bandwidth(a),d=new Array(a.length).fill(0);for(let t=0;t<a.length;t++)for(let i=t-3*e;i<=t+3*e+1;i++)if(!(i<0||i>=a.length||Math.abs(t-i)>=a.length)){var u=(i-t)*Math.exp(-.5*(i-t)**2/e**2)*Math.exp(-.5*(a[t]-a[i])**2*h[t]);d[t]+=u}for(var f=new Array,p=0;p<d.length-1;p++)d[p]<0&d[p+1]>=0&&f.push(p);f.push(d.length-1),f=f.concat(c).sort(((e,t)=>e-t)),f=Array.from(new Set(f));var g=0;for(p=0;p<f.length;p++){var m=a.slice(g,f[p]+1),w=m.reduce(((e,t)=>e+t))/m.length;a.fill(w,g,f[p]+1),g=f[p]+1}}p=0;for(var b=0;p<s.length;p++)o[p]&&(s[p]=a[b],b++);for(f=new Array,p=0;p<s.length-1;p++){Math.abs(s[p+1]-s[p])>.01&&f.push(p+1)}f.unshift(0),f.push(s.length),r=new Array(this.rd.length).fill(!1);for(p=1;p<f.length;p++){var F=[f[p-1],f[p]],v=[f[p-1],f[p-1]];if(!(p>1))continue;v[0]=f[p-2];var y=[f[p],f[p]];if(!(p<f.length-1))continue;y[1]=f[p+1];var A=F[1]-F[0],C=v[1]-v[0],_=y[1]-y[0];if(A<=1)continue;var x=new Ov(s.slice(F[0],F[1]));if(_<=15||C<=15||A<=15){var k=1.8*Math.sqrt(s[v[0]]/this.mean)*this.std;if(Math.abs(s[v[0]]-s[F[0]])<k)continue;if(k=1.8*Math.sqrt(s[y[0]]/this.mean)*this.std,Math.abs(s[y[0]]-s[F[0]])<k)continue}else{var I=s.slice(v[0],v[1]),S=new Ov(I),E=s.slice(y[0],y[1]),N=new Ov(E);if(qv(x.mean,x.std,x.data.length,S.mean,S.std,S.data.length)>.01/Tv*bin_size*(A+C))continue;if(qv(x.mean,x.std,x.data.length,N.mean,N.std,N.data.length)>.01/Tv*bin_size*(A+_))continue}if(Uv(this.mean,x.mean,x.std,x.data.length)>.05)continue;let e=a.slice(F[0],F[1]);var B=new Ov(e);r.fill(!0,F[0],F[1]),s.fill(B.mean,F[0],F[1])}})),i[e]=s})),i}call_mean_shift(e=3){for(var t=new Array(this.rd.length).fill(!1),i=new Array(this.rd.length),n=0;n<this.rd.length;n++)t[n]||(i[n]=this.rd[n]);return this.bin_bands.forEach(((n,r)=>{var s=t.map(((e,t)=>!e)),o=[];s.forEach(((e,t)=>{e&&o.push(this.rd[t])}));for(var a=[0],c=0,l=0;l<t.length;l++)t[l]?c>0&&(a.push(a[a.length-1]+c-1),c=0):c+=1;a.shift();for(var h=0;h<e;h++){var d=this.get_rd_signal_bandwidth(o),u=new Array(o.length).fill(0);for(l=0;l<o.length;l++)for(var f=l-3*n;f<=l+3*n+1;f++)if(!(f<0||f>=o.length||Math.abs(l-f)>=o.length)){var p=(f-l)*Math.exp(-.5*(f-l)**2/n**2)*Math.exp(-.5*(o[l]-o[f])**2*d[l]);u[l]+=p}var g=new Array;for(l=0;l<u.length-1;l++)u[l]<0&u[l+1]>=0&&g.push(l);g.push(u.length-1),g=g.concat(a).sort(((e,t)=>e-t)),g=Array.from(new Set(g));var m=0;for(l=0;l<g.length;l++){var w=o.slice(m,g[l]+1),b=w.reduce(((e,t)=>e+t))/w.length;o.fill(b,m,g[l]+1),m=g[l]+1}}for(l=0,f=0;l<i.length;l++)s[l]&&(i[l]=o[f],f++);for(g=new Array,l=0;l<i.length-1;l++){Math.abs(i[l+1]-i[l])>.01&&g.push(l+1)}g.unshift(0),g.push(i.length),t=new Array(this.rd.length).fill(!1);for(l=1;l<g.length;l++){var F=[g[l-1],g[l]],v=[g[l-1],g[l-1]];if(l>1){v[0]=g[l-2];var y=[g[l],g[l]];if(l<g.length-1){y[1]=g[l+1];var A=F[1]-F[0],C=v[1]-v[0],_=y[1]-y[0];if(!(A<=1)){var x=new Ov(i.slice(F[0],F[1]));if(_<=15||C<=15||A<=15){var k=1.8*Math.sqrt(i[v[0]]/this.mean)*this.std;if(Math.abs(i[v[0]]-i[F[0]])<k)continue;if(k=1.8*Math.sqrt(i[y[0]]/this.mean)*this.std,Math.abs(i[y[0]]-i[F[0]])<k)continue}else{var I=i.slice(v[0],v[1]),S=new Ov(I),E=i.slice(y[0],y[1]),N=new Ov(E);if(qv(x.mean,x.std,x.data.length,S.mean,S.std,S.data.length)>3.483106931382794e-9*(A+C))continue;if(qv(x.mean,x.std,x.data.length,N.mean,N.std,N.data.length)>3.483106931382794e-9*(A+_))continue}if(!(Uv(this.mean,x.mean,x.std,x.data.length)>.05)){var B=new Ov(this.rd.slice(F[0],F[1]));t.fill(!0,F[0],F[1]),i.fill(B.mean,F[0],F[1])}}}}}})),i}cnv_calling(e=1e5){var t=.25*this.mean,i=this.mean-t,n=this.mean+t,r=2971e6,s=this.meanShiftCaller(e),o={},a=[];return Object.entries(s).forEach((([c,l])=>{for(var h=!1;!h;){h=!0;var d=new Array(1).fill(0);for(let e=0;e<l.length-1;e++){Math.abs(l[e+1]-l[e])>.01&&d.push(e+1)}d.push(l.length);for(let e=0;e<d.length-2;e++){var u=Math.abs(l[d[e]]-l[d[e+1]]);if(u<t){var f=u+1,p=u+1;if(e>0&&(f=Math.abs(l[d[e]]-l[d[e-1]])),e<d.length-3&&(p=Math.abs(s[d[e+1]]-l[d[e+2]])),u<f&&u<p){h=!1;var g=new Ov(l.slice(d[e],d[e+2]));l.fill(g.mean,d[e],d[e+2]),d.splice(e+1,e+1)}}}}var m=[];Object.entries(this.rd[c]).forEach((([e,t])=>{m.push(t.binScore)}));for(var w,b=new Array(l.length).fill(\"\"),F=0,v=.05*e/r;F<l.length;){for(var y=F,A=F;F<l.length&l[F]<i;)F+=1;if((_=F)>A+1){var C=Pv(this.mean,this.std,m,A,_,v);if(C){var _=C;b.fill(\"D\",A,_)}}for(A=F;F<l.length&l[F]>n;)F+=1;(_=F)>A+1&&(C=Pv(this.mean,this.std,m,A,_,v))&&(_=C,b.fill(\"A\",A,_)),F==y&&(F+=1)}for(F=0;F<l.length;){for(;F<l.length&\"\"!=b[F];)F+=1;for(A=F;F<l.length&l[F]<i;)F+=1;(_=F)>A+1&&(Hv(this.mean,this.std,m,A,_)<1682935038707506e-26&&b.fill([\"d\"]*(_-A),A,_),F-=1),F+=1}(F=0)<l.length&&(w=b[F]),A=0;for(var x=[...m];F<l.length;){for(;b[F]==w&&!((F+=1)>=b.length););if(F>A){var k=new Ov(x.slice(A,F));x.fill(k.mean,A,F)}F<l.length&&(w=b[F]),A=F}for(o[c]=x,F=0;F<l.length;){if(\"\"==(w=b[F])){F+=1;continue}for(A=F;F<l.length&w==b[F];)F+=1;let t,i=new Ov(x.slice(A,F)).mean/this.mean;t=\"D\"==w?\"deletion\":\"duplication\";let n={chr:c,start:e*A+1,end:e*F,size:e*(F-A+1),value:2*i,event_type:t};a.push(n)}})),[o,a]}};class Vv{constructor(e,t){this.allVariants=e,this.rowBinSize=1e4,this.binSize=t,this.binFactor=parseInt(t/this.rowBinSize)}async read_rd_baf(e=\"ReadDepth\"){var t={};for(let e=this.allVariants.length-1;e>=0;e--){var i;let n=this.allVariants[e];this.allVariants.splice(e,1);let r=n.chr;i=Math.max(Math.floor(n.start/this.rowBinSize),0),t[r]||(t[r]=[]),t[r][i]||(t[r][i]={chr:r,start:i*this.rowBinSize,end:(i+1)*this.rowBinSize,dp_sum_score:0,dp_count:0,hets_count:0,hets:[]});const s=Object.values(n.calls);if(1!==s.length)throw Error(`Unexpected number of genotypes: ${s.length}.  CNVPytor expects 1 and only 1 genotype`);const o=s[0],a=o.info.DP;a&&(t[r][i].dp_sum_score+=Number.parseInt(a),t[r][i].dp_count++);let c=o.info.AD.split(\",\"),l=o.genotype;if(0==l[0]&&1==l[1]||1==l[0]&&0==l[1]){t[r][i].hets_count++;let e=parseInt(c[0]),n=parseInt(c[1]);t[r][i].hets.push({ref:e,alt:n})}}this.chromosomes=Object.keys(t);var n,r=this.adjust_bin_size(t);if(\"ReadDepth\"==e){n=new Wv(r,this.binSize).ReadDepth_caller();var s=this.formatDataStructure_BAF(r,\"max_likelihood\")}else if(\"2D\"==e){let e=new Dv(r,this.binSize),t=await e.call_2d();n=[t.binScore,[],t.segment_score];s=e.formatDataStructure_BAF(\"max_likelihood\",-1)}return[n,s]}formatDataStructure(e,t,i=1){const n=[];for(const[s,o]of Object.entries(e))for(let e of o){var r={...e};1!=i&&(r.value=e[t]/i*2),n.push(r)}return n}format_BAF_likelihood(e){const t=[];for(const[n,r]of Object.entries(e))for(let e of r){var i={...e};.5!=e.value&&(i.value=1-e.value,t.push(i))}return t}get_max_min_score(e){if(e.likelihood_score.length>0){const t=Math.max(...e.likelihood_score),i=e.likelihood_score.indexOf(t);e.value=Math.max(i/100,1-i/100),e.min_score=Math.min(i/100,1-i/100)}else e.score=0;return e}async getAllbins(){const e=await this.computeDepthFeatures();return new Fv.GetFit(e).fit_data(),e}formatDataStructure_BAF(e,t,i=-1){const n=[],r=[];for(const[a,c]of Object.entries(e))for(let e of c){var s={...e},o={...e};let a=e[t];.5!=a&&(o.value=i*(1-a),r.push(o)),s.value=i*a,n.push(s)}return[n,r]}adjust_bin_size(e){var t={};for(let r of this.chromosomes){t[r]||(t[r]=[]);for(let s=0;s<e[r].length/this.binFactor;s++){const o=s;t[r][s]||(t[r][s]={chr:r,start:o*this.binSize,end:(o+1)*this.binSize,dp_count:0,hets_count:0,binScore:0,likelihood_score:[],dp_sum_score:0});for(var i=s*this.binFactor;i<this.binFactor*s+this.binFactor;i++)if(e[r][i]&&(t[r][s].dp_sum_score+=e[r][i].dp_sum_score,t[r][s].dp_count+=e[r][i].dp_count,t[r][s].hets_count+=e[r][i].hets_count,0!=e[r][i].hets.length))for(let o of e[r][i].hets)if(0==t[r][s].likelihood_score.length)t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,t)=>jv(o.ref,o.alt,e)));else{var n=0;t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,i)=>{var a=t[r][s].likelihood_score[i]*jv(o.ref,o.alt,e);return n+=a,a})),t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,i)=>t[r][s].likelihood_score[i]/n))}t[r][s].binScore=100*parseInt(t[r][s].dp_sum_score/t[r][s].dp_count);const a=this.get_max_min_score(t[r][s]);t[r][s].max_likelihood=a.value}}return t}}function jv(e,t,i,n=!0){return Math.pow(i,e)*Math.pow(1-i,t)+Math.pow(i,t)*Math.pow(1-i,e)}class Wv{constructor(e,t){this.wigFeatures=e,this.binSize=t}ReadDepth_caller(){var e=new Fv.GetFit(this.wigFeatures),[t,i]=e.fit_data(),n=new Qv(this.wigFeatures,t,i),r=n.meanShiftCaller(this.binSize),s=n.cnv_calling();return Object.entries(this.wigFeatures).forEach((([e,t])=>{t.forEach(((t,i)=>{t.partition_level=parseInt(r[e][i]),t.partition_call=parseInt(s[0][e][i])}))})),[this.formatDataStructure(\"binScore\",t),this.formatDataStructure(\"partition_level\",t),this.formatDataStructure(\"partition_call\",t),s[1]]}formatDataStructure(e,t=1){const i=[];for(const[r,s]of Object.entries(this.wigFeatures))for(let r of s){var n={...r};1!=t&&(n.value=r[e]/t*2),i.push(n)}return i}}class Gv extends Hl{static DEFAULT_TRACK_HEIGHT=250;constructor(e,t){super(e,t)}init(e){this.featureType=\"numeric\",this.type=\"cnvpytor\",e.max||(this.defaultScale=!0,this.autoscale=!1),e.height||(e.height=Gv.DEFAULT_TRACK_HEIGHT),this.type=\"cnvpytor\",this.graphType=e.graphType||\"points\",this.bin_size=e.bin_size||1e5,this.signal_name=e.signal_name||\"rd_snp\",this.cnv_caller=e.cnv_caller||\"2D\",this.colors=e.colors||[\"gray\",\"black\",\"green\",\"blue\"],super.init(e)}get supportsWholeGenome(){return!0}get_signals(){let e=[];return\"rd_snp\"==this.signal_name?e=[\"RD_Raw\",\"RD_Raw_gc_coor\",this.cnv_caller,\"BAF1\",\"BAF2\"]:\"rd\"==this.signal_name?e=[\"RD_Raw\",\"RD_Raw_gc_coor\",this.cnv_caller]:\"snp\"==this.signal_name?e=[\"BAF1\",\"BAF2\"]:\"cnh\"==this.signal_name&&(e=[this.cnv_caller]),e}get_signal_colors(){return[{singal_name:\"RD_Raw\",color:this.colors[0]},{singal_name:\"RD_Raw_gc_coor\",color:this.colors[1]},{singal_name:\"ReadDepth\",color:this.colors[2]},{singal_name:\"2D\",color:this.colors[2]},{singal_name:\"BAF1\",color:this.colors[3]},{singal_name:\"BAF2\",color:this.colors[3]}]}async postInit(){if(\"vcf\"==this.config.format){let e;this.featureSource?e=Object.values(this.featureSource.getAllFeatures()).flat():(this.featureSource=this.featureSource||Ad(this.config,this.browser.genome),this.header=await this.getHeader(),e=this.featureSource.reader.features);const t=new Vv(e,this.bin_size);let i,n,r;this.wigFeatures_obj={},this.wigFeatures_obj[this.bin_size]={},\"2D\"==this.cnv_caller?(r=await t.read_rd_baf(\"2D\"),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size][\"2D\"]=i[2],this.available_callers=[\"2D\"]):(r=await t.read_rd_baf(),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size].ReadDepth=i[2],this.available_callers=[\"ReadDepth\"]),this.wigFeatures_obj[this.bin_size].RD_Raw=i[0],this.wigFeatures_obj[this.bin_size].RD_Raw_gc_coor=i[1],this.wigFeatures_obj[this.bin_size].BAF1=n[0],this.wigFeatures_obj[this.bin_size].BAF2=n[1],this.available_bins=[this.bin_size],this.set_available_callers()}else this.cnvpytor_obj=new mv(this.config.url,this.bin_size),this.wigFeatures_obj=await this.cnvpytor_obj.get_rd_signal(this.bin_size),this.available_bins=this.cnvpytor_obj.available_bins,this.available_callers=this.cnvpytor_obj.callers,this.set_available_callers();this.tracks=[];const e=[];this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(let t in this.wigFeatures_obj)for(const[i,n]of Object.entries(this.wigFeatures_obj[t]))if(this.signals.includes(i)){let t={type:\"wig\"};t.features=n,t.name=i,t.color=this.signal_colors.filter((e=>e.singal_name===i)).map((e=>e.color));const r=await this.browser.createTrack(t);r?(r.isMergedTrack=!0,r.autoscale=!1,this.tracks.push(r)):console.warn(\"Could not create track \"+t),\"function\"==typeof r.postInit&&e.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let e of this.tracks)e.autoscale=!1,e.dataRange=this.dataRange;return Promise.all(e)}set_available_callers(){this.available_callers.includes(this.cnv_caller)||(this.available_callers.length>0?this.cnv_caller=this.available_callers[0]:this.cnv_caller=null)}async getHeader(){if(!this.header){if(\"function\"==typeof this.featureSource.getHeader){const e=await this.featureSource.getHeader();e&&(this.callSets=e.callSets||[]),this.header=e}this.sampleKeys=this.callSets?this.callSets.map((e=>e.sample)):[],this.sampleNames=this.sampleKeys}return this.header}get height(){return this._height}set height(e){if(this._height=e,this.tracks)for(let t of this.tracks)t.height=e,t.config.height=e}menuItemList(){let e=[];void 0!==this.flipAxis&&e.push({label:\"Flip y-axis\",click:function(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),e=e.concat(this.numericDataMenuItems()),e.push(\"<hr/>\"),e.push(\"Bin Sizes\");for(let t of this.available_bins){const i=Dl(t,t===this.bin_size);e.push({object:Bt(i),click:async function(){this.bin_size=t,this.trackView.startSpinner(),await this.recreate_tracks(t),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}e.push(\"<hr/>\"),e.push(\"Signal Type\");let t={rd_snp:\"RD and BAF Likelihood\",rd:\"RD Signal\",snp:\"BAF Likelihood\"};for(let i in t){const n=Dl(t[i],i===this.signal_name);e.push({object:Bt(n),click:async function(){this.signal_name=i,await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}e.push(\"<hr/>\"),e.push(\"CNV caller\");for(let t of this.available_callers){const i=Dl(t,t===this.cnv_caller);e.push({object:Bt(i),click:async function(){this.cnv_caller=t,this.trackView.startSpinner(),await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}if(this.variantState){e.push(\"<hr/>\");for(let t of this.available_callers)e.push({label:\"Convert to variant track\",click:()=>{this.convertToVariant()}})}return e}async recreate_tracks(e){this.tracks=[];const t=[];e in this.wigFeatures_obj||(this.wigFeatures_obj={...this.wigFeatures_obj,...await this.cnvpytor_obj.get_rd_signal(e)}),this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(const[i,n]of Object.entries(this.wigFeatures_obj[e]))if(this.signals.includes(i)){let e={type:\"wig\"};e.features=n,e.name=i,e.color=this.signal_colors.filter((e=>e.singal_name===i)).map((e=>e.color));const r=await this.browser.createTrack(e);r?(r.isMergedTrack=!0,r.autoscale=!1,this.tracks.push(r)):console.warn(\"Could not create track \"+e),\"function\"==typeof r.postInit&&t.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let e of this.tracks)e.autoscale=!1,e.dataRange=this.dataRange;return Promise.all(t)}async getFeatures(e,t,i,n){if(this.tracks){const r=this.tracks.map((r=>r.getFeatures(e,t,i,n)));return Promise.all(r)}}getScaleFactor(e,t,i,n){return n?i/(Math.log10(t+1)-(e<=0?0:Math.log10(e+1))):i/(t-e)}computeYPixelValue(e,t){return(this.flipAxis?e-this.dataRange.min:this.dataRange.max-e)*t}computeYPixelValueInLogScale(e,t){let i=this.dataRange.max,n=this.dataRange.min;return i<=0?0:(n<=-1&&(n=0),n=n<=0?0:Math.log10(n+1),i=Math.log10(i+1),e=Math.log10(e+1),(this.flipAxis?e-n:i-e)*t)}draw(e){const t=e.features;if(!t)return;if(this.defaultScale&&(\"rd_snp\"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||-1,max:this.config.max||this.dataRange.max||5}:\"rd\"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||0,max:this.config.max||this.dataRange.max||5}:\"snp\"==this.signal_name&&(this.dataRange={min:this.config.min||this.dataRange.min||-1,max:this.config.max||this.dataRange.max||0})),this.autoscale&&(this.dataRange=function(e,t){let i=0,n=-Number.MAX_VALUE;for(let e of t)for(let t of e)void 0===t.value||Number.isNaN(t.value)||(i=Math.min(i,t.value),n=Math.max(n,t.value));return{min:i,max:n}}(e.referenceFrame.chr,t)),this.tracks)for(let i=0,n=this.tracks.length;i<n;i++){const n=Object.assign({},e);n.features=t[i],this.tracks[i].dataRange=this.dataRange,this.tracks[i].flipAxis=this.flipAxis,this.tracks[i].logScale=this.logScale,this.graphType&&(this.tracks[i].graphType=this.graphType),this.tracks[i].draw(n)}const i=this.getScaleFactor(this.dataRange.min,this.dataRange.max,e.pixelHeight,this.logScale),n=e=>this.logScale?this.computeYPixelValueInLogScale(e,i):this.computeYPixelValue(e,i);if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=n(t.y),r={strokeStyle:t.color,strokeWidth:1};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,r):xo.strokeLine(e.context,0,i,e.pixelWidth,i,r)}let r=n(2);xo.dashedLine(e.context,0,r,e.pixelWidth,r,5,{strokeStyle:\"lightgray\",strokeWidth:.5})}paintAxis(e,t,i){var n,r,s,o,a,c,l,h={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};if(void 0===this.dataRange||void 0===this.dataRange.max||void 0===this.dataRange.min)return;let d=void 0!==this.flipAxis&&this.flipAxis;function u(e){return e<0?Math.abs(e):0===e?\"0\":Math.abs(e)>=10||e%1==0?e.toFixed():Math.abs(e)>=1?e.toFixed(1):e.toFixed(2)}xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"}),n=(l=.95*t)-8,a={x:r=l,y:s=o=.01*i},xo.strokeLine(e,n,s,r,o,h),xo.fillText(e,u(d?this.dataRange.min:this.dataRange.max),n+4,s+12,h),c={x:r,y:s=o=.99*i},xo.strokeLine(e,n,s,r,o,h),xo.fillText(e,u(d?this.dataRange.max:this.dataRange.min),n+4,s-4,h),xo.strokeLine(e,a.x,a.y,c.x,c.y,h);const f=this.getScaleFactor(this.dataRange.min,this.dataRange.max,i,this.logScale),p=e=>this.logScale?this.computeYPixelValueInLogScale(e,f):this.computeYPixelValue(e,f),g=Math.ceil((this.dataRange.max-this.dataRange.min)/10);for(let t=Math.ceil(this.dataRange.min+1);t<Math.round(this.dataRange.max-.4);t+=g){const i=p(t);xo.strokeLine(e,45,i,50,i,h),xo.fillText(e,u(d?this.dataRange.max-t:t),44,i+4,h)}}popupData(e,t){const i=t||e.viewport.cachedFeatures;if(i&&i.length===this.tracks.length){const t=[];for(let n=0;n<this.tracks.length;n++){n>0&&t.push(\"<hr/>\"),t.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${this.tracks[n].name}</div>`);const r=this.tracks[n].popupData(e,i[n]);t.push(...r)}return t}}async convertToVariant(){this.variantState&&(Object.setPrototypeOf(this,Yv.prototype),this.init(this.variantState),await this.postInit(),this.trackView.clearCachedFeatures(),this.variantState.trackHeight&&this.trackView.setTrackHeight(this.variantState.trackHeight),this.trackView.checkContentHeight(),this.trackView.updateViews(),delete this.variantState)}}const $v=Mt,Kv=10;class Yv extends Hl{static defaults={displayMode:\"EXPANDED\",sortDirection:\"ASC\",showGenotypes:!0,expandedVariantHeight:10,squishedVariantHeight:2,squishedCallHeight:1,expandedCallHeight:10,expandedVGap:2,squishedVGap:1,expandedGroupGap:10,squishedGroupGap:5,featureHeight:14,noGenotypeColor:\"rgb(200,180,180)\",noCallColor:\"rgb(225, 225, 225)\",nonRefColor:\"rgb(200, 200, 215)\",mixedColor:\"rgb(200, 220, 200)\",homrefColor:\"rgb(200, 200, 200)\",homvarColor:\"rgb(17,248,254)\",hetvarColor:\"rgb(34,12,253)\",refColor:\"rgb(0,0,220)\",altColor:\"rgb(255,0,0)\",visibilityWindow:void 0,labelDisplayMode:void 0,type:\"variant\"};_sortDirections=new Map;constructor(e,t){super(e,t)}init(e){if(super.init(e),e.variantHeight&&(this.expandedVariantHeight=e.variantHeight),this.featureSource=Ad(e,this.browser.genome),this.colorTables=new Map,e.colorTable){const t=e.colorBy||\"*\";this.colorTables.set(t,new ao(e.colorTable))}if(this.strokecolor=e.strokecolor,this._context_hook=e.context_hook,e.color&&(this.colorBy=void 0),this.nVariantRows=1,e.samples)for(let t of e.samples)this.sampleKeys=e.samples;e.sort&&(this.initialSort=e.sort),this._colorByItems=new Map([[\"none\",\"None\"]])}async postInit(){if(this.header=await this.getHeader(),this.header.INFO){const e=new Set(Object.keys(this.header.INFO));this.config.colorBy?this.colorBy=this.config.colorBy:!this.config.color&&e.has(\"AF\")&&(this.colorBy=\"AF\"),e.has(\"AF\")&&this._colorByItems.set(\"AF\",\"Allele frequency\"),e.has(\"VT\")&&this._colorByItems.set(\"VT\",\"Variant Type\"),e.has(\"SVTYPE\")&&this._colorByItems.set(\"SVTYPE\",\"SV Type\")}if(this.config.colorBy&&!this._colorByItems.has(this.config.colorBy)&&this._colorByItems.set(this.config.colorBy,this.config.colorBy),!this.disposed){if(this.header&&!this.sampleKeys&&(this.sampleKeys=this.header.sampleNameMap?Array.from(this.header.sampleNameMap.keys()):[]),void 0===this.visibilityWindow&&!1!==this.config.indexed){const e=Ht(this.config.url)?this.config.url.name:this.config.url;$v(e)&&e.toLowerCase().includes(\"gnomad\")?this.visibilityWindow=1e3:\"function\"==typeof this.featureSource.defaultVisibilityWindow?this.visibilityWindow=await this.featureSource.defaultVisibilityWindow():this.visibilityWindow=1e6}return this}}get supportsWholeGenome(){return!this.config.indexURL||!0===this.config.supportsWholeGenome}get color(){return this._color||\"rgb(0,0,150)\"}set color(e){this._color=e,e&&(this.colorBy=void 0)}async getHeader(){return this.header||\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getSampleCount(){return this.sampleKeys?this.sampleKeys.length:0}async getFeatures(e,t,i,n){void 0===this.header&&(this.header=await this.getHeader());const r=await this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow});if(this.initialSort){const e=this.initialSort;if(void 0===e.option||\"GENOTYPE\"===e.option.toUpperCase())this.sortSamplesByGenotype(e,r);else if(\"ATTRIBUTE\"===e.option.toUpperCase()&&e.attribute){const t=\"ASC\"===e.direction?1:-1;this.sortByAttribute(e.attribute,t)}this.initialSort=void 0}return r}hasSamples(){return this.getSampleCount()>0}getSamples(){const e=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,i=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=t*((\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight)+e),r=Kv+t*(i+e);return{names:this.sampleKeys,yOffset:r,height:n}}computePixelHeight(e){if(!e||0===e.length)return Kv;const t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,i=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,n=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,r=\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s=!1===this.showGenotypes?0:this.getSampleCount()*t;return Kv+t*(n+i)+i+(s+1)*(r+i)}variantRowCount(e){this.nVariantRows=e}draw({context:e,pixelWidth:t,pixelHeight:i,bpPerPixel:n,bpStart:r,pixelTop:s,features:o}){xo.fillRect(e,0,s,t,i,{fillStyle:\"rgb(255, 255, 255)\"});const a=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,c=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,l=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=Kv+c*(l+a);let h=this.sampleColumns;const d=this.hasSamples();if(h&&d&&!1!==this.showGenotypes&&xo.strokeLine(e,0,this.variantBandHeight,t,this.variantBandHeight,{strokeStyle:\"rgb(224,224,224) \"}),o){const i=\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,a=r+t*n+1;for(let t of o){if(t.end<r)continue;if(t.start>a)break;const o=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,c=Kv+(\"COLLAPSED\"===this.displayMode?0:t.row*(o+s)),l=o;let h=(t.start-r)/n,u=(t.end-r)/n,f=Math.max(1,u-h);f<3?(f=3,h-=1):f>5&&(h+=1,f-=2);const p=t._f||t;let g;try{g=p.alleleFreq()}catch(e){console.log(e)}if(\"AF\"===this.colorBy&&g){const t=Math.min(1,g)*l,i=l-t;e.fillStyle=p.isFiltered()?this.refColorFiltered:this.refColor,e.fillRect(h,c,f,i),e.fillStyle=p.isFiltered()?this.altColorFiltered:this.altColor,e.fillRect(h,c+i,f,t)}else e.fillStyle=this.getColorForFeature(p),e.fillRect(h,c,f,l);let m=this.getVariantStrokecolor(p);if(m&&(e.strokeStyle=m,e.strokeRect(h,c,f,l)),this.callContextHook(p,e,h,c,f,l),d&&!1!==this.showGenotypes){const t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+s,this.sampleHeight=t*(i+s);let n=0;for(let t of this.sampleKeys){const r=this.header.sampleNameMap.get(t),o=p.calls[r];if(o){const t=\"COLLAPSED\"===this.displayMode?0:p.row,r=this.sampleYOffset+n*this.sampleHeight+t*(i+s);let a=!0,c=!0,l=!1;if(o.genotype)for(let e of o.genotype){if(\".\"===e){l=!0;break}0!==e&&(c=!1),0===e&&(a=!1)}o.genotype?e.fillStyle=l?this.noCallColor:c?this.homrefColor:a?this.homvarColor:this.hetvarColor:e.fillStyle=this.noGenotypeColor,e.fillRect(h,r,f,i)}n++}}}}else console.log(\"No feature list\")}get refColorFiltered(){return this._refColorFiltered||(this._refColorFiltered=_s.addAlpha(this.refColor,.2)),this._refColorFiltered}get altColorFiltered(){return this._altColorFiltered||(this._altColorFiltered=_s.addAlpha(this.altColor,.2)),this._altColorFiltered}getColorForFeature(e){const t=e._f||e;let i;if(this.colorBy&&\"none\"!==this.colorBy){const e=t.getAttributeValue(this.colorBy);i=void 0!==e?this.getVariantColorTable(this.colorBy).getColor(e):\"gray\"}else i=this.color?\"function\"==typeof this.color?this.color(e):this.color:\"NONVARIANT\"===t.type?this.nonRefColor:\"MIXED\"===t.type?this.mixedColor:this.color;return t.isFiltered()&&(i=_s.addAlpha(i,.2)),i}getVariantStrokecolor(e){const t=e._f||e;let i;return i=this.strokecolor?\"function\"==typeof this.strokecolor?this.strokecolor(t):this.strokecolor:void 0,i}callContextHook(e,t,i,n,r,s){if(this._context_hook&&\"function\"==typeof this._context_hook){const o=e._f||e;t.save(),this._context_hook(o,t,i,n,r,s),t.restore()}}clickedFeatures(e){let t=super.clickedFeatures(e);const i=\"EXPANDED\"===this.displayMode?this.expandedVGap:this.squishedVGap,n=i+(\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),r=e.y;if(r<=this.variantBandHeight){const e=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=Math.floor((r-Kv)/(e+i));\"COLLAPSED\"!==this.displayMode&&(t=t.filter((e=>e.row===n)))}else if(this.sampleKeys){const e=r-this.variantBandHeight,i=Math.floor(e/this.sampleHeight);if(i>=0&&i<this.sampleKeys.length){const r=Math.floor((e-i*this.sampleHeight)/n),s=\"COLLAPSED\"===this.displayMode?t:t.filter((e=>e.row===r)),o=this.sampleKeys[i],a=this.header.sampleNameMap.get(o);t=s.map((e=>{const t=e.calls[a];return t.genotypeString=function(e,t){if(e.genotype){let i=\"\";if(\".\"===t.alternateBases)i=\"No Call\";else{const n=t.alternateBases.split(\",\");for(let r of e.genotype)if(i.length>0&&(i+=\" | \"),\".\"===r)i+=\".\";else if(0===r)i+=t.referenceBases;else{i+=n[r-1].replace(\"<\",\"&lt;\")}}return i}}(t,e),t}))}}return t}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=this.browser.genome.id;let r=[];for(let e of t){const t=e._f||e;if(r.length>0&&r.push({html:'<hr style=\"border-top-width:2px ;border-color: #c9c3ba\" />'}),\"function\"==typeof t.popupData){const e=t.popupData(i,n);Array.prototype.push.apply(r,e)}}return r}menuItemList(){const e=[];if(this.header.INFO&&this.header.INFO){const t=this._colorByItems;e.push(\"<hr/>\");const i=Bt('<div class=\"igv-track-menu-category igv-track-menu-border-top\">');i.text(\"Color by:\"),e.push({name:void 0,object:i,click:void 0,init:void 0});for(let n of t.keys()){const r=this.colorBy===n;e.push(this.colorByCB({key:n,label:t.get(n)},r))}e.push(this.colorByCB({key:\"info\",label:\"Info field...\"}))}if(!0===Hf(this.browser.sampleInfo,this.sampleKeys)){e.push(\"<hr/>\"),e.push(\"Sort by attribute:\");for(const s of this.browser.sampleInfo.attributeNames)if(this.sampleKeys.some((e=>{const t=this.browser.sampleInfo.getAttributes(e);return t&&t[s]}))){const o=Bt(\"<div>\");function a(){const e=this._sortDirections.get(s)||1;this.sortByAttribute(s,e),this.config.sort={option:\"ATTRIBUTE\",attribute:s,direction:e>0?\"ASC\":\"DESC\"},this._sortDirections.set(s,-1*e)}o.html(`&nbsp;&nbsp;${s.split(Uu.emptySpaceReplacement).join(\" \")}`),e.push({object:o,click:a})}}e.push(\"<hr/>\"),this.getSampleCount()>0&&(e.push({object:Bt('<div class=\"igv-track-menu-border-top\">')}),e.push({object:Bt(Dl(\"Show Genotypes\",this.showGenotypes)),click:function(){this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.browser.sampleNameControl.performClickWithState(this.browser,this.showGenotypes),this.browser.sampleInfoControl.performClickWithState(this.browser,this.showGenotypes)}})),e.push({object:Bt('<div class=\"igv-track-menu-border-top\">')});for(let c of[\"COLLAPSED\",\"SQUISHED\",\"EXPANDED\"]){e.push({object:Bt(Dl({COLLAPSED:\"Collapse\",SQUISHED:\"Squish\",EXPANDED:\"Expand\"}[c],c===this.displayMode)),click:function(){this.displayMode=c,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return this.browser.circularView&&(e.push(\"<hr>\"),e.push({label:\"Add SVs to circular view\",click:function(){for(let e of this.trackView.viewports)this.sendChordsForViewport(e)}})),this.canCovertToPytor()&&(e.push(\"<hr>\"),e.push({label:\"Convert to CNVpytor track\",click:function(){this.convertToPytor()}})),e}contextMenuItemList(e){const t=[];if(this.hasSamples()&&this.showGenotypes){const i=e.viewport.referenceFrame,n=e.genomicLocation,r=i.toBP(2.5),s=this._sortDirections.get(\"genotype\")||1;this._sortDirections.set(\"genotype\",-1*s),t.push({label:\"Sort by genotype\",click:t=>{const i={direction:s,option:\"genotype\",chr:e.viewport.referenceFrame.chr,start:Math.floor(n-r),end:Math.ceil(n+r)},o=e.viewport.cachedFeatures;this.sortSamplesByGenotype(i,o),this.config.sort=i}}),t.push(\"<hr/>\")}if(this.browser.circularView){const i=e.viewport;t.push({label:\"Add SVs to Circular View\",click:()=>{this.sendChordsForViewport(i)}}),t.push(\"<hr/>\")}return t}async sortSamplesByGenotype({chr:e,position:t,start:i,end:n,direction:r},s){if(void 0===i&&(i=t-1),void 0===n&&(n=t),s||(s=await this.featureSource.getFeatures({chr:e,start:i,end:n})),!s)return;const o=new Map,a=\"ASC\"===r?1:-1;for(let e of s)if(!(e.end<i)){if(e.start>n)break;for(let t of e.calls){const e=t.sample,i=t.zygosityScore();o.set(e,o.has(e)?o.get(e)+i:i)}}this.sampleKeys.sort((function(e,t){let i=o.get(e)||0,n=o.get(t)||0;return a*(i-n)})),this.trackView.repaintViews()}sortByAttribute(e,t){this.config.sort={option:\"ATTRIBUTE\",attribute:e,direction:1===t?\"ASC\":\"DESC\"},this.sampleKeys=this.browser.sampleInfo.getSortedSampleKeysByAttribute(this.sampleKeys,e,t),this.trackView.repaintViews()}sendChordsForViewport(e){const t=e.referenceFrame;let i;if(\"all\"===t.chr){const e=this.featureSource.getAllFeatures(),t=Object.keys(e).map((t=>e[t]));i=[].concat(...t)}else i=this.featureSource.featureCache.queryFeatures(t.chr,t.start,t.end);Pm(i.filter((e=>{const t=e._f||e;return t.info&&t.info.CHR2&&t.info.END&&(t.info.CHR2!==t.chr||Math.abs(Number.parseInt(t.info.END)-t.pos)>1e6)})).map((e=>{const t=e._f||e,i=Number.parseInt(t.info.END),n=i-100,r=i+100;return{uniqueId:`${t.chr}:${t.start}-${t.end}_${t.info.CHR2}:${t.info.END}`,refName:zm(t.chr),start:t.start,end:t.end,mate:{refName:zm(t.info.CHR2),start:n,end:r}}})),this,t,.5)}colorByCB(e,t){const i=Bt(Dl(e.label,t));if(\"info\"!==e.key){function n(){const t=\"none\"===e.key?void 0:e.key;this.colorBy=t,this.config.colorBy=t,this.trackView.repaintViews()}return{name:void 0,object:i,click:n,init:void 0}}{function r(e){this.browser.inputDialog.present({label:\"Info field\",value:\"\",callback:e=>{e?(this.colorBy=e,this._colorByItems.set(e,e)):this.colorBy=void 0,this.trackView.repaintViews()}},e)}return{name:void 0,object:i,dialog:r,init:void 0}}}getState(){const e=super.getState();return this.color&&\"function\"!=typeof this.color&&(e.color=this.color),e}getVariantColorTable(e){if(this.colorTables.has(e))return this.colorTables.get(e);if(this.colorTables.has(\"*\"))return this.colorTables.get(\"*\");{let t;if(\"SVTYPE\"===e)t=Xv;else t=new oo(\"Set1\");return this.colorTables.set(e,t),t}}paintAxis(){}canCovertToPytor(){return!this.config.indexURL&&(!!this.header&&(1===Object.keys(this.sampleKeys).length&&this.header.FORMAT&&this.header.FORMAT.AD&&this.header.FORMAT.DP))}async convertToPytor(){this.variantState={...this.config,...this.getState()},this.variantState.trackHeight=this.height,this.trackView.startSpinner(),setTimeout((async()=>{try{const e=Object.assign({},this.config);Object.setPrototypeOf(this,Gv.prototype),this.init(e),await this.postInit(),this.trackView.clearCachedFeatures(),this.trackView.setTrackHeight(this.config.height||Gv.DEFAULT_TRACK_HEIGHT),this.trackView.checkContentHeight(),this.trackView.updateViews()}finally{this.trackView.stopSpinner()}}),100)}}const Xv=new ao({DEL:\"#ff2101\",INS:\"#001888\",DUP:\"#028401\",INV:\"#008688\",CNV:\"#8931ff\",BND:\"#891100\",\"*\":\"#002eff\"}),Zv={timeout:5e3,type:\"plain\",url:\"https://igv.org/genomes/locus.php?genome=$GENOME$&name=$FEATURE$\",coords:0};async function Jv(e,t){const i=e.searchConfig||Zv;let n;t=t.toUpperCase();const r=e.tracks.filter((e=>e.searchable));for(let e of r){const i=await e.search(t);if(i)return i}if(e.config&&!1!==e.config.search)try{return n=await async function(e,t,i){let n=i.url.replace(\"$FEATURE$\",t.toUpperCase());n.indexOf(\"$GENOME$\")>-1&&(n=n.replace(\"$GENOME$\",e.genome.id?e.genome.id:\"hg19\"));const r=i.timeout?{timeout:i.timeout}:void 0,s=await Qs.loadString(n,r);return function(e,t,i){let n;n=\"plain\"===i.type?function(e,t){const i=[],n=Dt(t);for(let t of n){const n=t.split(\"\\t\");if(n.length>=3){const t=n[1].split(\":\"),r=t[1].split(\"-\");i.push({chromosome:e.genome.getChromosomeName(t[0].trim()),start:parseInt(r[0].replace(/,/g,\"\")),end:parseInt(r[1].replace(/,/g,\"\")),name:n[0].toUpperCase()})}}return i}(e,t):JSON.parse(t);i.resultsField&&(n=n[i.resultsField]);if(n&&0!==n.length){const e=i.chromosomeField||\"chromosome\",t=i.startField||\"start\",r=i.endField||\"end\",s=i.coords||1;let o;o=Array.isArray(n)?n[0]:n,o.hasOwnProperty(e)&&o.hasOwnProperty(t)||console.error(\"Search service results must include chromosome and start fields: \"+o);const a=o[e];let c=o[t]-s,l=o[r];void 0===l&&(l=c+1);const h={chr:a,start:c,end:l};if(!o.type||o.type,i.geneField&&i.snpField){const e=o[i.geneField]||o[i.snpField];e&&(h.name=e.toUpperCase())}return h}return}(e,s,i)}(e,t,i),n}catch(e){console.log(\"Search service not available \"+e)}}function ey(e,t=!1){const i=e.split(\"\\t\");if(i.length>2)try{const e=i[0],t=parseInt(i[1].replace(/,/g,\"\"),10)-1,n=parseInt(i[2].replace(/,/g,\"\"),10);if(!isNaN(t)&&!isNaN(n))return{chr:e,start:t,end:n}}catch(e){}const n=e.split(\":\"),r={chr:n[0]};if(n.length>1){let e,i=n[1].split(\"-\");if(i.length>2){if(!n[1].startsWith(\"-\"))return;{const e=n[1].indexOf(\"-\",1);if(e>0){i=[n[1].substring(0,e),n[1].substring(e+1)]}}}if(e=i[0].replace(/,/g,\"\"),isNaN(e))return;if(r.start=parseInt(e,10)-1,r.end=r.start+1,1===i.length&&(r.start-=20,r.end+=20),2===i.length){if(e=i[1].replace(/,/g,\"\"),isNaN(e))return;if(r.end=parseInt(e,10),r.start<0&&!t){const e=-extent.start;r.start+=e,r.end+=e}}}return r}class ty extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"qtl\",this.name=e.name;const t=e.minLogP||e.min,i=e.maxLogP||e.max;this.dataRange={min:void 0!==t?t:3.5,max:i||25},this.autoscale=!i||e.autoscale,this.autoscalePercentile=void 0===e.autoscalePercentile?98:e.autoscalePercentile,this.background=e.background,this.divider=e.divider||\"rgb(225,225,225)\",this.dotSize=e.dotSize||2,this.height=e.height||100,this.disableButtons=e.disableButtons,this.featureSource=Ad(e,this.browser.genome)}paintAxis(e,t,i){const n=(this.dataRange.max-this.dataRange.min)/i,r={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"});const s=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let o=4;o<=this.dataRange.max;o+=s){const s=.85*t,a=s-5,c=s,l=i-(o-this.dataRange.min)/n;xo.strokeLine(e,a,l,c,l,r),l>8&&xo.fillText(e,o,a-1,l+2,r)}r.textAlign=\"center\",xo.fillText(e,\"-log10(pvalue)\",t/4,i/2,r,{rotate:{angle:-90}})}async getFeatures(e,t,i){const n=this.visibilityWindow;return await this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const{context:t,referenceFrame:i,pixelWidth:n,pixelHeight:r}=e;this.background&&xo.fillRect(t,0,0,n,r,{fillStyle:this.background}),xo.strokeLine(t,0,r-1,n,r-1,{strokeStyle:this.divider}),i.feature&&i.feature.match(/RS[0-9]+/);const s=i=>{const s=i?2*this.dotSize:this.dotSize,o=e.bpStart,a=(this.dataRange.max-this.dataRange.min)/r;for(let d of e.features){const u=(d.start-o+.5)/e.bpPerPixel;if(u<0)continue;if(u>n)break;const f=d.phenotype;let p;if(this.browser.qtlSelections.qtl?(l=this.browser.qtlSelections.qtl,h=d,p=l.chr===h.chr&&l.start===h.start&&l.pValue===h.pValue):p=this.browser.qtlSelections.snps.size>0?this.browser.qtlSelections.hasSnp(d.snp)&&this.browser.qtlSelections.hasPhenotype(f):this.browser.qtlSelections.hasPhenotype(f),!i||p){var c=-Math.log(d.pValue)/Math.LN10;if(c>=this.dataRange.min){let e;c>this.dataRange.max?(c=this.dataRange.max,e=!0):e=!1;const n=Math.max(0+s,r-Math.round((c-this.dataRange.min)/a));let o;d.px=u,d.py=n,d.radius=s,i&&p?(o=this.browser.qtlSelections.colorForGene(f),xo.setProperties(t,{fillStyle:o,strokeStyle:\"black\"})):(o=e?\"rgb(150, 150, 150)\":\"rgb(180, 180, 180)\",xo.setProperties(t,{fillStyle:o,strokeStyle:o})),xo.fillCircle(t,u,n,s),xo.strokeCircle(t,u,n,s)}}}var l,h};s(!1),s(!0)}popupData(e,t){if(void 0===t&&(t=e.viewport.cachedFeatures),!t||0===t.length)return[];const i=this.name,n=[];for(let r of this._clickedFeatures(e,t))n.length>0&&n.push(\"<hr/>\"),\"function\"==typeof r.popupData?n.push(...r.popupData(e)):n.push({name:\"snp id\",value:r.snp},{name:\"gene id\",value:r.gencodeId},{name:\"gene name\",value:r.geneSymbol},{name:\"p value\",value:r.pValue},{name:\"tissue\",value:i});return n}_clickedFeatures(e,t){const i=(e,t)=>Math.sqrt((e.px-t.canvasX)*(e.px-t.canvasX)+(e.py-t.canvasY)*(e.py-t.canvasY)),n=t.filter((t=>i(t,e)<6));if(n.length>1){n.sort(((t,n)=>i(t,e)-i(n,e)));const t=i(n[0],e);return n.filter((n=>i(n,e)<=t))}return n}contextMenuItemList(e){const t=[],i=e.viewport.cachedFeatures;if(i){const n=this._clickedFeatures(e,i);n.length>0&&(t.push({label:\"Highlight associated features\",click:async()=>{this.browser.qtlSelections.clear();for(let e of n)this.browser.qtlSelections.qtl=e,this.browser.qtlSelections.addPhenotype(e.phenotype);this.browser.repaintViews()}}),t.push(\"<hr>\"))}return t}menuItemList(){const e=[];return e.push(...this.numericDataMenuItems()),e.push(\"<hr/>\"),e.push({label:\"Search for...\",dialog:function(e){this.browser.inputDialog.present({label:\"Search for snp or phenotype\",value:\"\",callback:async e=>{if(e){e=e.trim().toUpperCase();const t=t=>((t.phenotype&&t.phenotype.toUpperCase())===e||t.snp&&t.snp.toUpperCase()===e)&&-Math.log(t.pValue)/Math.LN10>this.dataRange.min;let i,n,r,s=await this.featureSource.findFeatures(t);if(0==s.length){await this.browser.search(e)&&(s=await this.featureSource.findFeatures(t))}if(s.length>0){this.browser.qtlSelections.clear();const t=new Set;i=s[0].chr,n=s[0].start,r=s[0].end;for(let o of s)o.snp&&o.snp.toUpperCase()===e&&this.browser.qtlSelections.addSnp(o.snp),this.browser.qtlSelections.addPhenotype(o.phenotype),t.add(o.phenotype),o.chr===i&&(n=Math.min(n,o.start),r=Math.max(r,o.end));const o=this.browser.genome.getChromosomeName(i);for(let e of t){const t=await Jv(this.browser,e);t&&o===this.browser.genome.getChromosomeName(t.chr)&&(n=Math.min(n,t.start),r=Math.max(r,t.end))}const a=Math.floor(.1*(r-n));n=Math.max(0,n-a),r+=a,await this.browser.search(`${i}:${n}-${r}`)}}}},e)}}),e}doAutoscale(e){let t=this.config.max||25;if(e.length>0){const i=e.map((e=>-Math.log(e.pValue)/Math.LN10));i.sort(((e,t)=>e-t));t=i[Math.floor(i.length*(this.autoscalePercentile/100))]}return this.dataRange.max=Math.max(t,10),this.dataRange}}const iy={X:\"rgb(204, 153, 0)\",Y:\"rgb(153, 204, 0)\",Un:\"darkGray)\",1:\"rgb(80, 80, 255)\",2:\"rgb(206, 61, 50)\",\"2a\":\"rgb(210, 65, 55)\",\"2b\":\"rgb(215, 70, 60)\",3:\"rgb(116, 155, 88)\",4:\"rgb(240, 230, 133)\",5:\"rgb(70, 105, 131)\",6:\"rgb(186, 99, 56)\",7:\"rgb(93, 177, 221)\",8:\"rgb(128, 34, 104)\",9:\"rgb(107, 215, 107)\",10:\"rgb(213, 149, 167)\",11:\"rgb(146, 72, 34)\",12:\"rgb(131, 123, 141)\",13:\"rgb(199, 81, 39)\",14:\"rgb(213, 143, 92)\",15:\"rgb(122, 101, 165)\",16:\"rgb(228, 175, 105)\",17:\"rgb(59, 27, 83)\",18:\"rgb(205, 222, 183)\",19:\"rgb(97, 42, 121)\",20:\"rgb(174, 31, 99)\",21:\"rgb(231, 199, 111)\",22:\"rgb(90, 101, 94)\",23:\"rgb(204, 153, 0)\",24:\"rgb(153, 204, 0)\",25:\"rgb(51, 204, 0)\",26:\"rgb(0, 204, 51)\",27:\"rgb(0, 204, 153)\",28:\"rgb(0, 153, 204)\",29:\"rgb(10, 71, 255)\",30:\"rgb(71, 117, 255)\",31:\"rgb(255, 194, 10)\",32:\"rgb(255, 209, 71)\",33:\"rgb(153, 0, 51)\",34:\"rgb(153, 26, 0)\",35:\"rgb(153, 102, 0)\",36:\"rgb(128, 153, 0)\",37:\"rgb(51, 153, 0)\",38:\"rgb(0, 153, 26)\",39:\"rgb(0, 153, 102)\",40:\"rgb(0, 128, 153)\",41:\"rgb(0, 51, 153)\",42:\"rgb(26, 0, 153)\",43:\"rgb(102, 0, 153)\",44:\"rgb(153, 0, 128)\",45:\"rgb(214, 0, 71)\",46:\"rgb(255, 20, 99)\",47:\"rgb(0, 214, 143)\",48:\"rgb(20, 255, 177)\"};for(let DA of Object.keys(iy)){iy[\"chr\"+DA]=iy[DA]}for(let TA=1;TA<=48;TA++){if(10===TA)continue;const LA=ny(TA);iy[LA]=iy[TA.toString()]}function ny(e){if(!+e)return!1;for(var t=String(+e).split(\"\"),i=[\"\",\"C\",\"CC\",\"CCC\",\"CD\",\"D\",\"DC\",\"DCC\",\"DCCC\",\"CM\",\"\",\"X\",\"XX\",\"XXX\",\"XL\",\"L\",\"LX\",\"LXX\",\"LXXX\",\"XC\",\"\",\"I\",\"II\",\"III\",\"IV\",\"V\",\"VI\",\"VII\",\"VIII\",\"IX\"],n=\"\",r=3;r--;)n=(i[+t.pop()+10*r]||\"\")+n;return Array(+t.join(\"\")+1).join(\"M\")+n}class ry extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.useChrColors=void 0===e.useChrColors||e.useChrColors,this.trait=e.trait,this.posteriorProbability=e.posteriorProbability,this.valueProperty=\"bed\"===e.format?\"score\":\"value\",this.height=e.height||100,this.autoscale=e.autoscale,this.autoscalePercentile=void 0===e.autoscalePercentile?98:e.autoscalePercentile,this.background=e.background,this.divider=e.divider||\"rgb(225,225,225)\",this.dotSize=e.dotSize||3,this.popoverWindow=void 0===e.popoverWindow?1e8:e.popoverWindow,this.useChrColors?this.colorScale=new ao(e.colorTable||iy):e.color?this.colorScale=new ff(e.color):this.colorScale=new df(e.colorScale||{thresholds:[5e-8,5e-4,.5],colors:[\"rgb(255,50,50)\",\"rgb(251,100,100)\",\"rgb(251,170,170)\",\"rgb(227,238,249)\"]}),this.featureSource=Ad(e,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),this.autoscale||(this.posteriorProbability?this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?1:this.config.max}:this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?25:this.config.max}),this}get supportsWholeGenome(){return!0}async getFeatures(e,t,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const t=e.features,i=e.context,n=e.pixelWidth,r=e.pixelHeight;if(this.background&&xo.fillRect(i,0,0,n,r,{fillStyle:this.background}),xo.strokeLine(i,0,r-1,n,r-1,{strokeStyle:this.divider}),t){const s=e.bpPerPixel,o=e.bpStart,a=o+n*s+1;for(let e of t){const t=e.start;if(t<o)continue;if(t>a)break;let n;if(this.posteriorProbability)n=e[this.valueProperty];else{const t=e[this.valueProperty];if(!t)continue;n=-Math.log10(t)}const c=this.useChrColors?e._f?e._f.chr:e.chr:n,l=this.colorScale.getColor(c),h=(this.dataRange.max-this.dataRange.min)/r,d=Math.round((t-o)/s),u=Math.max(this.dotSize,r-Math.round((n-this.dataRange.min)/h));l&&xo.setProperties(i,{fillStyle:l,strokeStyle:\"black\"}),xo.fillCircle(i,d,u,this.dotSize),e.px=d,e.py=u}}}paintAxis(e,t,i){xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"});var n={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};const r=(this.dataRange.max-this.dataRange.min)/i;if(this.posteriorProbability){const t=.1;for(let s=this.dataRange.min;s<this.dataRange.max;s+=t){const t=i-Math.round((s-this.dataRange.min)/r);xo.strokeLine(e,45,t-2,50,t-2,n),xo.fillText(e,s.toFixed(1),44,t+2,n)}}else{const t=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let s=this.dataRange.min;s<this.dataRange.max;s+=t){const t=i-Math.round((s-this.dataRange.min)/r);xo.strokeLine(e,45,t,50,t,n),xo.fillText(e,Math.floor(s),44,t+4,n)}}n.textAlign=\"center\",this.posteriorProbability?xo.fillText(e,\"PPA\",t/2,i/2,n,{rotate:{angle:-90}}):xo.fillText(e,\"-log10(pvalue)\",t/2,i/2,n,{rotate:{angle:-90}})}popupData(e,t){void 0===t&&(t=e.viewport.cachedFeatures);let i=[];const n=e.viewport.trackView.track;if(t){let r=0;for(let s of t){const t=Math.abs(e.canvasX-s.px),o=Math.abs(e.canvasY-s.py);if(t<this.dotSize&&o<this.dotSize){if(r>0&&i.push(\"<HR/>\"),5==r){i.push(\"...\");break}if(s=s._f||s,\"function\"==typeof s.popupData)i=i.concat(s.popupData());else{const e=s[this.valueProperty],t=s.chr,r=Rt(s.start+1);i.push({name:\"chromosome\",value:t}),i.push({name:\"position\",value:r}),i.push({name:\"name\",value:s.name}),n.posteriorProbability?i.push({name:\"posterior probability\",value:e}):i.push({name:\"pValue\",value:e})}r++}}}return i}menuItemList(){return this.numericDataMenuItems()}doAutoscale(e){if(e.length>0){const t=this.valueProperty,i=this.posteriorProbability,n=e.map((function(e){const n=e[t];return{value:i?n:-Math.log(n)/Math.LN10}}));this.dataRange=qa(n)}else this.posteriorProbability?this.dataRange={min:this.config.min||0,max:this.config.max||1}:this.dataRange={min:this.config.max||25,max:this.config.min||0};return this.dataRange}}class sy extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.autoscale=e.autoscale||void 0===e.max,this.dataRange={min:e.min||0,max:e.max},this.windowFunction=e.windowFunction||\"mean\",this.paintAxis=cd,this.graphType=e.graphType||\"bar\",e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):this.featureSource=Ad(this.config,this.browser.genome),this.visibilityWindow=-1,this.featureSource.visibilityWindow=this.visibilityWindow}async postInit(){if(\"function\"==typeof this.featureSource.getHeader){if(this.header=await this.featureSource.getHeader(),this.disposed)return;if(this.sampleKeys=this.header.columnNames.slice(3),this.setTrackProperties(this.header),this.header.hasOwnProperty(\"clickToHighlight\")){let e=this.header.clickToHighlight;this.config.clickToHighlight=e,this.config.samplesClickedToHighlight={}}if(this.header.hasOwnProperty(\"highlight\")){this.config.highlightSamples={};let e=this.header.highlight;Array.isArray(e)||(e=[e]);for(let t of e){const e=t.split(\";\");2===e.length&&(this.config.highlightSamples[e[0]]=e[1])}}}}menuItemList(){return this.numericDataMenuItems()}async getFeatures(e,t,i){const n=await this.featureSource.getFeatures({chr:e,start:0,end:Number.MAX_SAFE_INTEGER,visibilityWindow:this.visibilityWindow});let r,s;for(let e=1;e<n.length-1;e++)if(void 0===r&&n[e].end>t&&(r=e-1),void 0===s&&n[e].start>i){s=e+1;break}return void 0===r&&(r=0),void 0===s&&(s=n.length),n.slice(r,s)}draw(e){const{features:t,context:i,bpPerPixel:n,bpStart:r,pixelWidth:s,pixelHeight:o}=e,a=e=>(this.dataRange.max-e)/(this.dataRange.max-this.dataRange.min)*o,c=function(e){let t=Math.floor((e-r)/n);return isNaN(t)&&console.warn(\"isNaN(x). feature start \"+Rt(e)+\" bp start \"+Rt(r)),t};if(t&&t.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const e=this.config.highlightSamples,n=this.config.onlyHandleClicksForHighlightedSamples,r=this.config.clickToHighlight;let s=-1,o={},l=[],h=[];this.clickDetectorCache={};for(let d of t){const t=c(d.start),u=c(d.end),f=s>=0?c(s):t;if(!isNaN(t)&&!isNaN(u)){this.clickDetectorCache[t]=[],this.clickDetectorCache[u]=[];for(let s=0;s<d.values.length;s++){const c=this.sampleKeys[s],p=d.values[s],g=a(p);if(t-f>=1){const s=o[c],h=a(s),d=e&&e[c];d?l.push([f,h,t,g,d]):r&&c in this.config.samplesClickedToHighlight?l.push([f,h,t,g,this.config.samplesClickedToHighlight[c]]):xo.strokeLine(i,f,h,t,g,{strokeStyle:\"#D9D9D9\"}),n&&!(c in e)||this.clickDetectorCache[t].push([f,h,t,g,c,d||\"gray\"])}if(u-t>=1){const s=e&&e[c];s?h.push([t,g,u,g,s]):r&&c in this.config.samplesClickedToHighlight?h.push([t,g,u,g,this.config.samplesClickedToHighlight[c]]):xo.strokeLine(i,t,g,u,g,{strokeStyle:\"gray\"}),n&&!(c in e)||this.clickDetectorCache[u].push([t,g,u,g,c,s||\"gray\"])}o[c]=p}s=d.end}}for(let e of l)xo.strokeLine(i,e[0],e[1],e[2],e[3],{strokeStyle:e[4],lineWidth:1.3});for(let e of h)xo.strokeLine(i,e[0],e[1],e[2],e[3],{strokeStyle:e[4],lineWidth:2})}(e=>{if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=a(t.y),n={strokeStyle:t.color,strokeWidth:2};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,n):xo.strokeLine(e.context,0,i,e.pixelWidth,i,n)}})(e)}doAutoscale(e){let t,i;return e.length>0?(t=Number.MAX_VALUE,i=-Number.MAX_VALUE,e.forEach((function(e){t=Math.min(t,...e.values),i=Math.max(i,...e.values)})),t-=.01,i+=.01):(t=0,i=100),{min:t,max:i}}clickedFeatures(e){const t=e.canvasX,i=e.canvasY;let n=null;for(n of Object.keys(this.clickDetectorCache))if(n=parseInt(n),n>=t)break;if(n){let e=Number.MAX_VALUE,o=[];const a=this.clickDetectorCache[n];for(let n of a){const r=n[0],s=n[2];if(t<r||t>s)return[];const a=n[1],c=n[3];if(i<Math.min(a,c)-10||i>Math.max(a,c)+10)continue;const l=oy(t,i,r,a,s,c);l<e&&(o=[{name:n[4],color:n[5]}],e=l)}if(e<5){if(this.config.clickToHighlight){if(o[0].name in this.config.samplesClickedToHighlight)delete this.config.samplesClickedToHighlight[o[0].name];else if(\"any\"===this.config.clickToHighlight){var r=[\"red\",\"darkblue\",\"green\",\"teal\",\"olivedrab\",\"orange\",\"maroon\",\"purple\",\"blue\",\"gold\"],s=r[Math.floor(Math.random()*(r.length+1))];this.config.samplesClickedToHighlight[o[0].name]=s}else this.config.samplesClickedToHighlight[o[0].name]=this.config.clickToHighlight;this.trackView.repaintViews()}return o}}return[]}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];return t.forEach((function(e){for(let t of Object.keys(e))Oa(e[t])&&i.push({name:t,value:e[t]})})),i}get supportsWholeGenome(){return!1}}function oy(e,t,i,n,r,s){const o=r-i,a=s-n,c=Math.abs(o*(n-t)-(i-e)*a),l=Math.sqrt(o*o+a*a);return l>0?c/l:0}class ay extends Hl{static defaults={height:300,theta:Math.PI/2,arcOrientation:\"UP\"};constructor(e,t){super(e,t),!1===e.arcOrientation?this.arcOrientation=\"DOWN\":!0===e.arcOrientation?this.arcOrientation=\"UP\":e.arcOrientation?this.arcOrientation=e.arcOrientation.toUpperCase():this.arcOrientation=\"UP\",\"bp\"===e.format?this.featureSource=new ly(e,t.genome):this.featureSource=new ud(e,t.genome)}async getFeatures(e,t,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const t=e.context,i=Math.PI/2,n=e.pixelWidth,r=e.pixelHeight;e.viewportWidth;const s=e.bpPerPixel,o=e.bpStart,a=s,c=\"UP\"===this.arcOrientation;xo.fillRect(t,0,e.pixelTop,n,r,{fillStyle:\"rgb(255, 255, 255)\"});const l=e.features;if(l){cy(l,1);for(let e of l)if(e.startLeft){let n=Math.round((e.startLeft-o)/a),r=Math.round((e.startRight-o)/a),s=Math.round((e.endLeft-o)/a),l=Math.round((e.endRight-o)/a);t.fillStyle=e.color,t.strokeStyle=e.color,t.beginPath();let h=(n+l)/2,d=(l-n)/2,u=this.height,f=Math.PI+(Math.PI/2-i),p=2*Math.PI-(Math.PI/2-i);c?(t.arc(h,u,d,f,p),t.lineTo(s,u)):(u=0,t.arc(h,u,d,p,f),t.lineTo(l,u));const g=(r+s)/2,m=(s-r)/2,w=u;c?(t.arc(g,w,m,p,f,!0),t.lineTo(n,w)):(t.arc(g,w,m,f,p,!0),t.lineTo(s,w)),t.stroke(),t.fill(),e.drawState={x1:h,y1:u,r1:d,x2:g,y2:w,r2:m,sa:f,ea:p}}else{let n=Math.round((e.start-o)/a),r=Math.round((e.end-o)/a);t.strokeStyle=e.color,t.beginPath();let s=(n+r)/2,l=(r-n)/2,h=this.height,d=Math.PI+(Math.PI/2-i),u=2*Math.PI-(Math.PI/2-i);c?t.arc(s,h,l,d,u):(h=0,t.arc(s,h,l,u,d)),t.stroke(),e.drawState={x1:s,y1:h,r1:l,sa:d,ea:u}}}}clickedFeatures(e){const t=super.clickedFeatures(e),i=[];cy(t,-1);for(let n of t){const t=n.drawState,r=e.canvasX-t.x1,s=e.canvasY-t.y1,o=Math.sqrt(r*r+s*s),a=t.r1+3;let c,l;if(void 0===t.x2)c=o,l=t.r1-3;else{const i=e.canvasX-t.x2,n=e.canvasY-t.y2;c=Math.sqrt(i*i+n*n),l=t.r2-3}if(o<a&&c>l){i.push(n);break}}return i}popupData(e,t){if(void 0===t&&(t=this.clickedFeatures(e)),t&&t.length>0)return this.extractPopupData(t[0],this.getGenomeId())}menuItemList(){return[{name:\"Toggle arc direction\",click:function(){this.arcOrientation=\"UP\"===this.arcOrientation?\"DOWN\":\"UP\",this.trackView.repaintViews()}}]}}function cy(e,t){e.sort((function(e,i){const n=void 0===e.score?-Number.MAX_VALUE:e.score,r=void 0===i.score?-Number.MAX_VALUE:i.score;return(void 0===t?1:t)*(n-r)}))}class ly{constructor(e,t){this.config=e,this.genome=t}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome;if(this.featureCache)return this.featureCache.queryFeatures(e,t,i);{const n=Ua(this.config),r=await Qs.loadByteArray(this.config.url,n);return this.featureCache=new Zs(function(e){if(!e)return null;const t=mh(e);let i,n=!0;const r=[],s=[],o=[];for(;void 0!==(i=t.nextLine());){const e=i.split(\"\\t\");if(n&&i.startsWith(\"color:\")){const t=\"rgb(\"+e[1]+\",\"+e[2]+\",\"+e[3]+\")\";r.push(t),e.length>4&&s.push(e[4])}else{n=!1;const t=e[0],i=Number.parseInt(e[1])-1,c=Number.parseInt(e[2])-1,l=Number.parseInt(e[3]),h=Number.parseInt(e[4]);var a=Number.parseInt(e[5]);const d=r[a];let u;u=i<=h?{chr:t,startLeft:Math.min(i,c),startRight:Math.max(i,c),endLeft:Math.min(l,h),endRight:Math.max(l,h),color:d,score:a}:{chr:t,startLeft:Math.min(l,h),startRight:Math.max(l,h),endLeft:Math.min(i,c),endRight:Math.max(i,c),color:d,score:a},u.start=u.startLeft,u.end=u.endRight,s.length>a&&(u.description=s[a]),o.push(u)}}return o}(r),s),this.featureCache.queryFeatures(e,t,i)}}}class hy{constructor(e){this.browser=e,this.type=\"ideogram\",this.height=16,this.order=Number.MIN_SAFE_INTEGER,this.disableButtons=!0,this.ignoreTrackMenu=!0}computePixelHeight(e){return this.height}draw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,features:r}){const s=t.chr,o=t.genome.getChromosome(s);if(void 0===o||i<=0||n<=0||\"all\"===s.toLowerCase())return;!function({ctx:e,chr:t,referenceFrame:i,genome:n,width:r,height:s,stainColors:o,features:a}){const c=1,l=.5*c,h=0;if(void 0===n)return;xo.fillRect(e,0,0,r,s,{fillStyle:_s.greyScale(255)});const d=a;if(d){const t=h+s/2,i=[],n=[];if(0===d.length)return;const a=r/d[d.length-1].end;e.beginPath(),xo.roundRect(e,l,l+h,r-2*l,s-2*l,(s-2*l)/2,0,1),e.clip();for(let r=0;r<d.length;r++){const l=d[r],u=a*l.start,f=a*l.end;\"c\"===l.type?(\"p\"===l.name.charAt(0)?(i[0]=u,n[0]=s+h,i[1]=u,n[1]=h,i[2]=f,n[2]=t):(i[0]=f,n[0]=s+h,i[1]=f,n[1]=h,i[2]=u,n[2]=t),e.fillStyle=\"rgb(150, 0, 0)\",e.strokeStyle=\"rgb(150, 0, 0)\",xo.polygon(e,i,n,1,0)):(e.fillStyle=dy(o,l),xo.fillRect(e,u,c+h,f-u,s-2*c))}}e.strokeStyle=_s.greyScale(41),xo.roundRect(e,l,l+h,r-2*l,s-2*l,(s-2*l)/2,0,1)}({ctx:e,features:r,chr:s,referenceFrame:t,genome:t.genome,width:i,height:n,stainColors:[]});const a=Math.round(t.bpPerPixel*i),c=t.start;let l=o.bpLength;const h=t.genome.getCytobands(s);if(h&&h.length>0&&h[h.length-1].end&&(l=Math.max(l,h[h.length-1].end),o.bpLength=l),a<l){const t=a/l,r=c/l;let s=Math.floor(r*i),o=Math.floor(t*i);s=Math.max(0,s),s=Math.min(i-o,s),e.save(),e.strokeStyle=\"red\",e.lineWidth=o<2?1:2;const h=s+e.lineWidth/2;o=o<2?1:o-e.lineWidth;const d=e.lineWidth/2,u=n-e.lineWidth;e.strokeRect(h,d,o,u),e.restore()}}dispose(){this.trackView=void 0}}function dy(e,t){if(\"c\"===t.type)return\"rgb(150, 10, 10)\";var i=t.stain,n=230;\"p\"===t.type&&(n=Math.floor(230-i/100*230));var r=e[n];return r||(r=\"rgb(\"+n+\",\"+n+\",\"+n+\")\",e[n]=r),r}let uy=new oo(\"Dark2\");[\"GT/AG\",\"CT/AC\",\"GC/AG\",\"CT/GC\",\"AT/AC\",\"GT/AT\",\"non-canonical\"].forEach((e=>{uy.getColor(e)}));class fy extends Hl{static defaults={margin:10,colorByNumReadsThreshold:5,height:100};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=e.type||\"junctions\",e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):this.featureSource=e.featureSource?e.featureSource:Ad(e,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get supportsWholeGenome(){return!1}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}computePixelHeight(e){return this.height}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=e.pixelHeight,a=r+s*n+1;if(this.isMergedTrack||xo.fillRect(i,0,e.pixelTop,s,o,{fillStyle:\"rgb(255, 255, 255)\"}),t){const s={};s.referenceFrame=e.viewport.referenceFrame,s.referenceFrameStart=s.referenceFrame.start,s.referenceFrameEnd=s.referenceFrameStart+s.referenceFrame.toBP(e.viewport.getWidth()),s.featureZoomOutTracker={};for(let e of t)if(!(e.end<r)){if(e.start>a)break;this.renderJunction(e,r,n,o,i,s)}}else console.log(\"No feature list\")}renderJunction(e,t,i,n,r,s){e.isVisible=!1;const o=Math.round((e.start-t)/i),a=Math.round((e.end-t)/i),c=(o+a)/2;if(a-o<=3){if(c in s.featureZoomOutTracker)return;s.featureZoomOutTracker[c]=!0}if(this.config.hideAnnotatedJunctions&&\"true\"===e.attributes.annotated_junction)return;if(this.config.hideUnannotatedJunctions&&\"false\"===e.attributes.annotated_junction)return;if(this.config.hideMotifs&&this.config.hideMotifs.includes(e.attributes.motif))return;if(this.config.hideStrand===e.strand)return;if(this.config.minJunctionEndsVisible){let t=0;if(e.start>=s.referenceFrameStart&&e.start<=s.referenceFrameEnd&&(t+=1),e.end>=s.referenceFrameStart&&e.end<=s.referenceFrameEnd&&(t+=1),t<this.config.minJunctionEndsVisible)return}let l,h,d,u;if(e.attributes.uniquely_mapped){if(l=parseInt(e.attributes.uniquely_mapped),l<this.config.minUniquelyMappedReads)return;if(h=parseInt(e.attributes.multi_mapped),d=l+h,d<this.config.minTotalReads)return;if(d>0&&h/d>this.config.maxFractionMultiMappedReads)return;if(e.attributes.maximum_spliced_alignment_overhang&&parseInt(e.attributes.maximum_spliced_alignment_overhang)<this.config.minSplicedAlignmentOverhang)return}if(e.attributes.num_samples_with_this_junction){if(u=parseInt(e.attributes.num_samples_with_this_junction),this.config.minSamplesWithThisJunction&&u<this.config.minSamplesWithThisJunction)return;if(this.config.maxSamplesWithThisJunction&&u>this.config.maxSamplesWithThisJunction)return;if(e.attributes.num_samples_total&&(e.attributes.percent_samples_with_this_junction=100*u/Number(e.attributes.num_samples_total),this.config.minPercentSamplesWithThisJunction&&(e.attributes.percent_samples_with_this_junction<this.config.minPercentSamplesWithThisJunction||e.attributes.percent_samples_with_this_junction>this.config.maxPercentSamplesWithThisJunction)))return}const f=this.margin,p=n,g=f+.5*p;let m=f;const w=f+p-10,b=(o+c)/2,F=(c+a)/2;let v,y,A=1;e.attributes.line_width?A=Number(e.attributes.line_width):(void 0===this.config.thicknessBasedOn||\"numUniqueReads\"===this.config.thicknessBasedOn?A=l:\"numReads\"===this.config.thicknessBasedOn?A=d:\"numSamplesWithThisJunction\"===this.config.thicknessBasedOn&&void 0!==u&&(A=u),A=1+Math.log(A+1)/Math.log(12)),void 0===this.config.bounceHeightBasedOn||\"random\"===this.config.bounceHeightBasedOn?v=(e.start+e.end)%7:\"distance\"===this.config.bounceHeightBasedOn?v=6*(e.end-e.start)/(s.referenceFrameEnd-s.referenceFrameStart):\"thickness\"===this.config.bounceHeightBasedOn&&(v=2*A),m+=p*Math.max(7-v,0)/10,y=e.attributes.color?e.attributes.color:void 0===this.config.colorBy||\"numUniqueReads\"===this.config.colorBy?l>this.config.colorByNumReadsThreshold?\"blue\":\"#AAAAAA\":\"numReads\"===this.config.colorBy?d>this.config.colorByNumReadsThreshold?\"blue\":\"#AAAAAA\":\"isAnnotatedJunction\"===this.config.colorBy?\"true\"===e.attributes.annotated_junction?\"#b0b0ec\":\"orange\":\"strand\"===this.config.colorBy?\"+\"===e.strand?\"#b0b0ec\":\"#ecb0b0\":\"motif\"===this.config.colorBy?uy.getColor(e.attributes.motif):\"#AAAAAA\";let C=\"\";e.attributes.label?C=e.attributes.label.replace(/_/g,\" \"):void 0===this.config.labelWith||\"uniqueReadCount\"===this.config.labelWith?C=l:\"totalReadCount\"===this.config.labelWith?C=d:\"numSamplesWithThisJunction\"===this.config.labelWith?void 0!==u&&(C=u):\"percentSamplesWithThisJunction\"===this.config.labelWith?void 0!==e.attributes.percent_samples_with_this_junction&&(C=e.attributes.percent_samples_with_this_junction.toFixed(0)+\"%\"):\"motif\"===this.config.labelWith&&void 0!==e.attributes.motif&&(C+=e.attributes.motif),\"uniqueReadCount\"===this.config.labelWithInParen?C+=\" (\"+l+\")\":\"totalReadCount\"===this.config.labelWithInParen?C+=\" (\"+d+\")\":\"multiMappedReadCount\"===this.config.labelWithInParen?h>0&&(C+=\" (+\"+h+\")\"):\"numSamplesWithThisJunction\"===this.config.labelWithInParen?void 0!==u&&(C+=\" (\"+u+\")\"):\"percentSamplesWithThisJunction\"===this.config.labelWithInParen?void 0!==e.attributes.percent_samples_with_this_junction&&(C+=\" (\"+e.attributes.percent_samples_with_this_junction.toFixed(0)+\"%)\"):\"motif\"===this.config.labelWithInParen&&void 0!==e.attributes.motif&&(C+=` ${e.attributes.motif}`),e.isVisible=!0,r.beginPath(),r.moveTo(o,w),r.bezierCurveTo(b,m,F,m,a,w),r.lineWidth=A,r.strokeStyle=y,r.stroke();const _=(e,t,i,n)=>{e.beginPath(),e.moveTo(t,i),e.lineTo(t-n/2,i-n),e.lineTo(t+n/2,i-n),e.lineTo(t,i),e.closePath(),e.fill()};if(e.attributes.left_shape||e.attributes.right_shape){r.fillStyle=y;const t=r.lineWidth>2?10:7;e.attributes.left_shape&&_(r,o,w,t),e.attributes.right_shape&&_(r,a,w,t)}r.fillText(C,c-r.measureText(C).width/2,(7*m+g)/8)}clickedFeatures(e){return super.clickedFeatures(e).filter((function(e){return e.isVisible&&e.attributes}))}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=[];for(let e of t){const t=\"function\"==typeof e.popupData?e.popupData(i):this.extractPopupData(e._f||e,this.getGenomeId());t&&(n.length>0&&n.push(\"<hr/><hr/>\"),Array.prototype.push.apply(n,t))}return n}dispose(){this.trackView=void 0}}const py={min:0,max:3e3,color:\"rgb(0,0,255)\"};class gy{constructor(e){e=e||py,this.max=e.max,this.min=e.min||0,this.cache=[],this.nbins=1e3,this.binsize=(this.max-this.min)/this.nbins,this.updateColor(e.color||\"rgb(0,0,255)\")}updateColor(e){const t=e.substring(4).replace(\")\",\"\").split(\",\");3===t.length&&(this.r=Number.parseInt(t[0].trim()),this.g=Number.parseInt(t[1].trim()),this.b=Number.parseInt(t[2].trim())),this.cache=[]}setMinMax(e,t){this.min=e,this.max=t,this.cache=[],this.binsize=(this.max-this.min)/this.nbins}getColor(e){if(e<this.min)return\"white\";const t=Math.floor((Math.min(this.max,e)-this.min)/this.binsize);if(void 0===this.cache[t]){const i=(ys.clamp(e,0,this.max)-0)/(this.max-0);this.cache[t]=`rgba(${this.r},${this.g},${this.b}, ${i})`}return this.cache[t]}toJson(){return{min:this.min,max:this.max,color:`rgb(${this.r},${this.g},${this.b})`}}static parse(e){const t=e.split(\",\"),i={min:Number.parseFloat(t[0]),max:Number.parseFloat(t[1]),color:`${t[2]},${t[3]},${t[4]}`};return new gy(i)}}class my extends Hl{static defaults={height:300,rowHeight:3,max:3e3,visibilityWindow:1e4};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"shoebox\",this.height=e.height||300,this.rowHeight=e.rowHeight||3,this.max=e.max||3e3,this.sampleKeys=[];for(let e=1;e<=100;e++)this.sampleKeys.push(e);const t=Object.assign({},this.config);t.format=\"shoebox\",this.featureSource=Ad(t,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))if(this.header&&this.setTrackProperties(this.header),this.config.colorScale&&this.config.colorScale.max&&this.config.colorScale.color)this.colorScale=new gy(this.config.colorScale);else{const e=this.dataRange.min,t=this.dataRange.max;this.colorScale=new gy({min:e,max:t,color:this.color})}}get color(){return this._color||\"rgb(0,0,255)\"}set color(e){this._color=e,this.colorScale&&this.colorScale.updateColor(e)}menuItemList(){const e=[];e.push(\"<hr/>\");let t=Bt(\"<div>\");return t.text(\"Set data range\"),e.push({object:t,dialog:function(){this.trackView.track.selected?this.browser.dataRangeDialog.configure(this.trackView.browser.getSelectedTrackViews()):this.browser.dataRangeDialog.configure(this.trackView),this.browser.dataRangeDialog.present(Bt(this.browser.columnContainer))}}),e}setDataRange({min:e,max:t}){this.dataRange.min=e,this.dataRange.max=t,this.colorScale.min=e,this.colorScale.max=t,this.trackView.repaintViews()}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys,height:this.rowHeight,yOffset:0}}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}draw({context:e,pixelTop:t,pixelWidth:i,pixelHeight:n,features:r,bpPerPixel:s,bpStart:o}){if(xo.fillRect(e,0,t,i,n,{fillStyle:\"rgb(255, 255, 255)\"}),r&&r.length>0){const a=this.rowHeight,c=t+n,l=o+i*s+1,h=a;for(let i of r){if(i.end<o||i.start>l)continue;const n=Math.round((i.start-o)/s),r=Math.round((i.end-o)/s),d=Math.max(1,r-n);let u=0;for(let r=i.values.length-1;r>=0;r--){const s=i.values[r],o=u*a;if(o+a<t||o>c)continue;const l=this.colorScale.getColor(s);e.fillStyle=l,e.fillRect(n,o,d,h),u++}}}}computePixelHeight(e){return e&&0!==e.length?e[0].values.length*this.rowHeight:0}clickedFeatures(e){const t=super.clickedFeatures(e),i=e.y;return t.filter((function(e){const t=e.pixelRect;return t&&i>=t.y&&i<=t.y+t.h}))}hoverText(e){const t=this.clickedFeatures(e);if(t&&t.length>0)return`${t[0].sample}: ${t[0].value}`}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){i.length>0&&(i.push(\"<hr/>\"),i.push(\"<hr/>\"));const t=e._f||e,n=\"function\"==typeof t.popupData?t.popupData(this.type,this.browser.genome.id):this.extractPopupData(t);Array.prototype.push.apply(i,n)}return i}get supportsWholeGenome(){return!1}getState(){const e=super.getState();return e.colorScale=this.colorScale.toJson(),e}}const wy=new Map([[\"ideogram\",(e,t)=>new hy(e,t)],[\"sequence\",(e,t)=>new Zd(e,t)],[\"feature\",(e,t)=>new Hd(e,t)],[\"seg\",(e,t)=>new Pf(e,t)],[\"mut\",(e,t)=>new Pf(e,t)],[\"maf\",(e,t)=>new Pf(e,t)],[\"shoebox\",(e,t)=>new my(e,t)],[\"wig\",(e,t)=>new ld(e,t)],[\"merged\",(e,t)=>new tf(e,t)],[\"alignment\",(e,t)=>new tw(e,t)],[\"interaction\",(e,t)=>new iw(e,t)],[\"interact\",(e,t)=>new iw(e,t)],[\"variant\",(e,t)=>new Yv(e,t)],[\"qtl\",(e,t)=>new ty(e,t)],[\"eqtl\",(e,t)=>new ty(e,t)],[\"gwas\",(e,t)=>new ry(e,t)],[\"arc\",(e,t)=>new ay(e,t)],[\"gcnv\",(e,t)=>new sy(e,t)],[\"junction\",(e,t)=>new fy(e,t)],[\"blat\",(e,t)=>new Vd(e,t)],[\"cnvpytor\",(e,t)=>new Gv(e,t)]]);class by{constructor(e,t){const i=(new DOMParser).parseFromString(e,\"text/xml\");this.processRootNode(i,t);const n=i.getElementsByTagName(\"Resource\"),r=i.getElementsByTagName(\"Track\"),s=r&&r.length>0,o=[];this.tracks=o;const a=new Map;Array.from(n).forEach((function(e,t){var i={url:e.getAttribute(\"path\"),indexURL:e.getAttribute(\"index\"),order:t};a.set(i.url,i),s||o.push(i)})),s&&Array.from(r).forEach((function(e){const t=e.getElementsByTagName(\"Track\");if(t&&t.length>0){const i={type:\"merged\",tracks:[]};Fy(e,i),o.push(i),Array.from(t).forEach((function(e){e.processed=!0;const t=e.getAttribute(\"id\"),n=a.get(t);n&&(i.tracks.push(n),Fy(e,n),n.autoscale=!1,i.height=n.height)}))}else if(!e.processed){const t=e.getAttribute(\"id\"),i=a.get(t);i&&(o.push(i),Fy(e,i))}}))}processRootNode(e,t){const i=e.getElementsByTagName(\"Session\");!i||i.length;const n=i.item(0),r=n.getAttribute(\"genome\"),s=n.getAttribute(\"locus\"),o=n.getAttribute(\"ucscID\");t&&t.hasOwnProperty(r)?this.genome=r:(this.reference={fastaURL:r},o&&(this.reference.id=o)),s&&(this.locus=s)}}function Fy(e,t){t.name=e.getAttribute(\"name\");const i=e.getAttribute(\"color\");i&&(t.color=\"rgb(\"+i+\")\");const n=e.getAttribute(\"altColor\");i&&(t.altColor=\"rgb(\"+n+\")\");const r=e.getAttribute(\"height\");r&&(t.height=parseInt(r));const s=e.getAttribute(\"autoScale\");s&&(t.autoscale=\"true\"===s);const o=e.getAttribute(\"autoscaleGroup\");o&&(t.autoscaleGroup=o);const a=e.getAttribute(\"windowFunction\");a&&(t.windowFunction=a);const c=e.getAttribute(\"visibilityWindow\")||e.getAttribute(\"featureVisibilityWindow\");c&&(t.visibilityWindow=c);const l=e.getAttribute(\"indexed\");l&&(t.indexed=\"true\"===l);const h=e.getAttribute(\"normalize\");h&&(t.normalize=\"true\"===h);const d=e.getElementsByTagName(\"DataRange\");if(d.length>0){const e=d.item(0);t.min=Number(e.getAttribute(\"minimum\")),t.max=Number(e.getAttribute(\"maximum\")),t.logScale=\"LOG\"===e.getAttribute(\"type\")}}class vy{constructor(e,t,i,n,r){this.genome=e,this.chr=t,this.start=i,this.end=n,this.bpPerPixel=r,this.id=s()}get center(){return(this.start+this.end)/2}get locusSearchString(){return`${this.chr}:${this.start+1}-${this.end}`}extend(e){const t=Math.min(e.start,this.start),i=Math.max(e.end,this.end),n=(i-t)/(this.end-this.start);this.start=t,this.end=i,this.bpPerPixel*=n}calculateEnd(e){return this.start+this.bpPerPixel*e}calculateCenter(e){return this.start+this.bpPerPixel*e/2}calculateBPP(e,t){return(e-this.start)/t}set(e){this.chr=e.chr,this.start=e.start,this.bpPerPixel=e.bpPerPixel}toPixels(e){return e/this.bpPerPixel}toBP(e){return this.bpPerPixel*e}shift(e){this.start+=e,this.end+=e}shiftPixels(e,t,i){const n=this.start,r=e*this.bpPerPixel;return this.start+=r,i&&this.clampStart(t),this.end=this.start+t*this.bpPerPixel,n!==this.start}clampStart(e){const t=this.genome.getChromosome(this.chr).bpStart||0;if(this.start=Math.max(t,this.start),e){const{bpLength:t}=this.genome.getChromosome(this.chr),i=t-e*this.bpPerPixel;this.start>i&&(this.start=i)}}async zoomWithScaleFactor(e,t,i,n){const r=void 0===n?this.start+this.toBP(i/2):n,s=this.start,o=this.bpPerPixel,a=this.getChromosome().bpLength,c=t<1?e.minimumBases()/i:a/i;this.bpPerPixel=t<1?Math.max(this.bpPerPixel*t,c):Math.min(this.bpPerPixel*t,c);const l=this.bpPerPixel*i;this.start=r-.5*l,this.clampStart(i),this.end=this.start+l;(s!==this.start||o!==this.bpPerPixel)&&await e.updateViews(!0)}getChromosome(){return this.genome.getChromosome(this.chr)}getMultiLocusLabelBPLengthOnly(e){const t=\"&nbsp\",i=Math.floor(this.start)+1,n=Math.round(this.start+this.bpPerPixel*e);return`${t}${this.chr}${t}${Wa(n-i)}${t}`}getMultiLocusLabelLocusOnly(e){const t=\"&nbsp\",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(e);return`${t}${i}:${n}-${r}${t}`}getMultiLocusLabel(e){const t=\"&nbsp\",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(e),s=Math.floor(this.start)+1;return`${t}${i}:${n}-${r}${t}${t}(${Wa(Math.round(this.start+this.bpPerPixel*e)-s)})${t}`}getPresentationLocusComponents(e){if(\"all\"===this.chr)return{chr:this.chr};{const t=Rt(Math.floor(this.start)+1),i=Rt(Math.round(this.start+this.bpPerPixel*e));return{chr:this.chr,start:t,end:i}}}getLocusString(){if(\"all\"===this.chr)return\"all\";return`${this.genome.getChromosomeDisplayName(this.chr)}:${Rt(Math.floor(this.start)+1)}-${Rt(Math.round(this.end))}`}description(e){console.log(` ${e||\"\"} referenceFrame - ${this.chr} bpp ${this.bpPerPixel.toFixed(3)} start ${Rt(Math.round(this.start))} end ${Rt(Math.round(this.end))} `)}overlaps(e){return this.chr===e.chr&&this.end>=e.start&&e.end>=this.start}}function yy(){return\"3.0.9\"}const Ay=\"Maximum sequence count exceeded\";class Cy{constructor(t,i){this.container=e({class:\"igv-chromosome-select-widget-container\"}),i.appendChild(this.container),this.select=document.createElement(\"select\"),this.select.setAttribute(\"name\",\"chromosome-select-widget\"),this.container.appendChild(this.select),this.select.addEventListener(\"change\",(()=>{this.select.blur(),\"\"!==this.select.value&&Ay!==this.select.value&&t.search(this.select.value)})),this.showAllChromosomes=!1!==t.config.showAllChromosomes,this.genome=t.genome}show(){this.container.style.display=\"flex\"}hide(){this.container.style.display=\"none\"}setValue(e){this.select.value=this.genome.getChromosomeDisplayName(e)}update(e){this.genome=e;const t=e.wgChromosomeNames.map((t=>e.getChromosomeDisplayName(t)))||[];if(this.showAllChromosomes&&e.chromosomeNames.length>1){const i=new Set(t);let n=0;for(let r of e.chromosomeNames){if(1e3==++n){t.push(Ay);break}i.has(r)||(r=e.getChromosomeDisplayName(r),t.push(r))}}this.select.innerHTML=\"\",e.showWholeGenomeView()&&t.unshift(\"all\");for(let i of t){const t=document.createElement(\"option\");t.setAttribute(\"value\",i),t.innerText=e.getChromosomeDisplayName(i),this.select.appendChild(t)}}}class _y{constructor(t,i){this.container=e({class:\"igv-windowsize-panel-container\"}),t.appendChild(this.container),i.on(\"locuschange\",(e=>{this.updatePanel(e)})),this.browser=i}show(){this.container.style.display=\"block\"}hide(){this.container.style.display=\"none\"}updatePanel(e){const t=this.browser.calculateViewportWidth(this.browser.referenceFrameList.length);this.container.innerText=1===e.length?Wa(Math.round(t*e[0].bpPerPixel)):\"\"}}class xy extends Ju{constructor(e,t,i,n){super(e,t,\"Select Tracks\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>multi select</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"multi-select\">\\n            <rect id=\"backdrop-copy-3\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-copy-3\" transform=\"translate(81, 427)\" fill=\"#737373\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy-2\" transform=\"translate(82, 277)\">\\n                <rect id=\"Rectangle\" fill-opacity=\"0.33\" fill=\"#CFCECE\" x=\"133\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke-opacity=\"0.32659528\" stroke=\"#CFCECE\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy\" transform=\"translate(81, 119)\" fill=\"#737373\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-17\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>multi select hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"multi-select-hover\">\\n            <rect id=\"backdrop-copy-4\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-copy-3\" transform=\"translate(81, 427)\" fill=\"#FFFFFF\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke=\"#FFFFFF\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy-2\" transform=\"translate(82, 277)\">\\n                <rect id=\"Rectangle\" fill-opacity=\"0.33\" fill=\"#CFCECE\" x=\"133\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke-opacity=\"0.33\" stroke=\"#CFCECE\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy\" transform=\"translate(81, 119)\" fill=\"#FFFFFF\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-17\" stroke=\"#FFFFFF\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n        </g>\\n    </g>\\n</svg>',!1),this.navbar=i,this.enableMultiTrackSelection=!1,this.button.addEventListener(\"mouseenter\",(e=>{!1===n&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(e=>{!1===n&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{this.setMultiTrackSelection(!this.enableMultiTrackSelection)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler)}setMultiTrackSelection(e){this.enableMultiTrackSelection=e,this.setState(this.enableMultiTrackSelection),!1===this.enableMultiTrackSelection&&this.navbar.overlayTrackButton.setVisibility(!1);for(const t of this.browser.trackViews)t.enableTrackSelection(e)}}class ky{constructor(t,i){this.browser=i,this.columnContainer=t,this.horizontalGuide=e({class:\"igv-cursor-guide-horizontal\"}),t.appendChild(this.horizontalGuide),this.verticalGuide=e({class:\"igv-cursor-guide-vertical\"}),t.appendChild(this.verticalGuide),this.addMouseHandler(i),this.setVisibility(i.config.showCursorGuide)}addMouseHandler(e){this.boundMouseMoveHandler=function(t){t.target.tagName;const{x:i,y:n}=a(t,this.columnContainer);if(this.horizontalGuide.style.top=`${n}px`,\"CANVAS\"===t.target.tagName){const n=function(e,t){for(;e.parentElement;){if(e.parentElement.classList.contains(t))return e.parentElement;e=e.parentElement}return}(t.target,\"igv-viewport\");if(n&&e.getRulerTrackView()){this.verticalGuide.style.left=`${i}px`;const r=e.root.querySelectorAll(\".igv-column\");let s;const o=n.parentElement;for(let e=0;e<r.length;e++)void 0===s&&o===r[e]&&(s=e);if(void 0!==s){const i=e.getRulerTrackView().viewports[s].mouseMove(t);if(i){const{start:e,bp:t,end:n}=i,r=(t-e)/(n-e);this.customMouseHandler&&this.customMouseHandler({start:e,bp:t,end:n,interpolant:r})}}}}}.bind(this),this.columnContainer.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandler(){this.columnContainer.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}setVisibility(e){!0===e?this.show():this.hide()}show(){this.verticalGuide.style.display=\"block\",this.horizontalGuide.style.display=\"block\"}hide(){if(this.verticalGuide.style.display=\"none\",this.horizontalGuide.style.display=\"none\",this.browser.getRulerTrackView())for(let e of this.browser.getRulerTrackView().viewports)e.$tooltip.hide()}}class Iy extends Ju{constructor(e,t){super(e,t,\"Crosshairs\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>cursor</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"cursor\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-3\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group\" transform=\"translate(5, 9)\" stroke-width=\"24\">\\n                <line x1=\"0.5\" y1=\"212.5\" x2=\"614.5\" y2=\"212.5\" id=\"Line\"></line>\\n                <line x1=\"-115.5\" y1=\"303.5\" x2=\"490.5\" y2=\"303.5\" id=\"Line-Copy\" transform=\"translate(187.5, 303.5) scale(-1, 1) rotate(90) translate(-187.5, -303.5)\"></line>\\n            </g>\\n            <circle id=\"Oval\" stroke-width=\"24\" cx=\"191.5\" cy=\"221.5\" r=\"88.5\"></circle>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>cursor hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"cursor-hover\">\\n            <rect id=\"Rectangle-Copy-5\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group-Copy-2\" transform=\"translate(5, 9)\" stroke=\"#FFFFFF\" stroke-width=\"24\">\\n                <line x1=\"0.5\" y1=\"212.5\" x2=\"614.5\" y2=\"212.5\" id=\"Line\"></line>\\n                <line x1=\"-115.5\" y1=\"303.5\" x2=\"490.5\" y2=\"303.5\" id=\"Line-Copy\" transform=\"translate(187.5, 303.5) scale(-1, 1) rotate(90) translate(-187.5, -303.5)\"></line>\\n            </g>\\n            <circle id=\"Oval\" stroke=\"#FFFFFF\" stroke-width=\"24\" cx=\"191.5\" cy=\"221.5\" r=\"88.5\"></circle>\\n        </g>\\n    </g>\\n</svg>',t.doShowCursorGuide),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowCursorGuide&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowCursorGuide&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowCursorGuide=!t.doShowCursorGuide,t.setCursorGuideVisibility(t.doShowCursorGuide),this.setState(t.doShowCursorGuide)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showCursorTrackingGuideButton)}}class Sy extends Ju{constructor(e,t){super(e,t,\"Center Line\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>centerline</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"centerline\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-2\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"6.5\" y1=\"312.5\" x2=\"618.5\" y2=\"312.5\" id=\"Line-Copy\" stroke-width=\"31\" transform=\"translate(312.5, 312.5) scale(-1, 1) rotate(90) translate(-312.5, -312.5)\"></line>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>centerline hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"centerline-hover\">\\n            <rect id=\"Rectangle-Copy-9\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"6.5\" y1=\"312.5\" x2=\"618.5\" y2=\"312.5\" id=\"Line-Copy\" stroke=\"#FFFFFF\" stroke-width=\"31\" transform=\"translate(312.5, 312.5) scale(-1, 1) rotate(90) translate(-312.5, -312.5)\"></line>\\n        </g>\\n    </g>\\n</svg>',t.config.showCenterGuide),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowCenterLine&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowCenterLine&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowCenterLine=!t.doShowCenterLine,t.setCenterLineVisibility(t.doShowCenterLine),this.setState(t.doShowCenterLine)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showCenterGuideButton)}}class Ey extends Ju{constructor(e,t){super(e,t,\"Track Labels\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>track labels</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"track-labels\" fill=\"#FFFFFF\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-27\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"group\" transform=\"translate(52.2778, 149.7248)\" stroke-width=\"24\">\\n                <path d=\"M448.444444,87.1189616 L448.444444,322.431462 L166.619398,322.431462 L19.2344421,204.775212 L166.619398,87.1189616 L448.444444,87.1189616 Z M244.028212,163.997434 C232.925565,163.997434 222.874656,168.493347 215.598982,175.760254 C208.318067,183.032394 203.815972,193.079106 203.815972,204.175675 C203.815972,215.272243 208.318067,225.318955 215.598982,232.591095 C222.874656,239.858002 232.925565,244.353915 244.028212,244.353915 C255.130858,244.353915 265.181767,239.858002 272.457442,232.591095 C279.738356,225.318955 284.240451,215.272243 284.240451,204.175675 C284.240451,193.079106 279.738356,183.032394 272.457442,175.760254 C265.181767,168.493347 255.130858,163.997434 244.028212,163.997434 Z\" id=\"backdrop\"></path>\\n                <path d=\"M495.232604,12 L495.232604,264.550423 L193.616935,264.550423 L35.4455183,138.275212 L193.616935,12 L495.232604,12 Z M168.133512,95.1660194 C156.441871,95.1660194 145.858581,99.8943121 138.197214,107.534302 C130.523695,115.18641 125.780417,125.758499 125.780417,137.434423 C125.780417,149.110347 130.523695,159.682435 138.197214,167.334543 C145.858581,174.974533 156.441871,179.702826 168.133512,179.702826 C179.825153,179.702826 190.408443,174.974533 198.06981,167.334543 C205.743329,159.682435 210.486607,149.110347 210.486607,137.434423 C210.486607,125.758499 205.743329,115.18641 198.06981,107.534302 C190.408443,99.8943121 179.825153,95.1660194 168.133512,95.1660194 Z\" id=\"hero\"></path>\\n            </g>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>track labels hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"track-labels-hover\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-29\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"group\" transform=\"translate(52.2778, 149.7248)\" fill=\"#FFFFFF\" stroke-width=\"24\">\\n                <path d=\"M448.444444,85.1189616 L448.444444,320.431462 L166.619398,320.431462 L19.2344421,202.775212 L166.619398,85.1189616 L448.444444,85.1189616 Z M244.028212,161.997434 C232.925565,161.997434 222.874656,166.493347 215.598982,173.760254 C208.318067,181.032394 203.815972,191.079106 203.815972,202.175675 C203.815972,213.272243 208.318067,223.318955 215.598982,230.591095 C222.874656,237.858002 232.925565,242.353915 244.028212,242.353915 C255.130858,242.353915 265.181767,237.858002 272.457442,230.591095 C279.738356,223.318955 284.240451,213.272243 284.240451,202.175675 C284.240451,191.079106 279.738356,181.032394 272.457442,173.760254 C265.181767,166.493347 255.130858,161.997434 244.028212,161.997434 Z\" id=\"backdrop\"></path>\\n                <path d=\"M495.232604,12 L495.232604,264.550423 L193.616935,264.550423 L35.4455183,138.275212 L193.616935,12 L495.232604,12 Z M168.133512,95.1660194 C156.441871,95.1660194 145.858581,99.8943121 138.197214,107.534302 C130.523695,115.18641 125.780417,125.758499 125.780417,137.434423 C125.780417,149.110347 130.523695,159.682435 138.197214,167.334543 C145.858581,174.974533 156.441871,179.702826 168.133512,179.702826 C179.825153,179.702826 190.408443,174.974533 198.06981,167.334543 C205.743329,159.682435 210.486607,149.110347 210.486607,137.434423 C210.486607,125.758499 205.743329,115.18641 198.06981,107.534302 C190.408443,99.8943121 179.825153,95.1660194 168.133512,95.1660194 Z\" id=\"hero\"></path>\\n            </g>\\n        </g>\\n    </g>\\n</svg>',t.config.showTrackLabels),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowTrackLabels&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowTrackLabels&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowTrackLabels=!t.doShowTrackLabels,t.setTrackLabelVisibility(t.doShowTrackLabels),this.setState(t.doShowTrackLabels)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showTrackLabelButton)}}class Ny extends Ju{constructor(e,t){super(e,t,[\"ROI\",\"Regions of Interest Table\"],ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>roi</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"roi\">\\n            <rect id=\"Rectangle-Copy-23\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <text id=\"ROI\" font-family=\"HelveticaNeue-Bold, Helvetica Neue\" font-size=\"258\" font-weight=\"bold\" fill=\"#737373\">\\n                <tspan x=\"81.445\" y=\"389\">ROI</tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>roi hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"roi-hover\">\\n            <rect id=\"Rectangle-Copy-24\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <text id=\"ROI\" font-family=\"HelveticaNeue-Bold, Helvetica Neue\" font-size=\"258\" font-weight=\"bold\" fill=\"#FFFFFF\">\\n                <tspan x=\"81.445\" y=\"389\">ROI</tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>',!1),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowROITable&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowROITable&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>this.buttonHandler(!t.doShowROITable))),this.setVisibility(!1)}buttonHandler(e){this.setState(e),this.browser.setROITableVisibility(e)}}class By extends Ju{constructor(e,t){super(e,t,\"Sample Info\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample info</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-info\">\\n            <rect id=\"Rectangle-Copy-6\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group-2\" transform=\"translate(8, 149)\">\\n                <rect id=\"Rectangle\" fill=\"#8DD3C7\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#FBB4AE\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#7FC97F\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#E41A1C\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#3F70AE\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"Group-2-Copy\" transform=\"translate(8, 251)\">\\n                <rect id=\"Rectangle\" fill=\"#E41A1C\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BC80BD\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#FFFFB3\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"Group-2-Copy-2\" transform=\"translate(314, 404) scale(-1, 1) translate(-314, -404)translate(8, 353)\">\\n                <rect id=\"Rectangle\" fill=\"#1B9E77\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BAD1E9\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#4DAF4A\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#CBF03E\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <rect id=\"Rectangle-Copy-10\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample info hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-info-hover\">\\n            <rect id=\"Rectangle-Copy-14\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-2\" transform=\"translate(314, 404) scale(-1, 1) translate(-314, -404)translate(8, 353)\">\\n                <rect id=\"Rectangle\" fill=\"#1B9E77\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BAD1E9\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#4DAF4A\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#CBF03E\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"row-1\" transform=\"translate(8, 251)\">\\n                <rect id=\"Rectangle\" fill=\"#E41A1C\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BC80BD\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#FFFFB3\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"row-0\" transform=\"translate(8, 149)\">\\n                <rect id=\"Rectangle\" fill=\"#8DD3C7\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#FBB4AE\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#7FC97F\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#E41A1C\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#3F70AE\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <rect id=\"Rectangle-Copy-15\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <rect id=\"scrim\" fill=\"#000000\" style=\"mix-blend-mode: hue;\" x=\"8\" y=\"149\" width=\"612\" height=\"306\"></rect>\\n        </g>\\n    </g>\\n</svg>',!1),this.showSampleInfo=!1,this.button.addEventListener(\"mouseenter\",(()=>{!1===this.showSampleInfo&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===this.showSampleInfo&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>{this.performClickWithState(t,void 0)}))}performClickWithState(e,t){this.showSampleInfo=void 0===t?!this.showSampleInfo:t;e.columnContainer.querySelector(\".igv-sample-info-column\").style.display=!1===this.showSampleInfo?\"none\":\"flex\",this.setState(this.showSampleInfo),e.layoutChange()}setButtonVisibility(e){this.showSampleInfo=e,this.setState(this.showSampleInfo),!0===this.showSampleInfo?this.show():this.hide()}}class My extends Ju{constructor(e,t){super(e,t,\"Sample Names\",'<svg width=\"90px\" height=\"20px\" viewBox=\"0 0 90 20\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"igv-navbar-button-group\">\\n            <rect id=\"Rectangle\" x=\"0.5\" y=\"0.5\" width=\"89\" height=\"18\" rx=\"6\"></rect>\\n            <text id=\"igv-text-button-label\" x=\"50%\" y=\"50%\" dy=\".1em\" font-family=\"Helvetica\" font-size=\"12\" font-weight=\"normal\" letter-spacing=\"-0.372\">\\n                <tspan id=\"igv-navbar-button-label\"></tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample names</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-names\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-13\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"80\" y1=\"465\" x2=\"541\" y2=\"464.5\" id=\"Line-3-Copy-3\" stroke-width=\"32\"></line>\\n            <line x1=\"80\" y1=\"312.5\" x2=\"542\" y2=\"313\" id=\"Line-3\" stroke-width=\"32\"></line>\\n            <line x1=\"80\" y1=\"158\" x2=\"541\" y2=\"158\" id=\"Line-3-Copy\" stroke-width=\"32\"></line>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample names hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-names-hover\">\\n            <rect id=\"Rectangle-Copy-18\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"80\" y1=\"465\" x2=\"541\" y2=\"464.5\" id=\"Line-3-Copy-3\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n            <line x1=\"80\" y1=\"312.5\" x2=\"542\" y2=\"313\" id=\"Line-3\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n            <line x1=\"80\" y1=\"158\" x2=\"541\" y2=\"158\" id=\"Line-3-Copy\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n        </g>\\n    </g>\\n</svg>',t.config.showSampleNames),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.showSampleNames&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.showSampleNames&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>{this.performClickWithState(t,void 0)})),!0===t.config.showSampleNameButton?this.show():this.hide()}performClickWithState(e,t){e.showSampleNames=void 0===t?!e.showSampleNames:t;e.columnContainer.querySelector(\".igv-sample-name-column\").style.display=!1===e.showSampleNames?\"none\":\"flex\",this.setState(e.showSampleNames),e.layoutChange()}}class Ry{constructor(t,i){this.parent=t,this.popover=e({class:\"igv-ui-dropdown\"}),t.appendChild(this.popover),this.popoverContent=e(),this.popover.appendChild(this.popoverContent),this.popover.style.display=\"none\",this.shim=i}configure(e){if(0===e.length)return;const t=nc(e,this.popover);for(const{object:e}of t)this.popoverContent.appendChild(e)}present(e){this.popover.style.display=\"block\";let{x:t,y:i}=a(e,this.parent);this.popover.style.left=`${t+this.shim.left}px`,this.popover.style.top=`${i+this.shim.top}px`}_present(e){this.popover.style.display=\"block\";let{x:t,y:i,width:n}=a(e,this.parent);t+=this.shim.left,i+=this.shim.top,this.popover.style.top=`${i}px`;const{width:r}=this.popover.getBoundingClientRect(),s=t+r,o=s-n;this.popover.style.left=`${s>n?t-o:t}px`}dismiss(){this.popover.style.display=\"none\"}}class Dy extends Ju{constructor(e,t){super(e,t,\"Save Image\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>save image</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"save-image\">\\n            <rect id=\"border\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"frame\" transform=\"translate(66, 66)\" fill=\"#737373\" fill-rule=\"nonzero\">\\n                <path d=\"M54.75,493 C39.69375,493 26.8046875,487.639062 16.0828125,476.917187 C5.3609375,466.195312 0,453.30625 0,438.25 L0,274 L54.75,274 L54.75,438.25 L219,438.25 L219,493 L54.75,493 Z\" id=\"Path\"></path>\\n                <path d=\"M274,493 L274,438.25 L438.25,438.25 L438.25,274 L493,274 L493,438.25 C493,453.30625 487.639062,466.195312 476.917187,476.917187 C466.195312,487.639062 453.30625,493 438.25,493 L274,493 Z\" id=\"Path\"></path>\\n                <path d=\"M0,219 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Hy(t,i,u.get(0)),!1===t.showNavigation&&this.$navigation.hide()}navbarDidResize(){const e=this.$navigation.width(),t=this.currentNavbarButtonClass();\"igv-navbar-text-button\"===t&&(this.textButtonContainerWidth=this.navbarRightContainer.getBoundingClientRect().width);const i=this.browser,n=i.isMultiLocusWholeGenomeView()||i.referenceFrameList&&mu.isWholeGenomeView(i.referenceFrameList[0].chr);n?this.windowSizePanel.hide():this.windowSizePanel.show();const{x:r,width:s}=this.navbarLeftContainer.getBoundingClientRect(),o=r+s,{x:a}=this.navbarRightContainer.getBoundingClientRect();let c;if(\"igv-navbar-text-button\"===t&&a-o<8)c=\"igv-navbar-icon-button\";else if(this.textButtonContainerWidth&&\"igv-navbar-icon-button\"===t){e-o-this.textButtonContainerWidth>8&&(c=\"igv-navbar-text-button\")}let l;c&&t!==c&&(this.currentClass=c,this.browser.fireEvent(\"navbar-resize\",[c])),l=n?\"igv-zoom-widget-hidden\":e>860?\"igv-zoom-widget\":\"igv-zoom-widget-900\",Bt(this.zoomWidget.zoomContainer).removeClass(),Bt(this.zoomWidget.zoomContainer).addClass(l)}setCenterLineButtonVisibility(e){e?this.centerLineButton.setVisibility(!e):this.centerLineButton.setVisibility(this.config.showCenterGuideButton)}setCursorGuideVisibility(e){e?this.cursorGuide.show():this.cursorGuide.hide()}updateGenome(e){let t=e.id&&e.id.length<20?e.id:`${e.id.substring(0,8)}...${e.id.substring(e.id.length-8)}`;this.$current_genome.text(t),this.$current_genome.attr(\"title\",e.description);!1!==this.config.showChromosomeWidget&&!1!==e.showChromosomeWidget&&e.chromosomeNames&&e.chromosomeNames.length>1?(this.chromosomeSelectWidget.update(e),this.chromosomeSelectWidget.show()):this.chromosomeSelectWidget.hide()}updateLocus(e,t){this.$searchInput&&this.$searchInput.val(e),this.chromosomeSelectWidget&&(this.chromosomeSelectWidget.select.value=t)}currentNavbarButtonClass(){return this.currentClass}setEnableTrackSelection(e){this.multiTrackSelectButton.setMultiTrackSelection(e)}getEnableTrackSelection(){return this.multiTrackSelectButton.enableMultiTrackSelection}hide(){this.$navigation.hide()}show(){this.$navigation.show()}}const Oy=(e,t)=>{const i=0===e?t.nextElementSibling:t.previousElementSibling;t.remove(),i.remove()},Uy=t=>{const i=e({class:\"igv-column-shim\"});Ya(i,t);const 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Vy=function(t,i){this.button=e({class:\"igv-navbar-button\"}),t.appendChild(this.button),this.button.textContent=\"circular view\",this.button.addEventListener(\"click\",(()=>{i.circularViewVisible=!i.circularViewVisible})),this.browser=i,this.setVisibility(i.config.showCircularViewButton),this.setState(i.circularViewVisible)};Vy.prototype.setVisibility=function(e){!0===e?this.show():this.hide()},Vy.prototype.setState=function(e){!0===e?this.button.classList.add(\"igv-navbar-button-clicked\"):this.button.classList.remove(\"igv-navbar-button-clicked\")},Vy.prototype.show=function(){this.button.style.display=\"block\",this.setState(this.browser.circularViewVisible)},Vy.prototype.hide=function(){this.button.style.display=\"none\"};class jy{constructor(t,i){this.browser=t,this.container=e({class:\"igv-roi-menu\"}),i.appendChild(this.container);const n=e();this.container.appendChild(n),u(n,(()=>this.container.style.display=\"none\")),this.body=e(),this.container.appendChild(this.body),this.container.style.display=\"none\"}async present(e,t,i,n,r,s){const o=this.menuItems(e,t,i,n,r,s);this.browser.menuPopup.presentTrackContextMenu(i,o)}menuItems(e,t,i,n,r,s){const o=e.name?[`<b>${e.name}</b><br/>`]:[];return\"name\"in t&&o.push(`<b>ROI Set: ${t.name}</b>`),o.length>0&&o.push(\"<hr/>\"),t.isUserDefined&&o.push({label:\"Set description ...\",click:()=>{const t={label:\"Description\",value:e.name||\"\",callback:()=>{const t=this.browser.inputDialog.value||\"\";e.name=t.trim(),this.browser.roiManager.repaintTable()}};this.browser.inputDialog.present(t,i)}}),Xa()&&e.end-e.start<1e6&&o.push({label:\"Copy reference sequence\",click:async()=>{this.container.style.display=\"none\";let t=await this.browser.genome.getSequence(e.chr,e.start,e.end);t||(t=\"Unknown sequence\");try{await navigator.clipboard.writeText(t)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),e.end-e.start<=25e3&&o.push({label:\"BLAT reference sequence\",click:async()=>{this.container.style.display=\"none\";const{chr:t,start:i,end:n}=e;let r=await this.browser.genome.getSequence(t,i,n);if(r){const e=`blat: ${t}:${i+1}-${n}`,s=`blat: ${t}:${i+1}-${n}`;jd({sequence:r,browser:this.browser,name:e,title:s})}}}),t.isUserDefined&&o.push(\"<hr/>\",{label:\"Delete\",click:async()=>{t.removeFeature(e);const i=await t.getAllFeatures();0===Object.keys(i).length&&n.deleteUserDefinedROISet(),n.deleteRegionWithKey(s.dataset.region,r),n.repaintTable()}}),o}dispose(){this.container.innerHTML=\"\"}}class Wy extends Pd{constructor(e){const t={browser:e,parent:e.columnContainer,headerTitle:\"Regions of 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n=e({class:\"igv-roi-table-button\"});this._footerDOM.appendChild(n),n.id=\"igv-roi-hide-show-button\",n.textContent=\"Hide all ROIs\",this.toggleROIButton=n,this.boundToggleDisplayButtonHandler=function(e){e.preventDefault(),e.stopPropagation(),this.browser.roiManager.toggleROIs()}.bind(this),this.toggleROIButton.addEventListener(\"click\",this.boundToggleDisplayButtonHandler)}setROIVisibility(e){const t=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let i=0;i<t.length;i++){const n=t[i];!1===e?$y(n,0):n.style.backgroundColor=n.dataset.color}this.toggleROIButton.textContent=!1===e?\"Show all ROIs\":\"Hide all ROIs\"}setTableRowSelectionState(e){super.setTableRowSelectionState(e);const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\");if(t.length>0&&t.length<2){const{locus:e}=Jy(t[0].dataset.region),{chr:i,start:n,end:r}=ey(e,this.browser.isSoftclipped());Gy(this.copySequenceButton,r-n<1e6)}else Gy(this.copySequenceButton,!1)}dispose(){document.removeEventListener(\"click\",this.boundGotoButtonHandler),document.removeEventListener(\"click\",this.boundCopySequenceButtonHandler),document.removeEventListener(\"click\",this.boundToggleDisplayButtonHandler),this.browser.roiTableControl.buttonHandler(!1),super.dispose()}static getColumnFormatConfiguration(e){return!0===e?[{label:\"Chr\",width:\"20%\"},{label:\"Start\",width:\"15%\"},{label:\"End\",width:\"15%\"},{label:\"Description\",width:\"30%\"},{label:\"ROI Set\",width:\"20%\"}]:[{label:\"Chr\",width:\"25%\"},{label:\"Start\",width:\"20%\"},{label:\"End\",width:\"20%\"},{label:\"Description\",width:\"35%\"}]}static gotoButtonHandler(e){e.stopPropagation();const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\"),i=[];for(let e of t){const{locus:t}=Jy(e.dataset.region);i.push(t)}for(let e of this.tableDOM.querySelectorAll(\".igv-roi-table-row\"))e.classList.remove(\"igv-roi-table-row-selected\");this.setTableRowSelectionState(!1),i.length>0&&this.browser.search(i.join(\" \"))}}function Gy(e,t){e.style.pointerEvents=t?\"auto\":\"none\",e.style.color=ro(t?\"licorice\":\"silver\"),e.style.borderColor=ro(t?\"licorice\":\"silver\")}function $y(e,t){const i=window.getComputedStyle(e).backgroundColor.match(/[\\d.]+/g);3===i.length&&i.push(1),i[3]=t,e.style.backgroundColor=`rgba(${i.join(\", \")})`}class Ky{constructor(e){this.browser=e,this.roiMenu=new jy(e,e.columnContainer),this.roiTable=new Wy(e,e.columnContainer),this.top=0,this.roiSets=[],this.boundLocusChangeHandler=Yy.bind(this),e.on(\"locuschange\",this.boundLocusChangeHandler);this.observer=new MutationObserver((()=>{const t=e.findTracks((e=>new Set([\"ideogram\",\"ruler\"]).has(e.type))),[i,n]=t.map((e=>e.trackView.viewports[0].$viewport.get(0))).map((e=>function(e){const t=window.getComputedStyle(e),i=parseInt(t.marginTop),n=parseInt(t.marginBottom),{top:r,bottom:s,height:o}=e.getBoundingClientRect();return{top:Math.floor(r)-i,bottom:Math.floor(s)+n,height:Math.floor(o)+i+n}}(e))),r=i?i.height:0,s=n?n.height:0,o=e.columnContainer.querySelectorAll(\".igv-roi-region\");if(o)for(const e of o)e.style.marginTop=`${r+s+-.5}px`})),this.observer.observe(e.columnContainer,{attributes:!0,childList:!0,subtree:!0})}async reset(){this.roiSets.length>0&&this.browser.roiTableControl.setVisibility(!0);const e=this.roiSets.map((e=>this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e})));e.length>0&&await Promise.all(e);const t=await this.getTableRecords();if(this.roiTable.renderTable(t),this.roiSets.length>0){const e=this.roiSets[0].isVisible;this.roiTable.setROIVisibility(e)}}async loadROI(e,t){const i=Array.isArray(e)?e:[e];for(let e of i)!e.name&&e.url&&(e.name=await ja(e.url)),e.url&&!e.format&&(e.format=await am(e)),this.roiSets.push(new ku(e,t));await this.reset()}clearROIs(){this.roiTable.clearTable();const e=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let t of e)t.remove();for(let e of this.roiSets)e.dispose();this.roiSets=[]}async getTableRecords(){const e=[];for(let t of this.roiSets){const i=t.name||\"\",n=await t.getAllFeatures();for(let t of Object.keys(n))for(let r of n[t])e.push({setName:i,feature:r})}return e}presentTable(){this.roiTable.present()}async repaintTable(){const e=await this.getTableRecords();this.roiTable.renderTable(e)}dismissTable(){this.roiTable.dismiss()}roiTableIsVisible(){return this.roiTable.isVisible()}async updateUserDefinedROISet(e){let t=await this.getUserDefinedROISet();void 0===t&&(t=this.initializeUserDefinedROISet()),t.addFeature(e),this.setROITableButtonVisibility(!0),await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t});const i=await this.getTableRecords();this.roiTable.renderTable(i)}setROITableButtonVisibility(e){this.browser.roiTableControl.setVisibility(e)}toggleROIs(){const e=!this.roiSets[0].isVisible;this.roiTable.setROIVisibility(e);for(const t of this.roiSets)t.isVisible=e}async renderAllROISets(){for(let e of this.roiSets)await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e})}async renderROISet({browser:e,pixelTop:t,roiSet:i}){const n=e.columnContainer.querySelectorAll(\".igv-column\");for(let r=0;r<n.length;r++){let{chr:s,start:o,end:a,bpPerPixel:c}=e.referenceFrameList[r];const l=n[r].querySelectorAll(\".igv-roi-region\");for(let e of l){const t=e.dataset.region,{chr:i,start:n,end:r}=Jy(t);(i!==s||r<o||n>a)&&e.remove()}const h=await i.getFeatures(s,o,a);if(h)for(let l of h){const h=Xy(s,l.start,l.end),{x:d,width:u}=Iu(Math.max(o,l.start),Math.min(a,l.end),o,c),f=n[r].querySelector(Zy(h));if(f)f.style.left=`${d}px`,f.style.width=`${u}px`;else{const s=this.createRegionElement(e.columnContainer,t,d,u,i,h,l);n[r].appendChild(s)}}}}createRegionElement(t,i,n,r,s,o,c){const l=e({class:\"igv-roi-region\"});l.style.top=`${i}px`,l.style.left=`${n}px`,l.style.width=`${r}px`,l.style.backgroundColor=s.color,l.dataset.color=s.color,l.dataset.region=o;const h=e();return l.appendChild(h),h.style.backgroundColor=s.headerColor,h.addEventListener(\"click\",(e=>{e.preventDefault(),e.stopPropagation(),a(e,t),this.roiMenu.present(c,s,e,this,t,l)})),l}renderSVGContext(e,t,{deltaX:i,deltaY:n}){for(const r of e.querySelectorAll(\".igv-roi-region\")){const{x:e,y:s,width:o,height:a}=r.getBoundingClientRect();t.fillStyle=r.style.backgroundColor,t.fillRect(e-i,s+n,o,a);const c=r.querySelector(\"div\"),{x:l,y:h,width:d,height:u}=c.getBoundingClientRect();t.fillStyle=c.style.backgroundColor,t.fillRect(l-i,h+n,d,u)}}getUserDefinedROISet(){return this.roiSets.find((e=>!0===e.isUserDefined))}deleteUserDefinedROISet(){this.roiSets=this.roiSets.filter((e=>!0!==e.isUserDefined))}initializeUserDefinedROISet(){const e=new ku({name:\"user defined\",isUserDefined:!0,features:[]},this.browser.genome);return this.roiSets.push(e),e}async deleteRegionWithKey(e,t){t.querySelectorAll(Zy(e)).forEach((e=>e.remove()));0===(await this.getTableRecords()).length&&(this.browser.roiTableControl.buttonHandler(!1),this.setROITableButtonVisibility(!1))}toJSON(){return this.roiSets.map((e=>e.toJSON()))}dispose(){this.browser.off(\"locuschange\",this.boundLocusChangeHandler);const e=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let t of e)t.remove();this.roiMenu&&this.roiMenu.dispose(),this.roiTable&&this.roiTable.dispose();for(let e of this.roiSets)e.dispose();for(let e of Object.keys(this))this[e]=void 0}}function Yy(){this.renderAllROISets()}function Xy(e,t,i){return`${e}-${t}-${i}`}function Zy(e){return`[data-region=\"${e}\"]`}function Jy(e){let t=e.split(\"-\"),i=parseInt(t.pop()),n=parseInt(t.pop()),r=t.join(\"-\");return{chr:r,start:n,end:i,locus:`${r}:${n}-${i}`,bedRecord:`${r}\\t${n}\\t${i}`}}class eA{constructor(e,t){this.name=e.name,this.featureSource=e.featureSource||Ad(e,t),this.color=e.color||_u}async getFeatures(e,t,i){return this.featureSource.getFeatures({chr:e,start:t,end:i})}draw(e){const{context:t,bpPerPixel:i,bpStart:n,pixelTop:r,pixelHeight:s,pixelWidth:o,features:a}=e;if(!a)return;const c=n+o*i+1;for(let{start:e,end:o}of a){if(o<n)continue;if(e>c)break;const{x:a,width:l}=Iu(e,o,n,i);xo.fillRect(t,a,r,l,s,{fillStyle:this.color})}}}class tA{aliasRecordCache=new Map;constructor(e,t,i){(t=t||{}).url=e,this.reader=new Zh(t,i)}async preload(e){await this.reader.preload();for(let t of e)await this.search(t)}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}async search(e){if(!this.aliasRecordCache.has(e)){const t=await this.reader.search(e);if(t)for(let e of Object.keys(t))\"start\"!==e&&\"end\"!==e&&this.aliasRecordCache.set(t[e],t)}return this.aliasRecordCache.get(e)}async getChromosomeNames(){return await this.reader.loadHeader(),Array.from(this.reader.chrNames)}}class iA{aliasRecordCache=new Map;constructor(e,t,i){this.aliasURL=e,this.config=t,this.genome=i}async preload(){return this.loadAliases()}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}async loadAliases(){const e=await Qs.loadString(this.aliasURL,Ua(this.config)),t=Dt(e),i=t[0];i.startsWith(\"#\")&&(this.headings=i.substring(1).split(\"\\t\").map((e=>e.trim())),this.altNameSets=this.headings.slice(1));const n=this.genome.chromosomeNames?new Set(this.genome.chromosomeNames):new Set;for(let e of t)if(!e.startsWith(\"#\")&&e.length>0){const t=e.split(\"\\t\");let i=t.find((e=>n.has(e)));i||(i=t[0]);const r={chr:i};for(let e=0;e<t.length;e++){r[this.headings?this.headings[e]:e]=t[e],this.aliasRecordCache.set(t[e],r)}this.aliasRecordCache.set(i.toLowerCase(),r),this.aliasRecordCache.set(i.toUpperCase(),r)}}async search(e){return 0===this.aliasRecordCache.size&&await this.loadAliases(),this.aliasRecordCache.get(e)}}class nA{constructor(e,t,i,n){this.start=e,this.end=t,this.name=i,this.stain=0,\"acen\"===n?this.type=\"c\":(this.type=n.charAt(1),\"p\"===this.type&&(this.stain=parseInt(n.substring(4))))}}class rA{cytobandMap=new Map;constructor(e,t,i){(t=t||{}).url=e,this.source=new od(t,i)}async getCytobands(e){if(this.cytobandMap.has(e))return this.cytobandMap.get(e);{let t=await this.#k(e);return t||(t=[]),this.cytobandMap.set(e,t),t}}async#k(e){return(await this.source.getFeatures({chr:e})).map((e=>new nA(e.start,e.end,e.name,e.gieStain)))}}class sA{cytobands=new Map;constructor(e,t){this.url=e,this.config=t}async getCytobands(e){return 0===this.cytobands.size&&await this.#I(),this.cytobands.get(e)}async#I(){let e,t;if(Ga(this.url)){const t=vs(this.url);e=\"\";const i=t.length;for(let n=0;n<i;n++)e+=String.fromCharCode(t[n])}else e=await Qs.loadString(this.url,Ua(this.config));let i=[];const n=Dt(e);for(let e of n){const n=e.split(\"\\t\"),r=n[0];if(t||(t=r),r!==t&&(this.cytobands.set(t,i),i=[],t=r),5===n.length){const e=parseInt(n[1]),t=parseInt(n[2]),r=n[3],s=n[4];i.push(new nA(e,t,r,s))}}}async getChromosomeNames(){return 0===this.cytobands.size&&await this.#I(),Array.from(this.cytobands.keys())}async getChromosomes(){0===this.cytobands.size&&await this.#I();const e=[];let t=0;for(let[i,n]of this.cytobands.entries())e.push(new lc(i,t++,n[n.length-1].end));return e}}class oA{aliasRecordCache=new Map;constructor(e,t){this.genomeID=e,this.update(e,t)}async preload(){}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}update(e,t){if(t){const i=[];for(let n of t){if(this.aliasRecordCache.has(n))continue;let t=!1;const r={chr:n};if(i.push(r),n.startsWith(\"gi|\")){const e=oA.getNCBIName(n);r[\"ncbi-gi-versioned\"]=e;const t=e.lastIndexOf(\".\");if(t>0){const e=e.substring(0,t);r[\"ncbi-gi\"]=e}}else{if(e.startsWith(\"hg\")||e.startsWith(\"GRCh\")||\"1kg_ref\"===e||\"b37\"===e)switch(n){case\"23\":r.ucsc=\"chrX\",t=!0;break;case\"24\":r.ucsc=\"chrY\",t=!0;break;case\"chrX\":r.ncbi=\"23\",t=!0;break;case\"chrY\":r.ncbi=\"24\",t=!0}else if(e.startsWith(\"mm\")||e.startsWith(\"GRCm\")||e.startsWith(\"rheMac\"))switch(n){case\"21\":r.ucsc=\"chrX\",t=!0;break;case\"22\":r.ucsc=\"chrY\",t=!0;break;case\"chrX\":r.ncbi=\"21\",t=!0;break;case\"chrY\":r.ncbi=\"22\",t=!0}if(t)continue;\"chrM\"===n?r.ncbi=\"MT\":\"MT\"===n?r.ucsc=\"chrM\":n.toLowerCase().startsWith(\"chr\")?r.ncbi=n.substring(3):Number.isInteger(Number(n))&&(r.ucsc=\"chr\"+n)}}for(let e of i){for(let t of Object.values(e))this.aliasRecordCache.set(t,e);this.aliasRecordCache.set(e.chr.toLowerCase(),e),this.aliasRecordCache.set(e.chr.toUpperCase(),e)}}}search(e){return this.aliasRecordCache.get(e)}static getNCBIName(e){const t=e.split(\"\\\\|\");return t[t.length-1]}}class aA{#S;static async createGenome(e,t){const i=new aA(e,t);return await i.init(),i}constructor(e,t){this.config=e,this.browser=t,this.id=e.id||function(e){return void 0!==e.id?e.id:e.fastaURL&&Mt(e.fastaURL)&&!e.fastaURL.startsWith(\"data:\")?e.fastaURL:e.fastaURL&&e.fastaURL.name?e.fastaURL.name:\"\"}(e),this.name=e.name,this.nameSet=e.nameSet}async init(){const e=this.config;if(this.sequence=await Nc(e,this.browser),e.chromSizesURL?this.chromosomes=await async function(e){const t=new Map;let i;if(Ga(e)){let t=vs(e);i=\"\";for(let e of t)i+=String.fromCharCode(e)}else i=await Qs.load(e,{});const n=Fc(i);let r=0;for(let e of n){const i=e.split(\"\\t\");if(i.length>1){const e=Number.parseInt(i[1]);t.set(i[0],new lc(i[0],r++,e))}}return t}(e.chromSizesURL):this.chromosomes=this.sequence.chromosomes||new Map,this.chromosomes.size>0&&(this.chromosomeNames=Array.from(this.chromosomes.keys())),e.chromAliasBbURL?(this.chromAlias=new tA(e.chromAliasBbURL,Object.assign({},e),this),this.chromosomeNames||(this.chromosomeNames=await this.chromAlias.getChromosomeNames())):e.aliasURL?this.chromAlias=new iA(e.aliasURL,Object.assign({},e),this):this.chromosomeNames&&(this.chromAlias=new oA(this.id,this.chromosomeNames)),e.cytobandBbURL)this.cytobandSource=new rA(e.cytobandBbURL,Object.assign({},e),this),this.chromosomeNames||(this.chromosomeNames=await this.cytobandSource.getChromosomeNames());else if(e.cytobandURL&&(this.cytobandSource=new sA(e.cytobandURL,Object.assign({},e)),this.chromosomeNames||(this.chromosomeNames=await this.cytobandSource.getChromosomeNames()),0===this.chromosomes.size)){const e=await this.cytobandSource.getChromosomes();for(let t of e)this.chromosomes.set(e.name,e)}if(!1!==e.wholeGenomeView&&this.chromosomes.size>0&&(e.chromosomeOrder?Array.isArray(e.chromosomeOrder)?this.#S=e.chromosomeOrder:this.#S=e.chromosomeOrder.split(\",\").map((e=>e.trim())):this.#S=function(e){const t=[];let i,n=1;for(let r of e.values()){if(i){if(r.bpLength<i/100)continue;i=((n-1)*i+r.bpLength)/n,t.push(r.name)}else i=r.bpLength,t.push(r.name);n++}return t}(this.chromosomes),await this.chromAlias.preload(this.#S)),this.wholeGenomeView=!1!==e.wholeGenomeView&&this.#S&&this.chromosomes.size>1,this.wholeGenomeView){const e=this.#S.reduce(((e,t)=>e+this.chromosomes.get(t).bpLength),0);this.chromosomes.set(\"all\",new lc(\"all\",0,e))}}get description(){return this.config.description||`${this.id}\\n${this.name}`}get infoURL(){return this.config.infoURL}showWholeGenomeView(){return this.wholeGenomeView}toJSON(){return Object.assign({},this.config,{tracks:void 0})}get initialLocus(){return this.config.locus?this.config.locus:this.getHomeChromosomeName()}getHomeChromosomeName(){return this.showWholeGenomeView()&&this.chromosomes.has(\"all\")?\"all\":this.chromosomeNames[0]}getChromosomeName(e){return this.chromAlias?this.chromAlias.getChromosomeName(e,this.chromosomes.keys()):e}getChromosomeDisplayName(e){return this.nameSet&&this.chromAlias&&this.chromAlias.getChromosomeAlias(e,this.nameSet)||e}getChromosome(e){return this.chromAlias&&(e=this.chromAlias.getChromosomeName(e)),this.chromosomes.get(e)}async loadChromosome(e){if(this.chromAlias){const t=await this.chromAlias.search(e);t&&(e=t.chr)}if(!this.chromosomes.has(e)){let t;const i=await this.sequence.getSequenceRecord(e);i&&(t=new lc(e,0,i.bpLength)),this.chromosomes.set(e,t)}return this.chromosomes.get(e)}async getAliasRecord(e){if(this.chromAlias)return this.chromAlias.search(e)}async getCytobands(e){if(this.cytobandSource){const t=this.getChromosomeName(e);return await this.cytobandSource.getCytobands(t)}}getChromosomes(){return this.chromosomes}get wgChromosomeNames(){return this.#S?this.#S.slice():void 0}get showChromosomeWidget(){return this.config.showChromosomeWidget}getGenomeCoordinate(e,t){var i=this.getCumulativeOffset(e);if(void 0!==i)return i+t}getChromosomeCoordinate(e){let t;void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=computeCumulativeOffsets.call(this));let i=0;for(let n of this.#S){const r=this.cumulativeOffsets[n];if(r>e){return{chr:t,position:e-i}}t=n,i=r}return{chr:this.#S[this.#S.length-1],position:0}}getCumulativeOffset(e){void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=function(){let e={},t=0;for(let i of this.#S){e[i]=Math.floor(t);t+=this.getChromosome(i).bpLength}return e}.call(this));const t=this.getChromosomeName(e);return this.cumulativeOffsets[t]}getGenomeLength(){if(!this.bpLength){let e=0;for(let t of this.#S){e+=this.chromosomes.get(t).bpLength}this.bpLength=e}return this.bpLength}async getSequence(e,t,i){return e=this.getChromosomeName(e),this.sequence.getSequence(e,t,i)}getSequenceInterval(e,t,i){return\"function\"==typeof this.sequence.getSequenceInterval?this.sequence.getSequenceInterval(e,t,i):void 0}}class cA{constructor(){this.clear()}clear(){this.phenotypeColors=new Map,this.snps=new Set,this.qtl=null}isEmpty(){return 0===this.phenotypeColors.size&&0===this.snps.size&&null===this.qtl}addSnp(e){e=e.toUpperCase(),this.snps.add(e)}addPhenotype(e){e=e.toUpperCase();const t=this.phenotypeColors.size;if(!this.phenotypeColors.has(e.toUpperCase())){const i=t<lA.length?lA[t]:_s.randomRGB(0,255);this.phenotypeColors.set(e.toUpperCase(),i)}}hasSnp(e){return e&&this.snps.has(e.toUpperCase())}hasPhenotype(e){return e&&this.phenotypeColors.has(e.toUpperCase())}hasQTL(e){return this.qtls.has(e)}colorForGene(e){return e?this.phenotypeColors.get(e.toUpperCase()):\"black\"}toJSON(){const e={};return this.phenotypeColors.size>0&&(e.phenotypes=Array.from(this.phenotypeColors.keys())),this.snps.size>0&&(e.snps=Array.from(this.snps)),this.qtl&&(e.qtl=this.qtl),e}static fromJSON(e){const t=new cA;if(e.phenotypes)for(let i of e.phenotypes)t.addPhenotype(i);if(e.snps)for(let i of e.snps)t.addSnp(i);return e.qtl&&(t.qtl=e.qtl),t}}const lA=[];lA.push(\"rgb(228,26,28)\"),lA.push(\"rgb(55,126,184)\"),lA.push(\"rgb(77,175,74)\"),lA.push(\"rgb(166,86,40)\"),lA.push(\"rgb(152,78,163)\"),lA.push(\"rgb(255,127,0)\"),lA.push(\"rgb(247,129,191)\"),lA.push(\"rgb(255,255,51)\"),lA.push(\"rgb(102,194,165)\"),lA.push(\"rgb(252,141,98)\"),lA.push(\"rgb(141, 160, 203)\"),lA.push(\"rgb(231, 138, 195)\"),lA.push(\"rgb(166, 216, 84)\"),lA.push(\"rgb(255, 217, 47)\"),lA.push(\"rgb(229, 196, 148)\"),lA.push(\"rgb( 141, 211, 199)\"),lA.push(\"rgb(255, 255, 179)\"),lA.push(\"rgb(190, 186, 218)\"),lA.push(\"rgb(251, 128, 114)\"),lA.push(\"rgb(128, 177, 211)\"),lA.push(\"rgb(253, 180, 98)\"),lA.push(\"rgb(179, 222, 105)\"),lA.push(\"rgb(252, 205, 229)\"),lA.push(\"rgb(188, 128, 189)\"),lA.push(\"rgb(204, 235, 197)\"),lA.push(\"rgb(255, 237, 111)\");class hA{constructor(t){this.parent=t,this.container=e({class:\"igv-ui-generic-dialog-container\"}),t.appendChild(this.container);const n=e({class:\"igv-ui-generic-dialog-header\"});this.container.appendChild(n),this.label=e({class:\"igv-ui-generic-dialog-one-liner\"}),this.container.appendChild(this.label),this.label.text=\"Unlabeled\",this.input_container=e({class:\"igv-ui-generic-dialog-input\"}),this.container.appendChild(this.input_container);let r='<input type=\"range\" id=\"igv-slider-dialog-input\" name=\"igv-slider-dialog-input\" />';this._input=document.createRange().createContextualFragment(r).firstChild,this.input_container.appendChild(this._input),r='<output id=\"igv-slider-dialog-output\" name=\"igv-slider-dialog-output\" for=\"igv-slider-dialog-input\"></output>',this._output=document.createRange().createContextualFragment(r).firstChild,this.input_container.appendChild(this._output);const s=e({class:\"igv-ui-generic-dialog-ok-cancel\"});this.container.appendChild(s),this.ok=e(),s.appendChild(this.ok),this.ok.textContent=\"OK\",this.cancel=e(),s.appendChild(this.cancel),this.cancel.textContent=\"Cancel\",i(this.container),this._input.addEventListener(\"input\",(()=>{const e=parseFloat(this._input.value)/this._scaleFactor;this.callback(e),this._output.value=`${e.toFixed(2)}`}),!1),this.ok.addEventListener(\"click\",(()=>{if(\"function\"==typeof this.callback){const e=parseFloat(this._input.value)/this._scaleFactor;this.callback(e),this.callback=void 0}this._input.value=void 0,i(this.container)}));const o=()=>{this._input.value=void 0,i(this.container)};this.cancel.addEventListener(\"click\",o),u(n,o),p(this.container,n)}get value(){return Ea.sanitize(this._input.value)}present(e,t){this.label.textContent=e.label,this._scaleFactor=e.scaleFactor;const[i,r,s]=[e.min,e.max,e.value].map((e=>Math.floor(this._scaleFactor*e).toString()));this._input.min=i,this._input.max=r,this._input.value=s;const o=parseFloat(s)/this._scaleFactor;this._output.value=`${o.toFixed(2)}`,this.callback=e.callback||e.click,n(this.container),this.clampLocation(t.clientX,t.clientY)}clampLocation(e,t){const{width:i,height:n}=this.container.getBoundingClientRect(),r=window.innerHeight,s=window.innerWidth,o=Math.min(r-n,t),a=Math.min(s-i,e);this.container.style.left=`${a}px`,this.container.style.top=`${o}px`}}class dA{qtlSelections=new cA;constructor(t,i){this.config=t,this.guid=s(),this.namespace=\".browser_\"+this.guid,this.parent=i;let n=i.shadowRoot;if(!n){n=i.attachShadow({mode:\"open\"});const e=new CSSStyleSheet;e.replaceSync('.igv-ui-dropdown {\\n  cursor: default;\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  z-index: 2048;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: 1px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div {\\n  overflow-y: auto;\\n  overflow-x: hidden;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div > div {\\n  padding: 4px;\\n  width: 100%;\\n  overflow-x: hidden;\\n  text-overflow: ellipsis;\\n  white-space: nowrap;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: 1px;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div > div:last-child {\\n  border-bottom-color: transparent;\\n  border-bottom-width: 0;\\n}\\n.igv-ui-dropdown > div > div:hover {\\n  cursor: pointer;\\n  background-color: rgba(0, 0, 0, 0.04);\\n}\\n\\n.igv-ui-popover {\\n  cursor: default;\\n  position: absolute;\\n  z-index: 2048;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: 1px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  background-color: white;\\n}\\n.igv-ui-popover > div:first-child {\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-width: 0;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-popover > div:first-child > div:first-child {\\n  margin-left: 4px;\\n}\\n.igv-ui-popover > div:first-child > div:last-child {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-popover > div:first-child > div:last-child:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-popover > div:last-child {\\n  user-select: text;\\n  overflow-y: auto;\\n  overflow-x: hidden;\\n  max-height: 400px;\\n  max-width: 800px;\\n  background-color: white;\\n  border-bottom-width: 0;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n}\\n.igv-ui-popover > div:last-child > div {\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  min-width: 220px;\\n  overflow-x: hidden;\\n  text-overflow: ellipsis;\\n  white-space: nowrap;\\n}\\n.igv-ui-popover > div:last-child > div > span {\\n  font-weight: bolder;\\n}\\n.igv-ui-popover > div:last-child hr {\\n  width: 100%;\\n}\\n\\n.igv-ui-alert-dialog-container {\\n  box-sizing: content-box;\\n  position: absolute;\\n  z-index: 2048;\\n  top: 50%;\\n  left: 50%;\\n  width: 400px;\\n  height: 200px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  outline: none;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 15px;\\n  font-weight: 400;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-ui-alert-dialog-container > div:first-child {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-alert-dialog-container > div:first-child div:first-child {\\n  padding-left: 8px;\\n}\\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body {\\n  -webkit-user-select: text;\\n  -moz-user-select: text;\\n  -ms-user-select: text;\\n  user-select: text;\\n  color: #373737;\\n  width: 100%;\\n  height: calc(100% - 24px - 64px);\\n  overflow-y: scroll;\\n}\\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body .igv-ui-alert-dialog-body-copy {\\n  margin: 16px;\\n  width: auto;\\n  height: auto;\\n  overflow-wrap: break-word;\\n  word-break: break-word;\\n  background-color: white;\\n  border: unset;\\n}\\n.igv-ui-alert-dialog-container > div:last-child {\\n  width: 100%;\\n  margin-bottom: 10px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-ui-alert-dialog-container > div:last-child div {\\n  margin: unset;\\n  width: 40px;\\n  height: 30px;\\n  line-height: 30px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  border-color: #2B81AF;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-ui-alert-dialog-container > div:last-child div:hover {\\n  cursor: pointer;\\n  border-color: #25597f;\\n  background-color: #25597f;\\n}\\n\\n.igv-ui-color-swatch {\\n  position: relative;\\n  box-sizing: content-box;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: wrap;\\n  justify-content: center;\\n  align-items: center;\\n  width: 32px;\\n  height: 32px;\\n  border-style: solid;\\n  border-width: 2px;\\n  border-color: white;\\n  border-radius: 4px;\\n}\\n\\n.igv-ui-color-swatch:hover {\\n  border-color: dimgray;\\n}\\n\\n.igv-ui-colorpicker-menu-close-button {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 32px;\\n  margin-top: 4px;\\n  margin-bottom: 4px;\\n  padding-right: 8px;\\n}\\n.igv-ui-colorpicker-menu-close-button i.fa {\\n  display: block;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  color: #5f5f5f;\\n}\\n.igv-ui-colorpicker-menu-close-button i.fa:hover,\\n.igv-ui-colorpicker-menu-close-button i.fa:focus,\\n.igv-ui-colorpicker-menu-close-button i.fa:active {\\n  cursor: pointer;\\n  color: #0f0f0f;\\n}\\n\\n.igv-ui-generic-dialog-container {\\n  box-sizing: content-box;\\n  position: fixed;\\n  top: 0;\\n  left: 0;\\n  width: 300px;\\n  height: fit-content;\\n  padding-bottom: 16px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  z-index: 2048;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-one-liner {\\n  color: #373737;\\n  width: 95%;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-top: 8px;\\n  padding-left: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input {\\n  margin-top: 8px;\\n  width: 95%;\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  padding-left: 8px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input > div {\\n  width: fit-content;\\n  height: 100%;\\n  font-size: 16px;\\n  text-align: right;\\n  padding-right: 8px;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\\n  width: 50%;\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input {\\n  margin-top: 8px;\\n  width: calc(100% - 16px);\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input[type=range] {\\n  width: 70%;\\n  -webkit-appearance: none;\\n  background: linear-gradient(90deg, white, black);\\n  outline: none;\\n  margin: 0;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input output {\\n  display: block;\\n  height: 100%;\\n  width: 20%;\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel {\\n  width: 100%;\\n  height: 28px;\\n  padding-top: 16px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div {\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:first-child {\\n  margin-left: 32px;\\n  margin-right: 0;\\n  background-color: #5ea4e0;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:last-child {\\n  margin-left: 0;\\n  margin-right: 32px;\\n  background-color: #c4c4c4;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n\\n.igv-ui-generic-container {\\n  box-sizing: content-box;\\n  position: absolute;\\n  z-index: 2048;\\n  background-color: white;\\n  cursor: pointer;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: wrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-container > div:first-child {\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  height: 24px;\\n  width: 100%;\\n  background-color: #dddddd;\\n}\\n.igv-ui-generic-container > div:first-child > div {\\n  display: block;\\n  color: #5f5f5f;\\n  cursor: pointer;\\n  width: 14px;\\n  height: 14px;\\n  margin-right: 8px;\\n  margin-bottom: 4px;\\n}\\n\\n.igv-ui-dialog {\\n  z-index: 2048;\\n  position: fixed;\\n  width: fit-content;\\n  height: fit-content;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  background-color: white;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-dialog .igv-ui-dialog-one-liner {\\n  width: 95%;\\n  height: 24px;\\n  line-height: 24px;\\n  text-align: left;\\n  margin: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n  font-weight: bold;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel {\\n  width: 100%;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div {\\n  margin: 16px;\\n  margin-top: 32px;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child {\\n  background-color: #5ea4e0;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child {\\n  background-color: #c4c4c4;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok {\\n  width: 100%;\\n  height: 36px;\\n  margin-top: 32px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok div {\\n  width: 98px;\\n  height: 36px;\\n  line-height: 36px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  border-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok div:hover {\\n  cursor: pointer;\\n  background-color: #25597f;\\n}\\n\\n.igv-ui-panel, .igv-ui-panel-row, .igv-ui-panel-column {\\n  z-index: 2048;\\n  background-color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  display: flex;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-ui-panel-column {\\n  display: flex;\\n  flex-direction: column;\\n}\\n\\n.igv-ui-panel-row {\\n  display: flex;\\n  flex-direction: row;\\n}\\n\\n.igv-ui-textbox {\\n  background-color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  display: flex;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-ui-table {\\n  background-color: white;\\n}\\n\\n.igv-ui-table thead {\\n  position: sticky;\\n  top: 0;\\n}\\n\\n.igv-ui-table th {\\n  text-align: left;\\n}\\n\\n.igv-ui-table td {\\n  padding-right: 20px;\\n}\\n\\n.igv-ui-table tr:hover {\\n  background-color: lightblue;\\n}\\n\\n.igv-ui-center-fixed {\\n  left: 50%;\\n  top: 50%;\\n  transform: translate(-50%, -50%);\\n}\\n\\n.igv-navbar {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  box-sizing: border-box;\\n  width: 100%;\\n  color: #444;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  line-height: 32px;\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  margin-top: 2px;\\n  margin-bottom: 6px;\\n  height: 32px;\\n  border-style: solid;\\n  border-radius: 3px;\\n  border-width: thin;\\n  border-color: #bfbfbf;\\n  background-color: #f3f3f3;\\n}\\n.igv-navbar .igv-navbar-left-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  height: 32px;\\n  line-height: 32px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-logo {\\n  width: 34px;\\n  height: 32px;\\n  margin-right: 8px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\\n  height: 32px;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  user-select: none;\\n  line-height: 32px;\\n  vertical-align: middle;\\n  text-align: center;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  height: 100%;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n  height: 100%;\\n  width: 125px;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\\n  display: block;\\n  cursor: pointer;\\n  width: 100px;\\n  height: 75%;\\n  outline: none;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  margin-left: 8px;\\n  height: 22px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 240px;\\n  height: 22px;\\n  line-height: 22px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\\n  cursor: text;\\n  width: 85%;\\n  height: 22px;\\n  line-height: 22px;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  text-align: left;\\n  padding-left: 8px;\\n  margin-right: 8px;\\n  outline: none;\\n  border-style: solid;\\n  border-radius: 3px;\\n  border-width: thin;\\n  border-color: #bfbfbf;\\n  background-color: white;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\\n  cursor: pointer;\\n  height: 16px;\\n  width: 16px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\\n  margin-left: 4px;\\n  user-select: none;\\n}\\n.igv-navbar .igv-navbar-right-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\\n  position: relative;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-hidden {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  height: 100%;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\\n  color: #737373;\\n  font-size: 18px;\\n  margin-left: 8px;\\n  user-select: none;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\\n  cursor: pointer;\\n  margin-left: unset;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: unset;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: 4px;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\\n  display: block;\\n  height: fit-content;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\\n  display: block;\\n  width: 125px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\\n  display: block;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\\n  color: #737373;\\n  font-size: 18px;\\n  height: 32px;\\n  line-height: 32px;\\n  margin-left: 8px;\\n  user-select: none;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\\n  cursor: pointer;\\n  margin-left: unset;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: unset;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: 4px;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\\n  width: 0;\\n  height: 0;\\n  display: none;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\\n  width: 0;\\n  height: 0;\\n  display: none;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\\n  display: block;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\\n  display: none;\\n}\\n\\n.igv-navbar-button {\\n  display: block;\\n  box-sizing: unset;\\n  padding-left: 6px;\\n  padding-right: 6px;\\n  height: 18px;\\n  text-transform: capitalize;\\n  user-select: none;\\n  line-height: 18px;\\n  text-align: center;\\n  vertical-align: middle;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 11px;\\n  font-weight: 200;\\n  color: #737373;\\n  background-color: #f3f3f3;\\n  border-color: #737373;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 6px;\\n}\\n\\n.igv-navbar-button:hover {\\n  cursor: pointer;\\n}\\n\\n.igv-navbar-button-clicked {\\n  color: white;\\n  background-color: #737373;\\n}\\n\\n.igv-navbar-icon-button {\\n  cursor: pointer;\\n  position: relative;\\n  width: 24px;\\n  height: 24px;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-icon-button > div:first-child {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: -18px;\\n  width: 24px;\\n  height: 24px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-icon-button > div:last-child {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 18px;\\n  width: 24px;\\n  height: 24px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n\\n.igv-navbar-text-button {\\n  cursor: pointer;\\n  position: relative;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  border: none;\\n  display: flex;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-navbar-text-button > div:nth-child(2) {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 0;\\n  width: 38px;\\n  height: 18px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-text-button > div:nth-child(3) {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 42px;\\n  width: 38px;\\n  height: 18px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n\\n#igv-text-button-label {\\n  text-anchor: middle;\\n  dominant-baseline: middle;\\n}\\n\\n.igv-navbar-text-button-svg-inactive rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n.igv-navbar-text-button-svg-inactive text {\\n  fill: #737373;\\n}\\n.igv-navbar-text-button-svg-inactive tspan {\\n  dominant-baseline: middle;\\n}\\n\\n.igv-navbar-text-button-svg-hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n.igv-navbar-text-button-svg-hover text {\\n  fill: white;\\n}\\n.igv-navbar-text-button-svg-hover tspan {\\n  dominant-baseline: middle;\\n}\\n\\n#igv-save-svg-group rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n#igv-save-svg-group text {\\n  fill: #737373;\\n}\\n\\n#igv-save-svg-group:hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n#igv-save-svg-group:hover text {\\n  fill: white;\\n}\\n\\n#igv-save-png-group rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n#igv-save-png-group text {\\n  fill: #737373;\\n}\\n\\n#igv-save-png-group:hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n#igv-save-png-group:hover text {\\n  fill: white;\\n}\\n\\n.igv-zoom-in-notice-container {\\n  z-index: 256;\\n  position: absolute;\\n  top: 8px;\\n  left: 50%;\\n  transform: translate(-50%, 0%);\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n  background-color: white;\\n}\\n.igv-zoom-in-notice-container > div {\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  padding-top: 2px;\\n  padding-bottom: 2px;\\n  width: 100%;\\n  height: 100%;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  color: #3f3f3f;\\n}\\n\\n.igv-zoom-in-notice {\\n  position: absolute;\\n  top: 10px;\\n  left: 50%;\\n}\\n.igv-zoom-in-notice div {\\n  position: relative;\\n  left: -50%;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #3f3f3f;\\n  background-color: rgba(255, 255, 255, 0.51);\\n  z-index: 64;\\n}\\n\\n.igv-container-spinner {\\n  position: absolute;\\n  top: 90%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  z-index: 1024;\\n  width: 24px;\\n  height: 24px;\\n  pointer-events: none;\\n  color: #737373;\\n}\\n\\n.igv-multi-locus-close-button {\\n  position: absolute;\\n  top: 2px;\\n  right: 0;\\n  padding-left: 2px;\\n  padding-right: 2px;\\n  width: 12px;\\n  height: 12px;\\n  color: #666666;\\n  background-color: white;\\n  z-index: 1000;\\n}\\n.igv-multi-locus-close-button > svg {\\n  vertical-align: top;\\n}\\n\\n.igv-multi-locus-close-button:hover {\\n  cursor: pointer;\\n  color: #434343;\\n}\\n\\n.igv-multi-locus-ruler-label {\\n  z-index: 64;\\n  position: absolute;\\n  top: 2px;\\n  left: 0;\\n  width: 100%;\\n  height: 12px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-multi-locus-ruler-label > div {\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  color: rgb(16, 16, 16);\\n  background-color: white;\\n}\\n.igv-multi-locus-ruler-label > div {\\n  cursor: pointer;\\n}\\n\\n.igv-multi-locus-ruler-label-square-dot {\\n  z-index: 64;\\n  position: absolute;\\n  left: 50%;\\n  top: 5%;\\n  transform: translate(-50%, 0%);\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\\n  width: 14px;\\n  height: 14px;\\n}\\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\\n  margin-left: 16px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  color: rgb(16, 16, 16);\\n}\\n\\n.igv-ruler-sweeper {\\n  display: none;\\n  pointer-events: none;\\n  position: absolute;\\n  top: 26px;\\n  bottom: 0;\\n  left: 0;\\n  width: 0;\\n  z-index: 99999;\\n  background-color: rgba(68, 134, 247, 0.25);\\n}\\n\\n.igv-ruler-tooltip {\\n  pointer-events: none;\\n  z-index: 128;\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: 1px;\\n  height: 32px;\\n  background-color: transparent;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ruler-tooltip > div {\\n  pointer-events: none;\\n  width: 128px;\\n  height: auto;\\n  padding: 1px;\\n  color: #373737;\\n  font-size: 10px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  background-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #373737;\\n}\\n\\n.igv-track-label {\\n  position: absolute;\\n  left: 8px;\\n  top: 8px;\\n  width: auto;\\n  height: auto;\\n  max-width: 50%;\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  text-align: center;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  border-color: #444;\\n  border-radius: 2px;\\n  border-style: solid;\\n  border-width: thin;\\n  background-color: white;\\n  z-index: 128;\\n  cursor: pointer;\\n}\\n\\n.igv-track-label:hover,\\n.igv-track-label:focus,\\n.igv-track-label:active {\\n  background-color: #e8e8e8;\\n}\\n\\n.igv-track-label-popup-shim {\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  padding-top: 4px;\\n}\\n\\n.igv-center-line {\\n  display: none;\\n  pointer-events: none;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  left: 50%;\\n  transform: translateX(-50%);\\n  z-index: 8;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  border-left-style: dashed;\\n  border-left-width: thin;\\n  border-right-style: dashed;\\n  border-right-width: thin;\\n}\\n\\n.igv-center-line-wide {\\n  background-color: rgba(0, 0, 0, 0);\\n  border-left-color: rgba(127, 127, 127, 0.51);\\n  border-right-color: rgba(127, 127, 127, 0.51);\\n}\\n\\n.igv-center-line-thin {\\n  background-color: rgba(0, 0, 0, 0);\\n  border-left-color: rgba(127, 127, 127, 0.51);\\n  border-right-color: rgba(0, 0, 0, 0);\\n}\\n\\n.igv-cursor-guide-horizontal {\\n  display: none;\\n  pointer-events: none;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  position: absolute;\\n  left: 0;\\n  right: 0;\\n  top: 50%;\\n  height: 1px;\\n  z-index: 32;\\n  margin-left: 50px;\\n  margin-right: 54px;\\n  border-top-style: dotted;\\n  border-top-width: thin;\\n  border-top-color: rgba(127, 127, 127, 0.76);\\n}\\n\\n.igv-cursor-guide-vertical {\\n  pointer-events: none;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  left: 50%;\\n  width: 1px;\\n  z-index: 32;\\n  border-left-style: dotted;\\n  border-left-width: thin;\\n  border-left-color: rgba(127, 127, 127, 0.76);\\n  display: none;\\n}\\n\\n.igv-user-feedback {\\n  position: fixed;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 512px;\\n  height: 360px;\\n  z-index: 2048;\\n  background-color: white;\\n  border-color: #a2a2a2;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #444;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-user-feedback div:first-child {\\n  position: relative;\\n  height: 24px;\\n  width: 100%;\\n  background-color: white;\\n  border-bottom-color: #a2a2a2;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-user-feedback div:first-child div {\\n  position: absolute;\\n  top: 2px;\\n  width: 16px;\\n  height: 16px;\\n  background-color: transparent;\\n}\\n.igv-user-feedback div:first-child div:first-child {\\n  left: 8px;\\n}\\n.igv-user-feedback div:first-child div:last-child {\\n  cursor: pointer;\\n  right: 8px;\\n}\\n.igv-user-feedback div:last-child {\\n  width: 100%;\\n  height: calc(100% - 24px);\\n  border-width: 0;\\n}\\n.igv-user-feedback div:last-child div {\\n  width: auto;\\n  height: auto;\\n  margin: 8px;\\n}\\n\\n.igv-generic-dialog-container {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: 300px;\\n  height: 200px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  z-index: 2048;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\\n  color: #373737;\\n  width: 95%;\\n  height: 24px;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-top: 8px;\\n  padding-left: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\\n  margin-top: 8px;\\n  width: 95%;\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  padding-left: 8px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\\n  width: 30%;\\n  height: 100%;\\n  font-size: 16px;\\n  text-align: right;\\n  padding-right: 8px;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\\n  width: 50%;\\n  font-size: 16px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input {\\n  margin-top: 8px;\\n  width: calc(100% - 16px);\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input input {\\n  font-size: 16px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\\n  width: 100%;\\n  height: 28px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\\n  margin-top: 32px;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\\n  margin-left: 32px;\\n  margin-right: 0;\\n  background-color: #5ea4e0;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\\n  margin-left: 0;\\n  margin-right: 32px;\\n  background-color: #c4c4c4;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok {\\n  width: 100%;\\n  height: 36px;\\n  margin-top: 32px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\\n  width: 98px;\\n  height: 36px;\\n  line-height: 36px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  border-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\\n  cursor: pointer;\\n  background-color: #25597f;\\n}\\n\\n.igv-generic-container {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  z-index: 2048;\\n  background-color: white;\\n  cursor: pointer;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: wrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-container div:first-child {\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  height: 24px;\\n  width: 100%;\\n  background-color: #dddddd;\\n}\\n.igv-generic-container div:first-child i {\\n  display: block;\\n  color: #5f5f5f;\\n  cursor: pointer;\\n  width: 14px;\\n  height: 14px;\\n  margin-right: 8px;\\n  margin-bottom: 4px;\\n}\\n\\n.igv-menu-popup {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: max-content;\\n  max-width: 400px;\\n  z-index: 512;\\n  cursor: pointer;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  color: #4b4b4b;\\n  background: white;\\n  border-radius: 4px;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-end;\\n  text-align: left;\\n}\\n.igv-menu-popup > div:not(:first-child) {\\n  width: 100%;\\n}\\n.igv-menu-popup > div:not(:first-child) > div {\\n  background: white;\\n}\\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\\n  padding-left: 4px;\\n  padding-right: 4px;\\n}\\n.igv-menu-popup > div:not(:first-child) > div:last-child {\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-color: transparent;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-menu-popup > div:not(:first-child) > div:hover {\\n  background: #efefef;\\n}\\n\\n.igv-menu-popup-shim {\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  padding-bottom: 1px;\\n  padding-top: 1px;\\n}\\n\\n.igv-menu-popup-header {\\n  position: relative;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-menu-popup-header div {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-menu-popup-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n\\n.igv-menu-popup-check-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 100%;\\n  height: 20px;\\n  margin-right: 4px;\\n  background-color: transparent;\\n}\\n.igv-menu-popup-check-container div {\\n  padding-top: 2px;\\n  padding-left: 8px;\\n}\\n.igv-menu-popup-check-container div:first-child {\\n  position: relative;\\n  width: 12px;\\n  height: 12px;\\n}\\n.igv-menu-popup-check-container div:first-child svg {\\n  position: absolute;\\n  width: 12px;\\n  height: 12px;\\n}\\n\\n.igv-user-feedback {\\n  position: fixed;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 512px;\\n  height: 360px;\\n  z-index: 2048;\\n  background-color: white;\\n  border-color: #a2a2a2;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #444;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-user-feedback div:first-child {\\n  position: relative;\\n  height: 24px;\\n  width: 100%;\\n  background-color: white;\\n  border-bottom-color: #a2a2a2;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-user-feedback div:first-child div {\\n  position: absolute;\\n  top: 2px;\\n  width: 16px;\\n  height: 16px;\\n  background-color: transparent;\\n}\\n.igv-user-feedback div:first-child div:first-child {\\n  left: 8px;\\n}\\n.igv-user-feedback div:first-child div:last-child {\\n  cursor: pointer;\\n  right: 8px;\\n}\\n.igv-user-feedback div:last-child {\\n  width: 100%;\\n  height: calc(100% - 24px);\\n  border-width: 0;\\n}\\n.igv-user-feedback div:last-child div {\\n  width: auto;\\n  height: auto;\\n  margin: 8px;\\n}\\n\\n.igv-loading-spinner-container {\\n  z-index: 1024;\\n  position: absolute;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 32px;\\n  height: 32px;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-loading-spinner-container > div {\\n  box-sizing: border-box;\\n  width: 100%;\\n  height: 100%;\\n  border-radius: 50%;\\n  border: 4px solid rgba(128, 128, 128, 0.5);\\n  border-top-color: rgb(255, 255, 255);\\n  animation: spin 1s ease-in-out infinite;\\n  -webkit-animation: spin 1s ease-in-out infinite;\\n}\\n\\n@keyframes spin {\\n  to {\\n    -webkit-transform: rotate(360deg);\\n    transform: rotate(360deg);\\n  }\\n}\\n@-webkit-keyframes spin {\\n  to {\\n    -webkit-transform: rotate(360deg);\\n    transform: rotate(360deg);\\n  }\\n}\\n.igv-roi-menu {\\n  position: absolute;\\n  z-index: 512;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  color: #4b4b4b;\\n  background-color: white;\\n  width: 192px;\\n  border-radius: 4px;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n}\\n.igv-roi-menu > div:first-child {\\n  height: 24px;\\n  border-top-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-roi-menu > div:first-child > div {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-roi-menu > div:first-child > div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-roi-menu > div:last-child {\\n  background-color: white;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-color: transparent;\\n  border-bottom-style: solid;\\n  border-bottom-width: 0;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  text-align: start;\\n  vertical-align: middle;\\n}\\n.igv-roi-menu > div:last-child > div {\\n  height: 24px;\\n  padding-left: 4px;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  border-bottom-color: #7f7f7f;\\n}\\n.igv-roi-menu > div:last-child > div:not(:first-child):hover {\\n  cursor: pointer;\\n  background-color: rgba(127, 127, 127, 0.1);\\n}\\n.igv-roi-menu > div:last-child div:first-child {\\n  font-style: italic;\\n  text-align: center;\\n  padding-right: 4px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n}\\n.igv-roi-menu > div:last-child > div:last-child {\\n  border-bottom-width: 0;\\n  border-bottom-color: transparent;\\n}\\n\\n.igv-roi-placeholder {\\n  font-style: normal;\\n  color: rgba(75, 75, 75, 0.6);\\n}\\n\\n.igv-roi-table {\\n  position: absolute;\\n  z-index: 1024;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  resize: both;\\n  overflow: hidden;\\n  width: min-content;\\n  max-width: 1600px;\\n  border-color: #7f7f7f;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  font-weight: 400;\\n  background-color: white;\\n  cursor: default;\\n}\\n.igv-roi-table > div {\\n  height: 24px;\\n  font-size: 14px;\\n  text-align: start;\\n  vertical-align: middle;\\n  line-height: 24px;\\n}\\n.igv-roi-table > div:first-child {\\n  border-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-top-width: 0;\\n  border-bottom-color: #7f7f7f;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-roi-table > div:first-child > div:first-child {\\n  text-align: center;\\n  white-space: nowrap;\\n  text-overflow: ellipsis;\\n  overflow: hidden;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  width: calc(100% - 4px - 12px);\\n}\\n.igv-roi-table > div:first-child > div:last-child {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7f7f7f;\\n}\\n.igv-roi-table > div:first-child > div:last-child > svg {\\n  display: block;\\n}\\n.igv-roi-table > div:first-child > div:last-child:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-roi-table > .igv-roi-table-description {\\n  padding: 4px;\\n  margin-left: 4px;\\n  word-break: break-all;\\n  overflow-y: auto;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-goto-explainer {\\n  margin-top: 5px;\\n  margin-left: 4px;\\n  color: #7F7F7F;\\n  font-style: italic;\\n  height: 24px;\\n  border-top: solid lightgray;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles {\\n  height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n  padding-right: 16px;\\n  background-color: white;\\n  border-top-color: #7f7f7f;\\n  border-top-style: solid;\\n  border-top-width: thin;\\n  border-bottom-color: #7f7f7f;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles > div {\\n  font-size: 14px;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-left: 4px;\\n  height: 24px;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  border-right-color: #7f7f7f;\\n  border-right-style: solid;\\n  border-right-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles > div:last-child {\\n  border-right: unset;\\n}\\n.igv-roi-table > .igv-roi-table-row-container {\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  overflow: auto;\\n  height: 360px;\\n  flex: 1 1 auto;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\\n  height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\\n  font-size: 14px;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-left: 4px;\\n  height: 24px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  border-right-color: transparent;\\n  border-right-style: solid;\\n  border-right-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:last-child {\\n  border-right: unset;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\\n  background-color: rgba(0, 0, 0, 0.04);\\n}\\n.igv-roi-table > div:last-child {\\n  min-height: 32px;\\n  height: 32px;\\n  line-height: 32px;\\n  border-top-color: #7f7f7f;\\n  border-top-style: solid;\\n  border-top-width: thin;\\n  border-bottom-color: transparent;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-width: 0;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n\\n.igv-roi-table-row-selected {\\n  background-color: rgba(0, 0, 0, 0.125);\\n}\\n\\n.igv-roi-table-button {\\n  cursor: pointer;\\n  height: 20px;\\n  user-select: none;\\n  line-height: 20px;\\n  text-align: center;\\n  vertical-align: middle;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 13px;\\n  font-weight: 400;\\n  color: black;\\n  padding-left: 6px;\\n  padding-right: 6px;\\n  background-color: rgb(239, 239, 239);\\n  border-color: black;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 3px;\\n}\\n\\n.igv-roi-table-button:hover {\\n  font-weight: 400;\\n  background-color: rgba(0, 0, 0, 0.13);\\n}\\n\\n.igv-roi-region {\\n  z-index: 64;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  pointer-events: none;\\n  overflow: visible;\\n  margin-top: 66px;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n}\\n.igv-roi-region > div {\\n  position: relative;\\n  width: 100%;\\n  height: 8px;\\n  pointer-events: auto;\\n}\\n\\n.igv-roi-menu-row {\\n  height: 24px;\\n  padding-left: 8px;\\n  font-size: small;\\n  text-align: start;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  background-color: white;\\n}\\n\\n.igv-roi-menu-row-edit-description {\\n  width: -webkit-fill-available;\\n  font-size: small;\\n  text-align: start;\\n  vertical-align: middle;\\n  background-color: white;\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  padding-bottom: 4px;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n}\\n.igv-roi-menu-row-edit-description > label {\\n  margin-left: 2px;\\n  margin-bottom: 0;\\n  display: block;\\n  width: -webkit-fill-available;\\n}\\n.igv-roi-menu-row-edit-description > input {\\n  display: block;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  margin-bottom: 1px;\\n  width: -webkit-fill-available;\\n}\\n\\n.igv-container {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  padding-top: 4px;\\n  user-select: none;\\n  -webkit-user-select: none;\\n  -ms-user-select: none;\\n  min-height: 160px;\\n}\\n\\n.igv-viewport {\\n  position: relative;\\n  margin-top: 5px;\\n  line-height: 1;\\n  overflow-x: hidden;\\n  overflow-y: hidden;\\n}\\n\\n.igv-viewport-content {\\n  position: relative;\\n  width: 100%;\\n}\\n.igv-viewport-content > canvas {\\n  position: relative;\\n  display: block;\\n}\\n\\n.igv-column-container {\\n  position: relative;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  width: 100%;\\n}\\n\\n.igv-column-shim {\\n  width: 1px;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  background-color: #545453;\\n}\\n\\n.igv-axis-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 50px;\\n}\\n.igv-axis-column > div {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 100%;\\n}\\n.igv-axis-column > div > div {\\n  z-index: 512;\\n  position: absolute;\\n  top: 8px;\\n  left: 8px;\\n  width: fit-content;\\n  height: fit-content;\\n  background-color: transparent;\\n  display: grid;\\n  align-items: start;\\n  justify-items: center;\\n}\\n.igv-axis-column > div > div > input {\\n  display: block;\\n  margin: unset;\\n  cursor: pointer;\\n}\\n\\n.igv-column {\\n  position: relative;\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-sample-info-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-sample-name-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-scrollbar-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 14px;\\n}\\n.igv-scrollbar-column > div {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 14px;\\n}\\n.igv-scrollbar-column > div > div {\\n  cursor: pointer;\\n  position: absolute;\\n  top: 0;\\n  left: 2px;\\n  width: 8px;\\n  border-width: 1px;\\n  border-style: solid;\\n  border-color: #c4c4c4;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n}\\n.igv-scrollbar-column > div > div:hover {\\n  background-color: #c4c4c4;\\n}\\n\\n.igv-track-drag-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 12px;\\n  background-color: white;\\n}\\n.igv-track-drag-column > .igv-track-drag-handle {\\n  z-index: 512;\\n  position: relative;\\n  cursor: pointer;\\n  margin-top: 5px;\\n  width: 100%;\\n  border-style: solid;\\n  border-width: 0;\\n  border-top-right-radius: 6px;\\n  border-bottom-right-radius: 6px;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-color {\\n  background-color: #c4c4c4;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-hover-color {\\n  background-color: #787878;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-selected-color {\\n  background-color: #0963fa;\\n}\\n.igv-track-drag-column > .igv-track-drag-shim {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 100%;\\n  border-style: solid;\\n  border-width: 0;\\n}\\n\\n.igv-gear-menu-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 28px;\\n}\\n.igv-gear-menu-column > div {\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  margin-top: 5px;\\n  width: 100%;\\n  background: white;\\n}\\n.igv-gear-menu-column > div > div {\\n  position: relative;\\n  margin-top: 4px;\\n  width: 16px;\\n  height: 16px;\\n  color: #7F7F7F;\\n}\\n.igv-gear-menu-column > div > div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n\\n/*# sourceMappingURL=igv.css.map */\\n'),n.adoptedStyleSheets=[e]}if(this.root=e({class:\"igv-container\"}),n.appendChild(this.root),this.spinner=e({class:\"igv-loading-spinner-container\"}),this.root.appendChild(this.spinner),this.spinner.appendChild(e()),this.spinner.style.width=\"64px\",this.spinner.style.height=\"64px\",this.stopSpinner(),this.alert=new La(this.root),this.columnContainer=e({class:\"igv-column-container\"}),this.root.appendChild(this.columnContainer),this.menuPopup=new Xu(this.columnContainer),this.menuUtils=new bo(this),this.initialize(t),this.trackViews=[],this.constants={dragThreshold:3,scrollThreshold:5,defaultColor:\"rgb(0,0,150)\",doubleClickDelay:t.doubleClickDelay||500},this.eventHandlers={},t.listeners)for(let e of Object.keys(t.listeners))this.on(e,t.listeners[e]);this.on(\"trackremoved\",(()=>{0===this.findTracks((e=>\"function\"==typeof e.getSamples)).length&&(this.sampleInfoControl.setButtonVisibility(!1),this.sampleNameViewportWidth=void 0,this.showSampleNames=!1,this.sampleNameControl.setState(this.showSampleNames),this.sampleNameControl.hide(),this.layoutChange())})),this.on(\"didchangecolumnlayout\",(()=>{if(yu.length>0){const e=yu.length;for(let t=0;t<e;t++)yu[t].dispose();yu.length=0}})),this.addEventHandlers(),this.sampleInfo=new Uu(this),this.createStandardControls(t),this.roiManager=new Ky(this)}get doShowROITable(){return this.roiManager.roiTableIsVisible()}startSpinner(){this.spinner.style.display=\"flex\"}stopSpinner(){this.spinner.style.display=\"none\"}initialize(e){this.flanking=e.flanking,this.crossDomainProxy=e.crossDomainProxy,this.formats=e.formats,this.trackDefaults=e.trackDefaults,this.nucleotideColors=e.nucleotideColors||Bc;for(let e of Object.keys(this.nucleotideColors))this.nucleotideColors[e.toLowerCase()]=this.nucleotideColors[e];this.doShowTrackLabels=e.showTrackLabels,this.doShowCenterLine=e.showCenterGuide,this.doShowCursorGuide=e.showCursorGuide,this.showSampleNames=e.showSampleNames,this.sampleNameViewportWidth=void 0,e.sampleNameViewportWidth&&(this.sampleNameViewportWidth=e.sampleNameViewportWidth),e.search&&(this.searchConfig={type:\"json\",url:e.search.url,coords:void 0===e.search.coords?1:e.search.coords,chromosomeField:e.search.chromosomeField||\"chromosome\",startField:e.search.startField||\"start\",endField:e.search.endField||\"end\",geneField:e.search.geneField||\"gene\",snpField:e.search.snpField||\"snp\",resultsField:e.search.resultsField})}createStandardControls(e){this.setTrackLabelVisibility(e.showTrackLabels),this.navbar=new Py(e,this),this.navbar.$navigation.insertBefore(Bt(this.columnContainer)),!1===e.showControls&&this.navbar.hide(),this.cursorGuide=new ky(this.columnContainer,this),this.inputDialog=new Na(this.root),this.inputDialog.container.id=`igv-input-dialog-${s()}`,this.dataRangeDialog=new _o(this,Bt(this.root)),this.dataRangeDialog.$container.get(0).id=`igv-data-range-dialog-${s()}`,this.genericColorPicker=new Ra({parent:this.columnContainer,width:432}),this.genericColorPicker.container.id=`igv-track-color-picker-${s()}`,this.sliderDialog=new hA(this.root),this.sliderDialog.container.id=`igv-slider-dialog-${s()}`}getSampleNameViewportWidth(){return void 0===this.sampleNameViewportWidth||!1===this.showSampleNames?0:this.sampleNameViewportWidth}getSampleInfoViewportWidth(){return this.getSampleInfoColumnWidth()}isMultiLocusMode(){return this.referenceFrameList&&this.referenceFrameList.length>1}isMultiLocusWholeGenomeView(){if(void 0===this.referenceFrameList||1===this.referenceFrameList.length)return!1;for(let e of this.referenceFrameList)if(\"all\"===e.chr.toLowerCase())return!0;return!1}currentLoci(){const e=e=>`${e.chr}:${e.start+1}-${e.end}`;return void 0===this.referenceFrameList||0===this.referenceFrameList.length?\"\":1===this.referenceFrameList.length?e(this.referenceFrameList[0]):this.referenceFrameList.map((t=>e(t)))}toSVG(){const{x:e,y:t,width:i,height:n}=this.columnContainer.getBoundingClientRect(),r=new lu({width:i,height:n,backdropColor:\"white\",multiLocusGap:0,viewbox:{x:0,y:0,width:i,height:n}}),s={deltaX:0,deltaY:-t};for(let e of this.trackViews)e.renderSVGContext(r,s);return s.deltaX=e,this.roiManager.renderSVGContext(this.columnContainer,r,s),r.getSerializedSvg(!0)}saveSVGtoFile(e,t){let i=this.toSVG();if(t){const e=document.createElement(\"svg\");e.innerHTML=i,t.append(e),t.appendChild(e)}const n=e||\"igvjs.svg\",r=URL.createObjectURL(new Blob([i],{type:\"application/octet-stream\"}));Pt(n,r),URL.revokeObjectURL(r)}savePNGtoFile(e){const t=this.toSVG(),i=new Blob([t],{type:\"image/svg+xml\"}),n=URL.createObjectURL(i),r=document.createElement(\"img\");r.addEventListener(\"load\",(()=>{const t=this.columnContainer.getBoundingClientRect(),i=window.devicePixelRatio,s=t.width*i,o=t.height*i,a=document.createElement(\"canvas\");a.width=s,a.height=o;const c=a.getContext(\"2d\");c.scale(i,i),c.drawImage(r,0,0);const l=a.toDataURL(\"image/png\");Pt(e=e||\"igvjs.png\",l),URL.revokeObjectURL(n)})),r.src=n}async loadSession(e){let t;return this.sampleInfo.initialize(),this.roiSets=[],t=e.url||e.file?await dA.loadSessionFile(e):e,this.loadSessionObject(t)}static async loadSessionFile(e){const t=e.url||e.file;let i;if(e.url&&Mt(e.url)&&(e.url.startsWith(\"blob:\")||e.url.startsWith(\"data:\"))){const t=dA.uncompressSession(e.url);i=JSON.parse(t)}else{let n=e.filename;if(n||(n=e.url?await ja(e.url):e.file.name),n.endsWith(\".xml\")){const e=mu.KNOWN_GENOMES,n=await Qs.loadString(t);i=new by(n,e)}else if(n.endsWith(\"hub.txt\")){i={reference:(await du.loadHub(t,e)).getGenomeConfig()}}else{if(!n.endsWith(\".json\"))throw Error(\"Unrecognized session file format:\"+n);i=await Qs.loadJson(t)}}return bA(i)}async loadSessionObject(e){this.cleanHouseForSession(),this.config=e,e.browsers&&(e=await async function(e){const t=e.browsers[0],i={},n=new Mf({url:t.url});await n.readHeaderAndFooter(),i.sampleNameViewportWidth=20,i.genome=\"hg38\";const r=t.state.split(\",\"),s=n.bpResolutions[Number.parseInt(r[2])],o=Number.parseInt(r[0]),a=Math.floor(Number.parseFloat(r[3])*s),c=a+Math.floor(1700*s);return i.locus=`${n.chromosomes[o].name}:${a}-${c}`,i.tracks=(t.tracks||[]).filter((e=>!(\"refgene\"===e.format||\"cellType\"===e.name))),i.tracks.push({type:\"shoebox\",url:t.url,name:t.name,colorScale:t.colorScale,_hicFile:n}),i}(e)),this.navbar.sampleInfoControl.setButtonVisibility(!1),this.showSampleNames=e.showSampleNames||!1,this.navbar.sampleNameControl.setState(!0===this.showSampleNames),e.sampleNameViewportWidth&&(this.sampleNameViewportWidth=e.sampleNameViewportWidth),$a(this.columnContainer,\"igv-axis-column\"),$a(this.columnContainer,\"igv-sample-info-column\"),$a(this.columnContainer,\"igv-sample-name-column\"),$a(this.columnContainer,\"igv-scrollbar-column\"),$a(this.columnContainer,\"igv-track-drag-column\"),$a(this.columnContainer,\"igv-gear-menu-column\");const t=e.reference||e.genome;if(!t)return void console.warn(\"No genome or reference object specified\");const i=Mt(t)?await mu.expandReference(this.alert,t):t;if(await this.loadReference(i,i.locus||e.locus),this.centerLineList=this.createCenterLineList(this.columnContainer),!1!==e.showIdeogram){const e=new hy(this);e.id=\"ideogram\";const t=new hf(this,this.columnContainer,e);this.trackViews.push(t)}if(!1!==e.showRuler){const e=new hf(this,this.columnContainer,new Wu(this));this.trackViews.push(e)}e.qtlSelections&&(this.qtlSelections=cA.fromJSON(e.qtlSelections)),this.roiManager.clearROIs(),e.roi?this.roiManager.loadROI(e.roi):await this.roiManager.reset();const n=[];if(e.sampleinfo)for(const t of e.sampleinfo)t.file?n.push(t.file):this.loadSampleInfo(t);const r=i.tracks||[],s=e.tracks?r.concat(e.tracks):r;0===s.filter((e=>\"sequence\"===e.type&&!e.url&&!e.fastaURL)).length&&s.push({type:\"sequence\",order:Wd,removable:!1});const o=s.filter((e=>void 0!==e.file)).map((({file:e})=>e)),a=s.filter((e=>void 0!==e.indexFile)).map((({indexFile:e})=>e));a.length>0&&o.push(...a),n.length>0&&o.push(...n),o.length>0&&alert(`Local files cannot be loaded automatically.\\nThis session contains references to these local files:\\n${o.map((e=>`    ${e}`)).join(\"\\n\")}`);const c=s.filter((e=>void 0===e.file));let l=1;for(let e of c)void 0===e.order&&(e.order=l++);await this.loadTrackList(c);for(let e of this.trackViews.filter((e=>\"ruler\"===e.track.type||\"ideogram\"===e.track.type)))await e.updateViews();return this.trackViews.some((e=>e.track.selected))&&this.navbar.setEnableTrackSelection(!0),this.updateUIWithReferenceFrameList(),this.updateLocusSearchWidget(),s}cleanHouseForSession(){for(let e of this.trackViews)e.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(\".igv-axis-column, .igv-column-shim, .igv-column, .igv-sample-info-column, .igv-sample-name-column, .igv-scrollbar-column, .igv-track-drag-column, .igv-gear-menu-column\").forEach((e=>e.remove())),this.trackViews=[],this.circularView&&this.circularView.clearChords()}async loadReference(e,t){let i;this.removeAllTracks(),this.roiManager.clearROIs(),this.navbar.setEnableTrackSelection(!1),i=e.gbkURL?await wd(e.gbkURL):await aA.createGenome(e,this);const n=void 0===this.genome||this.genome.id!==i.id;this.genome=i,this.navbar.updateGenome(i);let r=t||i.initialLocus;Array.isArray(r)&&(r=r.join(\" \"));if(!await this.search(r,!0))throw new Error(`Cannot set initial locus ${r}`);if(n){let t;if(e.hubURL){t=(await du.loadHub(e.hubURL)).getGroupedTrackConfigurations()}this.fireEvent(\"genomechange\",[{genome:i,trackConfigurations:t}]),this.circularView&&this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Hm(this.genome)})}}async loadGenome(e){let t;e.genarkAccession&&(e.url=hu(e.genarkAccession)),e.url&&(Mt(e.url)&&e.url.endsWith(\"/hub.txt\")?(e.hubURL=e.url,delete e.url):\"gbk\"===function(e){let t;if(e instanceof File)t=e.name;else{if(\"string\"!=typeof e)throw new Error(\"Input must be a File object or a URL string\");t=e}const i=t.split(\".\").pop();return i.split(\"?\")[0]}(e.url)&&(e.gbkURL=e.url,delete e.url));if(e.hubURL||e.url&&Mt(e.url)&&e.url.endsWith(\"/hub.txt\")){t=(await du.loadHub(e.hubURL||e.url,e)).getGenomeConfig()}else t=Mt(e)||!(e.url||e.fastaURL||e.twoBitURL||e.gbkURL)?await mu.expandReference(this.alert,e):e;let i;await this.loadReference(t),i=t.gbkURL||\"gbk\"===t.format?[{name:\"Annotations\",format:\"gbk\",url:t.gbkURL}]:t.tracks||[];return 0===i.filter((e=>\"sequence\"===e.type)).length&&i.push({type:\"sequence\",order:Wd}),await this.loadTrackList(i),await this.updateViews(),this.genome}async loadTrackHub(e){const t=bA((await du.loadHub(e.url,e)).getGenomeConfig());return this.loadGenome(t)}updateUIWithReferenceFrameList(){const e=this.referenceFrameList;this.isMultiLocusWholeGenomeView()||mu.isWholeGenomeView(e[0].chr),this.navbar.navbarDidResize(),mA(this.trackViews,this.doShowTrackLabels),this.doShowCenterLine&&mu.isWholeGenomeView(e[0].chr)&&this.navbar.centerLineButton.boundMouseClickHandler(),this.doShowCursorGuide&&mu.isWholeGenomeView(e[0].chr)&&this.navbar.cursorGuideButton.boundMouseClickHandler(),this.setCenterLineAndCenterLineButtonVisibility(mu.isWholeGenomeView(e[0].chr))}setCenterLineAndCenterLineButtonVisibility(e){e?this.navbar.centerLineButton.setVisibility(!1):this.navbar.centerLineButton.setVisibility(this.config.showCenterGuideButton);for(let t of this.centerLineList)e?this.setCenterLineVisibility(!e):this.setCenterLineVisibility(this.doShowCenterLine)}setTrackLabelVisibility(e){mA(this.trackViews,e)}setROITableVisibility(e){!0===e?this.roiManager.presentTable():this.roiManager.dismissTable()}setCursorGuideVisibility(e){e?this.cursorGuide.show():this.cursorGuide.hide()}setCustomCursorGuideMouseHandler(e){this.cursorGuide.customMouseHandler=e}setCenterLineVisibility(e){for(let t of this.centerLineList)!0===e?(t.show(),t.repaint()):t.hide()}async loadTrackList(e){let t=0;for(let i of e)void 0===i.order&&(i.order=t++);const i=[];for(let t of e)i.push(this._loadTrack(t));const n=await Promise.all(i);return this.trackViews.filter((function(e){return e.track.autoscaleGroup})).length>0&&this.updateViews(),n}async loadTrack(e){e.sync=!1!==e.sync;const t=this._loadTrack(e);return t&&e.autoscaleGroup&&(await t,this.updateViews()),t}async _loadTrack(e){Mt(e)&&(e=JSON.parse(e));try{if(e.hidden){const t=Ad(e,this.genome);return void await t.getFeatures({chr:\"1\",start:0,end:Number.MAX_SAFE_INTEGER})}const t=await this.createTrack(e);if(\"sampleinfo\"===e.type)return void this.layoutChange();if(void 0===t)return;return this.addTrack(e,t)}catch(t){let i=t.message||t.error||t.toString();const n={401:\"Access unauthorized\",403:\"Access forbidden\",404:\"Not found\"};n.hasOwnProperty(i)&&(i=n[i]),i=`${i} : ${Ht(e.url)?e.url.name:e.url}`;const r=new Error(i);throw console.error(r),r}}async addTrack(e,t){void 0===t.order&&(t.order=this.trackViews.length);const i=new hf(this,this.columnContainer,t);if(this.trackViews.push(i),mA(this.trackViews,this.doShowTrackLabels),\"function\"==typeof t.postInit)try{i.startSpinner(),await t.postInit()}finally{i.stopSpinner()}return t.autoscaleGroup||(e.sync?await i.updateViews():i.updateViews()),\"function\"==typeof t.hasSamples&&t.hasSamples()&&(this.sampleInfo.hasAttributes()&&this.sampleInfoControl.setButtonVisibility(!0),!1!==this.config.showSampleNameButton&&this.sampleNameControl.show()),this.reorderTracks(),this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()]),t.trackView.enableTrackSelection(this.navbar.getEnableTrackSelection()),t}async loadROI(e){return this.roiManager.loadROI(e,this.genome)}clearROIs(){this.roiManager.clearROIs()}async getUserDefinedROIs(){if(this.roiManager){const e=this.roiManager.getUserDefinedROISet();if(void 0===e)return[];const t=await e.getAllFeatures(),i=[];for(let e of Object.values(t))i.push(...e);return i}return[]}getRulerTrackView(){const e=this.trackViews.filter((({track:e})=>\"ruler\"===e.id));return e.length>0?e[0]:void 0}async createTrack(e){let t=await async function(e){return\"function\"==typeof e?e():e}\n",
-       "/*! pako 2.1.0 https://github.com/nodeca/pako @license (MIT AND Zlib) */(e.url||e.fastaURL);if(Mt(t)&&(t=t.trim()),t)if(e.format)e.format=e.format.toLowerCase();else if(e.fastaURL)e.format=\"fasta\";else if(e.sourceType)\"htsget\"===e.sourceType&&await Rh.inferFormat(e);else{const t=await am(e);t&&(e.format=t)}e.type&&Ha(e);let i=e.type?e.type.toLowerCase():void 0;if(!i){if(!e.format)throw Error(`Unrecognized track:  ${JSON.stringify(e)}`);if(\"hic\"===e.format){const t=new Mf(e);if(await t.readHeaderAndFooter(),!t.chromosomeIndexMap.celltype)throw Error(\"'.hic' files not supported\");i=\"shoebox\",e._hicFile=t}else if(i=za(e.format),\"bedtype\"===i){const t=Ad(e,this.genome);e._featureSource=t;const n=await t.trackType();i=n||\"annotation\"}e.type=i}if(this.trackDefaults&&i){const t=this.trackDefaults[i];if(t)for(let i in t)t.hasOwnProperty(i)&&void 0===e[i]&&(e[i]=t[i])}const n=function(e,t,i){let n;switch(e){case\"annotation\":case\"genes\":case\"fusionjuncspan\":case\"snp\":n=\"feature\";break;case\"seg\":case\"maf\":case\"mut\":n=\"seg\";break;case\"junctions\":case\"splicejunctions\":n=\"junction\";break;default:n=e}return wy.has(n)?wy.get(n)(t,i):void 0}(i,e,this);if(void 0!==n)return e.roi&&e.roi.length>0&&(n.roiSets=e.roi.map((e=>new eA(e,this.genome)))),n;this.alert.present(new Error(`Error creating track.  Could not determine track type for file: ${e.url||e}`),void 0)}reorderTracks(){this.trackViews.sort((function(e,t){const i=e=>\"ideogram\"===e.track.id?1:\"ruler\"===e.track.id?2:3,n=i(e),r=i(t);if(n===r){return(e.track.order||0)-(t.track.order||0)}return n-r}));for(let{axis:e,viewports:t,sampleInfoViewport:i,sampleNameViewport:n,outerScroll:r,dragHandle:s,gearContainer:o}of this.trackViews){e.remove();for(let{$viewport:e}of t)e.detach();i.viewport.remove(),n.viewport.remove(),r.remove(),s.remove(),o.remove()}const e=this.columnContainer.querySelectorAll(\".igv-column\");for(let{axis:t,viewports:i,sampleInfoViewport:n,sampleNameViewport:r,outerScroll:s,dragHandle:o,gearContainer:a}of this.trackViews){this.columnContainer.querySelector(\".igv-axis-column\").appendChild(t);for(let t=0;t<e.length;t++){const{$viewport:n}=i[t];e[t].appendChild(n.get(0))}this.columnContainer.querySelector(\".igv-sample-info-column\").appendChild(n.viewport),this.columnContainer.querySelector(\".igv-sample-name-column\").appendChild(r.viewport),this.columnContainer.querySelector(\".igv-scrollbar-column\").appendChild(s),this.columnContainer.querySelector(\".igv-track-drag-column\").appendChild(o),this.columnContainer.querySelector(\".igv-gear-menu-column\").appendChild(a)}}getTrackOrder(){return this.trackViews.filter((e=>e.track&&e.track.name)).map((e=>e.track.name))}getSelectedTrackViews(){return this.trackViews.filter((e=>!0===e.track.selected))}removeTrackByName(e){const t=this.trackViews.slice();for(let i of t)e===i.track.name&&this.removeTrack(i.track)}removeTrack(e){for(let t of this.trackViews)if(e===t.track){this._removeTrack(t.track);break}}_removeTrack(e){e.disposed||(this.trackViews.splice(this.trackViews.indexOf(e.trackView),1),this.fireEvent(\"trackremoved\",[e]),this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()]),e.trackView&&e.trackView.dispose())}removeAllTracks(){const e=this.trackViews;this.trackViews=[];for(let t of e)\"ruler\"!==t.track.id&&\"ideogram\"!==t.track.id?(this.fireEvent(\"trackremoved\",[t.track]),t.dispose()):this.trackViews.push(t)}get ideogramTrackView(){return this.trackViews[0]}get rulerTrackView(){return this.trackViews[1]}findTracks(e,t){let i=\"function\"==typeof e?t=>e(t.track):i=>t===i.track[e];return this.trackViews.filter(i).map((e=>e.track))}get tracks(){return this.trackViews.map((e=>e.track)).filter((e=>void 0!==e))}setTrackHeight(e){this.trackHeight=e,this.trackViews.forEach((function(t){t.setTrackHeight(e)}))}async visibilityChange(){this.layoutChange()}async layoutChange(){if(this.referenceFrameList.find((e=>e.bpPerPixel<0))){const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel=(t.end-t.start)/e}this.referenceFrameList&&this.navbar.navbarDidResize(),uA.call(this),await this.updateViews()}async updateViews(){const e=this.trackViews;this.updateLocusSearchWidget();for(let e of this.referenceFrameList)e.bpPerPixel<=10&&await this.genome.getSequence(e.chr,e.start,e.start+1);for(let e of this.centerLineList)e.repaint();if(this.dragObject)for(let t of e)await t.updateViews();else{const t={},i=[];for(const n of e)if(n.track.autoscaleGroup){const e=n.track.autoscaleGroup;t[e]||(t[e]=[]),t[e].push(n)}else i.push(n);if(Object.entries(t).length>0)for(const[e,i]of Object.entries(t)){const e=await Promise.all(i.map((e=>e.getInViewFeatures()))),t=qa(e.flat());for(const e of i)e.track.dataRange=Object.assign({},t),e.track.autoscale=!1;await Promise.all(i.map((e=>e.updateViews())))}await Promise.all(i.map((e=>e.updateViews())))}}repaintViews(){for(let e of this.trackViews)e.repaintViews()}updateLocusSearchWidget(){if(!this.referenceFrameList)return;const e=this.referenceFrameList,t=this.calculateViewportWidth(this.referenceFrameList.length);for(let i of e)i.end=i.start+i.bpPerPixel*t;const i=1===e.length?this.referenceFrameList[0].chr:\"\",n=this.referenceFrameList.map((e=>e.getLocusString())).join(\" \");this.navbar.updateLocus(n,i),this.fireEvent(\"locuschange\",[this.referenceFrameList])}calculateViewportWidth(e){let{width:t}=this.columnContainer.getBoundingClientRect();return t-=50+this.getSampleInfoViewportWidth()+this.getSampleNameViewportWidth()+14+12+28,t-=5*(e-1),Math.floor(t/e)}minimumBases(){return this.config.minimumBases}zoomIn(){this.zoomWithScaleFactor(.5)}zoomOut(){this.zoomWithScaleFactor(2)}async zoomWithScaleFactor(e,t,i){if(!this.referenceFrameList)return;const n=this.calculateViewportWidth(this.referenceFrameList.length);let r=i?[i]:this.referenceFrameList;for(let i of r)i.zoomWithScaleFactor(this,e,n,t)}async addMultiLocusPanel(e,t,i,n){if(!this.referenceFrameList)return;const r=this.calculateViewportWidth(1+this.referenceFrameList.length),s=this.calculateViewportWidth(this.referenceFrameList.length)/this.calculateViewportWidth(1+this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel*=s;const o=(i-t)/r,a=new vy(this.genome,e,t,i,o),c=n?this.referenceFrameList.indexOf(n):this.referenceFrameList.length-1,l=1+c,{$viewport:h}=this.trackViews[0].viewports[c],d=Uy(h.get(0).parentElement);if(this.fireEvent(\"didchangecolumnlayout\"),l===this.referenceFrameList.length){this.referenceFrameList.push(a);for(let e of this.trackViews){const t=zu(e,d,a);e.viewports.push(t)}}else{this.referenceFrameList.splice(l,0,a);for(let e of this.trackViews){const t=zu(e,d,a);e.viewports.splice(l,0,t)}}this.centerLineList=this.createCenterLineList(this.columnContainer),uA.call(this),await this.updateViews(!0)}createCenterLineList(e){const t=e.querySelectorAll(\".igv-center-line\");for(let e=0;e<t.length;e++)t[e].remove();const i=[],n=e.querySelectorAll(\".igv-column\");for(let e=0;e<n.length;e++)i.push(new Qy(this,this.referenceFrameList[e],n[e]));return i}async removeMultiLocusPanel(e){const t=this.referenceFrameList.indexOf(e),{$viewport:i}=this.trackViews[0].viewports[t];Oy(t,i.parent().get(0)),this.fireEvent(\"didchangecolumnlayout\");for(let{viewports:e}of this.trackViews)e[t].dispose(),e.splice(t,1);if(this.referenceFrameList.splice(t,1),1===this.referenceFrameList.length&&this.getRulerTrackView())for(let e of this.getRulerTrackView().viewports)e.dismissLocusLabel();const n=this.calculateViewportWidth(1+this.referenceFrameList.length)/this.calculateViewportWidth(this.referenceFrameList.length);await this.rescaleForMultiLocus(n)}async gotoMultilocusPanel(e){const t=this.referenceFrameList.indexOf(e);this.columnContainer.querySelectorAll(\".igv-column\").forEach(((e,i)=>{i===t||e.remove()})),this.columnContainer.querySelectorAll(\".igv-column-shim\").forEach((e=>e.remove()));for(let e of this.trackViews){const i=e.viewports[t];e.viewports.filter(((e,i)=>i!==t)).forEach((e=>e.dispose())),e.viewports=[i]}const i=this.calculateViewportWidth(1);e.bpPerPixel=(e.end-e.start)/i,this.referenceFrameList=[e],this.trackViews.forEach((({viewports:e})=>e.forEach((e=>e.setWidth(i))))),this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}async rescaleForMultiLocus(e){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel*=e;for(let{viewports:e}of this.trackViews)for(let i of e)i.setWidth(t);this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews()}async goto(e,t,i){await this.search(e+\":\"+t+\"-\"+i)}async doSearch(e,t){const i=await this.search(e,t);return i||this.alert.present(new Error(`Unrecognized locus: <b> ${e} </b>`)),i}async search(e,t){const i=await async function(e,t){if(void 0===t||\"\"===t.trim())return;const i=t.split(\" \");let n=[];const r=async t=>{if(\"all\"===t.trim().toLowerCase()||\"*\"===t)return e.genome.wholeGenomeView?{chr:\"all\",start:0,end:e.genome.getChromosome(\"all\").bpLength}:void 0;let i,n;if(t.includes(\":\")&&(i=ey(t,e.isSoftclipped()),i&&(n=await e.genome.loadChromosome(i.chr))),!n){i=void 0;const r=await Jv(e,t);r&&(i={chr:r.chr,start:r.start,end:r.end,name:(r.name||t).toUpperCase()}),i||(n=await e.genome.loadChromosome(t),n&&(i={chr:n.name}))}return i&&(n=n||await e.genome.loadChromosome(i.chr),i.chr=n.name,void 0===i.start&&void 0===i.end&&(i.start=0,i.end=n.bpLength)),i};for(let e of i){const t=await r(e);t&&n.push(t)}if(0===n.length){const e=await r(t.replaceAll(\" \",\"+\"));e&&n.push(e)}return 0===n.length?void 0:n}(this,e);if(i&&i.length>0){this.referenceFrameList=function(e,t,i,n,r,s){return e.map((e=>{const o=Object.assign({},e);if(i&&o.name&&(o.start=Math.max(0,o.start-i),o.end+=i),!s){const e=t.getChromosome(o.chr);Qa(e.bpLength,o,n)}return new vy(t,o.chr,o.start,o.end,(o.end-o.start)/r)}))}(i,this.genome,this.flanking,this.minimumBases(),this.calculateViewportWidth(i.length),this.isSoftclipped());for(let e of this.trackViews)e.removeViewportsFromColumnContainer();this.columnContainer.querySelectorAll(\".igv-column-shim, .igv-column\").forEach((e=>e.remove())),qy(this.columnContainer.querySelector(\".igv-sample-info-column\"),this.referenceFrameList.length),this.fireEvent(\"didchangecolumnlayout\");for(let e of this.trackViews)e.createViewports(this,this.columnContainer,this.referenceFrameList);return this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),t||await this.updateViews(),!0}return!1}async loadSampleInfo(e){await this.sampleInfo.loadSampleInfoFile(e.url);for(const{sampleInfoViewport:e}of this.trackViews)e.setWidth(this.getSampleInfoColumnWidth());this.findTracks((e=>\"function\"==typeof e.getSamples)).length>0&&(this.sampleInfoControl.performClickWithState(this,!0),this.sampleInfoControl.setButtonVisibility(!0));for(const{sampleInfoViewport:e}of this.trackViews)e.repaint()}getSampleInfoColumnWidth(){if(this.sampleInfo.attributeCount){const e=this.findTracks((e=>\"function\"==typeof e.getSamples)).length>0,t=this.sampleInfo.hasAttributes(),i=this.sampleInfoControl.showSampleInfo;return e&&t&&i?this.sampleInfo.attributeCount*Vu+8:0}return 0}on(e,t){this.eventHandlers[e]||(this.eventHandlers[e]=[]),this.eventHandlers[e].push(t)}un(e,t){this.off(e,t)}off(e,t){if(e)if(t){const i=this.eventHandlers[e];if(i&&0!==i.length){const n=i.indexOf(t);-1!==n&&this.eventHandlers[e].splice(n,1)}else console.warn(\"No handlers to remove for event: \"+e)}else this.eventHandlers[e]=[];else this.eventHandlers={}}fireEvent(e,t,i){const n=this.eventHandlers[e];if(void 0===n||0===n.length)return;const r=i||window;return n.map((function(e){return e.apply(r,t)}))[0]}dispose(){this.removeEventHandlers();for(let e of this.trackViews)e.dispose();this.roiManager&&this.roiManager.dispose()}toJSON(){const e={version:\"3.0.9\"};if(void 0!==this.showSampleNames&&(e.showSampleNames=this.showSampleNames),this.sampleNameViewportWidth&&(e.sampleNameViewportWidth=this.sampleNameViewportWidth),e.reference=this.genome.toJSON(),e.reference.fastaURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.fastaURL.name}.`);if(e.reference.indexURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.indexURL.name}.`);const t=[];let i=this.trackViews[0];for(let{referenceFrame:e}of i.viewports){const i=e.getLocusString();t.push(i)}e.locus=1===t.length?t[0]:t,e.roi=this.roiManager.toJSON(),this.qtlSelections.isEmpty()||(e.qtlSelections=this.qtlSelections.toJSON());const n=[],r=[];for(const{track:e}of this.trackViews)try{let t;\"function\"==typeof e.getState?t=Hl.localFileInspection(e.getState()):e.config&&(t=Hl.localFileInspection(e.config)),t&&(t.browser&&delete t.browser,t.order=e.order,n.push(t))}catch(t){const i=`Track: ${e.name}: ${t}`;console.error(i),r.push(i)}if(r.length>0){let e=1,t=\"Errors encountered saving session: </br>\";for(let i of r)t+=` (${e++}) ${i.toString()} <br/>`;throw Error(t)}e.tracks=n;const s=[];for(const e of n)for(const t of Object.keys(e))\"file\"!==t&&\"indexFile\"!==t||s.push(e[t]);const o=[];if(this.sampleInfo.sampleInfoFiles.length>0){const t=this.sampleInfo.toJSON();t.length>0&&(e.sampleinfo=t);for(const e of this.sampleInfo.sampleInfoFiles){const t=Hl.localFileInspection({url:e});t.file&&o.push(t.file)}o.length>0&&s.push(...o)}return s.length>0&&alert(`This session includes reference(s) to local file(s):\\n${s.map((e=>`    ${e}`)).join(\"\\n\")}\\nLocal files cannot be loaded automatically when a saved session is restored.`),e}compressedSession(){return function(e){const t=new Uint8Array(e.length);for(var i=0;i<e.length;i++)t[i]=e.charCodeAt(i);const n=new cs(t),r=String.fromCharCode.apply(null,n);return btoa(r).replace(/\\+/g,\".\").replace(/\\//g,\"_\").replace(/=/g,\"-\")}(JSON.stringify(this.toJSON()))}sessionURL(){const e=window.location.href.slice(),t=e.indexOf(\"?\");return(t>0?e.substring(0,t):e)+\"?sessionURL=blob:\"+this.compressedSession()}mouseDownOnViewport(e,t){var i;i=r(e),this.vpMouseDown={viewport:t,lastMouseX:i.x,mouseDownX:i.x,lastMouseY:i.y,mouseDownY:i.y,referenceFrame:t.referenceFrame}}cancelTrackPan(){const e=this.dragObject;this.dragObject=void 0,this.isScrolling=!1,this.vpMouseDown=void 0,e&&e.viewport.referenceFrame.start!==e.start&&(this.updateViews(),this.fireEvent(\"trackdragend\",[e.viewport]))}isTrackPanning(){return this.dragObject}isSoftclipped(){return void 0!==this.trackViews.find((e=>!0===e.track.showSoftClips))}startTrackDrag(e){this.dragTrack=e}updateTrackDrag(e){if(e&&this.dragTrack){const t=this.dragTrack,i=this.trackViews.indexOf(e),n=this.trackViews.indexOf(t),r=this.trackViews;r[i]=t,r[n]=e;const s=this.trackViews[i].track.order;this.trackViews[n].track.order=s;const o=r.length;let a=s;if(i<n)for(let e=i+1;e<o;e++){const t=r[e].track;if(!(t.order<=a))break;t.order=Math.min(Number.MAX_SAFE_INTEGER,a+1),a=t.order}else for(let e=i-1;e>0;e--){const t=r[e].track;if(!(t.order>=a))break;t.order=Math.max(-Number.MAX_SAFE_INTEGER,a-1),a=t.order}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()])):this.dragTrack=void 0}addEventHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers(),this.addKeyboardHandler()}removeEventHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers(),this.removeKeyboardHandler()}addWindowResizeHandler(){this.boundWindowResizeHandler=uA.bind(this),window.addEventListener(\"resize\",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener(\"resize\",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=pA.bind(this),this.root.addEventListener(\"mouseup\",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener(\"mouseup\",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=pA.bind(this),this.root.addEventListener(\"mouseleave\",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener(\"mouseleave\",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=fA.bind(this),this.boundColumnContainerTouchMoveHandler=fA.bind(this),this.boundColumnContainerMouseLeaveHandler=pA.bind(this),this.boundColumnContainerMouseUpHandler=pA.bind(this),this.boundColumnContainerTouchEndHandler=pA.bind(this),this.columnContainer.addEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener(\"touchmove\",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener(\"mouseleave\",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener(\"touchend\",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener(\"touchmove\",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener(\"mouseleave\",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener(\"touchend\",this.boundColumnContainerTouchEndHandler)}addKeyboardHandler(){this.keyUpHandler=gA.bind(this),document.addEventListener(\"keyup\",this.keyUpHandler)}removeKeyboardHandler(){console.log(\"Remove handler\"),document.addEventListener(\"keyup\",this.keyUpHandler)}static uncompressSession(e){let t;if(e.indexOf(\"/gzip;base64\")>0){t=vs(e);let i=\"\";for(let e of t)i+=String.fromCharCode(e);return i}return function(e){e=e.replace(/\\./g,\"+\").replace(/_/g,\"/\").replace(/-/g,\"=\");const t=atob(e),i=[];for(let e=0;e<t.length;e++)i.push(t.charCodeAt(e));const n=hs(i);let r=\"\";for(let e of n)r+=String.fromCharCode(e);return r}(e.substring(5))}createCircularView(e,t){var i;return t=!0===t,this.circularView=(i=this,new Bm(e,{onChordClick:(e,t,n)=>{const r=e.data,s=r.mate;function o(e){e.chr=i.genome.getChromosomeName(e.refName);let t=!1;for(let n of i.referenceFrameList){const i=lm.fromLocusString(n.getLocusString());if(i.contains(e)){t=!0;break}if(i.overlaps(e)){n.extend(e),t=!0;break}}if(!t){const t=2e3,n=(e.start+e.end)/2;i.addMultiLocusPanel(e.chr,n-t,n+t)}}o(r),o(s)}})),this.circularViewControl=new Vy(this.navbar.toggle_button_container,this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Hm(this.genome)}),this.circularViewVisible=t,this.circularView}get circularViewVisible(){return void 0!==this.circularView&&this.circularView.visible}set circularViewVisible(e){this.circularView&&(this.circularView.visible=e,this.circularViewControl.setState(e))}get sampleInfoControl(){return this.navbar.sampleInfoControl}get overlayTrackButton(){return this.navbar.overlayTrackButton}get roiTableControl(){return this.navbar.roiTableControl}get sampleInfoControl(){return this.navbar.sampleInfoControl}get sampleNameControl(){return this.navbar.sampleNameControl}}async function uA(){if(!this.referenceFrameList)return;const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList){const i=this.referenceFrameList.indexOf(t),{chr:n,genome:r}=t,{bpLength:s}=r.getChromosome(t.chr),o=t.toBP(e);mu.isWholeGenomeView(n)||o>s?t.bpPerPixel=s/e:t.end=t.start+t.toBP(e);for(let{viewports:t}of this.trackViews)t[i].setWidth(e)}this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}function fA(e){e.preventDefault();const{x:t,y:i}=r(e);if(this.vpMouseDown){const{viewport:e,referenceFrame:n}=this.vpMouseDown,r=Math.abs(t-this.vpMouseDown.mouseDownX)>Math.abs(i-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling)if(r)this.vpMouseDown.mouseDownX&&Math.abs(t-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:e,start:n.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(i-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const t=e.$viewport.height(),i=e.trackView.maxViewportContentHeight();this.vpMouseDown.r=t/i}if(this.dragObject){const i=!this.isSoftclipped();let r=this.vpMouseDown.lastMouseX-t;n.shiftPixels(r,e.$viewport.width(),i)&&this.updateViews(),this.fireEvent(\"trackdrag\")}if(this.isScrolling){const t=this.vpMouseDown.r*(this.vpMouseDown.lastMouseY-i);e.trackView.moveScroller(t)}this.vpMouseDown.lastMouseX=t,this.vpMouseDown.lastMouseY=i}}function pA(e){this.cancelTrackPan(),this.endTrackDrag()}async function gA(e){if(this.referenceFrameList&&!(this.referenceFrameList.length>1)&&(\"KeyF\"===e.code||\"KeyB\"===e.code)){const t=this.getSelectedTrackViews();if(t.length>0){const i=t[0].track;if(\"function\"==typeof i.nextFeatureAfter){const t=this.referenceFrameList[0],n=t.viewport?t.viewport.getWidth():this.calculateViewportWidth(this.referenceFrameList.length),r=\"all\"===t.chr.toLowerCase(),s=i.visibilityWindow;if(r||s&&s>0&&t.bpPerPixel*n>s)return;const o=\"KeyF\"===e.code,a=t.chr,c=t.center,l=await i.nextFeatureAfter(a,c,o);if(l){const i=await this.genome.getChromosomeName(l.chr);if(a===i){const i=(l.start+l.end)/2;if(e.shiftKey){const e=this.config.minimumBases||40,r=Math.max(e,1.1*(l.end-l.start));t.start=Math.max(0,i-r/2),t.end=i+r/2,t.bpPerPixel=(t.end-t.start)/n}else t.shift(i-c);this.updateViews()}else{t.chr=i;const r=(l.start+l.end)/2;if(e.shiftKey){const e=this.config.minimumBases||40,i=Math.max(e,1.1*(l.end-l.start));t.start=Math.max(0,r-i/2),t.end=t.start+i,t.bpPerPixel=(t.end-t.start)/n}else t.start=r-n*t.bpPerPixel/2,t.end=t.start+n*t.bpPerPixel;this.updateViews()}}}}}}function mA(e,t){for(let{viewports:i}of e)for(let e of i)e.$trackLabel&&(0===i.indexOf(e)&&!0===t?e.$trackLabel.show():e.$trackLabel.hide())}let wA=[];function bA(e){return void 0===e.minimumBases&&(e.minimumBases=40),void 0===e.showIdeogram&&(e.showIdeogram=!0),void 0===e.showCircularView&&(e.showCircularView=!1),void 0===e.showCircularViewButton&&(e.showCircularViewButton=!1),void 0===e.showTrackLabelButton&&(e.showTrackLabelButton=!0),void 0===e.showTrackLabels&&(e.showTrackLabels=!0),void 0===e.showCursorTrackingGuideButton&&(e.showCursorTrackingGuideButton=!0),void 0===e.showCursorGuide&&(e.showCursorGuide=e.showCursorTrackingGuide||!1),void 0===e.showCenterGuideButton&&(e.showCenterGuideButton=!0),void 0===e.showCenterGuide&&(e.showCenterGuide=!1),void 0===e.showSampleNames&&(e.showSampleNames=!1),void 0===e.showSVGButton&&(e.showSVGButton=!0),void 0===e.showControls&&(e.showControls=!0),void 0===e.showNavigation&&(e.showNavigation=!0),void 0===e.showRuler&&(e.showRuler=!0),void 0===e.flanking&&(e.flanking=1e3),void 0===e.pairsSupported&&(e.pairsSupported=!0),e.tracks||(e.tracks=[]),e}const FA=Qs.setApiKey;const vA=Qs.oauth;var yA={TrackUtils:Pa,IGVGraphics:xo,MenuUtils:bo,DataRangeDialog:_o,createTrack:async function(e,t){return await dA.prototype.createTrack.call(t,e)},createBrowser:async function(e,t){void 0===t&&(t={}),mu.KNOWN_GENOMES||await mu.initializeGenomes(t),bA(t),t.queryParametersSupported&&function(e){var t,i,n,r,s,o,a,c,l;let h,d,u;if(a=window.location.href,s={},t=a.indexOf(\"?\"),i=a.lastIndexOf(\"#\"),t>=0)for(i<0&&(i=a.length),n=t+1;n<i;)(r=a.indexOf(\"&\",n))<0&&(r=i),2===(o=a.substring(n,r).split(\"=\",2)).length?(c=o[0],l=decodeURIComponent(o[1]),\"file\"===c?h=l.split(\",\"):\"index\"===c?d=l.split(\",\"):\"name\"===c?u=l.split(\",\"):\"genome\"===c?!l.startsWith(\"https://\")&&!l.startsWith(\"http://\")||l.endsWith(\".json\")?(e[c]=l,e.reference=void 0):e.reference={fastaURL:l,indexURL:l+\".fai\"}:(\"reference\"===c&&(e.genome=void 0),e[c]=l),n=r+1):n++;if(h){e.tracks||(e.tracks=[]);for(let t=0;t<h.length;t++){if(h[t].endsWith(\".xml\")||h[t].endsWith(\".json\")){e.sessionURL=h[t];break}const i={url:h[t]};d&&d.length>t&&(i.indexURL=d[t]),u&&u.length>t&&(i.name=u[t]),e.tracks.push(i)}}}(t),t.apiKey&&Qs.setApiKey(t.apiKey),t.oauthToken&&Qs.setOauthToken(t.oauthToken),t.clientId&&!Ts()&&await async function(e){if(!google.accounts.oauth2.initTokenClient)throw new Error(\"Google accounts token client not loaded (https://accounts.google.com/gsi/client)\");if(Ts())throw new Error(\"Google client is already initialized\");const t={client_id:e.client_id||e.clientId,scope:e.scope||\"https://www.googleapis.com/auth/userinfo.profile\",state:e.state||\"igv\",error:e=>{throw new Error(e.type)},hint:e.hint,hosted_domain:e.hosted_domain},i=google.accounts.oauth2.initTokenClient(t);google.igv={tokenClient:i,apiKey:e.apiKey}}({client_id:t.clientId,apiKey:t.apiKey,scope:\"https://www.googleapis.com/auth/userinfo.profile\"});const i=new dA(t,e);wA.push(i),i.startSpinner();const n=t.sessionURL||t.session||t.hubURL;return n?await i.loadSession({url:n}):await i.loadSessionObject(t),i.stopSpinner(),i.navbar.navbarDidResize(),i},removeBrowser:function(e){e.dispose(),e.root.remove(),wA=wA.filter((t=>t!==e))},removeAllBrowsers:function(){for(let e of wA)e.dispose(),e.root.remove();wA=[]},visibilityChange:async function(){for(let e of wA)await e.visibilityChange()},setGoogleOauthToken:function(e){return Qs.setOauthToken(e)},setOauthToken:function(e,t){return Qs.setOauthToken(e,t)},oauth:vA,version:yy,setApiKey:FA,TrackBase:Hl,registerTrackClass:function(e,t){wy.set(e,((e,i)=>new t(e,i)))},registerTrackCreatorFunction:function(e,t){wy.set(e,t)},registerFileFormats:function(e,t){Sl[e]={fields:t}},loadSessionFile:dA.loadSessionFile};return yA}();\n",
-       "//# sourceMappingURL=igv.iife.js.map\n"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "/**\n",
-       " * Global handler for igv.js messages.  Messages have the form\n",
-       " * {\n",
-       " *     command  -- the command to execute\n",
-       " *     id -- the id of the igv.js browser, if applicable\n",
-       " *     data -- any data needed for the command\n",
-       " * }\n",
-       " */\n",
-       "\n",
-       "// Use a self-evaluating function to keep variables in this file scope, with the execption of the global handler\n",
-       "\n",
-       "(function () {\n",
-       "\n",
-       "    const isColab = window.google !== undefined && window.google.colab\n",
-       "    const isNotebook = !isColab && window.Jupyter !== undefined\n",
-       "\n",
-       "    let svgComm\n",
-       "    if (isNotebook) {\n",
-       "        svgComm = Jupyter.notebook.kernel.comm_manager.new_comm('svg', {})\n",
-       "    }\n",
-       "\n",
-       "    async function toSVG(displayID, locus, svg) {\n",
-       "        //console.log(isNotebook + \" \" + locus)\n",
-       "        if (isNotebook) {\n",
-       "            svgComm.send({\n",
-       "                \"display_id\": displayID,\n",
-       "                \"locus\": locus,\n",
-       "                \"svg\": svg\n",
-       "            })\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    console.log(\"Installing IGVMessageHandler\")\n",
-       "\n",
-       "    function convertUrlsAndPaths(session) {\n",
-       "        if (session.reference) {\n",
-       "            for (let pre of [\"fasta\", \"index\", \"cytoband\", \"cytobandBb\", \"compressedIndex\", \"alias\", \"aliasBb\",\n",
-       "            \"twoBit\", \"twoBitBpt\", \"chromAliasBb\", \"chromSizes\", \"trix\"]) {\n",
-       "                convert(session.reference, pre)\n",
-       "            }\n",
-       "            if (session.reference.tracks) {\n",
-       "                for (let t of session.reference.tracks) {\n",
-       "                    convert(t)\n",
-       "                    convert(t, \"index\")\n",
-       "                    if (!t.indexURL) {\n",
-       "                        t.indexed = false\n",
-       "                    }\n",
-       "                }\n",
-       "            }\n",
-       "        }\n",
-       "\n",
-       "        if (session.tracks) {\n",
-       "            for (let t of session.tracks) {\n",
-       "                convert(t)\n",
-       "                convert(t, \"index\")\n",
-       "                if (!t.indexURL) {\n",
-       "                    t.indexed = false\n",
-       "                }\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Return true if the sessionJson object contains only absolute URLs to resources\n",
-       "     */\n",
-       "    function safeToWeblink(sessionJson) {\n",
-       "        const unsafe = (url) => typeof url.startsWith != 'function' || !url.startsWith(\"http\")\n",
-       "        if (sessionJson.reference) {\n",
-       "            if (unsafe(sessionJson.reference.fastaURL)) return false\n",
-       "        }\n",
-       "        if (sessionJson.tracks) {\n",
-       "            const urls = sessionJson.tracks.filter(t => t.url).map(t => t.url)\n",
-       "            if (urls.some(unsafe)) return false\n",
-       "        }\n",
-       "        return true\n",
-       "    }\n",
-       "\n",
-       "    class MessageHandler {\n",
-       "\n",
-       "        constructor() {\n",
-       "            this.browserCache = new Map()\n",
-       "            this.messageQueue = new Queue()\n",
-       "        }\n",
-       "\n",
-       "        on(msg) {\n",
-       "            this.messageQueue.enqueue(msg)\n",
-       "            this.processQueue()\n",
-       "        }\n",
-       "\n",
-       "        async processQueue() {\n",
-       "\n",
-       "            const convertTrackData = (data) => {\n",
-       "                convert(data)\n",
-       "                convert(data, \"index\")\n",
-       "                if (!data.indexURL) {\n",
-       "                    data.indexed = false\n",
-       "                }\n",
-       "            }\n",
-       "\n",
-       "            if (!this.processing) {\n",
-       "                this.processing = true\n",
-       "                while (!this.messageQueue.isEmpty()) {\n",
-       "                    const msg = this.messageQueue.dequeue()\n",
-       "                    const command = msg.command\n",
-       "                    const browserID = msg.id\n",
-       "                    const data = msg.data\n",
-       "                    const browser = this.browserCache.get(browserID)\n",
-       "                    try {\n",
-       "                        switch (command) {\n",
-       "                            case \"createBrowser\":\n",
-       "\n",
-       "                                // custom button bar\n",
-       "                                const button_container = document.getElementById(`${browserID}_buttons`) // <= created from python\n",
-       "                                const customButtonDiv = document.createElement('div')\n",
-       "                                customButtonDiv.style = `background: #f3f3f3;padding: 5px;border-color: #bfbfbf;border-style: solid;border-width: thin;border-radius: 3px;`\n",
-       "                                button_container.appendChild(customButtonDiv)\n",
-       "\n",
-       "                                data.sync = true\n",
-       "                                convertUrlsAndPaths(data)\n",
-       "\n",
-       "                                const container = document.getElementById(`${browserID}_igvcontainer`)  // <= created from python\n",
-       "                                const newBrowser = await igv.createBrowser(container, data)\n",
-       "                                this.browserCache.set(browserID, newBrowser)\n",
-       "\n",
-       "                                // Add igv-notebook button bar\n",
-       "                                const toJsonButton = document.createElement('button')\n",
-       "                                toJsonButton.innerText = \"Save Session\"\n",
-       "                                toJsonButton.style = \"margin-right:5px\"\n",
-       "                                toJsonButton.addEventListener('click', (evt) => {\n",
-       "                                    let fn\n",
-       "                                    if (isNotebook) {\n",
-       "                                        fn = prompt(\"Filename:\", \"session.json\")\n",
-       "                                    } else {\n",
-       "                                        fn = \"session.json\"\n",
-       "                                    }\n",
-       "                                    if (fn) {\n",
-       "                                        const json = newBrowser.toJSON()\n",
-       "                                        const jsonString = JSON.stringify(json, null, '\\t')\n",
-       "                                        download(fn, jsonString)\n",
-       "                                    }\n",
-       "                                })\n",
-       "                                customButtonDiv.appendChild(toJsonButton)\n",
-       "\n",
-       "                                const webLinkNode = document.createElement('a')\n",
-       "                                webLinkNode.target = \"igvWeb\"\n",
-       "                                webLinkNode.innerText = \"Link to IGV-Web\"\n",
-       "                                webLinkNode.style.display = \"none\"\n",
-       "\n",
-       "                                const shareButton = document.createElement('button')\n",
-       "                                shareButton.innerText = \"Show IGV-Web Link\"\n",
-       "                                shareButton.style = \"margin-right:5px\"\n",
-       "                                shareButton.addEventListener('click', async (evt) => {\n",
-       "\n",
-       "                                    if (safeToWeblink(newBrowser.toJSON())) {\n",
-       "                                        const sessionURL = `https://igv.org/app?sessionURL=blob:${newBrowser.compressedSession()}`\n",
-       "                                        const shortURL = await shortenURL(sessionURL)\n",
-       "                                        webLinkNode.innerText = \"Link to IGV-Web\"\n",
-       "                                        webLinkNode.setAttribute(\"href\", shortURL)\n",
-       "                                        webLinkNode.style.display = \"inline-block\"\n",
-       "                                        shareButton.innerText = \"Update IGV-Web Link\"\n",
-       "                                    } else {\n",
-       "                                        webLinkNode.innerText = \"Cannot link -- non URL resources used\"\n",
-       "                                        webLinkNode.style.display = \"inline-block\"\n",
-       "                                    }\n",
-       "                                })\n",
-       "                                customButtonDiv.appendChild(shareButton)\n",
-       "                                customButtonDiv.appendChild(webLinkNode)\n",
-       "\n",
-       "                                if (isNotebook) {\n",
-       "                                    const toSVGButton = document.createElement('button')\n",
-       "                                    toSVGButton.innerText = \"To SVG\"\n",
-       "                                    toSVGButton.style = \"float:right\"\n",
-       "                                    toSVGButton.addEventListener('click', (evt) => {\n",
-       "                                        const locus = newBrowser.referenceFrameList.map(rf => rf.getLocusString()).join(' ')\n",
-       "                                        const svg = newBrowser.toSVG()\n",
-       "                                        toSVG(browserID, locus, svg)\n",
-       "                                    })\n",
-       "                                    customButtonDiv.appendChild(toSVGButton)\n",
-       "                                }\n",
-       "\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadSession\":\n",
-       "                                convertUrlsAndPaths(data)\n",
-       "                                browser.loadSessionObject(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadTrack\":\n",
-       "                                convertTrackData(data)\n",
-       "                                await browser.loadTrack(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadROI\":\n",
-       "                                if (Array.isArray(data)) {\n",
-       "                                    data.map(convertTrackData)\n",
-       "                                } else {\n",
-       "                                    convertTrackData(data)\n",
-       "                                }\n",
-       "                                await browser.loadROI(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"clearROIs\":\n",
-       "                                await browser.clearROIs()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"search\":\n",
-       "                                browser.search(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"zoomIn\":\n",
-       "                                browser.zoomIn()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"zoomOut\":\n",
-       "                                browser.zoomOut()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"remove\":\n",
-       "                                this.browserCache.delete(browserID)\n",
-       "                                document.getElementById(browserID).parentNode.removeChild(container)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"toSVG\":\n",
-       "                                const displayId = data\n",
-       "                                const svg = browser.toSVG()\n",
-       "                                const locus = browser.referenceFrameList.map(rf => rf.getLocusString()).join(' ')\n",
-       "                                toSVG(displayId, locus, svg)\n",
-       "                                break\n",
-       "\n",
-       "                            default:\n",
-       "                                console.error(\"Unrecognized method: \" + msg.command)\n",
-       "                        }\n",
-       "                    } catch (e) {\n",
-       "                        console.error(e)\n",
-       "                    }\n",
-       "                }\n",
-       "                this.processing = false\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Potentially convert a path to a local File-like object.\n",
-       "     * @param path\n",
-       "     * @returns {*}\n",
-       "     */\n",
-       "    function createNotebookFile(path) {\n",
-       "        if (!path ||\n",
-       "            path.startsWith(\"https://\") || path.startsWith(\"http://\") || path.startsWith(\"gs://\") || path.startsWith(\"data:\")) {\n",
-       "            return path\n",
-       "        } else {\n",
-       "            // Try to create a notebook file.  If no notebook file implementation is available for the kernel in\n",
-       "            // use (e.g. Jupyter Lab) treat as a URL.\n",
-       "            const nbFile = igv.createNotebookLocalFile({path})\n",
-       "            if (nbFile != null) {\n",
-       "                return nbFile\n",
-       "            } else {\n",
-       "                // Try to treat as relative URL.  This may or may not work\n",
-       "                return convertURL(path)\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Convert relative URLs to absolute.  Primarily for Jupyter Lab, not generally needed for Jupyter Notebook\n",
-       "     * @param url\n",
-       "     * @returns {*}\n",
-       "     */\n",
-       "    function convertURL(url) {\n",
-       "\n",
-       "        const pageURL = window.location.href\n",
-       "\n",
-       "        if (!url ||\n",
-       "            url.startsWith(\"https://\") ||\n",
-       "            url.startsWith(\"http://\") ||\n",
-       "            url.startsWith(\"gs://\") ||\n",
-       "            url.startsWith(\"data:\")) {\n",
-       "            return url\n",
-       "        } else if (isColab) {\n",
-       "            // Interpret relative url as a path.\n",
-       "            igv.createNotebookLocalFile({path: url})\n",
-       "        } else if (isNotebook) {\n",
-       "            // Jupyter Notebook\n",
-       "            //\n",
-       "            // Examples\n",
-       "            // https://hub-binder.mybinder.ovh/user/igvteam-igv-notebook-tnlb45ie/notebooks/examples/BamFiles-Jupyter.ipynb\n",
-       "            //   => https://hub-binder.mybinder.ovh/user/igvteam-igv-notebook-tnlb45ie/files/examples/data/gstt1_sample.bam\",\n",
-       "\n",
-       "            const baseURL = document.querySelector('body').getAttribute('data-base-url')\n",
-       "            const notebookPath = document.querySelector('body').getAttribute('data-notebook-path')\n",
-       "            const notebookName = document.querySelector('body').getAttribute('data-notebook-name')\n",
-       "            const notebookDir = notebookPath.slice(0, -1 * notebookName.length)\n",
-       "\n",
-       "            //`${location.origin}${base_path}files/${nb_dir}${url}`\n",
-       "            if (url.startsWith(\"/\")) {\n",
-       "                url = `files${url}`\n",
-       "                return encodeURI(`${location.origin}${baseURL}${url}`)\n",
-       "            } else {\n",
-       "                // URL is relative to notebook\n",
-       "                return encodeURI(`${location.origin}${baseURL}files/${notebookDir}${url}`)\n",
-       "            }\n",
-       "        } else if (pageURL.includes(\"/lab\")) {\n",
-       "\n",
-       "            console.log(\"Jupyter lab\")\n",
-       "            // Jupyter Lab\n",
-       "\n",
-       "            // Examples\n",
-       "            // http://localhost:8888/lab/workspaces/auto-N/tree/examples/BamFiles.ipynb\n",
-       "            //     =>  http://localhost:8888/files/examples/data/gstt1_sample.bam\n",
-       "            //\n",
-       "            // https://hub.gke2.mybinder.org/user/igvteam-igv-notebook-5ivkyktt/lab/tree/examples/BamFiles.ipynb\n",
-       "            //    => https://hub.gke2.mybinder.org/user/igvteam-igv-notebook-5ivkyktt/files/examples/data/gstt1_sample.bam\n",
-       "\n",
-       "            const baseIndex = pageURL.indexOf(\"/lab\")\n",
-       "            const baseURL = pageURL.substring(0, baseIndex)\n",
-       "\n",
-       "            if (url.startsWith(\"/\")) {\n",
-       "                return encodeURI(`${baseURL}/files${url}`)\n",
-       "            } else if (pageURL.includes(\"/tree/\")) {\n",
-       "                // Interpret URL as relative to notebook location.  This is not reliable, '/tree/' is not always in the page URL\n",
-       "                const treeIndex = pageURL.indexOf(\"/tree/\") + 6\n",
-       "                const lastSlashIndex = pageURL.lastIndexOf(\"/\")\n",
-       "                const notebookDir = pageURL.substring(treeIndex, lastSlashIndex)\n",
-       "                return encodeURI(`${baseURL}/files/${notebookDir}/${url}`)\n",
-       "            } else {\n",
-       "                // We don't know how to determine the notebook path\n",
-       "                console.warn(\"Page url missing '/tree/'.  Can't determine notebook path.\")\n",
-       "                return encodeURI(`${baseURL}/files/${url}`)\n",
-       "            }\n",
-       "        } else {\n",
-       "            // We should never get here,\n",
-       "            return encodeURI(url)\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    function convert(config, prefix) {\n",
-       "        const urlProp = prefix ? prefix + \"URL\" : \"url\"\n",
-       "        const pathProp = prefix ? prefix + \"Path\" : \"path\"\n",
-       "        if (config[pathProp]) {\n",
-       "            config[urlProp] = createNotebookFile(config[pathProp])\n",
-       "        } else if (config[urlProp]) {\n",
-       "            config[urlProp] = convertURL(config[urlProp])\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
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-       "        constructor() {\n",
-       "            this.elements = []\n",
-       "        }\n",
-       "\n",
-       "        enqueue(e) {\n",
-       "            this.elements.push(e)\n",
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-       "\n",
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-       "            return this.elements.length\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    window.igv.MessageHandler = new MessageHandler()\n",
-       "\n",
-       "    function download(filename, text) {\n",
-       "\n",
-       "        const data = URL.createObjectURL(new Blob([text], {type: \"application/octet-stream\"}))\n",
-       "        const element = document.createElement('a')\n",
-       "        element.setAttribute('href', data)\n",
-       "        element.setAttribute('download', filename)\n",
-       "        element.style.display = 'none'\n",
-       "        document.body.appendChild(element)\n",
-       "        element.click()\n",
-       "        document.body.removeChild(element)\n",
-       "    }\n",
-       "\n",
-       "    async function shortenURL(url) {\n",
-       "        const endpoint = \"https://2et6uxfezb.execute-api.us-east-1.amazonaws.com/dev/tinyurl/\"\n",
-       "        const enc = encodeURIComponent(url)\n",
-       "        const response = await fetch(`${endpoint}${enc}`)\n",
-       "        if (response.ok) {\n",
-       "            return response.text()\n",
-       "        } else {\n",
-       "            throw new Error(response.statusText)\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    console.log(\"igv.MessageHandler installed\")\n",
-       "\n",
-       "})()"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "/**\n",
-       " * Mock objects to emulate the browser \"File\" class for use with Jupyter and Colab notebooks.  These objects delegate\n",
-       " * actual file reading to python.\n",
-       " */\n",
-       "\n",
-       "// Use a self-evaluating function to keep variables in this file scope\n",
-       "\n",
-       "(function () {\n",
-       "\n",
-       "    const isColab =  window.google !== undefined && window.google.colab\n",
-       "    const isNotebook =  !isColab &&  window.Jupyter !== undefined\n",
-       "\n",
-       "    igv.createNotebookLocalFile = function (options) {\n",
-       "        if (isColab) {\n",
-       "            return new ColabLocalFile(options)\n",
-       "        } else if (isNotebook) {\n",
-       "            return new JupyterLocalFile(options)\n",
-       "        } else {\n",
-       "            return undefined;  //TODO -- throw error?\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    // Start up a Comm object if in a Jupyter Notebook environment (i.e. not Colab or JupyterLab).\n",
-       "    let comm\n",
-       "    const pendingRequests = new Map()\n",
-       "    if (isNotebook) {\n",
-       "        console.log('registering comm')\n",
-       "        comm = Jupyter.notebook.kernel.comm_manager.new_comm('file_request', {})\n",
-       "        // Register a handler\n",
-       "        comm.on_msg(function (msg) {\n",
-       "            const id = msg.content.data.id\n",
-       "            const data = msg.content.data.data\n",
-       "            pendingRequests.set(id, data)\n",
-       "        })\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Emulates a browser \"File\" for Jupyter notebooks.  File reading is delegated to python via Comms messaging.\n",
-       "     * Polling is used to synchronize the async message passing.\n",
-       "     *\n",
-       "     * NOTE: This will not work for JupyterLab\n",
-       "     */\n",
-       "    class JupyterLocalFile {\n",
-       "\n",
-       "        constructor({path, name, start, end}) {\n",
-       "            this.type = 'JupyterLocalFile'\n",
-       "            this.path = path\n",
-       "            this.name = name || path\n",
-       "            this.start = start\n",
-       "            this.end = end\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a new Blob object containing the data in the specified range of bytes of the blob on which it's called.\n",
-       "         * @param start An index into the Blob indicating the first byte to include in the new Blob\n",
-       "         * @param end  An index into the Blob indicating the first byte that will *not* be included in the new Blob\n",
-       "         * @param contentType\n",
-       "         * @returns {*}\n",
-       "         */\n",
-       "        slice(start, end) {\n",
-       "            return new JupyterLocalFile({path: this.path, name: this.name, start, end})\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with an ArrayBuffer containing the entire contents of the Blob as binary data.\n",
-       "         *\n",
-       "         * @returns {Promise<*>}\n",
-       "         */\n",
-       "        async arrayBuffer() {\n",
-       "\n",
-       "            const id = uniqueID()\n",
-       "            const path = this.path\n",
-       "            const promise = new Promise((resolve, reject) => {\n",
-       "                let count = 0\n",
-       "\n",
-       "                function poll() {\n",
-       "\n",
-       "                    if (count > 100) {\n",
-       "                        console.error(`error reading ${path}: timed out`)\n",
-       "                        reject(`error reading ${path}: timed out`)\n",
-       "                    }\n",
-       "\n",
-       "                    count++\n",
-       "                    if (pendingRequests.has(id)) {\n",
-       "                        const data = pendingRequests.get(id)\n",
-       "                        const dataString = atob(data)\n",
-       "                        const bytes = new Uint8Array(dataString.length)\n",
-       "                        for (var i = 0; i < dataString.length; i++) {\n",
-       "                            bytes[i] = dataString.charCodeAt(i)\n",
-       "                        }\n",
-       "                        pendingRequests.delete(id)\n",
-       "                        resolve(bytes.buffer)\n",
-       "                    } else {\n",
-       "                        setTimeout(poll, 100)\n",
-       "                    }\n",
-       "                }\n",
-       "\n",
-       "                poll()\n",
-       "            })\n",
-       "\n",
-       "            const msg = (this.start === undefined) ?\n",
-       "                {id: id, 'path': this.path, 'method': 'arrayBuffer'} :\n",
-       "                {id: id, 'path': this.path, 'method': 'arrayBuffer', 'start': this.start, 'end': this.end}\n",
-       "\n",
-       "            comm.send(msg)\n",
-       "\n",
-       "            return promise\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with a USVString containing the entire contents of the Blob interpreted as UTF-8 text.\n",
-       "         *\n",
-       "         * @returns {Promise<string>}\n",
-       "         */\n",
-       "        async text() {\n",
-       "            throw Error(\"text not implemented\")\n",
-       "        }\n",
-       "\n",
-       "        stream() {\n",
-       "            throw Error(\"stream not implemented\")\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Emulates a browser \"File\" for Colab environments.\n",
-       "     */\n",
-       "    class ColabLocalFile {\n",
-       "\n",
-       "        constructor({path, name, start, end}) {\n",
-       "            this.type = 'ColabLocalFile'\n",
-       "            this.path = path\n",
-       "            this.name = name || path\n",
-       "            this.start = start\n",
-       "            this.end = end\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a new Blob object containing the data in the specified range of bytes of the blob on which it's called.\n",
-       "         * @param start An index into the Blob indicating the first byte to include in the new Blob\n",
-       "         * @param end  An index into the Blob indicating the first byte that will *not* be included in the new Blob\n",
-       "         * @param contentType\n",
-       "         * @returns {*}\n",
-       "         */\n",
-       "        slice(start, end) {\n",
-       "            return new ColabLocalFile({path: this.path, name: this.name, start, end})\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with an ArrayBuffer containing the entire contents of the Blob as\n",
-       "         * binary data.\n",
-       "         */\n",
-       "        async arrayBuffer() {\n",
-       "\n",
-       "            const args = (this.start === undefined) ?\n",
-       "                [this.path] :\n",
-       "                [this.path, this.start.toString(), this.end.toString()]\n",
-       "\n",
-       "            const result = await google.colab.kernel.invokeFunction(\n",
-       "                'ReadFile', // The callback name.\n",
-       "                args, // The arguments.\n",
-       "                {}) // kwargs\n",
-       "            const data = result.data[\"text/plain\"]\n",
-       "            const dataString = atob(data.substring(2, data.length - 1))\n",
-       "            const bytes = new Uint8Array(dataString.length)\n",
-       "            for (var i = 0; i < dataString.length; i++) {\n",
-       "                bytes[i] = dataString.charCodeAt(i)\n",
-       "            }\n",
-       "            return bytes.buffer\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with a USVString containing the entire contents of the Blob interpreted as UTF-8 text.\n",
-       "         *\n",
-       "         * @returns {Promise<string>}\n",
-       "         */\n",
-       "        async text() {\n",
-       "            throw Error(\"text not implemented\")\n",
-       "        }\n",
-       "\n",
-       "        stream() {\n",
-       "            throw Error(\"stream not implemented\")\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    let counter = 0\n",
-       "\n",
-       "    function uniqueID() {\n",
-       "        return `${Math.random()}-${counter++}`\n",
-       "    }\n",
-       "\n",
-       "})()"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/html": [
-       "<div id=\"jb_4232033_buttons\"></div><div id=\"jb_4232033_igvcontainer\"></div>"
-      ],
-      "text/plain": [
-       "<IPython.core.display.HTML object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "window.igv.MessageHandler.on({\"id\": \"jb_4232033\", \"command\": \"createBrowser\", \"data\": {\"reference\": {\"id\": \"AgamP4\", \"name\": \"Anopheles gambiae (PEST)\", \"fastaURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai\", \"tracks\": [{\"name\": \"Genes\", \"type\": \"annotation\", \"format\": \"gff3\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz\", \"indexed\": false}]}, \"locus\": \"2L:2,422,600-2,422,700\", \"id\": \"jb_4232033\"}})"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "<igv_notebook.browser.Browser at 0x11d5b2ef0>"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "ag3.igv(region=\"2L:2,422,600-2,422,700\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "id": "72d27502",
+   "execution_count": null,
+   "id": "3",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "                                     \r"
-     ]
-    },
-    {
-     "data": {
-      "application/javascript": [
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r;for(hi(e,t-257,5),hi(e,i-1,5),hi(e,n-4,4),r=0;r<n;r++)hi(e,e.bl_tree[2*Yt[r]+1],3);yi(e,e.dyn_ltree,t-1),yi(e,e.dyn_dtree,i-1)})(e,e.l_desc.max_code+1,e.d_desc.max_code+1,o+1),bi(e,e.dyn_ltree,e.dyn_dtree)),pi(e),n&&gi(e)},ki={_tr_init:_i,_tr_stored_block:Ci,_tr_flush_block:xi,_tr_tally:(e,t,i)=>(e.pending_buf[e.sym_buf+e.sym_next++]=t,e.pending_buf[e.sym_buf+e.sym_next++]=t>>8,e.pending_buf[e.sym_buf+e.sym_next++]=i,0===t?e.dyn_ltree[2*i]++:(e.matches++,t--,e.dyn_ltree[2*(ei[i]+Qt+1)]++,e.dyn_dtree[2*ci(t)]++),e.sym_next===e.sym_end),_tr_align:e=>{hi(e,2,3),di(e,256,Xt),(e=>{16===e.bi_valid?(li(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=255&e.bi_buf,e.bi_buf>>=8,e.bi_valid-=8)})(e)}};var Ii=(e,t,i,n)=>{let r=65535&e,s=e>>>16&65535,o=0;for(;0!==i;){o=i>2e3?2e3:i,i-=o;do{r=r+t[n++]|0,s=s+r|0}while(--o);r%=65521,s%=65521}return r|s<<16};const Si=new Uint32Array((()=>{let e,t=[];for(var i=0;i<256;i++){e=i;for(var n=0;n<8;n++)e=1&e?3988292384^e>>>1:e>>>1;t[i]=e}return t})());var Ei=(e,t,i,n)=>{const r=Si,s=n+i;e^=-1;for(let i=n;i<s;i++)e=e>>>8^r[255&(e^t[i])];return~e},Ni={2:\"need dictionary\",1:\"stream end\",0:\"\",\"-1\":\"file error\",\"-2\":\"stream error\",\"-3\":\"data error\",\"-4\":\"insufficient memory\",\"-5\":\"buffer error\",\"-6\":\"incompatible version\"},Bi={Z_NO_FLUSH:0,Z_PARTIAL_FLUSH:1,Z_SYNC_FLUSH:2,Z_FULL_FLUSH:3,Z_FINISH:4,Z_BLOCK:5,Z_TREES:6,Z_OK:0,Z_STREAM_END:1,Z_NEED_DICT:2,Z_ERRNO:-1,Z_STREAM_ERROR:-2,Z_DATA_ERROR:-3,Z_MEM_ERROR:-4,Z_BUF_ERROR:-5,Z_NO_COMPRESSION:0,Z_BEST_SPEED:1,Z_BEST_COMPRESSION:9,Z_DEFAULT_COMPRESSION:-1,Z_FILTERED:1,Z_HUFFMAN_ONLY:2,Z_RLE:3,Z_FIXED:4,Z_DEFAULT_STRATEGY:0,Z_BINARY:0,Z_TEXT:1,Z_UNKNOWN:2,Z_DEFLATED:8};const{_tr_init:Mi,_tr_stored_block:Ri,_tr_flush_block:Di,_tr_tally:Ti,_tr_align:Li}=ki,{Z_NO_FLUSH:zi,Z_PARTIAL_FLUSH:Hi,Z_FULL_FLUSH:Pi,Z_FINISH:Oi,Z_BLOCK:Ui,Z_OK:qi,Z_STREAM_END:Qi,Z_STREAM_ERROR:Vi,Z_DATA_ERROR:ji,Z_BUF_ERROR:Wi,Z_DEFAULT_COMPRESSION:Gi,Z_FILTERED:$i,Z_HUFFMAN_ONLY:Ki,Z_RLE:Yi,Z_FIXED:Xi,Z_DEFAULT_STRATEGY:Zi,Z_UNKNOWN:Ji,Z_DEFLATED:en}=Bi,tn=258,nn=262,rn=42,sn=113,on=666,an=(e,t)=>(e.msg=Ni[t],t),cn=e=>2*e-(e>4?9:0),ln=e=>{let t=e.length;for(;--t>=0;)e[t]=0},hn=e=>{let t,i,n,r=e.w_size;t=e.hash_size,n=t;do{i=e.head[--n],e.head[n]=i>=r?i-r:0}while(--t);t=r,n=t;do{i=e.prev[--n],e.prev[n]=i>=r?i-r:0}while(--t)};let dn=(e,t,i)=>(t<<e.hash_shift^i)&e.hash_mask;const un=e=>{const t=e.state;let i=t.pending;i>e.avail_out&&(i=e.avail_out),0!==i&&(e.output.set(t.pending_buf.subarray(t.pending_out,t.pending_out+i),e.next_out),e.next_out+=i,t.pending_out+=i,e.total_out+=i,e.avail_out-=i,t.pending-=i,0===t.pending&&(t.pending_out=0))},fn=(e,t)=>{Di(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,un(e.strm)},pn=(e,t)=>{e.pending_buf[e.pending++]=t},gn=(e,t)=>{e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=255&t},mn=(e,t,i,n)=>{let r=e.avail_in;return r>n&&(r=n),0===r?0:(e.avail_in-=r,t.set(e.input.subarray(e.next_in,e.next_in+r),i),1===e.state.wrap?e.adler=Ii(e.adler,t,r,i):2===e.state.wrap&&(e.adler=Ei(e.adler,t,r,i)),e.next_in+=r,e.total_in+=r,r)},wn=(e,t)=>{let i,n,r=e.max_chain_length,s=e.strstart,o=e.prev_length,a=e.nice_match;const c=e.strstart>e.w_size-nn?e.strstart-(e.w_size-nn):0,l=e.window,h=e.w_mask,d=e.prev,u=e.strstart+tn;let f=l[s+o-1],p=l[s+o];e.prev_length>=e.good_match&&(r>>=2),a>e.lookahead&&(a=e.lookahead);do{if(i=t,l[i+o]===p&&l[i+o-1]===f&&l[i]===l[s]&&l[++i]===l[s+1]){s+=2,i++;do{}while(l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&s<u);if(n=tn-(u-s),s=u-tn,n>o){if(e.match_start=t,o=n,n>=a)break;f=l[s+o-1],p=l[s+o]}}}while((t=d[t&h])>c&&0!=--r);return o<=e.lookahead?o:e.lookahead},bn=e=>{const t=e.w_size;let i,n,r;do{if(n=e.window_size-e.lookahead-e.strstart,e.strstart>=t+(t-nn)&&(e.window.set(e.window.subarray(t,t+t-n),0),e.match_start-=t,e.strstart-=t,e.block_start-=t,e.insert>e.strstart&&(e.insert=e.strstart),hn(e),n+=t),0===e.strm.avail_in)break;if(i=mn(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=i,e.lookahead+e.insert>=3)for(r=e.strstart-e.insert,e.ins_h=e.window[r],e.ins_h=dn(e,e.ins_h,e.window[r+1]);e.insert&&(e.ins_h=dn(e,e.ins_h,e.window[r+3-1]),e.prev[r&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=r,r++,e.insert--,!(e.lookahead+e.insert<3)););}while(e.lookahead<nn&&0!==e.strm.avail_in)},Fn=(e,t)=>{let i,n,r,s=e.pending_buf_size-5>e.w_size?e.w_size:e.pending_buf_size-5,o=0,a=e.strm.avail_in;do{if(i=65535,r=e.bi_valid+42>>3,e.strm.avail_out<r)break;if(r=e.strm.avail_out-r,n=e.strstart-e.block_start,i>n+e.strm.avail_in&&(i=n+e.strm.avail_in),i>r&&(i=r),i<s&&(0===i&&t!==Oi||t===zi||i!==n+e.strm.avail_in))break;o=t===Oi&&i===n+e.strm.avail_in?1:0,Ri(e,0,0,o),e.pending_buf[e.pending-4]=i,e.pending_buf[e.pending-3]=i>>8,e.pending_buf[e.pending-2]=~i,e.pending_buf[e.pending-1]=~i>>8,un(e.strm),n&&(n>i&&(n=i),e.strm.output.set(e.window.subarray(e.block_start,e.block_start+n),e.strm.next_out),e.strm.next_out+=n,e.strm.avail_out-=n,e.strm.total_out+=n,e.block_start+=n,i-=n),i&&(mn(e.strm,e.strm.output,e.strm.next_out,i),e.strm.next_out+=i,e.strm.avail_out-=i,e.strm.total_out+=i)}while(0===o);return a-=e.strm.avail_in,a&&(a>=e.w_size?(e.matches=2,e.window.set(e.strm.input.subarray(e.strm.next_in-e.w_size,e.strm.next_in),0),e.strstart=e.w_size,e.insert=e.strstart):(e.window_size-e.strstart<=a&&(e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,e.insert>e.strstart&&(e.insert=e.strstart)),e.window.set(e.strm.input.subarray(e.strm.next_in-a,e.strm.next_in),e.strstart),e.strstart+=a,e.insert+=a>e.w_size-e.insert?e.w_size-e.insert:a),e.block_start=e.strstart),e.high_water<e.strstart&&(e.high_water=e.strstart),o?4:t!==zi&&t!==Oi&&0===e.strm.avail_in&&e.strstart===e.block_start?2:(r=e.window_size-e.strstart,e.strm.avail_in>r&&e.block_start>=e.w_size&&(e.block_start-=e.w_size,e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,r+=e.w_size,e.insert>e.strstart&&(e.insert=e.strstart)),r>e.strm.avail_in&&(r=e.strm.avail_in),r&&(mn(e.strm,e.window,e.strstart,r),e.strstart+=r,e.insert+=r>e.w_size-e.insert?e.w_size-e.insert:r),e.high_water<e.strstart&&(e.high_water=e.strstart),r=e.bi_valid+42>>3,r=e.pending_buf_size-r>65535?65535:e.pending_buf_size-r,s=r>e.w_size?e.w_size:r,n=e.strstart-e.block_start,(n>=s||(n||t===Oi)&&t!==zi&&0===e.strm.avail_in&&n<=r)&&(i=n>r?r:n,o=t===Oi&&0===e.strm.avail_in&&i===n?1:0,Ri(e,e.block_start,i,o),e.block_start+=i,un(e.strm)),o?3:1)},vn=(e,t)=>{let i,n;for(;;){if(e.lookahead<nn){if(bn(e),e.lookahead<nn&&t===zi)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),0!==i&&e.strstart-i<=e.w_size-nn&&(e.match_length=wn(e,i)),e.match_length>=3)if(n=Ti(e,e.strstart-e.match_start,e.match_length-3),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=3){e.match_length--;do{e.strstart++,e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart}while(0!=--e.match_length);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=dn(e,e.ins_h,e.window[e.strstart+1]);else n=Ti(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(fn(e,!1),0===e.strm.avail_out))return 1}return e.insert=e.strstart<2?e.strstart:2,t===Oi?(fn(e,!0),0===e.strm.avail_out?3:4):e.sym_next&&(fn(e,!1),0===e.strm.avail_out)?1:2},yn=(e,t)=>{let i,n,r;for(;;){if(e.lookahead<nn){if(bn(e),e.lookahead<nn&&t===zi)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),e.prev_length=e.match_length,e.prev_match=e.match_start,e.match_length=2,0!==i&&e.prev_length<e.max_lazy_match&&e.strstart-i<=e.w_size-nn&&(e.match_length=wn(e,i),e.match_length<=5&&(e.strategy===$i||3===e.match_length&&e.strstart-e.match_start>4096)&&(e.match_length=2)),e.prev_length>=3&&e.match_length<=e.prev_length){r=e.strstart+e.lookahead-3,n=Ti(e,e.strstart-1-e.prev_match,e.prev_length-3),e.lookahead-=e.prev_length-1,e.prev_length-=2;do{++e.strstart<=r&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart)}while(0!=--e.prev_length);if(e.match_available=0,e.match_length=2,e.strstart++,n&&(fn(e,!1),0===e.strm.avail_out))return 1}else if(e.match_available){if(n=Ti(e,0,e.window[e.strstart-1]),n&&fn(e,!1),e.strstart++,e.lookahead--,0===e.strm.avail_out)return 1}else e.match_available=1,e.strstart++,e.lookahead--}return e.match_available&&(n=Ti(e,0,e.window[e.strstart-1]),e.match_available=0),e.insert=e.strstart<2?e.strstart:2,t===Oi?(fn(e,!0),0===e.strm.avail_out?3:4):e.sym_next&&(fn(e,!1),0===e.strm.avail_out)?1:2};function An(e,t,i,n,r){this.good_length=e,this.max_lazy=t,this.nice_length=i,this.max_chain=n,this.func=r}const Cn=[new An(0,0,0,0,Fn),new An(4,4,8,4,vn),new An(4,5,16,8,vn),new An(4,6,32,32,vn),new An(4,4,16,16,yn),new An(8,16,32,32,yn),new An(8,16,128,128,yn),new An(8,32,128,256,yn),new An(32,128,258,1024,yn),new An(32,258,258,4096,yn)];function _n(){this.strm=null,this.status=0,this.pending_buf=null,this.pending_buf_size=0,this.pending_out=0,this.pending=0,this.wrap=0,this.gzhead=null,this.gzindex=0,this.method=en,this.last_flush=-1,this.w_size=0,this.w_bits=0,this.w_mask=0,this.window=null,this.window_size=0,this.prev=null,this.head=null,this.ins_h=0,this.hash_size=0,this.hash_bits=0,this.hash_mask=0,this.hash_shift=0,this.block_start=0,this.match_length=0,this.prev_match=0,this.match_available=0,this.strstart=0,this.match_start=0,this.lookahead=0,this.prev_length=0,this.max_chain_length=0,this.max_lazy_match=0,this.level=0,this.strategy=0,this.good_match=0,this.nice_match=0,this.dyn_ltree=new Uint16Array(1146),this.dyn_dtree=new Uint16Array(122),this.bl_tree=new Uint16Array(78),ln(this.dyn_ltree),ln(this.dyn_dtree),ln(this.bl_tree),this.l_desc=null,this.d_desc=null,this.bl_desc=null,this.bl_count=new Uint16Array(16),this.heap=new Uint16Array(573),ln(this.heap),this.heap_len=0,this.heap_max=0,this.depth=new Uint16Array(573),ln(this.depth),this.sym_buf=0,this.lit_bufsize=0,this.sym_next=0,this.sym_end=0,this.opt_len=0,this.static_len=0,this.matches=0,this.insert=0,this.bi_buf=0,this.bi_valid=0}const xn=e=>{if(!e)return 1;const t=e.state;return!t||t.strm!==e||t.status!==rn&&57!==t.status&&69!==t.status&&73!==t.status&&91!==t.status&&103!==t.status&&t.status!==sn&&t.status!==on?1:0},kn=e=>{if(xn(e))return an(e,Vi);e.total_in=e.total_out=0,e.data_type=Ji;const t=e.state;return t.pending=0,t.pending_out=0,t.wrap<0&&(t.wrap=-t.wrap),t.status=2===t.wrap?57:t.wrap?rn:sn,e.adler=2===t.wrap?0:1,t.last_flush=-2,Mi(t),qi},In=e=>{const t=kn(e);var i;return t===qi&&((i=e.state).window_size=2*i.w_size,ln(i.head),i.max_lazy_match=Cn[i.level].max_lazy,i.good_match=Cn[i.level].good_length,i.nice_match=Cn[i.level].nice_length,i.max_chain_length=Cn[i.level].max_chain,i.strstart=0,i.block_start=0,i.lookahead=0,i.insert=0,i.match_length=i.prev_length=2,i.match_available=0,i.ins_h=0),t},Sn=(e,t,i,n,r,s)=>{if(!e)return Vi;let o=1;if(t===Gi&&(t=6),n<0?(o=0,n=-n):n>15&&(o=2,n-=16),r<1||r>9||i!==en||n<8||n>15||t<0||t>9||s<0||s>Xi||8===n&&1!==o)return an(e,Vi);8===n&&(n=9);const a=new _n;return e.state=a,a.strm=e,a.status=rn,a.wrap=o,a.gzhead=null,a.w_bits=n,a.w_size=1<<a.w_bits,a.w_mask=a.w_size-1,a.hash_bits=r+7,a.hash_size=1<<a.hash_bits,a.hash_mask=a.hash_size-1,a.hash_shift=~~((a.hash_bits+3-1)/3),a.window=new Uint8Array(2*a.w_size),a.head=new Uint16Array(a.hash_size),a.prev=new Uint16Array(a.w_size),a.lit_bufsize=1<<r+6,a.pending_buf_size=4*a.lit_bufsize,a.pending_buf=new 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t}for(v=65535&b,F&=15,F&&(f<F&&(u+=_[i++]<<f,f+=8),v+=u&(1<<F)-1,u>>>=F,f-=F),f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=g[u&w];;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,16&F){if(y=65535&b,F&=15,f<F&&(u+=_[i++]<<f,f+=8,f<F&&(u+=_[i++]<<f,f+=8)),y+=u&(1<<F)-1,y>a){e.msg=\"invalid distance too far back\",k.mode=Zn;break e}if(u>>>=F,f-=F,F=r-s,y>F){if(F=y-F,F>l&&k.sane){e.msg=\"invalid distance too far back\",k.mode=Zn;break e}if(A=0,C=d,0===h){if(A+=c-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}else if(h<F){if(A+=c+h-F,F-=h,F<v){v-=F;do{x[r++]=d[A++]}while(--F);if(A=0,h<v){F=h,v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}}else if(A+=h-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}for(;v>2;)x[r++]=C[A++],x[r++]=C[A++],x[r++]=C[A++],v-=3;v&&(x[r++]=C[A++],v>1&&(x[r++]=C[A++]))}else{A=r-y;do{x[r++]=x[A++],x[r++]=x[A++],x[r++]=x[A++],v-=3}while(v>2);v&&(x[r++]=x[A++],v>1&&(x[r++]=x[A++]))}break}if(64&F){e.msg=\"invalid distance code\",k.mode=Zn;break e}b=g[(65535&b)+(u&(1<<F)-1)]}}break}}while(i<n&&r<o);v=f>>3,i-=v,f-=v<<3,u&=(1<<f)-1,e.next_in=i,e.next_out=r,e.avail_in=i<n?n-i+5:5-(i-n),e.avail_out=r<o?o-r+257:257-(r-o),k.hold=u,k.bits=f};const er=15,tr=new Uint16Array([3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0]),ir=new Uint8Array([16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78]),nr=new Uint16Array([1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0]),rr=new Uint8Array([16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64]);var sr=(e,t,i,n,r,s,o,a)=>{const c=a.bits;let l,h,d,u,f,p,g=0,m=0,w=0,b=0,F=0,v=0,y=0,A=0,C=0,_=0,x=null;const k=new Uint16Array(16),I=new Uint16Array(16);let S,E,N,B=null;for(g=0;g<=er;g++)k[g]=0;for(m=0;m<n;m++)k[t[i+m]]++;for(F=c,b=er;b>=1&&0===k[b];b--);if(F>b&&(F=b),0===b)return r[s++]=20971520,r[s++]=20971520,a.bits=1,0;for(w=1;w<b&&0===k[w];w++);for(F<w&&(F=w),A=1,g=1;g<=er;g++)if(A<<=1,A-=k[g],A<0)return-1;if(A>0&&(0===e||1!==b))return-1;for(I[1]=0,g=1;g<er;g++)I[g+1]=I[g]+k[g];for(m=0;m<n;m++)0!==t[i+m]&&(o[I[t[i+m]]++]=m);if(0===e?(x=B=o,p=20):1===e?(x=tr,B=ir,p=257):(x=nr,B=rr,p=0),_=0,m=0,g=w,f=s,v=F,y=0,d=-1,C=1<<F,u=C-1,1===e&&C>852||2===e&&C>592)return 1;for(;;){S=g-y,o[m]+1<p?(E=0,N=o[m]):o[m]>=p?(E=B[o[m]-p],N=x[o[m]-p]):(E=96,N=0),l=1<<g-y,h=1<<v,w=h;do{h-=l,r[f+(_>>y)+h]=S<<24|E<<16|N}while(0!==h);for(l=1<<g-1;_&l;)l>>=1;if(0!==l?(_&=l-1,_+=l):_=0,m++,0==--k[g]){if(g===b)break;g=t[i+o[m]]}if(g>F&&(_&u)!==d){for(0===y&&(y=F),f+=w,v=g-y,A=1<<v;v+y<b&&(A-=k[v+y],!(A<=0));)v++,A<<=1;if(C+=1<<v,1===e&&C>852||2===e&&C>592)return 1;d=_&u,r[d]=F<<24|v<<16|f-s}}return 0!==_&&(r[f+_]=g-y<<24|64<<16),a.bits=F,0};const{Z_FINISH:or,Z_BLOCK:ar,Z_TREES:cr,Z_OK:lr,Z_STREAM_END:hr,Z_NEED_DICT:dr,Z_STREAM_ERROR:ur,Z_DATA_ERROR:fr,Z_MEM_ERROR:pr,Z_BUF_ERROR:gr,Z_DEFLATED:mr}=Bi,wr=16180,br=16190,Fr=16191,vr=16192,yr=16194,Ar=16199,Cr=16200,_r=16206,xr=16209,kr=e=>(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24);function Ir(){this.strm=null,this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new Uint16Array(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}const Sr=e=>{if(!e)return 1;const t=e.state;return!t||t.strm!==e||t.mode<wr||t.mode>16211?1:0},Er=e=>{if(Sr(e))return ur;const t=e.state;return e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=wr,t.last=0,t.havedict=0,t.flags=-1,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new Int32Array(852),t.distcode=t.distdyn=new Int32Array(592),t.sane=1,t.back=-1,lr},Nr=e=>{if(Sr(e))return ur;const t=e.state;return t.wsize=0,t.whave=0,t.wnext=0,Er(e)},Br=(e,t)=>{let i;if(Sr(e))return ur;const n=e.state;return t<0?(i=0,t=-t):(i=5+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?ur:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,Nr(e))},Mr=(e,t)=>{if(!e)return ur;const i=new Ir;e.state=i,i.strm=e,i.window=null,i.mode=wr;const n=Br(e,t);return n!==lr&&(e.state=null),n};let Rr,Dr,Tr=!0;const Lr=e=>{if(Tr){Rr=new Int32Array(512),Dr=new Int32Array(32);let t=0;for(;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(sr(1,e.lens,0,288,Rr,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;sr(2,e.lens,0,32,Dr,0,e.work,{bits:5}),Tr=!1}e.lencode=Rr,e.lenbits=9,e.distcode=Dr,e.distbits=5},zr=(e,t,i,n)=>{let r;const s=e.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new Uint8Array(s.wsize)),n>=s.wsize?(s.window.set(t.subarray(i-s.wsize,i),0),s.wnext=0,s.whave=s.wsize):(r=s.wsize-s.wnext,r>n&&(r=n),s.window.set(t.subarray(i-n,i-n+r),s.wnext),(n-=r)?(s.window.set(t.subarray(i-n,i),0),s.wnext=n,s.whave=s.wsize):(s.wnext+=r,s.wnext===s.wsize&&(s.wnext=0),s.whave<s.wsize&&(s.whave+=r))),0};var Hr=(e,t)=>{let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_=0;const x=new Uint8Array(4);let k,I;const S=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(Sr(e)||!e.output||!e.input&&0!==e.avail_in)return ur;i=e.state,i.mode===Fr&&(i.mode=vr),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,d=a,u=c,C=lr;e:for(;;)switch(i.mode){case wr:if(0===i.wrap){i.mode=vr;break}for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(2&i.wrap&&35615===l){0===i.wbits&&(i.wbits=15),i.check=0,x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0),l=0,h=0,i.mode=16181;break}if(i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&l)<<8)+(l>>8))%31){e.msg=\"incorrect header check\",i.mode=xr;break}if((15&l)!==mr){e.msg=\"unknown compression method\",i.mode=xr;break}if(l>>>=4,h-=4,A=8+(15&l),0===i.wbits&&(i.wbits=A),A>15||A>i.wbits){e.msg=\"invalid window size\",i.mode=xr;break}i.dmax=1<<i.wbits,i.flags=0,e.adler=i.check=1,i.mode=512&l?16189:Fr,l=0,h=0;break;case 16181:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.flags=l,(255&i.flags)!==mr){e.msg=\"unknown compression method\",i.mode=xr;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=xr;break}i.head&&(i.head.text=l>>8&1),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0,i.mode=16182;case 16182:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.time=l),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,x[2]=l>>>16&255,x[3]=l>>>24&255,i.check=Ei(i.check,x,4,0)),l=0,h=0,i.mode=16183;case 16183:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.xflags=255&l,i.head.os=l>>8),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0,i.mode=16184;case 16184:if(1024&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length=l,i.head&&(i.head.extra_len=l),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0}else i.head&&(i.head.extra=null);i.mode=16185;case 16185:if(1024&i.flags&&(f=i.length,f>a&&(f=a),f&&(i.head&&(A=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Uint8Array(i.head.extra_len)),i.head.extra.set(n.subarray(s,s+f),A)),512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,i.length-=f),i.length))break e;i.length=0,i.mode=16186;case 16186:if(2048&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.name+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=16187;case 16187:if(4096&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.comment+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.comment=null);i.mode=16188;case 16188:if(512&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(4&i.wrap&&l!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=xr;break}l=0,h=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=Fr;break;case 16189:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}e.adler=i.check=kr(l),l=0,h=0,i.mode=br;case br:if(0===i.havedict)return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,dr;e.adler=i.check=1,i.mode=Fr;case Fr:if(t===ar||t===cr)break e;case vr:if(i.last){l>>>=7&h,h-=7&h,i.mode=_r;break}for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}switch(i.last=1&l,l>>>=1,h-=1,3&l){case 0:i.mode=16193;break;case 1:if(Lr(i),i.mode=Ar,t===cr){l>>>=2,h-=2;break e}break;case 2:i.mode=16196;break;case 3:e.msg=\"invalid block type\",i.mode=xr}l>>>=2,h-=2;break;case 16193:for(l>>>=7&h,h-=7&h;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if((65535&l)!=(l>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=xr;break}if(i.length=65535&l,l=0,h=0,i.mode=yr,t===cr)break e;case yr:i.mode=16195;case 16195:if(f=i.length,f){if(f>a&&(f=a),f>c&&(f=c),0===f)break e;r.set(n.subarray(s,s+f),o),a-=f,s+=f,c-=f,o+=f,i.length-=f;break}i.mode=Fr;break;case 16196:for(;h<14;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.nlen=257+(31&l),l>>>=5,h-=5,i.ndist=1+(31&l),l>>>=5,h-=5,i.ncode=4+(15&l),l>>>=4,h-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=xr;break}i.have=0,i.mode=16197;case 16197:for(;i.have<i.ncode;){for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.lens[S[i.have++]]=7&l,l>>>=3,h-=3}for(;i.have<19;)i.lens[S[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,k={bits:i.lenbits},C=sr(0,i.lens,0,19,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid code lengths set\",i.mode=xr;break}i.have=0,i.mode=16198;case 16198:for(;i.have<i.nlen+i.ndist;){for(;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(b<16)l>>>=m,h-=m,i.lens[i.have++]=b;else{if(16===b){for(I=m+2;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l>>>=m,h-=m,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=xr;break}A=i.lens[i.have-1],f=3+(3&l),l>>>=2,h-=2}else if(17===b){for(I=m+3;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=3+(7&l),l>>>=3,h-=3}else{for(I=m+7;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=11+(127&l),l>>>=7,h-=7}if(i.have+f>i.nlen+i.ndist){e.msg=\"invalid bit length repeat\",i.mode=xr;break}for(;f--;)i.lens[i.have++]=A}}if(i.mode===xr)break;if(0===i.lens[256]){e.msg=\"invalid code -- missing end-of-block\",i.mode=xr;break}if(i.lenbits=9,k={bits:i.lenbits},C=sr(1,i.lens,0,i.nlen,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid literal/lengths set\",i.mode=xr;break}if(i.distbits=6,i.distcode=i.distdyn,k={bits:i.distbits},C=sr(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,k),i.distbits=k.bits,C){e.msg=\"invalid distances set\",i.mode=xr;break}if(i.mode=Ar,t===cr)break e;case Ar:i.mode=Cr;case Cr:if(a>=6&&c>=258){e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,Jn(e,u),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,i.mode===Fr&&(i.back=-1);break}for(i.back=0;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(w&&!(240&w)){for(F=m,v=w,y=b;_=i.lencode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,i.length=b,0===w){i.mode=16205;break}if(32&w){i.back=-1,i.mode=Fr;break}if(64&w){e.msg=\"invalid literal/length code\",i.mode=xr;break}i.extra=15&w,i.mode=16201;case 16201:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=16202;case 16202:for(;_=i.distcode[l&(1<<i.distbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(!(240&w)){for(F=m,v=w,y=b;_=i.distcode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,64&w){e.msg=\"invalid distance code\",i.mode=xr;break}i.offset=b,i.extra=15&w,i.mode=16203;case 16203:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.offset+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=xr;break}i.mode=16204;case 16204:if(0===c)break e;if(f=u-c,i.offset>f){if(f=i.offset-f,f>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=xr;break}f>i.wnext?(f-=i.wnext,p=i.wsize-f):p=i.wnext-f,f>i.length&&(f=i.length),g=i.window}else g=r,p=o-i.offset,f=i.length;f>c&&(f=c),c-=f,i.length-=f;do{r[o++]=g[p++]}while(--f);0===i.length&&(i.mode=Cr);break;case 16205:if(0===c)break e;r[o++]=i.length,c--,i.mode=Cr;break;case _r:if(i.wrap){for(;h<32;){if(0===a)break e;a--,l|=n[s++]<<h,h+=8}if(u-=c,e.total_out+=u,i.total+=u,4&i.wrap&&u&&(e.adler=i.check=i.flags?Ei(i.check,r,u,o-u):Ii(i.check,r,u,o-u)),u=c,4&i.wrap&&(i.flags?l:kr(l))!==i.check){e.msg=\"incorrect data check\",i.mode=xr;break}l=0,h=0}i.mode=16207;case 16207:if(i.wrap&&i.flags){for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(4&i.wrap&&l!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=xr;break}l=0,h=0}i.mode=16208;case 16208:C=hr;break e;case xr:C=fr;break e;case 16210:return pr;default:return ur}return 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Object.values(this.allFeatures))for(let n of i)e(n)&&t.push(n);return t}queryFeatures(e,t,i){const n=this.treeMap[e];if(!n)return[];const r=n.findOverlapping(t,i);if(0===r.length)return[];{const n=[],s=this.allFeatures[e];if(s){for(let e of r){const r=e.value;for(let e=r.start;e<r.end;e++){let r=s[e];if(r.start>i)break;r.end>=t&&n.push(r)}}n.sort((function(e,t){return e.start-t.start}))}return n}}getAllFeatures(){return this.allFeatures}buildTreeMap(e,t){const i={},n=[];if(this.allFeatures={},e){for(let i of e){let e=i.chr;t&&(e=t.getChromosomeName(e));let r=this.allFeatures[e];r||(n.push(e),r=[],this.allFeatures[e]=r),r.push(i)}for(let e of n){const t=this.allFeatures[e];t.sort((function(e,t){return e.start===t.start?0:e.start>t.start?1:-1})),i[e]=Js(t)}}return i}}function Js(e){const t=new js,i=e.length,n=Math.max(10,Math.round(i/10));for(let r=0;r<i;r+=n){const s=Math.min(i,r+n),o=new eo(r,s),a=e[r].start;let c=a;for(let t=r;t<s;t++)c=Math.max(c,e[t].end);t.insert(a,c,o)}return t}class eo{constructor(e,t){this.start=e,this.end=t}}const to=function(e,t,i){if(e&&0!==e.length){const n=function(e){const t=new js,i=e.length,n=Math.max(10,Math.round(i/100));e.sort((function(e,t){return e.start===t.start?0:e.start>t.start?1:-1}));for(let r=0;r<i;r+=n){const s=Math.min(i,r+n),o=e.slice(r,s),a=o[0].start;let c=a;o.forEach((function(e){c=Math.max(c,e.end)})),t.insert(a,c,o)}return t}(e),r=n.findOverlapping(t,i);return 0===r.length?[]:(e=[],r.forEach((function(n){const r=n.value,s=r.length;for(let n=0;n<s;n++){const s=r[n];if(s.start>i)break;s.end>t&&e.push(s)}})),e.sort((function(e,t){return e.start-t.start})),e)}return[]};function io(e){if(3===(e=e.replace(/^#/,\"\")).length&&(e=e.split(\"\").map((e=>e+e)).join(\"\")),6!==e.length)throw new Error(\"Invalid HEX color.\");let t=parseInt(e,16);return`rgb(${t>>16&255}, ${t>>8&255}, ${255&t})`}const no={cantaloupe:{r:255,g:206,b:110},honeydew:{r:206,g:250,b:110},spindrift:{r:104,g:251,b:208},sky:{r:106,g:207,b:255},lavender:{r:210,g:120,b:255},carnation:{r:255,g:127,b:211},licorice:{r:0,g:0,b:0},snow:{r:255,g:255,b:255},salmon:{r:255,g:114,b:110},banana:{r:255,g:251,b:109},flora:{r:104,g:249,b:110},ice:{r:104,g:253,b:255},orchid:{r:110,g:118,b:255},bubblegum:{r:255,g:122,b:255},lead:{r:30,g:30,b:30},mercury:{r:232,g:232,b:232},tangerine:{r:255,g:136,b:2},lime:{r:131,g:249,b:2},sea_foam:{r:3,g:249,b:135},aqua:{r:0,g:140,b:255},grape:{r:137,g:49,b:255},strawberry:{r:255,g:41,b:135},tungsten:{r:58,g:58,b:58},silver:{r:208,g:208,b:208},maraschino:{r:255,g:33,b:1},lemon:{r:255,g:250,b:3},spring:{r:5,g:248,b:2},turquoise:{r:0,g:253,b:255},blueberry:{r:0,g:46,b:255},magenta:{r:255,g:57,b:255},iron:{r:84,g:84,b:83},magnesium:{r:184,g:184,b:184},mocha:{r:137,g:72,b:0},fern:{r:69,g:132,b:1},moss:{r:1,g:132,b:72},ocean:{r:0,g:74,b:136},eggplant:{r:73,g:26,b:136},maroon:{r:137,g:22,b:72},steel:{r:110,g:110,b:110},aluminum:{r:160,g:159,b:160},cayenne:{r:137,g:17,b:0},aspargus:{r:136,g:133,b:1},clover:{r:2,g:132,b:1},teal:{r:0,g:134,b:136},midnight:{r:0,g:24,b:136},plum:{r:137,g:30,b:136},tin:{r:135,g:134,b:135},nickel:{r:136,g:135,b:135}};function ro(e){const{r:t,g:i,b:n}=no[e];return`rgb(${t},${i},${n})`}const so={Set1:[\"rgb(228,26,28)\",\"rgb(55,126,184)\",\"rgb(77,175,74)\",\"rgb(166,86,40)\",\"rgb(152,78,163)\",\"rgb(255,127,0)\",\"rgb(247,129,191)\",\"rgb(153,153,153)\",\"rgb(255,255,51)\"],Dark2:[\"rgb(27,158,119)\",\"rgb(217,95,2)\",\"rgb(117,112,179)\",\"rgb(231,41,138)\",\"rgb(102,166,30)\",\"rgb(230,171,2)\",\"rgb(166,118,29)\",\"rgb(102,102,102)\"],Set2:[\"rgb(102, 194,165)\",\"rgb(252,141,98)\",\"rgb(141,160,203)\",\"rgb(231,138,195)\",\"rgb(166,216,84)\",\"rgb(255,217,47)\",\"rgb(229,196,148)\",\"rgb(179,179,179)\"],Set3:[\"rgb(141,211,199)\",\"rgb(255,255,179)\",\"rgb(190,186,218)\",\"rgb(251,128,114)\",\"rgb(128,177,211)\",\"rgb(253,180,98)\",\"rgb(179,222,105)\",\"rgb(252,205,229)\",\"rgb(217,217,217)\",\"rgb(188,128,189)\",\"rgb(204,235,197)\",\"rgb(255,237,111)\"],Pastel1:[\"rgb(251,180,174)\",\"rgb(179,205,227)\",\"rgb(204,235,197)\",\"rgb(222,203,228)\",\"rgb(254,217,166)\",\"rgb(255,255,204)\",\"rgb(229,216,189)\",\"rgb(253,218,236)\"],Pastel2:[\"rgb(173,226,207)\",\"rgb(253,205,172)\",\"rgb(203,213,232)\",\"rgb(244,202,228)\",\"rgb(230,245,201)\",\"rgb(255,242,174)\",\"rgb(243,225,206)\"],Accent:[\"rgb(127,201,127)\",\"rgb(190,174,212)\",\"rgb(253,192,134)\",\"rgb(255,255,153)\",\"rgb(56,108,176)\",\"rgb(240,2,127)\",\"rgb(191,91,23)\"]};class oo{constructor(e){this.colors=so[e],Array.isArray(this.colors)||(this.colors=[]),this.colorTable=new Map,this.nextIdx=0,this.colorGenerator=new co}getColor(e){return this.colorTable.has(e)||(this.nextIdx<this.colors.length?this.colorTable.set(e,this.colors[this.nextIdx]):this.colorTable.set(e,this.colorGenerator.get()),this.nextIdx++),this.colorTable.get(e)}}class ao{constructor(e){this.colorTable=e||{},this.nextIdx=0,this.colorGenerator=new co}getColor(e){if(!this.colorTable.hasOwnProperty(e)){if(this.colorTable.hasOwnProperty(\"*\"))return this.colorTable[\"*\"];this.colorTable[e]=this.colorGenerator.get()}return this.colorTable[e]}}function co(){this.hue=Math.random(),this.goldenRatio=.618033988749895,this.hexwidth=2}function lo(e,t,i,n){return`rgba(${e=ys.clamp(e,0,255)}, ${t=ys.clamp(t,0,255)}, ${i=ys.clamp(i,0,255)}, ${n=ys.clamp(n,0,1)})`}function ho(e,t){e=ys.clamp(e,0,255),t=ys.clamp(t,0,255);return`rgb(${Math.round(Math.random()*(t-e)+e).toString(10)},${Math.round(Math.random()*(t-e)+e).toString(10)},${Math.round(Math.random()*(t-e)+e).toString(10)})`}function uo(e){if(e.startsWith(\"rgb(\")){const[t,i]=e.split(\"(\"),[n]=i.split(\")\");return n.split(\",\").map((e=>parseInt(e)))}}co.prototype.hsvToRgb=function(e,t,i){var n=Math.floor(6*e),r=6*e-n,s=i*(1-t),o=i*(1-r*t),a=i*(1-(1-r)*t),c=255,l=255,h=255;switch(n){case 0:c=i,l=a,h=s;break;case 1:c=o,l=i,h=s;break;case 2:c=s,l=i,h=a;break;case 3:c=s,l=o,h=i;break;case 4:c=a,l=s,h=i;break;case 5:c=i,l=s,h=o}return[Math.floor(256*c),Math.floor(256*l),Math.floor(256*h)]},co.prototype.padHex=function(e){return e.length>this.hexwidth?e:new Array(this.hexwidth-e.length+1).join(\"0\")+e},co.prototype.get=function(e,t){this.hue+=this.goldenRatio,this.hue%=1,\"number\"!=typeof e&&(e=.5),\"number\"!=typeof t&&(t=.95);var i=this.hsvToRgb(this.hue,e,t);return\"#\"+this.padHex(i[0].toString(16))+this.padHex(i[1].toString(16))+this.padHex(i[2].toString(16))},new co;function fo(e,t,i){if(i<.005)return e;if(i>.995)return t;{let n,r,s,o,a,c;i<.5?(i/=.5,[n,r,s]=uo(e),[o,a,c]=uo(ro(\"snow\"))):(i=(i-.5)/.5,[n,r,s]=uo(ro(\"snow\")),[o,a,c]=uo(t));const[l,h,d]=[Math.floor(ys.lerp(n,o,i)),Math.floor(ys.lerp(r,a,i)),Math.floor(ys.lerp(s,c,i))];return function(e,t,i){return`rgb(${e=ys.clamp(e,0,255)}, ${t=ys.clamp(t,0,255)}, ${i=ys.clamp(i,0,255)})`}(l,h,d)}}const po=new Set([\"bedtype\",\"alignment\",\"annotation\",\"variant\",\"wig\",\"interact\",\"shoebox\"]),go=new Set([\"alignment\",\"annotation\",\"variant\",\"eqtl\",\"qtl\",\"snp\",\"shoebox\",\"wig\"]),mo=new Set([\"sequence\",\"ruler\",\"ideogram\"]),wo={};class bo{constructor(e){this.browser=e,this.initialize()}initialize(){const e=new c;e.add(\"...\");const t={parent:this.browser.root,content:e};this.dialog=new w(t),this.browser.root.appendChild(this.dialog.elem),i(this.dialog.elem)}trackMenuItemList(e){const t=[];return\"sequence\"!==e.track.config.type&&t.push(function(){const e=Bt(\"<div>\");function t(e){const t=()=>{const e=parseInt(this.browser.inputDialog.value,10);if(void 0!==e){const t=[];this.trackView.track.selected?t.push(...this.trackView.browser.getSelectedTrackViews().map((({track:e})=>e))):t.push(this);for(const i of t)i.trackView.autoHeight=!1,void 0!==i.minHeight&&i.minHeight>e&&(i.minHeight=e),void 0!==i.maxHeight&&i.maxHeight<e&&(i.minHeight=e),i.trackView.setTrackHeight(e,!0),i.trackView.checkContentHeight(),i.trackView.repaintViews()}},i={label:\"Track Height\",value:this.height,callback:t};this.browser.inputDialog.present(i,e)}return e.text(\"Set track height\"),{object:e,dialog:t}}()),!0===function(e){const t=e.browser.getSelectedTrackViews();return t&&t.length>1&&new Set(t).has(e)}(e)?t.push(...this.multiSelectMenuItems(e)):(\"sequence\"!==e.track.config.type&&t.push(function(){const e=Bt(\"<div>\");function t(e){const t=()=>{let e=this.browser.inputDialog.value;e=\"\"===e||void 0===e?\"untitled\":e.trim(),this.name=e},i={label:\"Track Name\",value:Ao(this)||\"unnamed\",callback:t};this.browser.inputDialog.present(i,e)}return e.text(\"Set track name\"),{object:e,click:t}}()),t.push(...this.defaultMenuItems(e))),!1!==e.track.removable&&(t.push(\"<hr/>\"),t.push(function(e){const t=e.track.selected?\"Remove tracks\":\"Remove track\",i=Bt(\"<div>\");function n(e){this.trackView.browser._removeTrack(this)}return i.text(t),{object:i,click:n,menuItemType:\"removeTrack\"}}(e))),t}defaultMenuItems(e){const t=[];return Co(e.track)&&(t.push(\"<hr/>\"),t.push(Fo({trackView:e,label:\"Set track color\",option:\"color\"})),t.push(vo({trackView:e,label:\"Unset track color\"})),\"wig\"!==e.track.config.type&&\"annotation\"!==e.track.config.type||(t.push(Fo({trackView:e,label:\"Set alt color\",option:\"altColor\"})),t.push(yo({trackView:e,label:\"Unset alt color\"})))),e.track.menuItemList&&t.push(...e.track.menuItemList()),function(e){const t=e.track;return t&&t.config&&void 0!==t.config.visibilityWindow||t&&go.has(t.type)}(e)&&(t.push(\"<hr/>\"),t.push(function(e){const t=Bt(\"<div>\");function i(t){const i=()=>{let e=this.browser.inputDialog.value;e=\"\"===e||void 0===e?-1:e.trim(),this.visibilityWindow=Number.parseInt(e),this.config.visibilityWindow=Number.parseInt(e),this.trackView.updateViews()},n={label:\"wig\"===e?\"Visibility window (bp). Enter 0 for whole chromosome, -1 for whole genome.\":\"Visibility window (bp). Enter 0 for whole chromosome.\",value:this.visibilityWindow,callback:i};this.browser.inputDialog.present(n,t)}return t.text(\"Set visibility window\"),{object:t,click:i}}(e.track.type))),t}multiSelectMenuItems(e){const t=[],i=e.browser.getSelectedTrackViews();var n;return!0===(n=i.map((({track:e})=>e.type)),1===[...new Set(n)].length)?(t.push(...this.defaultMenuItems(e)),\"wig\"===e.track.type&&(t.push(\"<hr/>\"),t.push(function(){const e=Bt(\"<div>\");function t(e){const t=so.Dark2,i=Math.floor(Math.random()*t.length),n=`auto-scale-group-${s()}`;wo[n]=t[i];const r=this.browser.getSelectedTrackViews();for(const{track:e}of r)e.autoscaleGroup=n;this.browser.updateViews()}return e.text(\"Group autoscale\"),{object:e,doAllMultiSelectedTracks:!0,click:t}}()))):Co(e.track)&&(t.push(\"<hr/>\"),t.push(Fo({trackView:e,label:\"Set track color\",option:\"color\"})),t.push(vo({trackView:e,label:\"Unset track color\"})),\"wig\"!==e.track.config.type&&\"annotation\"!==e.track.config.type||(t.push(Fo({trackView:e,label:\"Set alt color\",option:\"altColor\"})),t.push(yo({trackView:e,label:\"Unset alt color\"})))),t}}function Fo({trackView:e,label:t,option:i}){const n=Bt(\"<div>\");return n.text(t),{object:n,click:()=>e.presentColorPicker(i)}}function vo({trackView:e,label:t}){const i=Bt(\"<div>\");return i.text(t),{object:i,click:()=>{e.track.color=void 0,e.repaintViews()}}}function yo({trackView:e,label:t}){const i=Bt(\"<div>\");return i.text(t),{object:i,click:()=>{e.track.altColor=void 0,e.repaintViews()}}}function Ao(e){return e.name}function Co(e){return void 0===e.type||po.has(e.type)}class _o{constructor(e,t){this.browser=e,this.$container=Bt(\"<div>\",{class:\"igv-generic-dialog-container\"}),t.append(this.$container),this.$container.offset({left:0,top:0});const i=Bt(\"<div>\",{class:\"igv-generic-dialog-header\"});this.$container.append(i),u(i[0],(()=>{this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\"),this.$container.offset({left:0,top:0}),this.$container.hide()})),this.$minimum=Bt(\"<div>\",{class:\"igv-generic-dialog-label-input\"}),this.$container.append(this.$minimum);const n=Bt(\"<div>\");n.text(\"Minimum\"),this.$minimum.append(n),this.$minimum_input=Bt(\"<input>\"),this.$minimum.append(this.$minimum_input),this.$maximum=Bt(\"<div>\",{class:\"igv-generic-dialog-label-input\"}),this.$container.append(this.$maximum);const r=Bt(\"<div>\");r.text(\"Maximum\"),this.$maximum.append(r),this.$maximum_input=Bt(\"<input>\"),this.$maximum.append(this.$maximum_input);const s=Bt(\"<div>\",{class:\"igv-generic-dialog-ok-cancel\"});this.$container.append(s),this.$ok=Bt(\"<div>\"),s.append(this.$ok),this.$ok.text(\"OK\"),this.$cancel=Bt(\"<div>\"),s.append(this.$cancel),this.$cancel.text(\"Cancel\"),this.$cancel.on(\"click\",(()=>{this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\"),this.$container.offset({left:0,top:0}),this.$container.hide()})),p(this.$container.get(0),i.get(0)),this.$container.hide()}configure(e){let t;if(Array.isArray(e)){t={min:Number.MAX_SAFE_INTEGER,max:-Number.MAX_SAFE_INTEGER};for(const i of e)i.track.dataRange&&(t.min=Math.min(i.track.dataRange.min,t.min),t.max=Math.max(i.track.dataRange.max,t.max))}else t=e.track.dataRange;t&&(this.$minimum_input.val(t.min),this.$maximum_input.val(t.max)),this.$minimum_input.unbind(),this.$minimum_input.on(\"keyup\",(t=>{13===t.keyCode&&this.processResults(e),t.stopImmediatePropagation()})),this.$maximum_input.unbind(),this.$maximum_input.on(\"keyup\",(t=>{13===t.keyCode&&(t.stopImmediatePropagation(),this.processResults(e))})),this.$ok.unbind(),this.$ok.on(\"click\",(t=>{this.processResults(e)}))}processResults(e){if(\"\"!==this.$minimum_input.val()&&\"\"!==this.$maximum_input.val()){const t=Number(this.$minimum_input.val()),i=Number(this.$maximum_input.val());if(isNaN(t)||isNaN(i))this.browser.alert.present(new Error(\"Must input numeric values\"),void 0);else{const n=Array.isArray(e)?e:[e];for(const e of n)e.track.setDataRange({min:t,max:i})}this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\")}this.$container.offset({left:0,top:0}),this.$container.hide()}present(e){const t=e.offset().top,i=Bt(\"body\").scrollTop();this.$container.offset({left:e.width()-this.$container.width(),top:t+i}),this.$container.show()}}const xo={configureHighDPICanvas:function(e,t,i){const n=window.devicePixelRatio;e.canvas.style.width=`${t}px`,e.canvas.width=Math.floor(n*t),e.canvas.style.height=`${i}px`,e.canvas.height=Math.floor(n*i),e.scale(n,n)},setProperties:function(e,t){for(var i in t)if(t.hasOwnProperty(i)){var 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a=e=>{o.show(),i(n),e.preventDefault(),e.stopPropagation()};s.addEventListener(\"click\",a),s.addEventListener(\"touchend\",a),s.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}else s=e(),\"string\"==typeof t.label&&(s.innerHTML=t.label);if(t.click&&\"color\"!==t.type){function c(e){t.click(),i(n),e.preventDefault(),e.stopPropagation()}s.addEventListener(\"click\",c),s.addEventListener(\"touchend\",c),s.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}}return{object:s,init:t.init}}));return r}const rc=[[\"A\",\"T\"],[\"G\",\"C\"],[\"Y\",\"R\"],[\"W\",\"S\"],[\"K\",\"M\"],[\"D\",\"H\"],[\"B\",\"V\"]],sc=new Map;for(let _A of rc){const xA=_A[0],kA=_A[1];sc.set(xA,kA),sc.set(kA,xA),sc.set(xA.toLowerCase(),kA.toLowerCase()),sc.set(kA.toLowerCase(),xA.toLowerCase())}function oc(e){return sc.has(e)?sc.get(e):e}function ac(e){let t=\"\";for(let i of e)t+=sc.has(i)?sc.get(i):i;return t}function cc(e){let t=\"\",i=e.length;for(;i-- >0;){const n=e[i];t+=sc.has(n)?sc.get(n):n}return t}class lc{constructor(e,t,i,n){this.name=e,this.order=t,this.bpLength=i,this.altNames=n}getAltName(e){return this.altNames&&this.altNames.has(e)?this.altNames.get(e):this.name}}class hc{constructor(e,t,i,n){this.chr=e,this.start=t,this.end=i,this.features=n}contains(e,t,i){return this.chr===e&&this.start<=t&&this.end>=i}containsRange(e){return this.chr===e.chr&&this.start<=e.start&&this.end>=e.end}get locusString(){return`${this.chr}:${this.start+1}-${this.end}`}}class dc extends hc{constructor(e,t,i,n){super(e,t,i,n)}getSequence(e,t){if(e<this.start||t>this.end)return null;const i=e-this.start,n=t-e;return this.features?this.features.substring(i,i+n):null}hasSequence(e,t){return e>=this.start&&t<=this.end}}const uc=Dt,fc=new Set([\"fastaURL\",\"indexURL\",\"cytobandURL\",\"indexed\"]);class pc{#e;chromosomes=new Map;sequences=new Map;constructor(e){this.fastaURL=e.fastaURL,this.withCredentials=e.withCredentials;const t={};for(let i in e)e.hasOwnProperty(i)&&!fc.has(i)&&(t[i]=e[i]);this.config=t}async init(){return this.loadAll()}getSequenceRecord(e){return this.chromosomes.get(e)}get chromosomeNames(){return this.#e||(this.#e=Array.from(this.chromosomes.keys())),this.#e}getFirstChromosomeName(){return this.chromosomeNames[0]}async getSequence(e,t,i){if(0===this.sequences.size&&await this.loadAll(),!this.sequences.has(e))return;let n=this.sequences.get(e).find((e=>e.contains(t,i)));if(!n&&(n=this.sequences.get(e).find((e=>e.overlaps(t,i))),!n))return;t-=n.offset,i-=n.offset;let r=\"\";if(t<0)for(let e=t;e<Math.min(i,0);e++)r+=\"*\";if(i<=0)return r;const s=n.sequence,o=Math.min(i,s.length);return r+s.substring(t,o)}async loadAll(){let e;if(Ga(this.fastaURL)){let t=vs(this.fastaURL);e=\"\";for(let i of t)e+=String.fromCharCode(i)}else e=await Qs.load(this.fastaURL,Ua(this.config));const t=new Set,i=uc(e),n=i.length;let r,s=0,o=0,a={};for(;s<n;){if(r=i[s++].trim(),r.startsWith(\"#\")||0===r.length);else if(r.startsWith(\">\")){a&&a.seq&&c.call(this,a,o++);const e=r.substr(1).split(/\\s+/),t=e[0].split(\":\");if(a.chr=t[0],a.seq=\"\",a.offset=0,t.length>1&&t[1].indexOf(\"-\")>0){const i=t[1].split(\"-\");2===i.length&&/^[0-9]+$/.test(i[0])&&/^[0-9]+$/.test(i[1]);const n=Number.parseInt(i[0]);if(Number.parseInt(i[1])>n&&(a.offset=n-1),e.length>1&&e[1].startsWith(\"@len=\"))try{a.length=parseInt(e[1].trim().substring(5))}catch(e){a.length=void 0,console.error(`Error parsing sequence length for ${r}`)}else a.length=void 0}}else a.seq+=r;a&&a.seq&&c.call(this,a,o)}function c(e,i){const n=e.length||e.offset+e.seq.length;if(t.has(e.chr)){const t=this.chromosomes.get(e.chr);t.bpLength=Math.max(t.bpLength,n)}else this.sequences.set(e.chr,[]),this.chromosomes.set(e.chr,new lc(e.chr,i,n)),t.add(e.chr);this.sequences.get(e.chr).push(new gc(e.offset,e.seq))}}getSequenceInterval(e,t,i){const n=this.sequences.get(e);if(n)for(let r of n){const n=r.sequence,s=r.offset,o=s+n.length;if(s<=t&&o>=i)return new dc(e,s,o,n)}}}class gc{constructor(e,t){this.offset=e,this.sequence=t}contains(e,t){return this.offset<=e&&this.end>=t}overlaps(e,t){return this.offset<t&&this.end>e}get end(){return this.offset+this.sequence.length}}const mc=Dt,wc=new Set([\"fastaURL\",\"indexURL\",\"compressedIndexURL\",\"cytobandURL\",\"indexed\"]);class bc{#e;chromosomes=new Map;constructor(e){this.file=e.fastaURL,this.indexFile=e.indexURL,this.compressedIndexFile=e.compressedIndexURL,this.withCredentials=e.withCredentials;const t={};for(let i in e)e.hasOwnProperty(i)&&!wc.has(i)&&(t[i]=e[i]);this.config=t}getSequenceRecord(e){return this.chromosomes.get(e)}async init(){return this.getIndex()}get chromosomeNames(){return this.#e||(this.#e=Array.from(this.chromosomes.keys())),this.#e}getFirstChromosomeName(){return this.chromosomeNames[0]}async getIndex(){if(this.index)return this.index;{const e=await Qs.load(this.indexFile,Ua(this.config)),t=mc(e),i=t.length;let n=0,r=0;for(this.index={};n<i;){const e=t[n++].split(\"\\t\");if(5===e.length){const t=e[0],i=parseInt(e[1]),n={size:i,position:parseInt(e[2]),basesPerLine:parseInt(e[3]),bytesPerLine:parseInt(e[4])};this.index[t]=n,this.chromosomes.set(t,new lc(t,r++,i))}}return this.index}}async getCompressedIndex(){if(this.compressedIndex)return this.compressedIndex;if(!this.compressedIndexFile)return this.compressedIndex=[],this.compressedIndex;this.compressedIndex=[];const e=await Qs.loadArrayBuffer(this.compressedIndexFile,Ua(this.config)),t=e.byteLength;if(t<8)return console.log(\"Cannot parse GZI index file: length (\"+t+\" bytes) is insufficient to determine content of index.\"),this.compressedIndex;const i=e.slice(0,8),n=Number(new DataView(i).getBigUint64(0,!0)),r=8+2*n*8;if(t!=r)return console.log(\"Incorrect file size of reference genome index. Expected : \"+r+\". Received : \"+t),this.compressedIndex;this.compressedIndex.push([0,0]);for(let t=0;t<n;t++){const i=8+2*t*8,n=8+2*t*8+16,r=e.slice(i,n),s=new DataView(r),o=Number(s.getBigUint64(0,!0)),a=Number(s.getBigUint64(8,!0));this.compressedIndex.push([o,a])}return this.compressedIndex}async getRelevantCompressedBlockNumbers(e,t){if(e<0||t<0||t<e)return console.log(\"Incompatible query positions for reference-genome. Start:\"+e+\" | End:\"+t),[];await this.getCompressedIndex();let i=[];const n=this.compressedIndex.length-1;if(0==this.compressedIndex.length)return console.log(\"Compressed index does not contain any content\"),[];if(e>this.compressedIndex[n][1])return[n];let r=0,s=n,o=Math.floor(this.compressedIndex.length/2),a=this.compressedIndex.length+1,c=!1;for(let t=0;t<a;t++){const t=this.compressedIndex[o][1],i=o<this.compressedIndex.length-1?this.compressedIndex[o+1][1]:1/0;if(t<=e&&i>e){c=!0;break}t<e?r=o+1:s=o-1,o=Math.ceil((s-r)/2)+r}if(!c)return console.log(\"No blocks within compressed index found that correspond with query positions \"+e+\",\"+t),console.log(this.compressedIndex),[];i.push(o);for(let e=o+1;e<this.compressedIndex.length;e++){i.push(e);if(this.compressedIndex[e][1]>=t)break}const l=i[i.length-1];return l===this.compressedIndex.length-1&&this.compressedIndex[l][1]<t&&i.push(-1),i}async loadAndUncompressBlocks(e,t){if(await this.getCompressedIndex(),0==e.length)return\"\";let i=Array(e.length-1);for(let t=0;t<e.length-1;t++){const n=e[t],r=this.compressedIndex[n][0],s=e[t+1];let o=[];if(-1!=s){const e=this.compressedIndex[s][0]-r;o=await Qs.loadArrayBuffer(this.file,Ua(this.config,{range:{start:r,size:e}}))}else o=await Qs.loadArrayBuffer(this.file,Ua(this.config,{range:{start:r}}));const a=await gs(o);i[t]=a}let n=\"\";for(let e=0;e<i.length;e++)for(let t=0;t<i[e].length;t++){n+=String.fromCharCode(i[e][t])}const r=t-this.compressedIndex[e[0]][1];return n=n.substring(r),n}async readSequence(e,t,i){await this.getIndex(),await this.getCompressedIndex();const n=this.index[e];if(!n)return console.log(\"No index entry for chr: \"+e),this.index[e]=null,null;const r=Math.max(0,t),s=Math.min(n.size,i),o=n.bytesPerLine,a=n.basesPerLine,c=n.position,l=o-a,h=Math.floor(r/a),d=Math.floor(s/a),u=r-h*a,f=c+h*o+u,p=c+d*o+(s-d*a)-1,g=p-f+1;if(g<=0)return console.error(\"No sequence for \"+e+\":\"+t+\"-\"+i),null;let m;if(this.compressedIndexFile){let e=await this.getRelevantCompressedBlockNumbers(f,p);if(0===e.length)return console.log(\"No blocks in the compressed index that correspond with the requested byte positions (\"+f+\",\"+p+\")\"),null;m=await this.loadAndUncompressBlocks(e,f)}else m=await Qs.load(this.file,Ua(this.config,{range:{start:f,size:g}}));if(!m)return null;let w,b=\"\",F=0,v=m.length;for(u>0&&(w=Math.min(s-r,a-u),b+=m.substr(F,w),F+=w+l);F<v;)w=Math.min(a,v-F),b+=m.substr(F,w),F+=w+l;return b}}const Fc=Dt;class vc{#e;chromosomes=new Map;constructor(e){this.url=e}async init(){return this.loadAll()}getSequenceRecord(e){return this.chromosomes.get(e)}get chromosomeNames(){this.#e||(this.#e=Array.from(this.chromosomes.keys()))}async getSequence(e,t,i){return null}async loadAll(){let e;if(Ga(this.url)){let t=vs(this.fastaURL);e=\"\";for(let i of t)e+=String.fromCharCode(i)}else e=await Qs.load(this.url,{});const t=Fc(e);let i=0;for(let e of t){const t=e.split(\"\\t\");if(t.length>1){const e=Number.parseInt(t[1]),n=new lc(t[0],i++,e);this.chromosomes.set(t[0],n)}}}}class yc{constructor(e,t=!0){this.littleEndian=t,this.position=0,this.view=e,this.length=e.byteLength}dumpBytes(e=100){const t=this.position,i=[];for(let t=0;t<=e;t++)i.push(this.getByte());console.log(i.join(\" \")),this.setPosition(t)}setPosition(e){this.position=e}available(){return this.length-this.position}remLength(){return this.length-this.position}hasNext(){return this.position<this.length-1}getByte(){const e=this.view.getUint8(this.position,this.littleEndian);return this.position++,e}getShort(){const e=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,e}getUShort(){const e=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,e}getInt(){const e=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,e}getUInt(){const e=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,e}getLong(){var e=[];e[0]=this.view.getUint8(this.position),e[1]=this.view.getUint8(this.position+1),e[2]=this.view.getUint8(this.position+2),e[3]=this.view.getUint8(this.position+3),e[4]=this.view.getUint8(this.position+4),e[5]=this.view.getUint8(this.position+5),e[6]=this.view.getUint8(this.position+6),e[7]=this.view.getUint8(this.position+7);let t=0;if(this.littleEndian)for(let i=e.length-1;i>=0;i--)t=256*t+e[i];else for(let i=0;i<e.length;i++)t=256*t+e[i];return this.position+=8,t}getString(e){let t,i=\"\";for(;0!==(t=this.view.getUint8(this.position++))&&(i+=String.fromCharCode(t),!e||i.length!==e););return i}getFixedLengthString(e){let t=\"\";for(let i=0;i<e;i++){const e=this.view.getUint8(this.position++);e>0&&(t+=String.fromCharCode(e))}return t}getFloat(){var e=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,e}getDouble(){var e=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,e}skip(e){return this.position+=e,this.position}getVPointer(){var e=this.position,t=this.view.getUint8(e+1)<<8|this.view.getUint8(e),i=4294967296*(255&this.view.getUint8(e+6))+16777216*(255&this.view.getUint8(e+5))+65536*(255&this.view.getUint8(e+4))+256*(255&this.view.getUint8(e+3))+(255&this.view.getUint8(e+2));return this.position+=8,new Ac(i,t)}}class Ac{constructor(e,t){this.block=e,this.offset=t}isLessThan(e){return this.block<e.block||this.block===e.block&&this.offset<e.offset}isGreaterThan(e){return this.block>e.block||this.block===e.block&&this.offset>e.offset}isEqualTo(e){return this.block===e.block&&this.offset===e.offset}print(){return this.block+\":\"+this.offset}}class Cc{static magic=2026540177;littleEndian=!0;nodeCache=new Map;static async loadBpTree(e,t,i){return new Cc(e,t,i).init()}constructor(e,t,i){this.path=e,this.config=t,this.startOffset=i}async init(){const e=await this.#t(this.startOffset,32);let t=e.getInt();if(t!==Cc.magic&&(e.setPosition(0),this.littleEndian=!this.littleEndian,e.littleEndian=this.littleEndian,t=e.getInt(),t!==Cc.magic))throw Error(`Bad magic number ${t}`);const i=e.getInt(),n=e.getInt(),r=e.getInt(),s=e.getLong(),o=e.getLong(),a=this.startOffset+32;return this.header={magic:t,blockSize:i,keySize:n,valSize:r,itemCount:s,reserved:o,nodeOffset:a},this}async search(e){this.header||await this.init();const{keySize:t,valSize:i}=this.header;if(16!==i&&8!==i)throw Error(`Unexpected valSize ${i}`);const n=async e=>{if(this.nodeCache.has(e))return this.nodeCache.get(e);{let n=await this.#t(e,4);const r=n.getByte();n.getByte();const s=n.getUShort(),o=[];if(1===r){const r=s*(t+i);n=await this.#t(e+4,r);for(let e=0;e<s;e++){const e=n.getFixedLengthString(t),r=n.getLong();let s;if(16===i){const e=n.getInt();n.getInt(),s={offset:r,length:e}}else s={offset:r};o.push({key:e,value:s})}}else{const i=s*(t+8);n=await this.#t(e+4,i);for(let e=0;e<s;e++){const e=n.getFixedLengthString(t),i=n.getLong();o.push({key:e,offset:i})}}const a={type:r,count:s,items:o};return this.nodeCache.set(e,a),a}},r=async t=>{const i=await n(t);if(1!==i.type){let t=i.items[0].offset;for(let n=1;n<i.items.length;n++){const r=i.items[n].key;if(e.localeCompare(r)<0)break;t=i.items[n].offset}return r(t)}for(let t of i.items)if(e===t.key)return t.value};return r(this.header.nodeOffset)}async#t(e,t){const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:t}}));return new yc(new DataView(i),this.littleEndian)}}\n",
-       "/**\n",
-       "     * Note: Some portions of this code adapated from the GMOD two-bit.js project, @Copyright (c) 2017 Robert Buels\n",
-       "     * * https://github.com/GMOD/twobit-js/blob/master/src/twoBitFile.ts*\n",
-       "     */const _c=[\"T\",\"C\",\"A\",\"G\"],xc=[];for(let IA=0;IA<256;IA++)xc.push(_c[IA>>6&3]+_c[IA>>4&3]+_c[IA>>2&3]+_c[3&IA]);const kc=xc.map((e=>e.toLowerCase()));class Ic{littleEndian;metaIndex=new Map;constructor(e){this.url=e.twoBitURL||e.fastaURL,this.config=e,e.twoBitBptURL&&(this.bptURL=e.twoBitBptURL)}async init(){if(this.bptURL)this.index=await Cc.loadBpTree(this.bptURL,this.config,0);else{const e=await this._readIndex();this.index={search:async t=>e.has(t)?{offset:e.get(t)}:void 0}}}async readSequence(e,t,i){this.index||await this.init();const n=await this.getSequenceRecord(e);if(!n)return null;if(t<0)throw new TypeError(\"regionStart cannot be less than 0\");(void 0===i||i>n.dnaSize)&&(i=n.dnaSize);const r=this._getOverlappingBlocks(t,i,n.nBlocks),s=this._getOverlappingBlocks(t,i,n.maskBlocks),o=Math.floor(t/4),a=n.packedPos+o,c=Math.floor(i/4)-o+1,l=await Qs.loadArrayBuffer(this.url,{range:{start:a,size:c}}),h=new Uint8Array(l);let d=\"\";for(let e=t;e<i;e+=1){for(;s.length&&s[0].end<=e;)s.shift();const t=s[0]&&s[0].start<=e&&s[0].end>e;if(r[0]&&e>=r[0].start&&e<r[0].end){const t=r.shift();for(;e<t.end&&e<i;)d+=\"N\",e++;e--}else{const i=e%4,n=h[Math.floor(e/4)-o];d+=t?kc[n][i]:xc[n][i]}}return d}async _readIndex(){const e=new Map;let t=await Qs.loadArrayBuffer(this.url,{range:{start:0,size:64}}),i=new DataView(t),n=0;const r=i.getUint32(n,!0),s=i.getUint32(n,!1);n+=4;const o=440477507;if(r===o)this.littleEndian=!0;else{if(s!==o)throw Error(`Bad magic number ${o}`);this.littleEndian=!1}let a,c;this.version=i.getUint32(n,this.littleEndian),n+=4,this.sequenceCount=i.getUint32(n,this.littleEndian),n+=4,this.reserved=i.getUint32(n,this.littleEndian),n+=4;let l=20;for(let t=0;t<this.sequenceCount;t++){(!c||c.available()<1)&&(a=(this.sequenceCount-t)*l,c=await this._loadBinaryBuffer(n,a));const i=c.getByte();n+=1,c.available()<i+5&&(a=(this.sequenceCount-t)*l+100,c=await this._loadBinaryBuffer(n,a));const r=c.getString(i),s=c.getUInt();n+=i+4,e.set(r,s),l=Math.floor(l*(t/(t+1))+r.length/(t+1))}return e}async getSequenceRecord(e){if(!this.metaIndex.has(e)){if(!this.index)throw Error(\"TwobitSequence object must be initialized before accessing sequence\");let t=await this.index.search(e);if(!t)return;let i=t.offset,n=8,r=await this._loadBinaryBuffer(i,n);const s=r.getUInt(),o=r.getUInt();i+=n,n=8*o+4,r=await this._loadBinaryBuffer(i,n);const a=[];for(let e=0;e<o;e++)a.push(r.getUInt());const c=[];for(let e=0;e<o;e++)c.push(r.getUInt());const l=r.getUInt();i+=n,n=8*l+4,r=await this._loadBinaryBuffer(i,n);const h=[];for(let e=0;e<l;e++)h.push(r.getUInt());const d=[];for(let e=0;e<l;e++)d.push(r.getUInt());const u=[];for(let e=0;e<o;e++)u.push(new Sc(a[e],c[e]));const f=[];for(let e=0;e<l;e++)f.push(new Sc(h[e],d[e]));if(0!=r.getUInt())throw Error(\"Bad 2-bit file\");i+=n;const p={dnaSize:s,nBlocks:u,maskBlocks:f,packedPos:i,bpLength:s};this.metaIndex.set(e,p)}return this.metaIndex.get(e)}_getOverlappingBlocks(e,t,i){const n=[];for(let r of i){if(r.start>t)break;r.end<e||n.push(r)}return n}async _loadBinaryBuffer(e,t){const i=await Qs.loadArrayBuffer(this.url,{range:{start:e,size:t}});return new yc(new DataView(i),this.littleEndian)}}class Sc{constructor(e,t){this.start=e,this.size=t}get end(){return this.start+this.size}}class Ec{static#i=1e5;#n;#r=[];#s=10;constructor(e,t){this.sequenceReader=e,this.browser=t}get chromosomes(){return this.sequenceReader.chromosomes}async getSequenceRecord(e){return this.sequenceReader.getSequenceRecord(e)}async getSequence(e,t,i){let n=this.#r.find((n=>n.contains(e,t,i)));if(n||(n=await this.#o(e,t,i),this.#a(n),this.#r.push(n)),n){const e=t-n.start,r=i-t;return n.features?n.features.substring(e,e+r):null}}#a(e){this.#r=this.#r.filter((t=>!e.contains(t))),this.#r.length===this.#s&&this.#r.shift(),this.browser&&this.browser.referenceFrameList.length<100&&(this.#r=this.#r.filter((e=>void 0!==this.browser.referenceFrameList.find((t=>t.overlaps(e))))))}getSequenceInterval(e,t,i){return this.#r.find((n=>n.contains(e,t,i)))}async#o(e,t,i){let n=t,r=i;if(i-t<Ec.#i){const e=i-t,s=Math.round(t+e/2);n=Math.max(0,s-Ec.#i/2),r=n+Ec.#i}const s=new dc(e,n,r);if(this.#n&&this.#n[0].contains(e,t,i))return this.#n[1];{const t=new Promise((async(t,i)=>{s.features=await this.sequenceReader.readSequence(e,n,r),t(s)}));return this.#n=[s,t],t}}async init(){return this.sequenceReader.init()}get chromosomeNames(){return this.sequenceReader.chromosomeNames}getFirstChromosomeName(){return\"function\"==typeof this.sequenceReader.getFirstChromosomeName?this.sequenceReader.getFirstChromosomeName():void 0}#c(e){this.browser.referenceFrameList}}async function Nc(e,t){let i;return\"chromsizes\"===e.format?i=new vc(e.fastaURL||e.url):\"2bit\"===e.format||e.twoBitURL?i=new Ec(new Ic(e),t):Ga(e.fastaURL)||!e.indexURL?i=new pc(e):\"gbk\"===e.format||e.gbkURL||(i=new Ec(new bc(e),t)),await i.init(),i}const Bc={A:\"rgb(  0, 200,   0)\",C:\"rgb(  0,0,200)\",T:\"rgb(255,0,0)\",G:\"rgb(209,113,  5)\",N:\"rgb(80,80,80)\"};function Mc(e,t){if(e.length<6)return void console.log(\"Skipping line: \"+e.join(\" \"));var i={chr1:e[0],start1:Number.parseInt(e[1]),end1:Number.parseInt(e[2]),chr2:e[3],start2:Number.parseInt(e[4]),end2:Number.parseInt(e[5])};if(isNaN(i.start1)||isNaN(i.end1)||isNaN(i.start2)||isNaN(i.end2))return;t&&void 0===t.hiccups&&(t.hiccups=!!t.columnNames&&Dc(t.columnNames));const n=t&&t.hiccups,r=n?6:10;if(n||(e.length>6&&\".\"!==e[6]&&(i.name=e[6]),e.length>7&&\".\"!==e[7]&&(i.score=Number(e[7])),e.length>8&&\".\"!==e[8]&&(i.strand1=e[8]),e.length>9&&\".\"!==e[9]&&(i.strand2=e[9])),t){const n=t.colorColumn;n&&n<e.length&&(i.color=_s.createColorString(e[n]));const s=t.thicknessColumn;s&&s<e.length&&(i.thickness=e[s]),e.length>r&&t.columnNames&&t.columnNames.length===e.length&&(i.extras=e.slice(r))}return i.chr1===i.chr2&&(i.chr=i.chr1,i.start=Math.min(i.start1,i.start2),i.end=Math.max(i.end1,i.end2)),i}function Rc(e,t){if(!(e.length<8))return{chr:e[0],start:Number.parseInt(e[1]),end:Number.parseInt(e[2]),color:_s.createColorString(e[6]),value:Number(e[7])}}function Dc(e){return e&&(e.includes(\"fdrDonut\")||e.includes(\"fdr_donut\"))}function Tc(e,t){if(!(e.length<6))return{chr:e[0],start:Number.parseInt(e[1]),end:Number.parseInt(e[2]),chr1:e[8],start1:Number.parseInt(e[9]),end1:Number.parseInt(e[10]),chr2:e[13],start2:Number.parseInt(e[14]),end2:Number.parseInt(e[15]),name:e[3],score:Number(e[4]),value:Number(e[5]),color:\".\"===e[7]?void 0:\"0\"===e[7]?\"rgb(0,0,0)\":e[7]};console.log(\"Skipping line: \"+e.join(\" \"))}class Lc{constructor(e){this.message=e}}const zc=new Map([[\"%09\",\"\\t\"],[\"%0A\",\"\\n\"],[\"%0D\",\"\\r\"],[\"%25\",\"%\"],[\"%3B\",\";\"],[\"%3D\",\"=\"],[\"%26\",\"&\"],[\"%2C\",\",\"]]);function Hc(e){if(!e.includes(\"%\"))return e;let t=\"\";for(let i=0;i<e.length;i++)if(37===e.charCodeAt(i)&&i<e.length-2){const n=e.substring(i,i+3);zc.has(n)?t+=zc.get(n):t+=n,i+=2}else t+=e.charAt(i);return t}function Pc(e,t=\"=\"){const i=\"=\"===t;var n=[];for(let r of e.split(\";\")){r=r.trim();const e=r.indexOf(t);if(e>0&&e<r.length-1){let t=Hc(r.substring(0,e).trim()),s=Hc(r.substring(e+1).trim());i||(t=Oc(t),s=Oc(s)),n.push([t,s])}}return n}function Oc(e){return e.startsWith('\"')&&e.endsWith('\"')&&(e=e.substr(1,e.length-2)),e}function Uc(e,t,i=Number.MAX_SAFE_INTEGER){if(e.length<3)return;t&&t.gffTags;const n=e[0],r=parseInt(e[1]),s=e.length>2?parseInt(e[2]):r+1;if(isNaN(r)||isNaN(s))return new Lc(\"Unparsable bed record.\");const o=new nl({chr:n,start:r,end:s,score:1e3});let a=3;try{if(e.length>3&&a++<i){if(e[3].indexOf(\";\")>0&&e[3].indexOf(\"=\")>0){const i=Pc(e[3],\"=\");o.attributes={};for(let e of i)o.attributes[e[0]]=e[1],null!=t.nameField&&e[0]===t.nameField&&(o.name=e[1])}o.name||(o.name=\".\"===e[3]?\"\":e[3])}if(e.length>4&&a++<i&&(o.score=\".\"===e[4]?0:Number(e[4]),isNaN(o.score)))return o;if(e.length>5&&a++<i&&(o.strand=e[5],\".\"!==o.strand&&\"+\"!==o.strand&&\"-\"!==o.strand))return o;if(e.length>6&&a++<i&&(o.cdStart=parseInt(e[6]),isNaN(o.cdStart)))return o;if(e.length>7&&a++<i&&(o.cdEnd=parseInt(e[7]),isNaN(o.cdEnd)))return o;if(e.length>8&&a++<i&&\".\"!==e[8]&&\"0\"!==e[8]&&(o.color=_s.createColorString(e[8])),e.length>11&&a++<i){const t=parseInt(e[9]);if(t>1e3)return o;const i=e[10].replace(/,$/,\"\").split(\",\"),n=e[11].replace(/,$/,\"\").split(\",\");if(i.length!==n.length||t!==i.length)return o;const s=[];for(let e=0;e<t;e++){const t=r+parseInt(n[e]),o=t+parseInt(i[e]);s.push({start:t,end:o})}s.length>0&&(Yc(s,o.cdStart,o.cdEnd),o.exons=s)}if(t){let i=t.thicknessColumn,n=t.colorColumn;n&&n<e.length&&(o.color=_s.createColorString(e[n])),i&&i<e.length&&(o.thickness=e[i])}}catch(e){}return o}function qc(e,t){const i=Uc(e,t);return i&&e.length>14&&(i.signal=Number(e[12]),i.pValue=Number(e[13]),i.qValue=Number(e[14])),i}function Qc(e,t){const i=Uc(e,t,9);if(i){const t=[\"Coverage\",\"% Showing Methylation\",\"N-mod\",\"N-canonical\",\"N-other mod\",\"N-delete\",\"N-fail\",\"N-dff\",\"N-nocall\"];for(let n=9;n<e.length;n++){i[t[n-9]]=e[n]}}return i}function Vc(e,t){if(e.length<=15)return;return{swScore:Number.parseInt(e[1]),milliDiv:Number.parseInt(e[2]),milliDel:Number.parseInt(e[3]),milliIns:Number.parseInt(e[4]),chr:e[5],start:Number.parseInt(e[6]),end:Number.parseInt(e[7]),strand:e[9],repName:e[10],repClass:e[11],repFamily:e[12],repStart:Number.parseInt(e[13]),repEnd:Number.parseInt(e[14]),repLeft:Number.parseInt(e[15])}}function jc(e,t){var i=void 0===t.shift?0:1;if(e.length<=9+i)return;const n=parseInt(e[5+i]),r=parseInt(e[6+i]);var s={name:e[0+i],chr:e[1+i],strand:e[2+i],start:parseInt(e[3+i]),end:parseInt(e[4+i]),cdStart:n,cdEnd:r,id:e[0+i]};const o=Kc(parseInt(e[7+i]),e[8+i],e[9+i]);return Yc(o,n,r),s.exons=o,s}function Wc(e,t){var i=void 0===t.shift?0:1;if(e.length<=11+i)return;const n=parseInt(e[5+i]),r=parseInt(e[6+i]),s={name:e[11+i],chr:e[1+i],strand:e[2+i],start:parseInt(e[3+i]),end:parseInt(e[4+i]),cdStart:n,cdEnd:r,id:e[0+i]},o=Kc(parseInt(e[7+i]),e[8+i],e[9+i],e[14+i]);return Yc(o,n,r),s.exons=o,s}function Gc(e,t){var i=void 0===t.shift?0:1;if(e.length<=10+i)return;const n=parseInt(e[6+i]),r=parseInt(e[7+i]);var s={name:e[0+i],id:e[1+i],chr:e[2+i],strand:e[3+i],start:parseInt(e[4+i]),end:parseInt(e[5+i]),cdStart:n,cdEnd:r};const o=Kc(parseInt(e[8+i]),e[9+i],e[10+i]);return Yc(o,n,r),s.exons=o,s}function $c(e,t){if(e.length<21)return;const i=e[13],n=parseInt(e[15]),r=parseInt(e[16]),s=e[8].charAt(0),o=parseInt(e[17]),a=[],c=e[20].replace(/,$/,\"\").split(\",\"),l=e[18].replace(/,$/,\"\").split(\",\");for(let e=0;e<o;e++){const t=parseInt(c[e]),i=t+parseInt(l[e]);a.push({start:t,end:i})}return new rl({chr:i,start:n,end:r,strand:s,exons:a,tokens:e})}function Kc(e,t,i,n){const r=t.replace(/,$/,\"\").split(\",\"),s=i.replace(/,$/,\"\").split(\",\"),o=n?n.replace(/,$/,\"\").split(\",\"):void 0,a=[];for(let t=0;t<e;t++){const e={start:parseInt(r[t]),end:parseInt(s[t])};if(o){const i=parseInt(o[t]);-1!=i&&(e.readingFrame=i)}a.push(e)}return a}function Yc(e,t,i){for(let n of e){const e=n.end,r=n.start;e<t||r>i?n.utr=!0:(t>=r&&t<=e&&(n.cdStart=t),i>=r&&i<=e&&(n.cdEnd=i))}}function Xc(e,t){var i,n,r,s,o,a,c;if(!(e.length<9))return i=e[0],n=parseInt(e[1]),r=parseInt(e[2]),o=e[3],a=Number(e[4]),s=e[5].trim(),c=Number(e[6]),0===a&&(a=c),{chr:i,start:n,end:r,name:o,score:a,strand:s,signal:c,pValue:Number(e[7]),qValue:Number(e[8])}}function Zc(e,t){const i=Xc(e);return e.length>9&&(i.peak=Number(e[9])),i}function Jc(e,t){if(e.length<=3)return;const i={chr:e[0],start:parseInt(e[1]),end:parseInt(e[2]),value:Number(e[3])};if(t){let n=t.colorColumn;n&&n<e.length&&(i.color=_s.createColorString(e[n]))}return i}function el(e,t){const i=t.wig;if(i&&\"fixedStep\"===i.format){const t=i.index*i.step+i.start,n=t+i.span,r=Number(e[0]);return++i.index,isNaN(r)?null:{chr:i.chrom,start:t,end:n,value:r}}if(i&&\"variableStep\"===i.format){if(e.length<2)return null;const t=parseInt(e[0],10)-1,n=t+i.span,r=Number(e[1]);return isNaN(r)?null:{chr:i.chrom,start:t,end:n,value:r}}return Jc(e)}function tl(e,t){if(e.length<6)return;const i=[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"refNCBI\",\"refUCSC\",\"observed\",\"molType\",\"class\",\"valid\",\"avHet\",\"avHetSE\",\"func\",\"locType\",\"weight\",\"exceptions\",\"submitterCount\",\"submitters\",\"alleleFreqCount\",\"alleles\",\"alleleNs\",\"alleleFreqs\",\"bitfields\"],n={chr:e[1],start:Number.parseInt(e[2]),end:Number.parseInt(e[3]),name:e[4],score:Number.parseInt(e[5])},r=Math.min(e.length,i.length);for(let t=6;t<r;t++)n[i[t]]=e[t];return n}function il(e,t,i=Number.MAX_SAFE_INTEGER){if(e.length<4)return;const n=e[0],r=parseInt(e[1]),s=e.length>2?parseInt(e[2]):r+1;if(isNaN(r)||isNaN(s))return new Lc(\"Unparsable bed record.\");const o=new nl({chr:n,start:r,end:s,score:1e3}),a=[];for(let t=3;t<e.length;t++)a.push(Number.parseInt(e[t]));return o.values=a,o}class nl{constructor(e){Object.assign(this,e)}getAttributeValue(e){return this.hasOwnProperty(e)?this[e]:this.attributes?this.attributes[e]:void 0}}class rl{constructor(e){Object.assign(this,e)}get score(){const e=this.tokens,t=parseInt(e[0]),i=parseInt(e[2]),n=parseInt(e[1]),r=parseInt(e[4]),s=parseInt(e[6]),o=parseInt(e[10]);return Math.floor(1e3*(t+i-n-r-s)/o)}get matches(){return this.tokens[0]}get misMatches(){return this.tokens[1]}get repMatches(){return this.tokens[2]}get nCount(){return this.tokens[3]}get qNumInsert(){return this.tokens[4]}get qBaseInsert(){return this.tokens[5]}get tNumInsert(){return this.tokens[6]}get tBaseInsert(){return this.tokens[7]}popupData(){return[{name:\"chr\",value:this.chr},{name:\"start\",value:this.start+1},{name:\"end\",value:this.end},{name:\"strand\",value:this.strand},{name:\"score\",value:this.score},{name:\"match\",value:this.matches},{name:\"mis-match\",value:this.misMatches},{name:\"rep. match\",value:this.repMatches},{name:\"N's\",value:this.nCount},{name:\"Q gap count\",value:this.qNumInsert},{name:\"Q gap bases\",value:this.qBaseInsert},{name:\"T gap count\",value:this.tNumInsert},{name:\"T gap bases\",value:this.tBaseInsert}]}}const sl=new Set([\"transcript\",\"primary_transcript\",\"processed_transcript\",\"mRNA\",\"mrna\",\"lnc_RNA\",\"miRNA\",\"ncRNA\",\"rRNA\",\"scRNA\",\"snRNA\",\"snoRNA\",\"tRNA\"]),ol=new Set([\"CDS\",\"cds\"]),al=new Set([\"start_codon\",\"stop_codon\"]),cl=new Set([\"5UTR\",\"3UTR\",\"UTR\",\"five_prime_UTR\",\"three_prime_UTR\",\"3'-UTR\",\"5'-UTR\"]),ll=new Set([\"exon\",\"coding-exon\"]),hl=new Set;for(let SA of[ol,al,cl,ll])for(let EA of SA)hl.add(EA);function dl(e){return e.includes(\"intron\")}function ul(e){return ol.has(e)||al.has(e)}function fl(e){return cl.has(e)}function pl(e){return sl.has(e)||e.endsWith(\"RNA\")||e.endsWith(\"transcript\")}function gl(e){return hl.has(e)||e.endsWith(\"RNA\")||dl(e)}const ml=new Set([\"id\",\"parent\",\"name\"]);class wl{constructor(e){Object.assign(this,e),void 0!==e.phase&&\".\"!==e.phase&&(this.readingFrame=(3-parseInt(e.phase))%3)}popupData(e){const t=this.geneObject?this.geneObject.popupData():[];if(this.geneObject&&t.push(\"<hr/>\"),this.name&&t.push({name:\"Name\",value:this.name}),t.push({name:\"Type\",value:this.type}),t.push({name:\"Source\",value:this.source}),void 0!==this.score&&t.push({name:\"Score\",value:this.score}),t.push({name:\"Phase\",value:this.phase}),this.attributeString){const e=Pc(this.attributeString,this.delim);for(let[i,n]of e)void 0!==n&&n.length>0&&!ml.has(i.toLowerCase())&&t.push({name:i+\":\",value:n})}return t.push({name:\"Location\",value:`${this.chr}:${Rt(this.start+1)}-${Rt(this.end)}`}),t}getAttributeValue(e){if(this.hasOwnProperty(e))return this[e];if(this._attributeCache||(this._attributeCache=new Map),this._attributeCache.has(e))return this._attributeCache.get(e);{const t=Pc(this.attributeString,this.delim);let i;for(let[n,r]of t)if(n===e){i=r;break}return this._attributeCache.set(e,i),i}}}class bl extends wl{constructor(e){super(e),this.exons=[],this.parts=[]}addExon(e){this.exons.push(e),this.start=Math.min(this.start,e.start),this.end=Math.max(this.end,e.end)}addPart(e){this.parts.push(e)}assembleParts(){if(0===this.parts.length)return;this.parts.sort((function(e,t){return e.start-t.start}));let e=this.parts[0].start,t=this.parts[0].end;for(let i=1;i<this.parts.length;i++){const n=this.parts[i];if(!dl(n.type))if(n.start<=t)t=Math.max(t,n.end);else{this.findExonContaining({start:e,end:t})||this.exons.push({start:e,end:t,psuedo:!0}),e=n.start,t=n.end}}this.findExonContaining({start:e,end:t})||(this.exons.push({start:e,end:t,psuedo:!0}),this.start=Math.min(this.start,e),this.end=Math.max(this.end,t));for(let e of this.parts){const t=e.type;ul(t)?this.addCDS(e):fl(t)&&this.addUTR(e)}}findExonContaining({start:e,end:t}){for(let i of this.exons)if(i.end>=t&&i.start<=e)return i}addCDS(e){let t;const i=this.exons;for(let n of i)if(n.start<=e.start&&n.end>=e.end){t=n;break}t?(t.cdStart=t.cdStart?Math.min(e.start,t.cdStart):e.start,t.cdEnd=t.cdEnd?Math.max(e.end,t.cdEnd):e.end,t.readingFrame=e.readingFrame):console.error(\"No exon found spanning \"+e.start+\"-\"+e.end),this.cdStart=this.cdStart?Math.min(e.start,this.cdStart):e.start,this.cdEnd=this.cdEnd?Math.max(e.end,this.cdEnd):e.end}addUTR(e){let t;const i=this.exons;for(let n=0;n<i.length;n++)if(i[n].start<=e.start&&i[n].end>=e.end){t=i[n];break}t?e.start===t.start&&e.end===t.end?t.utr=!0:(e.end<t.end&&(t.cdStart=e.end),e.start>t.start&&(t.cdEnd=e.start)):console.error(\"No exon found spanning \"+cds.start+\"-\"+cds.end)}finish(){this.assembleParts();var e=this.cdStart,t=this.cdEnd;this.exons.sort((function(e,t){return e.start-t.start})),e&&this.exons.forEach((function(i){(i.end<e||i.start>t)&&(i.utr=!0)}))}popupData(e){const t=super.popupData(e);for(let i of this.exons)if(!i.pseudo&&e>=i.start&&e<i.end&&\"function\"==typeof i.popupData){t.push(\"<hr/>\");const n=i.popupData(e);for(let e of n)t.push(e)}for(let i of this.parts)if(e>=i.start&&e<i.end&&\"function\"==typeof i.popupData){t.push(\"<hr/>\");const n=i.popupData(e);for(let e of n)t.push(e)}return t}}function Fl(e,t){const i=t.format;if(e.length<9)return;const n=\"gff3\"===i?\"=\":\" \";return new wl({source:Hc(e[1]),type:e[2],chr:e[0],start:parseInt(e[3])-1,end:parseInt(e[4]),score:\".\"===e[5]?void 0:Number(e[5]),strand:e[6],phase:\".\"===e[7]?\".\":parseInt(e[7]),attributeString:e[8],delim:n})}function vl(e,t){const i=Fl(e,t);if(!i)return;const n=Pc(i.attributeString,i.delim);for(let[e,t]of n){const n=e.toLowerCase();\"color\"===n||\"colour\"===n?i.color=_s.createColorString(t):\"ID\"===e?i.id=t:\"Parent\"===e&&(i.parent=t)}return i}function yl(e,t){const i=Fl(e,t);if(!i)return;const n=Pc(i.attributeString,i.delim);let r,s;switch(i.type){case\"gene\":r=\"gene_id\";break;case\"transcript\":r=\"transcript_id\",s=\"gene_id\";break;default:s=\"transcript_id\"}for(let[e,t]of n){const n=e.toLowerCase();\"color\"===n||\"colour\"===n?i.color=_s.createColorString(t):e===r?i.id=t:e===s&&(i.parent=t)}return i}function Al(e,t){if(!(e.length<7)){var i=e[0],n=e[1],r=parseInt(e[2]),s=parseInt(e[3]),o=parseInt(e[4]),a=parseInt(e[5]),c=e[6],l={chr:i,name:n,junction_left:r,junction_right:s,num_junction_reads:o,num_spanning_frags:a,spanning_frag_coords:[],start:-1,end:-1},h=r,d=s;if(a>0)for(var u=c.split(\",\"),f=0;f<u.length;f++){var p=u[f].split(\"-\"),g=p[0],m=p[1];g<h&&(h=g),m>d&&(d=m),l.spanning_frag_coords.push({left:g,right:m})}return l.start=h,l.end=d,l}}function Cl(e,t){if(e.length<7)return null;const i={chr:e[0],start:parseInt(e[1])-1,end:parseInt(e[2]),\"Strongest SNP-risk allele\":e[3],\"Disease/Phenotype\":e[4],\"P-value\":e[5],\"Odds ratio or beta\":e[6]};return e.length>6&&(i.PUBMEDID=`<a target = \"blank\" href = \"https://www.ncbi.nlm.nih.gov/pubmed/${e[7]}\">${e[7]}</a>`),i}function _l(e,t){const i=t.customFormat;if(e.length<i.fields.length)return;const n=i.coords||0,r=e[i.chr],s=parseInt(e[i.start])-n,o={chr:r,start:s,end:void 0!==i.end?parseInt(e[i.end]):s+1};return i.fields&&i.fields.forEach((function(t,n){n!==i.chr&&n!==i.start&&n!==i.end&&(o[t]=e[n])})),o}function xl(e,t){const i=t.columnNames;if(!i)throw Error(\"Sample names are not defined.   Missing column headers?\");const n=i.length-3,r=e[0],s=parseInt(e[1]),o=parseInt(e[2]),a=e.slice(3).map(Number);return a.length==n?{chr:r,start:s,end:o,values:a}:void console.warn(`${r}:${s}-${o} row contains ${a.length} sample columns instead of the expected ${n} columns. Skipping...`)}const kl=[\"Name\",\"transcript_id\",\"gene_name\",\"gene\",\"gene_id\",\"alias\",\"locus\",\"name\"];class Il{constructor(e){this.format=e.format,this.nameField=e.nameField,this.filterTypes=void 0===e.filterTypes?new Set([\"chromosome\"]):new Set(e.filterTypes)}combineFeatures(e,t){let i;const n=this.filterTypes;if(e=e.filter((e=>void 0===n||!n.has(e.type))),\"gff3\"===this.format){const t=this.combineFeaturesById(e);i=this.combineFeaturesByType(t)}else i=this.combineFeaturesByType(e);return this.numberExons(i,t),this.nameFeatures(i),i}combineFeaturesById(e){const t=new Map,i=[];for(let n of e)if(gl(n.type)||pl(n.type)||!n.id)i.push(n);else{let e=t.get(n.chr);e||(e=new Map,t.set(n.chr,e));let i=e.get(n.id);i?i.push(n):e.set(n.id,[n])}for(let e of t.values())for(let t of e.values())if(t.length>1){const e=t[0];e.exons=[];for(let i of t)e.start=Math.min(e.start,i.start),e.end=Math.max(e.end,i.end),e.exons.push({start:i.start,end:i.end});i.push(e)}else i.push(t[0]);return i}combineFeaturesByType(e){const t=e.filter((e=>\"gene\"===e.type||e.type.endsWith(\"_gene\"))),i=Object.create(null);for(let e of t)i[e.id]=e;const n=Object.create(null),r=[],s=new Set,o=this.filterTypes;e=e.filter((e=>void 0===o||!o.has(e.type)));for(let t of e)if(pl(t.type)){const e=t.id;if(void 0!==e){const o=new bl(t);n[e]=o,r.push(o),s.add(t);const a=i[t.parent];a&&(o.geneObject=a,s.add(a))}}for(let t of e)if(gl(t.type)){const e=l(t);if(e)for(let i of e){let o=n[i];if(!o&&\"gtf\"===this.format){const e=Object.assign({},t);e.type=\"transcript\",o=new bl(e),n[i]=o,r.push(o)}if(void 0!==o){if(a=t.type,ll.has(a))if(e.length>1){const e=new wl(t);o.addExon(e)}else o.addExon(t);else o.addPart(t);s.add(t)}}}var a;r.forEach((function(e){\"function\"==typeof e.finish&&e.finish()}));const c=e.filter((e=>!s.has(e)));for(let e of c)r.push(e);return r;function l(e){return e.parent&&\"\"!==e.parent.trim()?e.parent.trim().split(\",\"):null}}numberExons(e,t){for(let i of e)if(i.exons&&(!t||i.end<=t.end&&i.start>t.start))for(let e=0;e<i.exons.length;e++){i.exons[e].number=\"-\"===i.strand?i.exons.length-e:e+1}}nameFeatures(e){for(let t of e)if(\"function\"==typeof t.getAttributeValue)if(this.nameField)t.name=t.getAttributeValue(this.nameField);else for(let e of kl){const i=t.getAttributeValue(e);if(i){t.name=i;break}}}}const Sl={gwascatalog:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"pubMedID\",\"author\",\"pubDate\",\"journal\",\"title\",\"trait\",\"initSample\",\"replSample\",\"region\",\"genes\",\"riskAllele\",\"riskAlFreq\",\"pValue\",\"pValueDesc\",\"orOrBeta\",\"ci95\",\"platform\",\"cnv\"]},wgrna:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"thickStart\",\"thickEnd\",\"type\"]},cpgislandext:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"length\",\"cpgNum\",\"gcNum\",\"perCpg\",\"perGc\",\"obsExp\"]},clinVarMain:{fields:[\"chr1\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"thickStart\",\"thickEnd\",\"reserved\",\"blockCount\",\"blockSizes\",\"chromStarts\",\"origName\",\"clinSign\",\"reviewStatus\",\"type\",\"geneId\",\"snpId\",\"nsvId\",\"rcvAcc\",\"testedInGtr\",\"phenotypeList\",\"phenotype\",\"origin\",\"assembly\",\"cytogenetic\",\"hgvsCod\",\"hgvsProt\",\"numSubmit\",\"lastEval\",\"guidelines\",\"otherIds\"]}};class El{constructor(e){this.config=e,this.header={},e.nameField&&(this.header.nameField=e.nameField),this.skipRows=0,e.decode?(this.decode=e.decode,this.delimiter=e.delimiter||\"\\t\"):e.format&&(this.header.format=e.format.toLowerCase(),this.setDecoder(this.header.format)),this.delimiter||(this.delimiter=\"\\t\")}async parseHeader(e){let t,i,n=this.header;for(;void 0!==(i=await e.nextLine());)if(i.startsWith(\"track\")||i.startsWith(\"#track\")){let e=Nl(i);Object.assign(n,e)}else if(i.startsWith(\"browser\"));else if(i.startsWith(\"#columns\")){let e=Bl(i);Object.assign(n,e)}else if(i.startsWith(\"##gff-version 3\"))n.format=\"gff3\";else if(i.startsWith(\"#gffTags\"))n.gffTags=!0;else{if(i.startsWith(\"fixedStep\")||i.startsWith(\"variableStep\"))break;if(i.startsWith(\"#\")){const e=i.split(this.delimiter||\"\\t\");e.length>1&&(t=e)}else{this.setDecoder(n.format);const e=i.split(this.delimiter||\"\\t\");try{const i=Object.assign({columnNames:t},n);if(this.decode(e,i))break;e.length>1&&(t=e)}catch(i){e.length>1&&(t=e)}}}if(t){n.columnNames=t;for(let e=0;e<t.length;e++)\"color\"===t[e]||\"colour\"===t[e]?n.colorColumn=e:\"thickness\"===t[e]&&(n.thicknessColumn=e)}return this.header=n,n}async parseFeatures(e){const t=[],i=this.decode,n=this.header.format,r=this.delimiter||\"\\t\";let s,o=0,a=0;for(;void 0!==(s=await e.nextLine());){if(o++,o<=this.skipRows)continue;if(!s||s.startsWith(\"track\")||s.startsWith(\"#\")||s.startsWith(\"browser\"))continue;if(\"wig\"===n&&s.startsWith(\"fixedStep\")){this.header.wig=Ml(s);continue}if(\"wig\"===n&&s.startsWith(\"variableStep\")){this.header.wig=Rl(s);continue}const e=s.split(r);if(e.length<1)continue;const c=i(e,this.header);c instanceof Lc?(a++,a>0&&console.error(`Error parsing line '${s}': ${c.message}`)):c&&t.push(c)}return i===Mc&&function(e){if(0==e.length)return;const t=e[0];if(void 0===t.score&&void 0!==t.name){for(let t of e)if(!Va(t.name)&&\".\"!==t.name)return;for(let t of e)t.score=Number(t.name),delete t.name}const i=e.filter((e=>e.chr1!==e.chr2));for(let t of i){const i=Object.assign({},t);i.dup=!0,e.push(i),t.chr=t.chr1,t.start=t.start1,t.end=t.end1,i.chr=i.chr2,i.start=i.start2,i.end=i.end2}}(t),\"gtf\"!==this.config.format&&\"gff3\"!==this.config.format&&\"gff\"!==this.config.format||!1===this.config.assembleGFF?t:new Il(this.config).combineFeatures(t)}setDecoder(e){switch(e){case\"broadpeak\":case\"regionpeak\":case\"peaks\":this.decode=Xc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"narrowpeak\":this.decode=Zc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedgraph\":this.decode=Jc,this.delimiter=/\\s+/;break;case\"wig\":this.decode=el,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gff3\":case\"gff\":this.decode=vl,this.delimiter=\"\\t\";break;case\"gtf\":this.decode=yl,this.delimiter=\"\\t\";break;case\"fusionjuncspan\":this.decode=Al,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gtexgwas\":this.skipRows=1,this.decode=Cl,this.delimiter=\"\\t\";break;case\"refflat\":this.decode=Gc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"genepred\":this.decode=jc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"genepredext\":this.decode=Wc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"ensgene\":this.decode=jc,this.header.shift=1,this.delimiter=this.config.delimiter||/\\s+/;break;case\"refgene\":this.decode=Wc,this.delimiter=this.config.delimiter||/\\s+/,this.header.shift=1;break;case\"bed\":this.decode=Uc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gappedpeak\":this.decode=qc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedmethyl\":this.decode=Qc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedpe\":case\"hiccups\":this.decode=Mc,this.delimiter=this.config.delimiter||\"\\t\";break;case\"bedpe-domain\":this.decode=Rc,this.headerLine=!0,this.delimiter=this.config.delimiter||\"\\t\";break;case\"bedpe-loop\":this.decode=Mc,this.delimiter=this.config.delimiter||\"\\t\",this.header={colorColumn:7};break;case\"interact\":this.decode=Tc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"snp\":this.decode=tl,this.delimiter=\"\\t\";break;case\"rmsk\":this.decode=Vc,this.delimiter=\"\\t\";break;case\"gcnv\":this.decode=xl,this.delimiter=\"\\t\";break;case\"shoebox\":this.decode=il,this.delimiter=\"\\t\";break;default:const t=function(e){return Sl&&Sl[e]?function(e){const t=e.fields,i=[\"chr\",\"start\",\"end\"];for(let n=0;n<t.length;n++)for(let r of i)r===t[n]&&(e[r]=n);return e}(Sl[e]):void 0}(e);void 0!==t?(this.decode=_l,this.header.customFormat=t,this.delimiter=t.delimiter||\"\\t\"):(this.decode=Uc,this.delimiter=this.config.delimiter||/\\s+/)}}}function Nl(e){const t={},i=e.split(/(?:\")([^\"]+)(?:\")|([^\\s\"]+)(?=\\s+|$)/g);let n;const r=[];for(let e of i)e&&0!==e.trim().length&&(e.endsWith(\"=\")?n=e:n?(r.push(n+e),n=void 0):r.push(e));for(let e of r){if(!e)return;var s=e.split(\"=\",2);if(2===s.length){const e=s[0].trim(),i=s[1].trim();if(t.hasOwnProperty(e)){let n=t[e];Array.isArray(n)?n.push(i):t[e]=[n,i]}else t[e]=i}}return\"interact\"==t.type?t.format=\"interact\":\"gcnv\"===t.type&&(t.format=\"gcnv\"),t}function Bl(e){let t={},i=e.split(/\\s+/);if(2===i.length){i[1].split(\";\").forEach((function(e){let i=e.split(\"=\");\"color\"===i[0]?t.colorColumn=Number.parseInt(i[1])-1:\"thickness\"===i[0]&&(t.thicknessColumn=Number.parseInt(i[1])-1)}))}return t}function Ml(e){const t=e.split(/\\s+/);return{format:\"fixedStep\",chrom:t[1].split(\"=\")[1],start:parseInt(t[2].split(\"=\")[1],10)-1,step:parseInt(t[3].split(\"=\")[1],10),span:t.length>4?parseInt(t[4].split(\"=\")[1],10):1,index:0}}function Rl(e){const t=e.split(/\\s+/);return{format:\"variableStep\",chrom:t[1].split(\"=\")[1],span:t.length>2?parseInt(t[2].split(\"=\")[1],10):1}}function Dl(t,i){const n=e({class:\"igv-menu-popup-check-container\"}),r=e();n.appendChild(r);const s=l(\"check\",!0===i?\"#444\":\"transparent\");r.appendChild(s);const o=e();return o.innerText=t,n.appendChild(o),n}function Tl(e,t){t=t||Number.MAX_SAFE_INTEGER;const i=[];e.sort((function(e,t){return e.start-t.start})),i.push(-1e3);for(let n of e){let e=0;const r=Math.min(i.length,t);for(e=0;e<r;e++)if(n.start>=i[e]){n.row=e,i[e]=n.end;break}n.row=e,i[e]=n.end}}async function Ll(e,t,i){const n=e=>{const i=Object.assign({},e);return i.chr=\"all\",i.start=t.getGenomeCoordinate(e.chr,e.start),i.end=t.getGenomeCoordinate(e.chr,e.end),i._f=e,i.exons&&delete i.exons,i},r=new Set(t.wgChromosomeNames),s=[];let o=0;for(let a of t.wgChromosomeNames){if(Array.isArray(e)){const i={};for(let n of e){const e=t.getChromosomeName(n.chr);i.hasOwnProperty(e)||(i[e]=[]),i[e].push(n)}e=i}const c=e[a];if(c){const e=i||1e4;for(let i of c){let a=t.getChromosomeName(i.chr);if(r.has(a))if(s.length<e)s.push(n(i));else{const t=e/(o+1);if(Math.random()<t){s[Math.floor(Math.random()*(e-1))]=n(i)}}o++}}}return s.sort((function(e,t){return e.start-t.start})),s}function zl(e,t){if(t=t||1e3,null==e||0===e.length)return;const i={},n=[];for(let t of e){const e=t.chr;let r=i[e];r||(r=[],i[e]=r,n.push(e)),r.push(t)}for(let e of n)Tl(i[e],t)}class Hl{static defaults={height:50,autoHeight:!1,visibilityWindow:void 0,color:void 0,altColor:void 0,supportHiDPI:!0,selected:!1};constructor(e,t){this.browser=t,this.init(e)}init(e){this.config=e,e.displayMode&&(e.displayMode=e.displayMode.toUpperCase());const t=Object.assign({},Hl.defaults);if(this.constructor.defaults)for(let e of Object.keys(this.constructor.defaults))t[e]=this.constructor.defaults[e];for(let n of Object.keys(t))this[n]=e.hasOwnProperty(n)?e[n]:t[n],\"color\"!==n&&\"altColor\"!==n||!this[n]||(this[n]=Mt(i=this[n])&&i.indexOf(\",\")>0&&!i.startsWith(\"rgb(\")&&!i.startsWith(\"rgba(\")?`rgb(${i})`:i);var i;e.name||e.label?this.name=e.name||e.label:Ht(e.url)?this.name=e.url.name:Mt(e.url)&&!e.url.startsWith(\"data:\")&&(this.name=zt(e.url)),this.url=e.url,this.config.type&&(this.type=this.config.type),this.id=void 0===this.config.id?this.name:this.config.id,this.order=e.order,this.autoscaleGroup=e.autoscaleGroup,this.removable=void 0===e.removable||e.removable,this.minHeight=e.minHeight||Math.min(25,this.height),this.maxHeight=e.maxHeight||Math.max(1e3,this.height),e.onclick&&(this.onclick=e.onclick,e.onclick=void 0),e.description&&(\"function\"==typeof e.description?this.description=e.description:this.description=()=>e.description),e.hoverTextFields?this.hoverText=Pl.bind(this):\"function\"==typeof this.config.hoverText&&(this.hoverText=this.config.hoverText)}get name(){return this._name}set name(e){this._name=e,this.trackView&&this.trackView.setTrackLabelName(e)}clearCachedFeatures(){this.trackView&&this.trackView.clearCachedFeatures()}updateViews(){this.trackView&&this.trackView.updateViews()}repaintViews(){this.trackView&&this.trackView.repaintViews()}getState(){const e={},t=Object.keys(this.config).filter((e=>{return!(void 0===(t=this.config[e])||\"function\"==typeof t||t instanceof Promise);var t}));for(const i of t)i.startsWith(\"_\")||(e[i]=this.config[i]);for(let t of Object.keys(e)){if(t.startsWith(\"_\"))continue;const i=this[t];void 0===i||!Oa(i)&&\"boolean\"!=typeof i&&\"metadata\"!==t||(e[t]=i)}const i=Object.assign({},Hl.defaults);if(this.constructor.defaults)for(let e of Object.keys(this.constructor.defaults))i[e]=this.constructor.defaults[e];for(let t of Object.keys(i))void 0!==this[t]&&i[t]!==this[t]&&(e[t]=this[t]);return!this.autoscale&&this.dataRange&&(e.min=this.dataRange.min,e.max=this.dataRange.max),this.autoscaleGroup&&(e.autoscaleGroup=this.autoscaleGroup),e}get supportsWholeGenome(){return!0===this.config.supportsWholeGenome}hasSamples(){return!1}getGenomeId(){return this.browser.genome?this.browser.genome.id:void 0}setTrackProperties(e){if(this.disposed)return;const t={};let i;for(let n of Object.keys(e))switch(n.toLowerCase()){case\"usescore\":t.useScore=1===e[n]||\"1\"===e[n]||\"on\"===e[n]||!0===e[n];break;case\"visibility\":switch(e[n]){case\"2\":case\"3\":case\"pack\":case\"full\":t.displayMode=\"EXPANDED\";break;case\"4\":case\"squish\":t.displayMode=\"SQUISHED\";break;case\"1\":case\"dense\":t.displayMode=\"COLLAPSED\"}break;case\"color\":case\"altcolor\":t[n]=e[n].startsWith(\"rgb(\")?e[n]:\"rgb(\"+e[n]+\")\";break;case\"featurevisiblitywindow\":case\"visibilitywindow\":t.visibilityWindow=Number.parseInt(e[n]);break;case\"maxheightpixels\":i=e[n].split(\":\"),3===i.length&&(t.minHeight=Number.parseInt(i[2]),t.height=Number.parseInt(i[1]),t.maxHeight=Number.parseInt(i[0]));break;case\"viewlimits\":if(!this.config.autoscale){i=e[n].split(\":\");let r,s=0;1==i.length?r=Number(i[0]):2==i.length&&(s=Number(i[0]),r=Number(i[1])),Number.isNaN(r)||Number.isNaN(s)?console.warn(`Unexpected viewLimits value in track line: ${e.viewLimits}`):(t.autoscale=!1,t.dataRange={min:s,max:r},this.viewLimitMin=s,this.viewLimitMax=r)}case\"name\":t[n]=e[n];break;case\"url\":t.infoURL=e[n];break;case\"type\":const r=e[n];Ol.has(r)?t[n]=Ol.get(r):t[n]=r;break;case\"graphtype\":t.graphType=e[n];break;default:t[n]=e[n]}for(let e of Object.keys(t))if(!this.config.hasOwnProperty(e)||\"name\"===e&&this.config._derivedName){let i=t[e];if(\"true\"===i&&(i=!0),\"false\"===i&&(i=!1),this[e]=i,\"height\"===e&&this.trackView)try{const e=Number.parseInt(i);this.trackView.setTrackHeight(e)}catch(e){console.error(e)}}}clickedFeatures(e){const t=e.viewport.cachedFeatures;if(!t||!Array.isArray(t)||0===t.length)return[];const i=e.genomicLocation,n=e.referenceFrame.bpPerPixel>.2?3*e.referenceFrame.bpPerPixel:.2;return to(t,i-n,i+n)}extractPopupData(e,t){const i=new Set([\"row\",\"color\",\"chr\",\"start\",\"end\",\"cdStart\",\"cdEnd\",\"strand\",\"alpha\"]),n=[];let r,s;for(let t in e)if(e.hasOwnProperty(t)&&!i.has(t)&&Oa(e[t])){let i=e[t];n.push({name:Lt(t),value:i}),\"alleles\"===t?r=e[t]:\"alleleFreqs\"===t&&(s=e[t])}if(r&&s){r.endsWith(\",\")&&(r=r.substr(0,r.length-1)),s.endsWith(\",\")&&(s=s.substr(0,s.length-1));let i=r.split(\",\"),o=s.split(\",\");if(o.length>1){let r=[];for(let e=0;e<o.length;e++)r.push({a:i[e],af:Number(o[e])});r.sort((function(e,t){return e.af-t.af}));let s=r[r.length-1].a;if(1===s.length)for(let i=r.length-2;i>=0;i--){let o=r[i].a;if(1===o.length){t||(t=this.getGenomeId());const i=Hl.getCravatLink(e.chr,e.start+1,s,o,t);console.log(i),i&&(n.push(\"<hr/>\"),n.push({html:i}),n.push(\"<hr/>\"))}}}}if(e.attributes)for(let t of Object.keys(e.attributes))n.push({name:t,value:e.attributes[t]});let o=`${e.chr}:${Rt(e.start+1)}-${Rt(e.end)}`;return e.strand&&(o+=` (${e.strand})`),n.push({name:\"Location\",value:o}),n}description(){const e=(e,t)=>`<div class=\"igv-track-label-popup-shim\"><b>${e}: </b>${t}</div>`;let t='<div class=\"igv-track-label-popup\">';if(this.url?Ht(this.url)?t+=e(\"Filename\",this.url.name):t+=e(\"URL\",this.url):t=this.name,this.config){if(this.config.metadata)for(let i of Object.keys(this.config.metadata)){t+=e(i,this.config.metadata[i])}for(let i of Object.keys(this.config)){if(i.startsWith(\"_\"))continue;let n=i.substr(0,1);if(n!==n.toLowerCase()){const n=this.config[i];n&&Oa(n)&&(t+=e(i,n))}}}return t+=\"</div>\",t}getColorForFeature(e){return\"function\"==typeof this.color?this.color(feature):this.color}numericDataMenuItems(){const e=[];e.push(\"<hr/>\");let t=Bt(\"<div>\");if(t.text(\"Set data range\"),e.push({object:t,dialog:function(){this.trackView.track.selected?this.browser.dataRangeDialog.configure(this.trackView.browser.getSelectedTrackViews()):this.browser.dataRangeDialog.configure(this.trackView),this.browser.dataRangeDialog.present(Bt(this.browser.columnContainer))}}),void 0!==this.logScale){function i(){this.logScale=!this.logScale,this.trackView.repaintViews()}t=Bt(Dl(\"Log scale\",this.logScale)),e.push({object:t,click:i})}return t=Bt(Dl(\"Autoscale\",this.autoscale)),e.push({object:t,click:function(){this.autoscaleGroup=void 0,this.autoscale=!this.autoscale,this.browser.updateViews()}}),e}setDataRange({min:e,max:t}){this.dataRange={min:e,max:t},this.autoscale=!1,this.autoscaleGroup=void 0,this.trackView.repaintViews()}async nextFeatureAfter(e,t,i){let n=this.trackView.viewports[0].cachedFeatures;if(n&&Array.isArray(n)&&n.length>0){if(this.browser.genome.getChromosomeName(n[0].chr)===e){const e=function(e,t,i=!0){const n=e=>(e.start+e.end)/2,r=i?(e,t)=>e.start-t.start+e.end-t.end:(e,t)=>t.start-e.start+t.end-e.end,s=Array.from(e);s.sort(r);let o=0,a=s.length;for(;o<a;){let e=Math.floor((o+a)/2);i?n(s[e])<=t?o=e+1:a=e:n(s[e])>=t?o=e+1:a=e}return s[o]}(n,t,i);if(e)return e}}if(\"function\"==typeof this.featureSource.nextFeature)return this.featureSource.nextFeature(e,t,i,this.visibilityWindow)}dispose(){this.disposed=!0;for(let e of Object.keys(this))this[e]=void 0}static getCravatLink(e,t,i,n,r){if(\"hg38\"===r||\"GRCh38\"===r){return`<a target=\"_blank\" href=\"https://run.opencravat.org/result/nocache/variant.html?chrom=${e.startsWith(\"chr\")?e:\"chr\"+e}&pos=${t}&ref_base=${i}&alt_base=${n}\"><b>Cravat ${i}->${n}</b></a>`}}static localFileInspection(e){const t=Object.assign({},e),i={url:\"file\",indexURL:\"indexFile\"};for(const e of[\"url\",\"indexURL\"])t[e]&&t[e]instanceof File&&(t[i[e]]=t[e].name,delete t[e]);return t}}function Pl(e){if(!this.hoverTextFields)return;const t=this.clickedFeatures(e);if(t&&t.length>0){let e=\"\";for(let i=0;i<t.length;i++){if(10===i){e+=\"; ...\";break}if(!t[i])continue;const n=t[i]._f||t[i];e.length>0&&(e+=\"\\n\"),e=\"\";for(let t of this.hoverTextFields)e.length>0&&(e+=\"\\n\"),n.hasOwnProperty(t)?e+=n[t]:\"function\"==typeof n.getAttribute&&(e+=n.getAttribute(t))}return e}}const Ol=new Map([[\"wiggle_0\",\"wig\"],[\"bed\",\"bed\"],[\"bigBed\",\"bigBed\"],[\"bigWig\",\"bigWig\"]]);class Ul{constructor(e){switch(this.type=e||\"seg\",this.type){case\"mut\":this.sampleColumn=3,this.chrColumn=0,this.startColumn=1,this.endColumn=2,this.dataColumn=4;break;case\"maf\":this.sampleColumn=15,this.chrColumn=4,this.startColumn=5,this.endColumn=6,this.dataColumn=8;break;default:this.sampleColumn=0,this.chrColumn=1,this.startColumn=2,this.endColumn=3}}async parseHeader(e){let t;for(;void 0!==(t=await e.nextLine());)if(!t.startsWith(\"#\")){const e=t.split(\"\\t\");this.header={headings:e};break}return this.header}async parseFeatures(e){const t=[];let i;this.header||(this.header=await this.parseHeader(e)),\"seg\"===this.type&&(this.dataColumn=this.header.headings.length-1),this.header.headings.length>5&&(i=this.extractExtraColumns(this.header.headings));const n=this.header.headings[this.dataColumn];let r;for(;void 0!==(r=await e.nextLine());){const e=r.split(\"\\t\"),s=\"seg\"===this.type?Number(e[this.dataColumn]):e[this.dataColumn];if(e.length>this.dataColumn){const r=new ql({sample:e[this.sampleColumn],chr:e[this.chrColumn],start:parseInt(e[this.startColumn])-1,end:parseInt(e[this.endColumn]),value:s,valueColumnName:n});if(i){const t=this.extractExtraColumns(e);r.setAttributes({names:i,values:t})}t.push(r)}}return t}extractExtraColumns(e){const t=[];for(let i=0;i<e.length;i++)i!==this.chrColumn&&i!==this.startColumn&&i!==this.endColumn&&i!==this.sampleColumn&&t.push(e[i]);return t}}class ql{constructor({sample:e,chr:t,start:i,end:n,value:r,valueColumnName:s}){this.sample=e,this.chr=t,this.start=i,this.end=n,this.value=r,this.valueColumnName=s}setAttributes({names:e,values:t}){this.attributeNames=e,this.attributeValues=t}getAttribute(e){if(this.attributeNames){const t=this.attributeNames.indexOf(e);if(t>=0)return this.attributeValues[t]}}popupData(e,t){const i=new Set([\"chr\",\"start\",\"end\",\"sample\",\"value\",\"row\",\"color\",\"sampleKey\",\"uniqueSampleKey\",\"sampleId\",\"chromosome\",\"uniquePatientKey\"]),n=this.chr+\":\"+Rt(this.start+1)+\"-\"+Rt(this.end),r=[{name:\"Sample\",value:this.sample},{name:\"Location\",value:n},{name:this.valueColumnName?Lt(this.valueColumnName):\"Value\",value:this.value}];if(\"mut\"===e&&\"hg38\"===t){const e=this.extractCravatLink(t);e&&(r.push(\"<hr/>\"),r.push({html:e}),r.push(\"<hr/>\"))}if(this.attributeNames&&this.attributeNames.length>0)for(let e=0;e<this.attributeNames.length;e++)!i.has(this.attributeNames[e])&this.valueColumnName!==this.attributeNames[e]&&r.push({name:Lt(this.attributeNames[e]),value:this.attributeValues[e]});return r}extractCravatLink(e){let t,i;if(this.attributeNames&&this.attributeNames.length>0)for(let n=0;n<this.attributeNames.length;n++)if(t||\"Reference_Allele\"!==this.attributeNames[n]||(t=this.attributeValues[n]),!i&&this.attributeNames[n].startsWith(\"Tumor_Seq_Allele\")&&this.attributeValues[n]!==t&&(i=this.attributeValues[n]),t&&i)return Hl.getCravatLink(this.chr,this.start+1,t,i,e)}}const Ql=new Map([[\"REF\",\"referenceBases\"],[\"ALT\",\"alternateBases\"],[\"QUAL\",\"quality\"],[\"FILTER\",\"filter\"]]);class Vl{constructor(e){this.chr=e[0],this.pos=parseInt(e[1]),this.names=e[2],this.referenceBases=e[3],this.alternateBases=e[4],this.quality=e[5],this.filter=e[6],this.info={};const t=e[7];if(t&&\".\"!==t)for(let e of t.split(\";\")){var i=e.split(\"=\");this.info[i[0]]=i[1]}this.init()}getAttributeValue(e){return Ql.has(e)&&(e=Ql.get(e)),this.hasOwnProperty(e)?this[e]:this.info[e]}init(){const e=this.referenceBases,t=this.alternateBases;if(this.info&&(this.info.VT?this.type=this.info.VT:this.info.SVTYPE?this.type=\"SV\":this.info.PERIOD&&(this.type=\"STR\")),void 0===this.type&&(this.type=function(e,t){const i=e.length;if(void 0===t)return\"UNKNOWN\";if(0===t.trim().length||\"<NON_REF>\"===t||\"<*>\"===t||\".\"===t)return\"NONVARIANT\";{const e=t.split(\",\").map((function(e){return 1===i&&1===e.length?\"SNP\":\"<NON_REF>\"===e?\"NONVARIANT\":e.length>i&&$l(e)?\"INSERTION\":e.length<i&&$l(e)?\"DELETION\":\"OTHER\"}));let n=e[0];for(let t of e)if(t!==n)return\"MIXED\";return n}}(e,t)),this.info.END)this.start=this.pos-1,this.info.CHR2&&this.info.CHR2!==this.chr?this.end=this.start+1:this.end=Number.parseInt(this.info.END);else if(\"NONVARIANT\"===this.type)this.start=this.pos-1,this.end=this.start+e.length;else{const i=t.split(\",\").filter((e=>e.length>0));this.alleles=[],this.start=void 0,this.end=void 0;for(let t of i)if(this.alleles.push(t),\"SV\"!==this.type&&$l(t)){let i=t.length,n=e.length;const r=Math.min(i,n);let s=0;for(;s<r&&e.charCodeAt(s)===t.charCodeAt(s);)s++,i--,n--;for(;i>0&&n>0;){const r=s+i-1,o=s+n-1;if(t.charCodeAt(r)!==e.charCodeAt(o))break;i--,n--}for(;i>0&&n>0;){const r=s,o=s;if(t.charCodeAt(r)!==e.charCodeAt(o))break;s++,i--,n--}const o=this.pos+s-1,a=o+n;this.start=void 0===this.start?o:Math.min(this.start,o),this.end=void 0===this.end?a:Math.max(this.end,a)}void 0===this.start&&(this.start=this.pos-1,this.end=this.pos),this.start===this.end&&(this.start-=.5,this.end+=.5)}}popupData(e,t){const i=`${Rt(this.pos)}`,n=this.start===this.end?`${Rt(this.start)} | ${Rt(this.start+1)}`:`${Rt(this.start+1)}-${Rt(this.end)}`,r=[{name:\"Chr\",value:this.chr},{name:\"Pos\",value:i},{name:\"Loc\",value:n},{name:\"ID\",value:this.names?this.names:\"\"},{name:\"Ref\",value:this.referenceBases},{name:\"Alt\",value:this.alternateBases.replace(\"<\",\"&lt;\")},{name:\"Qual\",value:this.quality},{name:\"Filter\",value:this.filter}];if(this.type&&r.push({name:\"Type\",value:this.type}),\"SNP\"===this.type){let e=this.referenceBases;if(1===e.length){let i=this.alternateBases.split(\",\");for(let n of i)if(1===n.length){let i=Hl.getCravatLink(this.chr,this.pos,e,n,t);i&&(r.push(\"<hr/>\"),r.push({html:i}))}}}const s=Object.keys(this.info);if(this.info&&s.length>0){r.push({html:'<hr style=\"border-top: dotted 1px;border-color: #c9c3ba\" />'});for(let e of s)r.push({name:e,value:Kl(decodeURIComponent(this.info[e]))})}return r}getInfo(e){return this.info?this.info[e]:void 0}isRefBlock(){return\"NONVARIANT\"===this.type}isFiltered(){return!(\".\"===this.filter||\"PASS\"===this.filter)}alleleFreq(){return this.info?this.info.AF:void 0}}class jl{constructor(e){this.mate=e,this.chr=e.info.CHR2,this.pos=Number.parseInt(e.info.END),this.start=this.pos-1,this.end=this.pos}get info(){return this.mate.info}get names(){return this.mate.names}get referenceBases(){return this.mate.referenceBases}get alternateBases(){return this.mate.alternateBases}get quality(){return this.mate.quality}get filter(){return this.mate.filter}get calls(){return this.mate.calls}getAttributeValue(e){return this.mate.getAttributeValue(e)}getInfo(e){this.mate.getInfo(e)}isFiltered(){return this.mate.isFiltered()}alleleFreq(){return this.mate.alleleFreq()}popupData(e,t){const i=[];return i.push(\"SV Breakpoint\"),i.push({name:\"Chr\",value:this.chr}),i.push({name:\"Pos\",value:`${Rt(this.pos)}`}),i.push({html:'<hr style=\"border-top: dotted 1px;border-color: #c9c3ba\" />'}),i.push(\"SV\"),i.push(...this.mate.popupData(e,t)),i}}class Wl{constructor({formatFields:e,sample:t,token:i}){this.info={},this.sample=t;const n=i.split(\":\");for(let t=0;t<n.length;t++){const i=n[t];if(t==e.genotypeIndex){this.genotype=[];for(let e of i.split(/[\\|\\/]/))this.genotype.push(\".\"===e?e:parseInt(e))}else this.info[e.fields[t]]=i}}get zygosity(){if(!this._zygosity)if(this.genotype){let e=!0,t=!0,i=!1;for(let n of this.genotype){if(\".\"===n){i=!0;break}0!==n&&(t=!1),0===n&&(e=!1)}this._zygosity=i?\"nocall\":t?\"homref\":e?\"homvar\":\"hetvar\"}else this._zygosity=\"unknown\";return this._zygosity}zygosityScore(){switch(this.zygosity){case\"homvar\":return 4;case\"hetvar\":return 3;case\"homref\":return 2;case\"nocall\":return 1;default:return 0}}#l(){switch(this.zygosity){case\"homref\":return\"Homozygous reference\";case\"homvar\":return\"Homozygous variant\";case\"hetvar\":return\"Heterozygous\";default:return\"\"}}popupData(e,t){const i=[];void 0!==this.sample&&i.push({name:\"Sample\",value:this.sample}),this.genotypeString&&i.push({name:\"Genotype\",value:this.genotypeString});const n=this.#l();n&&i.push({name:\"Zygosity\",value:n});var r=Object.keys(this.info);r.length&&i.push(\"<hr/>\");for(let e of r)i.push({name:e,value:decodeURIComponent(this.info[e])});return i}}const Gl=new Set([\"A\",\"C\",\"T\",\"G\"].map((e=>e.charCodeAt(0))));function $l(e){for(let t=0;t<e.length;t++)if(!Gl.has(e.charCodeAt(t)))return!1;return!0}function Kl(e,t){return void 0===t&&(t=\",\"),Array.isArray(e)?e.join(t):e}class Yl{construtor(){}async parseHeader(e,t){const i={};i.chrAliasTable=new Map;let n=await e.nextLine();if(!n.startsWith(\"##fileformat\"))throw new Error(\"Invalid VCF file: missing fileformat line\");for(i.version=n.substr(13);void 0!==(n=await e.nextLine())&&n.startsWith(\"#\");){let e;const s={};if(n.startsWith(\"##\")){if(n.startsWith(\"##INFO\")||n.startsWith(\"##FILTER\")||n.startsWith(\"##FORMAT\")){const t=n.indexOf(\"<\"),o=n.lastIndexOf(\">\");if(!(t>2&&o>0)){console.log(\"Malformed VCF header line: \"+n);continue}const a=n.substring(2,t-1);i[a]||(i[a]={});const c=Tt(n.substring(t+1,o-1),\",\");for(let t of c){var r=t.split(\"=\");r.length>1&&(\"ID\"===r[0]?e=r[1]:s[r[0]]=r[1])}e&&(i[a][e]=s)}else if(n.startsWith(\"##contig\")&&t){const e=n.indexOf(\"<ID=\");let r=n.indexOf(\",\",e);-1==r&&(r=n.indexOf(\">\",e));const s=n.substring(e+4,r),o=t.getChromosomeName(s);i.chrAliasTable.set(o,s)}}else if(n.startsWith(\"#CHROM\")){const e=n.split(\"\\t\");if(e.length>8){i.sampleNameMap=new Map;for(let t=9;t<e.length;t++)i.sampleNameMap.set(e[t],t-9)}}}return this.header=i,i}async parseFeatures(e){const t=[],i=this.header.sampleNameMap?Array.from(this.header.sampleNameMap.keys()):void 0,n=8+(i?i.length+1:0);let r;for(;void 0!==(r=await e.nextLine());)if(r&&!r.startsWith(\"#\")){const e=r.split(\"\\t\");if(e.length===n){const n=new Vl(e);if(n.header=this.header,t.push(n),e.length>9){const r=Xl(e[8].split(\":\"));n.calls=[];for(let t=9;t<e.length;t++){const s=i[t-9],o=e[t],a=new Wl({formatFields:r,sample:s,token:o});n.calls.push(a)}n.info&&n.info.CHR2&&n.info.END&&t.push(new jl(n))}}}return t}}function Xl(e){const t={genotypeIndex:-1,fields:e};for(let i=0;i<e.length;i++)\"GT\"===e[i]&&(t.genotypeIndex=i);return t}const Zl=Math.log10(Number.MIN_VALUE);class Jl{constructor(e){if(this.config=e,e.columns){if(void 0===e.columns.chromosome||void 0===e.columns.position||void 0===e.columns.value)throw Error(\"columns property must define chrCol, posCol, and valueCol\");this.posCol=e.columns.position-1,this.chrCol=e.columns.chromosome-1,this.valueCol=e.columns.value-1}else this.posCol=2,this.chrCol=1,this.valueCol=3}async parseHeader(e){const t=await e.nextLine();return this.parseHeaderLine(t)}parseHeaderLine(e){if(this.columns=e.split(/\\t/),!this.config.columns)for(let e=0;e<this.columns.length;e++){switch(this.columns[e].toLowerCase()){case\"chr\":case\"chromosome\":case\"chr_id\":this.chrCol=e;break;case\"bp\":case\"pos\":case\"position\":case\"chr_pos\":this.posCol=e;break;case\"p\":case\"pval\":case\"pvalue\":case\"p-value\":case\"p.value\":this.valueCol=e}}return this.columns}async parseFeatures(e){const t=[],i=e.nextLine();let n;this.columns||this.parseHeaderLine(i);const r=e=>{const t=e.indexOf(\"E\");if(t>0){if(Number.parseInt(e.substring(t+1))<Zl)return Number.MIN_VALUE}return Number(e)};for(;void 0!==(n=e.nextLine());){const e=n.split(/\\t/);if(e.length===this.columns.length){const i=e[this.posCol];if(i.indexOf(\";\")>0||0==i.length||i.indexOf(\"x\")>0)continue;const s=e[this.chrCol],o=r(e[this.valueCol]),a=parseInt(i)-1,c=a+1;t.push(new eh({chr:s,start:a,end:c,value:o,line:n,columns:this.columns}))}}return t}static isGWAS(e){const t=e.split(\"\\t\");if(t.length<5)return!1;const i=[[\"chr\",\"chromosome\",\"chr_id\",\"chrom\"],[\"bp\",\"pos\",\"position\",\"chr_pos\",\"chromEnd\"],[\"p\",\"pval\",\"p-value\",\"p.value\"]];for(let e of i)if(!t.some((t=>e.includes(t.toLowerCase()))))return!1;return!0}}class eh{constructor({chr:e,start:t,end:i,value:n,line:r,columns:s}){this.chr=e,this.start=t,this.end=i,this.value=n,this.line=r,this.columns=s}popupData(){const e=this.line.split(/\\t/);return this.columns.map((function(t,i){return{name:t,value:e[i]}}))}getAttribute(e){const t=this.line.split(/\\t/);for(let i=0;i<this.columns.length;i++)if(this.columns[i]===e)return t[i]}}var th=new RegExp(\"([^:]*)\\\\(([^)]*)\\\\)\"),ih=new RegExp(\"([^:]*):([^(]*)\\\\(([^)]*)\\\\)\");class nh{constructor(e){const t=e?e.decode:void 0;this.nameField=e?e.nameField:void 0,this.skipRows=0,this.decode=t||lh,this.delimiter=\"\\t\"}async parseHeader(e){let t,i;for(;(t=await e.nextLine())&&(t.startsWith(\"track\")||t.startsWith(\"#\")||t.startsWith(\"browser\"));)if(t.startsWith(\"track\")||t.startsWith(\"#track\")){let e=oh(t);i?Object.assign(i,e):i=e}else if(t.startsWith(\"#columns\")){let e=ah(t);i?Object.assign(i,e):i=e}else t.startsWith(\"##gff-version 3\")&&(this.format=\"gff3\",i||(i={}),i.format=\"gff3\");return this.header=i,i}async parseFeatures(e){const t=[],i=this.decode,n=this.delimiter||\"\\t\";let r,s=0;for(;void 0!==(r=e.nextLine());){if(s++,s<=this.skipRows||r.startsWith(\"track\")||r.startsWith(\"#\")||r.startsWith(\"browser\"))continue;let e=o();if(e.length<1)continue;if(!this.aed){this.aed=sh(e);continue}const n=i.call(this,e,undefined);n&&t.push(n)}return t;function o(){for(var e,t,i=[],s=\"\",o=!1;r||\"\"===r;){for(e=0;e<r.length;e++)(t=r.charAt(e))===n?o?s+=t:(i.push(s),s=\"\"):'\"'===t?e+1<r.length&&'\"'===r.charAt(e+1)?(o&&(s+='\"'),e++):o=!o:s+=t;if(!o)break;s+=\"\\n\",r=nextLine()}return i.push(s),i}}}function rh(e){var t=ih.exec(e);if(t)return{namespace:t[1],name:t[2],type:t[3]};if(t=th.exec(e))return{namespace:\"?\",name:t[1],type:t[2]};throw new Error(\"Error parsing the header row of AED file - column not in ns:name(ns:type) format\")}function sh(e){var t,i,n;for(t={columns:[],metadata:{}},i=0;i<e.length;i++)n=rh(e[i]),t.columns.push(n);return t}function oh(e){const t={},i=e.split(/(?:\")([^\"]+)(?:\")|([^\\s\"]+)(?=\\s+|$)/g);let n;const r=[];for(let e of i)e&&0!==e.trim().length&&(e.endsWith(\"=\")>0?n=e:n?(r.push(n+e),n=void 0):r.push(e));for(let e of r){if(!e)return;var s=e.split(\"=\",2);if(2===s.length){const e=s[0].trim(),i=s[1].trim();t[e]=i}}return t}function ah(e){let t={},i=e.split(/\\s+/);if(2===i.length){i[1].split(\";\").forEach((function(e){let i=e.split(\"=\");\"color\"===i[0]?t.colorColumn=Number.parseInt(i[1])-1:\"thickness\"===i[0]&&(t.thicknessColumn=Number.parseInt(i[1])-1)}))}return t}function ch(e,t){var i,n,r=e.columns;this.aed=e,this.allColumns=t,this.chr=null,this.start=null,this.end=null,this.score=1e3,this.strand=\".\",this.cdStart=null,this.cdEnd=null,this.name=null,this.color=null;for(let e=0;e<t.length;e++)if(i=t[e]){\"aed:Integer\"===(n=r[e]).type&&(i=parseInt(i));var s=[];if(n.namespace.length>0)for(let e=0;e<n.namespace.length;e++)s.push(n.namespace.charCodeAt(e));\"bio\"===n.namespace.trim()?\"sequence\"===n.name?this.chr=i:\"start\"===n.name?this.start=i:\"end\"===n.name?this.end=i:\"cdsMin\"===n.name?this.cdStart=i:\"cdsMax\"===n.name?this.cdEnd=i:\"strand\"===n.name&&(this.strand=i):\"aed\"===n.namespace?\"name\"===n.name&&(this.name=i):\"style\"===n.namespace&&\"color\"===n.name&&(this.color=_s.createColorString(i))}}function lh(e,t){var i,n,r,s,o,a,c=0,l=this.aed.columns;if(e.length===l.length){for(a=0;a<e.length;a++)s=l[a],\"\"!==(r=e[a])&&c++,\"name\"===s.name&&\"aed\"===s.namespace?i=r:\"value\"===s.name&&\"aed\"===s.namespace&&(n=r);if(2===c&&i&&n)return o=rh(i),this.aed.metadata[o.namespace]||(this.aed.metadata[o.namespace]={}),void(this.aed.metadata[o.namespace][o.name]||(this.aed.metadata[o.namespace][o.name]={type:o.type,value:n}));var h=new ch(this.aed,e);if(h.chr&&(h.start||0===h.start)&&h.end)return h;console.log(\"Cannot parse feature: \"+e.join(\",\"))}else console.log(\"Corrupted AED file row: \"+e.join(\",\"))}function hh(e,t){if(0===e.length)return e;if(e.sort((function(e,t){const i=e.minv.block-t.minv.block;return 0!==i?i:e.minv.offset-t.minv.offset})),e.length<=1)return e;t&&(e=e.filter((e=>e.maxv.isGreaterThan(t))));const i=[];let n;for(let t of e)n&&dh(n,t)?t.maxv.isGreaterThan(n.maxv)&&(n.maxv=t.maxv):(i.push(t),n=t);return i}function dh(e,t){const i=t.minv.block-e.maxv.block;return t.maxv.block-e.minv.block<5e6&&i<65e3}ch.prototype.popupData=function(){for(var e=[],t=this.aed,i=0;i<this.allColumns.length;i++){var n=this.allColumns[i],r=t.columns[i].name;\"sequence\"!==r&&\"color\"!==r&&n&&e.push({name:r,value:n})}return e};class uh{constructor(){this.tabix=!0}parse(e){const t=new yc(new DataView(e)),i=t.getInt();if(21582659!==i)throw 38359875===i?Error(\"CSI version 2 is not supported.  Please enter an issue at https://github.com/igvteam/igv.js\"):Error(\"Not a CSI index\");this.indices=[],this.blockMin=Number.MAX_SAFE_INTEGER,this.lastBlockPosition=[],this.sequenceIndexMap={},this.minShift=t.getInt(),this.depth=t.getInt();const n=[];let r=0;if(t.getInt()>=28){t.getInt(),t.getInt(),t.getInt(),t.getInt(),t.getInt(),t.getInt();const e=t.getInt(),i=t.position+e;let r=0;for(;t.position<i;){let e=t.getString();this.sequenceIndexMap[e]=r,n[r]=e,r++}}const s=this.bin_limit()+1,o=t.getInt();for(let e=0;e<o;e++){const i=[],n=[],o=t.getInt();for(let e=0;e<o;e++){const e=t.getInt();if(n[e]=t.getVPointer(),e>s)t.getInt(),t.getVPointer(),t.getVPointer(),t.getLong(),t.getLong();else{i[e]=[];const n=t.getInt();for(let s=0;s<n;s++){const n=t.getVPointer(),s=t.getVPointer();n&&s&&(n.block<this.blockMin&&(this.blockMin=n.block),s.block>r&&(r=s.block),i[e].push([n,s]))}}}o>0&&(this.indices[e]={binIndex:i,loffset:n})}this.lastBlockPosition=r}get sequenceNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(e,t,i){const n=this.indices[e];if(n){const e=this.reg2bins(t,i);if(0==e.length)return[];const r=[];for(let t of e)for(let e=t[0];e<=t[1];e++)if(n.binIndex[e]){const t=n.binIndex[e];for(let i of t){const t=i[0],n=i[1];r.push({minv:t,maxv:n,bin:e})}}let s=e[this.depth][0];do{if(n.binIndex[s])break;s>1+(this.getParentBin(s)<<3)?s--:s=this.getParentBin(s)}while(0!=s);return hh(r,n.loffset[s])}return[]}getParentBin(e){return 0==e?0:e-1>>3}reg2bins(e,t){(e-=1)<1&&(e=1),t>2**34&&(t=2**34),t-=1;let i=0,n=0,r=this.minShift+3*this.depth;const s=[];for(;i<=this.depth;r-=3,n+=1<<3*i,i+=1){const i=n+(e>>r),o=n+(t>>r);s.push([i,o])}return s}bin_limit(){return((1<<3*(this.depth+1))-1)/7}}class fh{constructor(){}async parse(e,t){const i=[];let n=Number.MAX_SAFE_INTEGER,r=0;const s=new yc(new DataView(e)),o=s.getInt(),a={};if(!(21578050===o||t&&21578324===o))throw new Error(indexURL+\" is not a \"+(t?\"tabix\":\"bai\")+\" file\");{const e=s.getInt();if(t){s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt();for(let t=0;t<e;t++){a[s.getString()]=t}}for(let t=0;t<e;t++){const e={},o=[],a=s.getInt();for(let t=0;t<a;t++){const t=s.getInt();if(37450===t)s.getInt(),s.getVPointer(),s.getVPointer(),s.getLong(),s.getLong();else{e[t]=[];const i=s.getInt();for(let o=0;o<i;o++){const i=s.getVPointer(),o=s.getVPointer();i&&o&&(i.block<n&&(n=i.block),o.block>r&&(r=o.block),e[t].push([i,o]))}}}const c=s.getInt();for(let e=0;e<c;e++){const e=s.getVPointer();o.push(e)}a>0&&(i[t]={binIndex:e,linearIndex:o})}this.firstBlockPosition=n,this.lastBlockPosition=r,this.indices=i,this.sequenceIndexMap=a,this.tabix=t}}get sequenceNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(e,t,i){const n=this.indices[e];if(n){const e=function(e,t){const i=[];t>=1<<29&&(t=1<<29);return--t,i.push([0,0]),i.push([1+(e>>26),1+(t>>26)]),i.push([9+(e>>23),9+(t>>23)]),i.push([73+(e>>20),73+(t>>20)]),i.push([585+(e>>17),585+(t>>17)]),i.push([4681+(e>>14),4681+(t>>14)]),i}(t,i),r=[];for(let t of e)for(let e=t[0];e<=t[1];e++)if(n.binIndex[e]){const t=n.binIndex[e];for(let e of t){const t=e[0],i=e[1];r.push({minv:t,maxv:i})}}const s=n.linearIndex.length;let o;const a=Math.min(t>>14,s-1),c=Math.min(i>>14,s-1);for(let e=a;e<=c;e++){const t=n.linearIndex[e];if(t){o=t;break}}return hh(r,o)}return[]}}class ph{constructor(){this.tribble=!0}async parse(e){let t=0;this.chrIndex={},this.lastBlockPosition=[];const i=new yc(new DataView(e));!function(e){e.getInt(),e.getInt();const t=e.getInt();if(e.getString(),e.getLong(),e.getLong(),e.getString(),e.getInt(),t>=3){let t=e.getInt();for(;t-- >0;)e.getString(),e.getString()}}(i);let n=i.getInt();for(;n-- >0;){let e=i.getString();const n=i.getInt(),r=i.getInt(),s=i.getInt();i.getInt(),i.getInt();let o=i.getLong();const a=[];for(let e=0;e<r;e++){const e=i.getLong();a.push({min:o,max:e}),o=e,e>t&&(t=e)}this.chrIndex[e]={chr:e,blocks:a,longestFeature:s,binWidth:n}}this.lastBlockPosition=t}get sequenceNames(){return Object.keys(this.chrIndex)}chunksForRange(e,t,i){const n=this.chrIndex[e];if(n){const e=n.blocks,r=n.longestFeature,s=n.binWidth,o=Math.max(t-r,0),a=Math.floor(o/s);if(a>=e.length)return[];{const t=Math.min(Math.floor((i-1)/s),e.length-1),n=e[a].min,r=e[t].max;if(0===r-n)return[];return[{minv:{block:n,offset:0},maxv:{block:r,offset:0}}]}}}}async function gh(e,t){let i=await Qs.loadArrayBuffer(e,Ua(t)),n=new DataView(i);if(31===n.getUint8(0)&&139===n.getUint8(1)){i=gs(i).buffer,n=new DataView(i)}switch(n.getInt32(0,!0)){case 21578050:return async function(e){const t=new fh;return await t.parse(e,!1),t}(i);case 21578324:return async function(e){const t=new fh;return await t.parse(e,!0),t}(i);case 21582659:return async function(e){const t=new uh;return t.parse(e),t}(i);case 1480870228:return async function(e){const t=new ph;return t.parse(e),t}(i);case 38359875:throw Error(\"CSI version 2 is not supported.\");default:throw Error(`Unrecognized index type: ${e}`)}}function mh(e){return\"string\"==typeof e||e instanceof String?new wh(e):new bh(e)}class wh{constructor(e){this.data=e,this.ptr=0}nextLine(){var e=this.ptr,t=this.data.indexOf(\"\\n\",e),i=this.data;if(t>0)return this.ptr=t+1,t>e&&\"\\r\"===i.charAt(t-1)?i.substring(e,t-1):i.substring(e,t);var n=i.length;return this.ptr=n,e>=n?void 0:i.substring(e)}}class bh{constructor(e){this.data=e,this.length=this.data.length,this.ptr=0}nextLine(){if(this.ptr>=this.data.length)return;let e=this.ptr;const t=this.data;let i=\"\",n=!1;for(;e<t.length;){var r=t[e],s=0,o=0;if(r<=127?(s=0,o=255&r):r<=223?(s=1,o=31&r):r<=239?(s=2,o=15&r):r<=244&&(s=3,o=7&r),t.length-e-s>0)for(var a=0;a<s;)o=o<<6|63&(r=t[e+a+1]),a+=1;else o=65533,s=t.length-e;e+=s+1;const c=String.fromCodePoint(o);if(\"\\r\"===c)n=!0;else{if(\"\\n\"===c)break;n&&(i+=\"\\r\",n=!1),i+=c}}return this.ptr=e,i}}class Fh{constructor(e){this.config=e,this.filePtr=0,this.bufferPtr=0,this.buffer}async nextLine(){let e;try{for(;;){const t=this.buffer?this.buffer.length:0;for(;this.bufferPtr<t;){const t=String.fromCharCode(this.buffer[this.bufferPtr++]);if(\"\\r\"!==t){if(\"\\n\"===t)return e;e=e?e+t:t}}if(this.eof)return e;await this.readNextBlock()}}catch(t){return console.warn(t),this.eof=!0,e}}async readNextBlock(){const e=Ua(this.config,{range:{start:this.filePtr,size:26}}),t=ms(await Qs.loadArrayBuffer(this.config.url,e));if(0===t)this.eof=!0,this.buffer=void 0;else{const e=Ua(this.config,{range:{start:this.filePtr,size:t}}),i=await Qs.loadArrayBuffer(this.config.url,e);i.byteLength<t&&(this.eof=!0),this.buffer=gs(i),0==this.buffer.byteLength&&(this.eof=!0),this.bufferPtr=0,this.filePtr+=i.byteLength}}}const vh=e=>{const t=ArrayBuffer.isView(e)?e:new Uint8Array(e);return 1+(t[17]<<8|t[16])};class yh{constructor(e){this.config=e,this.cacheBlocks=0!=e.cacheBlocks,this.cache=void 0}async getData(e,t){const i=e.block,n=t.block,r=0===t.offset,s=await this.getInflatedBlocks(i,n,r);if(1===s.length)return s[0];let o=0;for(const e of s)o+=e.byteLength;const a=new Uint8Array(o);let c=0;for(const e of s)a.set(e,c),c+=e.byteLength;return a}async getInflatedBlocks(e,t,i){if(this.cacheBlocks){const n=this.cache;if(n&&n.startBlock<=e&&(n.endBlock>=t||i&&n.nextEndBlock===t)){const i=e-n.startBlock,r=t-n.startBlock;return Ch(n.buffer,i,r)}{let r;if(!n||n.startBlock>t||n.endBlock<e)r=await this.loadBLockData(e,t,{skipEnd:i});else{const s=[];if(e<n.startBlock){const t=await this.loadBLockData(e,n.startBlock,{skipEnd:!0});s.push(t)}let o;if(e<=n.startBlock&&t>=n.endBlock)o=n.buffer;else{const i=Math.max(0,e-n.startBlock);let r;if(t>=n.endBlock)r=n.buffer.byteLength;else{const e=Ah(n.buffer);for(let i=0;i<e.length-1;i++)if(n.startBlock+e[i]===t){r=e[i+1];break}}o=n.buffer.slice(i,r)}if(s.push(o),t>n.endBlock){const e=await this.loadBLockData(n.endBlock,t,{skipStart:!0,skipEnd:i});s.push(e)}r=function(e){if(1===e.length)return e[0];let t=0;for(const i of e)t+=i.byteLength;const i=new Uint8Array(t);let n=0;for(const t of e)i.set(new Uint8Array(t),n),n+=t.byteLength;return i.buffer}(s)}let s=t;if(i){const e=Ah(r);t=e[e.length-1]}return this.cache={startBlock:e,endBlock:t,nextEndBlock:s,buffer:r},Ch(r)}}return Ch(await this.loadBLockData(e,t,{skipEnd:i}))}async loadBLockData(e,t,i){const n=this.config,r=i&&i.skipStart;let s=0;if(!(i&&i.skipEnd)){const e=Ua(n,{range:{start:t,size:26}}),i=await Qs.loadArrayBuffer(n.url,e);s=vh(i)}if(r){const t=Ua(n,{range:{start:e,size:26}}),i=await Qs.loadArrayBuffer(n.url,t);e+=vh(i)}const o=Ua(n,{range:{start:e,size:t+s-e}});return Qs.loadArrayBuffer(n.url,o)}}function Ah(e){const t=e.byteLength;let i=0;const n=[0];for(;i<t;){const r=new Uint8Array(e,i);i+=1+(r[17]<<8|r[16]),i<t&&n.push(i)}return n}function Ch(e,t,i){const n=[];let r=t=t||0;const s=e.byteLength-18;for(;r<s;)try{const t=new Uint8Array(e,r,18),s=t[11]<<8|t[10],o=t[17]<<8|t[16],a=12+s+r,c=e.byteLength-a,l=o-s-18;if(c<l||l<=0)break;const h=new Uint8Array(e,a,l),d=hs(h);if(n.push(d),i===r)break;r+=o+1}catch(e){console.error(e);break}return n}const _h=Math.log10(Number.MIN_VALUE);class xh{chrCol=-1;snpCol=-1;posCol=-1;pValueCol=-1;phenotypeColumn=-1;delimiter=\"\\t\";constructor(e){this.config=e}async parseHeader(e){const t=this.config;t.delimiter&&(this.delimiter=t.delimiter);const i=await e.nextLine(),n=this.parseHeaderLine(i);return t.chrColumn&&(this.chrColumn=t.chrColumn-1),t.snpColumn&&(this.snpColumn=t.snpColumn-1),t.posColumn&&(this.posColumn=t.posColumn-1),t.pValueColumn&&(this.pValueColumn=t.pValueColumn-1),t.phenotypeColumn&&(this.phenotypeColumn=t.phenotypeColumn-1),n}parseHeaderLine(e){this.columns=e.split(this.delimiter);for(let e=0;e<this.columns.length;e++){switch(this.columns[e].toLowerCase()){case\"chr\":case\"chromosome\":case\"chr_id\":case\"chrom\":this.chrColumn=e;break;case\"bp\":case\"pos\":case\"position\":case\"chr_pos\":case\"chromEnd\":this.posColumn=e;break;case\"p\":case\"pval\":case\"pvalue\":case\"p-value\":case\"p.value\":this.pValueColumn=e;break;case\"rsid\":case\"variant\":case\"snp\":this.snpColumn=e;break;case\"phenotype\":case\"gene\":case\"gene_id\":case\"molecular_trait_id\":this.phenotypeColumn=e}}return this.columns}async parseFeatures(e){const t=[],i=e.nextLine();let n;this.columns||this.parseHeaderLine(i);const r=e=>{const t=e.indexOf(\"E\");if(t>0){if(Number.parseInt(e.substring(t+1))<_h)return Number.MIN_VALUE}return Number(e)};for(;void 0!==(n=e.nextLine());){const e=n.split(this.delimiter);if(e.length===this.columns.length){const i=e[this.posColumn];if(i.indexOf(\";\")>0||0==i.length||i.indexOf(\"x\")>0)continue;const n=e[this.chrColumn],s=r(e[this.pValueColumn]),o=parseInt(i)-1,a=o+1,c=e[this.snpColumn],l=e[this.phenotypeColumn],h=new kh({chr:n,start:o,end:a,pValue:s,snp:c,phenotype:l},this.columns,e);t.push(h)}}return t}static isQTL(e){const t=e.split(\"\\t\");if(t.length<5)return!1;const i=[[\"chr\",\"chromosome\",\"chr_id\",\"chrom\"],[\"bp\",\"pos\",\"position\",\"chr_pos\",\"chromEnd\"],[\"p\",\"pval\",\"p-value\",\"p.value\"],[\"rsid\",\"variant\",\"snp\"],[\"phenotype\",\"gene\",\"gene_id\",\"molecular_trait_id\"]];for(let e of i)if(!t.some((t=>e.includes(t.toLowerCase()))))return!1;return!0}}class kh{constructor({chr:e,start:t,end:i,pValue:n,snp:r,phenotype:s},o,a){this.chr=e,this.start=t,this.end=i,this.pValue=n,this.snp=r,this.phenotype=s,this.headers=o,this.tokens=a}popupData(){const e=[];for(let t=0;t<this.headers.length;t++)e.push({name:this.headers[t],value:this.tokens[t]});return e}}class Ih{sequenceNames;constructor(e,t){if(this.config=e||{},this.genome=t,this.indexURL=e.indexURL,this.indexed=e.indexed||void 0!==this.indexURL,this.queryable=this.indexed,Ht(this.config.url))this.filename=this.config.url.name;else if(Ga(this.config.url))this.indexed=!1,this.dataURI=e.url;else{const t=Ot(this.config.url);this.filename=e.filename||t.file}this.parser=this.getParser(this.config),\"vcf\"!==this.config.format||this.config.indexURL||console.warn(\"Warning: index file not specified.  The entire vcf file will be loaded.\")}async defaultVisibilityWindow(){if(this.config.indexURL){const e=await this.getIndex();if(e&&e.lastBlockPosition){let t=0;const i=1e4;for(let i of e.sequenceNames){const e=this.genome.getChromosome(i);e&&(t+=e.bpLength)}return Math.round(t/e.lastBlockPosition*i)}}}async readFeatures(e,t,i){let n;this.dataURI||this.header||await this.readHeader();return await this.getIndex()?(this.indexed=!0,n=await this.loadFeaturesWithIndex(e,t,i)):this.dataURI?(this.indexed=!1,n=await this.loadFeaturesFromDataURI()):\"service\"===this.config.sourceType?n=await this.loadFeaturesFromService(e,t,i):(this.indexed=!1,n=await this.loadFeaturesNoIndex()),n.sort((function(e,t){return e.chr===t.chr?e.start-t.start:e.chr.localeCompare(t.chr)})),n}async readHeader(){if(this.dataURI)return await this.loadFeaturesFromDataURI(this.dataURI),this.header;if(this.config.indexURL){const e=await this.getIndex();if(!e)throw new Error(\"Unable to load index: \"+this.config.indexURL);let t;if(this.sequenceNames=new Set(e.sequenceNames),e.tabix)this._blockLoader=new yh(this.config),t=new Fh(this.config);else{const i=Object.values(e.chrIndex).flatMap((e=>e.blocks)).map((e=>e.max)).reduce(((e,t)=>Math.min(e,t)),Number.MAX_SAFE_INTEGER),n=Ua(this.config,{bgz:e.tabix,range:{start:0,size:i}});t=mh(await Qs.loadString(this.config.url,n))}return this.header=await this.parser.parseHeader(t),this.header}if(\"service\"!==this.config.sourceType){let e;if(this.config._filecontents)e=this.config._filecontents,delete this.config._filecontents;else{const t=Ua(this.config);e=await Qs.loadByteArray(this.config.url,t)}e.length<5e8&&(e=(new TextDecoder).decode(e));let t=mh(e);this.header=await this.parser.parseHeader(t),t=mh(e),this.features=await this.parser.parseFeatures(t),this.sequenceNames=new Set;for(let e of this.features)this.sequenceNames.add(e.chr);return this.header}if(this.config.seqnamesURL){const e=Ua(this.config,{}),t=await Qs.loadString(this.config.seqnamesURL,e);t&&(this.sequenceNames=new Set(t.split(\",\").map((e=>e.trim())).filter((e=>e))))}if(this.config.headerURL){const e=Ua(this.config,{}),t=mh(await Qs.loadString(this.config.headerURL,e));return this.header=await this.parser.parseHeader(t),this.header}}getParser(e){switch(e.format){case\"vcf\":return new Yl(e);case\"seg\":return new Ul(\"seg\");case\"mut\":return new Ul(\"mut\");case\"maf\":return new Ul(\"maf\");case\"gwas\":return new Jl(e);case\"qtl\":return new xh(e);case\"aed\":return new nh(e);default:return new El(e)}}async loadFeaturesNoIndex(){if(this.features){const e=this.features;return delete this.features,e}{const e=Ua(this.config),t=await Qs.loadByteArray(this.config.url,e);if(!this.header){const e=mh(t);this.header=await this.parser.parseHeader(e)}const i=mh(t),n=[];return await this._parse(n,i),n}}async loadFeaturesWithIndex(e,t,i){const n=this.config;this.parser;const r=this.index.tabix,s=r?this.index.sequenceIndexMap[e]:e;if(void 0===s)return[];const o=this.index.chunksForRange(s,t,i);if(o&&0!==o.length){const s=[];for(let a of o){let o;if(r)o=await this._blockLoader.getData(a.minv,a.maxv);else{const e=Ua(n,{range:{start:a.minv.block,size:a.maxv.block-a.minv.block+1}});o=await Qs.loadString(n.url,e)}const c=mh(a.minv.offset?o.slice(a.minv.offset):o);await this._parse(s,c,e,i,t)}return s}return[]}async loadFeaturesFromService(e,t,i){let n;n=\"function\"==typeof this.config.url?this.config.url({chr:e,start:t,end:i}):this.config.url.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i);const r=Ua(this.config),s=mh(await Qs.loadString(n,r)),o=[];return await this._parse(o,s),o}async _parse(e,t,i,n,r){let s=await this.parser.parseFeatures(t);if(s.sort((function(e,t){return e.chr===t.chr?e.start-t.start:e.chr.localeCompare(t.chr)})),void 0===i)for(let t of s)e.push(t);else{let t=!1;for(let o=0;o<s.length;o++){const a=s[o];if(a.chr===i){if(a.start>n){e.push(a);break}a.end>=r&&a.start<=n&&(t||(t=!0,o>0&&e.push(s[o-1])),e.push(a))}}}}async getIndex(){return this.index?this.index:this.config.indexURL?(this.index=await this.loadIndex(),this.index):void 0}async loadIndex(){return gh(this.config.indexURL,this.config)}async loadFeaturesFromDataURI(){if(this.features){const e=this.features;return delete this.features,e}{const e=vs(this.dataURI);let t=mh(e);this.header=await this.parser.parseHeader(t),this.header instanceof String&&this.header.startsWith(\"##gff-version 3\")&&(this.format=\"gff3\"),t=mh(e);const i=[];return await this._parse(i,t),i}}}const Sh=Mt;class Eh{constructor(e){this.config=e}async readFeatures(e,t,i){let n;n=\"function\"==typeof this.config.url?this.config.url({chr:e,start:t,end:i}):this.config.url.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i);let r,s=Object.assign({},this.config);void 0!==this.config.body&&(\"function\"==typeof this.config.body?s.body=this.config.body({chr:e,start:t,end:i}):s.body=this.config.body.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i));const o=await Qs.load(n,s);if(o&&(r=\"function\"==typeof this.config.parser?this.config.parser(o):Sh(o)?JSON.parse(o):o),this.config.mappings){let e=Object.keys(this.config.mappings);for(let t of r)for(let i of e)t[i]=t[this.config.mappings[i]]}return r}}const Nh=function(e,t){this.config=e,this.genome=t,this.expandQueryInterval=!1};Nh.prototype.readFeatures=function(e,t,i){const n=Math.max(0,Math.floor(t));let r=Math.ceil(i);if(this.genome){const t=this.genome.getChromosome(e);t&&r>t.bpLength&&(r=t.bpLength)}const s=this.config.url+\"?db=\"+this.config.db+\"&table=\"+this.config.tableName+\"&chr=\"+e+\"&start=\"+n+\"&end=\"+r;return Qs.loadJson(s,this.config).then((function(e){return e?(e.forEach((function(e){e.hasOwnProperty(\"exonStarts\")&&e.hasOwnProperty(\"exonEnds\")&&e.hasOwnProperty(\"exonCount\")&&e.hasOwnProperty(\"cdsStart\")&&e.hasOwnProperty(\"cdsEnd\")&&function(e){var t,i,n,r,s,o;t=e.exonCount,i=e.exonStarts.split(\",\"),n=e.exonEnds.split(\",\"),r=[];for(var a=0;a<t;a++){var c={start:s=parseInt(i[a]),end:o=parseInt(n[a])};(e.cdsStart>o||e.cdsEnd<e.cdsStart)&&(c.utr=!0),e.cdsStart>=s&&e.cdsStart<=o&&(c.cdStart=e.cdsStart),e.cdsEnd>=s&&e.cdsEnd<=o&&(c.cdEnd=e.cdsEnd),r.push(c)}e.exons=r}(e)})),e):null}))};class Bh{featureCaches=[];gtexChrs=new Set([\"chr1\",\"chr10\",\"chr11\",\"chr12\",\"chr13\",\"chr14\",\"chr15\",\"chr16\",\"chr17\",\"chr18\",\"chr19\",\"chr2\",\"chr20\",\"chr21\",\"chr22\",\"chr3\",\"chr4\",\"chr5\",\"chr6\",\"chr7\",\"chr8\",\"chr9\",\"chrM\",\"chrX\",\"chrY\"]);constructor(e){this.config=e,this.url=e.url,this.tissueId=e.tissueSiteDetailId,this.datasetId=e.datasetId||\"gtex_v8\"}async readFeatures(e,t,i){const n=e.startsWith(\"chr\")?e:\"MT\"===e?\"chrM\":\"chr\"+e;if(!this.gtexChrs.has(n))return[];const r=Math.floor(t),s=Math.ceil(i),o=this.datasetId,a=this.url+\"?chromosome=\"+n+\"&start=\"+r+\"&end=\"+s+\"&tissueSiteDetailId=\"+this.tissueId+\"&datasetId=\"+o,c=await Qs.loadJson(a,{withCredentials:this.config.withCredentials});return c&&c.singleTissueEqtl?c.singleTissueEqtl.map((e=>new Mh(e))):[]}}class Mh{constructor(e){this.chr=e.chromosome,this.start=e.pos-1,this.end=this.start+1,this.snp=e.snpId,this.phenotype=e.geneSymbol,this.pValue=e.pValue,this.json=e}popupData(){return Object.keys(this.json).map((e=>({name:e,value:this.json[e]})))}}class Rh{constructor(e,t){if(this.config=e,this.genome=t,!e.format)throw Error('Format is required, and must be either \"bam\" or \"cram\"');if(this.format=e.format.toUpperCase(),\"BAM\"!==this.format&&\"VCF\"!==this.format)throw Error(`htsget format ${e.format} is not supported`)}async readHeaderData(){const e=`${Dh(this.config)}?class=header&format=${this.format}`,t=await Qs.loadJson(e,Ua(this.config));return await this.loadUrls(t.htsget.urls)}async readData(e,t,i){const n=`${Dh(this.config)}?format=${this.format}&referenceName=${e}&start=${Math.floor(t)}&end=${Math.ceil(i)}`,r=await Qs.loadJson(n,Ua(this.config));return this.loadUrls(r.htsget.urls)}async loadUrls(e){const t=[];for(let i of e)if(i.url.startsWith(\"data:\"))t.push(Promise.resolve(Th(i.url)));else{const e=Ua(this.config||{});i.headers&&(e.headers=Object.assign(e.headers||{},i.headers)),t.push(Qs.loadArrayBuffer(i.url,e))}return function(e){let t=0;for(let i of e)t+=i.byteLength;let i=0;const n=new Uint8Array(t);for(let t of e){const e=new Uint8Array(t);n.set(e,i),i+=e.length}return n}(await Promise.all(t))}static async inferFormat(e){try{const t=Dh(e),i=`${t}${t.includes(\"?\")?\"&\":\"?\"}class=header`,n=await Qs.loadJson(i,Ua(e));if(n.htsget){const t=n.htsget.format;if(\"BAM\"!==t&&\"VCF\"!==t)throw Error(`htsget format ${t} is not supported`);e.format=t.toLowerCase(),e.sourceType=\"htsget\",e.name||(e.name=await ja(e.url))}}catch(e){}}}function Dh(e){if(e.url&&e.endpoint&&e.id)return e.url+e.endpoint+e.id;if(e.endpoint&&e.id)return e.endpoint+e.id;if(e.url)return e.url.startsWith(\"htsget://\")?e.url.replace(\"htsget://\",\"https://\"):e.url;throw Error(\"Must specify either 'url', or 'endpoint' and 'id\")}function Th(e){const t=e.split(\",\"),i=t[0].split(\":\")[1];let n=t[1];n=i.indexOf(\"base64\")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s<n.length;s++)r[s]=n.charCodeAt(s);return r}class Lh extends Rh{constructor(e,t){super(e,t),this.parser=new Yl}async readHeader(){if(!this.header){let e=await this.readHeaderData();fs(e)&&(e=ps(e));const t=mh(e);this.header=await this.parser.parseHeader(t,this.genome),this.chrAliasTable=this.header.chrAliasTable}return this.header}async readFeatures(e,t,i){if(this.config.format&&\"VCF\"!==this.config.format.toUpperCase())throw Error(`htsget format ${this.config.format} is not supported`);this.chrAliasTable||await this.readHeader();let n=this.chrAliasTable.has(e)?this.chrAliasTable.get(e):e,r=await this.readData(n,t,i);fs(r)&&(r=ps(r));const s=mh(r);return this.parser.parseFeatures(s)}}class zh{chrAliasTable=new Map;constructor(e,t){this.sequenceNames=new Set(e),this.genome=t}async getAliasName(e){if(!this.genome)return e;if(!this.chrAliasTable.has(e)){const t=await this.genome.getAliasRecord(e);if(t){let i;const n=Object.keys(t).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>t[e])).filter((e=>this.sequenceNames.has(e)));n.length>0&&(i=n[0]),this.chrAliasTable.set(e,i)}else this.chrAliasTable.set(e,void 0)}return this.chrAliasTable.get(e)}}class Hh{constructor(e){this.genome=e}async nextFeature(e,t,i,n){let r=this.genome.chromosomeNames||[e],s=r.indexOf(e);if(s<0)return;const o=Math.min(1e4,n||1e4);let a=i?t:Math.max(t-o,0);for(;s<r.length&&s>=0;){e=r[s];const c=this.genome.getChromosome(e).bpLength;for(;a<c&&a>=0;){let r=i?a+o:Math.min(t,a+o);const s=await this.getFeatures({chr:e,start:a,end:r,visibilityWindow:n});if(s){const e=(e,t)=>e.start-t.start+e.end-t.end,n=Array.from(s);n.sort(e);let r=i?0:n.length-1;for(;r>=0&&r<n.length;){const e=n[r],s=(e.start+e.end)/2;if(i){if(s>t)return e;r++}else{if(s<t)return e;r--}}}a=i?r:a-o}if(i)s++,a=0,t=0;else{if(s--,s<0)break;a=(t=this.genome.getChromosome(r[s]).bpLength)-o}}}async previousFeature(e,t,i,n){let r=this.genome.chromosomeNames||[e],s=r.indexOf(e);if(s<0)return;const o=Math.min(1e4,n||1e4);let a=i?t:Math.max(t-o,0);for(;s<r.length&&s>=0;){e=r[s];const c=this.genome.getChromosome(e).bpLength;for(;a<c&&a>=0;){let r=Math.min(t,a+o);const s=await this.getFeatures({chr:e,start:a,end:r,visibilityWindow:n});if(s){const e=(e,t)=>e.start-t.start+e.end-t.end,n=Array.from(s);n.sort(e);let r=i?0:n.length-1;for(;r>=0&&r<n.length;){const e=n[r],s=(e.start+e.end)/2;if(i){if(s>t)return e;r++}else{if(s<t)return e;r--}}}a=i?r:a-o}if(i)s++,a=0,t=0;else{if(s--,s<0)break;a=(t=this.genome.getChromosome(r[s]).bpLength)-o}}}}class Ph{constructor(e,t){this.config=e,this.genome=t,this.path=e.url,this.groupCache={},this.datasetCache={}}async readHeader(){if(void 0!==this.magic)return this;let e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:0,size:64e3}})),t=new yc(new DataView(e));if(this.magic=t.getInt(),this.version=t.getInt(),this.indexPos=t.getLong(),this.indexSize=t.getInt(),t.getInt(),this.version>=2){let e=t.getInt();for(this.windowFunctions=[];e-- >0;)this.windowFunctions.push(t.getString())}this.trackType=t.getString(),this.trackLine=t.getString();let i=t.getInt();for(this.trackNames=[];i-- >0;)this.trackNames.push(t.getString());this.genomeID=t.getString(),this.flags=t.getInt(),this.compressed=!!(1&this.flags),e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:this.indexPos,size:this.indexSize}})),t=new yc(new DataView(e)),this.datasetIndex={};let n=t.getInt();for(;n-- >0;){const e=t.getString(),i=t.getLong(),n=t.getInt();this.datasetIndex[e]={position:i,size:n}}for(this.groupIndex={},n=t.getInt();n-- >0;){const e=t.getString(),i=t.getLong(),n=t.getInt();this.groupIndex[e]={position:i,size:n}}return this}async readDataset(e,t,i){const n=e+\"_\"+t+\"_\"+i;if(this.datasetCache[n])return this.datasetCache[n];{await this.readHeader();const r=this.version<2?\"\":\"/\"+t,s=\"all\"===e.toLowerCase()||void 0===i?\"0\":i.toString();let o;o=\"raw\"===t?\"/\"+e+\"/raw\":\"/\"+e+\"/z\"+s+r;const a=this.datasetIndex[o];if(void 0===a)return;const c=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:a.position,size:a.size}}));if(!c)return;const l=new yc(new DataView(c));let h=l.getInt();const d={};for(;h-- >0;)d[l.getString()]=l.getString();const u=l.getString(),f=l.getFloat();let p=l.getInt();const g=[];for(;p-- >0;)g.push({position:l.getLong(),size:l.getInt()});const m={name:o,attributes:d,dataType:u,tileWidth:f,tiles:g};return this.datasetCache[n]=m,m}}async readRootGroup(){const e=this.genome,t=this.groupCache[\"/\"];if(t)return t;{const t=await this.readGroup(\"/\"),i=t.chromosomes,n=t.maxZoom;n&&(this.maxZoom=Number(n));const r=t.totalCount;r&&(t.totalCount=Number(r));const s={};return i&&i.split(\",\").forEach((function(t){const i=e.getChromosomeName(t);s[i]=t})),this.chrAliasTable=s,this.groupCache[\"/\"]=t,t}}async readGroup(e){const t=this.groupCache[e];if(t)return t;{await this.readHeader();const t=this.groupIndex[e];if(void 0===t)return;const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:t.position,size:t.size}}));if(!i)return;const n=new yc(new DataView(i)),r={name:e};let s=n.getInt();for(;s-- >0;){const e=n.getString(),t=n.getString();r[e]=t}return this.groupCache[e]=r,r}}async readTiles(e,t){if(e.sort((function(e,t){return e.position-t.position})),0===(e=e.filter((function(e){return e.size>0}))).length)return[];const i=[];for(let n of e){const e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:n.position,size:n.size}}));let r;try{r=this.compressed?ls(e).buffer:e}catch(e){console.error(e);continue}const s=new yc(new DataView(r)),o=s.getString();let a;switch(o){case\"fixedStep\":a=Oh(s,t);break;case\"variableStep\":a=Uh(s,t);break;case\"bed\":case\"bedWithName\":a=qh(s,t,o);break;default:throw\"Unknown tile type: \"+o}i.push(a)}return i}async readTile(e,t){let i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e.position,size:e.size}}));if(this.compressed){i=ls(i).buffer}const n=new yc(new DataView(i)),r=n.getString();switch(r){case\"fixedStep\":return Oh(n,t);case\"variableStep\":return Uh(n,t);case\"bed\":case\"bedWithName\":return qh(n,t,r);default:throw\"Unknown tile type: \"+r}}}function Oh(e,t){const i=e.getInt(),n=e.getInt(),r=e.getFloat(),s=[];let o=t;for(;o-- >0;){let t=i;const n=[];for(;t-- >0;)n.push(e.getFloat());s.push(n)}return{type:\"fixedStep\",start:n,span:r,data:s,nTracks:t,nPositions:i}}function Uh(e,t){const i=e.getInt(),n=e.getFloat(),r=e.getInt(),s=[];let o=r;for(;o-- >0;)s.push(e.getInt());e.getInt();const a=[];let c=t;for(;c-- >0;){o=r;const t=[];for(;o-- >0;)t.push(e.getFloat());a.push(t)}return{type:\"variableStep\",tileStart:i,span:n,start:s,data:a,nTracks:t,nPositions:r}}function qh(e,t,i){const n=e.getInt();let r=n;const s=[];for(;r-- >0;)s.push(e.getInt());r=n;const o=[];for(;r-- >0;)o.push(e.getInt());e.getInt();const a=[];let c=t;for(;c-- >0;){let t=n;const i=[];for(;t-- >0;)i.push(e.getFloat());a.push(i)}if(\"bedWithName\"===i){r=n;const t=[];for(;r-- >0;)t.push(e.getString())}return{type:i,start:s,end:o,data:a,nTracks:t,nPositions:n}}class Qh extends Hh{#h={};searchable=!1;constructor(e,t){super(t),this.genome=t,this.reader=new Ph(e,t),this.queryable=!0}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,windowFunction:r=\"mean\"}){return\"all\"===e.toLowerCase()?this.getWGValues(r,n):this._getFeatures(e,t,i,n,r)}async _getFeatures(e,t,i,n,r){const s=new hc(e,t,i),o=this.genome;if(!this.rootGroup&&(this.rootGroup=await this.reader.readRootGroup(),!this.normalizationFactor)){const e=this.rootGroup.totalCount;e&&(this.normalizationFactor=1e6/e)}s.bpPerPixel=n;const a=function(e,t,i){var n=i.getChromosome(e).bpLength;return Math.ceil(Math.log(Math.max(0,n/(700*t)))/Gh)}(e,n,o);let c=this.reader.chrAliasTable[e],l=this.reader.maxZoom;void 0===c&&(c=e),void 0===l&&(l=-1);const h=a>l?\"raw\":r,d=await this.reader.readDataset(c,h,a);if(null==d)return[];const u=d.tileWidth,f=Math.floor(t/u),p=Math.floor(i/u),g=await this.reader.readTiles(d.tiles.slice(f,p+1),1),m=[];for(let r of g)switch(r.type){case\"bed\":Vh(r,e,t,i,n,m);break;case\"variableStep\":jh(r,e,t,i,n,m);break;case\"fixedStep\":Wh(r,e,t,i,n,m);break;default:throw\"Unknown tile type: \"+r.type}return m.sort((function(e,t){return e.start-t.start})),m}get supportsWholeGenome(){return!0}get windowFunctions(){return this.reader.windowFunctions}async getWGValues(e,t){const i=this.#h[e];if(i&&i.bpPerPixel>.8*t&&i.bpPerPixel<1.2*t)return i.values;{const i=[],n=this.genome;if(this.genome.wgChromosomeNames)for(let r of n.wgChromosomeNames){const s=n.getChromosome(r).bpLength;t=s/1e3;const o=await this._getFeatures(r,0,s,t,e);if(o)for(let e of o){const t=Object.assign({},e);t.chr=\"all\",t.start=n.getGenomeCoordinate(e.chr,e.start),t.end=n.getGenomeCoordinate(e.chr,e.end),t._f=e,i.push(t)}}return this.#h[e]={values:i,bpPerPixel:t},i}}}function Vh(e,t,i,n,r,s){const o=e.nPositions,a=e.start,c=e.end,l=e.data[0];for(let e=0;e<o;e++){const r=a[e],o=c[e];if(!(o<i)){if(r>n)break;s.push({chr:t,start:r,end:o,value:l[e]})}}}function jh(e,t,i,n,r,s){const o=e.nPositions,a=e.start,c=e.span,l=e.data[0];for(let e=0;e<o;e++){const r=a[e],o=r+c;if(!(o<i)){if(r>n)break;s.push({chr:t,start:r,end:o,value:l[e]})}}}function Wh(e,t,i,n,r,s){const o=e.nPositions;let a=e.start;const c=e.span,l=e.data[0];for(let e=0;e<o;e++){const r=a+c;if(a>n)break;r>=i&&(Number.isNaN(l[e])||s.push({chr:t,start:a,end:r,value:l[e]})),a=r}}var Gh=Math.log(2);class $h{constructor(e,t,i,n){this.header=e,this.nameToId=t,this.idToName=i,this.sumLengths=n}static parseTree(e,t,i=!1){{const n=e.getInt(),r=e.getInt(),s=e.getInt(),o=e.getInt(),a=e.getLong(),c=e.getLong(),l={magic:n,blockSize:r,keySize:s,valSize:o,itemCount:a,reserved:c},h=new Map,d=[];let u=0;const f=n=>{n>=0&&(e.position=n);const r=e.getByte();e.getByte();const a=e.getUShort();if(1===r)for(let t=0;t<a;t++){let t,n=e.getFixedLengthString(s);if(8!==o)throw Error(`Unexpected \"valSize\" value in chromosome tree.  Expected 8, actual value is ${o}`);{t=e.getInt();const r=e.getInt();u+=r,i&&(n=i.getChromosomeName(n)),h.set(n,t),d[t]=n}}else for(let i=0;i<a;i++){e.getFixedLengthString(s);const i=e.getLong()-t,n=e.position;f(i),e.position=n}};return f(-1),new $h(l,h,d,u)}}}class Kh{static magic=610839776;littleEndian=!0;nodeCache=new Map;constructor(e,t,i){this.path=e,this.config=t,this.startOffset=i}async init(){const e=await this.#t(this.startOffset,48);let t=e.getInt();if(t!==Kh.magic&&(e.setPosition(0),this.littleEndian=!this.littleEndian,e.littleEndian=this.littleEndian,t=e.getInt(),t!==Kh.magic))throw Error(`Bad magic number ${t}`);const i=e.getUInt(),n=e.getLong(),r=e.getUInt(),s=e.getUInt(),o=e.getUInt(),a=e.getUInt(),c=e.getLong(),l=e.getUInt(),h=e.getUInt(),d=this.startOffset+48;return this.header={magic:t,blockSize:i,itemCount:n,startChromIx:r,startBase:s,endChromIx:o,endBase:a,endFileOffset:c,itemsPerSlot:l,reserved:h,rootNodeOffset:d},this}async#t(e,t){const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:t}}));return new yc(new DataView(i),this.littleEndian)}async findLeafItemsOverlapping(e,t,i,n){const r=[],s=async o=>{const a=await this.readNode(o);for(let o of a.items)Yh(o,e,t,i,n)&&(1===a.type?r.push(o):await s(o.childOffset))};return await s(this.header.rootNodeOffset),r}async readNode(e){const t=e;if(this.nodeCache.has(t))return this.nodeCache.get(t);let i=await this.#t(e,4);const n=i.getByte(),r=1===n;i.getByte();const s=i.getUShort();let o=s*(r?32:24);i=await this.#t(e+4,o);const a=[];for(let e=0;e<s;e++){let e={isLeaf:r,startChrom:i.getInt(),startBase:i.getInt(),endChrom:i.getInt(),endBase:i.getInt(),childOffset:i.getLong()};r&&(e.dataSize=i.getLong(),e.dataOffset=e.childOffset),a.push(e)}const c={type:n,items:a};return this.nodeCache.set(t,c),c}}function Yh(e,t,i,n,r){return e?(n>e.startChrom||n===e.startChrom&&r>=e.startBase)&&(t<e.endChrom||t===e.endChrom&&i<=e.endBase):(console.log(\"null item for \"+t+\" \"+i+\" \"+r),!1)}class Xh{ixFile;ixxFile;bufferCache=new Map;constructor(e,t){this.ixFile=t,this.ixxFile=e}async search(e,t){const i=e.split(\" \")[0].toLowerCase(),n=await this._getBuffer(i,t);if(!n)return;const r=n.slice(0,n.lastIndexOf(\"\\n\")).split(\"\\n\").filter((e=>!!e)),s=[];for(let e of r){const t=e.split(\" \")[0];if(t.startsWith(i)&&s.push(e),t.slice(0,i.length)>i)break}if(0!==s.length){const e=new Map;for(let t of s){const[i,...n]=t.split(\" \");e.set(i,n.map((e=>e.split(\",\")[0])))}return e}}async getIndex(e){return this.index||(this.index=await this._readIndex()),this.index}async _readIndex(e){return(await Qs.loadString(this.ixxFile)).split(\"\\n\").filter((e=>!!e)).map((e=>{const t=e.length-10,i=e.slice(0,t),n=e.slice(t);return[i,Number.parseInt(n,16)]}))}async _getBuffer(e,t){let i=0,n=65536;const r=await this.getIndex(t);for(let t=0;t<r.length;t++){const[s,o]=r[t],a=Math.min(s.length,e.length);s.slice(0,a)<e&&(i=o,n=o+65536)}const s=n-i;if(!(s<0)){if(this.bufferCache.has(i))return this.bufferCache.get(i);{const e=await Qs.loadString(this.ixFile,{range:{start:i,size:s}});return this.bufferCache.set(i,e),e}}}}class Zh{chrAliasTable=new Map;rpTreeCache=new Map;constructor(e,t){this.path=e.url,this.format=e.format||\"bigwig\",this.genome=t,this.config=e,this.bufferSize=512e3,this.loader=Ga(this.path)?new sd(vs(this.path).buffer):Qs;const i=e.trixURL||e.searchTrix;i&&(this._trix=new Xh(`${i}x`,i))}async preload(){const e=await Qs.loadArrayBuffer(this.path);this.loader=new sd(e)}async readWGFeatures(e,t){await this.loadHeader();const i=this.chromTree.idToName.length-1,n=this.chromTree.idToName[0],r=this.chromTree.idToName[i];return this.readFeatures(n,0,r,Number.MAX_VALUE,e,t)}async readFeatures(e,t,i,n,r,s=\"mean\"){t||(t=0),n||(n=Number.MAX_SAFE_INTEGER),await this.loadHeader();let o,a,c=await this.#d(e),l=await this.#d(i);if(void 0===c||void 0===l)return[];if(\"bigwig\"===this.type){const e=await this.getZoomHeaders();let t=r?function(e,t){let i;for(let n=0;n<t.length;n++){const r=t[n];if(r.reductionLevel<e){i=r;break}}return i}(r,e):void 0;t&&\"none\"!=s?(o=t.indexOffset,a=rd):(o=this.header.fullIndexOffset,a=id)}else o=this.header.fullIndexOffset,a=nd.call(this);const h=await this.loadRPTree(o),d=await h.findLeafItemsOverlapping(c,t,l,n);if(d&&0!==d.length){let e=Number.MAX_VALUE,i=0;for(let t of d)e=Math.min(e,t.dataOffset),i=Math.max(i,t.dataOffset+t.dataSize);const r=i-e,o=await this.loader.loadArrayBuffer(this.config.url,Ua(this.config,{range:{start:e,size:r}})),h=[];for(let i of d){const r=new Uint8Array(o,i.dataOffset-e,i.dataSize);let d;d=this.header.uncompressBuffSize>0?ls(r):r,a.call(this,new DataView(d.buffer),c,t,l,n,h,this.chromTree.idToName,s,this.littleEndian)}return h.sort((function(e,t){return e.start-t.start})),h}return[]}async#d(e){if(this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.chromTree.nameToId.get(e);if(void 0===t&&this.genome){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>this.chromTree.nameToId.has(e)));e.length>0&&(n=e[0],t=this.chromTree.nameToId.get(e[0]))}this.chrAliasTable.set(e,n)}return t}get searchable(){return\"bigbed\"===this.type}async search(e){if(this.header||await this.loadHeader(),!this.header||!this.header.extraIndexCount)return;const t=await this._searchForRegions(e);if(t){const i=await this._loadFeaturesForRange(t.offset,t.length);if(i){const t=i.filter((t=>{for(let i of Object.keys(t)){const n=t[i];if(Mt(n)&&n.toLowerCase()===e.toLowerCase())return!0}return!1}));return t.length>0?t.reduce(((e,t)=>e.end-e.start>t.end-t.start?e:t),i[0]):void 0}}}async _searchForRegions(e){const t=await this.#u();if(t){if(this._trix){const t=e.toLowerCase(),i=await this._trix.search(t);i&&i.has(t)&&(e=i.get(t)[0])}for(let i of t){const t=await i.search(e);if(t)return t}}}async#u(){if(void 0===this._searchTrees&&this.header.extraIndexOffsets&&this.header.extraIndexOffsets.length>0){this._searchTrees=[];for(let e of this.header.extraIndexOffsets){const t=await Cc.loadBpTree(this.path,this.config,e);this._searchTrees.push(t)}}return this._searchTrees}async getZoomHeaders(){return this.zoomLevelHeaders||await this.loadHeader(),this.zoomLevelHeaders}async loadHeader(){if(this.header)return this.header;{let e,t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:0,size:64}}));this.littleEndian=!0;const i=new yc(new DataView(t),this.littleEndian);let n=i.getUInt();if(2291137574===n)this.type=\"bigwig\";else if(2273964779===n)this.type=\"bigbed\";else{this.littleEndian=!1,i.littleEndian=!1,i.position=0;let e=i.getUInt();654085990===e?this.type=\"bigwig\":3958540679===e&&(this.type=\"bigbed\")}e={bwVersion:i.getUShort(),nZoomLevels:i.getUShort(),chromTreeOffset:i.getLong(),fullDataOffset:i.getLong(),fullIndexOffset:i.getLong(),fieldCount:i.getUShort(),definedFieldCount:i.getUShort(),autoSqlOffset:i.getLong(),totalSummaryOffset:i.getLong(),uncompressBuffSize:i.getInt(),extensionOffset:i.getLong()};const r=64;let s={start:r,size:e.totalSummaryOffset>0?e.totalSummaryOffset-r+40:Math.min(e.fullDataOffset,e.chromTreeOffset)-r};t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:s}));const o=new yc(new DataView(t),this.littleEndian),a=e.nZoomLevels;this.zoomLevelHeaders=[],this.firstZoomDataOffset=Number.MAX_SAFE_INTEGER;for(let e=1;e<=a;e++){const t=a-e,i=new Jh(t,o);this.firstZoomDataOffset=Math.min(i.dataOffset,this.firstZoomDataOffset),this.zoomLevelHeaders[t]=i}if(e.autoSqlOffset>0){o.position=e.autoSqlOffset-r;const t=o.getString();t&&(this.autoSql=function(e){let t;const i=[];let n=!1;const r=e.trim().split(/\\s*[\\r\\n]+\\s*/g);for(let e of r)if(e=e.trim(),e.length>0){if(e.startsWith(\"#\"))continue;if(e.startsWith(\"table\"))t=e.split(/\\s+/)[1].trim();else if(e.startsWith(\"(\"))n=!0;else if(e.startsWith(\")\"));else if(n){const t=e.indexOf(\";\");if(t>0){const n=e.substr(0,t).split(/\\s+/),r=e.substr(t+1).replace(/\"/g,\"\").trim();i.push({type:n[0],name:n[1],description:r})}}}return{table:t,fields:i}}(t))}e.totalSummaryOffset>0&&(o.position=e.totalSummaryOffset-r,this.totalSummary=new ed(o));const c=Math.min(2e5,Math.max(1e4,e.fullDataOffset-e.chromTreeOffset));if(this.chromTree=await this.#f(e.chromTreeOffset,c),this.chrNames=new Set(this.chromTree.idToName),\"bigbed\"===this.type){const t=await this.#p(e.fullDataOffset);this.featureDensity=t/this.chromTree.sumLengths}return this.header=e,e.extensionOffset>0&&await this.loadExtendedHeader(e.extensionOffset),this.header}}async#p(e){const t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:4}}));return new yc(new DataView(t),this.littleEndian).getInt()}async#f(e,t){let i=t;const n=async()=>{const t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:i}})),n=new yc(new DataView(t),this.littleEndian);return $h.parseTree(n,e,this.genome)};let r;for(;i<1e6;)try{return await n()}catch(e){r=e,i*=2}throw r}async loadExtendedHeader(e){let t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:64}})),i=new yc(new DataView(t),this.littleEndian);i.getUShort();const n=i.getUShort(),r=i.getLong();if(0===n)return;let s=56*n;t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:r,size:s}})),i=new yc(new DataView(t),this.littleEndian);const o=[],a=[],c=[];for(let e=0;e<n;e++){o.push(i.getUShort());const e=i.getUShort();c.push(i.getLong()),a.push(i.getInt());for(let t=0;t<e;t++)i.getUShort(),a.push(i.getUShort())}this.header.extraIndexCount=n,this.header.extraIndexOffsets=c}async loadRPTree(e){let t=this.rpTreeCache.get(e);return t||(t=new Kh(this.path,this.config,e),await t.init(),this.rpTreeCache.set(e,t),t)}async getType(){return await this.loadHeader(),this.type}async getTrackType(){return await this.loadHeader(),\"bigwig\"===this.type?\"wig\":this.autoSql&&\"chromatinInteract\"===this.autoSql.table?\"interact\":\"annotation\"}async _loadFeaturesForRange(e,t){const i=await this.loader.loadArrayBuffer(this.config.url,Ua(this.config,{range:{start:e,size:t}})),n=new Uint8Array(i),r=this.header.uncompressBuffSize>0?ls(n):n,s=[];return nd.call(this).call(this,new DataView(r.buffer),0,0,Number.MAX_SAFE_INTEGER,Number.MAX_SAFE_INTEGER,s,this.chromTree.idToName),s}}class Jh{constructor(e,t){this.index=e,this.reductionLevel=t.getInt(),this.reserved=t.getInt(),this.dataOffset=t.getLong(),this.indexOffset=t.getLong()}}class ed{constructor(e){e?(this.basesCovered=e.getLong(),this.minVal=e.getDouble(),this.maxVal=e.getDouble(),this.sumData=e.getDouble(),this.sumSquares=e.getDouble(),td.call(this)):(this.basesCovered=0,this.minVal=0,this.maxVal=0,this.sumData=0,this.sumSquares=0,this.mean=0,this.stddev=0)}}function td(){let e=this.basesCovered;if(e>0){this.mean=this.sumData/e,this.stddev=Math.sqrt(this.sumSquares/(e-1));let t=this.minVal<0?this.mean-2*this.stddev:0,i=this.maxVal>0?this.mean+2*this.stddev:0;this.defaultRange={min:t,max:i}}}function id(e,t,i,n,r,s,o,a,c){const l=new yc(e,c),h=l.getInt(),d=l.getInt();let u=d,f=l.getInt();const p=l.getInt(),g=l.getInt(),m=l.getByte();l.getByte();let w=l.getUShort();if(h>=t&&h<=n){let e=0;for(;w-- >0;){let a;switch(m){case 1:u=l.getInt(),f=l.getInt(),a=l.getFloat();break;case 2:u=l.getInt(),a=l.getFloat(),f=u+g;break;case 3:a=l.getFloat(),u=d+e*p,f=u+g,e++}if(!(h<t||h===t&&f<i)){if(h>n||h===n&&u>=r)break;if(Number.isFinite(a)){const e=o[h];s.push({chr:e,start:u,end:f,value:a})}}}}}function nd(){const e=function(e,t,i,n){if(\"biginteract\"===n||i&&(\"chromatinInteract\"===i.table||\"interact\"===i.table))return function(e,t){return e.chr1=t[5],e.start1=Number.parseInt(t[6]),e.end1=Number.parseInt(t[7]),e.chr2=t[10],e.start2=Number.parseInt(t[11]),e.end2=Number.parseInt(t[12]),e.name=t[0],e.score=Number(t[1]),e.value=Number(t[2]),e.color=\".\"===t[4]?void 0:\"0\"===t[4]?\"rgb(0,0,0)\":t[4],e};{const n=e-3;return function(r,s){if(n>0&&(r.name=s[0]),n>1&&(r.score=Number(s[1])),n>2&&(r.strand=s[2]),n>3&&(r.cdStart=parseInt(s[3])),n>4&&(r.cdEnd=parseInt(s[4])),n>5&&\".\"!==s[5]&&\"0\"!==s[5]&&\"-1\"!==s[5]){const e=_s.createColorString(s[5]);r.color=e.startsWith(\"rgb\")?e:void 0}if(n>8){const e=parseInt(s[6]),t=s[7].split(\",\"),i=s[8].split(\",\"),n=[];for(let s=0;s<e;s++){const e=r.start+parseInt(i[s]),o=e+parseInt(t[s]);n.push({start:e,end:o})}!function(e,t,i){for(let n of e){const e=n.end,r=n.start;e<t||r>i?n.utr=!0:(t>=r&&t<=e&&(n.cdStart=t),i>=r&&i<=e&&(n.cdEnd=i))}}(n,r.cdStart,r.cdEnd),r.exons=n}if(i)for(let n=e;n<t;n++)if(n<i.fields.length){const e=i.fields[n].name,t=s[n-3];r[e]=t}}}}(this.header.definedFieldCount,this.header.fieldCount,this.autoSql,this.format);return function(t,i,n,r,s,o,a,c,l){const h=new yc(t,l);for(;h.remLength()>=13;){const t=h.getInt(),c=a[t],l=h.getInt(),d=h.getInt(),u=h.getString();if(!(t<i||t===i&&d<n)){if(t>r||t===r&&l>=s)break;if(d>0){const t={chr:c,start:l,end:d};o.push(t);const i=u.split(\"\\t\");e(t,i)}}}}}function rd(e,t,i,n,r,s,o,a,c){const l=new yc(e,c);for(;l.remLength()>=32;){const e=l.getInt(),c=l.getInt(),h=l.getInt(),d=l.getInt(),u=l.getFloat(),f=l.getFloat(),p=l.getFloat();let g;switch(l.getFloat(),a){case\"min\":g=u;break;case\"max\":g=f;break;default:g=0===d?0:p/d}if(!(e<t||e===t&&h<i)){if(e>n||e===n&&c>=r)break;if(Number.isFinite(g)){const t=o[e];s.push({chr:t,start:c,end:h,value:g})}}}}class sd{constructor(e){this.data=e}loadArrayBuffer(e,t){const i=t.range;return i?this.data.slice(i.start,i.start+i.size):this.data}async dataViewForRange(e,t){const i=Math.min(this.data.byteLength-e.start,e.size);return t?new Uint8Array(this.data,e.start,i):new DataView(this.data,e.start,i)}}class od extends Hh{queryable=!0;#h={};windowFunctions=[\"mean\",\"min\",\"max\",\"none\"];constructor(e,t){super(t),this.reader=new Zh(e,t),this.genome=t,this.format=e.format||\"bigwig\"}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,windowFunction:r}){await this.reader.loadHeader();const s=\"bigwig\"===this.reader.type;let o;return o=\"all\"===e.toLowerCase()?s?await this.getWGValues(r,n):[]:await this.reader.readFeatures(e,t,e,i,n,r),s||Tl(o),o}async getHeader(){return this.reader.loadHeader()}async defaultVisibilityWindow(){return\"bigwig\"===this.reader.type?-1:this.reader.featureDensity?Math.floor(1e4/this.reader.featureDensity):-1}async getWGValues(e,t){const i=this.genome,n=this.#h[e];if(n&&n.bpPerPixel>.8*t&&n.bpPerPixel<1.2*t)return n.values;{const n=await this.reader.readWGFeatures(t,e);let r=[];for(let e of n){const t=e.chr,n=i.getCumulativeOffset(t);if(void 0===n)continue;const s=Object.assign({},e);s.chr=\"all\",s.start=n+e.start,s.end=n+e.end,s._f=e,r.push(s)}return r.sort(((e,t)=>e.start-t.start)),this.#h[e]={values:r,bpPerPixel:t},r}}supportsWholeGenome(){return\"bigwig\"===this.reader.type}async trackType(){return this.reader.getTrackType()}get searchable(){return this.reader.searchable}async search(e){return this.reader.search(e)}}const ad=.01;function cd(e,t,i,n){if(void 0===this.dataRange||void 0===this.dataRange.max||void 0===this.dataRange.min)return;xo.fillRect(e,0,0,t,i,{fillStyle:\"white\"}),n&&xo.fillRect(e,t-4-2,0,4,i,{fillStyle:n});const r=void 0!==this.flipAxis&&this.flipAxis,s=.95*t-8-5,o=.95*t-5,a={font:\"normal 10px Arial\",textAlign:\"right\",fillStyle:\"black\",strokeStyle:\"black\"};xo.strokeLine(e,s,ad*i,o,ad*i,a),xo.fillText(e,l(r?this.dataRange.min:this.dataRange.max),s+4,ad*i+12,a);const c=.99*i;function l(e){return 0===e?\"0\":Math.abs(e)>=10?e.toFixed():Math.abs(e)>=1?e.toFixed(1):Math.abs(e)>=.1?e.toFixed(2):e.toExponential(1)}xo.strokeLine(e,s,c,o,c,a),xo.fillText(e,l(r?this.dataRange.max:this.dataRange.min),s+4,c-4,a),xo.strokeLine(e,o,ad*i,o,c,a)}class ld extends Hl{static defaults={height:50,flipAxis:!1,logScale:!1,windowFunction:\"mean\",graphType:\"bar\",normalize:void 0,scaleFactor:void 0,overflowColor:\"rgb(255, 32, 255)\",baselineColor:\"lightGray\",summarize:!0,visibilityWindow:void 0};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"wig\",this.featureType=\"numeric\",this.resolutionAware=!0,this.paintAxis=cd;const t=e.format?e.format.toLowerCase():e.format;e.featureSource?(this.featureSource=e.featureSource,delete e.featureSource):this.featureSource=\"bigwig\"===t?new od(e,this.browser.genome):\"tdf\"===t?new Qh(e,this.browser.genome):Ad(e,this.browser.genome),void 0===e.max||!0===e.autoscale?this.autoscale=!0:this.dataRange={min:e.min||0,max:e.max}}async postInit(){const e=await this.getHeader();this.disposed||e&&this.setTrackProperties(e)}supportsWholeGenome(){return void 0===this.visibilityWindow||this.visibilityWindow<0}async getFeatures(e,t,i,n){const r=this.windowFunction,s=await this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow,windowFunction:r});if(this.normalize&&this.featureSource.normalizationFactor){const e=this.featureSource.normalizationFactor;for(let t of s)t.value*=e}if(this.scaleFactor){const e=this.scaleFactor;for(let t of s)t.value*=e}return!this.summarize||\"mean\"!==r&&\"min\"!==r&&\"max\"!==r?s:hd(s,t,n,r)}menuItemList(){const e=[];if(void 0!==this.flipAxis){function t(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}e.push(\"<hr>\"),e.push({label:\"Flip y-axis\",click:t})}return this.featureSource.windowFunctions&&e.push(...this.wigSummarizationItems()),e.push(...this.numericDataMenuItems()),e}wigSummarizationItems(){const e=this.featureSource.windowFunctions,t=[];t.push(\"<hr/>\"),t.push(\"<div>Windowing function</div>\");for(const i of e){const n=Bt(Dl(i,this.windowFunction===i));function r(){this.windowFunction=i,this.trackView.updateViews()}t.push({object:n,click:r})}return t}async getHeader(){return\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getScaleFactor(e,t,i,n){const r=!0===n?e<0?-Math.log10(Math.abs(e)+1):Math.log10(Math.abs(e)+1):e;return i/((!0===n?Math.log10(Math.abs(t)+1):t)-r)}computeYPixelValue(e,t){return(this.flipAxis?e-this.dataRange.min:this.dataRange.max-e)*t}computeYPixelValueInLogScale(e,t){let i=this.dataRange.max,n=this.dataRange.min;return n=n<0?-Math.log10(Math.abs(n)+1):Math.log10(Math.abs(n)+1),i=i<0?-Math.log10(Math.abs(i)+1):Math.log10(Math.abs(i)+1),e=e<0?-Math.log10(Math.abs(e)+1):Math.log10(e+1),(this.flipAxis?e-n:i-e)*t}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=e.pixelHeight-1,a=r+s*n+1,c=this.getScaleFactor(this.dataRange.min,this.dataRange.max,o,this.logScale),l=e=>this.logScale?this.computeYPixelValueInLogScale(e,c):this.computeYPixelValue(e,c);if(t&&t.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){let s,c=-1;const h=l(0);for(let d of t){if(d.end<r)continue;if(d.start>a)break;const t=(d.start-r)/n;if(isNaN(t))continue;let u=l(d.value);const f=(d.end-r)/n-t,p=e.alpha?_s.addAlpha(this.getColorForFeature(d),e.alpha):this.getColorForFeature(d);if(\"line\"===this.graphType)void 0!==s&&xo.strokeLine(i,c,s,t,u,{fillStyle:p,strokeStyle:p}),xo.strokeLine(i,t,u,t+f,u,{fillStyle:p,strokeStyle:p});else if(\"points\"===this.graphType){const e=this.config.pointSize||3,n=t+f/2;xo.fillCircle(i,n,u,e/2,{fillStyle:p,strokeStyle:p}),d.value>this.dataRange.max?xo.fillCircle(i,n,e/2,e/2,3,{fillStyle:this.overflowColor}):d.value<this.dataRange.min&&xo.fillCircle(i,n,o-e/2,e/2,3,{fillStyle:this.overflowColor})}else{const e=Math.min(o,u-h);xo.fillRect(i,t,h,f,e,{fillStyle:p}),d.value>this.dataRange.max?xo.fillRect(i,t,0,f,3,{fillStyle:this.overflowColor}):d.value<this.dataRange.min&&xo.fillRect(i,t,o-2,f,3,{fillStyle:this.overflowColor})}c=t+f,s=u}if(this.dataRange.min<0){let t=this.dataRange.max,n=this.dataRange.min;n=!0===this.logScale?n<0?-Math.log10(Math.abs(n)+1):Math.log10(Math.abs(n)+1):n,t=!0===this.logScale?t<0?-Math.log10(Math.abs(t)+1):Math.log10(Math.abs(t)+1):t;const r=t/(t-n),s=this.flipAxis?(1-r)*o:r*o;xo.strokeLine(i,0,s,e.pixelWidth,s,{strokeStyle:this.baselineColor})}}if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=l(t.y),n={strokeStyle:t.color,strokeWidth:2};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,n):xo.strokeLine(e.context,0,i,e.pixelWidth,i,n)}}popupData(e,t){if(void 0===t&&(t=this.clickedFeatures(e)),t&&t.length>0){const i=e.genomicLocation,n=[];t.sort((function(e,t){return Math.abs((e.start+e.end)/2-i)-Math.abs((t.start+t.end)/2-i)}));const r=t.length>10?t.slice(0,10):t;r.sort((function(e,t){return e.start-t.start}));for(let e of r)if(e){n.length>0&&n.push(\"<hr/>\");let t=e.end-e.start==1?Rt(Math.floor(e.start)+1):Rt(Math.floor(e.start)+1)+\"-\"+Rt(Math.floor(e.end));n.push({name:\"Position:\",value:t}),n.push({name:\"Value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\",value:Rt(e.value.toFixed(4))})}return r.length<t.length&&n.push(\"<hr/>...\"),n}return[]}get supportsWholeGenome(){return!this.config.indexURL&&!1!==this.config.supportsWholeGenome}getColorForFeature(e){let t=e.value<0&&this.altColor?this.altColor:this.color||\"rgb(150, 150, 150)\";return\"function\"==typeof t?t(e.value):t}dispose(){this.trackView=void 0}}function hd(e,t,i,n=\"mean\"){if(i<=1||!e||0===e.length)return e;const r=e[0].chr,s=i,o=[],a=e=>{const i=t+e.bin*s,a=i+s;let c;switch(n){case\"mean\":c=e.sumData/e.count;break;case\"max\":c=e.max;break;case\"min\":c=e.min;break;default:throw Error(`Unknown window function: ${n}`)}const l=`${n} of ${e.count} values`;o.push({chr:r,start:i,end:a,value:c,description:l})};let c;for(let i of e){let e=Math.floor((i.start-t)/s);const n=Math.floor((i.end-t)/s);if(c&&e===c.bin&&(c.add(i),e++),!c||n>c.bin){if(c&&a(c),n>e){const e=t+n*s;o.push({chr:r,start:i.start,end:e,value:i.value})}c=new dd(n,i)}}c&&a(c);const l=[];let h=o[0];for(let e of o)h.value===e.value&&e.start<=h.end?h.end=e.end:(l.push(h),h=e);return l.push(h),l}class dd{constructor(e,t){this.bin=e,this.sumData=t.value,this.count=1,this.min=t.value,this.max=t.value}add(e){this.sumData+=e.value,this.max=Math.max(e.value,this.max),this.min=Math.min(e.value,this.min),this.count++}get mean(){return this.sumData/this.count}}class ud extends Hh{constructor(e,t){super(t),this.config=e||{},this.genome=t,this.sourceType=void 0===e.sourceType?\"file\":e.sourceType,this.maxWGCount=e.maxWGCount||1e4,this.windowFunctions=[\"mean\",\"min\",\"max\",\"none\"];const i=new Set([\"bigwig\",\"bw\",\"bigbed\",\"bb\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\",\"tdf\"]);if(this.queryable=e.indexURL||!0===e.queryable,e.reader)this.reader=e.reader,this.queryable=!1!==e.queryable;else{if(\"ga4gh\"===e.sourceType)throw Error(\"Unsupported source type 'ga4gh'\");\"eqtl\"!==e.type&&\"qtl\"!==e.type||\"gtex-ws\"!==e.sourceType?\"htsget\"===e.sourceType?(this.reader=new Lh(e,t),this.queryable=!0):\"ucscservice\"===e.sourceType?(this.reader=new Nh(e.source),this.queryable=!0):\"custom\"===e.sourceType?(this.reader=new Eh(e.source),this.queryable=!1!==e.source.queryable):\"service\"===e.sourceType?(this.reader=new Ih(e,t),this.queryable=!0):(this.reader=new Ih(e,t),void 0!==e.queryable?this.queryable=e.queryable:(i.has(e.format)||this.reader.indexed)&&(this.queryable=!0)):(this.reader=new Bh(e),this.queryable=!0)}this.searchable=!1!==e.searchable}async defaultVisibilityWindow(){if(this.reader&&\"function\"==typeof this.reader.defaultVisibilityWindow)return this.reader.defaultVisibilityWindow()}async trackType(){const e=await this.getHeader();return e?e.type:void 0}async getHeader(){if(!this.header)if(this.reader&&\"function\"==typeof this.reader.readHeader){const e=await this.reader.readHeader();e?(this.header=e,e.format&&(this.config.format=e.format)):this.header={}}else this.header={};return this.header}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r,windowFunction:s}){const o=\"all\"===e.toLowerCase();if(t=t||0,i=i||Number.MAX_SAFE_INTEGER,(o&&!this.wgFeatures&&this.supportsWholeGenome()||this.config.disableCache||!this.featureCache||!this.featureCache.containsRange(new hc(e,t,i)))&&await this.loadFeatures(e,t,i,r),o){if(!this.wgFeatures)if(this.supportsWholeGenome())if(\"wig\"===this.config.type){const e=await Ll(this.featureCache.getAllFeatures(),this.genome,1e6);this.wgFeatures=hd(e,0,n,s)}else this.wgFeatures=await Ll(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount);else this.wgFeatures=[];return this.wgFeatures}return this.featureCache.queryFeatures(e,t,i)}async findFeatures(e){return this.featureCache?this.featureCache.findFeatures(e):[]}supportsWholeGenome(){return!this.queryable}getAllFeatures(){return this.queryable||!this.featureCache?[]:this.featureCache.getAllFeatures()}async loadFeatures(e,t,i,n){await this.getHeader();const r=this.reader;let s=t,o=i,a=e;if(!this.chrAliasManager&&this.reader&&this.reader.sequenceNames&&(this.chrAliasManager=new zh(this.reader.sequenceNames,this.genome)),this.chrAliasManager&&(a=await this.chrAliasManager.getAliasName(e)),(!n||n<=0)&&!1!==this.config.expandQuery){const e=this.genome?this.genome.getChromosome(a):void 0;s=0,o=Math.max(e?e.bpLength:Number.MAX_SAFE_INTEGER,i)}else if(n>i-t&&!1!==this.config.expandQuery){let e=Math.min(4.1*(i-t),n);this.config.minQuerySize&&e<this.config.minQuerySize&&(e=this.config.minQuerySize),s=Math.max(0,(t+i-e)/2),o=s+e}let c=await r.readFeatures(a,s,o);void 0===this.queryable&&(this.queryable=r.indexed);const l=this.queryable?new hc(e,s,o):void 0;if(c){if(\"wig\"!==this.config.format&&\"junctions\"!==this.config.type){zl(c,this.config.maxRows||Number.MAX_SAFE_INTEGER)}this.featureCache=new Zs(c,this.genome,l),this.searchable&&this.addFeaturesToDB(c,this.config)}else this.featureCache=new Zs([],l)}addFeaturesToDB(e,t){this.featureMap||(this.featureMap=new Map);const i=t.searchableFields||[\"name\",\"transcript_id\",\"gene_id\",\"gene_name\",\"id\"];for(let t of e)for(let e of i){let i;if(t.hasOwnProperty(e)?i=t[e]:\"function\"==typeof t.getAttributeValue&&(i=t.getAttributeValue(e)),i){if(i=i.replaceAll(\" \",\"+\").toUpperCase(),this.featureMap.has(i)){const e=this.featureMap.get(i);if(t.end-t.start<e.end-e.start)continue}this.featureMap.set(i,t)}}}search(e){if(this.featureMap)return this.featureMap.get(e.toUpperCase())}}class fd extends Hh{constructor(e,t){super(t),this.config=e,this.genome=t,this.queryable=!1,this.searchable=!1!==e.searchable,this.updateFeatures(e.features)}updateFeatures(e){zl(e=function(e,t){if(t)for(let i of e)i.chr=t.getChromosomeName(i.chr);return e}(e,this.genome)),this.config.mappings&&function(e,t){let i=Object.keys(t);e.forEach((function(e){i.forEach((function(i){e[i]=e[t[i]]}))}))}(e,this.config.mappings),this.featureCache=new Zs(e,this.genome),(this.searchable||this.config.searchableFields)&&this.addFeaturesToDB(e,this.config)}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome,o=s?s.getChromosomeName(e):e;return\"all\"===o.toLowerCase()?Ll(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.featureCache.queryFeatures(o,t,i)}getAllFeatures(){return this.featureCache.getAllFeatures()}supportsWholeGenome(){return!0}addFeaturesToDB(e,t){this.featureMap||(this.featureMap=new Map);const i=t.searchableFields||[\"name\"];for(let t of e)for(let e of i){let i;if(\"function\"==typeof t.getAttributeValue&&(i=t.getAttributeValue(e)),i||(i=t[e]),i){i=i.replaceAll(\" \",\"+\");const e=this.featureMap.get(i.toUpperCase());if(e&&e.end-e.start>t.end-t.start)continue;this.featureMap.set(i.toUpperCase(),t)}}}search(e){if(this.featureMap)return this.featureMap.get(e.toUpperCase())}}class pd{constructor({chr:e,locus:t,accession:i,aliases:n,features:r,sequence:s}){this.chr=e,this.locus=t,this.accession=i,this.aliases=n,this.features=r,this.sequence=s,this.bpLength=s.length}toJSON(){return{gbkURL:this.url}}getSequenceRecord(e){return{chr:this.chr,bpLength:this.bpLength}}get chromosomeNames(){return[this.chr]}getFirstChromosomeName(){return this.chr}get id(){return this.accession}get name(){return this.locus}get initialLocus(){return this.chr}get description(){return this.locus}get infoURL(){return this.url}showWholeGenomeView(){return!1}getHomeChromosomeName(){return this.chr}getChromosomeName(e){return e}getChromosomeDisplayName(e){return this.chr}getChromosome(e){if(e===this.chr)return{name:this.chr,bpLength:this.bpLength}}async loadChromosome(e){return this.getChromosome(e)}async getAliasRecord(e){}getCytobands(e){return[]}getChromosomes(){return[this.getChromosome(this.chr)]}get wgChromosomeNames(){}getGenomeCoordinate(e,t){if(e===this.chr)return t}getChromosomeCoordinate(e){return{chr:this.chr,position:e}}getCumulativeOffset(e){return 0}getGenomeLength(){return this.bpLength}async getSequence(e,t,i){return e===this.chr?this.sequence.substring(t,i):void 0}getSequenceInterval(e,t,i){return e===this.chr?new dc(this.chr,0,this.sequence.length,this.sequence):void 0}}const gd=/\\s+/,md=new Map;async function wd(e){let t=md.get(e);if(!t){t=function(e){if(!e)return null;const t=mh(e);let i=t.nextLine();const n=i.split(/\\s+/);if(\"LOCUS\"!==n[0].toUpperCase())throw Error(\"Expected `LOCUS` line.  Found: \"+i);const r=n[1].trim();let s,o;do{if(i=t.nextLine(),i.startsWith(\"ACCESSION\")){const e=i.split(gd);if(e.length<2)throw Error(\"Genbank file missing ACCESSION number.\");s=e[1].trim()}else if(i.startsWith(\"ALIASES\")){const e=i.split(gd);e.length>1&&(o=e[1].split(\",\"))}}while(i&&!i.startsWith(\"FEATURES\"));const a=s||r,c=function(e,t){const i=[];let n,r,s,o=0;for(;;)if(r=t.nextLine(),\"\"!==r){if(!r||r.startsWith(\"ORIGIN\"))break;if(r.length<6)o<10&&console(\"Unexpected line in genbank file (skipping): \"+r),o++;else if(\" \"!==r.charAt(5)){let t=r.substring(5,21).trim();s={chr:e,type:t,attributes:{},getAttributeValue:function(e){return this.attributes[e]}},n=r.substring(21),\"source\"!==t.toLowerCase()&&i.push(s)}else{let t=r.substring(21).trim();if(t.length>0)if(47===t.charCodeAt(0)){if(47===n.charCodeAt(0)){let e=n.split(\"=\",2);if(e.length>1){let t=e[0].length>1?e[0].substring(1):\"\",i=Fd(e[1]);s.attributes[t]=i}}else{const t=n.includes(\"complement\")?\"-\":\"+\";s.strand=t;let i=n.replace(\"join\",\"\").replace(\"order\",\"\").replace(\"complement\",\"\").replace(\"(\",\"\").replace(\")\",\"\");if(i.includes(\"..\")){i=i.replace(\"<\",\"\").replace(\">\",\"\");const n=bd(i,e,t),r=n[0];s.start=r.start;const o=n[n.length-1];s.end=o.end,n.length>1&&(s.exons=n)}else s.start=parseInt(i)-1,s.end=s.start+1}n=t}else n+=t}}return i}(a,t),l=function(e){let t,i=\"\";for(;(t=e.nextLine())&&!t.startsWith(\"//\");){t=t.trim();const e=t.split(/\\s+/);for(let t=1;t<e.length;t++)i+=e[t]}return i}(t);return new pd({chr:a,locus:r,accession:s,aliases:o,features:c,sequence:l})}(await Qs.loadString(e,{})),t.url=e,md.set(e,t)}return t}function bd(e,t,i){const n=e.split(\",\"),r=[];e.includes(\"complement\");for(const e of n){const n=e.split(\"..\");let s=0;try{s=parseInt(n[0])-1}catch(e){console.error(e)}let o=s+1;n.length>1&&(o=parseInt(n[1])),r.push({chr:t,start:s,end:o,strand:i})}return r.sort((function(e,t){return e.start-t.start})),r}function Fd(e){return e.startsWith('\"')&&e.endsWith('\"')&&(e=e.substring(1,e.length-2)),e}class vd extends Hh{constructor(e,t){super(t),this.config=e,this.searchable=!0}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){if(!this.featureSource){const e=await wd(this.config.url);this.featureSource=new fd({genome:this.config.genome,features:e.features,searchableFields:[\"gene\",\"db_xref\",\"locus_tag\",\"transcript_id\"]})}return this.featureSource.getFeatures({chr:e,start:t,end:i})}supportsWholeGenome(){return!1}search(e){return this.featureSource.search(e)}}const yd=new Set([\"bigwig\",\"bw\",\"bigbed\",\"bb\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\"]);function Ad(e,t){const i=e.format?e.format.toLowerCase():void 0;return e.features?new fd(e,t):yd.has(i)?new od(e,t):\"tdf\"===i?new Qh(e,t):\"gbk\"===i?new vd(e,t):new ud(e,t)}function Cd(e){return(3-e.readingFrame)%3}function _d(e){return e.cdStart||e.start}function xd(e){return e.cdEnd||e.end}const kd=.25;function Id(e,t,i){let n=(e.start-t)/i,r=(e.end-t)/i,s=r-n;return s<3&&(s=3,n-=1.5),{px:n,px1:r,pw:s}}function Sd(e,t,i,n,r,s){try{r.save(),r.fillStyle=this.color,r.strokeStyle=this.color;const n=this.getColorForFeature(e);let o,a;r.fillStyle=n,r.strokeStyle=n,\"SQUISHED\"===this.displayMode&&void 0!==e.row?(o=this.featureHeight/2,a=this.margin+this.squishedRowHeight*e.row):\"EXPANDED\"===this.displayMode&&void 0!==e.row?(o=this.featureHeight,a=this.margin+this.expandedRowHeight*e.row):(o=this.featureHeight,a=this.margin);const c=s.pixelWidth,l=a+o/2,h=o/2,d=l-h/2,u=e.exons?e.exons.length:0,f=Id(e,t,i),p=this.arrowSpacing,g=\"+\"===e.strand?1:\"-\"===e.strand?-1:0;if(0===u){const e=Math.max(0,f.px),t=Math.min(c,f.px1),i=t-e;if(r.fillRect(e,a,i,o),0!==g){r.fillStyle=\"white\",r.strokeStyle=\"white\";for(let i=e+p/2;i<t;i+=p)xo.strokeLine(r,i-2*g,l-2,i,l),xo.strokeLine(r,i-2*g,l+2,i,l);r.fillStyle=n,r.strokeStyle=n}}else{xo.strokeLine(r,f.px+1,l,f.px1-1,l);const u=Math.max(0,f.px)+p/2,m=Math.min(c,f.px1);for(let e=u;e<m;e+=p)xo.strokeLine(r,e-2*g,l-2,e,l),xo.strokeLine(r,e-2*g,l+2,e,l);for(let u=0;u<e.exons.length;u++){const f=e.exons[u];let m,w=Math.round((f.start-t)/i),b=Math.round((f.end-t)/i),F=Math.max(1,b-w);if(!(w+F<0)){if(w>c)break;if(f.utr)r.fillRect(w,d,F,h);else{if(f.cdStart&&(m=Math.round((f.cdStart-t)/i),r.fillRect(w,d,m-w,h),F-=m-w,w=m),f.cdEnd&&(m=Math.round((f.cdEnd-t)/i),r.fillRect(m,d,b-m,h),F-=b-m,b=m),F=Math.max(F,1),r.fillRect(w,a,F,o),void 0!==f.readingFrame&&s.bpPerPixel<kd&&s.sequenceInterval){const i=u>0&&void 0!==e.exons[u-1].readingFrame?e.exons[u-1]:void 0,n=u<e.exons.length-1&&void 0!==e.exons[u+1].readingFrame?e.exons[u+1]:void 0;Ed.call(this,r,e.strand,i,f,n,t,s.bpPerPixel,a,o,s.sequenceInterval)}if(F>p+5&&0!==g&&s.bpPerPixel>kd){r.fillStyle=\"white\",r.strokeStyle=\"white\";for(let e=w+p/2;e<b;e+=p)xo.strokeLine(r,e-2*g,l-2,e,l),xo.strokeLine(r,e-2*g,l+2,e,l);r.fillStyle=n,r.strokeStyle=n}}}}}s.drawLabel&&\"SQUISHED\"!==this.displayMode&&Nd.call(this,r,e,f.px,f.px1,a,s.referenceFrame,s)}finally{r.restore()}}function Ed(e,t,i,n,r,s,o,a,c,l){const h=[\"rgb(124,124,204)\",\"rgb(12, 12, 120)\"];e.save();const d=(t,i,n,r,d,u)=>{const f=Math.round((i-s)/o),p=Math.round((n-s)/o)-f;let g;if(void 0===r){if(l.hasSequence(i,n)){const e=l.getSequence(i,n);if(e&&3===e.length){const i=\"+\"===t?e:ac(e.split(\"\").reverse().join(\"\"));g=Gd[i]}}}else g=r;e.fillStyle=\"M\"===r||\"M\"===g&&0===u?\"#83f902\":\"STOP\"===g?\"#ff2101\":h[d],e.fillRect(f,a,p,c),g&&(e.save(),((t,i,n,r,s)=>{\"STOP\"===s&&(s=\"*\");const o=e.measureText(s).width;xo.fillText(e,s,n+(i-o)/2,r-4,{fillStyle:\"#ffffff\"})})(0,p,f,a+c,g),e.restore());const m=n-i;return m>0&&m<3?{start:i,end:n}:void 0},u=Cd(n);let f,p,g,m,w,b=_d(n),F=xd(n),v=1;if(\"+\"===t){for(u>0&&(b+=u),v=1,w=0,f=b;f<F;w++,f+=3)m=v%2,p=Math.min(F,f+3),g=d(t,f,p,void 0,v%2,w),++v;if(u>0||g){const e=u>0?Bd.call(this,t,u,b-u,b,g,i,n,r,l):Bd.call(this,t,void 0,void 0,void 0,g,i,n,r,l);if(e){const{left:i,rite:n}=e;i&&d(t,b-u,b,i.aminoAcidLetter,0,void 0),n&&d(t,g.start,g.end,n.aminoAcidLetter,m,void 0)}}}else{for(u>0&&(F-=u),v=1,w=0,w=0,p=F;p>b;w++,p-=3)m=v%2,f=Math.max(b,p-3),g=d(t,f,p,void 0,v%2,w),++v;if(u>0||g){const e=u>0?Bd.call(this,t,u,F,F+u,g,i,n,r,l):Bd.call(this,t,void 0,void 0,void 0,g,i,n,r,l);if(e){const{left:i,rite:n}=e;n&&d(t,F,F+u,n.aminoAcidLetter,0,void 0),i&&d(t,g.start,g.end,i.aminoAcidLetter,m,void 0)}}}e.restore()}function Nd(e,t,i,n,r,s,o){try{e.save();let s=t.name;if(void 0===s&&t.gene&&(s=t.gene.name),void 0===s&&(s=t.id||t.ID),!s||\".\"===s)return;let a=o.pixelXOffset||0;const c=Math.max(i,-a);let l,h=(c+Math.min(n,-a+o.viewportWidth))/2;\"COLLAPSED\"===this.displayMode&&\"SLANT\"===this.labelDisplayMode&&(l={rotate:{angle:45}});const d=function(e,t){return t?e+20:e+25}(r,l);let u=this.getColorForFeature(t),f=this.browser.qtlSelections.hasPhenotype(t.name);const p={textAlign:\"SLANT\"===this.labelDisplayMode?void 0:\"center\",fillStyle:u,strokeStyle:u},g=e.measureText(s),m=h-g.width/2,w=h+g.width/2,b=o.rowLastLabelX[t.row]||-Number.MAX_SAFE_INTEGER;(o.labelAllFeatures||m>b||f)&&(o.rowLastLabelX[t.row]=w,\"y\"===o.axis?(e.save(),xo.labelTransformWithContext(e,h),xo.fillText(e,s,h,d,p,l),e.restore()):(e.clearRect(h-g.width/2-1,d-g.actualBoundingBoxAscent-1,g.width+2,g.actualBoundingBoxAscent+g.actualBoundingBoxDescent+2),xo.fillText(e,s,h,d,p,l)))}finally{e.restore()}}function Bd(e,t,i,n,r,s,o,a,c){let l,h,d=\"\",u=\"\",f=\"\";const p={left:void 0,rite:void 0};if(\"+\"===e){if(t){if(u=c.getSequence(i,n),!u)return;if([l,h]=[xd(s)-(3-t),xd(s)],d=c.getSequence(l,h),!d)return;f=d+u,p.left={triplet:f,aminoAcidLetter:Gd[f]}}if(r){if(d=c.getSequence(r.start,r.end),!d)return;const e=Cd(a),t=_d(a);if(u=c.getSequence(t,t+e),!u)return;f=d+u,p.rite={triplet:f,aminoAcidLetter:Gd[f]}}}else{if(t){if(d=c.getSequence(i,n),void 0===d)return;if([l,h]=[_d(a),_d(a)+(3-t)],u=c.getSequence(l,h),void 0===u)return;f=d+u,f=ac(f.split(\"\").reverse().join(\"\")),p.rite={triplet:f,aminoAcidLetter:Gd[f]}}if(r){if(u=c.getSequence(r.start,r.end),void 0===u)return;const e=Cd(s),t=xd(s);if(d=c.getSequence(t-e,t),void 0===d)return;f=d+u,f=ac(f.split(\"\").reverse().join(\"\")),p.left={triplet:f,aminoAcidLetter:Gd[f]}}}return p}const Md=new Set([\"nonsense\",\"missense\",\"stop-loss\",\"frameshift\",\"cds-indel\"]),Rd=new Set([\"coding-synon\"]),Dd=new Set([\"splice-3\",\"splice-5\"]),Td=new Set([\"untranslated-5\",\"untranslated-3\"]);function Ld(e,t,i,n,r){var s,o,a,c,l,h,d=Id(e,t,i),u=this.margin,f=this.snpColors.length;switch(s=\"squished\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight,this.colorBy){case\"function\":c=e.func,h=c.split(\",\"),l=h.map((function(e){return Md.has(e)||Dd.has(e)?f-1:Rd.has(e)?f-2:Td.has(e)?f-3:0})),o=l.reduce((function(e,t){return Math.max(e,t)}));break;case\"class\":o=\"deletion\"===(a=e.class)?f-1:\"mnp\"===a?f-2:\"microsatellite\"===a||\"named\"===a?f-3:0}r.fillStyle=this.snpColors[o],r.fillRect(d.px,u,d.pw,s)}function zd(e,t,i,n,r){const s=\"EXPANDED\"===this.displayMode?this.expandedRowHeight:this.squishedRowHeight;let o=this.margin;\"COLLAPSED\"!==this.displayMode&&void 0!==e.row&&(o+=e.row*s);const a=o+.5*s,c=a-.5*s,l=a+.5*s,h=Math.round((e.junction_left-t)/i),d=Math.round((e.junction_right-t)/i);r.beginPath(),r.moveTo(h,a),r.bezierCurveTo(h,c,d,c,d,a),r.lineWidth=1+Math.log(e.num_junction_reads)/Math.log(2),r.strokeStyle=\"blue\",r.stroke();const u=e.spanning_frag_coords;for(let e=0;e<u.length;e++){const n=u[e],s=Math.round((n.left-t)/i),o=Math.round((n.right-t)/i);r.beginPath(),r.moveTo(s,a),r.bezierCurveTo(s,l,o,l,o,a),r.lineWidth=1,r.strokeStyle=\"purple\",r.stroke()}}class Hd extends Hl{static defaults={type:\"annotation\",maxRows:1e3,displayMode:\"EXPANDED\",margin:10,featureHeight:14,useScore:!1};constructor(e,t){super(e,t)}init(e){super.init(e),this.labelDisplayMode=e.labelDisplayMode,e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):\"blat\"!==e.type&&(this.featureSource=e.featureSource?e.featureSource:Ad(e,this.browser.genome)),\"FusionJuncSpan\"===e.type?(this.render=e.render||zd,this.squishedRowHeight=e.squishedRowHeight||50,this.expandedRowHeight=e.expandedRowHeight||50,this.height=e.height||this.margin+2*this.expandedRowHeight):\"snp\"===e.type?(this.render=e.render||Ld,this.snpColors=[\"rgb(0,0,0)\",\"rgb(0,0,255)\",\"rgb(0,255,0)\",\"rgb(255,0,0)\"],this.colorBy=\"function\",this.expandedRowHeight=e.expandedRowHeight||10,this.squishedRowHeight=e.squishedRowHeight||5,this.height=e.height||30):(this.render=e.render||Sd,this.arrowSpacing=30,function(e){e.browser.on&&(e.browser.on(\"trackdragend\",t),e.browser.on(\"trackremoved\",i));function t(){e.trackView&&\"SQUISHED\"!==e.displayMode&&e.trackView.repaintViews()}function i(n){e.browser.un&&e===n&&(e.browser.un(\"trackdragend\",t),e.browser.un(\"trackremoved\",i))}}(this),this.squishedRowHeight=e.squishedRowHeight||15,this.expandedRowHeight=e.expandedRowHeight||30,this.height=e.height||this.margin+2*this.expandedRowHeight,e.colorBy&&(e.colorBy.field&&(e.colorTable=e.colorBy.pallete||e.colorBy.palette,e.colorBy=e.colorBy.field),this.colorBy=e.colorBy,e.colorTable?this.colorTable=new ao(e.colorTable):this.colorTable=new oo(\"Set1\")))}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get searchable(){return this.featureSource.searchable}async search(e){return this.featureSource&&this.featureSource.searchable?this.featureSource.search(e):void 0}get supportsWholeGenome(){return void 0!==this.config.supportsWholeGenome?this.config.supportsWholeGenome:this.featureSource&&\"function\"==typeof this.featureSource.supportsWholeGenome?this.featureSource.supportsWholeGenome():!(void 0!==this.visibilityWindow||!1!==this.config.indexed&&this.config.indexURL)||void 0}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}computePixelHeight(e){if(\"COLLAPSED\"===this.displayMode)return this.margin+this.expandedRowHeight;{let t=0;if(e&&\"function\"==typeof e.forEach)for(let i of e)i.row&&i.row>t&&(t=i.row);return this.margin+(t+1)*(\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight)}}draw(e){const{features:t,context:i,bpPerPixel:n,bpStart:r,bpEnd:s,pixelWidth:o,pixelHeight:a,referenceFrame:c}=e;if(n<kd&&(e.sequenceInterval=this.browser.genome.getSequenceInterval(c.chr,r,s)),this.isMergedTrack||xo.fillRect(i,0,e.pixelTop,o,a,{fillStyle:\"rgb(255, 255, 255)\"}),t){const c=[];e.rowLastX=[],e.rowLastLabelX=[];for(let i of t)if(i.start>r&&i.end<s){const t=\"COLLAPSED\"===this.displayMode?0:i.row||0;c[t]?c[t]++:c[t]=1,e.rowLastX[t]=-Number.MAX_SAFE_INTEGER,e.rowLastLabelX[t]=-Number.MAX_SAFE_INTEGER}const l=o/Math.max(1,Math.max(...c.filter((e=>!isNaN(e)))));let h=[];const d=[];for(let o of t){if(o.end<r)continue;if(o.start>s)break;\"COLLAPSED\"===this.displayMode&&this.browser.qtlSelections.hasPhenotype(o.name)&&d.push(o);const t=\"COLLAPSED\"===this.displayMode?0:o.row;e.drawLabel=e.labelAllFeatures||l>10;const c=Math.ceil((o.end-r)/n),u=h[t];if(!u||c>u){this.render.call(this,o,r,n,a,i,e);const s=Math.floor((o.start-r)/n);u&&s-u<=0&&(i.globalAlpha=.5,xo.strokeLine(i,s,0,s,a,{strokeStyle:\"rgb(255, 255, 255)\"}),i.globalAlpha=1),h[t]=c}}for(let t of d)e.drawLabel=!0,this.render.call(this,t,r,n,a,i,e)}else console.log(\"No feature list\")}clickedFeatures(e){const t=e.y-this.margin,i=super.clickedFeatures(e);let n;switch(this.displayMode){case\"SQUISHED\":n=Math.floor(t/this.squishedRowHeight);break;case\"EXPANDED\":n=Math.floor(t/this.expandedRowHeight);break;default:n=void 0}return i.filter((function(e){return void 0===n||void 0===e.row||n===e.row}))}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=[];for(let e of t){const t=e._f||e,r=\"function\"==typeof t.popupData?t.popupData(i):this.extractPopupData(t);if(r){n.length>0&&n.push(\"<hr/><hr/>\");const s=this.infoURL||this.config.infoURL;for(let t of r)if(n.push(t),s&&t.name&&\"name\"===t.name.toLowerCase()&&t.value&&Mt(t.value)&&!t.value.startsWith(\"<\")){const i=s.replace(\"$$\",e.name);t.value=`<a target=_blank href=${i}>${t.value}</a>`}const o=\"gff\"===this.config.format||\"gff3\"===this.config.format||\"gtf\"===this.config.format;if(t.exons&&t.exons.length>1)for(let e=0;e<t.exons.length;e++){const r=t.exons[e];if(i>=r.start&&i<=r.end){const i=o?r.number:\"-\"===t.strand?t.exons.length-e:e+1;i&&(n.push(\"<hr/>\"),n.push({name:\"Exon Number\",value:i}));break}}}}return n}menuItemList(){const e=[];if(this.render===Ld){e.push(\"<hr/>\");for(const i of[\"function\",\"class\"]){const n=Bt(Dl(`Color by ${i}`,i===this.colorBy));function r(){this.colorBy=i,this.trackView.repaintViews()}e.push({object:n,click:r})}}e.push(\"<hr/>\");const t={COLLAPSED:\"Collapse\",SQUISHED:\"Squish\",EXPANDED:\"Expand\"};for(const s of[\"COLLAPSED\",\"SQUISHED\",\"EXPANDED\"]){const o=Bt(Dl(t[s],s===this.displayMode));function a(){this.displayMode=s,this.config.displayMode=s,this.trackView.checkContentHeight(),this.trackView.repaintViews()}e.push({object:o,click:a})}return e}contextMenuItemList(e){const t=this.clickedFeatures(e);if(void 0===t||0===t.length)return;t.length>1&&t.sort(((e,t)=>t.end-t.start-(e.end-e.start)));const i=t[0];if(i.end-i.start<=1e6){const e=[{label:\"View feature sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i.chr,i.start,i.end);e?\"-\"===i.strand&&(e=cc(e)):e=\"Unknown sequence\",this.browser.alert.present(e)}}];return Xa()&&void 0!==navigator.clipboard&&e.push({label:\"Copy feature sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i.chr,i.start,i.end);e?\"-\"===i.strand&&(e=cc(e)):e=\"Unknown sequence\";try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),e.push(\"<hr/>\"),e}}description(){if(Ld===this.render){let e=\"<html>\"+this.name+\"<hr/>\";return e+=\"<em>Color By Function:</em><br>\",e+='<span style=\"color:red\">Red</span>: Coding-Non-Synonymous, Splice Site<br>',e+='<span style=\"color:green\">Green</span>: Coding-Synonymous<br>',e+='<span style=\"color:blue\">Blue</span>: Untranslated<br>',e+='<span style=\"color:black\">Black</span>: Intron, Locus, Unknown<br><br>',e+=\"<em>Color By Class:</em><br>\",e+='<span style=\"color:red\">Red</span>: Deletion<br>',e+='<span style=\"color:green\">Green</span>: MNP<br>',e+='<span style=\"color:blue\">Blue</span>: Microsatellite, Named<br>',e+='<span style=\"color:black\">Black</span>: Indel, Insertion, SNP',e+=\"</html>\",e}return super.description()}getColorForFeature(e){const t=e._f||e;let i;if(e.name&&this.browser.qtlSelections.hasPhenotype(e.name))i=this.browser.qtlSelections.colorForGene(e.name);else if(this.altColor&&\"-\"===t.strand)i=\"function\"==typeof this.altColor?this.altColor(t):this.altColor;else if(this.color)i=\"function\"==typeof this.color?this.color(t):this.color;else if(this.colorBy){const e=t.getAttributeValue?t.getAttributeValue(this.colorBy):t[this.colorBy];i=this.colorTable.getColor(e)}else t.color&&(i=t.color);if(i||(i=\"rgb(0, 0, 150)\"),t.alpha&&1!==t.alpha)i=_s.addAlpha(i,t.alpha);else if(this.useScore&&t.score&&!Number.isNaN(t.score)){const e=function(e,t,i){const n=(t-e)/9,r=Math.floor((i-e)/n);return Math.min(1,.2+.8*r/9)}(this.config.min?this.config.min:this.viewLimitMin?this.viewLimitMin:0,this.config.max?this.config.max:this.viewLimitMax?this.viewLimitMax:1e3,t.score);t.alpha=e,i=_s.addAlpha(i,e)}return i}dispose(){this.trackView=void 0}}class Pd{constructor(t){if(this.config=t,this.browser=t.browser,this.columnFormat=t.columnFormat,this.tableRowSelectionList=[],this.tableDOM=e({class:\"igv-roi-table\"}),t.width){let[e]=t.width.split(\"px\");e=parseInt(e,10),this.tableDOM.style.width=`${Math.min(e,1600)}px`}t.parent.appendChild(this.tableDOM),this.headerDOM=t,this.tableColumnTitles=this.tableDOM,this.tableRowContainer=this.tableDOM,this.footerDOM=t.gotoButtonHandler}set headerDOM({browser:t,parent:i,headerTitle:n,dismissHandler:r}){const s=e();this.tableDOM.appendChild(s);const o=e();s.appendChild(o),o.innerHTML=n;const a=e();s.appendChild(a),a.appendChild(l(\"times\")),this.boundDismissHandler=function(e){e.stopPropagation(),r()}.bind(this),a.addEventListener(\"click\",this.boundDismissHandler);const{y:c}=t.root.getBoundingClientRect(),{y:h}=i.getBoundingClientRect(),d=-(h-c);p(this.tableDOM,s,{minX:0,minY:d}),this.tableDOM.style.display=\"none\",this._headerDOM=s}set tableColumnTitles(t){const i=e({class:\"igv-roi-table-column-titles\"});t.appendChild(i);for(const{label:t,width:n}of this.columnFormat){const r=e();i.appendChild(r),r.style.width=n,r.innerText=t}this._tableColumnTitlesDOM=i}get tableColumnTitles(){return this._tableColumnTitlesDOM}set tableRowContainer(t){const i=e({class:\"igv-roi-table-row-container\"});t.appendChild(i),this._tableRowContainerDOM=i}get tableRowContainer(){return this._tableRowContainerDOM}set footerDOM(t){const i=e();this.tableDOM.appendChild(i);const n=e({class:\"igv-roi-table-button\"});i.appendChild(n),n.id=\"igv-roi-table-view-button\",n.textContent=\"Go To\",n.style.pointerEvents=\"none\",this._footerDOM=i,this.gotoButton=n,this.boundGotoButtonHandler=t.bind(this),this.gotoButton.addEventListener(\"click\",this.boundGotoButtonHandler)}tableRowDOMHelper(e){e.addEventListener(\"mousedown\",(t=>{t.stopPropagation(),e.classList.toggle(\"igv-roi-table-row-selected\"),e.classList.contains(\"igv-roi-table-row-selected\")?e.classList.remove(\"igv-roi-table-row-hover\"):e.classList.add(\"igv-roi-table-row-hover\"),this.setTableRowSelectionState(e.classList.contains(\"igv-roi-table-row-selected\"))})),e.addEventListener(\"mouseover\",(t=>{e.classList.contains(\"igv-roi-table-row-selected\")?e.classList.remove(\"igv-roi-table-row-hover\"):e.classList.add(\"igv-roi-table-row-hover\")})),e.addEventListener(\"mouseout\",(t=>{e.classList.remove(\"igv-roi-table-row-hover\")}))}clearTable(){const e=this.tableRowContainer.querySelectorAll(\".igv-roi-table-row\");for(let t of e)t.remove()}setTableRowSelectionState(e){e?this.tableRowSelectionList.push(1):this.tableRowSelectionList.pop(),this.gotoButton.style.pointerEvents=this.tableRowSelectionList.length>0?\"auto\":\"none\"}present(){this.tableDOM.style.left=\"0px\";const{y:e}=this.browser.root.getBoundingClientRect(),{y:t}=this.config.parent.getBoundingClientRect();this.tableDOM.style.top=e-t+\"px\",this.tableDOM.style.display=\"flex\"}dismiss(){this.tableDOM.style.display=\"none\"}isVisible(){return\"none\"!==this.tableDOM.style.display}dispose(){this.tableDOM.innerHTML=\"\",this.tableDOM.remove();for(const e of Object.keys(this))this[e]=void 0;document.removeEventListener(\"click\",this.boundDismissHandler)}}class Od extends Pd{constructor(e){super(Object.assign({width:\"1024px\"},e)),this.descriptionDOM=e}set descriptionDOM(t){if(t.description){let i;i=e({class:\"igv-roi-table-description\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.style.height=\"auto\",i.innerHTML=\"BLAT result for query sequence:\",i=e({class:\"igv-roi-table-description\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.style.height=\"auto\",i.style.maxHeight=\"128px\",i.innerHTML=t.description,i=e({class:\"igv-roi-table-goto-explainer\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.innerHTML=\"Select one or more rows and click Go To to view the regions\"}}tableRowDOM(t){const i=e({class:\"igv-roi-table-row\"}),n=t.map((e=>isFinite(e)?Rt(e):e));for(let t=0;t<n.length;t++){const r=e();i.appendChild(r);const s=this.columnFormat[t];r.style.width=s.width||\"fit-content\",r.innerText=n[t]}return this.tableRowDOMHelper(i),i}renderTable(e){if(Array.from(this.tableRowContainer.querySelectorAll(\".igv-roi-table-row\")).forEach((e=>e.remove())),e.length>0)for(let t of e){const e=this.tableRowDOM(t);this.tableRowContainer.appendChild(e)}}static getColumnFormatConfiguration(){return[{label:\"chr\",width:\"7%\"},{label:\"start\",width:\"12%\"},{label:\"end\",width:\"12%\"},{label:\"strand\",width:\"5%\"},{label:\"score\",width:\"5%\"},{label:\"match\",width:\"5%\"},{label:\"mis-match\",width:\"7%\"},{label:\"rep. match\",width:\"7%\"},{label:\"N's\",width:\"3%\"},{label:\"Q gap count\",width:\"9%\"},{label:\"Q gap bases\",width:\"9%\"},{label:\"T gap count\",width:\"9%\"},{label:\"T gap bases\",width:\"9%\"}]}static gotoButtonHandler(e){e.stopPropagation();const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\"),i=[];for(const e of t){const t=[];e.querySelectorAll(\"div\").forEach((e=>t.push(e.innerText)));const[n,r,s]=t;i.push(`${n}:${r}-${s}`)}for(const e of this.tableDOM.querySelectorAll(\".igv-roi-table-row\"))e.classList.remove(\"igv-roi-table-row-selected\");this.setTableRowSelectionState(!1),this.browser.search(i.join(\" \"))}}const Ud=\"https://igv.org/services/blatUCSC.php\";async function qd({url:e,userSeq:t,db:i}){if(e=e||Ud,!i)throw Error(\"Blat database is not defined\");const n=await async function(e=\"\",t,i){const n=new URLSearchParams;n.append(\"userSeq\",t),n.append(\"db\",i);const r=await fetch(e,{method:\"post\",body:n});return r.json()}(e,t,i);n.fields;return n.blat.map($c)}const Qd=25e3;class Vd extends Hd{constructor(e,t){super(e,t),this.name||(this.name=\"Blat Results\"),this.sequence=e.sequence,this.table=void 0,e.features&&(this._features=e.features,this.featureSource=new fd({features:e.features},this.browser.genome),delete e.features)}async postInit(){if(!this.featureSource){const e=this.browser.genome.id,t=this.browser.config.blatServerURL,i=await qd({url:t,userSeq:this.sequence,db:e});this._features=i,this.featureSource=new fd({features:i},this.browser.genome)}}openTableView(){if(void 0===this.table){const e=this._features.map((e=>[e.chr,e.start+1,e.end,e.strand,e.score,e.matches,e.misMatches,e.repMatches,e.nCount,e.qNumInsert,e.qBaseInsert,e.tNumInsert,e.tBaseInsert])),t={browser:this.browser,parent:this.browser.columnContainer,headerTitle:this.config.title,description:this.sequence,dismissHandler:()=>{this.table.dismiss(),this.table.dispose(),this.table=void 0},columnFormat:Od.getColumnFormatConfiguration(),gotoButtonHandler:Od.gotoButtonHandler};this.table=new Od(t),this.table.renderTable(e)}this.table.present()}menuItemList(){const e=super.menuItemList();return e.push(\"<hr/>\"),e.push({label:\"Open table view\",click:function(){this.openTableView()}}),e}dispose(){super.dispose(),this.table&&this.table.popover.parentElement.removeChild(this.table.popover)}}async function jd({sequence:e,browser:t,name:i,title:n}){if(e.length>Qd)t.alert.present(`Sequence size exceeds maximum allowed length (${e.length} > 25000)`);else try{const r=t.genome.id,s=t.config.blatServerURL||\"https://igv.org/services/blatUCSC.php\",o={type:\"blat\",name:i||\"blat results\",title:n||\"blat results\",sequence:e,altColor:\"rgb(176, 176, 236)\",color:\"rgb(236, 176, 176)\",searchable:!1,features:await qd({url:s,userSeq:e,db:r})};(await t.loadTrack(o)).openTableView()}catch(e){t.alert.present(`Error performing blat search:  ${e}`)}}const Wd=Number.MIN_SAFE_INTEGER,Gd={TTT:\"F\",TTC:\"F\",TTA:\"L\",TTG:\"L\",CTT:\"L\",CTC:\"L\",CTA:\"L\",CTG:\"L\",ATT:\"I\",ATC:\"I\",ATA:\"I\",ATG:\"M\",GTT:\"V\",GTC:\"V\",GTA:\"V\",GTG:\"V\",TCT:\"S\",TCC:\"S\",TCA:\"S\",TCG:\"S\",CCT:\"P\",CCC:\"P\",CCA:\"P\",CCG:\"P\",ACT:\"T\",ACC:\"T\",ACA:\"T\",ACG:\"T\",GCT:\"A\",GCC:\"A\",GCA:\"A\",GCG:\"A\",TAT:\"Y\",TAC:\"Y\",TAA:\"STOP\",TAG:\"STOP\",CAT:\"H\",CAC:\"H\",CAA:\"Q\",CAG:\"Q\",AAT:\"N\",AAC:\"N\",AAA:\"K\",AAG:\"K\",GAT:\"D\",GAC:\"D\",GAA:\"E\",GAG:\"E\",TGT:\"C\",TGC:\"C\",TGA:\"STOP\",TGG:\"W\",CGT:\"R\",CGC:\"R\",CGA:\"R\",CGG:\"R\",AGT:\"S\",AGC:\"S\",AGA:\"R\",AGG:\"R\",GGT:\"G\",GGC:\"G\",GGA:\"G\",GGG:\"G\"},$d={},Kd=[\"A\",\"G\",\"C\",\"T\",\"Y\",\"R\",\"W\",\"S\",\"K\",\"M\",\"D\",\"V\",\"H\",\"B\",\"N\",\"X\"],Yd=[\"T\",\"C\",\"G\",\"A\",\"R\",\"Y\",\"W\",\"S\",\"M\",\"K\",\"H\",\"B\",\"D\",\"V\",\"N\",\"X\"];for(let NA=0;NA<Kd.length;NA++)$d[Kd[NA]]=Yd[NA],$d[Kd[NA].toLowerCase()]=Yd[NA].toLowerCase();const Xd=115;class Zd{constructor(e,t){this.config=e,this.browser=t,this.type=\"sequence\",this.removable=!0===e.removable,this.name=e.name,this.id=e.id,this.sequenceType=e.sequenceType||\"dna\",this.disableButtons=!1,this.order=e.order||Wd,this.ignoreTrackMenu=!1,this.reversed=!0===e.reversed,this.frameTranslate=!0===e.frameTranslate,this.height=this.frameTranslate?Xd:25,e.url&&(e.fastaURL=e.url),e.fastaURL||(this.id=e.id||\"sequence\")}menuItemList(){return[{name:this.reversed?\"Forward\":\"Reverse\",click:()=>{this.reversed=!this.reversed,this.trackView.repaintViews()}},{name:this.frameTranslate?\"Close Translation\":\"Three-frame Translate\",click:()=>{if(this.frameTranslate=!this.frameTranslate,this.frameTranslate){for(let e of this.trackView.viewports)e.setContentHeight(Xd);this.trackView.setTrackHeight(Xd)}else{for(let e of this.trackView.viewports)e.setContentHeight(25);this.trackView.setTrackHeight(25)}this.trackView.repaintViews()}}]}contextMenuItemList(e){const t=e.viewport;if(t.referenceFrame.bpPerPixel<=1){const e=t.getWidth()*t.referenceFrame.bpPerPixel,i=t.referenceFrame.chr,n=Math.floor(t.referenceFrame.start),r=Math.ceil(n+e),s=[{label:this.reversed?\"View visible sequence (reversed)...\":\"View visible sequence...\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);e?this.reversed&&(e=cc(e)):e=\"Unknown sequence\",this.browser.alert.present(e)}}];return Xa()&&s.push({label:\"Copy visible sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);e?this.reversed&&(e=cc(e)):e=\"Unknown sequence\";try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),s.push({label:\"BLAT read sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);if(e){this.reversed&&(e=cc(e));const t=`blat: ${i}:${n+1}-${r}`,s=`blat: ${i}:${n+1}-${r}`;jd({sequence:e,browser:this.browser,name:t,title:s})}}}),s.push(\"<hr/>\"),s}}translateSequence(e){const t=[[],[],[]];for(let i of[0,1,2]){let n=i;for(;e.length-n>=3;){let r=e.slice(n,n+3);this.reversed&&(r=r.split(\"\").reverse().join(\"\"));const s=Gd[r.toUpperCase()]||\"\";t[i].push({codons:r,aminoA:s}),n+=3}}return t}async getSequenceSource(){return this.config.fastaURL?(this.fasta||(this.fasta=new Jd(this.config,this.browser.genome),await this.fasta.init()),this.fasta):this.browser.genome}async getFeatures(e,t,i,n){if(t=Math.floor(t),i=Math.floor(i),n&&n>10)return null;{const n=await this.getSequenceSource();return{bpStart:t,sequence:await n.getSequence(e,t,i)}}}draw(e){const t=e.context;if(e.features){let i=e.features.sequence;if(!i)return;this.reversed&&(i=i.split(\"\").map((function(e){return $d[e]})).join(\"\"));const n=e.features.bpStart,r=1+e.bpStart+e.pixelWidth*e.bpPerPixel;for(let s=Math.floor(e.bpStart);s<=r;s++){const r=Math.floor(s-n);if(r>=0&&r<i.length){const n=(s-e.bpStart)/e.bpPerPixel,o=1/e.bpPerPixel,a=i[r],c=this.fillColor(a.toUpperCase());if(e.bpPerPixel>.1)xo.fillRect(t,n,5,o,10,{fillStyle:c});else{const i=n+.5*(o-t.measureText(a).width);\"y\"===e.axis?(t.save(),xo.labelTransformWithContext(t,i),xo.strokeText(t,a,i,15,{strokeStyle:c}),t.restore()):xo.strokeText(t,a,i,15,{strokeStyle:c})}}}if(this.frameTranslate){let r=25;const s=this.translateSequence(i);for(let i=0;i<s.length;i++){const o=s[i];for(let s=0;s<o.length;s++){let a=0==s%2?\"rgb(160,160,160)\":\"rgb(224,224,224)\";const c=o[s],l=n+i+3*s-e.bpStart,h=Math.floor(l/e.bpPerPixel),d=Math.floor((l+3)/e.bpPerPixel),u=Math.round((h+d)/2);if(d<0)continue;if(h>e.pixelWidth)break;let f=c.aminoA;c.aminoA.indexOf(\"STOP\")>-1?(a=\"rgb(255, 0, 0)\",f=\"STOP\"):\"M\"===c.aminoA&&(a=\"rgb(0, 153, 0)\",f=\"START\"),xo.fillRect(t,h,r,d-h,25,{fillStyle:a}),e.bpPerPixel<=.1&&xo.strokeText(t,f,u-t.measureText(f).width/2,r+15)}r+=30}}}}get supportsWholeGenome(){return!1}computePixelHeight(e){return this.height=this.frameTranslate?Xd:25,this.height}fillColor(e){return this.color?this.color:\"dna\"===this.sequenceType?this.browser.nucleotideColors[e]||\"gray\":\"rgb(0, 0, 150)\"}getState(){const e={type:\"sequence\"};return this.order!==Wd&&(e.order=this.order),this.reversed&&(e.revealed=!0),e}}class Jd{constructor(e,t){this.config=e,this.genome=t}async init(){this.fasta=await Nc(this.config),this.chrNameMap=new Map;for(let e of this.fasta.chromosomeNames)this.chrNameMap.set(this.genome.getChromosomeName(e),e)}async getSequence(e,t,i){const n=this.chrNameMap.has(e)?this.chrNameMap.get(e):e;return this.fasta.getSequence(n,t,i)}}class eu{constructor(e,t,i,n){this.guid=s(),this.trackView=e,this.referenceFrame=i,this.browser=e.browser,this.$viewport=Bt('<div class=\"igv-viewport\">'),t.appendChild(this.$viewport.get(0)),e.track.height&&(this.$viewport.get(0).style.height=`${e.track.height}px`),e.track instanceof Zd&&(this.alert=new Ta(this.$viewport.get(0))),this.contentTop=0,this.contentHeight=this.$viewport.height(),this.$viewport.width(n),this.initializationHelper()}initializationHelper(){}showMessage(e){this.messageDiv||(this.messageDiv=document.createElement(\"div\"),this.messageDiv.className=\"igv-viewport-message\",this.$viewport.append(Bt(this.messageDiv))),this.messageDiv.textContent=e,this.messageDiv.style.display=\"inline-block\"}hideMessage(e){this.messageDiv&&(this.messageDiv.style.display=\"none\")}setTrackLabel(e){}startSpinner(){}stopSpinner(){}checkZoomIn(){return!0}shift(){}setTop(e){this.contentTop=e,this.$viewport.height()}async loadFeatures(){}clearCache(){}repaint(){}draw(e,t,i){console.log(\"Viewport - draw(drawConfiguration, features, roiFeatures)\")}checkContentHeight(e){let t=this.trackView.track;if(e=e||this.cachedFeatures,\"FILL\"===t.displayMode)this.setContentHeight(this.$viewport.height());else if(\"function\"==typeof t.computePixelHeight&&e&&e.length>0){let i=t.computePixelHeight(e);i!==this.contentHeight&&this.setContentHeight(i)}}getContentHeight(){return this.contentHeight}setContentHeight(e){this.contentHeight=e}isLoading(){return!1}saveSVG(){}isVisible(){return this.$viewport.width()}setWidth(e){this.$viewport.width(e)}getWidth(){return this.$viewport.width()}getContentTop(){return this.contentTop}containsPosition(e,t){console.log(\"Viewport - containsPosition(chr, position)\")}addMouseHandlers(){}removeMouseHandlers(){}dispose(){this.$viewport.get(0).remove();for(let e of Object.keys(this))this[e]=void 0}}\n",
-       "/*!!\n",
-       "     *  Canvas 2 Svg v1.0.19\n",
-       "     *  A low level canvas to SVG converter. Uses a mock canvas context to build an SVG document.\n",
-       "     *\n",
-       "     *  Licensed under the MIT license:\n",
-       "     *  http://www.opensource.org/licenses/mit-license.php\n",
-       "     *\n",
-       "     *  Author:\n",
-       "     *  Kerry Liu\n",
-       "     *\n",
-       "     *  Copyright (c) 2014 Gliffy Inc.\n",
-       "     */function tu(e,t){var i,n=Object.keys(t);for(i=0;i<n.length;i++)e=e.replace(new RegExp(\"\\\\{\"+n[i]+\"\\\\}\",\"gi\"),t[n[i]]);return e}function iu(e){var t,i,n;if(!e)throw new Error(\"cannot create a random attribute name for an undefined object\");t=\"ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz\",i=\"\";do{for(i=\"\",n=0;n<12;n++)i+=t[Math.floor(51*Math.random())]}while(e[i]);return i}function nu(e){var t={alphabetic:\"alphabetic\",hanging:\"hanging\",top:\"text-before-edge\",bottom:\"text-after-edge\",middle:\"central\"};return t[e]||t.alphabetic}function ru(e){var t=Math.sqrt(e[0]*e[0]+e[1]*e[1]);return[e[0]/t,e[1]/t]}const su=function(e,t){var i,n,r,s={};for(e=e.split(\",\"),t=t||10,i=0;i<e.length;i+=2)n=\"&\"+e[i+1]+\";\",r=parseInt(e[i],t),s[n]=\"&#\"+r+\";\";return 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stroke\"},font:{canvas:\"10px sans-serif\"},shadowColor:{canvas:\"#000000\"},shadowOffsetX:{canvas:0},shadowOffsetY:{canvas:0},shadowBlur:{canvas:0},textAlign:{canvas:\"start\"},textBaseline:{canvas:\"alphabetic\"},lineDash:{svgAttr:\"stroke-dasharray\",canvas:[],svg:null,apply:\"stroke\"}};class au{constructor(e,t){this.__root=e,this.__ctx=t}addColorStop(e,t){var i,n=this.__ctx.__createElement(\"stop\");n.setAttribute(\"offset\",e),t&&-1!==t.indexOf(\"rgba\")?(i=/rgba\\(\\s*(\\d+)\\s*,\\s*(\\d+)\\s*,\\s*(\\d+)\\s*,\\s*(\\d?\\.?\\d*)\\s*\\)/gi.exec(t),n.setAttribute(\"stop-color\",tu(\"rgb({r},{g},{b})\",{r:i[1],g:i[2],b:i[3]})),n.setAttribute(\"stop-opacity\",i[4])):n.setAttribute(\"stop-color\",t),this.__root.appendChild(n)}}class cu{constructor(e,t){this.__root=e,this.__ctx=t}}class lu{constructor(e){if(!(this instanceof lu))return new 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e,t,i=Object.keys(ou);for(e=0;e<i.length;e++)this[t=i[e]]=ou[t].canvas}__applyStyleState(e){var t,i,n=Object.keys(e);for(t=0;t<n.length;t++)this[i=n[t]]=e[i]}__getStyleState(){var e,t,i={},n=Object.keys(ou);for(e=0;e<n.length;e++)i[t=n[e]]=this[t];return i}__applyStyleToCurrentElement(e){var t=this.__currentElement,i=this.__currentElementsToStyle;i&&(t.setAttribute(e,\"\"),t=i.element,i.children.forEach((function(t){t.setAttribute(e,\"\")})));var n,r,s,o,a,c=Object.keys(ou);for(n=0;n<c.length;n++)if(r=ou[c[n]],s=this[c[n]],r.apply)if(s instanceof cu){if(s.__ctx)for(;s.__ctx.__defs.childNodes.length;)o=s.__ctx.__defs.childNodes[0].getAttribute(\"id\"),this.__ids[o]=o,this.__defs.appendChild(s.__ctx.__defs.childNodes[0]);t.setAttribute(r.apply,tu(\"url(#{id})\",{id:s.__root.getAttribute(\"id\")}))}else if(s instanceof au)t.setAttribute(r.apply,tu(\"url(#{id})\",{id:s.__root.getAttribute(\"id\")}));else 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\"+w:w,l.setAttribute(\"transform\",b),o.appendChild(l)}}}else\"CANVAS\"!==p.nodeName&&\"IMG\"!==p.nodeName||((h=this.__createElement(\"image\")).setAttribute(\"width\",i),h.setAttribute(\"height\",n),h.setAttribute(\"preserveAspectRatio\",\"none\"),(g||m||r!==p.width||s!==p.height)&&((d=this.__document.createElement(\"canvas\")).width=i,d.height=n,d.getContext(\"2d\").drawImage(p,g,m,r,s,0,0,i,n),p=d),h.setAttribute(\"transform\",w),h.setAttributeNS(\"http://www.w3.org/1999/xlink\",\"xlink:href\",\"CANVAS\"===p.nodeName?p.toDataURL():p.getAttribute(\"src\")),o.appendChild(h))}createPattern(e,t){let i,n=this.__document.__createElement(\"pattern\"),r=iu(this.__ids);return n.setAttribute(\"id\",r),n.setAttribute(\"width\",e.width),n.setAttribute(\"height\",e.height),\"CANVAS\"===e.nodeName||\"IMG\"===e.nodeName?(i=this.__createElement(\"image\"),i.setAttribute(\"width\",e.width),i.setAttribute(\"height\",e.height),i.setAttributeNS(\"http://www.w3.org/1999/xlink\",\"xlink:href\",\"CANVAS\"===e.nodeName?e.toDataURL():e.getAttribute(\"src\")),n.appendChild(i),this.__defs.appendChild(n)):e instanceof lu&&(n.appendChild(e.__root.childNodes[1]),this.__defs.appendChild(n)),new cu(n,this)}setLineDash(e){e&&e.length>0?this.lineDash=e.join(\",\"):this.lineDash=null}drawFocusRing(){}createImageData(){}getImageData(){}putImageData(){}globalCompositeOperation(){}setTransform(){}}function hu(e){if(e.startsWith(\"GCF\")||e.startsWith(\"GCA\")&&e.length>=13){return\"https://hgdownload.soe.ucsc.edu/hubs/\"+e.substring(0,3)+\"/\"+e.substring(4,7)+\"/\"+e.substring(7,10)+\"/\"+e.substring(10,13)+\"/\"+e+\"/hub.txt\"}}class du{static supportedTypes=new Set([\"bigBed\",\"bigWig\",\"bigGenePred\",\"vcfTabix\"]);static filterTracks=new Set([\"cytoBandIdeo\",\"assembly\",\"gap\",\"gapOverlap\",\"allGaps\",\"cpgIslandExtUnmasked\",\"windowMasker\"]);static async loadHub(e){const t=e.lastIndexOf(\"/\"),i=e.substring(0,t+1),n=await pu(e);let r;if(\"genome\"===n[1].type){const e=n[1];if(e.hasProperty(\"groups\")){const t=i+e.getProperty(\"groups\");r=await pu(t)}if(e.hasProperty(\"chromSizes\")){const t=i+e.getProperty(\"chromSizes\"),n=await async function(e){try{const t=(await fetch(e,{method:\"HEAD\"})).headers;return t.has(\"content-length\")?t.get(\"content-length\"):null}catch(e){return null}}(t);null!==n&&Number.parseInt(n)<1e6&&e.setProperty(\"chromSizesURL\",t)}}return new du(e,n,r)}constructor(e,t,i){this.url=e;const n=e.lastIndexOf(\"/\");if(this.baseURL=e.substring(0,n+1),\"hub\"!==t[0].type)throw Error(\"Unexpected hub.txt file -- does the first line start with 'hub'?\");if(this.hubStanza=t[0],\"on\"!==this.hubStanza.getProperty(\"useOneFile\"))throw Error(\"Only 'useOneFile' hubs are currently supported\");if(t.length<2)throw Error(\"Expected at least 2 stanzas, hub and genome\");if(\"genome\"!==t[1].type)throw Error(`Unexpected hub file -- expected \"genome\" stanza but found \"${t[1].type}\"`);this.genomeStanza=t[1],this.trackStanzas=[];for(let e=2;e<t.length;e++)\"track\"===t[e].type&&this.trackStanzas.push(t[e]);if(i){this.groupStanzas=i,this.groupPriorityMap=new Map;for(let e of i)e.hasProperty(\"priority\")&&this.groupPriorityMap.set(e.getProperty(\"name\"),10*Number.parseInt(e.getProperty(\"priority\")))}}getDefaultPosition(){return this.genomeStanza.getProperty(\"defaultPos\")}getGenomeConfig(e={}){const t=this.genomeStanza.getProperty(\"genome\"),i=this.hubStanza.getProperty(\"shortLabel\")||this.genomeStanza.getProperty(\"scientificName\")||this.genomeStanza.getProperty(\"organism\")||this.genomeStanza.getProperty(\"description\"),n=i+(i?` (${t})`:` ${t}`),r={hubURL:this.url,id:t,name:n,twoBitURL:this.baseURL+this.genomeStanza.getProperty(\"twoBitPath\"),nameSet:\"ucsc\"};if(this.genomeStanza.hasProperty(\"chromSizesURL\")?r.chromSizesURL=this.genomeStanza.getProperty(\"chromSizesURL\"):(r.wholeGenomeView=!1,r.showChromosomeWidget=!1),this.genomeStanza.hasProperty(\"defaultPos\")){const e=this.genomeStanza.getProperty(\"defaultPos\");if(e){const t=e.lastIndexOf(\":\");r.locus=t>0?e.substring(0,t):e}}this.genomeStanza.hasProperty(\"blat\")&&(r.blat=this.baseURL+this.genomeStanza.getProperty(\"blat\")),this.genomeStanza.hasProperty(\"chromAliasBb\")&&(r.chromAliasBbURL=this.baseURL+this.genomeStanza.getProperty(\"chromAliasBb\")),this.genomeStanza.hasProperty(\"chromAlias\")&&(r.aliasURL=this.baseURL+this.genomeStanza.getProperty(\"chromAlias\")),this.genomeStanza.hasProperty(\"twoBitBptURL\")&&(r.twoBitBptURL=this.baseURL+this.genomeStanza.getProperty(\"twoBitBptURL\")),this.genomeStanza.hasProperty(\"twoBitBptUrl\")&&(r.twoBitBptURL=this.baseURL+this.genomeStanza.getProperty(\"twoBitBptUrl\")),e.includeChromSizes&&this.genomeStanza.hasProperty(\"chromSizes\")&&(r.chromSizesURL=this.baseURL+this.genomeStanza.getProperty(\"chromSizes\")),this.hubStanza.hasProperty(\"longLabel\")?r.description=this.hubStanza.getProperty(\"longLabel\").replace(\"/\",\"\\n\"):(r.description=r.id,this.genomeStanza.hasProperty(\"description\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"description\")}`),this.genomeStanza.hasProperty(\"organism\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"organism\")}`),this.genomeStanza.hasProperty(\"scientificName\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"scientificName\")}`),this.genomeStanza.hasProperty(\"htmlPath\")&&(r.infoURL=this.baseURL+this.genomeStanza.getProperty(\"htmlPath\")));const s=this.trackStanzas.filter((e=>\"cytoBandIdeo\"===e.name&&e.hasProperty(\"bigDataUrl\")));s.length>0&&(r.cytobandBbURL=this.baseURL+s[0].getProperty(\"bigDataUrl\"));return r.tracks=this.#g((e=>!du.filterTracks.has(e.name)&&\"hide\"!==e.getProperty(\"visibility\"))),r}getGroupedTrackConfigurations(){const e=new Map;for(let t of this.#g()){if(\"cytoBandIdeo\"===t.name)continue;const i=t.group||\"other\";e.has(i)?e.get(i).push(t):e.set(i,[t])}const t=this.groupStanzas?new Map(this.groupStanzas.map((e=>[e.getProperty(\"name\"),e]))):new Map;return Array.from(e.keys()).map((i=>({label:t.has(i)?t.get(i).getProperty(\"label\"):i,tracks:e.get(i)})))}#g(e){return this.trackStanzas.filter((t=>du.supportedTypes.has(t.format)&&t.hasProperty(\"bigDataUrl\")&&(!e||e(t)))).map((e=>this.#m(e)))}#m(e){const t=e.format,i={id:e.getProperty(\"track\"),name:e.getProperty(\"shortLabel\"),format:t,url:this.baseURL+e.getProperty(\"bigDataUrl\"),displayMode:e.displayMode};if(\"vcfTabix\"===t&&(i.indexURL=i.url+\".tbi\"),e.hasProperty(\"longLabel\")&&e.hasProperty(\"html\")?(i.description&&(i.description+=\"<br/>\"),i.description=`<a target=\"_blank\" href=\"${this.baseURL+e.getProperty(\"html\")}\">${e.getProperty(\"longLabel\")}</a>`):e.hasProperty(\"longLabel\")&&(i.description=e.getProperty(\"longLabel\")),e.hasProperty(\"autoScale\")&&(i.autoscale=\"on\"===e.getProperty(\"autoScale\").toLowerCase()),e.hasProperty(\"maxHeightPixels\")){const t=e.getProperty(\"maxHeightPixels\").split(\":\");i.maxHeight=Number.parseInt(t[0]),i.height=Number.parseInt(t[1]),i.minHeight=Number.parseInt(t[2])}if(e.hasProperty(\"color\")){const t=e.getProperty(\"color\");i.color=t.indexOf(\",\")>0?`rgb(${t})`:t}if(e.hasProperty(\"altColor\")){const t=e.getProperty(\"altColor\");i.altColor=t.indexOf(\",\")>0?`rgb(${t})`:t}if(e.hasProperty(\"viewLimits\")){const t=e.getProperty(\"viewLimits\").split(\":\");let n,r;t.length>1&&(n=Number.parseInt(t[0]),r=Number.parseInt(t[1])),Number.isNaN(r)||Number.isNaN(n)?console.warn(`Unexpected viewLimits value in track line: ${properties.viewLimits}`):(i.min=n,i.max=r)}if(e.hasProperty(\"itemRgb\"),\"hide\"===e.getProperty(\"visibility\")&&(i.visible=!1),e.hasProperty(\"url\")&&(i.infoURL=e.getProperty(\"url\")),e.hasProperty(\"searchIndex\")&&(i.searchIndex=e.getProperty(\"searchIndex\")),e.hasProperty(\"searchTrix\")&&(i.trixURL=this.baseURL+e.getProperty(\"searchTrix\")),e.hasProperty(\"group\")&&(i.group=e.getProperty(\"group\"),this.groupPriorityMap&&this.groupPriorityMap.has(i.group))){const e=this.groupPriorityMap.get(i.group)+1;i.order=e,this.groupPriorityMap.set(i.group,e)}return i}}function uu(e){const t=e.indexOf(\" \");return t>0?e.substring(0,t):e}class fu{properties=new Map;constructor(e,t){this.type=e,this.name=t}setProperty(e,t){this.properties.set(e,t)}getProperty(e){return this.properties.has(e)?this.properties.get(e):this.parent?this.parent.getProperty(e):void 0}hasProperty(e){return!!this.properties.has(e)||!!this.parent&&this.parent.hasProperty(e)}get format(){const e=this.getProperty(\"type\");if(e)return uu(e)}get displayMode(){let e=this.getProperty(\"visibility\");if(!e)return\"COLLAPSED\";switch(e=e.toLowerCase(),e){case\"dense\":default:return\"COLLAPSED\";case\"pack\":return\"EXPANDED\";case\"squish\":return\"SQUISHED\"}}}async function pu(e){const t=await fetch(e),i=(await t.text()).split(/\\n|\\r\\n|\\r/g),n=[];let r,s=!0;for(let e of i){const t=gu(e),i=e.indexOf(\" \",t);if(i<0)s=!0;else{const o=e.substring(t,i).trim();if(o.startsWith(\"#\"))continue;const a=e.substring(i+1).trim();if(s){const e=new fu(o,a);n.push(e),r=e,s=!1}r.setProperty(o,a)}}return function(e){const t=new Map;for(let i of e)t.set(i.name,i);for(let i of e)if(i.properties.has(\"parent\")){const e=uu(i.properties.get(\"parent\"));i.parent=t.get(e)}return e}(n)}function gu(e){let t=0;for(t=0;t<e.length;t++){const i=e.charAt(t);if(\" \"!==i&&\"\\t\"!==i)break}return t}const mu={initializeGenomes:async function(e){if(!mu.KNOWN_GENOMES){const t={};if(!1!==e.loadDefaultGenomes){const r=\"https://igv.org/genomes/genomes.json\";n(await Qs.loadJson(r,{timeout:5e3}))}const i=e.genomeList||e.genomes;if(i)if(\"string\"==typeof i){n(await Qs.loadJson(i,{}))}else n(i);function n(e){return e.forEach((function(e){t[e.id]=e})),t}mu.KNOWN_GENOMES=t}},isWholeGenomeView:function(e){return\"all\"===e.toLowerCase()},expandReference:async function(e,t){if(Mt(t)&&t.startsWith(\"{\"))try{t=JSON.parse(t)}catch(e){}let i;if(Mt(t)?i=t:t.genome?i=t.genome:void 0===t.id||t.fastaURL||t.twobitURL||(i=t.id),i){let t=mu.KNOWN_GENOMES[i];if(!t){if((i.startsWith(\"GCA_\")||i.startsWith(\"GCF_\"))&&i.length>=13)try{const e=hu(i);t=(await du.loadHub(e)).getGenomeConfig()}catch(e){console.error(e)}t||e.present(new Error(`Unknown genome id: ${i}`),void 0)}return t}return t}};let wu,bu,Fu=0,vu=0,yu=[];class Au extends eu{constructor(e,t,i,n){super(e,t,i,n)}initializationHelper(){this.$spinner=Bt(\"<div>\",{class:\"igv-loading-spinner-container\"}),this.$viewport.append(this.$spinner),this.$spinner.append(Bt(\"<div>\"));const e=this.trackView.track;\"sequence\"!==e.type&&(this.$zoomInNotice=this.createZoomInNotice(this.$viewport)),\"sequence\"!==e.id&&(this.$trackLabel=Bt('<div class=\"igv-track-label\">'),this.$viewport.append(this.$trackLabel),this.setTrackLabel(e.name||\"\"),!1===this.browser.doShowTrackLabels&&this.$trackLabel.hide()),this.stopSpinner(),this.addMouseHandlers()}setContentHeight(e){super.setContentHeight(e),this.featureCache&&(this.featureCache.redraw=!0)}setTrackLabel(e){this.$trackLabel.empty(),this.$trackLabel.html(e);const t=this.$trackLabel.text();this.$trackLabel.attr(\"title\",t)}startSpinner(){this.$spinner.show()}stopSpinner(){this.$spinner&&this.$spinner.hide()}checkZoomIn(){if(this.trackView.track&&\"sequence\"===this.trackView.track.type&&this.referenceFrame.bpPerPixel>10)return Bt(this.canvas).remove(),this.canvas=void 0,!1;if(!this.viewIsReady())return!1;if((()=>{if(\"all\"!==this.referenceFrame.chr.toLowerCase()||this.trackView.track.supportsWholeGenome){const e=this.trackView.track.visibilityWindow;return void 0!==e&&e>0&&this.referenceFrame.bpPerPixel*this.$viewport.width()>e}return!0})()){if(this.canvas&&(Bt(this.canvas).remove(),this.canvas=void 0),this.trackView.track.autoHeight){const e=this.trackView.minHeight||0;this.setContentHeight(e)}return this.$zoomInNotice&&this.$zoomInNotice.show(),!1}return this.$zoomInNotice&&this.$zoomInNotice.hide(),!0}shift(){const e=this.referenceFrame;this.canvas&&this.canvas._data&&this.canvas._data.referenceFrame.chr===this.referenceFrame.chr&&this.canvas._data.bpPerPixel===e.bpPerPixel&&(this.canvas._data.pixelShift=Math.round((this.canvas._data.bpStart-e.start)/e.bpPerPixel),this.canvas.style.left=this.canvas._data.pixelShift+\"px\")}genomicRange(){return{start:this.referenceFrame.start,end:this.referenceFrame.start+this.referenceFrame.bpPerPixel*this.$viewport.width()}}setTop(e){if(super.setTop(e),this.canvas){const t=this.$viewport.height(),i=e+this.canvas._data.pixelTop,n=i+this.canvas._data.pixelHeight;(i>0||n<t)&&this.repaint()}else this.repaint();if(this.canvas&&this.canvas._data){let t=e+this.canvas._data.pixelTop;this.canvas.style.top=`${t}px`}}async loadFeatures(){const e=this.referenceFrame,t=e.chr,i=await this.browser.genome.loadChromosome(t),n=i?i.bpLength:Number.MAX_SAFE_INTEGER,r=this.$viewport.width()*e.bpPerPixel,s=Math.floor(Math.max(0,e.start-r)),o=Math.ceil(Math.min(n,e.start+r+r));if(!this.loading||this.loading.start!==s||this.loading.end!==o){this.loading={start:s,end:o},this.startSpinner();try{const i=this.trackView.track,n=await this.getFeatures(i,t,s,o,e.bpPerPixel);if(n){let r=[];if(i.roiSets&&i.roiSets.length>0)for(let n of i.roiSets){const i=await n.getFeatures(t,s,o,e.bpPerPixel);r.push({track:n,features:i})}const a=i&&i.resolutionAware,c=this.windowFunction;return this.featureCache=new Cu(t,s,o,e.bpPerPixel,n,r,a,c),this.loading=!1,this.hideMessage(),this.stopSpinner(),this.featureCache}}catch(e){this.trackView&&!0!==this.trackView.disposed&&(this.showMessage(\"Error loading track data\"),this.browser.alert.present(e),console.error(e))}finally{this.loading=!1,this.stopSpinner()}}}get track(){return this.trackView.track}get windowFunction(){return this.track?this.track.windowFunction:void 0}repaintDimensions(){const e=mu.isWholeGenomeView(this.referenceFrame.chr),t=e?this.$viewport.width():3*this.$viewport.width(),i=this.referenceFrame.bpPerPixel;return{bpStart:this.referenceFrame.start-(e?0:this.$viewport.width()*i),bpEnd:e?Number.MAX_SAFE_INTEGER:this.referenceFrame.start+2*this.$viewport.width()*i+1,pixelWidth:t}}repaint(){if(void 0===this.featureCache)return;const{features:e,roiFeatures:t}=this.featureCache,{bpStart:i,bpEnd:n,pixelWidth:r}=this.repaintDimensions(),s=this.$viewport.height(),o=this.getContentHeight(),a=t?Math.max(o,s):o,c=Math.min(a,3*s);if(0===r||0===c)return void(this.canvas&&Bt(this.canvas).remove());const l=Math.max(0,-this.contentTop-Math.floor(c/3)),h=this.referenceFrame.bpPerPixel,d=Math.round((i-this.referenceFrame.start)/h),u=(this.contentTop||0)+l,f=document.createElement(\"canvas\");f.style.position=\"relative\",f.style.display=\"block\",f.style.width=r+\"px\",f.style.height=c+\"px\",f.style.left=d+\"px\",f.style.top=u+\"px\";const p=\"FILL\"===this.trackView.track.displayMode||!1!==this.trackView.track.supportHiDPI?window.devicePixelRatio:1;f.width=p*r,f.height=p*c;const g=f.getContext(\"2d\");g.scale(p,p),g.translate(0,-l);const m={context:g,pixelXOffset:d,pixelWidth:r,pixelHeight:c,pixelTop:l,bpStart:i,bpEnd:n,bpPerPixel:h,pixelShift:d,windowFunction:this.windowFunction,referenceFrame:this.referenceFrame,selection:this.selection,viewport:this,viewportWidth:this.$viewport.width()};this.draw(m,e,t),this.canvas&&Bt(this.canvas).remove(),f._data=m,this.canvas=f,this.$viewport.append(Bt(f))}refresh(){if(!this.canvas||!this.featureCache)return;const e=this.canvas._data;e.context.clearRect(0,0,this.canvas.width,this.canvas.height);const{features:t,roiFeatures:i}=this.featureCache;this.draw(e,t,i)}draw(e,t,i){if(t&&(e.features=t,this.trackView.track.draw(e)),i&&i.length>0)for(let t of i)e.features=t.features,t.track.draw(e)}containsPosition(e,t){return this.referenceFrame.chr===e&&t>=this.referenceFrame.start&&t<=this.referenceFrame.calculateEnd(this.getWidth())}isLoading(){return this.loading}savePNG(){if(!this.canvas)return;const e=this.canvas._data,t=e?e.pixelTop:0,i=window.devicePixelRatio,n=this.$viewport.width()*i,r=this.$viewport.height()*i,s=-Bt(this.canvas).position().left*i,o=(-this.contentTop-t)*i,a=this.canvas.getContext(\"2d\").getImageData(s,o,n,r),c=document.createElement(\"canvas\"),l=c.getContext(\"2d\");c.width=a.width,c.height=a.height,l.putImageData(a,0,0);Pt((this.$trackLabel.text()?this.$trackLabel.text():\"image\")+\".png\",c.toDataURL(\"image/png\"))}saveSVG(){let{width:e,height:t}=this.browser.columnContainer.getBoundingClientRect();const i=new lu({width:e,height:8e3,backdropColor:\"white\",multiLocusGap:0,viewbox:{x:0,y:0,width:e,height:8e3}}),n={deltaX:32,deltaY:32};this.renderSVGContext(i,n,!1),i.setHeight(t);const r=(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\"),o=this.browser.referenceFrameList.indexOf(this.referenceFrame),a=i.getSerializedSvg(!0),c=URL.createObjectURL(new Blob([a],{type:\"application/octet-stream\"}));Pt(`${`${r}_referenceFrame_${o}_guid_${s()}`}.svg`,c)}renderSVGContext(e,{deltaX:t,deltaY:i},n=!0){if(!(this.$zoomInNotice&&this.$zoomInNotice.is(\":visible\"))){const{width:n,height:r}=this.$viewport.get(0).getBoundingClientRect(),o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${s()}`,a=t,c=i+this.contentTop,l=-this.contentTop;e.saveWithTranslationAndClipRect(o,a,c,n,r,l);const{start:h,bpPerPixel:d}=this.referenceFrame,u=Math.round((h-this.referenceFrame.start)/d),f={context:e,viewport:this,referenceFrame:this.referenceFrame,top:l,pixelTop:l,pixelWidth:n,pixelHeight:r,pixelXOffset:u,pixelShift:u,bpStart:h,bpEnd:h+n*d,bpPerPixel:d,viewportWidth:n,selection:this.selection},p=this.featureCache?this.featureCache.features:void 0,g=this.featureCache?this.featureCache.roiFeatures:void 0;this.draw(f,p,g),e.restore()}if(n&&this.$trackLabel&&this.browser.doShowTrackLabels){const{x:n,y:r,width:s,height:o}=((e,t)=>{const{x:i,y:n,width:r,height:s}=e.getBoundingClientRect(),{x:o,y:a,width:c,height:l}=t.getBoundingClientRect();return{x:o-i,y:a-n,width:c,height:l}})(this.$viewport.get(0),this.$trackLabel.get(0));this.renderTrackLabelSVG(e,t+n,i+r,s,o)}}renderTrackLabelSVG(e,t,i,n,r){const o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_track_label_guid_${s()}`;e.saveWithTranslationAndClipRect(o,t,i,n,r,0),e.fillStyle=\"white\",e.fillRect(0,0,n,r),e.font=\"12px Arial\",e.fillStyle=\"rgb(68, 68, 68)\";const{width:a}=e.measureText(this.$trackLabel.text()),c=.25*(n-a),l=.7*(r-12);e.fillText(this.$trackLabel.text(),c,r-l),e.strokeStyle=\"rgb(68, 68, 68)\",e.strokeRect(0,0,n,r),e.restore()}get cachedFeatures(){return this.featureCache?this.featureCache.features:[]}clearCache(){this.featureCache=void 0,this.canvas&&(this.canvas._data=void 0)}async getFeatures(e,t,i,n,r){if(this.featureCache&&this.featureCache.containsRange(t,i,n,r,this.windowFunction))return this.featureCache.features;if(\"function\"==typeof e.getFeatures){const s=await e.getFeatures(t,i,n,r,this);return this.checkContentHeight(s),s}}needsRepaint(){if(!this.canvas)return!0;const e=this.canvas._data;return!e||this.referenceFrame.start<e.bpStart||this.referenceFrame.end>e.bpEnd||this.referenceFrame.chr!==e.referenceFrame.chr||this.referenceFrame.bpPerPixel!=e.bpPerPixel||this.windowFunction!=e.windowFunction}needsReload(){if(!this.featureCache)return!0;const{chr:e,bpPerPixel:t}=this.referenceFrame,{bpStart:i,bpEnd:n}=this.repaintDimensions();return!this.featureCache.containsRange(e,i,n,t,this.windowFunction)}createZoomInNotice(e){const t=Bt(\"<div>\",{class:\"igv-zoom-in-notice-container\"});e.append(t);const i=Bt(\"<div>\");return t.append(i),i.text(\"Zoom in to see features\"),t.hide(),t}viewIsReady(){return this.browser&&this.browser.referenceFrameList&&this.referenceFrame}addMouseHandlers(){const e=this.$viewport.get(0);this.addViewportContextMenuHandler(e);const t=e=>{this.enableClick=!0,this.browser.mouseDownOnViewport(e,this),r(e)};e.addEventListener(\"mousedown\",t),e.addEventListener(\"touchstart\",t);const i=e=>{this.browser.dragObject||this.browser.isScrolling?(this.browser.cancelTrackPan(),this.enableClick=!1):(this.browser.cancelTrackPan(),this.browser.endTrackDrag())};e.addEventListener(\"mouseup\",i),e.addEventListener(\"touchend\",i),\"function\"==typeof this.trackView.track.hoverText&&e.addEventListener(\"mousemove\",(e=>{if(0===e.buttons&&Date.now()-vu>100){vu=Date.now();const t=this.createClickState(e);if(t){const e=this.trackView.track.hoverText(t);e?this.$viewport[0].setAttribute(\"title\",e):this.$viewport[0].removeAttribute(\"title\")}}})),this.addViewportClickHandler(this.$viewport.get(0)),this.trackView.track.name&&\"sequence\"!==this.trackView.track.config.type&&this.addTrackLabelClickHandler(this.$trackLabel.get(0))}addViewportContextMenuHandler(e){e.addEventListener(\"contextmenu\",(e=>{if(this.browser.dragObject)return!1;const t=this.createClickState(e);if(void 0===t)return!1;e.preventDefault();let i=[];if(\"function\"==typeof this.trackView.track.contextMenuItemList){const e=this.trackView.track.contextMenuItemList(t);e&&(i=e)}i.length>0&&i.push({label:Bt(\"<HR>\")}),i.push({label:\"Save Image (PNG)\",click:()=>this.savePNG()}),i.push({label:\"Save Image (SVG)\",click:()=>this.saveSVG()}),this.browser.menuPopup.presentTrackContextMenu(e,i)}))}addViewportClickHandler(e){e.addEventListener(\"click\",(e=>{if(this.enableClick&&this.canvas){if(3===e.which||e.ctrlKey)return;if(this.browser.dragObject||this.browser.isScrolling)return;e.preventDefault();const t=a(e,this.$viewport.get(0)).x,i=a(e,this.canvas).x,n=this.referenceFrame;Math.floor(n.start+n.toBP(i));const r=Date.now();if(r-Fu<this.browser.constants.doubleClickDelay){wu&&(window.clearTimeout(wu),wu=void 0);const e=Math.round(n.start+n.toBP(t));let i;if(\"all\"===this.referenceFrame.chr.toLowerCase()){const t=this.browser.genome.getChromosomeCoordinate(e).chr;if(1===this.browser.referenceFrameList.length)i=t;else{const e=this.browser.referenceFrameList.map((({locusSearchString:e})=>e));e[this.browser.referenceFrameList.indexOf(this.referenceFrame)]=t,i=e.join(\" \")}this.browser.search(i)}else this.browser.zoomWithScaleFactor(.5,e,this.referenceFrame)}else\"function\"==typeof this.trackView.track.popupData&&(wu=setTimeout((()=>{const t=this.getPopupContent(e);if(t)if(!1===e.shiftKey){if(bu&&bu.dispose(),yu.length>0){for(const e of yu)e.dispose();yu.length=0}bu=new tc(this.$viewport.get(0).parentElement,!0,void 0,(()=>{bu.dispose()})),bu.presentContentWithEvent(e,t)}else{let i=new tc(this.$viewport.get(0).parentElement,!0,void 0,(()=>{const e=yu.indexOf(i);yu.splice(e,1),i.dispose()}));yu.push(i),i.presentContentWithEvent(e,t)}window.clearTimeout(wu),wu=void 0}),this.browser.constants.doubleClickDelay));Fu=r}}))}addTrackLabelClickHandler(e){e.addEventListener(\"click\",(e=>{e.stopPropagation();const{track:t}=this.trackView;let i;\"function\"==typeof t.description?i=t.description():t.description&&(i=`<div>${t.description}</div>`),i&&(void 0===this.popover&&(this.popover=new tc(this.browser.columnContainer,!0,t.name||\"\",void 0)),this.popover.presentContentWithEvent(e,i))}))}createClickState(e){if(!this.canvas)return;const t=this.referenceFrame,i=a(e,this.$viewport.get(0)),n=a(e,this.canvas),r=t.start+t.toBP(i.x);return{event:e,viewport:this,referenceFrame:t,genomicLocation:r,y:i.y-this.contentTop,canvasX:n.x,canvasY:n.y}}getPopupContent(e){const t=this.createClickState(e);if(void 0===t)return;let i=this.trackView.track;const n=i.popupData(t),r=this.browser.fireEvent(\"trackclick\",[i,n]);let s;return void 0===r||!0===r?n&&n.length>0&&(s=n.map((e=>{if(e.name){const t=`<span>${e.name}</span>&nbsp&nbsp&nbsp${e.value}`;return`<div title=\"${e.value}\">${t}</div>`}return\"<hr>\"===e?e:e.html?e.html:`<div title=\"${e}\">${e}</div>`})).join(\"\")):\"string\"==typeof r&&(s=r),s}dispose(){this.popover&&this.popover.dispose(),super.dispose()}}class Cu{constructor(e,t,i,n,r,s,o,a){this.chr=e,this.bpStart=t,this.bpEnd=i,this.bpPerPixel=n,this.features=r,this.roiFeatures=s,this.multiresolution=o,this.windowFunction=a}containsRange(e,t,i,n,r){if(r&&r!==this.windowFunction)return!1;const s=this.multiresolution?this.bpPerPixel/n:1;return t>=this.bpStart&&i<=this.bpEnd&&e===this.chr&&s>.5&&s<2}overlapsRange(e,t,i){return this.chr===e&&i>=this.bpStart&&t<=this.bpEnd}}const _u=function(e,t){const{r:i,g:n,b:r}=no[e];return`rgba(${i},${n},${r},${t})`}(\"nickel\",2/16),xu=_u;class ku{constructor(e,t){if(this.url=e.url,e.name&&(this.name=e.name),this.isUserDefined=e.isUserDefined,e.featureSource)this.featureSource=e.featureSource;else if(e.features)this.featureSource=new Su(e.features,t);else{if(!e.format)throw Error(\"ROI configuration must define either features or file format\");this.featureSource=Ad(e,t)}!0===this.isUserDefined?(this.color=e.color||xu,this.headerColor=\"rgba(155,185,129)\"):(this.color=e.color||_u,this.headerColor=\"rgb(190,190,190)\"),this.isVisible=void 0===e.isVisible||e.isVisible}async getFeatures(e,t,i){return this.featureSource.getFeatures({chr:e,start:t,end:i})}async getAllFeatures(){return\"function\"==typeof this.featureSource.getAllFeatures?await this.featureSource.getAllFeatures():{}}addFeature(e){this.featureSource.addFeature(e)}removeFeature(e){this.featureSource.removeFeature(e)}toJSON(){if(this.url)return{name:this.name,color:this.color,url:this.url,isUserDefined:this.isUserDefined,isVisible:this.isVisible};{const e=this.featureSource.getAllFeatures(),t=[];for(let i of Object.keys(e))for(let n of e[i])t.push(n);return{name:this.name,color:this.color,features:t,isUserDefined:this.isUserDefined,isVisible:this.isVisible}}}dispose(){for(let e of Object.keys(this))this[e]=void 0}}function Iu(e,t,i,n){let r=Math.round((e-i)/n);let s=Math.round((t-i)/n)-r;return s<3&&(s=3,r-=1),{x:r,width:s}}class Su{constructor(e,t){this.featureMap={},this.genome=t;for(let i of e){const e=t?t.getChromosomeName(i.chr):i.chr;let n=this.featureMap[e];n||(n=[],this.featureMap[e]=n),n.push(i)}for(let e of Object.keys(this.featureMap))this.featureMap[e].sort(((e,t)=>e.start-t.start))}async getFeatures({chr:e,start:t,end:i}){if(\"all\"===e.toLowerCase())return Ll(this.featureMap,this.genome);{const n=this.featureMap[e];return n?n.filter((e=>e.end>t&&e.start<i)):[]}}getAllFeatures(){return this.featureMap}supportsWholeGenome(){return!0}addFeature(e){let t=this.featureMap[e.chr];t||(t=[],this.featureMap[e.chr]=t),t.push(e),t.sort(((e,t)=>e.start-t.start))}removeFeature({chr:e,start:t,end:i}){if(this.featureMap[e]){const n=`${e}-${t}-${i}`;this.featureMap[e]=this.featureMap[e].filter((e=>n!==`${e.chr}-${e.start}-${e.end}`)),0===this.featureMap[e].length&&delete this.featureMap[e]}}}class Eu{constructor(t,i,n,r){this.rulerViewport=t,this.rulerSweeper=e({class:\"igv-ruler-sweeper\"}),i.appendChild(this.rulerSweeper),this.browser=n,this.referenceFrame=r,this.isMouseHandlers=void 0,this.addBrowserObserver()}addBrowserObserver(){this.boundObserverHandler=(()=>{this.referenceFrame&&(mu.isWholeGenomeView(this.referenceFrame.chr)?this.removeMouseHandlers():this.addMouseHandlers())}).bind(this),this.browser.on(\"locuschange\",this.boundObserverHandler)}removeBrowserObserver(){this.browser.off(\"locuschange\",this.boundObserverHandler)}addMouseHandlers(){if(!0===this.isMouseHandlers)return;let e,t,i,n,r,s;this.boundContentMouseDownHandler=function(s){e=!0,t=!0;const{x:o}=a(s,this.rulerViewport.contentDiv);n=i=o,r=1,this.rulerSweeper.style.display=\"block\",this.rulerSweeper.style.backgroundColor=!0===s.shiftKey?xu:\"rgba(68, 134, 247, 0.25)\",this.rulerSweeper.style.left=`${n}px`,this.rulerSweeper.style.width=`${r}px`}.bind(this),this.rulerViewport.contentDiv.addEventListener(\"mousedown\",this.boundContentMouseDownHandler),this.boundDocumentMouseMoveHandler=function(o){let c;if(e&&t){const{x:e}=a(o,this.rulerViewport.contentDiv);c=Math.max(Math.min(e,this.rulerViewport.contentDiv.clientWidth),0),s=c-i,r=Math.abs(s),this.rulerSweeper.style.width=`${r}px`,s<0&&(n=i+s,this.rulerSweeper.style.left=`${n}px`)}}.bind(this),document.addEventListener(\"mousemove\",this.boundDocumentMouseMoveHandler),this.boundDocumentMouseUpHandler=function(i){let s;if(!0===e&&!0===t&&(e=t=void 0,this.rulerSweeper.style.display=\"none\",r>1)){s={start:Math.floor(this.referenceFrame.calculateEnd(n)),end:Math.floor(this.referenceFrame.calculateEnd(n+r))};!0===i.shiftKey?this.browser.roiManager.updateUserDefinedROISet(Object.assign({chr:this.referenceFrame.chr},s)):(Qa(this.browser.genome.getChromosome(this.referenceFrame.chr).bpLength,s,this.browser.minimumBases()),function(e,t,i){e.start=Math.round(t.start),e.end=Math.round(t.end),e.bpPerPixel=(e.end-e.start)/i}(this.referenceFrame,s,this.rulerViewport.contentDiv.clientWidth),this.browser.updateViews(this.referenceFrame))}}.bind(this),document.addEventListener(\"mouseup\",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!0}removeMouseHandlers(){this.rulerViewport.contentDiv.removeEventListener(\"mousedown\",this.boundContentMouseDownHandler),document.removeEventListener(\"mousemove\",this.boundDocumentMouseMoveHandler),document.removeEventListener(\"mouseup\",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!1}dispose(){this.removeBrowserObserver(),this.removeMouseHandlers(),this.rulerSweeper.remove()}}function Nu(e){if(Bu[e])return Bu[e];if(Bu[\"chr\"+e]){const t=Bu[\"chr\"+e];return Bu[e]=t,t}{const t=_s.randomRGB(0,255);return Bu[e]=t,t}}const Bu={chrX:\"rgb(204, 153, 0)\",chrY:\"rgb(153, 204, 0)\",chrUn:\"rgb(50, 50, 50)\",chr1:\"rgb(80, 80, 255)\",chrI:\"rgb(139, 155, 187)\",chr2:\"rgb(206, 61, 50)\",chrII:\"rgb(206, 61, 50)\",chr2a:\"rgb(216, 71, 60)\",chr2b:\"rgb(226, 81, 70)\",chr3:\"rgb(116, 155, 88)\",chrIII:\"rgb(116, 155, 88)\",chr4:\"rgb(240, 230, 133)\",chrIV:\"rgb(240, 230, 133)\",chr5:\"rgb(70, 105, 131)\",chr6:\"rgb(186, 99, 56)\",chr7:\"rgb(93, 177, 221)\",chr8:\"rgb(128, 34, 104)\",chr9:\"rgb(107, 215, 107)\",chr10:\"rgb(213, 149, 167)\",chr11:\"rgb(146, 72, 34)\",chr12:\"rgb(131, 123, 141)\",chr13:\"rgb(199, 81, 39)\",chr14:\"rgb(213, 143, 92)\",chr15:\"rgb(122, 101, 165)\",chr16:\"rgb(228, 175, 105)\",chr17:\"rgb(59, 27, 83)\",chr18:\"rgb(205, 222, 183)\",chr19:\"rgb(97, 42, 121)\",chr20:\"rgb(174, 31, 99)\",chr21:\"rgb(231, 199, 111)\",chr22:\"rgb(90, 101, 94)\",chr23:\"rgb(204, 153, 0)\",chr24:\"rgb(153, 204, 0)\",chr25:\"rgb(51, 204, 0)\",chr26:\"rgb(0, 204, 51)\",chr27:\"rgb(0, 204, 153)\",chr28:\"rgb(0, 153, 204)\",chr29:\"rgb(10, 71, 255)\",chr30:\"rgb(71, 117, 255)\",chr31:\"rgb(255, 194, 10)\",chr32:\"rgb(255, 209, 71)\",chr33:\"rgb(153, 0, 51)\",chr34:\"rgb(153, 26, 0)\",chr35:\"rgb(153, 102, 0)\",chr36:\"rgb(128, 153, 0)\",chr37:\"rgb(51, 153, 0)\",chr38:\"rgb(0, 153, 26)\",chr39:\"rgb(0, 153, 102)\",chr40:\"rgb(0, 128, 153)\",chr41:\"rgb(0, 51, 153)\",chr42:\"rgb(26, 0, 153)\",chr43:\"rgb(102, 0, 153)\",chr44:\"rgb(153, 0, 128)\",chr45:\"rgb(214, 0, 71)\",chr46:\"rgb(255, 20, 99)\",chr47:\"rgb(0, 214, 143)\",chr48:\"rgb(20, 255, 177)\"};let Mu,Ru;class Du extends Au{constructor(e,t,i,n){super(e,t,i,n)}get contentDiv(){return this.$viewport.get(0)}initializationHelper(){let e;this.$multiLocusCloseButton=Bt(\"<div>\",{class:\"igv-multi-locus-close-button\"}),this.$viewport.append(this.$multiLocusCloseButton),this.$multiLocusCloseButton.get(0).appendChild(l(\"times-circle\")),this.$multiLocusCloseButton.click((()=>{this.browser.removeMultiLocusPanel(this.referenceFrame)})),this.$rulerLabel=Bt(\"<div>\",{class:\"igv-multi-locus-ruler-label\"}),this.$viewport.append(this.$rulerLabel),e=document.createElement(\"div\"),this.$rulerLabel.append(Bt(e)),this.$rulerLabel.get(0).addEventListener(\"click\",(async e=>{e.stopPropagation(),await this.browser.gotoMultilocusPanel(this.referenceFrame)})),this.$tooltip=Bt(\"<div>\",{class:\"igv-ruler-tooltip\"}),this.$tooltip.height(this.$viewport.height()),this.$viewport.append(this.$tooltip),this.$tooltipContent=Bt(\"<div>\"),this.$tooltip.append(this.$tooltipContent),this.rulerSweeper=new Eu(this,this.$viewport.get(0).parentElement,this.browser,this.referenceFrame),this.attachMouseHandlers(mu.isWholeGenomeView(this.referenceFrame.chr)),this.$tooltip.hide(),this.dismissLocusLabel()}presentLocusLabel(e){this.$multiLocusCloseButton.show(),this.$rulerLabel.show(),this.$rulerLabel.get(0).style.backgroundColor=Nu(this.referenceFrame.chr);const t=this.$rulerLabel.get(0).querySelector(\"div\"),{width:i}=this.$rulerLabel.get(0).getBoundingClientRect();t.innerHTML=`${this.referenceFrame.getMultiLocusLabel(e)}`;const{width:n}=t.getBoundingClientRect();n/i>.5&&(t.innerHTML=`${this.referenceFrame.getMultiLocusLabelBPLengthOnly(e)}`)}dismissLocusLabel(){this.$rulerLabel.hide(),this.$multiLocusCloseButton.hide()}attachMouseHandlers(e){if(this.namespace=`.ruler_track_viewport_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}`,this.$viewport.off(this.namespace),!0===e){const e=this.browser.referenceFrameList.indexOf(this.referenceFrame),t=`click${this.namespace}`;this.$viewport.on(t,(t=>{const{x:i}=a(t,this.$viewport.get(0)),n=Math.round(this.referenceFrame.start+this.referenceFrame.toBP(i));let r;const{chr:s}=this.browser.genome.getChromosomeCoordinate(n);if(1===this.browser.referenceFrameList.length)r=s;else{let t=this.browser.referenceFrameList.map((({locusSearchString:e})=>e));t[e]=s,r=t.join(\" \")}this.browser.search(r)})),this.$viewport.get(0).style.cursor=\"pointer\"}else this.$viewport.get(0).style.cursor=\"default\"}mouseMove(e){if(!0===this.browser.doShowCursorGuide){void 0===Ru?(Ru=this,this.$tooltip.show()):Ru.guid!==this.guid?(Ru.$tooltip&&Ru.$tooltip.hide(),this.$tooltip.show(),Ru=this):this.$tooltip.show();if(this.browser.isMultiLocusWholeGenomeView()||mu.isWholeGenomeView(this.referenceFrame.chr))return void this.$tooltip.hide();const{x:t}=a(e,this.$viewport.get(0)),{start:i,end:n,bpPerPixel:r}=this.referenceFrame,s=Math.round(.5+i+Math.max(0,t)*r);this.$tooltipContent.text(Rt(s));const{width:o}=this.$tooltipContent.get(0).getBoundingClientRect(),{width:c}=this.$viewport.get(0).getBoundingClientRect();return this.$tooltip.css({left:`${ys.clamp(t,0,c-o)}px`}),clearTimeout(Mu),Mu=setTimeout((()=>{this.$tooltip&&this.$tooltip.hide()}),1e4),{start:i,bp:s,end:n}}}startSpinner(){}stopSpinner(){}dispose(){this.rulerSweeper.dispose(),super.dispose()}}class Tu extends Au{featureCache=new Lu;constructor(e,t,i,n){super(e,t,i,n)}initializationHelper(){this.canvas=document.createElement(\"canvas\"),this.canvas.className=\"igv-ideogram-canvas\",this.$viewport.append(Bt(this.canvas)),this.ideogram_ctx=this.canvas.getContext(\"2d\"),this.addMouseHandlers()}async getFeatures(e,t,i,n){return this.featureCache.containsRange(e)?this.featureCache.get(e):this.loadFeatures()}async loadFeatures(){const e=this.referenceFrame.chr,t=await this.referenceFrame.genome.getCytobands(e);return this.featureCache.set(e,t),t}repaint(){if(void 0===this.featureCache)return;const{width:e,height:t}=this.$viewport[0].getBoundingClientRect();xo.configureHighDPICanvas(this.ideogram_ctx,e,t);const i=this.referenceFrame.chr,n=this.featureCache.get(i),r={context:this.ideogram_ctx,pixelWidth:e,pixelHeight:t,referenceFrame:this.referenceFrame,features:n};this.trackView.track.draw(r)}addMouseHandlers(){this.addViewportClickHandler(this.$viewport.get(0))}addViewportClickHandler(e){this.boundClickHandler=function(e){const{xNormalized:t,width:i}=a(e,this.ideogram_ctx.canvas),{bpLength:n}=this.browser.genome.getChromosome(this.referenceFrame.chr),r=this.referenceFrame.bpPerPixel*i/n;let s=t;s-r/2<0&&(s=r/2);s+r/2>1&&(s=1-r/2);const o=Math.round((s-r/2)*n),c=Math.round((s+r/2)*n);this.referenceFrame.start=o,this.referenceFrame.end=c,this.referenceFrame.bpPerPixel=(c-o)/i,this.browser.updateViews(this.referenceFrame,this.browser.trackViews,!0)}.bind(this),e.addEventListener(\"click\",this.boundClickHandler)}setWidth(e){this.$viewport.width(e)}renderSVGContext(e,{deltaX:t,deltaY:i},n=!0){const{width:r,height:o}=this.$viewport.get(0).getBoundingClientRect(),a=`ideogram_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${s()}`,c=t,l=i+this.contentTop,h=-this.contentTop;e.saveWithTranslationAndClipRect(a,c,l,r,o,h),this.trackView.track.draw({context:e,pixelWidth:r,pixelHeight:o,referenceFrame:this.referenceFrame,features:this.featureCache.get(this.referenceFrame.chr)}),e.restore()}startSpinner(){}stopSpinner(){}}class Lu{features=new Map;containsRange(e){return this.features.has(e)}set(e,t){this.features.set(e,t)}get(e){return this.features.get(e)}}function zu(e,t,i,n){if(\"ruler\"===e.track.type)return new Du(e,t,i,n);if(\"ideogram\"===e.track.id)return new Tu(e,t,i,n);{const r=new Au(e,t,i,n);return i.viewport=r,r}}const Hu=[\"rgb(255, 0, 0)\",\"rgb(0, 255, 0)\",\"rgb(0, 0, 255)\",\"rgb(255, 0, 255)\",\"rgb(0, 255, 255)\",\"rgb(128, 0, 128)\",\"rgb(255, 165, 0)\",\"rgb(255, 105, 180)\",\"rgb(255, 127, 80)\",\"rgb(220, 20, 60)\",\"rgb(255, 99, 71)\",\"rgb(173, 216, 230)\",\"rgb(144, 238, 144)\",\"rgb(224, 255, 255)\",\"rgb(250, 250, 210)\",\"rgb(152, 251, 152)\",\"rgb(70, 130, 180)\",\"rgb(102, 205, 170)\"].map((e=>{const[t,i,n]=e.split(\",\"),[r,s]=t.split(\"(\"),[o,a]=n.split(\")\");return[s,i,o]})),Pu=ro(\"magnesium\"),Ou=[\"#sampleTable\",\"#sampleMapping\",\"#colors\"];class Uu{static emptySpaceReplacement=\"|\";sampleDictionary={};attributeNames=[];sampleMappingDictionary={};colorDictionary={};attributeRangeLUT={};constructor(e){e.tracks.some((e=>\"function\"==typeof e.getSamples)).length>0&&e.sampleInfoControl.setButtonVisibility(!0),this.initialize()}initialize(){this.sampleInfoFiles=[],this.attributeNames=[],this.sampleDictionary={},this.sampleMappingDictionary={},this.colorDictionary={},this.attributeRangeLUT={},this.initialized=!1}get attributeCount(){return this.attributeNames?this.attributeNames.length:0}isInitialized(){return this.initialized}hasAttributes(){return this.attributeCount>0}getAttributes(e){const t=0===Object.keys(this.sampleMappingDictionary)?e:this.sampleMappingDictionary[e]||e;return this.sampleDictionary[t]}async loadSampleInfoFile(e){try{const t=await Qs.loadString(e);this.#w(t),this.sampleInfoFiles.push(e)}catch(e){console.error(e.message)}}#w(e){const t=function(e){const t={},i=e.split(/\\r?\\n|\\r/).map((e=>e.trim())).filter((e=>\"\"!==e));let n;Ou.includes(i[0])||(n=\"#sampleTable\",t[n]=[]);for(const e of i)Ou.includes(e)?(n=e,t[n]=[]):n&&!1===e.startsWith(\"#\")&&t[n].push(e);return t}(e);for(const[e,i]of Object.entries(t))switch(e){case\"#sampleTable\":this.#b(i);break;case\"#sampleMapping\":this.#F(i);break;case\"#colors\":this.#v(i)}this.initialized=!0}getAttributeColor(e,t){let i;if(\"-\"===t)i=ro(\"snow\");else if(\"string\"==typeof t&&this.colorDictionary[t])i=this.colorDictionary[t]();else if(this.colorDictionary[e])i=this.colorDictionary[e](t);else if(\"string\"==typeof t)i=\"NA\"===t?Pu:function(e){let t=0;for(let i=0;i<e.length;i++)t=e.charCodeAt(i)+((t<<5)-t);let i=[];for(let e=0;e<3;e++){const n=t>>8*e&255;i.push(n)}return`rgb(${i.join(\", \")})`}(t);else{const[n,r]=this.attributeRangeLUT[e],s=.2,o=Math.max((t-n)/(r-n),s),[a,c,l]=Hu[Object.keys(this.attributeRangeLUT).indexOf(e)];i=`rgba(${a},${c},${l},${o})`}return i}getSortedSampleKeysByAttribute(e,t,i){i=i||1;const n=e.filter((e=>\"number\"==typeof this.getAttributes(e)[t])),r=e.filter((e=>\"string\"==typeof this.getAttributes(e)[t])),s=(e,n)=>{const r=this.getAttributes(e)[t],s=this.getAttributes(n)[t];return\"string\"==typeof r&&\"string\"==typeof s?i*r.localeCompare(s):\"number\"==typeof r&&\"number\"==typeof s?i*(r-s):void 0};return n.sort(s),r.sort(s),-1===i?[...n,...r]:[...r,...n]}toJSON(){const e=[];for(const t of this.sampleInfoFiles){const i={url:t},n=Hl.localFileInspection(i);e.push(n)}return e}#b(e){const t=e.shift().split(\"\\t\").filter((e=>e.length>0));t.shift();const i=t.map((e=>e.split(\" \").join(Uu.emptySpaceReplacement))),n=e.filter((e=>e.length>0));let r;for(const e of n){const t=e.split(\"\\t\"),n=t.shift();void 0===r&&(r={}),r[n]={};for(let e=0;e<t.length;e++){const s={};\"\"===t[e]?s[i[e]]=\"-\":s[i[e]]=t[e],Object.assign(r[n],s)}}for(const[e,t]of Object.entries(r))r[e]=Qu(t);const s=function(e,t){const i={};for(const n of Object.values(t))for(const t of e){let e=n[t];void 0===i[t]&&(i[t]=[]),i[t].push(e)}const n=e=>\"number\"==typeof e,r=e=>\"string\"==typeof e;for(const e of Object.keys(i)){const t=i[e],s=new Set(t),o=Array.from(s);if(!0===o.some(r)&&!0===o.some(n)?i[e]=o.filter((e=>!r(e))):i[e]=o,!i[e].some(r)){const t=i[e].slice();i[e]=[Math.min(...t),Math.max(...t)]}}return i}(i,r);qu(this.attributeRangeLUT,s);const o=new Set(this.attributeNames);for(const e of i)o.has(e)||this.attributeNames.push(e);qu(this.sampleDictionary,r)}#F(e){for(const t of e){const[e,i]=t.split(\"\\t\");this.sampleMappingDictionary[e]=i}}#v(e){const t=(e,t,i)=>{let n;switch(t){case 0:n=e.split(\" \").join(Uu.emptySpaceReplacement);break;case 1:n=e.includes(\":\")?e.split(\":\").map((e=>parseFloat(e))):e;break;case 2:case 3:n=`rgb(${e})`}return n},i=e.map((e=>e.split(\"\\t\").map(t))),n=i.filter((e=>3===e.length&&!e.includes(\"*\"))).filter((([e,t,i])=>!Array.isArray(t))),r={};for(const e of n){const[t,i,n]=e;void 0===r[t]&&(r[t]={}),r[t][i.toUpperCase()]=n}for(const[e,t]of Object.entries(r)){const i=Object.assign({},t);this.colorDictionary[e]=e=>{const t=e.toUpperCase();return i[t]||ro(\"snow\")}}const s=i.filter((e=>Array.isArray(e[1])));for(const e of s){const[t,i]=e[1],n=e[0];if(3===e.length){const[r,s,o]=uo(e[2]);this.colorDictionary[n]=e=>{e=ys.clamp(e,t,i);return lo(r,s,o,(e-t)/(i-t))}}else if(4===e.length){const[t,i]=e[1],[n,r,s,o]=e;this.colorDictionary[n]=e=>{e=ys.clamp(e,t,i);return fo(s,o,(e-t)/(i-t))}}}const o=i.filter((e=>3===e.length&&e.includes(\"*\")));for(const e of o)if(\"*\"===e[1]){const[t,i,n]=e;this.colorDictionary[t]=e=>{if(\"NA\"===e)return Pu;{const[i,r]=this.attributeRangeLUT[t],s=(e-i)/(r-i),[o,a,c]=uo(n);return lo(o,a,c,s)}}}else if(\"*\"===e[0]){const[t,i,n]=e;this.colorDictionary[i]=()=>n}}}function qu(e,t){for(const[i,n]of Object.entries(t))i in e&&e[i]===n||(e[i]=n)}function Qu(e){const t=Object.assign({},e);for(const[e,i]of Object.entries(t))\"string\"!=typeof i||isNaN(i)||(t[e]=Number(i));return t}const Vu=16,ju=Rt;class Wu{constructor(e){this.browser=e,this.height=40,this.name=\"\",this.id=\"ruler\",this.disableButtons=!0,this.ignoreTrackMenu=!0,this.order=.01*Number.MIN_SAFE_INTEGER,this.removable=!1,this.type=\"ruler\"}async getFeatures(e,t,i){return[]}computePixelHeight(e){return this.height}draw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpPerPixel:r,bpStart:s}){mu.isWholeGenomeView(t.chr)?this.drawWholeGenome({context:e,pixelWidth:i,pixelHeight:n,bpPerPixel:r}):this.doDraw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpStart:s})}drawWholeGenome({context:e,pixelWidth:t,pixelHeight:i,bpPerPixel:n}){e.save(),xo.fillRect(e,0,0,t,i,{fillStyle:\"white\"});for(let t of this.browser.genome.wgChromosomeNames){let r=this.browser.genome.getCumulativeOffset(t),s=this.browser.genome.getChromosome(t).bpLength,o=Math.round(r/n),a=Math.round(s/n);this.renderChromosomeRect(e,o,0,a,i,t)}e.restore()}doDraw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpStart:r}){e.clearRect(0,0,i,n);const s=function(e,t){if(e<10)return new Gu(1,\"bp\",1);const i=Math.floor(Math.log10(e));let n=\"bp\",r=1;i>9?(n=\"gb\",r=1e9):i>6?(n=\"mb\",r=1e6):i>3&&(n=\"kb\",r=1e3);const s=Math.pow(10,i-1),o=e/s,a=75,c=Math.pow(10,i-1),l=Math.pow(10,i)/2;return new Gu(o<a&&!0!==t?c:l,n,r)}(Math.floor(t.toBP(i)),e.isSVG);let o=Math.floor(r/s.majorTick)-1;const{tickDelta:a,labelLength:c}=function(e,t,i,n,r){const s=l(t,c(1+n,r),i)-l(t,c(n,r),i),o=`${Rt(Math.floor(c(n,r)/r.unitMultiplier))} ${r.majorUnit}`,a=Math.floor(e.measureText(o).width);return{tickDelta:s,labelLength:a};function c(e,t){return Math.floor(e*t.majorTick)}function l(e,t,i){return Math.round(e.toPixels(t-1-i+.5))}}(e,t,r,o,s);let l,h;this.browser.referenceFrameList.indexOf(t);let d=a;const u=.25*c;do{h=Math.floor(o*s.majorTick);const i=`${Rt(Math.floor(h/s.unitMultiplier))} ${s.majorUnit}`;l=Math.round(t.toPixels(h-1-r+.5));const n=Math.round(l-e.measureText(i).width/2);n>0&&u+c<=d&&(xo.fillText(e,i,n,this.height-8),d=0),l>0&&xo.strokeLine(e,l,this.height-6,l,this.height-2),h=Math.floor((1+o)*s.majorTick);let f=l+(Math.round(t.toPixels(h-1-r+.5))-l)/2;f>0&&xo.strokeLine(e,f,this.height-6,f,this.height-2),++o,d+=a}while(l<i);xo.strokeLine(e,0,this.height-2,i,this.height-2)}renderChromosomeRect(e,t,i,n,r,s){e.textAlign=\"center\",e.textBaseline=\"middle\",e.font=\"12px sans-serif\",xo.strokeLine(e,t+n,i,t+n,i+r,{strokeStyle:_s.greyScale(191)});const o=(s=this.browser.genome.getChromosomeDisplayName(s)).startsWith(\"chr\")?s.substring(3):s;n>e.measureText(o).width&&xo.fillText(e,o,t+n/2,i+r/2,{fillStyle:_s.greyScale(68)})}get supportsWholeGenome(){return!0}dispose(){}}class Gu{constructor(e,t,i){this.majorTick=e,this.minorTick=e/10,this.majorUnit=t,this.unitMultiplier=i}description(e){console.log((e||\"\")+\" tick \"+ju(this.majorTick)+\" label width \"+ju(this.labelWidthBP)+\" multiplier \"+this.unitMultiplier)}}class $u{constructor(t,i,n){this.guid=s(),this.trackView=t,this.browser=t.browser,this.viewport=e({class:\"igv-viewport\"}),i.appendChild(this.viewport),this.viewport.style.height=`${t.track.height}px`,null===this.viewport.previousElementSibling&&(this.viewport.style.zIndex=16,this.viewport.style.overflow=\"visible\"),this.canvas=document.createElement(\"canvas\"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext(\"2d\"),this.ctx.font=\"10px verdana\",this.contentTop=0,this.hitList=void 0,this.sortDirection=1,this.setWidth(n),this.addMouseHandlers()}resizeCanvas(){const e=window.devicePixelRatio,t=this.browser.getSampleInfoViewportWidth();let i;if(this.browser.trackViews.length>1&&null===this.viewport.previousElementSibling){const[e,t]=[this.browser.ideogramTrackView.track,this.browser.rulerTrackView.track];i=e.height+t.height}else i=this.viewport.clientHeight;if(this.canvas.width!==t*e||this.canvas.height!==i*e){const n=this.canvas;n.width=t*e,n.height=i*e,n.style.width=`${t}px`,n.style.height=`${i}px`,this.ctx=this.canvas.getContext(\"2d\"),this.ctx.scale(e,e),null===this.viewport.previousElementSibling&&xo.fillRect(this.ctx,0,0,this.ctx.canvas.width,this.ctx.canvas.height,{fillStyle:ro(\"snow\")})}}setTop(e){\"function\"==typeof this.trackView.track.getSamples&&(this.contentTop=e,this.repaint())}setWidth(e){this.viewport.innerWidth=e,this.resizeCanvas()}setHeight(e){const t=this.browser.getSampleInfoViewportWidth();this.viewport.style.width=`${t}px`,this.viewport.style.height=`${e}px`;const i=window.devicePixelRatio;this.canvas.width=t*i,this.canvas.height=e*i,this.canvas.style.width=`${t}px`,this.canvas.style.height=`${e}px`,this.ctx=this.canvas.getContext(\"2d\"),this.ctx.scale(i,i),null===this.viewport.previousElementSibling&&xo.fillRect(this.ctx,0,0,this.ctx.canvas.width,this.ctx.canvas.height,{fillStyle:ro(\"snow\")})}async repaint(){if(this.resizeCanvas(),\"function\"==typeof this.trackView.track.getSamples){const e=this.trackView.track.getSamples();e.names&&e.names.length>0&&this.draw({context:this.ctx,samples:e})}else null===this.viewport.previousElementSibling&&(this.browser.rulerTrackView&&this.browser.rulerTrackView.setTrackHeight(!0===this.browser.sampleInfoControl.showSampleInfo?this.calculateSampleInfoColumnHeight():40,!0),this.renderSampleInfoColumns(this.ctx))}calculateSampleInfoColumnHeight(){const e=this.browser.sampleInfo.attributeNames.map((e=>this.ctx.measureText(e).width));return 4+Math.min(Math.max(...e),128)}draw({context:e,samples:t}){if(e.clearRect(0,0,e.canvas.width,e.canvas.height),e.fillStyle=ro(\"snow\"),e.fillRect(0,0,e.canvas.width,e.canvas.height),t&&t.names.length>0){const i=this.browser.sampleInfo.attributeNames,n=this.viewport.getBoundingClientRect().height;let r=1;const s=t.height;r=s-2*r<=1?0:1;let o=this.contentTop+t.yOffset;this.hitList={};for(const a of t.names){if(o>n)break;if(o+s>0){const t=this.browser.sampleInfo.getAttributes(a);if(t){const n=Object.entries(t);for(const t of n){const[n,a]=t;e.fillStyle=this.browser.sampleInfo.getAttributeColor(n,a);const c=8+i.indexOf(n)*Vu,l=o+r,h=s-2*r;e.fillRect(c,l,15,h);const d=`${Math.floor(c)}#${Math.floor(l)}#16#${Math.ceil(h)}`;this.hitList[d]=`${n}#${a}`}}}o+=s}}}renderSampleInfoColumns(e){const t=(e,t,i,n,r,s)=>{e.save(),e.font=\"10px verdana\",e.translate(i+r/2,n+s),e.rotate(-Math.PI/2),e.textAlign=\"left\",e.fillStyle=ro(\"lead\"),e.fillText(t,2,2),e.restore()},i=this.browser.sampleInfo.attributeNames;this.hitList={};for(let n=0;n<i.length;n++){const r=8+n*Vu,s=15,o=Math.round(e.canvas.height/window.devicePixelRatio);xo.fillRect(e,r,0,s,o,{fillStyle:ro(\"snow\")}),t(e,i[n],r,0,s,o);const a=`${Math.floor(r)}#0#${s}#${Math.ceil(o)}`;this.hitList[a]=`${i[n]}`}}renderSVGContext(e,{deltaX:t,deltaY:i}){if(\"function\"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:o,height:a}=this.viewport.getBoundingClientRect(),c=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_sample_names_guid_${s()}`;e.saveWithTranslationAndClipRect(c,t,i+r,o,a,-r),this.draw({context:e,samples:n}),e.restore()}}addMouseHandlers(){this.addMouseMoveHandler()}addMouseMoveHandler(){this.boundMouseMoveHandler=function(e){if(this.hitList){const t=Object.entries(this.hitList);if(null===this.viewport.previousElementSibling){const i=(t,i)=>{const{marginTop:n}=window.getComputedStyle(i),{x:r,y:s}=a(e,this.browser.columnContainer.querySelector(\".igv-sample-info-column\"));return{x:Math.floor(r),y:Math.floor(s-parseInt(n,10))}},n=this.browser.columnContainer.querySelector(\".igv-sample-info-column\"),{x:r,y:s}=i(n,this.viewport);n.setAttribute(\"title\",\"\");for(const[e,i]of t){const[t,o,a,c]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(r<t||r>t+a||s<o||s>o+c)){n.setAttribute(\"title\",`${i}`);break}}}else{const{x:i,y:n}=a(e,this.viewport);this.viewport.setAttribute(\"title\",\"\");for(const[e,r]of t){const[t,s,o,a]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(i<t||i>t+o||n<s||n>s+a)){const[e,t]=r.split(\"#\");this.viewport.setAttribute(\"title\",`${e.split(Uu.emptySpaceReplacement).join(\" \")}: ${\"-\"===t?\"\":t}`);break}}}}}.bind(this),this.viewport.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandlers(){this.viewport.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}show(){this.viewport.style.display=\"block\"}hide(){this.viewport.style.display=\"none\"}}class Ku{constructor(t,i,n,r){this.guid=s(),this.trackView=t,this.browser=t.browser,this.viewport=e({class:\"igv-viewport\"}),i.appendChild(this.viewport),t.track.height&&(this.viewport.style.height=`${t.track.height}px`),this.canvas=document.createElement(\"canvas\"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext(\"2d\"),this.trackScrollDelta=0,this.contentTop=0,this.hitList=void 0,this.sortDirection=1,this.setWidth(r),this.addMouseHandlers()}checkCanvas(){const e=this.browser.sampleNameViewportWidth||0;this.ctx.canvas.width=e*window.devicePixelRatio,this.ctx.canvas.style.width=`${e}px`,this.ctx.canvas.height=this.viewport.clientHeight*window.devicePixelRatio,this.ctx.canvas.style.height=`${this.viewport.clientHeight}px`,this.ctx.scale(window.devicePixelRatio,window.devicePixelRatio)}setTop(e){if(\"function\"==typeof this.trackView.track.getSamples){this.contentTop=e;const t=this.trackView.track.getSamples();this.repaint(t)}}setWidth(e){this.viewport.innerWidth=e,this.checkCanvas()}async repaint(e){if(e.names.length>0&&!0===this.browser.showSampleNames&&(this.checkCanvas(),this.draw({context:this.ctx,samples:e}),void 0===this.browser.sampleNameViewportWidth)){const t=e.names.map((e=>this.ctx.measureText(e).width));this.browser.sampleNameViewportWidth=Math.min(200,4+Math.ceil(Math.max(...t))),this.browser.layoutChange()}}draw({context:e,samples:t}){if(xo.fillRect(e,0,0,e.canvas.width,t.height,{fillStyle:ro(\"snow\")}),t&&t.names.length>0){const i=this.viewport.getBoundingClientRect().height,n=t.height,r=n-2<=1?0:1;let s=this.contentTop+t.yOffset;this.hitList={};for(const o of t.names){if(s>i)break;if(s+n>0){const t=n-2*r;Yu(e,o,0+2,s+r,e.canvas.width,t)}s+=n}}}renderSVGContext(e,{deltaX:t,deltaY:i}){if(\"function\"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:o,height:a}=this.viewport.getBoundingClientRect(),c=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_sample_names_guid_${s()}`;e.saveWithTranslationAndClipRect(c,t,i+r,o,a,-r),this.draw({context:e,samples:n}),e.restore()}}addMouseHandlers(){this.boundClickHandler=function(e){e.preventDefault();const t={label:\"Name Panel Width\",value:this.browser.sampleNameViewportWidth,callback:e=>{this.browser.sampleNameViewportWidth=parseInt(e),this.browser.layoutChange()}};this.browser.inputDialog.present(t,e)}.bind(this),this.viewport.addEventListener(\"contextmenu\",this.boundClickHandler),this.boundMouseMoveHandler=function(e){if(this.hitList){const t=Object.entries(this.hitList),{x:i,y:n}=a(e,this.viewport);this.viewport.setAttribute(\"title\",\"\");for(const[e,r]of t){const[t,s,o,a]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(i<t||i>t+o||n<s||n>s+a)){this.viewport.setAttribute(\"title\",`${r}`);break}}}}.bind(this),this.viewport.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandlers(){this.viewport.removeEventListener(\"contextmenu\",this.boundClickHandler),this.viewport.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}}function Yu(e,t,i,n,r,s){const o=Math.min(s,10);e.font=`${o}px sans-serif`,e.textAlign=\"start\",e.fillStyle=ro(\"lead\");const a=i,c=e.measureText(t),l=n+s/2+(c.actualBoundingBoxAscent+c.actualBoundingBoxDescent)/2;e.fillText(t,a,l)}class Xu{constructor(t){this.popover=e({class:\"igv-menu-popup\"}),t.appendChild(this.popover),this.parent=t;const i=e({class:\"igv-menu-popup-header\"});this.popover.appendChild(i),u(i,(()=>this.popover.style.display=\"none\")),this.popoverContent=e(),this.popover.appendChild(this.popoverContent),p(this.popover,i),i.addEventListener(\"click\",(e=>{e.stopPropagation(),e.preventDefault()})),this.popover.style.display=\"none\"}presentMenuList(e,t){if(Zu(this.parent),t.length>0){this.popoverContent.innerHTML=\"\";const i=this.parseMenuList(e,t);for(let e of i){e.init&&e.init();let t=e.object;0===i.indexOf(e)&&t.removeClass(\"igv-track-menu-border-top\"),t.hasClass(\"igv-track-menu-border-top\")||t.hasClass(\"igv-menu-popup-check-container\")||t.is(\"div\")&&t.addClass(\"igv-menu-popup-shim\"),this.popoverContent.appendChild(t.get(0))}this.popover.style.display=\"flex\";const{width:n}=this.popover.getBoundingClientRect();this.popover.style.left=-n+\"px\",this.popover.style.top=\"0px\"}}parseMenuList(e,t){return t.map(((t,i)=>{let n;if(t.name?(n=Bt(\"<div>\"),n.text(t.name)):t.object?n=t.object:\"string\"==typeof t.label?(n=Bt(\"<div>\"),n.html(t.label)):\"string\"==typeof t&&(n=t.startsWith(\"<\")?Bt(t):Bt(\"<div>\"+t+\"</div>\")),0===i&&n.addClass(\"igv-track-menu-border-top\"),t.click||t.dialog){const i=i=>{if(i.preventDefault(),i.stopPropagation(),t.click)if(e.track.selected){const n=e.browser.getSelectedTrackViews();if(!0===t.doAllMultiSelectedTracks)t.click.call(e.track,i);else if(\"removeTrack\"===t.menuItemType){const r=()=>{e.browser.overlayTrackButton.setVisibility(!1);for(const{track:e}of n)t.click.call(e,i)},s={html:`Are you sure you want to delete ${n.length} tracks?`,callback:r};e.browser.menuUtils.dialog.present(s,i)}else for(const{track:e}of n)t.click.call(e,i)}else t.click.call(e.track,i);else t.dialog&&t.dialog.call(e.track,i);this.popover.style.display=\"none\"};n.on(\"click\",i),n.on(\"touchend\",(e=>i(e))),n.on(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}return{object:n,init:t.init||void 0}}))}presentTrackContextMenu(t,n){this.popoverContent.innerHTML=\"\";const r=function(t,n){return t.map((t=>{let r;if(\"string\"==typeof t&&\"<hr/>\"===t)r=document.createElement(\"hr\");else if(\"string\"==typeof t)r=e({class:\"context-menu\"}),r.innerHTML=t;else if(\"Node\"==typeof t)r=t;else{if(\"function\"==typeof t.init&&t.init(),\"checkbox\"===t.type)r=Dl(\"Show all bases\",t.value);else if(\"color\"===t.type){const s=new Ra(n.parentElement);s.configure({color:\"grey\"}),r=e({class:\"context-menu\"}),\"string\"==typeof t.label&&(r.innerHTML=t.label);const o=e=>{s.show(),i(n),e.preventDefault(),e.stopPropagation()};r.addEventListener(\"click\",o),r.addEventListener(\"touchend\",o),r.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}else r=e({class:\"context-menu\"}),\"string\"==typeof t.label&&(r.innerHTML=t.label);if(t.click&&\"color\"!==t.type){function a(e){t.click(),i(n),e.preventDefault(),e.stopPropagation()}r.addEventListener(\"click\",a),r.addEventListener(\"touchend\",a),r.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}}return{el:r,init:t.init}}))}(n,this.popover);for(let{el:e}of r)this.popoverContent.appendChild(e);!function(e,t){t.style.display=\"flex\";const{x:i,y:n}=a(e,t.parentNode),{width:r}=t.getBoundingClientRect(),s=i+r,{width:o}=t.parentNode.getBoundingClientRect();t.style.left=`${s>o?i-(s-o):i}px`,t.style.top=`${n}px`}(t,this.popover)}hide(){this.popover.style.display=\"none\"}dispose(){this.popoverContent.innerHTML=\"\",this.popover.innerHTML=\"\",Object.keys(this).forEach((function(e){this[e]=void 0}))}}const Zu=e=>{const t=e.querySelectorAll(\".igv-menu-popup\");for(const e of t)e.style.display=\"none\"};class Ju{constructor(t,i,n,r,s,o,a){this.browser=i,this.button=e({class:\"igv-navbar-text-button\"}),t.appendChild(this.button),Array.isArray(n)?(this.textContent=n[0],this.title=n[1]):this.textContent=this.title=n,this.buttonLabel=r,this.imageDictionary={image:`url(\"data:image/svg+xml,${encodeURIComponent(s)}\")`,imageHover:`url(\"data:image/svg+xml,${encodeURIComponent(o)}\")`},this.responsiveKey=\"text\",this.configureButton(this.textContent,this.title),this.setState(a),i.on(\"navbar-resize\",(e=>{this.navbarResizeHandler(e)}))}navbarResizeHandler(e){const t=\"igv-navbar-icon-button\"===e?\"image\":\"text\";t!==this.responsiveKey&&(this.responsiveKey=t,this.configureButton(this.textContent,this.title),this.setState(void 0))}configureButton(e,t){this.groupElement=void 0,this.button.title=t,this.button.innerHTML=\"\",this.button.style.backgroundImage=\"none\",this.button.classList.remove(\"igv-navbar-icon-button\"),this.button.classList.remove(\"igv-navbar-text-button\"),\"text\"===this.responsiveKey?this.configureTextButton(e):this.configureIconButton()}configureTextButton(e){console.log(`text ${this.title}`),this.button.classList.add(\"igv-navbar-text-button\");const t=document.createElement(\"div\");t.innerHTML=this.buttonLabel;const i=t.firstChild;this.button.appendChild(i),this.groupElement=i.querySelector(\"#igv-navbar-button-group\");i.querySelector(\"#igv-navbar-button-label\").textContent=e}configureIconButton(){console.log(`icon ${this.title}`),this.button.classList.add(\"igv-navbar-icon-button\")}setState(e){void 0!==e&&(this.doHover=e),\"text\"===this.responsiveKey?this.setTextButtonState(this.doHover):this.setIconButtonState(this.doHover)}setTextButtonState(e){this.groupElement.classList.remove(...this.groupElement.classList);const t=!0===e?\"igv-navbar-text-button-svg-hover\":\"igv-navbar-text-button-svg-inactive\";this.groupElement.classList.add(t)}setIconButtonState(e){this.button.style.backgroundImage=!0===e?this.imageDictionary.imageHover:this.imageDictionary.image}show(){this.button.style.display=\"flex\"}hide(){this.button.style.display=\"none\"}setVisibility(e){!0===e?this.show():this.hide()}}const ef='<svg width=\"80px\" height=\"18px\" viewBox=\"0 0 80 18\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"igv-navbar-button-group\">\\n            <rect id=\"Rectangle\" x=\"0.5\" y=\"0.5\" width=\"79\" height=\"17\" rx=\"6\"></rect>\\n            <text id=\"igv-text-button-label\" x=\"50%\" y=\"50%\" dy=\".1em\" font-family=\"Helvetica\" font-size=\"12\" font-weight=\"normal\" letter-spacing=\"-0.372\">\\n                <tspan id=\"igv-navbar-button-label\"></tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>';class tf extends Hl{static defaults={autoscale:void 0,alpha:.5,height:50};constructor(e,t,i){super(e,t),this.type=\"merged\",this.paintAxis=cd,this.graphType=e.graphType,this.tracks=i||[]}async postInit(){if(this.config.tracks){for(let e of this.config.tracks){const t=await this.browser.createTrack(e);t?this.tracks.push(t):console.warn(\"Could not create track \"+e),\"function\"==typeof t.postInit&&await t.postInit()}this.config.tracks.every((e=>void 0!==e.autoscale||void 0!==e.max))||(this.config.autoscale=void 0===this.config.max)}for(let e of this.tracks)e.isMergedTrack=!0;if(this.config.autoscale?this.autoscale=this.config.autoscale:void 0!==this.config.max&&this.setDataRange({min:this.config.min||0,max:this.config.max}),void 0!==this.config.flipAxis)for(let e of this.tracks)e.flipAxis=this.config.flipAxis;if(void 0!==this.config.logScale)for(let e of this.tracks)e.logScale=this.config.logScale;this.resolutionAware=this.tracks.some((e=>e.resolutionAware))}set flipAxis(e){this.config.flipAxis=e;for(let t of rf(this.tracks))t.flipAxis=e}get flipAxis(){return rf(this.tracks).every((e=>e.flipAxis))}set logScale(e){this.config.logScale=e;for(let t of rf(this.tracks))t.logScale=e}get logScale(){return rf(this.tracks).every((e=>e.logScale))}get height(){return this._height}set height(e){if(this.config.height=e,this._height=e,this.tracks)for(let t of this.tracks)t.height=e,t.config.height=e}set autoscale(e){if(this._autoscale=e,!1===e&&this.tracks)for(let e of this.tracks)e.autoscale=!1}get autoscale(){return this._autoscale}set autoscaleGroup(e){if(this.tracks)for(let t of this.tracks)t.autoscaleGroup=e}get autoscaleGroup(){if(this.tracks&&this.tracks.length>0){const e=this.tracks[0].autoscaleGroup;return this.tracks.some((t=>e!==t.autoscaleGroup))?void 0:e}}setDataRange({min:e,max:t}){this.autoscale=!1;for(const i of rf(this.tracks))i.dataRange={min:e,max:t},i.autoscale=!1,i.autoscaleGroup=!1}set dataRange({min:e,max:t}){for(const i of rf(this.tracks))i.dataRange={min:e,max:t}}get dataRange(){if(this.tracks){const e=rf(this.tracks);if(e.length>0){const t=e[0].dataRange;if(e.every((e=>e.dataRange&&e.dataRange.min===t.min&&e.dataRange.max===t.max)))return t}}}menuItemList(){const e=[];return rf(this.tracks).length>0&&(void 0!==this.flipAxis&&e.push({label:\"Flip y-axis\",click:function(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),e.push(...this.numericDataMenuItems())),e.push(\"<hr/>\"),e.push(this.overlayTrackAlphaAdjustmentMenuItem()),e.push(this.trackSeparationMenuItem()),e}async getFeatures(e,t,i,n){const r=this.tracks.map((r=>r.getFeatures(e,t,i,n))),s=await Promise.all(r);if(s.every((e=>0===e.length)))return new nf([],[]);{const e=this.tracks.map((e=>e.name));return new nf(s,e)}}draw(e){const t=e.features;for(let i=0,n=this.tracks.length;i<n;i++){const n=Object.assign({},e);n.features=t.featureArrays[i],n.alpha=this.alpha,this.graphType&&(this.tracks[i].graphType=this.graphType),this.tracks[i].draw(n)}}popupData(e){const t=this.clickedFeatures(e);if(t&&t.length===this.tracks.length){const i=[];let n=!0;for(let r=0;r<t.length;r++)if(r>0&&i.push(\"<hr/>\"),i.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${t[r].trackName}</div>`),t[r].features.length>0){n=!1;const s=this.tracks[r].popupData(e,t[r].features);i.push(...s)}else i.push(\"Missing or 0 value(s)\");return!0===n?[]:i}}clickedFeatures(e){const t=e.viewport.cachedFeatures;if(!t||!t.featureArrays||!Array.isArray(t.featureArrays)||0===t.featureArrays.length)return[];const i=e.genomicLocation,n=[],r=e.referenceFrame.bpPerPixel>.2?3*e.referenceFrame.bpPerPixel:.2,s=i-r,o=i+r;for(let e=0;e<t.featureArrays.length;e++){const i=to(t.featureArrays[e],s,o);n.push({trackName:t.trackNames[e],features:i})}return n}get supportsWholeGenome(){return this.tracks.every((e=>e.supportsWholeGenome))}getState(){const e=super.getState(),t=[];for(let e of this.tracks)t.push(e.getState());return e.tracks=t,e}updateScales(e){let t;if(this.autoscale){t=!0;let i=[];for(let t of e){if(t.featureCache&&t.featureCache.features){const e=t.referenceFrame,n=e.start,r=n+e.toBP(t.getWidth()),s=t.featureCache.features;this.autoscale&&(i.push({value:s.getMax(n,r)}),i.push({value:s.getMin(n,r)}))}const e=qa(i);for(const t of rf(this.tracks))t.dataRange=e}}else{let i=-1;for(let n of this.tracks)if(++i,n.autoscale){t=!0;let r=[];for(let t of e)if(t.featureCache&&t.featureCache.features){const e=t.referenceFrame,n=e.start,s=n+e.toBP(t.getWidth()),o=t.featureCache.features.featureArrays[i];if(o)for(let e of o)if(!(e.end<n)){if(e.start>s)break;r.push(e)}}n.dataRange=qa(r)}}return t}overlayTrackAlphaAdjustmentMenuItem(){const t=e();return t.innerText=\"Set transparency\",{object:Bt(t),dialog:function(e){const t={label:\"Transparency\",value:this.alpha,min:0,max:1,scaleFactor:1e3,callback:e=>{this.alpha=Math.max(.001,e),this.repaintViews()}};this.browser.sliderDialog.present(t,e)}}}trackSeparationMenuItem(){const e=Bt(\"<div>\");return e.text(\"Separate tracks\"),{object:e,click:function(e){const t=this.autoscale,i=this.name,n=this.tracks,r=this.browser,s=this.order;r.removeTrack(this);for(let e of n)e.order=s,t&&(e.autoscaleGroup=i),e.isMergedTrack=!1,r.addTrack(e.config,e);r.updateViews()}}}}class nf{constructor(e,t){this.featureArrays=e,this.trackNames=t}getMax(e,t){let i=-Number.MAX_VALUE;for(let n of this.featureArrays)if(Array.isArray(n))for(let r of n)if(!(void 0===r.value||Number.isNaN(r.value)||r.end<e)){if(r.start>t)break;i=Math.max(i,r.value)}return i!==-Number.MAX_VALUE?i:100}getMin(e,t){let i=0;for(let n of this.featureArrays)if(Array.isArray(n))for(let r of n)if(void 0!==r.value&&!Number.isNaN(r.value)){if(r.end<e)continue;if(r.start>t)break;i=Math.min(i,r.value)}return i}}const rf=e=>e?e.filter((e=>void 0!==e.dataRange||void 0!==e.autoscale||void 0!==e.autoscaleGroup)):[];class sf extends Ju{constructor(e,t){super(e,t,\"Overlay Tracks\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>Overlay Tracks</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"Overlay-Tracks\">\\n            <rect id=\"backdrop\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"layer-group\" transform=\"translate(3, 127)\">\\n                <rect id=\"a\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#A1A1A1\" x=\"12\" y=\"12\" width=\"332\" height=\"139\"></rect>\\n                <rect id=\"a---hold-out\" fill=\"#A1A1A1\" x=\"9\" y=\"25\" width=\"324\" height=\"115\"></rect>\\n                <rect id=\"b\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#C9C9C9\" x=\"81\" y=\"103\" width=\"474\" height=\"139\"></rect>\\n                <rect id=\"c\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#ECECEC\" x=\"238\" y=\"214\" width=\"372\" height=\"139\"></rect>\\n                <rect id=\"c---hold-out\" fill=\"#ECECEC\" x=\"250\" y=\"226\" width=\"372\" height=\"115\"></rect>\\n            </g>\\n            <rect id=\"over-border\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>Overlay Tracks Hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"Overlay-Tracks-Hover\">\\n            <rect id=\"backdrop-copy\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"layer-group\" transform=\"translate(3, 127)\">\\n                <rect id=\"a\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#A1A1A1\" x=\"12\" y=\"12\" width=\"332\" height=\"139\"></rect>\\n                <rect id=\"a---hold-out\" fill=\"#A1A1A1\" x=\"9\" y=\"25\" width=\"324\" height=\"115\"></rect>\\n                <rect id=\"b\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#C9C9C9\" x=\"81\" y=\"103\" width=\"474\" height=\"139\"></rect>\\n                <rect id=\"c\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#ECECEC\" x=\"238\" y=\"214\" width=\"372\" height=\"139\"></rect>\\n                <rect id=\"c---hold-out\" fill=\"#ECECEC\" x=\"250\" y=\"226\" width=\"372\" height=\"115\"></rect>\\n            </g>\\n            <rect id=\"over-border-copy\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>',!1),this.button.addEventListener(\"mouseenter\",(()=>this.setState(!0))),this.button.addEventListener(\"mouseleave\",(()=>this.setState(!1)));this.boundMouseClickHandler=(()=>{this.setVisibility(!1),of.call(this)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(!0)}}function of(e){if(!0===af(this.browser)){const e=this.browser.getSelectedTrackViews().map((({track:e})=>e));for(const t of e)t.selected=!1;const t=[];for(let i of e)\"merged\"===i.type?t.push(...i.tracks):t.push(i);const i={name:\"Overlay\",type:\"merged\",autoscale:!1,alpha:.5,height:Math.max(...e.map((({height:e})=>e))),order:Math.min(...e.map((({order:e})=>e)))},n=new tf(i,this.browser,t);for(const t of e){const e=this.browser.trackViews.indexOf(t.trackView);this.browser.trackViews.splice(e,1),t.trackView.dispose()}this.browser.addTrack(i,n),n.trackView.updateViews()}}function af(e){const t=e.getSelectedTrackViews();if(t&&t.length>1){const e=new Set([\"wig\",\"merged\"]);return t.filter((({track:t})=>e.has(t.type))).length>1}return!1}const cf=new Set([\"sequence\",\"ruler\",\"ideogram\"]),lf=new Set([\"ruler\",\"sequence\",\"ideogram\"]);class hf{constructor(e,t,i){this.namespace=`trackview-${s()}`,this.browser=e,this.track=i,i.trackView=this,this.addDOMToColumnContainer(e,t,e.referenceFrameList)}startSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].startSpinner()}stopSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].stopSpinner()}addDOMToColumnContainer(e,t,i){this.axis=this.createAxis(e,this.track),this.createViewports(e,t,i),this.sampleInfoViewport=new $u(this,e.columnContainer.querySelector(\".igv-sample-info-column\"),e.getSampleInfoViewportWidth()),this.sampleNameViewport=new Ku(this,e.columnContainer.querySelector(\".igv-sample-name-column\"),void 0,e.getSampleNameViewportWidth()),this.createTrackScrollbar(e),this.createTrackDragHandle(e),this.createTrackGearPopup(e)}createViewports(e,t,i){this.viewports=[];const n=e.calculateViewportWidth(i.length),r=t.querySelectorAll(\".igv-column\");for(let e=0;e<r.length;e++){const t=zu(this,r[e],i[e],n);this.viewports.push(t)}}createAxis(t,i){const n=e();if(this.axis=n,t.columnContainer.querySelector(\".igv-axis-column\").appendChild(n),n.dataset.tracktype=i.type,n.style.height=`${i.height}px`,\"function\"==typeof i.paintAxis){const{width:e,height:t}=n.getBoundingClientRect();this.axisCanvas=document.createElement(\"canvas\"),this.axisCanvas.style.width=`${e}px`,this.axisCanvas.style.height=`${t}px`,n.appendChild(this.axisCanvas)}if(!1===mo.has(this.track.type)){this.trackSelectionContainer=e(),n.appendChild(this.trackSelectionContainer);const t='<input type=\"checkbox\" name=\"track-select\">',i=document.createRange().createContextualFragment(t).firstChild;this.trackSelectionContainer.appendChild(i),i.checked=this.track.selected||!1,i.addEventListener(\"change\",(e=>{e.preventDefault(),e.stopPropagation(),this.track.selected=e.target.checked,this.setDragHandleSelectionState(e.target.checked),this.browser.overlayTrackButton.setVisibility(af(this.browser))})),this.enableTrackSelection(!1)}return n}resizeAxisCanvas(e,t){this.axis.style.width=`${e}px`,this.axis.style.height=`${t}px`,\"function\"==typeof this.track.paintAxis&&(this.axisCanvas.style.width=`${e}px`,this.axisCanvas.style.height=`${t}px`)}renderSVGContext(e,{deltaX:t,deltaY:i}){!function(e,t,i,n,r){if(\"function\"==typeof t.paintAxis){const{y:o,width:a,height:c}=i.getBoundingClientRect(),l=`${(t.name||t.id).replace(/\\W/g,\"\")}_axis_guid_${s()}`;e.saveWithTranslationAndClipRect(l,n,o+r,a,c,0),t.paintAxis(e,a,c),e.restore()}}(e,this.track,this.axisCanvas,t,i);const{width:n}=this.axis.getBoundingClientRect(),{y:r}=this.viewports[0].$viewport.get(0).getBoundingClientRect();let o={deltaX:n+t,deltaY:r+i};for(let t of this.viewports){t.renderSVGContext(e,o);const{width:i}=t.$viewport.get(0).getBoundingClientRect();o.deltaX+=i}if(!0===this.browser.sampleInfo.isInitialized()&&!0===this.browser.sampleInfoControl.showSampleInfo){this.sampleInfoViewport.renderSVGContext(e,o);const{width:t}=this.sampleInfoViewport.viewport.getBoundingClientRect();o.deltaX+=t}!0===this.browser.showSampleNames&&this.sampleNameViewport.renderSVGContext(e,o)}presentColorPicker(e){if(!1===lf.has(this.track.type)){const t=[],i=this.track.color||this.track.defaultColor;Mt(i)&&t.push(i),this.track.altColor&&Mt(this.track.altColor)&&t.push(this.track.altColor);let n=t.map((e=>e.startsWith(\"#\")?e:e.startsWith(\"rgb(\")?_s.rgbToHex(e):_s.colorNameToHex(e))),r={color:e=>{this.track.color=io(e),this.repaintViews()},altColor:e=>{this.track.altColor=io(e),this.repaintViews()}};const s=this.browser.getSelectedTrackViews();s.length>0&&new Set(s).has(this)?(r={color:e=>{for(let t of s)t.track.color=e,t.repaintViews()}},this.browser.genericColorPicker.configure(n,r)):this.browser.genericColorPicker.configure(n,r),this.browser.genericColorPicker.setActiveColorHandler(e),this.browser.genericColorPicker.show()}}setTrackHeight(e,t){t||(this.track.minHeight&&(e=Math.max(this.track.minHeight,e)),this.track.maxHeight&&(e=Math.min(this.track.maxHeight,e))),this.track.height=e,this.resizeAxisCanvas(this.axis.clientWidth,this.track.height),\"function\"==typeof this.track.paintAxis&&this.paintAxis();for(let{$viewport:t}of this.viewports)t.height(e);if(this.sampleInfoViewport.setHeight(e),this.sampleNameViewport.viewport.style.height=`${e}px`,\"function\"!=typeof this.track.computePixelHeight)for(let t of this.viewports)t.setContentHeight(e);this.repaintViews(),this.updateScrollbar(),this.dragHandle.style.height=`${e}px`,this.gearContainer.style.height=`${e}px`}updateScrollbar(){const e=this.viewports[0].$viewport.height();if(this.outerScroll.style.height=`${e}px`,!1===cf.has(this.track.type)){const t=this.maxViewportContentHeight(),i=Math.round(e/t*e);t>e?(this.innerScroll.style.display=\"block\",this.innerScroll.style.height=`${i}px`):this.innerScroll.style.display=\"none\"}}moveScroller(e){const t=Bt(this.innerScroll).position().top+e,i=Math.min(Math.max(0,t),this.outerScroll.clientHeight-this.innerScroll.clientHeight);Bt(this.innerScroll).css(\"top\",`${i}px`);const n=this.maxViewportContentHeight(),r=-Math.round(i*(n/this.viewports[0].$viewport.height()));for(let e of this.viewports)e.setTop(r);this.sampleInfoViewport.setTop(r),this.sampleNameViewport.trackScrollDelta=e,this.sampleNameViewport.setTop(r)}isLoading(){for(let e of this.viewports)if(e.isLoading())return!0}repaintViews(){for(let e of this.viewports)e.isVisible()&&e.repaint();\"function\"==typeof this.track.paintAxis&&this.paintAxis(),this.repaintSampleInfo(),this.repaintSamples()}repaintSampleInfo(){this.sampleInfoViewport.repaint()}repaintSamples(){if(\"function\"==typeof this.track.getSamples){const e=this.track.getSamples();e.names&&e.names.length>0&&this.sampleNameViewport.repaint(e)}}setTrackLabelName(e){this.viewports.forEach((t=>t.setTrackLabel(e)))}resize(e){for(let t of this.viewports)t.setWidth(e)}async updateViews(){if(!this.browser||!this.browser.referenceFrameList)return;const e=this.viewports.filter((e=>e.isVisible()));if(e.forEach((e=>e.shift())),this.browser.dragObject)return;const t=e.filter((e=>e.needsRepaint())).filter((e=>e.checkZoomIn())),i=e.filter((e=>e.checkZoomIn())).filter((e=>e.needsReload()));for(let e of i)await e.loadFeatures();if(this.disposed)return;if(this.track&&\"function\"==typeof this.track.variantRowCount&&i.length>0){let e=0;for(let t of this.viewports)t.featureCache&&t.featureCache.features&&(e=Math.max(e,t.featureCache.features.reduce(((e,t)=>Math.max(e,t.row||0)),0)));if(this.track.nVariantRows!==e+1){this.track.variantRowCount(e+1);for(let e of this.viewports)e.checkContentHeight()}}let n;if(\"merged\"===this.track.type)n=this.track.updateScales(e);else if(this.track.autoscale){let t=[];for(let i of e){const e=i.referenceFrame,n=e.start,r=n+e.toBP(i.getWidth());if(i.featureCache&&i.featureCache.features)if(\"function\"==typeof i.featureCache.features.getMax){const e=i.featureCache.features.getMax(n,r);if(t.push({value:e}),\"function\"==typeof i.featureCache.features.getMin){const e=i.featureCache.features.getMin(n,r);t.push({value:e})}}else{const e=to(i.featureCache.features,n,r);for(let i of e)t.push(i)}}\"function\"==typeof this.track.doAutoscale?this.track.dataRange=this.track.doAutoscale(t):this.track.dataRange=qa(t)}const r=this.track.autoscale||this.track.autoscaleGroup||\"ruler\"===this.track.type||n||this.track.groupBy;for(let i of e)t.includes(i)?i.repaint():r&&i.refresh();this.adjustTrackHeight(),this.repaintSampleInfo(),this.repaintSamples(),this.updateRulerViewportLabels()}clearCachedFeatures(){for(let e of this.viewports)e.clearCache()}updateRulerViewportLabels(){const e=this.browser.calculateViewportWidth(this.viewports.length);for(let t of this.viewports)\"ruler\"===this.track.type&&(this.viewports.length>1?t.presentLocusLabel(e):t.dismissLocusLabel())}async getInViewFeatures(){if(!this.browser||!this.browser.referenceFrameList)return[];let e=[];const t=this.viewports.filter((e=>e.isVisible()));for(let i of t){const t=i.referenceFrame,{chr:n,start:r,bpPerPixel:s}=i.referenceFrame,o=r+t.toBP(i.getWidth());if((!i.featureCache||!i.featureCache.containsRange(n,r,o,s))&&await i.loadFeatures(),i.featureCache&&i.featureCache.features)if(\"function\"==typeof i.featureCache.features.getMax){const t=i.featureCache.features.getMax(r,o);e.push({value:t})}else{const t=\"function\"==typeof i.featureCache.queryFeatures?i.featureCache.queryFeatures(n,r,o):to(i.featureCache.features,r,o);e=e.concat(t)}}return e}checkContentHeight(){for(let e of this.viewports)e.checkContentHeight();this.adjustTrackHeight()}adjustTrackHeight(){var e=this.maxViewportContentHeight();if(this.track.autoHeight?this.setTrackHeight(e,!1):this.track.paintAxis&&this.paintAxis(),!1===cf.has(this.track.type)){const t=this.viewports[0].getContentTop(),i=this.viewports[0].$viewport.height(),n=Math.min(0,i-e);if(t<n)for(let e of this.viewports)e.setTop(n);this.updateScrollbar()}}viewportsToReload(e){return this.viewports.filter((t=>{if(!t.isVisible())return!1;if(t.checkZoomIn()){const i=t.referenceFrame,n=t.referenceFrame.chr,r=i.start,s=r+i.toBP(Bt(t.contentDiv).width()),o=i.bpPerPixel;return e||!t.tile||t.tile.invalidate||!t.tile.containsRange(n,r,s,o)}return!1}))}createTrackScrollbar(t){const i=e();if(t.columnContainer.querySelector(\".igv-scrollbar-column\").appendChild(i),i.style.height=`${this.track.height}px`,this.outerScroll=i,!1===cf.has(this.track.type)){const n=e();i.appendChild(n),this.innerScroll=n,this.addTrackScrollMouseHandlers(t)}}createTrackDragHandle(t){\"sequence\"!==this.track.type&&!0===mo.has(this.track.type)?this.dragHandle=e({class:\"igv-track-drag-shim\"}):(this.dragHandle=e({class:\"igv-track-drag-handle\"}),this.dragHandle.classList.add(\"igv-track-drag-handle-color\")),t.columnContainer.querySelector(\".igv-track-drag-column\").appendChild(this.dragHandle),this.dragHandle.style.height=`${this.track.height}px`,this.addTrackDragMouseHandlers(t)}createTrackGearPopup(t){if(this.gearContainer=e(),t.columnContainer.querySelector(\".igv-gear-menu-column\").appendChild(this.gearContainer),this.gearContainer.style.height=`${this.track.height}px`,!0===this.track.ignoreTrackMenu);else{function i(e){if(e.preventDefault(),e.stopPropagation(),\"none\"===this.trackGearPopup.popover.style.display){for(const e of t.trackViews.filter((e=>e!==this&&void 0!==e.trackGearPopup)))e.trackGearPopup.popover.style.display=\"none\";this.trackGearPopup.presentMenuList(this,t.menuUtils.trackMenuItemList(this))}else this.trackGearPopup.popover.style.display=\"none\"}this.gear=e(),this.gearContainer.appendChild(this.gear),this.gear.appendChild(l(\"cog\")),this.trackGearPopup=new Xu(this.gear),this.boundTrackGearClickHandler=i.bind(this),this.gear.addEventListener(\"click\",this.boundTrackGearClickHandler)}}addTrackScrollMouseHandlers(e){this.boundTrackScrollMouseDownHandler=function(t){t.stopPropagation();const{y:i}=r(t);Bt(this.innerScroll).data(\"yDown\",i.toString()),this.boundColumnContainerMouseMoveHandler=function(e){e.stopPropagation();const{y:t}=r(e);this.moveScroller(t-parseInt(Bt(this.innerScroll).data(\"yDown\"))),Bt(this.innerScroll).data(\"yDown\",t.toString())}.bind(this),e.columnContainer.addEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler)}.bind(this),this.innerScroll.addEventListener(\"mousedown\",this.boundTrackScrollMouseDownHandler),this.boundColumnContainerMouseUpHandler=function(t){e.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler)}.bind(this),e.columnContainer.addEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),e.columnContainer.addEventListener(\"mouseleave\",this.boundColumnContainerMouseUpHandler)}removeTrackScrollMouseHandlers(){!1===cf.has(this.track.type)&&(this.innerScroll.removeEventListener(\"mousedown\",this.boundTrackScrollMouseDownHandler),this.browser.columnContainer.removeEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.browser.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.browser.columnContainer.removeEventListener(\"mouseleave\",this.boundColumnContainerMouseMoveHandler))}addTrackDragMouseHandlers(e){if(\"sequence\"===this.track.type||!1===mo.has(this.track.type)){let t;function i(i){i.preventDefault(),t=i.target,!1===this.track.selected&&(t.classList.remove(\"igv-track-drag-handle-color\"),t.classList.add(\"igv-track-drag-handle-hover-color\")),e.startTrackDrag(this)}function n(i){e.endTrackDrag(),t&&i.target!==t&&!1===this.track.selected&&(t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.add(\"igv-track-drag-handle-color\")),t=void 0}function r(i){i.preventDefault(),void 0===t&&!1===this.track.selected&&(i.target.classList.remove(\"igv-track-drag-handle-color\"),i.target.classList.add(\"igv-track-drag-handle-hover-color\")),e.updateTrackDrag(this)}function s(e){e.preventDefault(),void 0===t&&!1===this.track.selected&&(e.target.classList.remove(\"igv-track-drag-handle-hover-color\"),e.target.classList.add(\"igv-track-drag-handle-color\"))}this.boundTrackDragMouseDownHandler=i.bind(this),this.dragHandle.addEventListener(\"mousedown\",this.boundTrackDragMouseDownHandler),this.boundDocumentTrackDragMouseUpHandler=n.bind(this),document.addEventListener(\"mouseup\",this.boundDocumentTrackDragMouseUpHandler),this.boundTrackDragMouseEnterHandler=r.bind(this),this.dragHandle.addEventListener(\"mouseenter\",this.boundTrackDragMouseEnterHandler),this.dragHandle.addEventListener(\"mouseout\",(e=>{e.preventDefault(),void 0===t&&!1===this.track.selected&&(e.target.classList.remove(\"igv-track-drag-handle-hover-color\"),e.target.classList.add(\"igv-track-drag-handle-color\"))})),this.boundTrackDragMouseOutHandler=s.bind(this),this.dragHandle.addEventListener(\"mouseout\",this.boundTrackDragMouseOutHandler)}}removeTrackDragMouseHandlers(){\"ideogram\"===this.track.type||\"ruler\"===this.track.type||(this.dragHandle.removeEventListener(\"mousedown\",this.boundTrackDragMouseDownHandler),document.removeEventListener(\"mouseup\",this.boundDocumentTrackDragMouseUpHandler),this.dragHandle.removeEventListener(\"mouseup\",this.boundTrackDragMouseEnterHandler),this.dragHandle.removeEventListener(\"mouseout\",this.boundTrackDragMouseOutHandler))}removeTrackGearMouseHandlers(){!0===this.track.ignoreTrackMenu||this.gear.removeEventListener(\"click\",this.boundTrackGearClickHandler)}removeDOMFromColumnContainer(){this.axis.remove(),this.removeViewportsFromColumnContainer(),this.sampleInfoViewport.dispose(),this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove()}removeViewportsFromColumnContainer(){for(let e of this.viewports)e.$viewport.remove()}dispose(){this.axis.remove();for(let e of this.viewports)e.dispose();this.sampleInfoViewport.dispose(),this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove(),\"function\"==typeof this.track.dispose&&this.track.dispose();for(let e of Object.keys(this))this[e]=void 0;this.alert&&this.alert.container.remove(),this.disposed=!0}paintAxis(){if(\"function\"==typeof this.track.paintAxis){const{width:e,height:t}=this.axisCanvas.getBoundingClientRect(),i=window.devicePixelRatio||1;this.axisCanvas.height=i*t,this.axisCanvas.width=i*e;const n=this.axisCanvas.getContext(\"2d\");if(n.scale(i,i),this.track.autoscaleGroup){if(void 0===wo[this.track.autoscaleGroup]){const e=so.Dark2,t=Math.floor(Math.random()*so.Dark2.length);wo[this.track.autoscaleGroup]=e[t]}const i=_s.addAlpha(wo[this.track.autoscaleGroup],.75);this.track.paintAxis(n,e,t,i)}else this.track.paintAxis(n,e,t,void 0)}}maxViewportContentHeight(){return Math.max(...this.viewports.map((e=>e.getContentHeight())))}enableTrackSelection(e){const t=this.trackSelectionContainer;if(t&&!mo.has(this.track.type))if(!1!==e)t.style.display=\"grid\";else{this.track.selected=!1;t.querySelector(\"[name=track-select]\").checked=this.track.selected,this.dragHandle&&this.setDragHandleSelectionState(!1),t.style.display=\"none\"}}setDragHandleSelectionState(e){const t=this.dragHandle;e?(t.classList.remove(\"igv-track-drag-handle-color\"),t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.add(\"igv-track-drag-handle-selected-color\")):(t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.remove(\"igv-track-drag-handle-selected-color\"),t.classList.add(\"igv-track-drag-handle-color\"))}}function df(e){this.thresholds=e.thresholds,this.colors=e.colors}function uf(e){this.scale=e,this.lowColor=\"rgb(\"+e.lowR+\",\"+e.lowG+\",\"+e.lowB+\")\",this.highColor=\"rgb(\"+e.highR+\",\"+e.highG+\",\"+e.highB+\")\",this.diff=e.high-e.low}df.prototype.getColor=function(e){for(let t of this.thresholds)if(e<t)return this.colors[this.thresholds.indexOf(t)];return this.colors[this.colors.length-1]},uf.prototype.getColor=function(e){var t,i=this.scale;return e<=i.low?this.lowColor:e>=i.high?this.highColor:(t=(e-i.low)/this.diff,\"rgb(\"+Math.floor(i.lowR+t*(i.highR-i.lowR))+\",\"+Math.floor(i.lowG+t*(i.highG-i.lowG))+\",\"+Math.floor(i.lowB+t*(i.highB-i.lowB))+\")\")};class ff{constructor(e){this.color=e}getColor(){return this.color}}const pf={threshold:2e3,r:0,g:0,b:255};class gf{constructor(e){e=e||pf,this.threshold=e.threshold,this.r=e.r,this.g=e.g,this.b=e.b,this.cache=[],this.nbins=2e3,this.binsize=this.threshold/this.nbins}setThreshold(e){this.threshold=e,this.cache=[],this.binsize=this.threshold/this.nbins}getThreshold(){return this.threshold}setColorComponents(e){this.r=e.r,this.g=e.g,this.b=e.b,this.cache=[]}getColorComponents(){return{r:this.r,g:this.g,b:this.b}}equals(e){return JSON.stringify(this)===JSON.stringify(e)}getColor(e){const t=Math.floor(Math.min(this.threshold,e)/this.binsize);if(void 0===this.cache[t]){const i=(ys.clamp(e,0,this.threshold)-0)/(this.threshold-0);this.cache[t]=`rgba(${this.r},${this.g},${this.b}, ${i})`}return this.cache[t]}stringify(){return this.threshold+\",\"+this.r+\",\"+this.g+\",\"+this.b}static parse(e){var t,i;return e.startsWith(\"R:\")?(t=e.substring(2).split(\":\"),(i=new RatioColorScale(Number.parseFloat(t[0]))).positiveScale=n(t[1]),i.negativeScale=n(t[2]),i):n(e);function n(e){var t,i;return t={threshold:(i=e.split(\",\"))[0],r:i[1],g:i[2],b:i[3]},new gf(t)}}}class mf{constructor(e){this.config=e,this.url=e.path||e.url}async read(e,t){const i={start:e,size:t};return Qs.loadArrayBuffer(this.url,{range:i})}}class wf{constructor(e){this.file=e}async read(e,t){const i=this.file;return void 0!==e?i.slice(e,e+t).arrayBuffer():i.arrayBuffer()}}class bf{constructor(e,t){this.file=e,this.rateLimiter=t}async read(e,t){const i=this.file,n=this.rateLimiter;return new Promise((function(r,s){n.limiter((async function(i){try{const n=await i.read(e,t);r(n)}catch(e){s(e)}}))(i)}))}}class Ff{constructor(e){this.file=e.file,this.size=e.size||64e3,this.position=0,this.bufferStart=0,this.bufferLength=0,this.buffer=void 0}async read(e,t){const i=e,n=e+t,r=this.bufferStart,s=this.bufferStart+this.bufferLength;if(t>this.size)return this.buffer=void 0,this.bufferStart=0,this.bufferLength=0,this.file.read(e,t);if(i>=r&&n<=s){const e=i-r,n=e+t;return this.buffer.slice(e,n)}if(i<r&&n>r){const n=r-i,s=await this.file.read(e,n),o=t-n;if(o>0){const e=this.buffer.slice(0,o);return vf(s,e)}return s}if(!(i<s&&n>s))return this.buffer=await this.file.read(e,this.size),this.bufferStart=e,this.bufferLength=this.buffer.byteLength,this.buffer.slice(0,t);{const e=s-i,n=this.bufferLength-e,r=this.buffer.slice(n,this.bufferLength),o=t-e;if(!(o>0))return r;try{this.buffer=await this.file.read(s,this.size),this.bufferStart=s,this.bufferLength=this.buffer.byteLength;const e=this.buffer.slice(0,o);return vf(r,e)}catch(e){if(e.code&&416===e.code)return r;throw e}}}}var vf=function(e,t){var i=new Uint8Array(e.byteLength+t.byteLength);return i.set(new Uint8Array(e),0),i.set(new Uint8Array(t),e.byteLength),i.buffer};const yf=function(e,t){this.littleEndian=void 0===t||t,this.position=0,this.view=e,this.length=e.byteLength};function Af(e,t){this.block=e,this.offset=t}yf.prototype.available=function(){return this.length-this.position},yf.prototype.remLength=function(){return this.length-this.position},yf.prototype.hasNext=function(){return this.position<this.length-1},yf.prototype.getByte=function(){var e=this.view.getUint8(this.position,this.littleEndian);return this.position++,e},yf.prototype.getShort=function(){var e=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,e},yf.prototype.getUShort=function(){var e=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,e},yf.prototype.getInt=function(){var e=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getUInt=function(){var e=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getLong=function(){var e=[];e[0]=this.view.getUint8(this.position),e[1]=this.view.getUint8(this.position+1),e[2]=this.view.getUint8(this.position+2),e[3]=this.view.getUint8(this.position+3),e[4]=this.view.getUint8(this.position+4),e[5]=this.view.getUint8(this.position+5),e[6]=this.view.getUint8(this.position+6),e[7]=this.view.getUint8(this.position+7);var t=0;if(this.littleEndian)for(var i=e.length-1;i>=0;i--)t=256*t+e[i];else for(i=0;i<e.length;i++)t=256*t+e[i];return this.position+=8,t},yf.prototype.getString=function(e){for(var t,i=\"\";0!=(t=this.view.getUint8(this.position++))&&(i+=String.fromCharCode(t),!e||i.length!=e););return i},yf.prototype.getFixedLengthString=function(e){var t,i,n=\"\";for(t=0;t<e;t++)(i=this.view.getUint8(this.position++))>0&&(n+=String.fromCharCode(i));return n},yf.prototype.getFixedLengthTrimmedString=function(e){var t,i,n=\"\";for(t=0;t<e;t++)(i=this.view.getUint8(this.position++))>32&&(n+=String.fromCharCode(i));return n},yf.prototype.getFloat=function(){var e=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getDouble=function(){var e=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,e},yf.prototype.skip=function(e){return this.position+=e,this.position},yf.prototype.getVPointer=function(){var e=this.position,t=this.view.getUint8(e+1)<<8|this.view.getUint8(e),i=4294967296*(255&this.view.getUint8(e+6))+16777216*(255&this.view.getUint8(e+5))+65536*(255&this.view.getUint8(e+4))+256*(255&this.view.getUint8(e+3))+(255&this.view.getUint8(e+2));return this.position+=8,new Af(i,t)},Af.prototype.isLessThan=function(e){return this.block<e.block||this.block===e.block&&this.offset<e.offset},Af.prototype.isGreaterThan=function(e){return this.block>e.block||this.block===e.block&&this.offset>e.offset},Af.prototype.print=function(){return this.block+\":\"+this.offset};class Cf{constructor(e,t){this.chr1=e,this.chr2=t}getKey(){return this.chr1.name+\"_\"+this.chr2.name+\"_\"+this.zoom.unit+\"_\"+this.zoom.binSize}getBlockNumbers(e,t,i){if(e.chr==this.chr2&&t.chr===this.chr1){const i=e;e=t,t=i}const n=this.chr1===this.chr2,r=this.zoom.binSize,s=this.blockBinCount,o=this.blockColumnCount;return i<9||!n?function(){const i=e.start/r,a=e.end/r,c=t.start/r,l=t.end/r,h=Math.floor(i/s),d=Math.floor((a-1)/s),u=Math.floor(c/s),f=Math.floor((l-1)/s),p=[];for(let e=u;e<=f;e++)for(let t=h;t<=d;t++){let i;i=n&&e<t?t*o+e:e*o+t,p.includes(i)||p.push(i)}return p}():function(){const i=e.start/r,n=e.end/r,a=t.start/r,c=t.end/r,l=Math.floor((i+a)/2/s),h=Math.floor((n+c)/2/s),d=Math.floor(Math.log2(1+Math.abs(i-c)/Math.sqrt(2)/s)),u=Math.floor(Math.log2(1+Math.abs(n-a)/Math.sqrt(2)/s)),f=(n-a)*(i-c)<0?0:Math.min(d,u),p=Math.max(d,u),g=[];for(let e=f;e<=p;e++)for(let t=l;t<=h;t++){const i=e*o+t;g.push(i)}return g}()}static parseMatrixZoomData(e,t,i){const n=new Cf(e,t),r=i.getString(),s=i.getInt(),o=i.getFloat(),a=i.getFloat(),c=i.getFloat(),l=i.getFloat(),h=i.getInt();n.blockBinCount=i.getInt(),n.blockColumnCount=i.getInt();const d=i.getInt();n.zoom={index:s,unit:r,binSize:h},n.blockIndex=new _f(d,i);const u=o/(e.size/h)/(t.size/h);return n.averageCount=u,n.sumCounts=o,n.stdDev=c,n.occupiedCellCount=a,n.percent95=l,n}}class _f{constructor(e,t){for(this.blockIndex={};e-- >0;){const e=t.getInt(),i=t.getLong(),n=t.getInt();this.blockIndex[e]={filePosition:i,size:n}}}getBlockIndexEntry(e){return this.blockIndex[e]}}class xf{constructor(e,t,i){this.chr1=e,this.chr2=t,this.bpZoomData=[],this.fragZoomData=[];for(let e of i)\"BP\"===e.zoom.unit?this.bpZoomData.push(e):this.fragZoomData.push(e)}findZoomForResolution(e,t){const i=\"FRAG\"===t?this.fragZoomData:this.bpZoomData;for(let t=1;t<i.length;t++){if(i[t].zoom.binSize<e)return t-1}return i.length-1}getZoomData(e,t){const i=\"BP\"===(t=t||\"BP\")?this.bpZoomData:this.fragZoomData;for(let t=0;t<i.length;t++){var n=i[t];if(e===n.zoom.binSize)return n}}getZoomDataByIndex(e,t){return(\"FRAG\"===t?this.fragZoomData:this.bpZoomData)[e]}static getKey(e,t){if(e>t){const i=e;e=t,t=i}return`${e}_${t}`}static parseMatrix(e,t){const i=new yf(new DataView(e)),n=i.getInt(),r=i.getInt(),s=t[n],o=t[r];let a=i.getInt();const c=[];for(;a-- >0;){const e=Cf.parseMatrixZoomData(s,o,i);c.push(e)}return new xf(n,r,c)}}class kf{constructor(e,t,i){this.bin1=e,this.bin2=t,this.counts=i}getKey(){return this.bin1+\"_\"+this.bin2}}class If{constructor(e=10){this.max=e,this.map=new Map}get(e){let t=this.map.get(e);return t&&(this.map.delete(e),this.map.set(e,t)),t}set(e,t){this.map.has(e)?this.map.delete(e):this.map.size===this.max&&this.map.delete(this.first()),this.map.set(e,t)}has(e){return this.map.has(e)}clear(){this.map.clear()}first(){return this.map.keys().next().value}}class Sf{constructor(e,t,i,n){this.file=e,this.filePosition=t,this.nValues=i,this.dataType=n,this.cache=void 0}async getValues(e,t){if(!this.cache||e<this.cache.start||t>this.cache.end){const i=Math.max(0,e-1e3),n=Math.min(this.nValues,t+1e3),r=this.filePosition+i*this.dataType,s=n-i,o=s*this.dataType,a=await this.file.read(r,o);if(!a)return;const c=new yf(new DataView(a)),l=[];for(let e=0;e<s;e++)l[e]=8===this.dataType?c.getDouble():c.getFloat();this.cache={start:i,end:n,values:l}}const i=e-this.cache.start,n=i+(t-e);return this.cache.values.slice(i,n)}getKey(){return Sf.getKey(this.type,this.chrIdx,this.unit,this.resolution)}static getNormalizationVectorKey(e,t,i,n){return e+\"_\"+t+\"_\"+i+\"_\"+n}}var 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mf(e);(t=this.url).indexOf(\"drive.google.com\")>=0||t.indexOf(\"www.googleapis.com/drive\")>0?this.file=new bf(i,Bf):this.file=i}}var t}async init(){this.initialized||(await this.readHeaderAndFooter(),this.initialized=!0)}async getVersion(){if(void 0===this.version){const e=await this.file.read(0,128);if(!e)return;const t=new yf(new DataView(e));return this.magic=t.getString(),this.version=t.getInt(),this.version}return this.version}async getMetaData(){return await this.init(),this.meta}async readHeaderAndFooter(){let e=await this.file.read(0,16);if(!e||0===e.byteLength)throw Error(\"File content is empty\");let t=new yf(new DataView(e));if(this.magic=t.getString(),this.version=t.getInt(),this.version<5)throw Error(\"Unsupported hic version: \"+this.version);this.footerPosition=t.getLong(),await this.readFooter();const i=Object.values(this.masterIndex).reduce(((e,t)=>Math.min(e,t.start)),Number.MAX_VALUE)-16;e=await this.file.read(16,i),t=new yf(new DataView(e)),this.genomeId=t.getString(),this.version>=9&&(this.normVectorIndexPosition=t.getLong(),this.normVectorIndexSize=t.getLong()),this.attributes={};let n=t.getInt();for(;n-- >0;)this.attributes[t.getString()]=t.getString();this.chromosomes=[],this.chromosomeIndexMap={};let r=t.getInt(),s=0;for(;r-- >0;){const e={index:s,name:t.getString(),size:this.version<9?t.getInt():t.getLong()};\"all\"===e.name.toLowerCase()&&(this.wholeGenomeChromosome=e,this.wholeGenomeResolution=Math.round(2*e.size)),this.chromosomes.push(e),this.chromosomeIndexMap[e.name]=e.index,s++}this.bpResolutions=[];let o=t.getInt();for(;o-- >0;)this.bpResolutions.push(t.getInt());if(this.loadFragData){this.fragResolutions=[];let e=t.getInt();if(e>0)for(;e-- >0;)this.fragResolutions.push(t.getInt())}this.chrAliasTable={};for(let e of Object.keys(this.chromosomeIndexMap))e.startsWith(\"chr\")?this.chrAliasTable[e.substr(3)]=e:\"MT\"===e?this.chrAliasTable.chrM=e:this.chrAliasTable[\"chr\"+e]=e;this.meta={version:this.version,genome:this.genomeId,chromosomes:this.chromosomes,resolutions:this.bpResolutions}}async readFooter(){const e=this.version<9?8:12;let t=await this.file.read(this.footerPosition,e);if(!t)return null;let i=new yf(new DataView(t));const n=this.version<9?i.getInt():i.getLong();let r=i.getInt();const s=196*r;for(t=await this.file.read(this.footerPosition+e,Math.min(s,n)),i=new yf(new DataView(t)),this.masterIndex={};r-- >0;){const e=i.getString(),t=i.getLong(),n=i.getInt();this.masterIndex[e]={start:t,size:n}}if(this.expectedValueVectors={},this.version>5){const e=this.version<9?4:8;this.normExpectedValueVectorsPosition=this.footerPosition+e+n}return this}async printIndexStats(){let e,t=0,i=0;await await this.init();for(let n of Object.keys(this.masterIndex)){const r=this.masterIndex[n];t+=r.size,r.size>i&&(i=r.size,e=n)}console.log(`${i}  ${e}  ${this.config.url}`)}async getMatrix(e,t){const i=xf.getKey(e,t);if(this.matrixCache.has(i))return this.matrixCache.get(i);{const n=await this.readMatrix(e,t);return this.matrixCache.set(i,n),n}}async readMatrix(e,t){if(await this.init(),e>t){const i=e;e=t,t=i}const i=xf.getKey(e,t),n=this.masterIndex[i];if(!n)return;const r=await this.file.read(n.start,n.size);return r?xf.parseMatrix(r,this.chromosomes):void 0}async getContactRecords(e,t,i,n,r,s=!1){await this.init();const o=this.chromosomeIndexMap[this.getFileChrName(t.chr)],a=this.chromosomeIndexMap[this.getFileChrName(i.chr)];if(o>a||o===a&&t.start>=i.end){const e=t;t=i,i=e}const c=await this.getBlocks(t,i,n,r);if(!c||0===c.length)return[];const l=[],h=t.start/r,d=t.end/r,u=i.start/r,f=i.end/r,p=Math.floor(h),g=Math.ceil(d),m=Math.floor(u),w=Math.ceil(f);for(let o of c)if(o){let a,c,b=e&&\"NONE\"!==e;const F=this.getFileChrName(t.chr),v=this.getFileChrName(i.chr);if(b){const t=await this.getNormalizationVector(e,F,n,r),i=F===v?t:await this.getNormalizationVector(e,v,n,r);t&&i?(a=await t.getValues(p,g),c=await i.getValues(m,w)):b=!1}for(let e of o.records)if(s||e.bin1>=h&&e.bin1<d&&e.bin2>=u&&e.bin2<f)if(b){const t=e.bin1,i=e.bin2,n=a[t-p]*c[i-m];if(0!==n&&!isNaN(n)){const r=e.counts/n;l.push(new kf(t,i,r))}}else l.push(e);void 0===this.percentile95&&o.records.length>10&&(this.percentile95=Lf(o.records,95))}return l}async getBlocks(e,t,i,n){const r=(e,t)=>`${t.getKey()}_${e}`;await this.init();const s=this.getFileChrName(e.chr),o=this.getFileChrName(t.chr),a=this.chromosomeIndexMap[s],c=this.chromosomeIndexMap[o];if(void 0===a)return console.log(\"No chromosome named: \"+e.chr),[];if(void 0===c)return console.log(\"No chromosome named: \"+t.chr),[];const l=await this.getMatrix(a,c);if(!l)return console.log(\"No matrix for \"+e.chr+\"-\"+t.chr),[];const h=l.getZoomData(n,i);if(!h){let i=`No data avalailble for resolution: ${n}  for map ${e.chr}-${t.chr}`;throw new Error(i)}const d=h.getBlockNumbers(e,t,this.version),u=[],f=[];for(let e of d){const t=r(e,h);this.blockCache.has(n,t)?u.push(this.blockCache.get(n,t)):f.push(e)}const p=f.map((e=>this.readBlock(e,h))),g=await Promise.all(p);for(let e of g)e&&this.blockCache.set(n,r(e.blockNumber,h),e);return u.concat(g)}async readBlock(e,t){const i=await t.blockIndex.getBlockIndexEntry(e);if(i){let n=await this.file.read(i.filePosition,i.size);if(!n)return;n=new ls(new Uint8Array(n)).buffer;const r=new yf(new DataView(n)),s=r.getInt(),o=[];if(this.version<7)for(let e=0;e<s;e++){const e=r.getInt(),t=r.getInt(),i=r.getFloat();o.push(new kf(e,t,i))}else{const e=r.getInt(),t=r.getInt(),i=1===r.getByte(),n=!(this.version<9)&&1==r.getByte(),s=!(this.version<9)&&1==r.getByte(),a=r.getByte();if(1===a){const a=s?r.getInt():r.getShort();for(let c=0;c<a;c++){const a=t+(s?r.getInt():r.getShort()),c=n?r.getInt():r.getShort();for(let t=0;t<c;t++){const t=e+(n?r.getInt():r.getShort()),s=i?r.getFloat():r.getShort();o.push(new kf(t,a,s))}}}else{if(2!=a)throw new Error(\"Unknown block type: \"+a);{const n=r.getInt(),s=r.getShort();for(let a=0;a<n;a++){const n=Math.floor(a/s),c=e+(a-n*s),l=t+n;if(i){const e=r.getFloat();isNaN(e)||o.push(new kf(c,l,e))}else{const e=r.getShort();-32768!=e&&o.push(new kf(c,l,e))}}}}}return new Df(e,t,o,i)}}async hasNormalizationVector(e,t,i,n){let r;if(await this.init(),Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}const s=Rf(e,r,i.toString(),n),o=await this.getNormVectorIndex();return o&&o[s]}async isNormalizationValueAvailableAtResolution(e,t,i,n){let r;if(Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}return void 0!==(await this.getNormVectorIndex())[Rf(e,r,i.toString(),n)]}async getNormalizationVector(e,t,i,n){let r;if(await this.init(),Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}const s=Rf(e,r,i.toString(),n);if(this.normVectorCache.has(s))return this.normVectorCache.get(s);const o=await this.getNormVectorIndex();if(!o)return void console.log(\"Normalization vectors not present in this file\");if(!1===await this.isNormalizationValueAvailableAtResolution(e,t,i,n)){const t=`Normalization option ${e} not available at resolution ${n}. Will use NONE.`;return console.log(t),void(this.alert&&this.alert(t))}const a=o[s],c=await this.file.read(a.filePosition,8);if(!c)return;const l=new yf(new DataView(c)),h=this.version<9?l.getInt():l.getLong(),d=this.version<9?8:4,u=this.version<9?a.filePosition+4:a.filePosition+8,f=new Sf(this.file,u,h,d);return this.normVectorCache.set(s,f),f}async getNormVectorIndex(){if(!(this.version<6)){if(!this.normVectorIndex){if(!this.config.nvi&&this.remote&&this.url){const e=new URL(this.url),t=encodeURIComponent(e.hostname+e.pathname);Ef.hasOwnProperty(t)&&(this.config.nvi=Ef[t])}if(this.config.nvi){const e=decodeURIComponent(this.config.nvi).split(\",\"),t={start:parseInt(e[0]),size:parseInt(e[1])};return this.readNormVectorIndex(t)}try{return await this.readNormExpectedValuesAndNormVectorIndex(),this.normVectorIndex}catch(e){\"416\"===e.code||416===e.code?this.normExpectedValueVectorsPosition=void 0:console.error(e)}}return this.normVectorIndex}}async getNormalizationOptions(){return await this.getNormVectorIndex(),this.normalizationTypes}async readNormVectorIndex(e){await this.init(),this.normalizationVectorIndexRange=e;const t=await this.file.read(e.start,e.size),i=new yf(new DataView(t));this.normVectorIndex={};let n=i.getInt();for(;n-- >0;)this.parseNormVectorEntry(i);return this.normVectorIndex}async readNormExpectedValuesAndNormVectorIndex(){if(await this.init(),void 0===this.normExpectedValueVectorsPosition)return;const e=await this.skipExpectedValues(this.normExpectedValueVectorsPosition);let t=4,i=await this.file.read(e,4);if(0===i.byteLength)return;const n=new yf(new DataView(i)).getInt(),r={start:e+t,size:30*n};i=await this.file.read(r.start,r.size),this.normalizedExpectedValueVectors={},this.normVectorIndex={},await async function i(n,r){const s=new yf(new DataView(r));for(;n-- >0;){if(s.available()<100){n++,t+=s.position;const r=Math.max(1e3,30*n),o={start:e+t,size:r},a=await this.file.read(o.start,o.size);return i.call(this,n,a)}this.parseNormVectorEntry(s)}t+=s.position}.call(this,n,i),this.config.nvi=e.toString()+\",\"+t}async skipExpectedValues(e){const t=this.version,i=new Ff({file:this.file,size:256e3}),n={start:e,size:4},r=await i.read(n.start,n.size),s=new yf(new DataView(r)).getInt();return 0===s?e+4:async function e(n,r){let s={start:n,size:500},o=0,a=n,c=await i.read(s.start,s.size),l=new yf(new DataView(c));l.getString(),l.getString(),l.getInt();const h=t<9?l.getInt():l.getLong();o+=l.position+h*(t<9?8:4),s={start:n+o,size:4},c=await i.read(s.start,s.size),l=new yf(new DataView(c));const d=l.getInt();return o+=4+d*(4+(t<9?8:4)),r--,0===r?a+o:e(a+o,r)}(e+4,s)}getZoomIndexForBinSize(e,t){let i;if(\"BP\"===(t=t||\"BP\"))i=this.bpResolutions;else{if(\"FRAG\"!==t)throw new Error(\"Invalid unit: \"+t);i=this.fragResolutions}for(let t=0;t<i.length;t++)if(i[t]===e)return t;return-1}parseNormVectorEntry(e){const t=e.getString(),i=e.getInt(),n=e.getString(),r=e.getInt(),s=e.getLong(),o=this.version<9?e.getInt():e.getLong(),a=t+\"_\"+i+\"_\"+n+\"_\"+r;this.normalizationTypes.includes(t)||this.normalizationTypes.push(t),this.normVectorIndex[a]={filePosition:s,size:o}}getFileChrName(e){return this.chrAliasTable.hasOwnProperty(e)?this.chrAliasTable[e]:e}}function Rf(e,t,i,n){return e+\"_\"+t+\"_\"+i+\"_\"+n}class Df{constructor(e,t,i,n){this.blockNumber=e,this.zoomData=t,this.records=i,this.idx=n}}class Tf{constructor(){this.resolution=void 0,this.map=new If(6)}set(e,t,i){this.resolution!==e&&this.map.clear(),this.resolution=e,this.map.set(t,i)}get(e,t){return this.resolution===e?this.map.get(t):void 0}has(e,t){return this.resolution===e&&this.map.has(t)}}function Lf(e,t){const i=e.map((e=>e.counts));i.sort((function(e,t){return e-t}));return i[Math.floor(t/100*e.length)]}class zf{constructor(e,t){this.config=e,this.genome=t,this.hicFile=e._hicFile?e._hicFile:new Mf(e),e._hicFile=void 0}async getHeader(){return await this.hicFile.init(),this.hicFile}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){this.hicFile.initialized||await this.hicFile.init();const s=this.hicFile.bpResolutions,o=s[s.length-1];return(await this.hicFile.getContactRecords(void 0,{chr:e,start:t,end:i},{chr:\"celltype\",start:0,end:1e8},\"BP\",o)).map((t=>{const i=t.bin1*o;return{chr:e,start:i,end:i+o,value:t.counts,sample:t.bin2.toString()}}))}supportsWholeGenome(){return!1}}function Hf(e,t){const i=new Set(e.attributeNames),n=t[0];if(void 0===e.getAttributes(n))return!1;{const t=Object.keys(e.getAttributes(n));for(const e of t)if(!1===i.has(e))return!1}return!0}class Pf extends Hl{#y=new Map;constructor(e,t){super(e,t)}init(e){if(super.init(e),this.type=e.type||\"seg\",\"maf\"===this.type&&(this.type=\"mut\"),this.isLog=e.isLog,this.displayMode=e.displayMode||\"EXPANDED\",this.height=e.height||300,this.maxHeight=e.maxHeight||500,this.squishedRowHeight=e.sampleSquishHeight||e.squishedRowHeight||2,this.expandedRowHeight=e.sampleExpandHeight||e.expandedRowHeight||13,this.sampleHeight=this.squishedRowHeight,this.sampleKeys=[],e.samples){for(let t of e.samples)this.sampleKeys.push(t);this.explicitSamples=!0}if(e.color)this.color=e.color;else if(e.colorTable)this.colorTable=new ao(e.colorTable);else switch(this.type){case\"mut\":this.colorTable=new ao(qf);break;case\"shoebox\":e.colorScale&&(this.sbColorScale=gf.parse(e.colorScale));break;default:this.posColorScale=new uf(e.posColorScale||Of),this.negColorScale=new uf(e.negColorScale||Uf)}const t=Object.assign({},this.config);t.maxWGCount=t.maxWGCount||Number.MAX_SAFE_INTEGER,\"shoebox\"===this.type?(this.featureSource=new zf(t,this.browser.genome),this.height=e.height||500,this.maxHeight=e.maxHeight||800,this.isLog=!1,this.squishedRowHeight=e.squishedRowHeight||1,this.displayMode=e.displayMode||\"SQUISHED\",this.visibilityWindow=void 0===e.visibilityWindow?1e6:e.visibilityWindow):this.featureSource=Ad(t,this.browser.genome),this.initialSort=e.sort}async postInit(){\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader(),this.disposed)||this.header&&this.setTrackProperties(this.header)}menuItemList(){const e=[];if(!0===Hf(this.browser.sampleInfo,this.sampleKeys)){e.push(\"<hr/>\"),e.push(\"Sort by attribute:\");for(const n of this.browser.sampleInfo.attributeNames){if(this.sampleKeys.some((e=>{const t=this.browser.sampleInfo.getAttributes(e);return t&&t[n]}))){const r=Bt(\"<div>\");function s(){const e=this.#y.get(n)||1;this.sortByAttribute(n,e),this.#y.set(n,-1*e),this.config.sort={option:\"ATTRIBUTE\",attribute:n,direction:1===e?\"ASC\":\"DESC\"}}r.html(`&nbsp;&nbsp;${n.split(Uu.emptySpaceReplacement).join(\" \")}`),e.push({object:r,click:s})}}}const t={SQUISHED:\"Squish\",EXPANDED:\"Expand\",FILL:\"Fill\"};if(\"shoebox\"===this.type&&this.sbColorScale){function o(e){this.browser.inputDialog.present({label:\"Color Scale Threshold\",value:this.sbColorScale.threshold,callback:()=>{const e=Number(this.browser.inputDialog.value,10);e&&(this.sbColorScale.setThreshold(e),this.trackView.repaintViews())}},e)}e.push(\"<hr/>\"),e.push({object:Bt(\"<div>Set color scale threshold</div>\"),dialog:o})}e.push(\"<hr/>\"),e.push(\"DisplayMode:\");const i=\"seg\"===this.type||\"shoebox\"===this.type?[\"SQUISHED\",\"EXPANDED\",\"FILL\"]:[\"SQUISHED\",\"EXPANDED\"];for(let a of i){const c=Dl(t[a],a===this.displayMode);e.push({object:Bt(c),click:function(){this.displayMode=a,this.config.displayMode=a,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)}})}return e}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys,height:this.sampleHeight,yOffset:0}}async getFeatures(e,t,i){const n=await this.featureSource.getFeatures({chr:e,start:t,end:i});if(this.updateSampleKeys(n),this.initialSort){const e=this.initialSort;if(void 0===e.option||\"VALUE\"===e.option.toUpperCase())this.sortByValue(e,n);else if(\"ATTRIBUTE\"===e.option.toUpperCase()&&e.attribute){const t=\"DESC\"===e.direction?1:-1;this.sortByAttribute(e.attribute,t)}this.initialSort=void 0}return n}draw({context:e,pixelTop:t,pixelWidth:i,pixelHeight:n,features:r,bpPerPixel:s,bpStart:o}){if(xo.fillRect(e,0,t,i,n,{fillStyle:\"rgb(255, 255, 255)\"}),r&&r.length>0){if(this.checkForLog(r),\"shoebox\"===this.type&&!this.sbColorScale){const e=this.featureSource.hicFile.percentile95||2e3;this.sbColorScale=new gf({threshold:e,r:0,g:0,b:255})}const a={};let c;switch(this.sampleKeys.forEach((function(e,t){a[e]=t})),this.displayMode){case\"FILL\":this.sampleHeight=n/this.sampleKeys.length,c=0;break;case\"SQUISHED\":this.sampleHeight=this.squishedRowHeight,c=0;break;default:this.sampleHeight=this.expandedRowHeight,c=1}const l=this.sampleHeight;for(let e of r)e.pixelRect=void 0;const h=t+n,d=o+i*s+1,u=s;this.sampleYStart=void 0;for(let i of r){if(i.end<o||i.start>d)continue;const n=i.sampleKey||i.sample;i.row=a[n];const r=i.row*l+c;void 0===this.sampleYStart&&(this.sampleYStart=r);if(r+l<t||r>h)continue;const s=Math.max(i.start,o);let f=Math.round((s-o)/u);const p=Math.min(i.end,d),g=Math.round((p-o)/u);let m,w,b=Math.max(1,g-f);if(this.color?m=\"function\"==typeof this.color?this.color(i):this.color:this.colorTable&&(m=this.colorTable.getColor(i.value.toLowerCase())),\"mut\"===this.type)w=l-2*c,b<3&&(b=3,f-=1);else if(\"shoebox\"===this.type){m=this.sbColorScale.getColor(i.value);let e=l;if(l<.25){const t=.1+2*Math.abs(t.value);e=Math.min(1,t*l)}w=e-2*c}else{let e=i.value;this.isLog||(e=ys.log2(e/2)),m=e<-.1?this.negColorScale.getColor(e):e>.1?this.posColorScale.getColor(e):\"white\";let t=l;if(l<.25){const i=.1+2*Math.abs(e);t=Math.min(1,i*l)}w=t-2*c}i.pixelRect={x:f,y:r,w:b,h:w},e.fillStyle=m,e.fillRect(f,r,b,w)}}}checkForLog(e){if(void 0===this.isLog){this.isLog=!1;for(let t of e)if(t.value<0)return void(this.isLog=!0)}}computePixelHeight(e){if(!e)return 0;const t=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight;return this.updateSampleKeys(e),this.sampleKeys.length*t}async sortByValue(e,t){const i=e.chr;let n,r;if(e.position?(n=e.position-1,r=n+1):(n=e.start,r=e.end),t||(t=await this.featureSource.getFeatures({chr:i,start:n,end:r})),!t)return;this.updateSampleKeys(t);const s={},o=\"ASC\"===e.direction?1:-1,a=()=>{const e=r-n+1;for(let i of t){if(i.end<n)continue;if(i.start>r)break;const t=Math.max(n,i.start),o=(Math.min(r,i.end)-t)/e,a=i.sampleKey||i.sample,c=s[a]||0;s[a]=c+o*i.value}this.sampleKeys.sort((function(e,t){let i=s[e],n=s[t];return i||(i=o*Number.MAX_VALUE),n||(n=o*Number.MAX_VALUE),i===n?0:i>n?o:-1*o}))},c=()=>{for(let e of t){if(e.end<n)continue;if(e.start>r)break;const t=e.sampleKey||e.sample;(!s.hasOwnProperty(t)||e.value.localeCompare(s[t])>0)&&(s[t]=e.value)}this.sampleKeys.sort((function(e,t){let i=s[e]||\"\",n=s[t]||\"\";return o*i.localeCompare(n)}))};\"mut\"===this.type?c():a(),this.trackView.repaintViews()}sortByAttribute(e,t){this.sampleKeys=this.browser.sampleInfo.getSortedSampleKeysByAttribute(this.sampleKeys,e,t),this.trackView.repaintViews()}clickedFeatures(e){const t=super.clickedFeatures(e),i=e.y;return t.filter((function(e){const t=e.pixelRect;return t&&i>=t.y&&i<=t.y+t.h}))}hoverText(e){const t=this.clickedFeatures(e);if(t&&t.length>0)return`${t[0].sample}: ${t[0].value}`}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){i.length>0&&(i.push(\"<hr/>\"),i.push(\"<hr/>\"));const t=e._f||e,n=\"function\"==typeof t.popupData?t.popupData(this.type,this.browser.genome.id):this.extractPopupData(t);Array.prototype.push.apply(i,n)}return i}contextMenuItemList(e){const t=e.genomicLocation,i=t=>{const i=e.viewport.cachedFeatures;this.sortByValue(t,i)},n=e.referenceFrame.toBP(2.5);return[\"DESC\",\"ASC\"].map((r=>{const s=\"DESC\"===r?\"descending\":\"ascending\";return{label:\"seg\"===this.type||\"shoebox\"===this.type?`Sort by value (${s})`:`Sort by type (${s})`,click:()=>{const s={option:\"VALUE\",direction:r,chr:e.referenceFrame.chr,start:Math.floor(t-n),end:Math.floor(t+n)};i(s),this.config.sort=s}}}))}get supportsWholeGenome(){return(!1===this.config.indexed||!this.config.indexURL)&&!1!==this.config.supportsWholeGenome}updateSampleKeys(e){if(this.explicitSamples)return;const t=new Set(this.sampleKeys);for(let i of e){const e=i.sampleKey||i.sample;t.has(e)||(this.sampleKeys.push(e),t.add(e))}}}const Of={low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0},Uf={low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255},qf={indel:\"rgb(0,200,0)\",\"targeted region\":\"rgb(236,155,43)\",truncating:\"rgb(\\t150,0,0)\",\"non-coding transcript\":\"rgb(0,0,150)\",synonymous:\"rgb(109,165,95)\",silent:\"rgb(109,135,80)\",missense_mutation:\"rgb(72,130,187)\",missense:\"rgb(72,130,187)\",\"splice site\":\"rgb(143,83,155)\",splice_region:\"rgb(143,83,155)\",nonsense:\"rgb(216, 57,81)\",nonsense_mutation:\"rgb(216, 57,81)\",frame_shift_del:\"rgb(226,135,65)\",frame_shift_ins:\"rgb(226,135,65)\",in_frame_del:\"rgb(247,235,94)\",in_frame_ins:\"rgb(247,235,94)\",\"*other*\":\"rgb(159,91,50)\"};class Qf{constructor(e){this.paired=!0,this.firstAlignment=e,this.chr=e.chr,this.readName=e.readName,e.start<e.mate.position?(this.start=e.start,this.scStart=e.scStart,this.connectingStart=e.start+e.lengthOnRef,this.connectingEnd=e.mate.position):(this.start=e.mate.position,this.scStart=this.start,this.connectingStart=e.mate.position,this.connectingEnd=e.start),this.end=Math.max(e.mate.position,e.start+e.lengthOnRef),this.lengthOnRef=this.end-this.start;let t=Math.max(this.end,e.scStart+e.scLengthOnRef);this.scLengthOnRef=t-this.scStart}setSecondAlignment(e){this.secondAlignment=e;const t=this.firstAlignment;e.start>t.start?this.connectingEnd=e.start:this.connectingStart=e.start+e.lengthOnRef,this.start=Math.min(t.start,e.start),this.end=Math.max(t.start+t.lengthOnRef,e.start+e.lengthOnRef),this.lengthOnRef=this.end-this.start,this.scStart=Math.min(t.scStart,e.scStart);const i=Math.max(t.scStart+t.scLengthOnRef,e.scStart+e.scLengthOnRef);this.scLengthOnRef=i-this.scStart}containsLocation(e,t){const i=t?this.scStart:this.start,n=t?this.scLengthOnRef:this.lengthOnRef;return e>=i&&e<=i+n}alignmentContaining(e,t){return this.firstAlignment.containsLocation(e,t)?this.firstAlignment:this.secondAlignment&&this.secondAlignment.containsLocation(e,t)?this.secondAlignment:void 0}popupData(e){let t=this.firstAlignment.popupData(e);return this.secondAlignment&&(t.push(\"-------------------------------\"),t=t.concat(this.secondAlignment.popupData(e))),t}isPaired(){return!0}isMateMapped(){return!0}isProperPair(){return this.firstAlignment.isProperPair()}get fragmentLength(){return Math.abs(this.firstAlignment.fragmentLength)}get firstOfPairStrand(){return this.firstAlignment.firstOfPairStrand}get pairOrientation(){return this.firstAlignment.pairOrientation}hasTag(e){return this.firstAlignment.hasTag(e)||this.secondAlignment&&this.secondAlignment.hasTag(e)}getGroupValue({option:e,tag:t}){switch(e){case\"strand\":return this.isNegativeStrand()?\"-\":\"+\";case\"FIRST_IN_PAIR_STRAND\":return this.isPaired()?this.isFirstOfPair()?this.isNegativeStrand()?\"-\":\"+\":this.isSecondOfPair()?this.isNegativeStrand()?\"+\":\"-\":void 0:void 0;case\"START\":return this.start;case\"INSERT_SIZE\":return this.fragmentLength;case\"MATE_CHR\":return this.mate?this.mate.chr:void 0;case\"MQ\":return this.mq;case\"ALIGNED_READ_LENGTH\":return this.lengthOnRef;case\"TAG\":return this.tags()[t];case\"PHASE\":return this.tags().HP;case\"READ_ORDER\":return this.isPaired()&&this.isFirstOfPair()?\"FIRST\":this.isPaired()&&this.isSecondOfPair()?\"SECOND\":\"\";default:return}}}class Vf{static instances=new Map;static getKey(e,t,i){const n=\"\"+e+t+i;return Vf.instances.has(n)||Vf.instances.set(n,new Vf(e,t,i)),Vf.instances.get(n)}constructor(e,t,i){this.base=e,this.strand=t,this.modification=i,this.canonicalBase=\"+\"===this.strand?this.base:oc(this.base)}getCanonicalBase(){}toString(){return\"\"+this.base+this.strand+this.modification}static compare(e,t){const i=e.modification,n=t.modification;return i===n?e.strand.charAt(0)-t.strand.charAt(0):jf.has(i)&jf.has(n)?jf.get(i)-jf.get(n):jf.has(i)?1:jf.has(n)?-1:i>n?1:-1}}const jf=new Map([\"NONE_C\",\"NONE_T\",\"NONE_G\",\"NONE_A\",\"m\",\"h\",\"f\",\"c\",\"C\",\"g\",\"e\",\"b\",\"T\",\"U\",\"a\",\"A\",\"o\",\"G\",\"n\",\"N\"].map(((e,t)=>[e,t])));class Wf{constructor(e,t,i,n){this.base=e,this.modification=i,this.strand=t,this.likelihoods=n,this.canonicalBase=\"+\"==this.strand?this.base:oc(this.base),this.key=Vf.getKey(e,t,i)}containsPosition(e){return this.likelihoods.has(e)}is5mC(){return this.modification.equals(\"m\")&&(\"C\"===this.base&&\"+\"===this.strand||\"G\"===this.base&&\"-\"===this.strand)}fullName(){return Gf.get(this.modification)||this.modification}}const Gf=new Map;Gf.set(\"m\",\"5mC\"),Gf.set(\"h\",\"5hmC\"),Gf.set(\"f\",\"5fC\"),Gf.set(\"c\",\"5caC\"),Gf.set(\"g\",\"5hmU\"),Gf.set(\"e\",\"5fU\"),Gf.set(\"b\",\"5caU\"),Gf.set(\"a\",\"6mA\"),Gf.set(\"o\",\"8xoG\"),Gf.set(\"n\",\"Xao\"),Gf.set(\"C\",\"Unknown C\"),Gf.set(\"T\",\"Unknown T\"),Gf.set(\"A\",\"Unknown A\"),Gf.set(\"G\",\"Unknown G\"),Gf.set(\"N\",\"Unknown\");const $f=new Map([[\"m\",\"5mC\"],[\"h\",\"5hmC\"],[\"f\",\"5fC\"],[\"c\",\"5caC\"],[\"g\",\"5hmU\"],[\"e\",\"5fU\"],[\"b\",\"5caU\"],[\"a\",\"6mA\"],[\"o\",\"8xoG\"],[\"n\",\"Xao\"],[\"C\",\"Unknown C\"],[\"T\",\"Unknown T\"],[\"A\",\"Unknown A\"],[\"G\",\"Unknown G\"],[\"N\",\"Unknown\"]]);function Kf(e){return $f.has(e)?$f.get(e):\"Uknown\"}function Yf(e){if(!e)return!1;const t=e.length;if(0==t)return!1;for(let i=0;i<t;i++){const t=e.charAt(i);if(t<\"0\"||t>\"9\")return!1}return!0}function Xf(e){return e<0?e+256:e}class Zf{allModifications=new Set;simplexModifications=new Set;maxLikelihoods=new Map;nomodLikelihoods=new Map;lastThreshold;incrementCounts(e){if(!e.blocks)return;const t=e.getBaseModificationSets();if(t)for(let i of e.blocks)if(\"S\"!==i.type)for(let e=0;e<i.len;e++){let n,r=e+i.seqOffset,s=0,o=-1,a=255;for(let e of t){const t=Vf.getKey(e.base,e.strand,e.modification);this.allModifications.add(t);const i=e.likelihoods;if(e.containsPosition(r)){const c=Xf(i.get(r));a-=c,c>o&&(s=e.canonicalBase,o=c,n=t)}}if(0!=s){const t=i.start+e,r=Vf.getKey(s,\"+\",\"NONE_\"+s);this.allModifications.add(r);const c=(e,t,i,n)=>{let r=n.get(i);r||(r=new Map,n.set(i,r));let s=r.get(e);s||(s=[],r.set(e,s)),s.push(t)};c(t,o,n,this.maxLikelihoods),a>o?c(t,a,r,this.nomodLikelihoods):c(t,o,n,this.nomodLikelihoods)}}}getCount(e,t,i,n){this.lastThreshold=i;const r=255*i,s=n?this.nomodLikelihoods.get(t):this.maxLikelihoods.get(t);if(!s)return 0;const o=s.get(e);if(o){let e=0;for(let t of o){Xf(t)>=r&&e++}return e}return 0}getLikelihoodSum(e,t,i,n){this.lastThreshold=i;const r=255*i,s=(n?this.nomodLikelihoods.get(t):this.maxLikelihoods.get(t)).get(e);if(s){let e=0;for(let t of s){const i=Xf(t);i>=r&&(e+=i)}return e}return 0}popupData(e,t){const i=[];i.push(\"<b>Modifications with likelihood > \"+100*this.lastThreshold+\"%</b>\");for(let n of this.maxLikelihoods.keys()){if(this.maxLikelihoods.get(n).has(e)){let r=\"basemod2\"===t;const s=this.getCount(e,n,this.lastThreshold,r);if(s>0){const t=this.getLikelihoodSum(e,n,this.lastThreshold,r)/s*.3921568,o=Kf(n.modification);i.push(o+\" (\"+n.base+n.strand+\"): \"+s+\"  @ average likelihood \"+Math.round(t)+\"%\")}}}return i}computeSimplex(){const e=new Set(Array.from(this.allModifications).filter((e=>\"-\"===e.strand)).map((e=>e.modification)));for(let t of this.allModifications)\"+\"!==t.strand||e.has(t.modification)||(this.simplexModifications.add(t.modification),this.simplexModifications.add(\"NONE_\"+t.getCanonicalBase()))}}class Jf{constructor(){this.alignments=[],this.score=void 0}findAlignment(e,t=!1){const i=(e,i)=>i>=e.start&&i<e.start+(t?e.fragmentLength:e.lengthOnRef);let n;for(let r=0;r<this.alignments.length;r++){const s=this.alignments[r];if(e>=s.start&&e<s.start+(t?s.fragmentLength:s.lengthOnRef)){s.paired?s.firstAlignment&&i(s.firstAlignment,e)?n=s.firstAlignment:s.secondAlignment&&i(s.secondAlignment,e)&&(n=s.secondAlignment):n=s;break}}return n}getSortValue({position:e,option:t,tag:i,sortAsPairs:n},r){t||(t=\"BASE\");const s=this.findAlignment(e,n);if(void 0===s)return Number.MAX_VALUE;switch(t){case\"NUCLEOTIDE\":case\"BASE\":return function(e,t,i){let n;const r=Math.floor(i)-t.start;r<t.sequence.length&&(n=t.sequence.charAt(r));if(!n)return 0;const s=e.readBaseAt(i),o=e.readBaseQualityAt(i),a=t.coverageMap,c=Math.floor(i-a.bpStart),l=a.coverage[c];let h=0;if(e.insertions)for(let t of e.insertions)t.start===i&&(h=-l.ins);if(s)if(n=n.toUpperCase(),\"N\"===s&&0===h)h=2;else if(n!==s&&\"=\"!==s||0!==h){if(\"X\"===s||n!==s){h-=l[\"pos\"+s]+l[\"neg\"+s]+o/1e3}}else h=4-o/1e3;else{const e=l.del;e>0?h-=e:0===h&&(h=1)}return h}(s,r,e);case\"strand\":return s.strand?1:-1;case\"START\":return s.start;case\"TAG\":return s.tags()[i];case\"READ_NAME\":return s.readName;case\"INSERT_SIZE\":return-Math.abs(s.fragmentLength);case\"GAP_SIZE\":return-s.gapSizeAt(e);case\"MATE_CHR\":return s.mate?s.mate.chr:Number.MAX_VALUE;case\"MQ\":return void 0===s.mq?Number.MAX_VALUE:-s.mq;case\"ALIGNED_READ_LENGTH\":return-s.lengthOnRef;default:return Number.MAX_VALUE}}}var ep={fr:{F1R2:\"LR\",F2R1:\"LR\",F1F2:\"LL\",F2F1:\"LL\",R1R2:\"RR\",R2R1:\"RR\",R1F2:\"RL\",R2F1:\"RL\"},rf:{R1F2:\"LR\",R2F1:\"LR\",R1R2:\"LL\",R2R1:\"LL\",F1F2:\"RR\",F2F1:\"RR\",F1R2:\"RL\",F2R1:\"RL\"},ff:{F2F1:\"LR\",R1R2:\"LR\",F2R1:\"LL\",R1F2:\"LL\",R2F1:\"RR\",F1R2:\"RR\",R2R1:\"RL\",F1F2:\"RL\"}};class tp{#A=[];baseModificationKeys=new Set;constructor(e,t,i,{samplingWindowSize:n,samplingDepth:r,alleleFreqThreshold:s,colorBy:o}){this.alleleFreqThreshold=void 0===s?.2:s,this.samplingWindowSize=n||100,this.samplingDepth=r||1e3,this.chr=e,this.start=Math.floor(t),this.end=Math.ceil(i),this.length=i-t,this.coverageMap=new np(e,t,i,this.alleleFreqThreshold),this.downsampledIntervals=[],o&&o.startsWith(\"basemod\")&&(this.baseModCounts=new Zf),this.alignments=[],this.pairsCache=new Map,this.downsampledReads=new Set,this.currentBucket=new ip(this.start,this.start+this.samplingWindowSize,this),this.hasPairs=!1}pack({viewAsPairs:e,showSoftClips:t,expectedPairOrientation:i,groupBy:n,displayMode:r}){let s=this.allAlignments();s=e?function(e){const t=new Map,i=e.map((e=>{if(ap(e)){let i=t.get(e.readName);return i?(i.setSecondAlignment(e),t.delete(e.readName),i):(i=new Qf(e),t.set(e.readName,i),i)}return e}));return i}(s):function(e){return e.flatMap((e=>e instanceof Qf?[e.firstAlignment,e.secondAlignment].filter(Boolean):[e]))}(s),this.packAlignmentRows(s,t,i,n,r),this.alignments&&delete this.alignments}packAlignmentRows(e,t,i,n,r){this.#A=[];const s=(e,i)=>{e.sort((function(e,i){return t?e.scStart-i.scStart:e.start-i.start}));const n=new op(i);let r,s=0,o=0;const a=new Set,c=()=>{r=new Jf,n.push(r),s=0,o=0,a.clear()};for(c();e.length>0;)if(o>=0&&o<e.length){const i=e[o];a.add(i),r.alignments.push(i),s=t?i.scStart+i.scLengthOnRef+2:i.start+i.lengthOnRef+2,o=cp(e,(e=>(t?e.scStart:e.start)>s),o)}else e=e.filter((e=>!a.has(e))),c();return n},o=(e,t)=>{e.sort((function(e,t){return e.start-t.start}));const i=new op(t),{start:n,end:r}=this.viewport.genomicRange();for(let t of e)if(t.end<n||t.start>r)this.#A.push(t);else{const e=new Jf;e.alignments.push(t),i.push(e)}return i};if(!e||0===e.length)return new Map;{const t=new Map;if(n)for(let r of e){const e=lp(r,n,i)||\"\";t.has(e)||t.set(e,[]),t.get(e).push(r)}else t.set(\"\",e);const a=new Map,c=Array.from(t.keys()).sort(function(e,t){switch(e){case\"pairOrientation\":return function(e){const t=[\"LL\",\"RR\",\"RL\",\"LR\",\"\"];return(e,i)=>t.indexOf(e)-t.indexOf(i)}();case\"strand\":case\"firstOfPairStrand\":return up;default:return e&&e.startsWith(\"base:\")?dp:fp}}(n));for(let e of c){const i=t.get(e),n=\"FULL\"===r?o(i,e):s(i,e);a.set(e,n)}this.packedGroups=a}}push(e){this.hasPairs=this.hasPairs||e.isPaired(),this.coverageMap.incCounts(e);const t=e.getBaseModificationSets();if(t)for(let e of t)this.baseModificationKeys.add(e.key);this.baseModCounts&&this.baseModCounts.incrementCounts(e),this.downsampledReads.has(e.readName)?this.currentBucket.downsampledCount++:(e.start>=this.currentBucket.end&&(this.finishBucket(),this.currentBucket=new ip(e.start,e.start+this.samplingWindowSize,this)),this.currentBucket.addAlignment(e))}finish(){void 0!==this.currentBucket&&this.finishBucket(),this.hasAlignments=this.alignments.length>0,this.alignments.sort((function(e,t){return e.start-t.start})),this.baseModCounts&&this.baseModCounts.computeSimplex(),delete this.currentBucket,delete this.pairsCache,delete this.downsampledReads}contains(e,t,i){return this.chr===e&&this.start<=t&&this.end>=i}hasDownsampledIntervals(){return this.downsampledIntervals&&this.downsampledIntervals.length>0}finishBucket(){this.alignments=this.alignments.concat(this.currentBucket.alignments),this.currentBucket.downsampledCount>0&&this.downsampledIntervals.push(new sp(this.currentBucket.start,this.currentBucket.end,this.currentBucket.downsampledCount))}allAlignments(){if(this.alignments)return this.alignments;if(this.packedGroups){const e=Array.from(this.packedGroups.values()).flatMap((e=>e.rows.flatMap((e=>e.alignments))));if(this.#A&&this.#A.length>0)for(let t of this.#A)e.push(t);return e}return[]}getMax(e,t){return this.coverageMap.getMax(e,t)}sortRows(e){if(this.packedGroups)for(let t of this.packedGroups.values())t.sortRows(e,this)}}class ip{constructor(e,t,{samplingDepth:i,downsampledReads:n,pairsCache:r}){this.start=e,this.end=t,this.alignments=[],this.downsampledCount=0,this.samplingDepth=i,this.downsampledReads=n,this.pairsCache=r,this.hasPairs=!1}addAlignment(e){this.hasPairs=this.hasPairs||e.isPaired();const t=this.hasPairs?Math.ceil(this.samplingDepth/2):this.samplingDepth;if(ap(e)){const t=this.pairsCache.get(e.readName);if(t)return t.setSecondAlignment(e),void this.pairsCache.delete(e.readName)}if(this.alignments.length<t)if(ap(e)){const t=new Qf(e);this.pairsCache.set(e.readName,t),this.alignments.push(t)}else this.alignments.push(e);else{const i=Math.floor(Math.random()*(t+this.downsampledCount-1));if(i<t){const t=this.alignments[i];if(this.pairsCache.has(t.readName)&&this.pairsCache.delete(t.readName),ap(e)){const t=new Qf(e);this.pairsCache.set(e.readName,t),this.alignments[i]=t}else this.alignments[i]=e;this.downsampledReads.add(t.readName)}else this.downsampledReads.add(e.readName);this.downsampledCount++}}}class np{constructor(e,t,i,n){this.chr=e,this.bpStart=t,this.length=i-t,this.coverage=new Array(this.length),this.maximum=0,this.threshold=n,this.qualityWeight=!0}getMax(e,t){let i=0;const n=this.coverage.length;for(let r=0;r<n;r++){const n=this.bpStart+r;if(n>t)break;const s=this.coverage[r];n>=e&&s&&(i=Math.max(i,s.total))}return i}incCounts(e){var t=this;if(void 0===e.blocks?i(e):e.blocks.forEach((function(e){i(e)})),e.gaps)for(let i of e.gaps)if(\"D\"===i.type){const e=i.start-t.bpStart;for(let n=e;n<e+i.len;n++)n<0||(this.coverage[n]||(this.coverage[n]=new rp(t.threshold)),this.coverage[n].del++)}if(e.insertions)for(let i of e.insertions){const e=i.start-this.bpStart;e<0||(this.coverage[e]||(this.coverage[e]=new rp(t.threshold)),this.coverage[e].ins++)}function i(i){if(\"S\"===i.type)return;const n=e.seq,r=e.qual,s=i.seqOffset;for(let o=i.start-t.bpStart,a=0;a<i.len;o++,a++){t.coverage[o]||(t.coverage[o]=new rp(t.threshold));const i=null==n?\"N\":n.charAt(s+a),c=e.strand?\"pos\"+i:\"neg\"+i,l=r&&s+a<r.length?r[s+a]:30;t.coverage[o][c]+=1,t.coverage[o][\"qual\"+i]+=l,t.coverage[o].total+=1,t.coverage[o].qual+=l,t.maximum=Math.max(t.coverage[o].total,t.maximum)}}}getPosCount(e,t){const i=e-this.bpStart;if(i<0||i>=this.coverage.length)return 0;const n=this.coverage[i];switch(t){case\"A\":case\"a\":return n.posA;case\"C\":case\"c\":return n.posC;case\"T\":case\"t\":return n.posT;case\"G\":case\"g\":return n.posG;case\"N\":case\"n\":return n.posN;default:return 0}}getNegCount(e,t){const i=e-this.bpStart;if(i<0||i>=this.coverage.length)return 0;const n=this.coverage[i];switch(t){case\"A\":case\"a\":return n.negA;case\"C\":case\"c\":return n.negC;case\"T\":case\"t\":return n.negT;case\"G\":case\"g\":return n.negG;case\"N\":case\"n\":return n.negN;default:return 0}}getCount(e,t){return this.getPosCount(e,t)+this.getNegCount(e,t)}getTotalCount(e){const t=e-this.bpStart;return t>=0&&t<this.coverage.length?this.coverage[t].total:0}}class rp{constructor(e){this.qualityWeight=!0,this.posA=0,this.negA=0,this.posT=0,this.negT=0,this.posC=0,this.negC=0,this.posG=0,this.negG=0,this.posN=0,this.negN=0,this.pos=0,this.neg=0,this.qualA=0,this.qualT=0,this.qualC=0,this.qualG=0,this.qualN=0,this.qual=0,this.total=0,this.del=0,this.ins=0,this.threshold=e}hoverText(){const e=this.posA+this.posT+this.posC+this.posG+this.posN,t=this.negA+this.negT+this.negC+this.negG+this.negN;return`${this.total} (${e}+, ${t}-)`}isMismatch(e){const t=this.threshold*(this.qualityWeight&&this.qual?this.qual:this.total);let i=0;for(let t of[\"A\",\"T\",\"C\",\"G\"])t!==e&&(i+=this.qualityWeight&&this.qual?this[\"qual\"+t]:this[\"pos\"+t]+this[\"neg\"+t]);return i>=t}}class sp{constructor(e,t,i){this.start=e,this.end=t,this.counts=i}popupData(e){return[{name:\"start\",value:Math.floor(this.start+1)},{name:\"end\",value:this.end},{name:\"# downsampled:\",value:this.counts}]}}class op{pixelTop=0;pixelBottom=0;rows=[];constructor(e){this.name=this.name}push(e){this.rows.push(e)}get length(){return this.rows.length}sortRows(e,t){const i=[],n=[];for(let t of this.rows){void 0!==t.findAlignment(e.position,e.sortAsPairs)?i.push(t):n.push(t)}i.sort(((i,n)=>{const r=e.direction,s=i.getSortValue(e,t),o=n.getSortValue(e,t);if(void 0===o&&void 0!==o)return 1;if(void 0!==s&&void 0===o)return-1;const a=s>o?1:s<o?-1:0;return!0===r?a:-a}));for(let e of n)i.push(e);this.rows=i}}function ap(e){return e.isPaired()&&e.mate&&e.isMateMapped()&&e.chr===e.mate.chr&&(e.isFirstOfPair()||e.isSecondOfPair())&&!(e.isSecondary()||e.isSupplementary())}function cp(e,t,i){let n=i-1,r=e.length;for(;1+n<r;){const i=n+(r-n>>1);t(e[i])?r=i:n=i}return r}function lp(e,t,i){let n,r,s;if(t.startsWith(\"tag:\"))n=t.substring(4),t=\"tag\";else if(t.startsWith(\"base:\")){const e=t.split(\":\");3===e.length&&(t=\"base\",r=e[1],s=Number.parseInt(e[2].replaceAll(\",\",\"\"))-1)}switch(t){case\"strand\":return e.strand?\"+\":\"-\";case\"firstOfPairStrand\":const t=e.firstOfPairStrand;return void 0===t?\"\":t?\"+\":\"-\";case\"mateChr\":return e.mate&&e.isMateMapped()?e.mate.chr:\"\";case\"pairOrientation\":return ep[i][e.pairOrientation]||\"\";case\"chimeric\":return e.tags().SA?\"chimeric\":\"\";case\"supplementary\":return e.isSupplementary?\"supplementary\":\"\";case\"readOrder\":return e.isPaired()&&e.isFirstOfPair()?\"first\":e.isPaired()&&e.isSecondOfPair()?\"second\":\"\";case\"phase\":return e.tags().HP||\"\";case\"tag\":return e.tags()[n]||\"\";case\"base\":if(e.chr===r&&e.start<=s&&e.end>s){const t=e.readBaseAt(s);return t||\"GAP\"}return\"\";default:return}}const hp=new Map([[\"A\",1],[\"T\",2],[\"C\",3],[\"G\",4],[\"N\",5],[\"GAP\",5],[\"\",7]]);function dp(e,t){return hp.has(e)&&hp.has(t)?hp.get(e)-hp.get(t):e.localeCompare(t,void 0,{sensitivity:\"base\"})}function up(e,t){return e===t?0:e&&t?-e.localeCompare(t):e?1:-1}function fp(e,t){if(e||t){if(e){if(t){if(e===t)return 0;if(Va(e)&&(Va(t),1))return Number.parseFloat(e)-Number.parseFloat(t);{let i=e.toString(),n=t.toString();return i.localeCompare(n,void 0,{sensitivity:\"base\"})}}return-1}return 1}return 0}class pp{constructor(e){const t=e.split(\",\");this.chr=t[0],this.start=parseInt(t[1]),this.strand=t[2].charAt(0),this.mapQ=parseInt(t[4]),this.numMismatches=parseInt(t[5]),this.lenOnRef=function(e){let t=0,i=\"\";for(let n=0;n<e.length;n++){const r=e.charCodeAt(n);if(r>47&&r<58)i+=e.charAt(n);else{switch(r){case 78:case 68:case 77:case 61:case 88:t+=parseInt(i.toString())}i=\"\"}}return t}(t[3])}printString(){return this.chr+\":\"+Rt(this.start)+\"-\"+Rt(this.start+this.lenOnRef)+\" (\"+this.strand+\") = \"+Rt(this.lenOnRef)+\"bp @MAPQ: \"+this.mapQ+\" NM: \"+this.numMismatches}}function gp(e){return e.split(\";\").filter((e=>e.length>0)).map((e=>new pp(e)))}const mp={c:1,C:1,s:2,S:2,i:4,I:4,f:4};class wp{constructor(){this.hidden=!1}isMapped(){return!(4&this.flags)}isPaired(){return!!(1&this.flags)}isProperPair(){return!!(2&this.flags)}isFirstOfPair(){return!!(64&this.flags)}isSecondOfPair(){return!!(128&this.flags)}isSecondary(){return!!(256&this.flags)}isSupplementary(){return!!(2048&this.flags)}isFailsVendorQualityCheck(){return!!(512&this.flags)}isDuplicate(){return!!(1024&this.flags)}isMateMapped(){return!(8&this.flags)}isNegativeStrand(){return!!(16&this.flags)}isMateNegativeStrand(){return!!(32&this.flags)}hasTag(e){const t=this.tagDict||function(e){let t=0;const i=e.length,n={};for(;t<i;){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const s=String.fromCharCode(e[t++]);let o;if(\"A\"===s)o=String.fromCharCode(e[t]),t++;else if(\"i\"===s||\"I\"===s)o=vp(e,t),t+=4;else if(\"c\"===s)o=Cp(e,t),t++;else if(\"C\"===s)o=_p(e,t),t++;else if(\"s\"===s||\"S\"===s)o=yp(e,t),t+=2;else if(\"f\"===s)o=Ap(e,t),t+=4;else if(\"Z\"===s)for(o=\"\";;){var r=e[t++];if(0===r)break;o+=String.fromCharCode(r)}else{if(\"B\"!==s){o=\"Error unknown type: \"+s,n[i]=o;break}{const r=String.fromCharCode(e[t++]);let s=mp[r];if(void 0===s){n[i]=`Error: unknown element type '${r}'`;break}const a=vp(e,t);t+=4;const c=t+a*s;o=[];const l=new DataView(e.buffer);for(;t<c;){switch(r){case\"c\":o.push(l.getInt8(t));break;case\"C\":o.push(l.getUint8(t));break;case\"s\":o.push(l.getInt16(t));break;case\"S\":o.push(l.getUint16(t));break;case\"i\":o.push(l.getInt32(t));break;case\"I\":o.push(l.getUint32(t));break;case\"f\":o.push(l.getFloat32(t))}t+=s}}}n[i]=o}return n}(this.tagBA);return t.hasOwnProperty(e)}tags(){return this.tagDict}getTag(e){return this.tags()[e]}get firstOfPairStrand(){if(this.isPaired()){if(this.isFirstOfPair())return this.strand;if(this.isMateMapped())return this.mate.strand}}containsLocation(e,t){const i=t?this.scStart:this.start,n=t?this.scLengthOnRef:this.lengthOnRef;return e>=i&&e<=i+n}popupData(e){const t=[];if(e=Math.floor(e),this.insertions){const n=this.seq;for(let r of this.insertions){var i=r.start;if(e===i||e===i-1)return t.push({name:\"Insertion\",value:n.substr(r.seqOffset,r.len)}),t.push({name:\"Location\",value:i}),t}}t.push({name:\"Read Name\",value:this.readName}),t.push(\"<hr/>\"),t.push({name:\"Alignment Start\",value:Rt(1+this.start),borderTop:!0}),t.push({name:\"Read Strand\",value:!0===this.strand?\"(+)\":\"(-)\",borderTop:!0});let n=this.cigar;if(n&&n.length>50){const e=25;n=`${n.substring(0,e-2)} ... ${n.substring(n.length-e+2)}`}t.push({name:\"Cigar\",value:n}),t.push({name:\"Mapping Quality\",value:this.mq}),t.push({name:\"Secondary\",value:a(this.isSecondary())}),t.push({name:\"Supplementary\",value:a(this.isSupplementary())}),t.push({name:\"Duplicate\",value:a(this.isDuplicate())}),t.push({name:\"Failed QC\",value:a(this.isFailsVendorQualityCheck())}),this.isPaired()&&(t.push(\"<hr/>\"),t.push({name:\"First in Pair\",value:!this.isSecondOfPair(),borderTop:!0}),t.push({name:\"Mate is Mapped\",value:a(this.isMateMapped())}),this.pairOrientation&&t.push({name:\"Pair Orientation\",value:this.pairOrientation}),this.isMateMapped()&&(t.push({name:\"Mate Chromosome\",value:this.mate.chr}),t.push({name:\"Mate Start\",value:this.mate.position+1}),t.push({name:\"Mate Strand\",value:!0===this.mate.strand?\"(+)\":\"(-)\"}),t.push({name:\"Insert Size\",value:this.fragmentLength})));const r=this.tags();if(r.hasOwnProperty(\"SA\")){t.push(\"<hr/>\"),t.push({name:\"Supplementary Alignments\",value:\"\"});const e=gp(r.SA);if(e){t.push(\"<ul>\");for(let i of e)t.push(`<li>${i.printString()}</li>`);t.push(\"</ul>\")}}const s=new Set([\"SA\",\"MD\"]);t.push(\"<hr/>\");for(let e in r)s.has(e)||t.push({name:e,value:r[e]});t.push({name:\"Hidden Tags\",value:\"SA, MD\"}),t.push(\"<hr/>\"),t.push({name:\"Genomic Location: \",value:Rt(1+e)}),t.push({name:\"Read Base:\",value:this.readBaseAt(e)}),t.push({name:\"Base Quality:\",value:this.readBaseQualityAt(e)});const o=this.getBaseModificationSets();if(o){const i=this.positionToReadIndex(e);if(void 0!==i){let e=!1;for(let n of o)if(n.containsPosition(i)){e||(t.push(\"<hr/>\"),t.push(\"<b>Base modifications:</b>\"),e=!0);const r=Math.round(100/255*Xf(n.likelihoods.get(i)));t.push(`${n.fullName()} @ likelihood =  ${r}%`)}}}return t;function a(e){return e?\"Yes\":\"No\"}}readBaseAt(e){const t=Fp(this.blocks,e);if(t){if(\"*\"===this.seq)return\"*\";{const i=t.seqIndexAt(e);return this.seq[i]}}}readBaseQualityAt(e){const t=Fp(this.blocks,e);if(t){if(\"*\"===this.qual)return 30;{const i=t.seqIndexAt(e);return i>=0&&this.qual&&i<this.qual.length?this.qual[i]:30}}}gapSizeAt(e){if(this.gaps)for(let t of this.gaps)if(e>=t.start&&e<t.start+t.len)return t.len;return 0}softClippedBlocks(){let e,t,i;for(let n of this.blocks)\"S\"===n.type?i?t=n:e=n:\"H\"!==n.type&&(i=!0);return{left:e,right:t}}getBaseModificationSets(){if(!this.baseModificationSets&&(this.tagDict.MM||this.tagDict.Mm)){const e=this.tagDict.MM||this.tagDict.Mm,t=this.tagDict.ML||this.tagDict.Ml;!Mt(e)||t&&!Array.isArray(t)||(0===e.length?this.baseModificationSets=bp:this.baseModificationSets=function(e,t,i,n){n&&(i=cc(i));const r=[],s=e.split(\";\");let o=0;for(let e of s){const s=e.split(\",\"),a=s[0].charAt(0),c=s[0].charAt(1),l=s[0].endsWith(\".\");if(1==s.length);else{const e=s[0].endsWith(\".\")||s[0].endsWith(\"?\")?s[0].substring(2,s[0].length-1):s[0].substring(2);let h=[];if(e.length>1)if(Yf(e))h.push(e);else for(let t=0;t<e.length;t++)h.push(e.substring(t,t+1));else h.push(e);const d=new Map;for(let e of h)d.set(e,new Map);let u=1,f=Number.parseInt(s[u++]),p=0,g=0;for(;p<i.length;){if(\"N\"===a||i[p]===a){const e=n?i.length-1-p:p;if(g===f){for(let i of h){const n=t?t[o++]:255;d.get(i).set(e,n)}if(u<s.length)f=Number.parseInt(s[u++]),g=0;else{if(!l)break;f=-1}}else{if(l)for(let t of h)d.get(t).set(e,0);g++}}p++}for(let e of h)r.push(new Wf(a,c,e,d.get(e)))}}return r}(e,t,this.seq,this.isNegativeStrand()))}return this.baseModificationSets}getGroupValue(e,t,i){const n=this;switch(e){case\"strand\":return n.strand?\"+\":\"-\";case\"firstOfPairStrand\":const e=n.firstOfPairStrand;return void 0===e?\"\":e?\"+\":\"-\";case\"mateChr\":return n.mate&&n.isMateMapped()?n.mate.chr:\"\";case\"pairOrientation\":return ep[i][n.pairOrientation]||\"\";case\"chimeric\":return n.tags().SA?\"chimeric\":\"\";case\"supplementary\":return n.isSupplementary?\"supplementary\":\"\";case\"readOrder\":return n.isPaired()&&n.isFirstOfPair()?\"first\":n.isPaired()&&n.isSecondOfPair()?\"second\":\"\";case\"phase\":return n.tags().HP||\"\";case\"tag\":return n.tags()[t]||\"\";default:return}}positionToReadIndex(e){const t=Fp(this.blocks,e);return t?e-t.start+t.seqOffset:void 0}}const bp=new Set;function Fp(e,t){for(let i=0;i<e.length;i++){const n=e[i];if(t>=n.start&&t<n.start+n.len)return n}}function vp(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function yp(e,t){return e[t+1]<<8|e[t]}function Ap(e,t){return new DataView(e.buffer).getFloat32(t)}function Cp(e,t){return new DataView(e.buffer).getInt8(t)}function _p(e,t){return new DataView(e.buffer).getUint8(t)}class xp{constructor(e){e&&Object.assign(this,e)}seqIndexAt(e){return Math.floor(e)-this.start+this.seqOffset}}class kp{constructor(e){e||(e={}),this.vendorFailed=e.vendorFailed=!1!==e.vendorFailed,this.duplicate=e.duplicate=!1!==e.duplicate,this.secondary=e.secondary||!1,this.supplementary=e.supplementary||!1,this.mq=e.mq||0,e.readgroups&&(this.readgroups=new Set(e.readgroups))}pass(e){if(!e.isMapped())return!1;if(this.vendorFailed&&e.isFailsVendorQualityCheck())return!1;if(this.duplicate&&e.isDuplicate())return!1;if(this.secondary&&e.isSecondary())return!1;if(this.supplementary&&e.isSupplementary())return!1;if(e.mq<this.mq)return!1;if(this.readgroups){const t=e.tags().RG;return this.readgroups.has(t)}return!0}}const Ip=Dp(new Uint8Array([66,65,77,1]),0),Sp=[\"=\",\"A\",\"C\",\"M\",\"G\",\"R\",\"S\",\"V\",\"T\",\"W\",\"Y\",\"H\",\"K\",\"D\",\"B\",\"N\"],Ep=[\"M\",\"I\",\"D\",\"N\",\"S\",\"H\",\"P\",\"=\",\"X\",\"?\",\"?\",\"?\",\"?\",\"?\",\"?\",\"?\"],Np={c:1,C:1,s:2,S:2,i:4,I:4,f:4},Bp=1e4,Mp={readHeader:async function(e,t,i){const n=gs(await Qs.loadArrayBuffer(e,t));return Mp.decodeBamHeader(n,i)},decodeBamHeader:function(e){const t=Dp(e,0);if(t!==Ip)throw new Error(\"BAM header errror: bad magic number.  This could be caused by either a corrupt or missing file.\");const i=Dp(e,4);let n=\"\";for(var r=0;r<i;++r)n+=String.fromCharCode(e[r+8]);const s=Dp(e,i+8);let o=i+12;const a={},c=[];for(r=0;r<s;++r){const t=Dp(e,o);let i=\"\";for(var l=0;l<t-1;++l)i+=String.fromCharCode(e[o+4+l]);a[i]=r,c[r]=i,o=o+8+t}return{magicNumber:t,size:o,chrNames:c,chrToIndex:a}},bam_tag2cigar:function(e,t,i,n,r,s){function o(e){return\"C\"===e||\"c\"===e||\"A\"===e?1:\"S\"===e||\"s\"===e?2:\"I\"===e||\"i\"===e||\"f\"===e?4:0}if(1!==s.length||r.start<0)return!1;for(var a=i+(n+1>>1)+n;a+4<t;){if(\"CG\"===String.fromCharCode(e[a])+String.fromCharCode(e[a+1]))break;var c=String.fromCharCode(e[a+2]);if(\"B\"===c)a+=8+o(c=String.fromCharCode(e[a+3]))*Dp(e,a+4);else if(\"Z\"===c||\"H\"===c)for(a+=3;0!==e[a++];);else a+=3+o(c)}if(a>=t)return!1;if(\"B\"!==String.fromCharCode(e[a+2])||\"I\"!==String.fromCharCode(e[a+3]))return!1;var l=Dp(e,a+4),h=a+8;if(h+4*l>t)return!1;var d=\"\",u=0;s.length=0,a=h;for(var f=0;f<l;++f,a+=4){var p=Dp(e,a),g=p>>4,m=Ep[15&p];\"M\"!==m&&\"EQ\"!==m&&\"X\"!==m&&\"D\"!==m&&\"N\"!==m&&\"=\"!==m||(u+=g),d=d+g+m,s.push({len:g,ltr:m})}return r.cigar=d,r.lengthOnRef=u,!0},decodeBamRecords:function(e,t,i,n,r,s,o,a){for(;t<e.length;){const u=t+Dp(e,t)+4,f=new wp,p=Dp(e,t+4),g=Dp(e,t+8);if(u>e.length)return;if(p<0){t=u;continue}if(void 0!==r&&(p>r||g>o))return!0;if(void 0!==r&&p<r){t=u;continue}const m=Dp(e,t+12),w=(65280&m)>>8,b=255&m,F=Dp(e,t+16),v=(4294901760&F)>>16,y=65535&F,A=Dp(e,t+20),C=Dp(e,t+24),_=Dp(e,t+28),x=Dp(e,t+32);let k=[];for(let i=0;i<b-1;++i)k.push(String.fromCharCode(e[t+36+i]));k=k.join(\"\");let I=0,S=\"\",E=t+36+b;const N=[];let B;for(let t=0;t<y;++t){var c=Dp(e,E),l=c>>4,h=Ep[15&c];\"M\"!==h&&\"EQ\"!==h&&\"X\"!==h&&\"D\"!==h&&\"N\"!==h&&\"=\"!==h||(I+=l),S=S+l+h,E+=4,B={len:l,ltr:h},N.push(B)}if(f.chr=n[p],f.start=g,f.flags=v,f.strand=!(16&v),f.readName=k,f.cigar=S,f.lengthOnRef=I,f.fragmentLength=x,f.mq=w,Mp.bam_tag2cigar(e,u,E,A,f,N),f.end=f.start+f.lengthOnRef,f.end<s){t=u;continue}let M=[];const R=A+1>>1;for(let t=0;t<R;++t){var d=e[E+t];M.push(Sp[(240&d)>>4]),M.push(Sp[15&d])}M=M.slice(0,A).join(\"\"),E+=R;const D=[];for(let t=0;t<A;++t)D.push(e[E+t]);E+=A,C>=0&&(f.mate={chr:n[C],position:_,strand:!(32&v)}),f.seq=M,f.qual=D;const T=new Uint8Array(e.buffer.slice(E,u));f.tagDict=zp(T),this.setPairOrientation(f),(void 0===a||a.pass(f))&&(Rp(f,N),i.push(f)),t=u}},decodeSamRecords:function(e,t,i,n,r,s){var o,a,c,l,h,d,u,f,p,g;for(l=(o=Dt(e)).length,!1,a=0;a<l;a++)if(h=o[a].split(\"\\t\"),(p=new wp).chr=h[2],p.start=Number.parseInt(h[3])-1,p.flags=Number.parseInt(h[1]),p.readName=h[0],p.strand=!(16&p.flags),p.mq=Number.parseInt(h[4]),p.cigar=h[5],p.fragmentLength=Number.parseInt(h[8]),p.seq=h[9],\"*\"!==p.chr&&p.isMapped()&&p.chr===i){if(p.start>r)break;if(f=0,(g=Tp(p.cigar)).forEach((function(e){var t=e.len,i=e.ltr;\"M\"!==i&&\"EQ\"!==i&&\"X\"!==i&&\"D\"!==i&&\"N\"!==i&&\"=\"!==i||(f+=t)})),p.lengthOnRef=f,!(p.start+f<n)){for(d=h[10],p.qual=[],c=0;c<d.length;c++)p.qual[c]=d.charCodeAt(c)-33;p.tagDict=h.length<11?{}:Lp(h.slice(11)),p.isMateMapped()&&(u=h[6],p.mate={chr:\"=\"===u?p.chr:u,position:Number.parseInt(h[7]),strand:!(32&p.flags)}),this.setPairOrientation(p),(void 0===s||s.pass(p))&&(Rp(p,g),t.push(p))}}},setReaderDefaults:function(e,t){e.filter=\"function\"==typeof t.filter?{pass:t.filter}:new kp(t.filter),t.readgroup&&(e.filter.readgroups=new Set([t.readgroup])),e.alleleFreqThreshold=void 0===t.alleleFreqThreshold?.2:t.alleleFreqThreshold,e.samplingWindowSize=void 0===t.samplingWindowSize?100:t.samplingWindowSize,e.samplingDepth=void 0===t.samplingDepth?500:t.samplingDepth,e.samplingDepth>Bp&&(console.log(\"Warning: attempt to set sampling depth > maximum value of \"+Bp),e.samplingDepth=Bp)},setPairOrientation:function(e){if(e.isMapped()&&e.mate&&e.isMateMapped()&&e.mate.chr===e.chr){var t=e.strand?\"F\":\"R\",i=e.mate,n=i.strand?\"F\":\"R\",r=\" \",s=\" \";e.isFirstOfPair()?(r=\"1\",s=\"2\"):e.isSecondOfPair()&&(r=\"2\",s=\"1\");var o=[],a=e.fragmentLength,c=e.end-e.start;if(0===a)a=(e.start<i.position?i.position+c:i.position-c)-e.start;a>0?(o[0]=t,o[1]=r,o[2]=n,o[3]=s):(o[2]=t,o[3]=r,o[0]=n,o[1]=s),e.pairOrientation=o.join(\"\")}}};function Rp(e,t){const i=[];let n,r,s=0,o=e.start;e.scStart=e.start,e.scLengthOnRef=e.lengthOnRef;for(let a of t){let t;switch(a.ltr){case\"H\":case\"P\":break;case\"S\":t=o,e.scLengthOnRef+=a.len,0===i.length&&(e.scStart-=a.len,t-=a.len),i.push(new xp({start:t,seqOffset:s,len:a.len,type:\"S\"})),s+=a.len;break;case\"N\":case\"D\":void 0===r&&(r=[]),r.push({start:o,len:a.len,type:a.ltr}),o+=a.len;break;case\"I\":void 0===n&&(n=[]),n.push(new xp({start:o,len:a.len,seqOffset:s,type:\"I\"})),s+=a.len;break;case\"M\":case\"EQ\":case\"=\":case\"X\":i.push(new xp({start:o,seqOffset:s,len:a.len,type:\"M\"})),s+=a.len,o+=a.len;break;default:console.log(\"Error processing cigar element: \"+a.len+a.ltr)}}e.blocks=i,e.insertions=n,e.gaps=r}function Dp(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function Tp(e){var t,i,n,r,s,o,a,c,l;for(t=[],i=[],s=null,r=e.length,n=0;n<r;n++)o=e.charAt(n),l=void 0,(l=o.charCodeAt(0))>=48&&l<=57?i.push(o):(a=o,c=Number.parseInt(i.join(\"\")),i=[],null!==s&&s.ltr===a?s.len+=c:(s={len:c,ltr:a},t.push(s)));return t}function Lp(e){var t={};return e.forEach((function(e){var i=e.split(\":\");t[i[0]]=i[2]})),t}function zp(e){let t=0;const i=e.length,n={},r=new DataView(e.buffer);for(;t<i;){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const o=String.fromCharCode(e[t++]);let a;if(\"A\"===o)a=String.fromCharCode(e[t]),t++;else if(\"i\"===o||\"I\"===o)a=r.getInt32(t,!0),t+=4;else if(\"c\"===o)a=r.getInt8(t,!0),t++;else if(\"C\"===o)a=r.getUint8(t,!0),t++;else if(\"s\"===o||\"S\"===o)a=r.getInt16(t,!0),t+=2;else if(\"f\"===o)a=r.getFloat32(t,!0),t+=4;else if(\"Z\"===o)for(a=\"\";;){var s=e[t++];if(0===s)break;a+=String.fromCharCode(s)}else{if(\"B\"!==o){a=\"Error unknown type: \"+o,n[i]=a;break}{const s=String.fromCharCode(e[t++]);let o=Np[s];if(void 0===o){n[i]=`Error: unknown element type '${s}'`;break}const c=r.getInt32(t,!0);t+=4;const l=t+c*o;for(a=[];t<l;){switch(s){case\"c\":a.push(r.getInt8(t,!0));break;case\"C\":a.push(r.getUint8(t,!0));break;case\"s\":a.push(r.getInt16(t,!0));break;case\"S\":a.push(r.getUint16(t,!0));break;case\"i\":a.push(r.getInt32(t,!0));break;case\"I\":a.push(r.getUint32(t,!0));break;case\"f\":a.push(r.getFloat32(t,!0))}t+=o}}}n[i]=a}return n}class Hp{chrAliasTable=new Map;constructor(e,t){this.config=e,this.genome=t,this.bamPath=e.url,this.isDataUri=Ga(e.url),Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(!this.alignmentCache){let e;if(this.isDataUri){const t=function(e){const t=e.split(\",\"),i=t[0].split(\":\")[1];let n=t[1];n=i.indexOf(\"base64\")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s<n.length;s++)r[s]=n.charCodeAt(s);return r}(this.bamPath);e=gs(t.buffer)}else{e=gs(await Qs.loadArrayBuffer(this.bamPath,Ua(this.config)))}this.alignmentCache=this.#C(e)}const n=await this.#_(e),r=this.alignmentCache.queryFeatures(n,t,i),s=new tp(e,t,i,this.config);for(let e of r)s.push(e);return s.finish(),s}#C(e){const t=[];return this.header=Mp.decodeBamHeader(e),Mp.decodeBamRecords(e,this.header.size,t,this.header.chrNames,void 0,0,Number.MAX_SAFE_INTEGER,this.filter),new Zs(t,this.genome)}async#_(e){const t=new Set(this.header.chrNames);if(t.has(e))return e;if(this.chrAliasTable.has(e))return this.chrAliasTable.get(e);if(this.genome){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>t.has(e)));e.length>0&&(n=e[0])}return this.chrAliasTable.set(e,n),n}return e}}class Pp{chrAliasTable=new Map;constructor(e,t){this.config=e,this.genome=t,this.bamPath=e.url,this.baiPath=e.indexURL,Mp.setReaderDefaults(this,e),this._blockLoader=new yh(e)}async readAlignments(e,t,i){const n=await this.#x(e),r=new tp(e,t,i,this.config);if(void 0===n)return r;{const e=(await this.getIndex()).chunksForRange(n,t,i);if(!e||0===e.length)return r;for(let s of e){const e=await this._blockLoader.getData(s.minv,s.maxv);if(Mp.decodeBamRecords(e,s.minv.offset,r,this.header.chrNames,n,t,i,this.filter))break}return r.finish(),r}}async#x(e){if(await this.getHeader(),this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.header.chrToIndex[e];if(void 0===t){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>void 0!==this.header.chrToIndex[e]));e.length>0&&(n=e[0],t=this.header.chrToIndex[e[0]])}this.chrAliasTable.set(e,n)}return t}async getHeader(){if(!this.header){const e=this.genome,t=await this.getIndex();let i;if(t.firstBlockPosition){const e=Ua(this.config,{range:{start:t.firstBlockPosition,size:26}}),n=ms(await Qs.loadArrayBuffer(this.bamPath,e));i=t.firstBlockPosition+n}else i=64e3;const n=Ua(this.config,{range:{start:0,size:i}});this.header=await Mp.readHeader(this.bamPath,n,e)}return this.header}async getIndex(){return this.index||(this.index=await gh(this.baiPath,this.config)),this.index}async getChrIndex(){if(this.chrToIndex)return this.chrToIndex;{const e=await this.getHeader();return this.chrToIndex=e.chrToIndex,this.indexToChr=e.chrNames,this.chrNames=new Set(e.chrNames),this.chrToIndex}}}class Op{constructor(e,t){this.config=e,this.genome=t;const i={};e.sources.sequences.forEach((function(n){const r=t?t.getChromosomeName(n):n;i[r]=function(e,t,i){const n={url:e.sources.url.replace(\"$CHR\",i)};e.sources.indexURL&&(n.indexURL=e.sources.indexURL.replace(\"$CHR\",i));const r=Object.assign(e,n);return new Pp(r,t)}(e,t,n)})),this.bamReaders=i,Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(this.bamReaders.hasOwnProperty(e)){let n=this.bamReaders[e];return await n.readAlignments(e,t,i)}return new tp(e,t,i,this.config)}}const Up=function(e,t){this.config=e,this.genome=t,Mp.setReaderDefaults(this,e)};function qp(){const e=this,t=this.genome;if(this.header)return Promise.resolve(this.header);{const i=this.config.url+\"?file=\"+this.config.alignmentFile+\"&options=-b,-H\",n=Ua(this.config);return Mp.readHeader(i,n,t).then((function(t){return e.header=t,t}))}}Up.prototype.readAlignments=function(e,t,i){var n=this;return qp.call(n).then((function(r){var s,o;return s=r.chrAliasTable.hasOwnProperty(e)?r.chrAliasTable[e]:e,o=n.config.url+\"?reference=\"+n.config.referenceFile+\"&file=\"+n.config.alignmentFile+\"&region=\"+s+\":\"+t+\"-\"+i,Qs.loadString(o,Ua(n.config)).then((function(o){var a;return r.chrToIndex[s],a=new tp(e,t,i,n.config),Mp.decodeSamRecords(o,a,s,t,i,n.filter),a}))}))};class Qp extends Rh{constructor(e,t){super(e,t),Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(!this.header){const e=gs((await this.readHeaderData()).buffer);this.header=Mp.decodeBamHeader(e,this.genome),this.chrAliasTable=new Map;for(let e of this.header.chrNames)this.chrAliasTable.set(e,this.genome.getChromosomeName(e))}let n=this.chrAliasTable.has(e)?this.chrAliasTable.get(e):e;const r=gs((await this.readData(n,t,i)).buffer);this.header=Mp.decodeBamHeader(r,this.genome);const s=this.header.chrToIndex[e],o=new tp(e,t,i,this.config);return Mp.decodeBamRecords(r,this.header.size,o,this.header.chrNames,s,t,i,this.filter),o.finish(),o}}\n",
-       "/*! For license information please see cram-bundle.js.LICENSE.txt */for(var Vp=(()=>{var e={4923:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(8712),s=i(5931),o=i(9747);function a(e,t){const[i,n,r,s,o,a]=t,c=i;e[c]||(e[c]=[]),e[c].push({start:n,span:r,containerStart:s,sliceStart:o,sliceBytes:a})}t.default=class{constructor(e){this.filehandle=(0,s.open)(e.url,e.path,e.filehandle)}parseIndex(){return n(this,void 0,void 0,(function*(){const e={},t=31===(i=yield this.filehandle.readFile())[0]&&139===i[1]?(0,r.unzip)(i):i;var i;if(t.length>4&&21578050===t.readUInt32LE(0))throw new o.CramMalformedError(\"invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support\");let n=[],s=\"\";for(const i of t)if(i>=48&&i<=57||!s&&45===i)s+=String.fromCharCode(i);else if(9===i)n.push(Number.parseInt(s,10)),s=\"\";else if(10===i)n.push(Number.parseInt(s,10)),s=\"\",a(e,n),n=[];else if(13!==i&&32!==i)throw new o.CramMalformedError(\"invalid .crai index file\");return s&&n.push(Number.parseInt(s,10)),6===n.length&&a(e,n),Object.entries(e).forEach((([t,i])=>{const n=i;e[t]=n.sort(((e,t)=>e.start-t.start||e.span-t.span))})),e}))}getIndex(){return this.parseIndexP||(this.parseIndexP=this.parseIndex().catch((e=>{throw this.parseIndexP=void 0,e}))),this.parseIndexP}hasDataForReferenceSequence(e){return n(this,void 0,void 0,(function*(){return!!(yield this.getIndex())[e]}))}getEntriesForRange(e,t,i){return n(this,void 0,void 0,(function*(){const n=(yield this.getIndex())[e];if(!n)return[];const r=e=>{const n=e.start,r=e.start+e.span;return n>i?-1:r<=t?1:0},s=[];for(const e of n)0===r(e)&&s.push(e);return s}))}}},9508:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=class{constructor(e,t){this.parameters=e,this.dataType=t}}},368:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`)}decode(e,t,i,n){return(0,o.getBits)(t.content,n.coreBlock,this.parameters.length)-this.parameters.offset}}t.default=a},8635:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=n(i(9508)),s=i(400);class o extends r.default{constructor(e,t,i){super(e,t),this.instantiateCodec=i}decode(e,t,i,n){const r=this._getLengthCodec().decode(e,t,i,n),s=this._getDataCodec(),o=new Uint8Array(r);for(let a=0;a<r;a+=1)o[a]=s.decode(e,t,i,n);return o}_getLengthCodec(){const e=this.parameters.lengthsEncoding;return this.instantiateCodec(e,\"int\")}_getDataCodec(){const e=this.parameters.valuesEncoding;return this.instantiateCodec(e,\"byte\")}}t.default=o,\"_getLengthCodec _getDataCodec\".split(\" \").forEach((e=>{(0,s.tinyMemoize)(o,e)}))},4839:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{decode(e,t,i,n){const{blockContentId:s}=this.parameters,o=i[s];if(!o)throw new r.CramMalformedError(`no block found with content ID ${s}`);const a=n.externalBlocks.getCursor(s);return this._decodeByteArray(o,a)}_decodeByteArray(e,t){const i=e.content,{stopByte:n}=this.parameters,r=t.bytePosition;let s=t.bytePosition;for(;i[s]!==n&&s<i.length;){if(s===i.length)throw new o.CramBufferOverrunError(\"byteArrayStop reading beyond length of data buffer?\");s+=1}return t.bytePosition=s+1,i.subarray(r,s)}}t.default=a},8153:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(400),a=i(612);class c extends s.default{constructor(e,t){if(super(e,t),\"int\"===this.dataType)this._decodeData=this._decodeInt;else{if(\"byte\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by EXTERNAL codec`);this._decodeData=this._decodeByte}}decode(e,t,i,n){const{blockContentId:s}=this.parameters,o=i[s];if(!o)throw new r.CramMalformedError(`no block found with content ID ${s}}`);const a=n.externalBlocks.getCursor(s);return this._decodeData(o,a)}_decodeInt(e,t){const[i,n]=(0,o.parseItf8)(e.content,t.bytePosition);return t.bytePosition=t.bytePosition+n,i}_decodeByte(e,t){if(t.bytePosition>=e.content.length)throw new a.CramBufferOverrunError(\"attempted to read beyond end of block. this file seems truncated.\");return e.content[t.bytePosition++]}}t.default=c},8185:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`)}decode(e,t,i,n){let r=1;for(;0===(0,o.getBits)(t.content,n.coreBlock,1);)r+=1;return((0,o.getBits)(t.content,n.coreBlock,r-1)|1<<r-1)-this.parameters.offset}}t.default=a},612:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.CramBufferOverrunError=void 0,t.getBits=function(e,t,n){let r=0;if(t.bytePosition+(7-t.bitPosition+n)/8>e.length)throw new i(\"read error during 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t=0;t<this.parameters.numCodes;t++)e[t]={symbol:this.parameters.symbols[t],bitLength:this.parameters.bitLengths[t]};e=e.sort(((e,t)=>e.bitLength-t.bitLength||e.symbol-t.symbol)),this.codeBook={},e.forEach((e=>{this.codeBook[e.bitLength]||(this.codeBook[e.bitLength]=[]),this.codeBook[e.bitLength].push(e.symbol)}))}buildCodes(){this.codes={};let e=0,t=-1;Object.entries(this.codeBook).forEach((([i,n])=>{const s=Number.parseInt(i,10);n.forEach((i=>{const n={bitLength:s,value:i,bitCode:0};t+=1;const o=s-e;if(t<<=o,n.bitCode=t,e+=o,function(e){let t=e-(e>>1)&1431655765;return t=(858993459&t)+(t>>2&858993459),16843009*(t+(t>>4)&252645135)>>24}(t)>s)throw new r.CramMalformedError(\"Symbol out of range\");this.codes[i]=n}))}))}buildCaches(){this.sortedCodes=Object.values(this.codes).sort(((e,t)=>e.bitLength-t.bitLength||e.bitCode-t.bitCode)),this.sortedValuesByBitCode=this.sortedCodes.map((e=>e.value)),this.sortedBitCodes=this.sortedCodes.map((e=>e.bitCode)),this.sortedBitLengthsByBitCode=this.sortedCodes.map((e=>e.bitLength));const e=Math.max(...this.sortedBitCodes);this.bitCodeToValue=new Array(e+1).fill(-1);for(let e=0;e<this.sortedBitCodes.length;e+=1)this.bitCodeToValue[this.sortedCodes[e].bitCode]=e}decode(e,t,i,n){return this._decode(e,t,n.coreBlock)}_decodeZeroLengthCode(){return this.sortedCodes[0].value}_decode(e,t,i){const n=t.content;let s=0,a=0;for(let e=0;e<this.sortedCodes.length;e+=1){const t=this.sortedCodes[e].bitLength;a<<=t-s,a|=(0,o.getBits)(n,i,t-s),s=t;{const i=this.bitCodeToValue[a];if(i>-1&&this.sortedBitLengthsByBitCode[i]===t)return this.sortedValuesByBitCode[i];for(let i=e;this.sortedCodes[i+1].bitLength===t&&i<this.sortedCodes.length;i+=1)e+=1}}throw new r.CramMalformedError(\"Huffman symbol not found.\")}}t.default=a},6524:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.instantiateCodec=function e(t,i){const n=(s=\"ignore\"===i?0:t.codecId,u[s]);var s;if(!n)throw new r.CramUnimplementedError(`no codec implemented for codec ID ${t.codecId}`);return new n(t.parameters,i,e)};const r=i(9747),s=n(i(4341)),o=n(i(8153)),a=n(i(4839)),c=n(i(8635)),l=n(i(368)),h=n(i(8185)),d=n(i(99)),u={1:o.default,3:s.default,4:c.default,5:a.default,6:l.default,7:d.default,9:h.default}},99:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new 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0===a?(r=this.parameters.K,s=(0,o.getBits)(t.content,n.coreBlock,r)):(r=a+this.parameters.K-1,s=1<<r|(0,o.getBits)(t.content,n.coreBlock,r)),s-this.parameters.offset}}t.default=a},7295:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default={CRAM_FLAG_PRESERVE_QUAL_SCORES:1,CRAM_FLAG_DETACHED:2,CRAM_FLAG_MATE_DOWNSTREAM:4,CRAM_FLAG_NO_SEQ:8,CRAM_FLAG_MASK:15,CRAM_M_REVERSE:1,CRAM_M_UNMAP:2,BAM_FPAIRED:1,BAM_FPROPER_PAIR:2,BAM_FUNMAP:4,BAM_FMUNMAP:8,BAM_FREVERSE:16,BAM_FMREVERSE:32,BAM_FREAD1:64,BAM_FREAD2:128,BAM_FSECONDARY:256,BAM_FQCFAIL:512,BAM_FDUP:1024,BAM_FSUPPLEMENTARY:2048,BAM_CMATCH:0,BAM_CINS:1,BAM_CDEL:2,BAM_CREF_SKIP:3,BAM_CSOFT_CLIP:4,BAM_CHARD_CLIP:5,BAM_CPAD:6,BAM_CEQUAL:7,BAM_CDIFF:8,BAM_CBACK:9,BAM_CIGAR_STR:\"MIDNSHP:XB\",BAM_CIGAR_SHIFT:4,BAM_CIGAR_MASK:15,BAM_CIGAR_TYPE:246183}},7219:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0});const 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t[0][e[0]>>6&3]=\"C\",t[0][e[0]>>4&3]=\"G\",t[0][e[0]>>2&3]=\"T\",t[0][3&e[0]]=\"N\",t[1][e[1]>>6&3]=\"A\",t[1][e[1]>>4&3]=\"G\",t[1][e[1]>>2&3]=\"T\",t[1][3&e[1]]=\"N\",t[2][e[2]>>6&3]=\"A\",t[2][e[2]>>4&3]=\"C\",t[2][e[2]>>2&3]=\"T\",t[2][3&e[2]]=\"N\",t[3][e[3]>>6&3]=\"A\",t[3][e[3]>>4&3]=\"C\",t[3][e[3]>>2&3]=\"G\",t[3][3&e[3]]=\"N\",t[4][e[4]>>6&3]=\"A\",t[4][e[4]>>4&3]=\"C\",t[4][e[4]>>2&3]=\"G\",t[4][3&e[4]]=\"T\",t}(e.preservation.SM),this.dataSeriesEncoding=e.dataSeriesEncoding,this.tagEncoding=e.tagEncoding}getCodecForTag(e){const t=this.tagCodecCache[e];if(t)return t;{const t=this.tagEncoding[e];if(!t)throw new Error(\"Error, no tag encoding\");const i=(0,n.instantiateCodec)(t,\"byteArray\");return this.tagCodecCache[e]=i,i}}getTagNames(e){return this.tagIdsDictionary[e]}getCodecForDataSeries(e){let t=this.dataSeriesCodecCache[e];if(void 0===t){const i=this.dataSeriesEncoding[e];if(i){const o=s[e];if(!o)throw new r.CramMalformedError(`data series name ${e} not defined in 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0:e.numRecords))return null;const{majorVersion:t}=yield this.file.getDefinition(),i=(0,h.getSectionParsers)(t),n=yield this.getFirstBlock();if(void 0===n)return;if(\"COMPRESSION_HEADER\"!==n.contentType)throw new o.CramMalformedError(`invalid content type ${n.contentType} in compression header block`);const r=(0,a.parseItem)(n.content,i.cramCompressionHeader.parser,0,n.contentPosition);return Object.assign(Object.assign({},n),{parsedContent:r})}))}getFirstBlock(){return n(this,void 0,void 0,(function*(){const e=yield this.getHeader();if(e)return this.file.readBlock(e._endPosition)}))}getCompressionScheme(){return n(this,void 0,void 0,(function*(){const e=yield this.getCompressionHeaderBlock();if(e)return new l.default(e.parsedContent)}))}getSlice(e,t){return new c.default(this,e,t)}_readContainerHeader(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield 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\").forEach((e=>{(0,a.tinyMemoize)(d,e)}))},6794:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(8287),o=r(i(928)),a=r(i(7392)),c=r(i(6960)),l=r(i(235)),h=i(1307),d=i(9747),u=i(8712),f=r(i(9989)),p=i(3165),g=r(i(78)),m=i(5931),w=i(400),b=i(5417);class F{constructor(e){var t;if(this.file=(0,m.open)(e.url,e.path,e.filehandle),this.validateChecksums=!0,this.fetchReferenceSequenceCallback=e.seqFetch,this.options={checkSequenceMD5:e.checkSequenceMD5,cacheSize:null!==(t=e.cacheSize)&&void 0!==t?t:2e4},this.featureCache=new a.default({maxSize:this.options.cacheSize}),function(){const e=new Uint32Array([287454020]),t=new Uint8Array(e.buffer);return 68===t[0]?0:17===t[0]?1:2}()>0)throw new Error(\"Detected big-endian machine, may be unable to run\")}read(e,t,i,n){return this.file.read(e,t,i,n)}stat(){return this.file.stat()}getDefinition(){return n(this,void 0,void 0,(function*(){const{maxLength:e,parser:t}=(0,p.cramFileDefinition)(),i=s.Buffer.allocUnsafe(e);yield this.file.read(i,0,e,0);const n=t(i).value;if(2!==n.majorVersion&&3!==n.majorVersion)throw new d.CramUnimplementedError(`CRAM version ${n.majorVersion} not supported`);return n}))}getSamHeader(){return n(this,void 0,void 0,(function*(){const e=yield this.getContainerById(0);if(!e)throw new d.CramMalformedError(\"file contains no containers\");const t=yield e.getFirstBlock();if(void 0===t)return(0,b.parseHeaderText)(\"\");const i=t.content,n=i.readInt32LE(0),r=i.toString(\"utf8\",4,4+n);return this.header=r,(0,b.parseHeaderText)(r)}))}getHeaderText(){return n(this,void 0,void 0,(function*(){return yield this.getSamHeader(),this.header}))}getContainerById(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t);let n=i.cramFileDefinition.maxLength;const{size:r}=yield this.file.stat(),{cramContainerHeader1:s}=i;let o;for(let t=0;t<=e;t++){if(n+s.maxLength+8>=r)return;o=this.getContainerAtPosition(n);const i=yield o.getHeader();if(!i)throw new d.CramMalformedError(`container ${e} not found in file`);if(0===t){n=i._endPosition;for(let e=0;e<i.numBlocks;e++){const e=yield this.readBlock(n);if(void 0===e)return;n=e._endPosition}}else n+=i._size+i.length}return o}))}checkCrc32(e,t,i,r){return n(this,void 0,void 0,(function*(){const n=s.Buffer.allocUnsafe(t);yield this.file.read(n,0,t,e);const a=o.default.unsigned(n);if(a!==i)throw new d.CramMalformedError(`crc mismatch in ${r}: recorded CRC32 = ${i}, but calculated CRC32 = ${a}`)}))}containerCount(){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.getDefinition(),t=(0,p.getSectionParsers)(e),{size:i}=yield this.file.stat(),{cramContainerHeader1:n}=t;let r=0,s=t.cramFileDefinition.maxLength;for(;s+n.maxLength+8<i;){const e=yield this.getContainerAtPosition(s).getHeader();if(!e)break;if(0===r){s=e._endPosition;for(let t=0;t<e.numBlocks;t++){const e=yield this.readBlock(s);if(void 0===e)return;s=e._endPosition}}else s+=e._size+e.length;r+=1}return r}))}getContainerAtPosition(e){return new g.default(this,e)}readBlockHeader(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t),{cramBlockHeader:n}=i,{size:r}=yield this.file.stat();if(e+n.maxLength>=r)return;const o=s.Buffer.allocUnsafe(n.maxLength);return yield this.file.read(o,0,n.maxLength,e),(0,w.parseItem)(o,n.parser,0,e)}))}_parseSection(e,t){return n(this,arguments,void 0,(function*(e,t,i=e.maxLength,n){let r;if(n)r=n;else{const{size:e}=yield this.file.stat();if(t+i>=e)return;r=s.Buffer.allocUnsafe(i),yield this.file.read(r,0,i,t)}const o=(0,w.parseItem)(r,e.parser,0,t);if(o._size!==i)throw new d.CramMalformedError(`section read error: requested size ${i} does not equal parsed size ${o._size}`);return o}))}_uncompress(e,t,i){return n(this,void 0,void 0,(function*(){if(\"gzip\"===e)(0,u.unzip)(t).copy(i);else if(\"bzip2\"===e){const e=l.default.array(t);let n,r=l.default.header(e),o=0;do{n=l.default.decompress(e,r),-1!==n&&(s.Buffer.from(n).copy(i,o),o+=n.length,r-=n.length)}while(-1!==n)}else if(\"lzma\"===e){const e=new Response(new h.XzReadableStream((n=t,new ReadableStream({start(e){e.enqueue(n),e.close()}}))));s.Buffer.from(yield e.arrayBuffer()).copy(i)}else if(\"rans\"===e)(0,f.default)(t,i);else if(\"rans4x16\"===e)c.default.r4x16_uncompress(t,i);else if(\"arith\"===e)c.default.arith_uncompress(t,i);else if(\"fqzcomp\"===e)c.default.fqzcomp_uncompress(t,i);else{if(\"tok3\"!==e)throw new d.CramUnimplementedError(`${e} decompression not yet implemented`);c.default.tok3_uncompress(t,i)}var n}))}readBlock(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t),n=yield this.readBlockHeader(e);if(void 0===n)return;const r=n._endPosition,o=s.Buffer.allocUnsafe(n.uncompressedSize),a=Object.assign(Object.assign({},n),{_endPosition:r,contentPosition:r,content:o});if(\"raw\"!==n.compressionMethod){const e=s.Buffer.allocUnsafe(n.compressedSize);yield this.read(e,0,n.compressedSize,r),yield this._uncompress(n.compressionMethod,e,o)}else yield this.read(o,0,n.uncompressedSize,r);if(t>=3){const t=yield this._parseSection(i.cramBlockCrc32,r+n.compressedSize);if(void 0===t)return;a.crc32=t.crc32,this.validateChecksums&&(yield this.checkCrc32(e,n._size+n.compressedSize,t.crc32,\"block data\")),a._endPosition=t._endPosition,a._size=a.compressedSize+i.cramBlockCrc32.maxLength}else a._endPosition=r+a.compressedSize,a._size=a.compressedSize;return a}))}}t.default=F,\"getDefinition getSectionParsers getSamHeader\".split(\" \").forEach((e=>{(0,w.tinyMemoize)(F,e)}))},7390:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=t.CramRecord=void 0;var r=i(8401);Object.defineProperty(t,\"CramRecord\",{enumerable:!0,get:function(){return n(r).default}});var s=i(6794);Object.defineProperty(t,\"default\",{enumerable:!0,get:function(){return n(s).default}})},8401:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.MateFlagsDecoder=t.CramFlagsDecoder=t.BamFlagsDecoder=t.MateFlags=t.CramFlags=t.BamFlags=void 0;const r=n(i(7295)),s={a:0,A:0,c:1,C:1,g:2,G:2,t:3,T:3,n:4,N:4};function o(e){const t={};for(const[i,n]of e)t[`is${n}`]=e=>!!(e&i),t[`set${n}`]=e=>e|i;return t}t.BamFlags=[[1,\"Paired\"],[2,\"ProperlyPaired\"],[4,\"SegmentUnmapped\"],[8,\"MateUnmapped\"],[16,\"ReverseComplemented\"],[32,\"MateReverseComplemented\"],[64,\"Read1\"],[128,\"Read2\"],[256,\"Secondary\"],[512,\"FailedQc\"],[1024,\"Duplicate\"],[2048,\"Supplementary\"]],t.CramFlags=[[1,\"PreservingQualityScores\"],[2,\"Detached\"],[4,\"WithMateDownstream\"],[8,\"DecodeSequenceAsStar\"]],t.MateFlags=[[1,\"OnNegativeStrand\"],[2,\"Unmapped\"]],t.BamFlagsDecoder=o(t.BamFlags),t.CramFlagsDecoder=o(t.CramFlags),t.MateFlagsDecoder=o(t.MateFlags),t.default=class{constructor({flags:e,cramFlags:t,readLength:i,mappingQuality:n,lengthOnRef:r,qualityScores:s,mateRecordNumber:o,readBases:a,readFeatures:c,mateToUse:l,readGroupId:h,readName:d,sequenceId:u,uniqueId:f,templateSize:p,alignmentStart:g,tags:m}){this.flags=e,this.cramFlags=t,this.readLength=i,this.mappingQuality=n,this.lengthOnRef=r,this.qualityScores=s,a&&(this.readBases=a),this.readGroupId=h,this.readName=d,this.sequenceId=u,this.uniqueId=f,this.templateSize=p,this.alignmentStart=g,this.tags=m,c&&(this.readFeatures=c),l&&(this.mate={flags:l.mateFlags,readName:l.mateReadName,sequenceId:l.mateSequenceId,alignmentStart:l.mateAlignmentStart}),o&&(this.mateRecordNumber=o)}isPaired(){return!!(this.flags&r.default.BAM_FPAIRED)}isProperlyPaired(){return!!(this.flags&r.default.BAM_FPROPER_PAIR)}isSegmentUnmapped(){return!!(this.flags&r.default.BAM_FUNMAP)}isMateUnmapped(){return!!(this.flags&r.default.BAM_FMUNMAP)}isReverseComplemented(){return!!(this.flags&r.default.BAM_FREVERSE)}isMateReverseComplemented(){return!!(this.flags&r.default.BAM_FMREVERSE)}isRead1(){return!!(this.flags&r.default.BAM_FREAD1)}isRead2(){return!!(this.flags&r.default.BAM_FREAD2)}isSecondary(){return!!(this.flags&r.default.BAM_FSECONDARY)}isFailedQc(){return!!(this.flags&r.default.BAM_FQCFAIL)}isDuplicate(){return!!(this.flags&r.default.BAM_FDUP)}isSupplementary(){return!!(this.flags&r.default.BAM_FSUPPLEMENTARY)}isDetached(){return!!(this.cramFlags&r.default.CRAM_FLAG_DETACHED)}hasMateDownStream(){return!!(this.cramFlags&r.default.CRAM_FLAG_MATE_DOWNSTREAM)}isPreservingQualityScores(){return!!(this.cramFlags&r.default.CRAM_FLAG_PRESERVE_QUAL_SCORES)}isUnknownBases(){return!!(this.cramFlags&r.default.CRAM_FLAG_NO_SEQ)}getReadBases(){if(!this.readBases&&this._refRegion){const e=function(e,t){if(!e.lengthOnRef&&!e.readLength)return null;if(e.isUnknownBases())return null;const i=e.alignmentStart-t.start;if(!e.readFeatures)return t.seq.slice(i,i+(e.lengthOnRef||0)).toUpperCase();let n=\"\",r=i,s=0;for(;n.length<e.readLength;)if(s<e.readFeatures.length){const i=e.readFeatures[s];if(\"Q\"===i.code||\"q\"===i.code)s+=1;else if(i.pos===n.length+1)if(s+=1,\"b\"===i.code){const e=i.data;n+=e,r+=e.length}else\"B\"===i.code?(n+=i.data[0],r+=1):\"X\"===i.code?(n+=i.sub,r+=1):\"I\"===i.code?n+=i.data:\"D\"===i.code?r+=i.data:\"i\"===i.code?n+=i.data:\"N\"===i.code?r+=i.data:\"S\"===i.code?n+=i.data:\"P\"===i.code||i.code;else if(s<e.readFeatures.length){const e=t.seq.slice(r,r+i.pos-n.length-1);n+=e,r+=e.length}}else{const i=t.seq.slice(r,r+e.readLength-n.length);n+=i,r+=i.length}return n.toUpperCase()}(this,this._refRegion);e&&(this.readBases=e)}return this.readBases}getPairOrientation(){if(!this.isSegmentUnmapped()&&this.isPaired()&&!this.isMateUnmapped()&&this.mate&&this.sequenceId===this.mate.sequenceId){const e=this.isReverseComplemented()?\"R\":\"F\",t=this.isMateReverseComplemented()?\"R\":\"F\";let i=\" \",n=\" \";this.isRead1()?(i=\"1\",n=\"2\"):this.isRead2()&&(i=\"2\",n=\"1\");const r=[];let s=this.templateLength||this.templateSize;if(void 0===s)throw new Error(\"One of templateSize and templateLength must be set\");return this.alignmentStart>this.mate.alignmentStart&&s>0&&(s=-s),s>0?(r[0]=e,r[1]=i,r[2]=t,r[3]=n):(r[2]=e,r[3]=i,r[0]=t,r[1]=n),r.join(\"\")}return null}addReferenceSequence(e,t){this.readFeatures&&this.readFeatures.forEach((i=>{\"X\"===i.code&&function(e,t,i,n){const r=n.refPos-t.start,o=t.seq.charAt(r);o&&(n.ref=o);let a=s[o];void 0===a&&(a=4);const c=i.substitutionMatrix[a][n.data];c&&(n.sub=c)}(0,e,t,i)})),!this.readBases&&e.start<=this.alignmentStart&&e.end>=this.alignmentStart+(this.lengthOnRef||this.readLength)-1&&(this._refRegion=e)}toJSON(){const e={};return Object.keys(this).forEach((t=>{t.startsWith(\"_\")||(e[t]=this[t])})),e.readBases=this.getReadBases(),e}}},3165:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.cramFileDefinition=r,t.cramBlockHeader=s,t.cramBlockCrc32=o,t.cramTagDictionary=c,t.cramPreservationMap=l,t.isMappedSliceHeader=function(e){return\"number\"==typeof e.refSeqId},t.getSectionParsers=function(e){return{cramFileDefinition:r(),cramBlockHeader:s(),cramBlockCrc32:o(),cramDataSeriesEncodingMap:p(),cramTagEncodingMap:g(),cramCompressionHeader:{parser:(e,t)=>{const{value:i,offset:n}=l().parser(e,t);t=n;const{value:r,offset:s}=p().parser(e,t);t=s;const{value:o,offset:a}=g().parser(e,t);return t=a,{value:{dataSeriesEncoding:h(r),preservation:h(i),tagEncoding:h(o)},offset:t}}},cramEncoding:{parser:(e,t)=>f(e,t)},cramUnmappedSliceHeader:d(e),cramMappedSliceHeader:u(e),cramContainerHeader1:m(e),cramContainerHeader2:w(e)}};const n=i(400);function r(){return{parser:(e,t=0)=>{const i=e,n=new DataView(i.buffer,i.byteOffset,i.length);let r=0;const s=e.subarray(r,r+4).toString();r+=4;const o=n.getUint8(r);r+=1;const a=n.getUint8(r);r+=1;const c=i.subarray(r,r+20).toString().replaceAll(\"\\0\",\"\");return r+=20,{value:{magic:s,majorVersion:o,minorVersion:a,fileId:c},offset:r}},maxLength:26}}function s(){return{parser:(e,t=0)=>{const i=e,r=new DataView(i.buffer,i.byteOffset,i.length);let s=0;const o=r.getUint8(s),a=[\"raw\",\"gzip\",\"bzip2\",\"lzma\",\"rans\",\"rans4x16\",\"arith\",\"fqzcomp\",\"tok3\"][o];if(!a)throw new Error(`compression method number ${o} not implemented`);s+=1;const c=r.getUint8(s),l=[\"FILE_HEADER\",\"COMPRESSION_HEADER\",\"MAPPED_SLICE_HEADER\",\"UNMAPPED_SLICE_HEADER\",\"EXTERNAL_DATA\",\"CORE_DATA\"][c];if(!l)throw new Error(`invalid block content type id ${c}`);s+=1;const[h,d]=(0,n.parseItf8)(e,s);s+=d;const[u,f]=(0,n.parseItf8)(e,s);s+=f;const[p,g]=(0,n.parseItf8)(e,s);return s+=g,{offset:s,value:{uncompressedSize:p,compressedSize:u,contentId:h,contentType:l,compressionMethod:a}}},maxLength:17}}function o(){return{parser:(e,t)=>{const i=e,n=new DataView(i.buffer,i.byteOffset,i.length).getUint32(t,!0);return{offset:t+=4,value:{crc32:n}}},maxLength:4}}function a(e,t,i){const n=e.toString(\"utf8\",t,i),r=[];for(let e=0;e<n.length;e+=3)r.push(n.slice(e,e+3));return r}function c(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const s=e.subarray(t,t+i);t+=i;const o=[];let c=0,l=0;for(;l<s.length;l++)s[l]||(o.push(a(s,c,l)),c=l+1);return l>c&&o.push(a(s,c,l)),{value:{size:i,ents:o},offset:t}}}}function l(){return{parser:(e,t)=>{const i=e,r=new DataView(i.buffer,i.byteOffset,i.length),[s,o]=(0,n.parseItf8)(e,t);t+=o;const[a,l]=(0,n.parseItf8)(e,t);t+=l;const h=[];for(let i=0;i<a;i++){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);if(t+=2,\"MI\"===i||\"UI\"===i||\"PI\"===i||\"RN\"===i||\"AP\"===i||\"RR\"===i)h.push({key:i,value:!!r.getUint8(t)}),t+=1;else if(\"SM\"===i)h.push({key:i,value:[r.getUint8(t),r.getUint8(t+1),r.getUint8(t+2),r.getUint8(t+3),r.getUint8(t+4)]}),t+=5;else{if(\"TD\"!==i)throw new Error(`unknown key ${i}`);{const{offset:n,value:r}=c().parser(e,t);h.push({key:i,value:r.ents}),t=n}}}return{value:{mapSize:s,mapCount:a,ents:h},offset:t}}}}function h(e){const t={};for(const{key:i,value:n}of e.ents)t[i]&&console.warn(`duplicate key ${i} in map`),t[i]=n;return t}function d(e){return{parser:(t,i)=>{const[r,s]=(0,n.parseItf8)(t,i);i+=s;let o=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);i+=r,o=e}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);i+=r,o=e}else console.warn(\"recordCounter=0\");const[a,c]=(0,n.parseItf8)(t,i);i+=c;const[l,h]=(0,n.parseItf8)(t,i);i+=h;const d=[];for(let e=0;e<l;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,d.push(e)}let u;return e>=2&&(u=[...t.subarray(i,i+16)],i+=16),{value:{recordCounter:o,md5:u,contentIds:d,numContentIds:l,numBlocks:a,numRecords:r},offset:i}},maxLength:e=>40+5*e}}function u(e){return{parser:(t,i)=>{const[r,s]=(0,n.parseItf8)(t,i);i+=s;const[o,a]=(0,n.parseItf8)(t,i);i+=a;const[c,l]=(0,n.parseItf8)(t,i);i+=l;const[h,d]=(0,n.parseItf8)(t,i);i+=d;let u=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);i+=r,u=e}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);i+=r,u=e}else console.warn(\"majorVersion is <2, recordCounter set to 0\");const[f,p]=(0,n.parseItf8)(t,i);i+=p;const[g,m]=(0,n.parseItf8)(t,i);i+=m;const w=[];for(let e=0;e<g;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,w.push(e)}const[b,F]=(0,n.parseItf8)(t,i);let v;return i+=F,e>=2&&(v=[...t.subarray(i,i+16)],i+=16),{value:{md5:v,numBlocks:f,numRecords:h,numContentIds:g,refSeqSpan:c,refSeqId:r,refSeqStart:o,recordCounter:u,refBaseBlockId:b,contentIds:w},offset:i}},maxLength:e=>60+5*e}}function f(e,t){const i=e,r=new DataView(i.buffer,i.byteOffset,i.length),[s,o]=(0,n.parseItf8)(e,t);t+=o;const[a,c]=(0,n.parseItf8)(e,t);t+=c;const l={};if(0===s);else if(1===s){const[i,r]=(0,n.parseItf8)(e,t);l.blockContentId=i,t+=r}else if(2===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.M=s,t+=o}else if(3===s){const i=(0,n.parseItf8)(e,t),r=i[0];t+=i[1];const s=[];for(let i=0;i<r;i++){const i=(0,n.parseItf8)(e,t);s.push(i[0]),t+=i[1]}l.symbols=s;const o=(0,n.parseItf8)(e,t),a=i[0];l.numLengths=a,l.numCodes=r,l.numLengths=a,t+=o[1];const c=[];for(let i=0;i<a;i++){const i=(0,n.parseItf8)(e,t);t+=i[1],c.push(i[0])}l.bitLengths=c}else if(4===s){const{value:i,offset:n}=f(e,t);l.lengthsEncoding=i,t=n;const{value:r,offset:s}=f(e,t);l.valuesEncoding=r,t=s}else if(5===s){l.stopByte=r.getUint8(t),t+=1;const[i,s]=(0,n.parseItf8)(e,t);l.blockContentId=i,t+=s}else if(6===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.length=s,t+=o}else if(7===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.K=s,t+=o}else if(8===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.log2m=s,t+=o}else{if(9!==s)throw new Error(`unknown codecId ${s}`);{const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r}}return{value:{codecId:s,parametersBytes:a,parameters:l},offset:t}}function p(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const[s,o]=(0,n.parseItf8)(e,t);t+=o;const a=[];for(let i=0;i<s;i++){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const{value:n,offset:r}=f(e,t);t=r,a.push({key:i,value:n})}return{value:{mapSize:i,ents:a,mapCount:s},offset:t}}}}function g(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const[s,o]=(0,n.parseItf8)(e,t);t+=o;const a=[];for(let i=0;i<s;i++){const[i,r]=(0,n.parseItf8)(e,t);t+=r;const s=String.fromCharCode(i>>16&255)+String.fromCharCode(i>>8&255)+String.fromCharCode(255&i),{value:o,offset:c}=f(e,t);t=c,a.push({key:s,value:o})}return{value:{mapSize:i,ents:a,mapCount:s},offset:t}}}}function m(e){return{maxLength:52,parser:(t,i)=>{const r=t,s=new DataView(r.buffer,r.byteOffset,r.length).getInt32(i,!0);i+=4;const[o,a]=(0,n.parseItf8)(t,i);i+=a;const[c,l]=(0,n.parseItf8)(t,i);i+=l;const[h,d]=(0,n.parseItf8)(t,i);i+=d;const[u,f]=(0,n.parseItf8)(t,i);i+=f;let p,g=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);g=e,i+=r}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);g=e,i+=r}else console.warn(\"setting recordCounter=0\");if(e>1){const[e,r]=(0,n.parseLtf8)(t,i);p=e,i+=r}const[m,w]=(0,n.parseItf8)(t,i);i+=w;const[b,F]=(0,n.parseItf8)(t,i);return{value:{length:s,refSeqId:o,refSeqStart:c,alignmentSpan:h,numBlocks:m,numLandmarks:b,numBases:p,recordCounter:g,numRecords:u},offset:i+=F}}}}function w(e){return{parser:(t,i)=>{const r=t,s=new DataView(r.buffer,r.byteOffset,r.length),[o,a]=(0,n.parseItf8)(t,i);i+=a;const c=[];for(let e=0;e<o;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,c.push(e)}let l;return e>=3&&(l=s.getUint32(i,!0),i+=4),{value:Object.assign(Object.assign({},void 0===l?{}:{crc32:l}),{numLandmarks:o,landmarks:c}),offset:i}},maxLength:e=>5+5*e+4}}},6484:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,c,l,h,d,u,f){let p=t(\"BF\");const g=t(\"CF\");if(!(0,s.isMappedSliceHeader)(c.parsedContent))throw new Error(\"slice header not mapped\");const m=u>1&&-2===c.parsedContent.refSeqId?t(\"RI\"):c.parsedContent.refSeqId,w=t(\"RL\");let b=t(\"AP\");i.APdelta&&(b+=d.lastAlignmentStart),d.lastAlignmentStart=b;const F=t(\"RG\");let v,y,A,C;if(i.readNamesIncluded&&(v=o(t(\"RN\"))),r.CramFlagsDecoder.isDetached(g)){const e=t(\"MF\");let n;i.readNamesIncluded||(n=o(t(\"RN\")),v=n);const s=t(\"NS\"),a=t(\"NP\");(e||s>-1)&&(y={mateFlags:e,mateSequenceId:s,mateAlignmentStart:a,mateReadName:n}),A=t(\"TS\"),r.MateFlagsDecoder.isUnmapped(e)&&(p=r.BamFlagsDecoder.setMateUnmapped(p)),r.MateFlagsDecoder.isOnNegativeStrand(e)&&(p=r.BamFlagsDecoder.setMateReverseComplemented(p))}else r.CramFlagsDecoder.isWithMateDownstream(g)&&(C=t(\"NF\")+f+1);const _=t(\"TL\");if(_<0)throw new n.CramMalformedError(\"invalid TL index\");const x={},k=i.getTagNames(_),I=k.length;for(let t=0;t<I;t+=1){const n=k[t],r=n.slice(0,2),s=n.slice(2,3),o=i.getCodecForTag(n).decode(e,l,h,d);x[r]=\"number\"==typeof o?o:a(s,o)}let S,E,N,B,M;if(r.BamFlagsDecoder.isSegmentUnmapped(p))if(r.CramFlagsDecoder.isDecodeSequenceAsStar(g))M=null,B=null;else{const e=new Array(w);for(let i=0;i<e.length;i+=1)e[i]=t(\"BA\");if(M=String.fromCharCode(...e),r.CramFlagsDecoder.isPreservingQualityScores(g)){B=new Array(w);for(let i=0;i<e.length;i+=1)B[i]=t(\"QS\")}}else{const e=t(\"FN\");if(e&&(S=function(e,t,i,r,s){let o=0,a=e-1;const c=new Array(t);function l([e,t]){const n=i(t);if(\"character\"===e)return String.fromCharCode(n);if(\"string\"===e){let e=\"\";for(let t=0;t<n.byteLength;t++)e+=String.fromCharCode(n[t]);return e}return\"numArray\"===e?n.toArray():n}for(let e=0;e<t;e+=1){const t=String.fromCharCode(i(\"FC\")),r=i(\"FP\"),h={B:[\"character\",\"BA\"],S:[\"string\",s>1?\"SC\":\"IN\"],X:[\"number\",\"BS\"],D:[\"number\",\"DL\"],I:[\"string\",\"IN\"],i:[\"character\",\"BA\"],b:[\"string\",\"BB\"],q:[\"numArray\",\"QQ\"],Q:[\"number\",\"QS\"],H:[\"number\",\"HC\"],P:[\"number\",\"PD\"],N:[\"number\",\"RS\"]}[t];if(!h)throw new n.CramMalformedError(`invalid read feature code \"${t}\"`);let d=l(h);const u={B:[\"number\",\"QS\"]}[t];u&&(d=[d,l(u)]),o+=r;const f=o;a+=r;const p=a;\"D\"===t||\"N\"===t?a+=d:\"I\"===t||\"S\"===t?a-=d.length:\"i\"===t&&(a-=1),c[e]={code:t,pos:f,refPos:p,data:d}}return c}(b,e,t,0,u)),E=w,S)for(const{code:e,data:t}of S)\"D\"===e||\"N\"===e?E+=t:\"I\"===e||\"S\"===e?E-=t.length:\"i\"===e&&(E-=1);if(Number.isNaN(E)&&(console.warn(`${v||`${m}:${b}`} record has invalid read features`),E=w),N=t(\"MQ\"),r.CramFlagsDecoder.isPreservingQualityScores(g)){B=new Array(w);for(let e=0;e<B.length;e++)B[e]=t(\"QS\")}}return{readLength:w,sequenceId:m,cramFlags:g,flags:p,alignmentStart:b,readGroupId:F,readName:v,mateToUse:y,templateSize:A,mateRecordNumber:C,readFeatures:S,lengthOnRef:E,mappingQuality:N,qualityScores:B,readBases:M,tags:x}};const n=i(9747),r=i(8401),s=i(3165);function o(e){let t=\"\";for(let i=0;i<e.length&&0!==e[i];i++)t+=String.fromCharCode(e[i]);return t}function a(e,t){if(\"Z\"===e)return o(t);if(\"A\"===e)return String.fromCharCode(t[0]);if(\"I\"===e)return new Uint32Array(t.buffer)[0];if(\"i\"===e)return new Int32Array(t.buffer)[0];if(\"s\"===e)return new Int16Array(t.buffer)[0];if(\"S\"===e)return new Uint16Array(t.buffer)[0];if(\"c\"===e)return new Int8Array(t.buffer)[0];if(\"C\"===e)return t[0];if(\"f\"===e)return new Float32Array(t.buffer)[0];if(\"H\"===e)return Number.parseInt(o(t).replace(/^0x/,\"\"),16);if(\"B\"===e)return function(e){const t=String.fromCharCode(e[0]),i=new DataView(e.buffer).getUint32(1,!0),n=new Array(i);if(e=e.slice(5),\"c\"===t){const t=new Int8Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"C\"===t){const t=new Uint8Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"s\"===t){const t=new Int16Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"S\"===t){const t=new Uint16Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"i\"===t){const t=new Int32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"I\"===t){const t=new Uint32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else{if(\"f\"!==t)throw new Error(`unknown type: ${t}`);{const t=new Float32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}}return n}(t);throw new n.CramMalformedError(`Unrecognized tag type ${e}`)}},6771:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(9747),o=i(400),a=r(i(7295)),c=r(i(6484)),l=r(i(8401)),h=i(3165),d=i(612);function u(e,t,i,n){const r=!!(n.mate||void 0!==n.mateRecordNumber&&n.mateRecordNumber!==t);i.readName||(i.readName=String(i.uniqueId),n.readName=i.readName),i.mate={sequenceId:n.sequenceId,alignmentStart:n.alignmentStart,uniqueId:n.uniqueId},n.readName&&(i.mate.readName=n.readName),n.mate||void 0!==n.mateRecordNumber||(n.mate={sequenceId:i.sequenceId,alignmentStart:i.alignmentStart,uniqueId:i.uniqueId},i.readName&&(n.mate.readName=i.readName)),i.flags|=a.default.BAM_FPAIRED,n.flags&a.default.BAM_FUNMAP&&(i.flags|=a.default.BAM_FMUNMAP),i.flags&a.default.BAM_FUNMAP&&(n.flags|=a.default.BAM_FMUNMAP),n.flags&a.default.BAM_FREVERSE&&(i.flags|=a.default.BAM_FMREVERSE),i.flags&a.default.BAM_FREVERSE&&(n.flags|=a.default.BAM_FMREVERSE),void 0===i.templateLength&&(r?function(e,t,i){const n=function t(i){const n=[i];if(void 0!==i.mateRecordNumber&&i.mateRecordNumber>=0){const r=e[i.mateRecordNumber];if(!r)throw new s.CramMalformedError(\"intra-slice mate record not found, this file seems malformed\");n.push(...t(r))}return n}(i),r=n.map((e=>e.alignmentStart)),o=n.map((e=>e.alignmentStart+e.readLength-1)),a=Math.max(...o)-Math.min(...r)+1;a>=0&&n.forEach((e=>{if(void 0!==e.templateLength)throw new s.CramMalformedError(\"mate pair group has some members that have template lengths already, this file seems malformed\");e.templateLength=a}))}(e,0,i):function(e,t){const i=Math.min(e.alignmentStart,t.alignmentStart),n=Math.max(e.alignmentStart+e.readLength-1,t.alignmentStart+t.readLength-1)-i+1;e.templateLength=n,t.templateLength=n}(i,n)),i.mateRecordNumber=void 0}class f{constructor(e,t,i){this.container=e,this.containerPosition=t,this.sliceSize=i,this.file=e.file}getHeader(){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.file.getDefinition(),t=(0,h.getSectionParsers)(e),i=yield this.container.getHeader();if(!i)throw new Error(\"no container header detected\");const n=yield this.file.readBlock(i._endPosition+this.containerPosition);if(void 0===n)throw new Error(\"block header undefined\");if(\"MAPPED_SLICE_HEADER\"===n.contentType){const e=(0,o.parseItem)(n.content,t.cramMappedSliceHeader.parser,0,i._endPosition);return Object.assign(Object.assign({},n),{parsedContent:e})}if(\"UNMAPPED_SLICE_HEADER\"===n.contentType){const e=(0,o.parseItem)(n.content,t.cramUnmappedSliceHeader.parser,0,i._endPosition);return Object.assign(Object.assign({},n),{parsedContent:e})}throw new s.CramMalformedError(`error reading slice header block, invalid content type ${n.contentType}`)}))}getBlocks(){return n(this,void 0,void 0,(function*(){const e=yield this.getHeader();let t=e._endPosition;const i=new Array(e.parsedContent.numBlocks);for(let e=0;e<i.length;e++){const n=yield this.file.readBlock(t);if(void 0===n)throw new Error(\"block undefined\");i[e]=n,t=i[e]._endPosition}return i}))}getCoreDataBlock(){return n(this,void 0,void 0,(function*(){return(yield this.getBlocks())[0]}))}_getBlocksContentIdIndex(){return n(this,void 0,void 0,(function*(){const e=yield this.getBlocks(),t={};return e.forEach((e=>{\"EXTERNAL_DATA\"===e.contentType&&(t[e.contentId]=e)})),t}))}getBlockByContentId(e){return n(this,void 0,void 0,(function*(){return(yield this._getBlocksContentIdIndex())[e]}))}getReferenceRegion(){return n(this,void 0,void 0,(function*(){const e=(yield this.getHeader()).parsedContent;if(!(0,h.isMappedSliceHeader)(e))throw new Error(\"slice header not mapped\");if(e.refSeqId<0)return;const t=yield this.container.getCompressionScheme();if(void 0===t)throw new Error(\"compression scheme undefined\");if(e.refBaseBlockId>=0){const t=yield this.getBlockByContentId(e.refBaseBlockId);if(!t)throw new s.CramMalformedError(\"embedded reference specified, but reference block does not exist\");return{seq:t.data.toString(\"utf8\"),start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan}}if(t.referenceRequired||this.file.fetchReferenceSequenceCallback){if(!this.file.fetchReferenceSequenceCallback)throw new Error(\"reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence\");const t=yield this.file.fetchReferenceSequenceCallback(e.refSeqId,e.refSeqStart,e.refSeqStart+e.refSeqSpan-1);if(t.length!==e.refSeqSpan)throw new s.CramArgumentError(\"seqFetch callback returned a reference sequence of the wrong length\");return{seq:t,start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan}}}))}getAllRecords(){return this.getRecords((()=>!0))}_fetchRecords(){return n(this,void 0,void 0,(function*(){var e,t;const{majorVersion:i}=yield this.file.getDefinition(),n=yield this.container.getCompressionScheme();if(void 0===n)throw new Error(\"compression scheme undefined\");const r=yield this.getHeader(),a=yield this._getBlocksContentIdIndex();if(i>1&&this.file.options.checkSequenceMD5&&(0,h.isMappedSliceHeader)(r.parsedContent)&&r.parsedContent.refSeqId>=0&&\"0000000000000000\"!==(null===(e=r.parsedContent.md5)||void 0===e?void 0:e.join(\"\"))){const e=yield this.getReferenceRegion();if(e){const{seq:i,start:n,end:a}=e,c=(0,o.sequenceMD5)(i),l=null===(t=r.parsedContent.md5)||void 0===t?void 0:t.map((e=>(e<16?\"0\":\"\")+e.toString(16))).join(\"\");if(c!==l)throw new s.CramMalformedError(`MD5 checksum reference mismatch for ref ${r.parsedContent.refSeqId} pos ${n}..${a}. recorded MD5: ${l}, calculated MD5: ${c}`)}}const f=yield this.getCoreDataBlock(),p={lastAlignmentStart:(0,h.isMappedSliceHeader)(r.parsedContent)?r.parsedContent.refSeqStart:0,coreBlock:{bitPosition:7,bytePosition:0},externalBlocks:{map:new Map,getCursor(e){let t=this.map.get(e);return void 0===t&&(t={bitPosition:7,bytePosition:0},this.map.set(e,t)),t}}},g=e=>{const t=n.getCodecForDataSeries(e);if(!t)throw new s.CramMalformedError(`no codec defined for ${e} data series`);return t.decode(this,f,a,p)},m=new Array(r.parsedContent.numRecords);for(let t=0;t<m.length;t+=1)try{const e=(0,c.default)(this,g,n,r,f,a,p,i,t);m[t]=new l.default(Object.assign(Object.assign({},e),{uniqueId:r.contentPosition+r.parsedContent.recordCounter+t+1}))}catch(e){if(e instanceof d.CramBufferOverrunError){console.warn(\"read attempted beyond end of buffer, file seems truncated.\");break}throw e}for(let e=0;e<m.length;e+=1){const{mateRecordNumber:t}=m[e];void 0!==t&&t>=0&&u(m,e,m[e],m[t])}return m}))}getRecords(e){return n(this,void 0,void 0,(function*(){const t=this.container.filePosition+this.containerPosition;let i=this.file.featureCache.get(t.toString());i||(i=this._fetchRecords(),this.file.featureCache.set(t.toString(),i));const r=(yield i).filter(e);if(r.length&&this.file.fetchReferenceSequenceCallback){const e=yield this.getHeader();if((0,h.isMappedSliceHeader)(e.parsedContent)&&(e.parsedContent.refSeqId>=0||-2===e.parsedContent.refSeqId)){const t=e.parsedContent.refSeqId>=0?e.parsedContent.refSeqId:void 0,i=yield this.container.getCompressionScheme();if(void 0===i)throw new Error(\"compression scheme undefined\");const s={};for(const e of r){const i=void 0!==t?t:e.sequenceId;let n=s[i];n||(n={id:i,start:e.alignmentStart,end:Number.NEGATIVE_INFINITY,seq:null},s[i]=n);const r=e.alignmentStart+(e.lengthOnRef||e.readLength)-1;r>n.end&&(n.end=r),e.alignmentStart<n.start&&(n.start=e.alignmentStart)}yield Promise.all(Object.values(s).map((e=>n(this,void 0,void 0,(function*(){-1!==e.id&&e.start<=e.end&&this.file.fetchReferenceSequenceCallback&&(e.seq=yield this.file.fetchReferenceSequenceCallback(e.id,e.start,e.end))})))));for(const e of r){const n=s[void 0!==t?t:e.sequenceId];if(null==n?void 0:n.seq){const t=n.seq;e.addReferenceSequence(Object.assign(Object.assign({},n),{seq:t}),i)}}}}return r}))}}t.default=f,\"getHeader getBlocks _getBlocksContentIdIndex\".split(\" \").forEach((e=>{(0,o.tinyMemoize)(f,e)}))},400:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.itf8Size=function(e){return-128&e?-16384&e?-2097152&e?-268435456&e?5:4:3:2:1},t.parseItf8=function(e,t){let i=t;const n=e[i];let r;if(n<128?(r=n,i+=1):n<192?(r=16383&(n<<8|e[i+1]),i+=2):n<224?(r=2097151&(n<<16|e[i+1]<<8|e[i+2]),i+=3):n<240?(r=268435455&(n<<24|e[i+1]<<16|e[i+2]<<8|e[i+3]),i+=4):(r=(15&n)<<28|e[i+1]<<20|e[i+2]<<12|e[i+3]<<4|15&e[i+4],i+=5),i>e.length)throw new o.CramBufferOverrunError(\"Attempted to read beyond end of buffer; this file seems truncated.\");return[r,i-t]},t.parseLtf8=function(e,t){let i=t;const n=e[i];let r;if(n<128)r=n,i+=1;else if(n<192)r=16383&(e[i]<<8|e[i+1]),i+=2;else if(n<224)r=2097151&(e[i]<<16|e[i+1]<<8|e[i+2]),r=(63&n)<<16|e.readUInt16LE(i+1),i+=3;else if(n<240)r=268435455&(e[i]<<24|e[i+1]<<16|e[i+2]<<8|e[i+3]),i+=4;else if(n<248)r=(15&e[i])*Math.pow(2,32)+(e[i+1]<<24)|e[i+2]<<16|e[i+3]<<8|e[i+4],i+=5;else if(n<252)r=((7&e[i])<<8|e[i+1])*Math.pow(2,32)+(e[i+2]<<24)|e[i+3]<<16|e[i+4]<<8|e[i+5],i+=6;else if(n<254)r=((3&e[i])<<16|e[i+1]<<8|e[i+2])*Math.pow(2,32)+(e[i+3]<<24)|e[i+4]<<16|e[i+5]<<8|e[i+6],i+=7;else if(n<255){if(r=s.default.fromBytesBE(e.slice(i+1,i+8)),r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new Error(\"integer overflow\");r=r.toNumber(),i+=8}else{if(r=s.default.fromBytesBE(e.slice(i+1,i+9)),r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new Error(\"integer overflow\");r=r.toNumber(),i+=9}return[r,i-t]},t.parseItem=function(e,t,i=0,n=0){const{offset:r,value:s}=t(e,i);return Object.assign(Object.assign({},s),{_endPosition:r+n,_size:r-i})},t.tinyMemoize=function(e,t){const i=e.prototype[t],n=`_memo_${t}`;e.prototype[t]=function(){if(!(n in this)){const e=i.call(this);this[n]=e,Promise.resolve(e).catch((()=>{delete this[n]}))}return this[n]}},t.sequenceMD5=function(e){return(0,r.default)(e.toUpperCase().replaceAll(/[^\\u0021-\\u007e]/g,\"\"))};const r=n(i(3503)),s=n(i(8570)),o=i(612)},9747:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.CramArgumentError=t.CramSizeLimitError=t.CramMalformedError=t.CramUnimplementedError=t.CramError=void 0;class i extends Error{}t.CramError=i;class n extends Error{}t.CramUnimplementedError=n,t.CramMalformedError=class extends i{},t.CramSizeLimitError=class extends i{},t.CramArgumentError=class extends i{}},7806:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.IndexedCramFile=t.CraiIndex=t.CramRecord=t.CramFile=void 0;var r=i(7390);Object.defineProperty(t,\"CramFile\",{enumerable:!0,get:function(){return n(r).default}}),Object.defineProperty(t,\"CramRecord\",{enumerable:!0,get:function(){return r.CramRecord}});var s=i(4923);Object.defineProperty(t,\"CraiIndex\",{enumerable:!0,get:function(){return n(s).default}});var o=i(6014);Object.defineProperty(t,\"IndexedCramFile\",{enumerable:!0,get:function(){return n(o).default}})},6014:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(9747),o=r(i(7390));t.default=class{constructor(e){var t;if(this.cram=null!==(t=e.cram)&&void 0!==t?t:new o.default({url:e.cramUrl,path:e.cramPath,filehandle:e.cramFilehandle,seqFetch:e.seqFetch,checkSequenceMD5:e.checkSequenceMD5,cacheSize:e.cacheSize}),!(this.cram instanceof o.default))throw new Error(\"invalid arguments: no cramfile\");this.index=e.index}getRecordsForRange(e,t,i){return n(this,arguments,void 0,(function*(e,t,i,n={}){if(n.viewAsPairs=n.viewAsPairs||!1,n.pairAcrossChr=n.pairAcrossChr||!1,n.maxInsertSize=n.maxInsertSize||2e5,\"string\"==typeof e)throw new s.CramUnimplementedError(\"string sequence names not yet supported\");const r=e,o=yield this.index.getEntriesForRange(r,t,i),a=n=>n.sequenceId===e&&n.alignmentStart<=i&&void 0!==n.lengthOnRef&&n.alignmentStart+n.lengthOnRef-1>=t,c=yield Promise.all(o.map((e=>this.getRecordsInSlice(e,a))));let l=Array.prototype.concat(...c);if(n.viewAsPairs){const e={},t={};for(const i of l){const n=i.readName;if(void 0===n)throw new Error(\"readName undefined\");const r=i.uniqueId;e[n]||(e[n]=0),e[n]+=1,t[r]=1}const i={};Object.entries(e).forEach((([e,t])=>{1===t&&(i[e]=!0)}));const s=[];for(const e of l){const t=e.readName;if(void 0===t)throw new Error(\"readName undefined\");if(i[t]&&e.mate&&(e.mate.sequenceId===r||n.pairAcrossChr)&&Math.abs(e.alignmentStart-e.mate.alignmentStart)<n.maxInsertSize){const t=this.index.getEntriesForRange(e.mate.sequenceId,e.mate.alignmentStart,e.mate.alignmentStart+1);s.push(t)}}const o=yield Promise.all(s);let a=[];for(const e of o)a.push(...e);a=a.sort(((e,t)=>e.toString().localeCompare(t.toString()))).filter(((e,t,i)=>!t||e.toString()!==i[t-1].toString()));const c=[];for(const e of a){let n=this.cram.featureCache.get(e.toString());n||(n=this.getRecordsInSlice(e,(()=>!0)),this.cram.featureCache.set(e.toString(),n));const r=n.then((e=>{const n=[];for(const r of e){if(void 0===r.readName)throw new Error(\"readName undefined\");i[r.readName]&&!t[r.uniqueId]&&n.push(r)}return n}));c.push(r)}const h=yield Promise.all(c);if(h.length){const e=h.reduce(((e,t)=>e.concat(t)));l=l.concat(e)}}return l}))}getRecordsInSlice({containerStart:e,sliceStart:t,sliceBytes:i},n){return this.cram.getContainerAtPosition(e).getSlice(t,i).getRecords(n)}hasDataForReferenceSequence(e){return this.index.hasDataForReferenceSequence(e)}}},5931:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.RemoteFile=t.LocalFile=void 0,t.open=function(e,t,i){if(i)return i;if(e)return new n.RemoteFile(e);if(t)return new n.LocalFile(t);throw new Error(\"no url, path, or filehandle provided, cannot open\")};const n=i(1113);var r=i(1113);Object.defineProperty(t,\"LocalFile\",{enumerable:!0,get:function(){return r.LocalFile}}),Object.defineProperty(t,\"RemoteFile\",{enumerable:!0,get:function(){return r.RemoteFile}})},6476:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.RANS_BYTE_L=t.TOTFREQ=t.TF_SHIFT=void 0,t.TF_SHIFT=12,t.TOTFREQ=4096,t.RANS_BYTE_L=1<<23},997:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,n){let a=e.getInt(),c=e.getInt(),l=e.getInt(),h=e.getInt();const d=n.remaining(),u=-4&d;for(let r=0;r<u;r+=4){const d=t.R[o.default.get(a,s.TF_SHIFT)],u=t.R[o.default.get(c,s.TF_SHIFT)],f=t.R[o.default.get(l,s.TF_SHIFT)],p=t.R[o.default.get(h,s.TF_SHIFT)];n.putAt(r,d),n.putAt(r+1,u),n.putAt(r+2,f),n.putAt(r+3,p),a=o.default.advanceSymbolStep(a,i[255&d],s.TF_SHIFT),c=o.default.advanceSymbolStep(c,i[255&u],s.TF_SHIFT),l=o.default.advanceSymbolStep(l,i[255&f],s.TF_SHIFT),h=o.default.advanceSymbolStep(h,i[255&p],s.TF_SHIFT),a=o.default.renormalize(a,e),c=o.default.renormalize(c,e),l=o.default.renormalize(l,e),h=o.default.renormalize(h,e)}let f;switch(n.setPosition(u),3&d){case 0:break;case 1:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f);break;case 2:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(c,s.TF_SHIFT)],o.default.advanceSymbol(c,e,i[255&f],s.TF_SHIFT),n.put(f);break;case 3:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(c,s.TF_SHIFT)],o.default.advanceSymbol(c,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(l,s.TF_SHIFT)],o.default.advanceSymbol(l,e,i[255&f],s.TF_SHIFT),n.put(f);break;default:throw new r.CramMalformedError(\"invalid output size encountered during rANS decoding\")}n.setPosition(0)};const r=i(9747),s=i(6476),o=n(i(488))},7960:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,n){const o=t.remaining();let a=e.getInt(),c=e.getInt(),l=e.getInt(),h=e.getInt();const d=o>>2;let u=0,f=d,p=2*d,g=3*d,m=0,w=0,b=0,F=0;for(;u<d;u+=1,f+=1,p+=1,g+=1){const o=255&i[m].R[s.default.get(a,r.TF_SHIFT)],d=255&i[w].R[s.default.get(c,r.TF_SHIFT)],v=255&i[b].R[s.default.get(l,r.TF_SHIFT)],y=255&i[F].R[s.default.get(h,r.TF_SHIFT)];t.putAt(u,o),t.putAt(f,d),t.putAt(p,v),t.putAt(g,y),a=s.default.advanceSymbolStep(a,n[m][o],r.TF_SHIFT),c=s.default.advanceSymbolStep(c,n[w][d],r.TF_SHIFT),l=s.default.advanceSymbolStep(l,n[b][v],r.TF_SHIFT),h=s.default.advanceSymbolStep(h,n[F][y],r.TF_SHIFT),a=s.default.renormalize(a,e),c=s.default.renormalize(c,e),l=s.default.renormalize(l,e),h=s.default.renormalize(h,e),m=o,w=d,b=v,F=y}for(;g<o;g+=1){const o=255&i[F].R[s.default.get(h,r.TF_SHIFT)];t.putAt(g,o),h=s.default.advanceSymbol(h,e,n[F][o],r.TF_SHIFT),F=o}};const r=i(6476),s=n(i(488))},488:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0});const n=i(9747),r=i(6476);class s{constructor(){this.F=void 0,this.C=void 0}}function o(e,t,i,n){return i*(e>>n)+(e&(1<<n)-1)-t}t.default={FC:s,AriDecoder:class{constructor(){this.fc=new Array(256);for(let e=0;e<this.fc.length;e+=1)this.fc[e]=new s;this.R=null}},DecodingSymbol:class{constructor(){this.start=void 0,this.freq=void 0}},symbolInit:function(e,t,i){if(!(t<=65536))throw new n.CramMalformedError(\"assertion failed: start <= 1<<16\");if(!(i<=65536-t))throw new n.CramMalformedError(\"assertion failed: freq <= 1<<16\");e.start=t,e.freq=i},advanceStep:o,advanceSymbolStep:function(e,t,i){return o(e,t.start,t.freq,i)},get:function(e,t){return e&(1<<t)-1},advanceSymbol:function(e,t,i,n){return function(e,t,i,n,s){if((e=n*(e>>s)+(e&(1<<s)-1)-i)<r.RANS_BYTE_L)do{e=e<<8|255&t.get()}while(e<r.RANS_BYTE_L);return e}(e,t,i.start,i.freq,n)},renormalize:function(e,t){if(e<r.RANS_BYTE_L)do{e=e<<8|255&t.get()}while(e<r.RANS_BYTE_L);return e}}},1971:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.readStatsO0=function(e,t,i){let n=0,r=0,c=255&e.get();do{null==t.fc[c]&&(t.fc[c]=new o.default.FC),t.fc[c].F=255&e.get(),t.fc[c].F>=128&&(t.fc[c].F&=-129,t.fc[c].F=(127&t.fc[c].F)<<8|255&e.get()),t.fc[c].C=r,o.default.symbolInit(i[c],t.fc[c].C,t.fc[c].F),t.R||(t.R=new Array(s.TOTFREQ)),t.R.fill(c,r,r+t.fc[c].F),r+=t.fc[c].F,0===n&&c+1===(255&e.getByteAt(e.position()))?(c=255&e.get(),n=255&e.get()):0!==n?(n-=1,c+=1):c=255&e.get()}while(0!==c);a(r<s.TOTFREQ)},t.readStatsO1=function(e,t,i){let n=0,r=255&e.get();do{let c=0,l=0,h=255&e.get();null==t[r]&&(t[r]=new o.default.AriDecoder);do{null==t[r].fc[h]&&(t[r].fc[h]=new o.default.FC),t[r].fc[h].F=255&e.get(),t[r].fc[h].F>=128&&(t[r].fc[h].F&=-129,t[r].fc[h].F=(127&t[r].fc[h].F)<<8|255&e.get()),t[r].fc[h].C=l,0===t[r].fc[h].F&&(t[r].fc[h].F=s.TOTFREQ),null==i[r][h]&&(i[r][h]=new o.default.RansDecSymbol),o.default.symbolInit(i[r][h],t[r].fc[h].C,t[r].fc[h].F),null==t[r].R&&(t[r].R=new Array(s.TOTFREQ)),t[r].R.fill(h,l,l+t[r].fc[h].F),l+=t[r].fc[h].F,a(l<=s.TOTFREQ),0===c&&h+1===(255&e.getByteAt(e.position()))?(h=255&e.get(),c=255&e.get()):0!==c?(c-=1,h+=1):h=255&e.get()}while(0!==h);0===n&&r+1===(255&e.getByteAt(e.position()))?(r=255&e.get(),n=255&e.get()):0!==n?(n-=1,r+=1):r=255&e.get()}while(0!==r)};const r=i(9747),s=i(6476),o=n(i(488));function a(e){if(!e)throw new r.CramMalformedError(\"assertion failed\")}},9989:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i=0){if(0===e.length)return t.fill(0),t;const n=new d(e,i),u=n.get();if(0!==u&&1!==u)throw new s.CramMalformedError(`Invalid rANS order ${u}`);if(n.getInt()!==n.remaining()-h)throw new s.CramMalformedError(\"Incorrect input length.\");const f=n.getInt(),p=new d(t||r.Buffer.allocUnsafe(f));if(p.length<f)throw new s.CramMalformedError(`Output buffer too small to fit ${f} bytes.`);switch(u){case 0:return function(e,t){const i=new o.default.AriDecoder,n=new Array(256);for(let e=0;e<n.length;e+=1)n[e]=new o.default.DecodingSymbol;return(0,a.readStatsO0)(e,i,n),(0,c.default)(e,i,n,t),t}(n,p);case 1:return function(e,t){const i=new Array(256);for(let e=0;e<i.length;e+=1)i[e]=new o.default.AriDecoder;const n=new Array(256);for(let e=0;e<n.length;e+=1){n[e]=new Array(256);for(let t=0;t<n[e].length;t+=1)n[e][t]=new o.default.DecodingSymbol}return(0,a.readStatsO1)(e,i,n),(0,l.default)(e,t,i,n),t}(n,p);default:throw new s.CramMalformedError(`Invalid rANS order: ${u}`)}};const r=i(8287),s=i(9747),o=n(i(488)),a=i(1971),c=n(i(997)),l=n(i(7960)),h=4;class d{constructor(e,t=0){this._buffer=e,this._position=t,this.length=e.length}get(){const e=this._buffer[this._position];return this._position+=1,e}getByte(){return this.get()}getByteAt(e){return this._buffer[e]}position(){return this._position}put(e){return this._buffer[this._position]=e,this._position+=1,e}putAt(e,t){return this._buffer[e]=t,t}setPosition(e){return this._position=e,e}getInt(){const e=this._buffer.readInt32LE(this._position);return this._position+=4,e}remaining(){return this._buffer.length-this._position}}},5417:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.parseHeaderText=function(e){const t=e.split(/\\r?\\n/),i=[];for(const e of t){const[t,...n]=e.split(/\\t/);t&&i.push({tag:t.slice(1),data:n.map((e=>{const t=e.indexOf(\":\");return-1!==t?{tag:e.slice(0,t),value:e.slice(t+1)}:{tag:e,value:\"\"}}))})}return i}},8712:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.unzip=function(e){return r.Buffer.from((0,n.inflate)(e))};const n=i(1668),r=i(8287)},635:(e,t,i)=>{var n=i(8287).Buffer;const r=i(4646),s=i(8706),o=i(9614),a=i(235),c=128;e.exports=class{decode(e){return this.stream=new s(e),this.decodeStream(this.stream)}decodeStream(e,t=0){var i=this.stream.ReadByte();16&i||(t=this.stream.ReadUint7());var n,r=t,s=1&i;if(8&i)return this.decodeStripe(this.stream,t);if(i&c&&([n,r]=this.decodePackMeta(this.stream)),32&i)var o=this.decodeCat(this.stream,r);else o=4&i?this.decodeExt(this.stream,r):64&i?s?this.decodeRLE1(this.stream,r):this.decodeRLE0(this.stream,r):s?this.decode1(this.stream,r):this.decode0(this.stream,r);return i&c&&(o=this.decodePack(o,n,t)),o}encode(e,t){if(this.stream=new s(\"\",0,1.1*e.length+100),this.stream.WriteByte(t),16&t||this.stream.WriteUint7(e.length),8&t)return n.concat([this.stream.buf.slice(0,this.stream.pos),this.encodeStripe(this.stream,e,t>>8)]);var i,r=1&t,o=e.length;return t&c&&([i,e,o]=this.encodePack(e)),t&c&&this.stream.WriteStream(i),64&t?r?this.encodeRLE1(e,o,this.stream):this.encodeRLE0(e,o,this.stream):r?this.encode1(e,o,this.stream):this.encode0(e,o,this.stream)}decode0(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);var a=new o(s),c=new r(e);c.RangeStartDecode(e);for(var l=0;l<t;l++)i[l]=a.ModelDecode(e,c);return i}encode0(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new o(n);i.WriteByte(n);var c=new r(i);for(s=0;s<t;s++)a.ModelEncode(i,c,e[s]);return c.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decode1(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new Array(s),c=0;c<s;c++)a[c]=new o(s);var l=new r(e);l.RangeStartDecode(e);var h=0;for(c=0;c<t;c++)i[c]=a[h].ModelDecode(e,l),h=i[c];return i}encode1(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new Array(n);for(s=0;s<n;s++)a[s]=new o(n);i.WriteByte(n);var c=new r(i),l=0;for(s=0;s<t;s++)a[l].ModelEncode(i,c,e[s]),l=e[s];return c.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeExt(e,t){var i=new n.allocUnsafe(t),r=a.array(e.buf.slice(e.pos)),s=a.header(r),o=0;do{var c=a.decompress(r,s);-1!=c&&(n.from(c).copy(i,o),o+=c.length,s-=c.length)}while(-1!=c);return i}encodeExt(e,t){}decodeRLE0(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new o(s),c=new Array(258),l=0;l<=257;l++)c[l]=new o(4);var h=new r(e);for(h.RangeStartDecode(e),l=0;l<t;){i[l]=a.ModelDecode(e,h);for(var d=c[i[l]].ModelDecode(e,h),u=d,f=256;3==d;)d=c[f].ModelDecode(e,h),f=257,u+=d;for(var p=1;p<=u;p++)i[l+p]=i[l];l+=u+1}return i}encodeRLE0(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new o(n),c=new Array(258);for(s=0;s<=257;s++)c[s]=new o(4);i.WriteByte(n);var l=new r(i);for(s=0;s<t;){a.ModelEncode(i,l,e[s]);for(var h=1;s+h<t&&e[s+h]==e[s];)h++;h--;var d=e[s];e[s],s+=h+1;var u=h>=3?3:h;for(c[d].ModelEncode(i,l,u),h-=u,d=256;3==u;)u=h>=3?3:h,c[d].ModelEncode(i,l,u),d=257,h-=u}return l.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeRLE1(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new Array(s),c=0;c<s;c++)a[c]=new o(s);var l=new Array(258);for(c=0;c<=257;c++)l[c]=new o(4);var h=new r(e);h.RangeStartDecode(e);var d=0;for(c=0;c<t;){i[c]=a[d].ModelDecode(e,h),d=i[c];for(var u=l[i[c]].ModelDecode(e,h),f=u,p=256;3==u;)u=l[p].ModelDecode(e,h),p=257,f+=u;for(var g=1;g<=f;g++)i[c+g]=i[c];c+=f+1}return i}encodeRLE1(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new Array(n);for(s=0;s<n;s++)a[s]=new o(n);var c=new Array(258);for(s=0;s<=257;s++)c[s]=new o(4);i.WriteByte(n);for(var l=new r(i),h=(s=0,0);s<t;){a[h].ModelEncode(i,l,e[s]);for(var d=1;s+d<t&&e[s+d]==e[s];)d++;d--;var u=e[s];h=e[s],s+=d+1;var f=d>=3?3:d;for(c[u].ModelEncode(i,l,f),d-=f,u=256;3==f;)f=d>=3?3:d,c[u].ModelEncode(i,l,f),u=257,d-=f}return l.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodePackMeta(e){this.nsym=e.ReadByte();for(var t=new Array(this.nsym),i=0;i<this.nsym;i++)t[i]=e.ReadByte();return[t,e.ReadUint7()]}decodePack(e,t,i){var r=new n.allocUnsafe(i);if(this.nsym<=1)for(var s=0;s<i;s++)r[s]=t[0];else if(this.nsym<=2){s=0;for(var o=0;s<i;s++){if(s%8==0)var a=e[o++];r[s]=t[1&a],a>>=1}}else if(this.nsym<=4)for(s=0,o=0;s<i;s++)s%4==0&&(a=e[o++]),r[s]=t[3&a],a>>=2;else{if(!(this.nsym<=16))return e;for(s=0,o=0;s<i;s++)s%2==0&&(a=e[o++]),r[s]=t[15&a],a>>=4}return r}packMeta(e){for(var t=new s(\"\",0,1024),i=new Array(256),n=0;n<e.length;n++)i[e[n]]=1;var r=0;for(n=0;n<256;n++)i[n]&&(i[n]=++r);for(t.WriteByte(r),n=0;n<256;n++)i[n]&&(t.WriteByte(n),i[n]--);return[t,i,r]}encodePack(e){var t,i,r;[t,i,r]=this.packMeta(e);var s=e.length,o=0;if(r<=1)return t.WriteUint7(0),[t,new n.allocUnsafe(0),0];if(r<=2){for(var a=new n.allocUnsafe(Math.floor((s+7)/8)),c=(o=0,0);o<(-8&s);o+=8,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<1)+(i[e[o+2]]<<2)+(i[e[o+3]]<<3)+(i[e[o+4]]<<4)+(i[e[o+5]]<<5)+(i[e[o+6]]<<6)+(i[e[o+7]]<<7);if(o<s){a[c]=0;for(var l=0;o<s;)a[c]|=i[e[o++]]<<l,l++;c++}return t.WriteUint7(c),[t,a,a.length]}if(r<=4){for(a=new n.allocUnsafe(Math.floor((s+3)/4)),o=0,c=0;o<(-4&s);o+=4,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<2)+(i[e[o+2]]<<4)+(i[e[o+3]]<<6);if(o<s){for(a[c]=0,l=0;o<s;)a[c]|=i[e[o++]]<<l,l+=2;c++}return t.WriteUint7(c),[t,a,a.length]}if(r<=16){for(a=new n.allocUnsafe(Math.floor((s+1)/2)),o=0,c=0;o<(-2&s);o+=2,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<4);return o<s&&(a[c++]=i[e[o++]]),t.WriteUint7(c),[t,a,a.length]}return t.WriteUint7(e.length),[t,e,e.length]}encodeStripe(e,t,i){0==i&&(i=4);for(var n=new Array(i),r=new Array(i),o=0;o<i;o++)r[o]=Math.floor(t.length/i)+(t.length%i>o),n[o]=new Array(r[o]);for(var a=0,c=0;c<t.length;c+=i,a++)for(var l=0;l<i;l++)a<n[l].length&&(n[l][a]=t[c+l]);var h=new Array(i),d=0;for(o=0;o<i;o++){var u=this.encode(n[o],0),f=this.encode(n[o],1);h[o]=f.length<u.length?f:u,d+=h[o].length}var p=new s(\"\",0,d+5*i+1);for(p.WriteByte(i),o=0;o<i;o++)p.WriteUint7(h[o].length);for(o=0;o<i;o++)p.WriteData(h[o],h[o].length);return p.buf.slice(0,p.buf.pos)}decodeStripe(e,t){for(var i=e.ReadByte(),r=new Array(i),s=new Array(i),o=0;o<i;o++)r[o]=e.ReadUint7();var a=new Array(i);for(o=0;o<i;o++)s[o]=Math.floor(t/i)+(t%i>o),a[o]=this.decodeStream(e,s[o]);var c=new n.allocUnsafe(t);for(o=0;o<i;o++)for(var l=0;l<s[o];l++)c[l*i+o]=a[o][l];return c}decodeCat(e,t){for(var i=new n.allocUnsafe(t),r=0;r<t;r++)i[r]=e.ReadByte();return i}}},4646:e=>{e.exports=class{constructor(e){this.low=0,this.range=4294967295,this.code=0,this.FFnum=0,this.carry=0,this.cache=0}RangeStartDecode(e){for(var t=0;t<5;t++)this.code=(this.code<<8)+e.ReadByte();this.code&=4294967295,this.code>>>=0}RangeGetFrequency(e){return this.range=Math.floor(this.range/e),Math.floor(this.code/this.range)}RangeDecode(e,t,i,n){for(this.code-=t*this.range,this.range*=i;this.range<1<<24;)this.range*=256,this.code=256*this.code+e.ReadByte()}RangeShiftLow(e){if(this.low<4278190080|this.carry){for(e.WriteByte(this.cache+this.carry);this.FFnum;)e.WriteByte(this.carry-1),this.FFnum--;this.cache=this.low>>>24,this.carry=0}else this.FFnum++;this.low<<=8,this.low>>>=0}RangeEncode(e,t,i,n){var r=this.low;for(this.range=Math.floor(this.range/n),this.low+=t*this.range,this.low>>>=0,this.range*=i,this.low<r&&(0!=this.carry&&console.log(\"ERROR: Multiple carry\"),this.carry=1);this.range<1<<24;)this.range*=256,this.RangeShiftLow(e)}RangeFinishEncode(e){for(var t=0;t<5;t++)this.RangeShiftLow(e)}}},9614:e=>{e.exports=class{constructor(e=256){this.total_freq=e,this.max_sym=e-1,this.S=new Array,this.F=new Array;for(var t=0;t<=this.max_sym;t++)this.S[t]=t,this.F[t]=1}ModelDecode(e,t){for(var i=t.RangeGetFrequency(this.total_freq),n=0,r=0;n+this.F[r]<=i;)n+=this.F[r++];t.RangeDecode(e,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise();var s=this.S[r];if(r>0&&this.F[r]>this.F[r-1]){var o=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=o,o=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=o}return s}ModelRenormalise(){this.total_freq=0;for(var e=0;e<=this.max_sym;e++)this.F[e]-=Math.floor(this.F[e]/2),this.total_freq+=this.F[e]}ModelEncode(e,t,i){for(var n=0,r=0;this.S[r]!=i;r++)n+=this.F[r];if(t.RangeEncode(e,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise(),i=this.S[r],r>0&&this.F[r]>this.F[r-1]){var s=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=s,s=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=s}}}},6038:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706),s=i(9614),o=i(4646);function a(e,t,i){for(var n=0,r=0,s=-1,o=new Array(1024);r<i;){var a=e.ReadByte();if(o[n++]=a,r+=a,a==s){var c=e.ReadByte();for(r+=a*c;c--;)o[n++]=a}s=a}var l=0;for(n=0,r=0;r<i;){var h=0;do{var d=o[n++];h+=d}while(255==d);for(;h--;)t[r++]=l;l++}}function c(e,t,i){var n=e.context;return t.qctx=(t.qctx<<e.qshift)+e.qtab[i],n+=(t.qctx&(1<<e.qbits)-1)<<e.qloc,e.do_pos&&(n+=e.ptab[Math.min(t.p,1023)]<<e.ploc),e.do_delta&&(n+=e.dtab[Math.min(t.delta,255)]<<e.dloc,t.delta+=t.prevq!=i?1:0,t.prevq=i),e.do_sel&&(n+=t.s<<e.sloc),t.p--,65535&n}function l(e){var t={};t.context=e.ReadUint16(),t.pflags=e.ReadByte(),t.do_dedup=2&t.pflags,t.fixed_len=4&t.pflags,t.do_sel=8&t.pflags,t.do_qmap=16&t.pflags,t.do_pos=32&t.pflags,t.do_delta=64&t.pflags,t.do_qtab=128&t.pflags,t.max_sym=e.ReadByte();var i=e.ReadByte();if(t.qbits=i>>4,t.qshift=15&i,i=e.ReadByte(),t.qloc=i>>4,t.sloc=15&i,i=e.ReadByte(),t.ploc=i>>4,t.dloc=15&i,t.qmap=new Array(256),16&t.pflags)for(var n=0;n<t.max_sym;n++)t.qmap[n]=e.ReadByte();else for(n=0;n<256;n++)t.qmap[n]=n;if(t.qtab=new Array(1024),t.qbits>0&&128&t.pflags)a(e,t.qtab,256);else for(n=0;n<256;n++)t.qtab[n]=n;return t.ptab=new Array(1024),32&t.pflags&&a(e,t.ptab,1024),t.dtab=new Array(256),64&t.pflags&&a(e,t.dtab,256),t}function h(e,t,i,n,r,s){i.max_sel>0?r.s=n.sel.ModelDecode(e,t):r.s=0,r.x=i.stab[r.s];var o=i.params[r.x];if(o.fixed_len>=0){var a=n.len[0].ModelDecode(e,t);a|=n.len[1].ModelDecode(e,t)<<8,a|=n.len[2].ModelDecode(e,t)<<16,a|=n.len[3].ModelDecode(e,t)<<24,o.fixed_len>0&&(o.fixed_len=-a)}else a=-o.fixed_len;r.len=a,i.do_rev&&(s[r.rec]=n.rev.ModelDecode(e,t)),r.is_dup=0,2&o.pflags&&n.dup.ModelDecode(e,t)&&(r.is_dup=1),r.p=a,r.delta=0,r.qctx=0,r.prevq=0,r.rec++}function d(e,t,i){for(var n=0,r=0,s=new Array(2*i),o=0;n<i;){for(var a=n;n<i&&t[n]==r;)n++;var c=n-a;do{var l=Math.min(255,c);s[o++]=l,c-=l}while(255==l);r++}var h=-1,d=new Array(2*i),u=0;for(n=0;n<o;){var f=s[n++];if(d[u++]=f,f==h){for(a=n;n<o&&s[n]==h&&n-a<255;)n++;d[u++]=n-a}else h=f}e.WriteData(d,u)}e.exports={decode:function(e,t){return function(e,t){var i=e.ReadUint7(),r=function(e){var t={max_sym:0};if(5==e.ReadByte()){var i=e.ReadByte(),n=1&i?e.ReadByte():1,r=i.nparam>1?i.nparam-1:0,s=new Array(256);if(2&i)r=e.ReadByte(),a(e,s,256);else{for(var o=0;o<n;o++)s[o]=o;for(;o<256;o++)s[o]=n-1}t.do_rev=4&i,t.stab=s,t.max_sel=r,t.params=new Array(t.nparam);for(var c=0;c<n;c++)t.params[c]=l(e),t.max_sym<t.params[c].max_sym&&(t.max_sym=t.params[c].max_sym);return t}console.error(\"Invalid FQZComp version number\")}(e);if(r){var d=r.params,u=new Array(t.length),f=function(e){var t={};t.qual=new Array(65536);for(var i=0;i<65536;i++)t.qual[i]=new s(e.max_sym+1);for(t.len=new Array(4),i=0;i<4;i++)t.len[i]=new s(256);return t.rev=new s(2),t.dup=new s(2),e.max_sel>0&&(t.sel=new s(e.max_sel+1)),t}(r),p=new o(e);p.RangeStartDecode(e);for(var g=new n.allocUnsafe(i),m={qctx:0,prevq:0,delta:0,p:0,s:0,x:0,len:0,is_dup:0,rec:0},w=0;w<i;){if(0==m.p){if(h(e,p,r,f,m,u),m.is_dup>0&&f.dup.ModelDecode(e,p)){for(var b=0;b<len;b++)g[w+b]=g[w+b-m.len];w+=m.len,m.p=0;continue}t.push(m.len);var F=(d=r.params[m.x]).context}var v=f.qual[F].ModelDecode(e,p);g[w++]=d.qmap[v],F=c(d,m,v)}return r.do_rev&&function(e,t,i,n){for(var r=0,s=0;s<t;){if(i[r])for(var o=0,a=n[r]-1;o<a;){var c=e[s+o];e[s+o]=e[s+a],e[s+a]=c,o++,a--}s+=n[r++]}}(g,i,u,t),g}}(new r(e),t)},encode:function(e,t,i){for(var n=new Array(2),a=new Array(2),c=new Array(2),l=new Array(2),h=new Array(256),u=0;u<2;u++)n[u]=new Array(256),a[u]=new Array(256),c[u]=new Array(1024),l[u]=new Array(256);(p=new r(\"\",0,1.1*e.length+100)).WriteUint7(e.length);var f=function(e,t,i,n){for(var r=i[0],s=0;s<i.length&&i[s]==r;s++);var o=s==i.length?1:0,a=0,c=0;for(s=0;s<256;s++)n[0][s]=0;var l=0,h=0;for(s=0;s<e.length;s++)0==h&&(h=t[l<t.length-1?l++:l]),n[0][e[s]]++,h--;for(s=0;s<256;s++)n[0][s]&&(c<s&&(c=s),a++);var d=5,u=0;return a<=16&&(u=1,d=a<=2?1:a<=4?2:a<=8?3:4),[{qbits:8+(d>4),qshift:d,qloc:7,pbits:7,pshift:t[0]>128?1:0,ploc:0,dbits:d>4?0:1,dshift:3,dloc:15,sbits:0,sloc:15,do_stab:0,context:0,max_sym:c,nsym:a,do_qmap:u,do_dedup:0,fixed_len:1==t.length?1:0,do_sel:0,do_rev:0,do_pos:1,do_delta:d<=4?1:0,do_qtab:0,qbits:8+(d>4)-(0==o),sbits:1,sloc:15-(d<=4),do_stab:1,do_sel:1}]}(e,t,i,n),p=function(e,t,i,n,r,s,o){for(var a=[0,1,1,1,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7],c=0;c<t.length;c++)o[c]=c;for(;c<256;c++)o[c]=t.length-1;e.WriteByte(5);var l=(t.length>1?1:0)|(t[0].do_stab?2:0);if(e.WriteByte(l),1&l&&e.WriteByte(t.length),2&l){var h=1<<t[0].sbits;h>0&&h--,e.WriteByte(h),d(e,o,256)}for(var u=0;u<t.length;u++){if(e.WriteUint16(t[u].context),e.WriteByte((t[u].do_qtab?128:0)|(t[u].do_delta?64:0)|(t[u].do_pos?32:0)|(t[u].do_qmap?16:0)|(t[u].do_sel?8:0)|(t[u].fixed_len?4:0)|(t[u].do_dedup?2:0)),t[u].do_qmap?e.WriteByte(t[u].nsym):e.WriteByte(t[u].max_sym),e.WriteByte(t[u].qbits<<4|t[u].qshift),e.WriteByte(t[u].qloc<<4|t[u].sloc),e.WriteByte(t[u].ploc<<4|t[u].dloc),t[u].do_qmap){t[u].max_sym=t[u].nsym;var f=0;for(c=0;c<256;c++)i[u][c]&&(e.WriteByte(c),i[u][c]=f++);for(;f<t[u].nsym;f++)e.WriteByte(0)}else for(c=0;c<256;c++)i[u][c]=c;if(t[u].qbits>0){for(c=0;c<256;c++)n[u][c]=c;t[u].do_qtab&&d(e,n[u],256)}if(t[u].pbits>0){for(c=0;c<1024;c++)r[u][c]=Math.min((1<<t[u].pbits)-1,c>>t[u].pshift);d(e,r[u],1024)}if(t[u].dbits>0){for(c=0;c<256;c++)a[c]>(1<<t[u].dbits)-1&&(a[c]=(1<<t[u].dbits)-1);for(c=0;c<256;c++)s[u][c]=a[Math.min(a.length-1,c>>t[u].dshift)];d(e,s[u],256)}}return e}(p,f,n,a,c,l,h);return function(e,t,i,n,r,a,c,l,h,d){var u=1<<r[0].sbits;u>0&&u--;for(var f=t.length,p=0,g=0;g<r.length;g++)p<r[g].max_sym&&(p=r[g].max_sym);for(var m=new Array(65536),w=0;w<65536;w++)m[w]=new s(p+1);var b=new Array(4);for(w=0;w<4;w++)b[w]=new s(256);new s(2),new s(2);for(var F=new s(u+1),v=new o(t),y=(g=0,w=0,0);w<f;){if(0==g){var A=n[y];r[0].sbits>0&&F.ModelEncode(e,v,A);var C=d[A],_=i[Math.min(i.length-1,y++)];r[C].fixed_len?r[C].fixed_len>0&&(b[0].ModelEncode(e,v,255&_),b[1].ModelEncode(e,v,_>>8&255),b[2].ModelEncode(e,v,_>>16&255),b[3].ModelEncode(e,v,_>>24&255),r[C].fixed_len=-1):(b[0].ModelEncode(e,v,255&_),b[1].ModelEncode(e,v,_>>8&255),b[2].ModelEncode(e,v,_>>16&255),b[3].ModelEncode(e,v,_>>24&255)),r[C].do_dedup&&process.exit(1),g=_;var x=0,k=r[C].context,I=0,S=0}var E=t[w++],N=a[C][E];m[k].ModelEncode(e,v,N),I=(I<<r[C].qshift)+c[C][N],k=r[C].context,k+=(I&(1<<r[C].qbits)-1)<<r[C].qloc,r[C].pbits>0&&(k+=l[C][Math.min(g,1023)]<<r[C].ploc),r[C].dbits>0&&(k+=h[C][Math.min(x,255)]<<r[C].dloc,x+=S!=N?1:0,S=N),r[C].do_sel&&(k+=A<<r[C].sloc),k&=65535,g--}return v.RangeFinishEncode(e),e.buf.slice(0,e.pos)}(p,e,t,i,f,n,a,c,l,h)}}},6960:(e,t,i)=>{var n=i(8287).Buffer,r=i(5460),s=i(8223),o=i(635),a=i(6038),c=i(5997);e.exports={r4x8_uncompress:function(e,t){r.decode(e).copy(t,0,0)},r4x16_uncompress:function(e,t){s.decode(e).copy(t,0,0)},arith_uncompress:function(e,t){o.decode(e).copy(t,0,0)},fqzcomp_uncompress:function(e,t){var i=new Array;a.decode(e,i).copy(t,0,0)},tok3_uncompress:function(e,t){var i=c.decode(e,0,\"\\0\");n.from(i,\"binary\").copy(t,0,0)}}},8706:(e,t,i)=>{var n=i(8287).Buffer;e.exports=class{constructor(e,t=0,i=0){0!=i?(this.buf=n.allocUnsafe(i),this.length=i):(this.buf=e,this.length=e.length),this.pos=t}EOF(){return this.pos>=this.length}ReadData(e){var t=this.buf.slice(this.pos,this.pos+e);return this.pos+=e,t}ReadByte(){const e=this.buf[this.pos];return this.pos++,e}ReadChar(){const e=this.buf[this.pos];return this.pos++,String.fromCharCode(e)}ReadUint16(){return this.ReadByte()|this.ReadByte()<<8}ReadUint32(){const e=this.buf.readInt32LE(this.pos);return this.pos+=4,e}ReadString(){var e=\"\";do{var t=this.buf[this.pos++];t&&(e+=String.fromCharCode(t))}while(t);return e}ReadUint7(){var e=0;do{var t=this.ReadByte();e=e<<7|127&t}while(128&t);return e}ReadITF8(){var e=this.buf[this.pos];return this.pos++,e>=240?(e=(15&e)<<28,e+=(this.buf[this.pos+0]<<20)+(this.buf[this.pos+1]<<12)+(this.buf[this.pos+2]<<4)+(this.buf[this.pos+3]>>4),this.pos+=4):e>=224?(e=(15&e)<<24,e+=(this.buf[this.pos+0]<<16)+(this.buf[this.pos+1]<<8)+(0|this.buf[this.pos+2]),this.pos+=3):e>=192?(e=(31&e)<<16,e+=(this.buf[this.pos+0]<<8)+(0|this.buf[this.pos+1]),this.pos+=2):e>=128&&(e=(63&e)<<8,e+=this.buf[this.pos],this.pos++),e}WriteByte(e){this.buf[this.pos++]=e}WriteChar(e){this.buf[this.pos++]=e.charCodeAt(0)}WriteString(e){for(var t=0;t<e.length;t++)this.buf[this.pos++]=e.charCodeAt(t);this.buf[this.pos++]=0}WriteData(e,t){for(var i=0;i<t;i++)this.buf[this.pos++]=e[i]}WriteStream(e){this.WriteData(e.buf,e.pos)}WriteUint16(e){this.WriteByte(255&e),this.WriteByte(e>>8&255)}WriteUint32(e){this.buf.writeInt32LE(e,this.pos),this.pos+=4}WriteUint7(e){var t=0,i=e;do{t+=7,i>>=7}while(i>0);do{t-=7,this.WriteByte((e>>t&127)+((t>0)<<7))}while(t>0)}WriteITF8(e){e<0&&(e=1+e),e<=127?this.buf[this.pos++]=e:e<=16383?(this.buf[this.pos++]=128|Math.floor(e/256),this.buf[this.pos++]=255&e):e<131071?(this.buf[this.pos++]=192|Math.floor(e/65536),this.buf[this.pos++]=255&Math.floor(e/256),this.buf[this.pos++]=255&e):e<268435455?(this.buf[this.pos++]=224|Math.floor(e/16777216),this.buf[this.pos++]=255&Math.floor(e/65536),this.buf[this.pos++]=255&Math.floor(e/256),this.buf[this.pos++]=255&e):(this.buf[this.pos++]=240|Math.floor(e/268435456),this.buf[this.pos++]=255&Math.floor(e/1048576),this.buf[this.pos++]=255&Math.floor(e/4096),this.buf[this.pos++]=255&Math.floor(e/4),this.buf[this.pos++]=15&e)}WriteByteNeg(e){this.buf[--this.pos]=e}}},5460:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706);function s(e){return 4095&e}function o(e,t){for(var i=0;t>=e[i+1];)i++;return i}function a(e){for(var t=new 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o=0,a=0,c=0;for(i=0,n=0;n<256;n++)0!=e[n]&&(o<e[n]&&(o=e[n],a=n),e[n]=Math.floor(e[n]*s),0==e[n]&&(e[n]=1),i+=e[n]);i<r?e[a]+=r-i:i-r<e[a]/2&&e[a]>2?e[a]-=i-r:i!=r&&(s=r/i,c=1)}while(c)}function b(e,t){for(var i=0,n=0;n<256;n++)i+=e[n];if(0!=i&&i!=1<<t){for(var r=0;i<1<<t;)i*=2,r++;for(n=0;n<256;n++)e[n]<<=r}}function F(e,t){for(var i=0,n=0;n<256;n++)if(t[n])if(i>0)i--;else if(e.WriteByte(n),n>0&&t[n-1]>0){for(i=n+1;i<256&&t[i];i++);i-=n+1,e.WriteByte(i)}e.WriteByte(0)}function v(e){const t=e.length;var i=new r(\"\",0,780),s=new Array(256);!function(e,t){for(var i=0;i<256;i++)t[i]=0;for(i=0;i<e.length;i++)t[e[i]]++}(e,s);var o=Math.ceil(Math.log2(t));o>12&&(o=12),w(s,o),function(e,t){F(e,t);for(var i=0;i<256;i++)t[i]&&e.WriteUint7(t[i])}(i,s),w(s,12);var a=new Array(256);a[0]=0;for(var c=1;c<256;c++)a[c]=a[c-1]+s[c-1];var l=new Array(4);for(c=0;c<4;c++)l[c]=32768;var u=new r(\"\",1.05*t+100|0,1.05*t+100|0);for(c=t-1;c>=0;c--)l[c%4]=d(l[c%4],u,a[e[c]],s[e[c]],12);for(c=3;c>=0;c--)h(l[c],u);return n.concat([i.buf.slice(0,i.pos),u.buf.slice(u.pos,u.length)],i.pos+u.length-u.pos)}e.exports={decode:function(e){return f(new r(e),0)},encode:p}},5997:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706),s=i(8223);var o=new(i(635));function a(e,t){for(var i=e+\"\";i.length<t;)i=\"0\"+i;return i}function c(e,t,i,n){var r=e[0][0].ReadByte(),s=n-e[0][r].ReadUint32();if(5==r)return t[n]=t[s],i[n]=i[s],t[n];var o=1;t[n]=\"\",i[n]=new Array(256);do{switch(r=e[o][0].ReadByte()){case 2:i[n][o]=e[o][2].ReadChar();break;case 1:i[n][o]=e[o][1].ReadString();break;case 7:i[n][o]=e[o][7].ReadUint32();break;case 3:var c=e[o][3].ReadUint32(),l=e[o][4].ReadByte();i[n][o]=a(c,l);break;case 8:i[n][o]=(0|i[s][o])+e[o][8].ReadByte();break;case 9:c=(0|i[s][o])+e[o][9].ReadByte(),l=i[s][o].length,i[n][o]=a(c,l);break;case 10:i[n][o]=i[s][o];break;default:i[n][o]=\"\"}t[n]+=i[n][o++]}while(12!=r);return t[n]}function l(e,t,i,n,r,s){for(var o=0;o<n.length;o++)if(!(i>0&&5==t[o][0].type)&&t[o][i])switch(e[0].WriteByte(t[o][i].type),t[o][i].type){case 6:e[6].WriteUint32(t[o][i].val);break;case 5:e[5].WriteUint32(t[o][i].val);break;case 1:e[1].WriteString(t[o][i].val);break;case 2:e[2].WriteChar(t[o][i].val);break;case 7:e[7].WriteUint32(t[o][i].val);break;case 3:e[3].WriteUint32(t[o][i].val),e[4].WriteByte(t[o][i].val.length);break;case 8:case 9:e[t[o][i].type].WriteByte(t[o][i].val)}}function h(e,t,i,n){for(var r=0;r<=12;r++)if(!(e[r].pos<=0)){n.WriteByte(r+(0==r?128:0)),e[r]=e[r].buf.slice(0,e[r].pos);var s=d(e[r],i);n.WriteUint7(s.length),n.WriteData(s,s.length)}}function d(e,t){var i,n=1<<30,r=[0,1,64,65,128,129,201];for(var a in r){var c=r[a];if(!(1&c&&e.length<100||8&c&&e.length%4!=0)){try{var l=t?o.encode(e,c):s.encode(e,c)}catch(e){l=0}l&&n>l.length&&(n=l.length,i=l)}}return i}function u(e,t,i,n,r){var s=0,o=r-1;e[r]=new Array(256),t[n]?e[r][0]={type:5,val:r-t[n]}:e[r][0]={type:6,val:0==r?0:1},t[n]=r;for(var a=n.match(/([a-zA-Z0-9]{1,9})|([^a-zA-Z0-9]+)/g),c=0;c<a.length;c++){var l=c+1,h=1,d=a[c];if(a[c].match(/^0+[0-9]*$/g)?h=3:a[c].match(/^[0-9]+$/g)?h=7:1==a[c].length&&(h=2),o>=0&&e[o][l])if(e[o][l].str==a[c])h=10,d=\"\";else if(7==e[o][l].type||8==e[o][l].type){var u=d-e[o][l].str;i[l]++,u>=0&&u<256&&i[l]>r/2&&(h=8,d=u)}else 3!=e[o][l].type&&9!=e[o][l].type||e[o][l].str.length!=d.length||(u=d-e[o][l].str,i[l]++,u>=0&&u<256&&i[l]>r/2&&(h=9,d=u));e[r][l]={str:a[c],val:d,type:h},s<e[r][l].val.length+3&&(s=e[r][l].val.length+3)}return e[r][++l]={type:12},[l+1,s]}e.exports={encode:function(e,t){var i=e.toString();\"\\n\"==i[i.length-1]&&(i=i.substring(0,i.length-1));var n=i.split(\"\\n\"),s=new r(\"\",0,2*i.length+1e4);s.WriteUint32(i.length),s.WriteUint32(n.length),s.WriteByte(t);for(var o=new Array(n.length),a={},c=new Array(256).fill(0),d=0,f=0,p=0;p<n.length;p++){var[g,m]=u(o,a,c,n[p],p);d<g&&(d=g),f<m&&(f=m)}for(var w=0;w<d;w++){for(var b=new Array(13),F=0;F<=12;F++)b[F]=new r(\"\",0,n.length*f);l(b,o,w,n),h(b,0,t,s)}return s.buf.slice(0,s.pos)},decode:function(e,t,i){(e=new r(e)).ReadUint32();var a=e.ReadUint32(),l=e.ReadByte(),h=function(e,t,i,a){for(var c=-1,l=new Array(256);!e.EOF();){var h=e.ReadByte(),d=128&h,u=64&h,f=63&h;if(d&&(l[++c]=new Array(13)),0!=f&&d){var p=new Array(a-1).fill(10);l[c][0]=new r(n.from([f].concat(p)))}if(u){var g=e.ReadByte(),m=e.ReadByte();l[c][f]=new r(l[g][m].buf)}else{var w=e.ReadUint7(),b=e.ReadData(w);l[c][f]=i?o.decode(b):s.decode(b),l[c][f]=new r(l[c][f])}}return l}(e,0,l,a),d=new Array(a),u=new Array(a),f=\"\";void 0===i&&(i=\"\\n\");for(var p=0;p<a;p++)f+=c(h,d,u,p)+i;return f}}},7526:(e,t)=>{t.byteLength=function(e){var t=a(e),i=t[0],n=t[1];return 3*(i+n)/4-n},t.toByteArray=function(e){var t,i,s=a(e),o=s[0],c=s[1],l=new r(function(e,t,i){return 3*(t+i)/4-i}(0,o,c)),h=0,d=c>0?o-4:o;for(i=0;i<d;i+=4)t=n[e.charCodeAt(i)]<<18|n[e.charCodeAt(i+1)]<<12|n[e.charCodeAt(i+2)]<<6|n[e.charCodeAt(i+3)],l[h++]=t>>16&255,l[h++]=t>>8&255,l[h++]=255&t;return 2===c&&(t=n[e.charCodeAt(i)]<<2|n[e.charCodeAt(i+1)]>>4,l[h++]=255&t),1===c&&(t=n[e.charCodeAt(i)]<<10|n[e.charCodeAt(i+1)]<<4|n[e.charCodeAt(i+2)]>>2,l[h++]=t>>8&255,l[h++]=255&t),l},t.fromByteArray=function(e){for(var t,n=e.length,r=n%3,s=[],o=16383,a=0,l=n-r;a<l;a+=o)s.push(c(e,a,a+o>l?l:a+o));return 1===r?(t=e[n-1],s.push(i[t>>2]+i[t<<4&63]+\"==\")):2===r&&(t=(e[n-2]<<8)+e[n-1],s.push(i[t>>10]+i[t>>4&63]+i[t<<2&63]+\"=\")),s.join(\"\")};for(var i=[],n=[],r=\"undefined\"!=typeof Uint8Array?Uint8Array:Array,s=\"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/\",o=0;o<64;++o)i[o]=s[o],n[s.charCodeAt(o)]=o;function a(e){var t=e.length;if(t%4>0)throw new Error(\"Invalid string. 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Received type number');return d(e)}return l(e,t,i)}function l(e,t,i){if(\"string\"==typeof e)return function(e,t){if(\"string\"==typeof t&&\"\"!==t||(t=\"utf8\"),!c.isEncoding(t))throw new TypeError(\"Unknown encoding: \"+t);const i=0|g(e,t);let n=a(i);const r=n.write(e,t);return r!==i&&(n=n.slice(0,r)),n}(e,t);if(ArrayBuffer.isView(e))return function(e){if(K(e,Uint8Array)){const t=new Uint8Array(e);return f(t.buffer,t.byteOffset,t.byteLength)}return u(e)}(e);if(null==e)throw new TypeError(\"The first argument must be one of type string, Buffer, ArrayBuffer, Array, or Array-like Object. Received type \"+typeof e);if(K(e,ArrayBuffer)||e&&K(e.buffer,ArrayBuffer))return f(e,t,i);if(\"undefined\"!=typeof SharedArrayBuffer&&(K(e,SharedArrayBuffer)||e&&K(e.buffer,SharedArrayBuffer)))return f(e,t,i);if(\"number\"==typeof e)throw new TypeError('The \"value\" argument must not be of type number. Received type number');const n=e.valueOf&&e.valueOf();if(null!=n&&n!==e)return c.from(n,t,i);const r=function(e){if(c.isBuffer(e)){const t=0|p(e.length),i=a(t);return 0===i.length||e.copy(i,0,0,t),i}return void 0!==e.length?\"number\"!=typeof e.length||Y(e.length)?a(0):u(e):\"Buffer\"===e.type&&Array.isArray(e.data)?u(e.data):void 0}(e);if(r)return r;if(\"undefined\"!=typeof Symbol&&null!=Symbol.toPrimitive&&\"function\"==typeof e[Symbol.toPrimitive])return c.from(e[Symbol.toPrimitive](\"string\"),t,i);throw new TypeError(\"The first argument must be one of type string, Buffer, ArrayBuffer, Array, or Array-like Object. 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reading blob\"))},t.onabort=()=>{n(new Error(\"blob reading was aborted\"))},t.onload=()=>{t.result&&\"string\"!=typeof t.result?i(t.result):n(new Error(\"unknown error reading blob\"))},t.readAsArrayBuffer(e)}))}class l{constructor(e){this.blob=e,this.size=e.size}async read(e,t=0,i,n=0){if(!i)return{bytesRead:0,buffer:e};const r=n,o=r+i,a=await c(this.blob.slice(r,o)),l=s.Buffer.from(a);return{bytesRead:l.copy(e,t),buffer:l}}async readFile(e){const t=\"string\"==typeof e?e:null==e?void 0:e.encoding;if(\"utf8\"===t)return function(e){const t=new FileReader;return new Promise(((i,n)=>{t.onerror=()=>{t.abort(),n(new Error(\"problem reading blob\"))},t.onabort=()=>{n(new Error(\"blob reading was aborted\"))},t.onload=()=>{t.result&&\"string\"==typeof t.result?i(t.result):n(new Error(\"unknown error reading blob\"))},t.readAsText(e)}))}(this.blob);if(t)throw new Error(`unsupported encoding: ${t}`);const i=await c(this.blob);return s.Buffer.from(i)}async stat(){return{size:this.size}}async close(){}}function h(e,t={}){return new a(e,t)}function d(e,t,i,n={}){if(void 0!==i)return i;if(void 0!==e)return h(e,n);if(void 0!==t)return new(r())(t,n);throw new Error(\"no url, path, or filehandle provided, cannot open\")}},251:(e,t)=>{t.read=function(e,t,i,n,r){var s,o,a=8*r-n-1,c=(1<<a)-1,l=c>>1,h=-7,d=i?r-1:0,u=i?-1:1,f=e[t+d];for(d+=u,s=f&(1<<-h)-1,f>>=-h,h+=a;h>0;s=256*s+e[t+d],d+=u,h-=8);for(o=s&(1<<-h)-1,s>>=-h,h+=n;h>0;o=256*o+e[t+d],d+=u,h-=8);if(0===s)s=1-l;else{if(s===c)return o?NaN:1/0*(f?-1:1);o+=Math.pow(2,n),s-=l}return(f?-1:1)*o*Math.pow(2,s-n)},t.write=function(e,t,i,n,r,s){var o,a,c,l=8*s-r-1,h=(1<<l)-1,d=h>>1,u=23===r?Math.pow(2,-24)-Math.pow(2,-77):0,f=n?0:s-1,p=n?1:-1,g=t<0||0===t&&1/t<0?1:0;for(t=Math.abs(t),isNaN(t)||t===1/0?(a=isNaN(t)?1:0,o=h):(o=Math.floor(Math.log(t)/Math.LN2),t*(c=Math.pow(2,-o))<1&&(o--,c*=2),(t+=o+d>=1?u/c:u*Math.pow(2,1-d))*c>=2&&(o++,c/=2),o+d>=h?(a=0,o=h):o+d>=1?(a=(t*c-1)*Math.pow(2,r),o+=d):(a=t*Math.pow(2,d-1)*Math.pow(2,r),o=0));r>=8;e[i+f]=255&a,f+=p,a/=256,r-=8);for(o=o<<r|a,l+=r;l>0;e[i+f]=255&o,f+=p,o/=256,l-=8);e[i+f-p]|=128*g}},8570:e=>{e.exports=i;var t=null;try{t=new WebAssembly.Instance(new WebAssembly.Module(new Uint8Array([0,97,115,109,1,0,0,0,1,13,2,96,0,1,127,96,4,127,127,127,127,1,127,3,7,6,0,1,1,1,1,1,6,6,1,127,1,65,0,11,7,50,6,3,109,117,108,0,1,5,100,105,118,95,115,0,2,5,100,105,118,95,117,0,3,5,114,101,109,95,115,0,4,5,114,101,109,95,117,0,5,8,103,101,116,95,104,105,103,104,0,0,10,191,1,6,4,0,35,0,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,126,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,127,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,128,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,129,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,130,34,4,66,32,135,167,36,0,32,4,167,11])),{}).exports}catch(e){}function i(e,t,i){this.low=0|e,this.high=0|t,this.unsigned=!!i}function n(e){return!0===(e&&e.__isLong__)}i.prototype.__isLong__,Object.defineProperty(i.prototype,\"__isLong__\",{value:!0}),i.isLong=n;var r={},s={};function o(e,t){var i,n,o;return t?(o=0<=(e>>>=0)&&e<256)&&(n=s[e])?n:(i=c(e,(0|e)<0?-1:0,!0),o&&(s[e]=i),i):(o=-128<=(e|=0)&&e<128)&&(n=r[e])?n:(i=c(e,e<0?-1:0,!1),o&&(r[e]=i),i)}function a(e,t){if(isNaN(e))return t?w:m;if(t){if(e<0)return w;if(e>=f)return A}else{if(e<=-p)return C;if(e+1>=p)return y}return e<0?a(-e,t).neg():c(e%u|0,e/u|0,t)}function c(e,t,n){return new i(e,t,n)}i.fromInt=o,i.fromNumber=a,i.fromBits=c;var l=Math.pow;function h(e,t,i){if(0===e.length)throw Error(\"empty string\");if(\"NaN\"===e||\"Infinity\"===e||\"+Infinity\"===e||\"-Infinity\"===e)return m;if(\"number\"==typeof t?(i=t,t=!1):t=!!t,(i=i||10)<2||36<i)throw RangeError(\"radix\");var n;if((n=e.indexOf(\"-\"))>0)throw Error(\"interior hyphen\");if(0===n)return h(e.substring(1),t,i).neg();for(var r=a(l(i,8)),s=m,o=0;o<e.length;o+=8){var c=Math.min(8,e.length-o),d=parseInt(e.substring(o,o+c),i);if(c<8){var u=a(l(i,c));s=s.mul(u).add(a(d))}else s=(s=s.mul(r)).add(a(d))}return s.unsigned=t,s}function d(e,t){return\"number\"==typeof e?a(e,t):\"string\"==typeof e?h(e,t):c(e.low,e.high,\"boolean\"==typeof t?t:e.unsigned)}i.fromString=h,i.fromValue=d;var u=4294967296,f=u*u,p=f/2,g=o(1<<24),m=o(0);i.ZERO=m;var w=o(0,!0);i.UZERO=w;var b=o(1);i.ONE=b;var F=o(1,!0);i.UONE=F;var v=o(-1);i.NEG_ONE=v;var y=c(-1,2147483647,!1);i.MAX_VALUE=y;var A=c(-1,-1,!0);i.MAX_UNSIGNED_VALUE=A;var C=c(0,-2147483648,!1);i.MIN_VALUE=C;var _=i.prototype;_.toInt=function(){return this.unsigned?this.low>>>0:this.low},_.toNumber=function(){return this.unsigned?(this.high>>>0)*u+(this.low>>>0):this.high*u+(this.low>>>0)},_.toString=function(e){if((e=e||10)<2||36<e)throw RangeError(\"radix\");if(this.isZero())return\"0\";if(this.isNegative()){if(this.eq(C)){var t=a(e),i=this.div(t),n=i.mul(t).sub(this);return i.toString(e)+n.toInt().toString(e)}return\"-\"+this.neg().toString(e)}for(var r=a(l(e,6),this.unsigned),s=this,o=\"\";;){var c=s.div(r),h=(s.sub(c.mul(r)).toInt()>>>0).toString(e);if((s=c).isZero())return h+o;for(;h.length<6;)h=\"0\"+h;o=\"\"+h+o}},_.getHighBits=function(){return this.high},_.getHighBitsUnsigned=function(){return this.high>>>0},_.getLowBits=function(){return this.low},_.getLowBitsUnsigned=function(){return this.low>>>0},_.getNumBitsAbs=function(){if(this.isNegative())return this.eq(C)?64:this.neg().getNumBitsAbs();for(var e=0!=this.high?this.high:this.low,t=31;t>0&&!(e&1<<t);t--);return 0!=this.high?t+33:t+1},_.isZero=function(){return 0===this.high&&0===this.low},_.eqz=_.isZero,_.isNegative=function(){return!this.unsigned&&this.high<0},_.isPositive=function(){return this.unsigned||this.high>=0},_.isOdd=function(){return!(1&~this.low)},_.isEven=function(){return!(1&this.low)},_.equals=function(e){return n(e)||(e=d(e)),(this.unsigned===e.unsigned||this.high>>>31!=1||e.high>>>31!=1)&&this.high===e.high&&this.low===e.low},_.eq=_.equals,_.notEquals=function(e){return!this.eq(e)},_.neq=_.notEquals,_.ne=_.notEquals,_.lessThan=function(e){return this.comp(e)<0},_.lt=_.lessThan,_.lessThanOrEqual=function(e){return this.comp(e)<=0},_.lte=_.lessThanOrEqual,_.le=_.lessThanOrEqual,_.greaterThan=function(e){return this.comp(e)>0},_.gt=_.greaterThan,_.greaterThanOrEqual=function(e){return this.comp(e)>=0},_.gte=_.greaterThanOrEqual,_.ge=_.greaterThanOrEqual,_.compare=function(e){if(n(e)||(e=d(e)),this.eq(e))return 0;var t=this.isNegative(),i=e.isNegative();return t&&!i?-1:!t&&i?1:this.unsigned?e.high>>>0>this.high>>>0||e.high===this.high&&e.low>>>0>this.low>>>0?-1:1:this.sub(e).isNegative()?-1:1},_.comp=_.compare,_.negate=function(){return!this.unsigned&&this.eq(C)?C:this.not().add(b)},_.neg=_.negate,_.add=function(e){n(e)||(e=d(e));var t=this.high>>>16,i=65535&this.high,r=this.low>>>16,s=65535&this.low,o=e.high>>>16,a=65535&e.high,l=e.low>>>16,h=0,u=0,f=0,p=0;return f+=(p+=s+(65535&e.low))>>>16,u+=(f+=r+l)>>>16,h+=(u+=i+a)>>>16,h+=t+o,c((f&=65535)<<16|(p&=65535),(h&=65535)<<16|(u&=65535),this.unsigned)},_.subtract=function(e){return n(e)||(e=d(e)),this.add(e.neg())},_.sub=_.subtract,_.multiply=function(e){if(this.isZero())return m;if(n(e)||(e=d(e)),t)return c(t.mul(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned);if(e.isZero())return m;if(this.eq(C))return e.isOdd()?C:m;if(e.eq(C))return this.isOdd()?C:m;if(this.isNegative())return e.isNegative()?this.neg().mul(e.neg()):this.neg().mul(e).neg();if(e.isNegative())return this.mul(e.neg()).neg();if(this.lt(g)&&e.lt(g))return a(this.toNumber()*e.toNumber(),this.unsigned);var i=this.high>>>16,r=65535&this.high,s=this.low>>>16,o=65535&this.low,l=e.high>>>16,h=65535&e.high,u=e.low>>>16,f=65535&e.low,p=0,w=0,b=0,F=0;return b+=(F+=o*f)>>>16,w+=(b+=s*f)>>>16,b&=65535,w+=(b+=o*u)>>>16,p+=(w+=r*f)>>>16,w&=65535,p+=(w+=s*u)>>>16,w&=65535,p+=(w+=o*h)>>>16,p+=i*f+r*u+s*h+o*l,c((b&=65535)<<16|(F&=65535),(p&=65535)<<16|(w&=65535),this.unsigned)},_.mul=_.multiply,_.divide=function(e){if(n(e)||(e=d(e)),e.isZero())throw Error(\"division by zero\");var i,r,s;if(t)return this.unsigned||-2147483648!==this.high||-1!==e.low||-1!==e.high?c((this.unsigned?t.div_u:t.div_s)(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned):this;if(this.isZero())return this.unsigned?w:m;if(this.unsigned){if(e.unsigned||(e=e.toUnsigned()),e.gt(this))return w;if(e.gt(this.shru(1)))return F;s=w}else{if(this.eq(C))return e.eq(b)||e.eq(v)?C:e.eq(C)?b:(i=this.shr(1).div(e).shl(1)).eq(m)?e.isNegative()?b:v:(r=this.sub(e.mul(i)),s=i.add(r.div(e)));if(e.eq(C))return this.unsigned?w:m;if(this.isNegative())return e.isNegative()?this.neg().div(e.neg()):this.neg().div(e).neg();if(e.isNegative())return this.div(e.neg()).neg();s=m}for(r=this;r.gte(e);){i=Math.max(1,Math.floor(r.toNumber()/e.toNumber()));for(var o=Math.ceil(Math.log(i)/Math.LN2),h=o<=48?1:l(2,o-48),u=a(i),f=u.mul(e);f.isNegative()||f.gt(r);)f=(u=a(i-=h,this.unsigned)).mul(e);u.isZero()&&(u=b),s=s.add(u),r=r.sub(f)}return s},_.div=_.divide,_.modulo=function(e){return n(e)||(e=d(e)),t?c((this.unsigned?t.rem_u:t.rem_s)(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned):this.sub(this.div(e).mul(e))},_.mod=_.modulo,_.rem=_.modulo,_.not=function(){return c(~this.low,~this.high,this.unsigned)},_.and=function(e){return n(e)||(e=d(e)),c(this.low&e.low,this.high&e.high,this.unsigned)},_.or=function(e){return n(e)||(e=d(e)),c(this.low|e.low,this.high|e.high,this.unsigned)},_.xor=function(e){return n(e)||(e=d(e)),c(this.low^e.low,this.high^e.high,this.unsigned)},_.shiftLeft=function(e){return 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e=this.high,t=this.low;return[e>>>24,e>>>16&255,e>>>8&255,255&e,t>>>24,t>>>16&255,t>>>8&255,255&t]},i.fromBytes=function(e,t,n){return n?i.fromBytesLE(e,t):i.fromBytesBE(e,t)},i.fromBytesLE=function(e,t){return new i(e[0]|e[1]<<8|e[2]<<16|e[3]<<24,e[4]|e[5]<<8|e[6]<<16|e[7]<<24,t)},i.fromBytesBE=function(e,t){return new i(e[4]<<24|e[5]<<16|e[6]<<8|e[7],e[0]<<24|e[1]<<16|e[2]<<8|e[3],t)}},3503:(e,t,i)=>{var n,r,s,o,a;n=i(3939),r=i(2151).utf8,s=i(652),o=i(2151).bin,(a=function(e,t){e.constructor==String?e=t&&\"binary\"===t.encoding?o.stringToBytes(e):r.stringToBytes(e):s(e)?e=Array.prototype.slice.call(e,0):Array.isArray(e)||e.constructor===Uint8Array||(e=e.toString());for(var i=n.bytesToWords(e),c=8*e.length,l=1732584193,h=-271733879,d=-1732584194,u=271733878,f=0;f<i.length;f++)i[f]=16711935&(i[f]<<8|i[f]>>>24)|4278255360&(i[f]<<24|i[f]>>>8);i[c>>>5]|=128<<c%32,i[14+(c+64>>>9<<4)]=c;var p=a._ff,g=a._gg,m=a._hh,w=a._ii;for(f=0;f<i.length;f+=16){var 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e.state=c,c.strm=e,c.wrap=a,c.gzhead=null,c.w_bits=n,c.w_size=1<<c.w_bits,c.w_mask=c.w_size-1,c.hash_bits=s+7,c.hash_size=1<<c.hash_bits,c.hash_mask=c.hash_size-1,c.hash_shift=~~((c.hash_bits+F-1)/F),c.window=new r.Buf8(2*c.w_size),c.head=new r.Buf16(c.hash_size),c.prev=new r.Buf16(c.w_size),c.lit_bufsize=1<<s+6,c.pending_buf_size=4*c.lit_bufsize,c.pending_buf=new r.Buf8(c.pending_buf_size),c.d_buf=1*c.lit_bufsize,c.l_buf=3*c.lit_bufsize,c.level=t,c.strategy=o,c.method=i,U(e)}n=[new H(0,0,0,0,(function(e,t){var i=65535;for(i>e.pending_buf_size-5&&(i=e.pending_buf_size-5);;){if(e.lookahead<=1){if(T(e),0===e.lookahead&&t===l)return 1;if(0===e.lookahead)break}e.strstart+=e.lookahead,e.lookahead=0;var n=e.block_start+i;if((0===e.strstart||e.strstart>=n)&&(e.lookahead=e.strstart-n,e.strstart=n,N(e,!1),0===e.strm.avail_out))return 1;if(e.strstart-e.block_start>=e.w_size-y&&(N(e,!1),0===e.strm.avail_out))return 1}return 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1;if(0===e.lookahead)break}if(e.match_length=0,e.lookahead>=F&&e.strstart>0&&(n=a[r=e.strstart-1])===a[++r]&&n===a[++r]&&n===a[++r]){o=e.strstart+v;do{}while(n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&r<o);e.match_length=v-(o-r),e.match_length>e.lookahead&&(e.match_length=e.lookahead)}if(e.match_length>=F?(i=s._tr_tally(e,1,e.match_length-F),e.lookahead-=e.match_length,e.strstart+=e.match_length,e.match_length=0):(i=s._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++),i&&(N(e,!1),0===e.strm.avail_out))return 1}return e.insert=0,4===t?(N(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(N(e,!1),0===e.strm.avail_out)?1:2}(r,t):n[r.level].func(r,t);if(3!==p&&4!==p||(r.status=x),1===p||3===p)return 0===e.avail_out&&(r.last_flush=-1),h;if(2===p&&(1===t?s._tr_align(r):5!==t&&(s._tr_stored_block(r,0,0,!1),3===t&&(S(r.head),0===r.lookahead&&(r.strstart=0,r.block_start=0,r.insert=0))),E(e),0===e.avail_out))return r.last_flush=-1,h}return 4!==t?h:r.wrap<=0?1:(2===r.wrap?(B(r,255&e.adler),B(r,e.adler>>8&255),B(r,e.adler>>16&255),B(r,e.adler>>24&255),B(r,255&e.total_in),B(r,e.total_in>>8&255),B(r,e.total_in>>16&255),B(r,e.total_in>>24&255)):(M(r,e.adler>>>16),M(r,65535&e.adler)),E(e),r.wrap>0&&(r.wrap=-r.wrap),0!==r.pending?h:1)},t.deflateEnd=function(e){var t;return e&&e.state?(t=e.state.status)!==A&&69!==t&&73!==t&&91!==t&&t!==C&&t!==_&&t!==x?k(e,d):(e.state=null,t===_?k(e,-3):h):d},t.deflateSetDictionary=function(e,t){var i,n,s,a,c,l,u,f,p=t.length;if(!e||!e.state)return d;if(2===(a=(i=e.state).wrap)||1===a&&i.status!==A||i.lookahead)return d;for(1===a&&(e.adler=o(e.adler,t,p,0)),i.wrap=0,p>=i.w_size&&(0===a&&(S(i.head),i.strstart=0,i.block_start=0,i.insert=0),f=new r.Buf8(i.w_size),r.arraySet(f,t,p-i.w_size,i.w_size,0),t=f,p=i.w_size),c=e.avail_in,l=e.next_in,u=e.input,e.avail_in=p,e.next_in=0,e.input=t,T(i);i.lookahead>=F;){n=i.strstart,s=i.lookahead-(F-1);do{i.ins_h=(i.ins_h<<i.hash_shift^i.window[n+F-1])&i.hash_mask,i.prev[n&i.w_mask]=i.head[i.ins_h],i.head[i.ins_h]=n,n++}while(--s);i.strstart=n,i.lookahead=F-1,T(i)}return i.strstart+=i.lookahead,i.block_start=i.strstart,i.insert=i.lookahead,i.lookahead=0,i.match_length=i.prev_length=F-1,i.match_available=0,e.next_in=l,e.input=u,e.avail_in=c,i.wrap=a,h},t.deflateInfo=\"pako deflate (from Nodeca project)\"},7414:e=>{e.exports=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name=\"\",this.comment=\"\",this.hcrc=0,this.done=!1}},7293:e=>{e.exports=function(e,t){var i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_,x,k;i=e.state,n=e.next_in,x=e.input,r=n+(e.avail_in-5),s=e.next_out,k=e.output,o=s-(t-e.avail_out),a=s+(e.avail_out-257),c=i.dmax,l=i.wsize,h=i.whave,d=i.wnext,u=i.window,f=i.hold,p=i.bits,g=i.lencode,m=i.distcode,w=(1<<i.lenbits)-1,b=(1<<i.distbits)-1;e:do{p<15&&(f+=x[n++]<<p,p+=8,f+=x[n++]<<p,p+=8),F=g[f&w];t:for(;;){if(f>>>=v=F>>>24,p-=v,0==(v=F>>>16&255))k[s++]=65535&F;else{if(!(16&v)){if(64&v){if(32&v){i.mode=12;break e}e.msg=\"invalid literal/length code\",i.mode=30;break e}F=g[(65535&F)+(f&(1<<v)-1)];continue t}for(y=65535&F,(v&=15)&&(p<v&&(f+=x[n++]<<p,p+=8),y+=f&(1<<v)-1,f>>>=v,p-=v),p<15&&(f+=x[n++]<<p,p+=8,f+=x[n++]<<p,p+=8),F=m[f&b];;){if(f>>>=v=F>>>24,p-=v,16&(v=F>>>16&255)){if(A=65535&F,p<(v&=15)&&(f+=x[n++]<<p,(p+=8)<v&&(f+=x[n++]<<p,p+=8)),(A+=f&(1<<v)-1)>c){e.msg=\"invalid distance too far back\",i.mode=30;break e}if(f>>>=v,p-=v,A>(v=s-o)){if((v=A-v)>h&&i.sane){e.msg=\"invalid distance too far back\",i.mode=30;break e}if(C=0,_=u,0===d){if(C+=l-v,v<y){y-=v;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}}else if(d<v){if(C+=l+d-v,(v-=d)<y){y-=v;do{k[s++]=u[C++]}while(--v);if(C=0,d<y){y-=v=d;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}}}else if(C+=d-v,v<y){y-=v;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}for(;y>2;)k[s++]=_[C++],k[s++]=_[C++],k[s++]=_[C++],y-=3;y&&(k[s++]=_[C++],y>1&&(k[s++]=_[C++]))}else{C=s-A;do{k[s++]=k[C++],k[s++]=k[C++],k[s++]=k[C++],y-=3}while(y>2);y&&(k[s++]=k[C++],y>1&&(k[s++]=k[C++]))}break}if(64&v){e.msg=\"invalid distance code\",i.mode=30;break e}F=m[(65535&F)+(f&(1<<v)-1)]}}break}}while(n<r&&s<a);n-=y=p>>3,f&=(1<<(p-=y<<3))-1,e.next_in=n,e.next_out=s,e.avail_in=n<r?r-n+5:5-(n-r),e.avail_out=s<a?a-s+257:257-(s-a),i.hold=f,i.bits=p}},1447:(e,t,i)=>{var n=i(9805),r=i(3269),s=i(4823),o=i(7293),a=i(1998),c=0,l=-2,h=1,d=12,u=30,f=852,p=592;function g(e){return(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24)}function m(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new n.Buf16(320),this.work=new n.Buf16(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}function w(e){var t;return e&&e.state?(t=e.state,e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=h,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new n.Buf32(f),t.distcode=t.distdyn=new n.Buf32(p),t.sane=1,t.back=-1,c):l}function b(e){var t;return e&&e.state?((t=e.state).wsize=0,t.whave=0,t.wnext=0,w(e)):l}function F(e,t){var i,n;return e&&e.state?(n=e.state,t<0?(i=0,t=-t):(i=1+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?l:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,b(e))):l}function v(e,t){var i,n;return e?(n=new m,e.state=n,n.window=null,(i=F(e,t))!==c&&(e.state=null),i):l}var y,A,C=!0;function _(e){if(C){var t;for(y=new n.Buf32(512),A=new n.Buf32(32),t=0;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(a(1,e.lens,0,288,y,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;a(2,e.lens,0,32,A,0,e.work,{bits:5}),C=!1}e.lencode=y,e.lenbits=9,e.distcode=A,e.distbits=5}function x(e,t,i,r){var s,o=e.state;return null===o.window&&(o.wsize=1<<o.wbits,o.wnext=0,o.whave=0,o.window=new n.Buf8(o.wsize)),r>=o.wsize?(n.arraySet(o.window,t,i-o.wsize,o.wsize,0),o.wnext=0,o.whave=o.wsize):((s=o.wsize-o.wnext)>r&&(s=r),n.arraySet(o.window,t,i-r,s,o.wnext),(r-=s)?(n.arraySet(o.window,t,i-r,r,0),o.wnext=r,o.whave=o.wsize):(o.wnext+=s,o.wnext===o.wsize&&(o.wnext=0),o.whave<o.wsize&&(o.whave+=s))),0}t.inflateReset=b,t.inflateReset2=F,t.inflateResetKeep=w,t.inflateInit=function(e){return v(e,15)},t.inflateInit2=v,t.inflate=function(e,t){var i,f,p,m,w,b,F,v,y,A,C,k,I,S,E,N,B,M,R,D,T,L,z,H,P=0,O=new n.Buf8(4),U=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];if(!e||!e.state||!e.output||!e.input&&0!==e.avail_in)return l;(i=e.state).mode===d&&(i.mode=13),w=e.next_out,p=e.output,F=e.avail_out,m=e.next_in,f=e.input,b=e.avail_in,v=i.hold,y=i.bits,A=b,C=F,L=c;e:for(;;)switch(i.mode){case h:if(0===i.wrap){i.mode=13;break}for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(2&i.wrap&&35615===v){i.check=0,O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0),v=0,y=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&v)<<8)+(v>>8))%31){e.msg=\"incorrect header check\",i.mode=u;break}if(8!=(15&v)){e.msg=\"unknown compression method\",i.mode=u;break}if(y-=4,T=8+(15&(v>>>=4)),0===i.wbits)i.wbits=T;else if(T>i.wbits){e.msg=\"invalid window size\",i.mode=u;break}i.dmax=1<<T,e.adler=i.check=1,i.mode=512&v?10:d,v=0,y=0;break;case 2:for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(i.flags=v,8!=(255&i.flags)){e.msg=\"unknown compression method\",i.mode=u;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=u;break}i.head&&(i.head.text=v>>8&1),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0,i.mode=3;case 3:for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.head&&(i.head.time=v),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,O[2]=v>>>16&255,O[3]=v>>>24&255,i.check=s(i.check,O,4,0)),v=0,y=0,i.mode=4;case 4:for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.head&&(i.head.xflags=255&v,i.head.os=v>>8),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0,i.mode=5;case 5:if(1024&i.flags){for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.length=v,i.head&&(i.head.extra_len=v),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&((k=i.length)>b&&(k=b),k&&(i.head&&(T=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Array(i.head.extra_len)),n.arraySet(i.head.extra,f,m,k,T)),512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,i.length-=k),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===b)break e;k=0;do{T=f[m+k++],i.head&&T&&i.length<65536&&(i.head.name+=String.fromCharCode(T))}while(T&&k<b);if(512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,T)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===b)break e;k=0;do{T=f[m+k++],i.head&&T&&i.length<65536&&(i.head.comment+=String.fromCharCode(T))}while(T&&k<b);if(512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,T)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=u;break}v=0,y=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=d;break;case 10:for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}e.adler=i.check=g(v),v=0,y=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=w,e.avail_out=F,e.next_in=m,e.avail_in=b,i.hold=v,i.bits=y,2;e.adler=i.check=1,i.mode=d;case d:if(5===t||6===t)break e;case 13:if(i.last){v>>>=7&y,y-=7&y,i.mode=27;break}for(;y<3;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}switch(i.last=1&v,y-=1,3&(v>>>=1)){case 0:i.mode=14;break;case 1:if(_(i),i.mode=20,6===t){v>>>=2,y-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg=\"invalid block type\",i.mode=u}v>>>=2,y-=2;break;case 14:for(v>>>=7&y,y-=7&y;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if((65535&v)!=(v>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=u;break}if(i.length=65535&v,v=0,y=0,i.mode=15,6===t)break e;case 15:i.mode=16;case 16:if(k=i.length){if(k>b&&(k=b),k>F&&(k=F),0===k)break e;n.arraySet(p,f,m,k,w),b-=k,m+=k,F-=k,w+=k,i.length-=k;break}i.mode=d;break;case 17:for(;y<14;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(i.nlen=257+(31&v),v>>>=5,y-=5,i.ndist=1+(31&v),v>>>=5,y-=5,i.ncode=4+(15&v),v>>>=4,y-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=u;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;y<3;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.lens[U[i.have++]]=7&v,v>>>=3,y-=3}for(;i.have<19;)i.lens[U[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,z={bits:i.lenbits},L=a(0,i.lens,0,19,i.lencode,0,i.work,z),i.lenbits=z.bits,L){e.msg=\"invalid code lengths set\",i.mode=u;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;N=(P=i.lencode[v&(1<<i.lenbits)-1])>>>16&255,B=65535&P,!((E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(B<16)v>>>=E,y-=E,i.lens[i.have++]=B;else{if(16===B){for(H=E+2;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v>>>=E,y-=E,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=u;break}T=i.lens[i.have-1],k=3+(3&v),v>>>=2,y-=2}else if(17===B){for(H=E+3;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}y-=E,T=0,k=3+(7&(v>>>=E)),v>>>=3,y-=3}else{for(H=E+7;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}y-=E,T=0,k=11+(127&(v>>>=E)),v>>>=7,y-=7}if(i.have+k>i.nlen+i.ndist){e.msg=\"invalid bit length 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e;b--,v+=f[m++]<<y,y+=8}if(N&&!(240&N)){for(M=E,R=N,D=B;N=(P=i.lencode[D+((v&(1<<M+R)-1)>>M)])>>>16&255,B=65535&P,!(M+(E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}v>>>=M,y-=M,i.back+=M}if(v>>>=E,y-=E,i.back+=E,i.length=B,0===N){i.mode=26;break}if(32&N){i.back=-1,i.mode=d;break}if(64&N){e.msg=\"invalid literal/length code\",i.mode=u;break}i.extra=15&N,i.mode=22;case 22:if(i.extra){for(H=i.extra;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.length+=v&(1<<i.extra)-1,v>>>=i.extra,y-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;N=(P=i.distcode[v&(1<<i.distbits)-1])>>>16&255,B=65535&P,!((E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(!(240&N)){for(M=E,R=N,D=B;N=(P=i.distcode[D+((v&(1<<M+R)-1)>>M)])>>>16&255,B=65535&P,!(M+(E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}v>>>=M,y-=M,i.back+=M}if(v>>>=E,y-=E,i.back+=E,64&N){e.msg=\"invalid distance code\",i.mode=u;break}i.offset=B,i.extra=15&N,i.mode=24;case 24:if(i.extra){for(H=i.extra;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.offset+=v&(1<<i.extra)-1,v>>>=i.extra,y-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=u;break}i.mode=25;case 25:if(0===F)break e;if(k=C-F,i.offset>k){if((k=i.offset-k)>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=u;break}k>i.wnext?(k-=i.wnext,I=i.wsize-k):I=i.wnext-k,k>i.length&&(k=i.length),S=i.window}else S=p,I=w-i.offset,k=i.length;k>F&&(k=F),F-=k,i.length-=k;do{p[w++]=S[I++]}while(--k);0===i.length&&(i.mode=21);break;case 26:if(0===F)break e;p[w++]=i.length,F--,i.mode=21;break;case 27:if(i.wrap){for(;y<32;){if(0===b)break e;b--,v|=f[m++]<<y,y+=8}if(C-=F,e.total_out+=C,i.total+=C,C&&(e.adler=i.check=i.flags?s(i.check,p,C,w-C):r(i.check,p,C,w-C)),C=F,(i.flags?v:g(v))!==i.check){e.msg=\"incorrect data check\",i.mode=u;break}v=0,y=0}i.mode=28;case 28:if(i.wrap&&i.flags){for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=u;break}v=0,y=0}i.mode=29;case 29:L=1;break e;case u:L=-3;break e;case 31:return-4;default:return l}return e.next_out=w,e.avail_out=F,e.next_in=m,e.avail_in=b,i.hold=v,i.bits=y,(i.wsize||C!==e.avail_out&&i.mode<u&&(i.mode<27||4!==t))&&x(e,e.output,e.next_out,C-e.avail_out)?(i.mode=31,-4):(A-=e.avail_in,C-=e.avail_out,e.total_in+=A,e.total_out+=C,i.total+=C,i.wrap&&C&&(e.adler=i.check=i.flags?s(i.check,p,C,e.next_out-C):r(i.check,p,C,e.next_out-C)),e.data_type=i.bits+(i.last?64:0)+(i.mode===d?128:0)+(20===i.mode||15===i.mode?256:0),(0===A&&0===C||4===t)&&L===c&&(L=-5),L)},t.inflateEnd=function(e){if(!e||!e.state)return l;var t=e.state;return t.window&&(t.window=null),e.state=null,c},t.inflateGetHeader=function(e,t){var i;return e&&e.state&&2&(i=e.state).wrap?(i.head=t,t.done=!1,c):l},t.inflateSetDictionary=function(e,t){var i,n=t.length;return e&&e.state?0!==(i=e.state).wrap&&11!==i.mode?l:11===i.mode&&r(1,t,n,0)!==i.check?-3:x(e,t,n,n)?(i.mode=31,-4):(i.havedict=1,c):l},t.inflateInfo=\"pako inflate (from Nodeca project)\"},1998:(e,t,i)=>{var n=i(9805),r=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],s=[16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78],o=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0],a=[16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64];e.exports=function(e,t,i,c,l,h,d,u){var f,p,g,m,w,b,F,v,y,A=u.bits,C=0,_=0,x=0,k=0,I=0,S=0,E=0,N=0,B=0,M=0,R=null,D=0,T=new n.Buf16(16),L=new n.Buf16(16),z=null,H=0;for(C=0;C<=15;C++)T[C]=0;for(_=0;_<c;_++)T[t[i+_]]++;for(I=A,k=15;k>=1&&0===T[k];k--);if(I>k&&(I=k),0===k)return l[h++]=20971520,l[h++]=20971520,u.bits=1,0;for(x=1;x<k&&0===T[x];x++);for(I<x&&(I=x),N=1,C=1;C<=15;C++)if(N<<=1,(N-=T[C])<0)return-1;if(N>0&&(0===e||1!==k))return-1;for(L[1]=0,C=1;C<15;C++)L[C+1]=L[C]+T[C];for(_=0;_<c;_++)0!==t[i+_]&&(d[L[t[i+_]]++]=_);if(0===e?(R=z=d,b=19):1===e?(R=r,D-=257,z=s,H-=257,b=256):(R=o,z=a,b=-1),M=0,_=0,C=x,w=h,S=I,E=0,g=-1,m=(B=1<<I)-1,1===e&&B>852||2===e&&B>592)return 1;for(;;){F=C-E,d[_]<b?(v=0,y=d[_]):d[_]>b?(v=z[H+d[_]],y=R[D+d[_]]):(v=96,y=0),f=1<<C-E,x=p=1<<S;do{l[w+(M>>E)+(p-=f)]=F<<24|v<<16|y}while(0!==p);for(f=1<<C-1;M&f;)f>>=1;if(0!==f?(M&=f-1,M+=f):M=0,_++,0==--T[C]){if(C===k)break;C=t[i+d[_]]}if(C>I&&(M&m)!==g){for(0===E&&(E=I),w+=x,N=1<<(S=C-E);S+E<k&&!((N-=T[S+E])<=0);)S++,N<<=1;if(B+=1<<S,1===e&&B>852||2===e&&B>592)return 1;l[g=M&m]=I<<24|S<<16|w-h}}return 0!==M&&(l[w+M]=C-E<<24|64<<16),u.bits=I,0}},4674:e=>{e.exports={2:\"need dictionary\",1:\"stream end\",0:\"\",\"-1\":\"file error\",\"-2\":\"stream error\",\"-3\":\"data error\",\"-4\":\"insufficient memory\",\"-5\":\"buffer error\",\"-6\":\"incompatible version\"}},3665:(e,t,i)=>{var n=i(9805);function r(e){for(var t=e.length;--t>=0;)e[t]=0}var s=15,o=16,a=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0],c=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13],l=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7],h=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],d=new Array(576);r(d);var u=new Array(60);r(u);var f=new Array(512);r(f);var p=new Array(256);r(p);var g=new Array(29);r(g);var m,w,b,F=new Array(30);function v(e,t,i,n,r){this.static_tree=e,this.extra_bits=t,this.extra_base=i,this.elems=n,this.max_length=r,this.has_stree=e&&e.length}function y(e,t){this.dyn_tree=e,this.max_code=0,this.stat_desc=t}function A(e){return e<256?f[e]:f[256+(e>>>7)]}function C(e,t){e.pending_buf[e.pending++]=255&t,e.pending_buf[e.pending++]=t>>>8&255}function 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M(e,t,i){var n,r,s,o,l=0;if(0!==e.last_lit)do{n=e.pending_buf[e.d_buf+2*l]<<8|e.pending_buf[e.d_buf+2*l+1],r=e.pending_buf[e.l_buf+l],l++,0===n?x(e,r,t):(x(e,(s=p[r])+256+1,t),0!==(o=a[s])&&_(e,r-=g[s],o),x(e,s=A(--n),i),0!==(o=c[s])&&_(e,n-=F[s],o))}while(l<e.last_lit);x(e,256,t)}function R(e,t){var i,n,r,o=t.dyn_tree,a=t.stat_desc.static_tree,c=t.stat_desc.has_stree,l=t.stat_desc.elems,h=-1;for(e.heap_len=0,e.heap_max=573,i=0;i<l;i++)0!==o[2*i]?(e.heap[++e.heap_len]=h=i,e.depth[i]=0):o[2*i+1]=0;for(;e.heap_len<2;)o[2*(r=e.heap[++e.heap_len]=h<2?++h:0)]=1,e.depth[r]=0,e.opt_len--,c&&(e.static_len-=a[2*r+1]);for(t.max_code=h,i=e.heap_len>>1;i>=1;i--)B(e,o,i);r=l;do{i=e.heap[1],e.heap[1]=e.heap[e.heap_len--],B(e,o,1),n=e.heap[1],e.heap[--e.heap_max]=i,e.heap[--e.heap_max]=n,o[2*r]=o[2*i]+o[2*n],e.depth[r]=(e.depth[i]>=e.depth[n]?e.depth[i]:e.depth[n])+1,o[2*i+1]=o[2*n+1]=r,e.heap[1]=r++,B(e,o,1)}while(e.heap_len>=2);e.heap[--e.heap_max]=e.heap[1],function(e,t){var i,n,r,o,a,c,l=t.dyn_tree,h=t.max_code,d=t.stat_desc.static_tree,u=t.stat_desc.has_stree,f=t.stat_desc.extra_bits,p=t.stat_desc.extra_base,g=t.stat_desc.max_length,m=0;for(o=0;o<=s;o++)e.bl_count[o]=0;for(l[2*e.heap[e.heap_max]+1]=0,i=e.heap_max+1;i<573;i++)(o=l[2*l[2*(n=e.heap[i])+1]+1]+1)>g&&(o=g,m++),l[2*n+1]=o,n>h||(e.bl_count[o]++,a=0,n>=p&&(a=f[n-p]),c=l[2*n],e.opt_len+=c*(o+a),u&&(e.static_len+=c*(d[2*n+1]+a)));if(0!==m){do{for(o=g-1;0===e.bl_count[o];)o--;e.bl_count[o]--,e.bl_count[o+1]+=2,e.bl_count[g]--,m-=2}while(m>0);for(o=g;0!==o;o--)for(n=e.bl_count[o];0!==n;)(r=e.heap[--i])>h||(l[2*r+1]!==o&&(e.opt_len+=(o-l[2*r+1])*l[2*r],l[2*r+1]=o),n--)}}(e,t),I(o,h,e.bl_count)}function D(e,t,i){var n,r,s=-1,o=t[1],a=0,c=7,l=4;for(0===o&&(c=138,l=3),t[2*(i+1)+1]=65535,n=0;n<=i;n++)r=o,o=t[2*(n+1)+1],++a<c&&r===o||(a<l?e.bl_tree[2*r]+=a:0!==r?(r!==s&&e.bl_tree[2*r]++,e.bl_tree[32]++):a<=10?e.bl_tree[34]++:e.bl_tree[36]++,a=0,s=r,0===o?(c=138,l=3):r===o?(c=6,l=3):(c=7,l=4))}function 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v(d,a,257,286,s),w=new v(u,c,0,30,s),b=new v(new Array(0),l,0,19,7)}(),L=!0),e.l_desc=new y(e.dyn_ltree,m),e.d_desc=new y(e.dyn_dtree,w),e.bl_desc=new y(e.bl_tree,b),e.bi_buf=0,e.bi_valid=0,S(e)},t._tr_stored_block=z,t._tr_flush_block=function(e,t,i,n){var r,s,o=0;e.level>0?(2===e.strm.data_type&&(e.strm.data_type=function(e){var t,i=4093624447;for(t=0;t<=31;t++,i>>>=1)if(1&i&&0!==e.dyn_ltree[2*t])return 0;if(0!==e.dyn_ltree[18]||0!==e.dyn_ltree[20]||0!==e.dyn_ltree[26])return 1;for(t=32;t<256;t++)if(0!==e.dyn_ltree[2*t])return 1;return 0}(e)),R(e,e.l_desc),R(e,e.d_desc),o=function(e){var t;for(D(e,e.dyn_ltree,e.l_desc.max_code),D(e,e.dyn_dtree,e.d_desc.max_code),R(e,e.bl_desc),t=18;t>=3&&0===e.bl_tree[2*h[t]+1];t--);return e.opt_len+=3*(t+1)+5+5+4,t}(e),r=e.opt_len+3+7>>>3,(s=e.static_len+3+7>>>3)<=r&&(r=s)):r=s=i+5,i+4<=r&&-1!==t?z(e,t,i,n):4===e.strategy||s===r?(_(e,2+(n?1:0),3),M(e,d,u)):(_(e,4+(n?1:0),3),function(e,t,i,n){var r;for(_(e,t-257,5),_(e,i-1,5),_(e,n-4,4),r=0;r<n;r++)_(e,e.bl_tree[2*h[r]+1],3);T(e,e.dyn_ltree,t-1),T(e,e.dyn_dtree,i-1)}(e,e.l_desc.max_code+1,e.d_desc.max_code+1,o+1),M(e,e.dyn_ltree,e.dyn_dtree)),S(e),n&&E(e)},t._tr_tally=function(e,t,i){return e.pending_buf[e.d_buf+2*e.last_lit]=t>>>8&255,e.pending_buf[e.d_buf+2*e.last_lit+1]=255&t,e.pending_buf[e.l_buf+e.last_lit]=255&i,e.last_lit++,0===t?e.dyn_ltree[2*i]++:(e.matches++,t--,e.dyn_ltree[2*(p[i]+256+1)]++,e.dyn_dtree[2*A(t)]++),e.last_lit===e.lit_bufsize-1},t._tr_align=function(e){_(e,2,3),x(e,256,d),function(e){16===e.bi_valid?(C(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=255&e.bi_buf,e.bi_buf>>=8,e.bi_valid-=8)}(e)}},4442:e=>{e.exports=function(){this.input=null,this.next_in=0,this.avail_in=0,this.total_in=0,this.output=null,this.next_out=0,this.avail_out=0,this.total_out=0,this.msg=\"\",this.state=null,this.data_type=2,this.adler=0}},7392:e=>{class t{constructor(e={}){if(!(e.maxSize&&e.maxSize>0))throw new TypeError(\"`maxSize` must be a number greater than 0\");this.maxSize=e.maxSize,this.cache=new Map,this.oldCache=new Map,this._size=0}_set(e,t){this.cache.set(e,t),this._size++,this._size>=this.maxSize&&(this._size=0,this.oldCache=this.cache,this.cache=new Map)}get(e){if(this.cache.has(e))return this.cache.get(e);if(this.oldCache.has(e)){const t=this.oldCache.get(e);return this.oldCache.delete(e),this._set(e,t),t}}set(e,t){return this.cache.has(e)?this.cache.set(e,t):this._set(e,t),this}has(e){return this.cache.has(e)||this.oldCache.has(e)}peek(e){return this.cache.has(e)?this.cache.get(e):this.oldCache.has(e)?this.oldCache.get(e):void 0}delete(e){const t=this.cache.delete(e);return t&&this._size--,this.oldCache.delete(e)||t}clear(){this.cache.clear(),this.oldCache.clear(),this._size=0}*keys(){for(const[e]of this)yield e}*values(){for(const[,e]of this)yield e}*[Symbol.iterator](){for(const e of this.cache)yield e;for(const e of this.oldCache){const[t]=e;this.cache.has(t)||(yield e)}}get size(){let e=0;for(const t of this.oldCache.keys())this.cache.has(t)||e++;return this._size+e}}e.exports=t},1307:function(e,t,i){var n;n=e=>(()=>{var 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\"},t=>{t.exports=e}],i={};function 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-       "/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */var Jp={read:function(e,t,i,n,r){var s,o,a=8*r-n-1,c=(1<<a)-1,l=c>>1,h=-7,d=i?r-1:0,u=i?-1:1,f=e[t+d];for(d+=u,s=f&(1<<-h)-1,f>>=-h,h+=a;h>0;s=256*s+e[t+d],d+=u,h-=8);for(o=s&(1<<-h)-1,s>>=-h,h+=n;h>0;o=256*o+e[t+d],d+=u,h-=8);if(0===s)s=1-l;else{if(s===c)return o?NaN:1/0*(f?-1:1);o+=Math.pow(2,n),s-=l}return(f?-1:1)*o*Math.pow(2,s-n)},write:function(e,t,i,n,r,s){var o,a,c,l=8*s-r-1,h=(1<<l)-1,d=h>>1,u=23===r?Math.pow(2,-24)-Math.pow(2,-77):0,f=n?0:s-1,p=n?1:-1,g=t<0||0===t&&1/t<0?1:0;for(t=Math.abs(t),isNaN(t)||t===1/0?(a=isNaN(t)?1:0,o=h):(o=Math.floor(Math.log(t)/Math.LN2),t*(c=Math.pow(2,-o))<1&&(o--,c*=2),(t+=o+d>=1?u/c:u*Math.pow(2,1-d))*c>=2&&(o++,c/=2),o+d>=h?(a=0,o=h):o+d>=1?(a=(t*c-1)*Math.pow(2,r),o+=d):(a=t*Math.pow(2,d-1)*Math.pow(2,r),o=0));r>=8;e[i+f]=255&a,f+=p,a/=256,r-=8);for(o=o<<r|a,l+=r;l>0;e[i+f]=255&o,f+=p,o/=256,l-=8);e[i+f-p]|=128*g}};\n",
-       "/*!\n",
-       "     * The buffer module from node.js, for the browser.\n",
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-       "     * @author   Feross Aboukhadijeh <https://feross.org>\n",
-       "     * @license  MIT\n",
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e>>>=0,t||Ig(e,4,this.length),Jp.read(this,e,!1,23,4)},ng.prototype.readDoubleLE=function(e,t){return e>>>=0,t||Ig(e,8,this.length),Jp.read(this,e,!0,52,8)},ng.prototype.readDoubleBE=function(e,t){return e>>>=0,t||Ig(e,8,this.length),Jp.read(this,e,!1,52,8)},ng.prototype.writeUintLE=ng.prototype.writeUIntLE=function(e,t,i,n){if(e=+e,t>>>=0,i>>>=0,!n){Sg(this,e,t,i,Math.pow(2,8*i)-1,0)}let r=1,s=0;for(this[t]=255&e;++s<i&&(r*=256);)this[t+s]=e/r&255;return t+i},ng.prototype.writeUintBE=ng.prototype.writeUIntBE=function(e,t,i,n){if(e=+e,t>>>=0,i>>>=0,!n){Sg(this,e,t,i,Math.pow(2,8*i)-1,0)}let r=i-1,s=1;for(this[t+r]=255&e;--r>=0&&(s*=256);)this[t+r]=e/s&255;return t+i},ng.prototype.writeUint8=ng.prototype.writeUInt8=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,1,255,0),this[t]=255&e,t+1},ng.prototype.writeUint16LE=ng.prototype.writeUInt16LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,65535,0),this[t]=255&e,this[t+1]=e>>>8,t+2},ng.prototype.writeUint16BE=ng.prototype.writeUInt16BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,65535,0),this[t]=e>>>8,this[t+1]=255&e,t+2},ng.prototype.writeUint32LE=ng.prototype.writeUInt32LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,4294967295,0),this[t+3]=e>>>24,this[t+2]=e>>>16,this[t+1]=e>>>8,this[t]=255&e,t+4},ng.prototype.writeUint32BE=ng.prototype.writeUInt32BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,4294967295,0),this[t]=e>>>24,this[t+1]=e>>>16,this[t+2]=e>>>8,this[t+3]=255&e,t+4},ng.prototype.writeBigUInt64LE=Gg((function(e,t=0){return Eg(this,e,t,BigInt(0),BigInt(\"0xffffffffffffffff\"))})),ng.prototype.writeBigUInt64BE=Gg((function(e,t=0){return Ng(this,e,t,BigInt(0),BigInt(\"0xffffffffffffffff\"))})),ng.prototype.writeIntLE=function(e,t,i,n){if(e=+e,t>>>=0,!n){const n=Math.pow(2,8*i-1);Sg(this,e,t,i,n-1,-n)}let r=0,s=1,o=0;for(this[t]=255&e;++r<i&&(s*=256);)e<0&&0===o&&0!==this[t+r-1]&&(o=1),this[t+r]=(e/s|0)-o&255;return t+i},ng.prototype.writeIntBE=function(e,t,i,n){if(e=+e,t>>>=0,!n){const n=Math.pow(2,8*i-1);Sg(this,e,t,i,n-1,-n)}let r=i-1,s=1,o=0;for(this[t+r]=255&e;--r>=0&&(s*=256);)e<0&&0===o&&0!==this[t+r+1]&&(o=1),this[t+r]=(e/s|0)-o&255;return t+i},ng.prototype.writeInt8=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,1,127,-128),e<0&&(e=255+e+1),this[t]=255&e,t+1},ng.prototype.writeInt16LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,32767,-32768),this[t]=255&e,this[t+1]=e>>>8,t+2},ng.prototype.writeInt16BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,32767,-32768),this[t]=e>>>8,this[t+1]=255&e,t+2},ng.prototype.writeInt32LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,2147483647,-2147483648),this[t]=255&e,this[t+1]=e>>>8,this[t+2]=e>>>16,this[t+3]=e>>>24,t+4},ng.prototype.writeInt32BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,2147483647,-2147483648),e<0&&(e=4294967295+e+1),this[t]=e>>>24,this[t+1]=e>>>16,this[t+2]=e>>>8,this[t+3]=255&e,t+4},ng.prototype.writeBigInt64LE=Gg((function(e,t=0){return Eg(this,e,t,-BigInt(\"0x8000000000000000\"),BigInt(\"0x7fffffffffffffff\"))})),ng.prototype.writeBigInt64BE=Gg((function(e,t=0){return Ng(this,e,t,-BigInt(\"0x8000000000000000\"),BigInt(\"0x7fffffffffffffff\"))})),ng.prototype.writeFloatLE=function(e,t,i){return Mg(this,e,t,!0,i)},ng.prototype.writeFloatBE=function(e,t,i){return Mg(this,e,t,!1,i)},ng.prototype.writeDoubleLE=function(e,t,i){return Rg(this,e,t,!0,i)},ng.prototype.writeDoubleBE=function(e,t,i){return Rg(this,e,t,!1,i)},ng.prototype.copy=function(e,t,i,n){if(!ng.isBuffer(e))throw new TypeError(\"argument should be a Buffer\");if(i||(i=0),n||0===n||(n=this.length),t>=e.length&&(t=e.length),t||(t=0),n>0&&n<i&&(n=i),n===i)return 0;if(0===e.length||0===this.length)return 0;if(t<0)throw new RangeError(\"targetStart out of bounds\");if(i<0||i>=this.length)throw new RangeError(\"Index out of range\");if(n<0)throw new RangeError(\"sourceEnd out of bounds\");n>this.length&&(n=this.length),e.length-t<n-i&&(n=e.length-t+i);const r=n-i;return this===e&&\"function\"==typeof Uint8Array.prototype.copyWithin?this.copyWithin(t,i,n):Uint8Array.prototype.set.call(e,this.subarray(i,n),t),r},ng.prototype.fill=function(e,t,i,n){if(\"string\"==typeof e){if(\"string\"==typeof t?(n=t,t=0,i=this.length):\"string\"==typeof i&&(n=i,i=this.length),void 0!==n&&\"string\"!=typeof n)throw new TypeError(\"encoding must be a string\");if(\"string\"==typeof n&&!ng.isEncoding(n))throw new TypeError(\"Unknown encoding: \"+n);if(1===e.length){const t=e.charCodeAt(0);(\"utf8\"===n&&t<128||\"latin1\"===n)&&(e=t)}}else\"number\"==typeof e?e&=255:\"boolean\"==typeof e&&(e=Number(e));if(t<0||this.length<t||this.length<i)throw new RangeError(\"Out of range index\");if(i<=t)return this;let r;if(t>>>=0,i=void 0===i?this.length:i>>>0,e||(e=0),\"number\"==typeof e)for(r=t;r<i;++r)this[r]=e;else{const s=ng.isBuffer(e)?e:ng.from(e,n),o=s.length;if(0===o)throw new TypeError('The value \"'+e+'\" is invalid for argument \"value\"');for(r=0;r<i-t;++r)this[r+t]=s[r%o]}return this};const Dg={};function Tg(e,t,i){Dg[e]=class extends i{constructor(){super(),Object.defineProperty(this,\"message\",{value:t.apply(this,arguments),writable:!0,configurable:!0}),this.name=`${this.name} [${e}]`,this.stack,delete this.name}get code(){return e}set code(e){Object.defineProperty(this,\"code\",{configurable:!0,enumerable:!0,value:e,writable:!0})}toString(){return`${this.name} [${e}]: ${this.message}`}}}function Lg(e){let t=\"\",i=e.length;const n=\"-\"===e[0]?1:0;for(;i>=n+4;i-=3)t=`_${e.slice(i-3,i)}${t}`;return`${e.slice(0,i)}${t}`}function zg(e,t,i,n,r,s){if(e>i||e<t){const n=\"bigint\"==typeof t?\"n\":\"\";let r;throw r=s>3?0===t||t===BigInt(0)?`>= 0${n} and < 2${n} ** ${8*(s+1)}${n}`:`>= -(2${n} ** 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Received ${r}`,n}),RangeError);const Og=/[^+/0-9A-Za-z-_]/g;function Ug(e,t){let i;t=t||1/0;const n=e.length;let r=null;const s=[];for(let o=0;o<n;++o){if(i=e.charCodeAt(o),i>55295&&i<57344){if(!r){if(i>56319){(t-=3)>-1&&s.push(239,191,189);continue}if(o+1===n){(t-=3)>-1&&s.push(239,191,189);continue}r=i;continue}if(i<56320){(t-=3)>-1&&s.push(239,191,189),r=i;continue}i=65536+(r-55296<<10|i-56320)}else r&&(t-=3)>-1&&s.push(239,191,189);if(r=null,i<128){if((t-=1)<0)break;s.push(i)}else if(i<2048){if((t-=2)<0)break;s.push(i>>6|192,63&i|128)}else if(i<65536){if((t-=3)<0)break;s.push(i>>12|224,i>>6&63|128,63&i|128)}else{if(!(i<1114112))throw new Error(\"Invalid code point\");if((t-=4)<0)break;s.push(i>>18|240,i>>12&63|128,i>>6&63|128,63&i|128)}}return s}function qg(e){return Zp.toByteArray(function(e){if((e=(e=e.split(\"=\")[0]).trim().replace(Og,\"\")).length<2)return\"\";for(;e.length%4!=0;)e+=\"=\";return e}(e))}function Qg(e,t,i,n){let r;for(r=0;r<n&&!(r+i>=t.length||r>=e.length);++r)t[r+i]=e[r];return r}function Vg(e,t){return e instanceof t||null!=e&&null!=e.constructor&&null!=e.constructor.name&&e.constructor.name===t.name}function jg(e){return e!=e}const Wg=function(){const e=\"0123456789abcdef\",t=new Array(256);for(let i=0;i<16;++i){const n=16*i;for(let r=0;r<16;++r)t[n+r]=e[i]+e[r]}return t}();function Gg(e){return\"undefined\"==typeof BigInt?$g:e}function $g(){throw new Error(\"BigInt not supported\")}class Kg{constructor(e,t){this.position=0,this.url=e,this.config=t,Ht(e)||!1===t.cacheFetches?this.useCache=!1:(this.useCache=!0,this.cache=new Yg({fetch:(e,t)=>this._fetch(e,t),fetchSize:t.fetchSize||1e4}))}async _fetch(e,t){const i={start:e,size:t};this._stat={size:void 0};const n=await Qs.loadArrayBuffer(this.url,Ua(this.config,{range:i}));return ng.from(n)}async read(e,t=0,i=1/0,n=0){if(this.useCache)await this.cache.get(e,t,n,i);else{(await this._fetch(n,i)).copy(e,t)}return{bytesRead:i,buffer:e}}async readFile(){const e=await Qs.loadArrayBuffer(this.url,Ua(this.config));return ng.from(e)}async stat(){if(!this._stat){const e=ng.allocUnsafe(10);if(await this.read(e,0,10,0),!this._stat)throw new Error(`unable to determine size of file at ${this.url}`)}return this._stat}}class Yg{constructor({fetch:e,fetchSize:t=3e4}){this.fetch=e,this.position=0,this.buffer=ng.allocUnsafe(0),this.fetchSize=t}async get(e,t,i,n){if(e.length<t+n)throw new Error(\"output buffer not big enough for request\");if(i>=this.position&&i+n<=this.position+this.buffer.length);else{const e=Math.max(n,this.fetchSize);this.buffer=await this.fetch(i,e),this.position=i}const r=t,s=i-this.position,o=s+n;this.buffer.copy(e,r,s,o)}}class Xg{chrAliasTable=new Map;constructor(e,t,i){this.config=e,this.browser=i,this.genome=t,this.cramFile=new Vp.CramFile({filehandle:e.fileHandle?e.fileHandle:new Kg(e.url,e),seqFetch:e.seqFetch||async function(e,t,i){const n=this.genome,r=await this.getHeader(),s=n.getChromosomeName(r.indexToChr[e]);return this.genome.getSequence(s,t-1,i)}.bind(this),checkSequenceMD5:void 0===e.checkSequenceMD5||e.checkSequenceMD5});const n=e.indexFileHandle?e.indexFileHandle:new Kg(e.indexURL,e);this.indexedCramFile=new Vp.IndexedCramFile({cram:this.cramFile,index:new Vp.CraiIndex({filehandle:n}),fetchSizeLimit:e.fetchSizeLimit||1e9}),Mp.setReaderDefaults(this,e)}async getHeader(){if(!this.header){const e=await this.cramFile.getSamHeader(),t={},i=[],n=[];for(let r of e)if(\"SQ\"===r.tag){for(let e of r.data)if(\"SN\"===e.tag){const n=e.value;t[n]=i.length,i.push(n);break}}else\"RG\"===r.tag&&n.push(r.data);this.header={indexToChr:i,chrToIndex:t,chrNames:Object.keys(t),readGroups:n}}return this.header}async#x(e){if(await this.getHeader(),this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.header.chrToIndex[e];if(void 0===t){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>void 0!==this.header.chrToIndex[e]));e.length>0&&(n=e[0],t=this.header.chrToIndex[e[0]])}this.chrAliasTable.set(e,n)}return t}async readAlignments(e,t,i){const n=await this.getHeader(),r=await this.#x(e),s=new tp(e,t,i,this.config);if(void 0===r)return s;try{const e=await this.indexedCramFile.getRecordsForRange(r,t,i);for(let a of e){const e=a.sequenceId,c=a.alignmentStart,l=c+a.lengthOnRef;if(e<0)continue;if(e>r||c>i)return;if(e<r)continue;if(l<t)continue;const h=o(a,n.chrNames);this.filter.pass(h)&&s.push(h)}return s.finish(),s}catch(e){let t=e.message;throw t&&t.indexOf(\"MD5\")>=0&&(t=\"Sequence mismatch. Is this the correct genome for the loaded CRAM?\"),this.browser.alert.present(new Error(t)),e}function o(e,t){const i=new wp;if(i.chr=t[e.sequenceId],i.start=e.alignmentStart-1,i.lengthOnRef=e.lengthOnRef,i.flags=e.flags,i.strand=!(16&e.flags),i.fragmentLength=e.templateLength||e.templateSize,i.mq=e.mappingQuality,i.end=e.alignmentStart+e.lengthOnRef,i.readGroupId=e.readGroupId,e.mate&&void 0!==e.mate.sequenceId){const n=void 0!==e.mate.flags?!(1&e.mate.flags):!(32&e.flags);i.mate={chr:t[e.mate.sequenceId],position:e.mate.alignmentStart,strand:n}}return i.seq=e.getReadBases(),i.qual=e.qualityScores,i.tagDict=e.tags,i.readName=e.readName,function(e,t){const i=[];let n,r,s=0,o=\"\";if(t.scStart=t.start,t.scLengthOnRef=t.lengthOnRef,e.readFeatures)for(let a of e.readFeatures){const e=a.code,c=a.data,l=a.pos-1,h=a.refPos-1;switch(e){case\"S\":case\"I\":case\"i\":case\"N\":case\"D\":if(l>s){const e=l-s;i.push(new xp({start:h-e,seqOffset:s,len:e,type:\"M\"})),s+=e,o+=e+\"M\"}if(\"S\"===e){let n=h;t.scLengthOnRef+=c.length,0===l&&(t.scStart-=c.length,n-=c.length);const r=c.length;i.push(new xp({start:n,seqOffset:s,len:r,type:\"S\"})),s+=r,o+=r+e}else if(\"I\"===e||\"i\"===e){void 0===n&&(n=[]);const t=\"i\"===e?1:c.length;n.push(new xp({start:h,len:t,seqOffset:s,type:\"I\"})),s+=t,o+=t+e}else\"D\"!==e&&\"N\"!==e||(r||(r=[]),r.push({start:h,len:c,type:e}),o+=c+e);break;case\"H\":case\"P\":o+=c+e}}const a=e.readLength-s;a>0&&(i.push(new xp({start:e.alignmentStart+e.lengthOnRef-a-1,seqOffset:s,len:a,type:\"M\"})),o+=a+\"M\");t.blocks=i,t.insertions=n,t.gaps=r,t.cigar=o}(e,i),i.mate&&i.start>i.mate.position&&i.fragmentLength>0&&(i.fragmentLength=-i.fragmentLength),Mp.setPairOrientation(i),i}}}const Zg=2291137574,Jg=2273964779,em=[84,68,70,52],tm=new Uint8Array([66,65,77,1]),im=[67,82,65,77],nm=[31,139],rm=4,sm=new Set([\"narrowpeak\",\"broadpeak\",\"regionpeak\",\"peaks\",\"bedgraph\",\"wig\",\"gff3\",\"gff\",\"gtf\",\"fusionjuncspan\",\"refflat\",\"seg\",\"aed\",\"bed\",\"bedMethyl\",\"vcf\",\"bb\",\"bigbed\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\",\"bw\",\"bigwig\",\"bam\",\"tdf\",\"refgene\",\"genepred\",\"genepredext\",\"bedpe\",\"bp\",\"snp\",\"rmsk\",\"cram\",\"gwas\",\"maf\",\"mut\",\"hiccups\",\"fasta\",\"fa\",\"fna\",\"pytor\",\"hic\",\"qtl\"]);function om(e,t){const i=Math.min(e.length,t.length);if(0==i)return!1;for(let n=0;n<i;n++)if(e[n]!==t[n])return!1;return!0}async function am(e){let t;const i=e.filename||await ja(e.url);return i&&(t=await function(e){if(!e)return;if((e=e.toLowerCase()).endsWith(\"refgene.txt.gz\")||e.endsWith(\"refgene.txt.bgz\")||e.endsWith(\"refgene.txt\")||e.endsWith(\"refgene.sorted.txt.gz\")||e.endsWith(\"refgene.sorted.txt.bgz\"))return\"refgene\";e.endsWith(\".gz\")&&(e=e.substring(0,e.length-3));e.endsWith(\".bgz\")&&(e=e.substring(0,e.length-4));(e.endsWith(\".txt\")||e.endsWith(\".tab\")||e.endsWith(\".tsv\"))&&(e=e.substring(0,e.length-4));const t=e.lastIndexOf(\".\"),i=t<0?e:e.substring(t+1);switch(i){case\"bw\":return\"bigwig\";case\"bb\":return\"bigbed\";case\"fasta\":case\"fa\":case\"fna\":return\"fasta\";default:return sm.has(i)?i:void 0}}(i)),t||(t=await async function(e){const t=e.url;let i=Ua(e,{range:{start:0,size:1e3}}),n=await Qs.loadArrayBuffer(t,i),r=new Uint8Array(n);if(om(r,nm)){if(0!==(r[3]&rm)&&66===r[12]&&67===r[13]){i=Ua(e,{range:{start:0,size:ms(n)}}),n=await Qs.loadArrayBuffer(t,i),r=gs(n)}else i=Ua(e,{}),n=await Qs.loadArrayBuffer(t,i),r=ps(n),e._filecontents=r}if(om(r,tm))return\"bam\";if(om(r,im))return\"cram\";const s=!0;let o=new yc(new DataView(n),s).getUInt();if(o===Zg)return\"bigwig\";if(o===Jg)return\"bigbed\";if(om(r,em))return\"tdf\";const a=new TextDecoder(\"utf-8\").decode(r),c=a.split(/\\r?\\n/)[0];if(c.startsWith(\"##fileformat=VCF\"))return\"vcf\";if(c.startsWith(\"##gff-version 3\"))return\"gff3\";if(c.startsWith(\"##gff-version\"))return\"gff\";if(c.startsWith(\"##fileformat=\"))return c.substring(13).toLowerCase();if(xh.isQTL(c))return\"qtl\";if(Jl.isGWAS(c))return\"gwas\";if(Dc(c.split(\"\\t\")))return\"hiccups\";return null}(e)),t}class cm{constructor(e,t){const i=t.genome;if(this.config=e,this.genome=i,Ga(e.url)&&(this.config.indexed=!1),\"ga4gh\"===e.sourceType)throw Error(\"Unsupported source type 'ga4gh'\");if(\"pysam\"===e.sourceType)this.bamReader=new Up(e,i);else if(\"htsget\"===e.sourceType)this.bamReader=new Qp(e,i);else if(\"shardedBam\"===e.sourceType)this.bamReader=new Op(e,i);else if(\"cram\"===e.format)this.bamReader=new Xg(e,i,t);else{if(!this.config.indexURL&&!1!==e.indexed)if(Mt(this.config.url)){const e=function(e,t){if(Mt(e)){if(e.includes(\"?\")){const i=e.indexOf(\"?\");return e.substring(0,i)+\".\"+t+e.substring(i)}return e+\".\"+t}}(this.config.url,\"bai\");e?(console.warn(`Warning: no indexURL specified for ${this.config.url}.  Guessing ${e}`),this.config.indexURL=e):(console.warning(`Warning: no indexURL specified for ${this.config.url}.`),this.config.indexed=!1)}else console.warning(`Warning: no indexURL specified for ${this.config.name}.`),this.config.indexed=!1;!1!==this.config.indexed?this.bamReader=new Pp(e,i):this.bamReader=new Hp(e,i)}}async getAlignments(e,t,i){const n=this.genome,r=await this.bamReader.readAlignments(e,t,i);if(r.hasAlignments){const t=await n.getSequence(e,r.start,r.end);if(t)return r.coverageMap.refSeq=t,r.sequence=t,r;console.error(\"No sequence for: \"+e+\":\"+r.start+\"-\"+r.end)}return r}}class lm{constructor({chr:e,start:t,end:i}){this.chr=e,this.start=t,this.end=i}contains(e){return e.chr===this.chr&&e.start>=this.start&&e.end<=this.end}overlaps(e){return e.chr===this.chr&&!(e.end<this.start||e.start>this.end)}extend(e){e.chr===this.chr&&(this.start=Math.min(e.start,this.start),this.end=Math.max(e.end,this.end))}getLocusString(){if(\"all\"===this.chr)return\"all\";{const e=Rt(Math.floor(this.start)+1),t=Rt(Math.round(this.end));return`${this.chr}:${e}-${t}`}}static fromLocusString(e){if(\"all\"===e)return new lm({chr:\"all\"});const t=e.split(\":\"),i=t[0],n=t[1].split(\"-\"),r=Number.parseInt(n[0].replace(/,/g,\"\"))-1,s=Number.parseInt(n[1].replace(/,/g,\"\"));return new lm({chr:i,start:r,end:s})}}\n",
-       "/*!\n",
-       "     * vanilla-picker v2.12.1\n",
-       "     * https://vanilla-picker.js.org\n",
-       "     *\n",
-       "     * Copyright 2017-2021 Andreas Borgen (https://github.com/Sphinxxxx), Adam Brooks (https://github.com/dissimulate)\n",
-       "     * Released under the ISC license.\n",
-       "     */var hm=function(e,t){if(!(e instanceof t))throw new TypeError(\"Cannot call a class as a function\")},dm=function(){function e(e,t){for(var i=0;i<t.length;i++){var n=t[i];n.enumerable=n.enumerable||!1,n.configurable=!0,\"value\"in n&&(n.writable=!0),Object.defineProperty(e,n.key,n)}}return function(t,i,n){return i&&e(t.prototype,i),n&&e(t,n),t}}(),um=function(e,t){if(Array.isArray(e))return e;if(Symbol.iterator in Object(e))return function(e,t){var i=[],n=!0,r=!1,s=void 0;try{for(var o,a=e[Symbol.iterator]();!(n=(o=a.next()).done)&&(i.push(o.value),!t||i.length!==t);n=!0);}catch(e){r=!0,s=e}finally{try{!n&&a.return&&a.return()}finally{if(r)throw s}}return i}(e,t);throw new TypeError(\"Invalid attempt to destructure non-iterable instance\")};String.prototype.startsWith=String.prototype.startsWith||function(e){return 0===this.indexOf(e)},String.prototype.padStart=String.prototype.padStart||function(e,t){for(var i=this;i.length<e;)i=t+i;return i};var fm={cb:\"0f8ff\",tqw:\"aebd7\",q:\"-ffff\",qmrn:\"7fffd4\",zr:\"0ffff\",bg:\"5f5dc\",bsq:\"e4c4\",bck:\"---\",nch:\"ebcd\",b:\"--ff\",bvt:\"8a2be2\",brwn:\"a52a2a\",brw:\"deb887\",ctb:\"5f9ea0\",hrt:\"7fff-\",chcT:\"d2691e\",cr:\"7f50\",rnw:\"6495ed\",crns:\"8dc\",crms:\"dc143c\",cn:\"-ffff\",Db:\"--8b\",Dcn:\"-8b8b\",Dgnr:\"b8860b\",Dgr:\"a9a9a9\",Dgrn:\"-64-\",Dkhk:\"bdb76b\",Dmgn:\"8b-8b\",Dvgr:\"556b2f\",Drng:\"8c-\",Drch:\"9932cc\",Dr:\"8b--\",Dsmn:\"e9967a\",Dsgr:\"8fbc8f\",DsTb:\"483d8b\",DsTg:\"2f4f4f\",Dtrq:\"-ced1\",Dvt:\"94-d3\",ppnk:\"1493\",pskb:\"-bfff\",mgr:\"696969\",grb:\"1e90ff\",rbrc:\"b22222\",rwht:\"af0\",stg:\"228b22\",chs:\"-ff\",gnsb:\"dcdcdc\",st:\"8f8ff\",g:\"d7-\",gnr:\"daa520\",gr:\"808080\",grn:\"-8-0\",grnw:\"adff2f\",hnw:\"0fff0\",htpn:\"69b4\",nnr:\"cd5c5c\",ng:\"4b-82\",vr:\"0\",khk:\"0e68c\",vnr:\"e6e6fa\",nrb:\"0f5\",wngr:\"7cfc-\",mnch:\"acd\",Lb:\"add8e6\",Lcr:\"08080\",Lcn:\"e0ffff\",Lgnr:\"afad2\",Lgr:\"d3d3d3\",Lgrn:\"90ee90\",Lpnk:\"b6c1\",Lsmn:\"a07a\",Lsgr:\"20b2aa\",Lskb:\"87cefa\",LsTg:\"778899\",Lstb:\"b0c4de\",Lw:\"e0\",m:\"-ff-\",mgrn:\"32cd32\",nn:\"af0e6\",mgnt:\"-ff\",mrn:\"8--0\",mqm:\"66cdaa\",mmb:\"--cd\",mmrc:\"ba55d3\",mmpr:\"9370db\",msg:\"3cb371\",mmsT:\"7b68ee\",\"\":\"-fa9a\",mtr:\"48d1cc\",mmvt:\"c71585\",mnLb:\"191970\",ntc:\"5fffa\",mstr:\"e4e1\",mccs:\"e4b5\",vjw:\"dead\",nv:\"--80\",c:\"df5e6\",v:\"808-0\",vrb:\"6b8e23\",rng:\"a5-\",rngr:\"45-\",rch:\"da70d6\",pgnr:\"eee8aa\",pgrn:\"98fb98\",ptrq:\"afeeee\",pvtr:\"db7093\",ppwh:\"efd5\",pchp:\"dab9\",pr:\"cd853f\",pnk:\"c0cb\",pm:\"dda0dd\",pwrb:\"b0e0e6\",prp:\"8-080\",cc:\"663399\",r:\"--\",sbr:\"bc8f8f\",rb:\"4169e1\",sbrw:\"8b4513\",smn:\"a8072\",nbr:\"4a460\",sgrn:\"2e8b57\",ssh:\"5ee\",snn:\"a0522d\",svr:\"c0c0c0\",skb:\"87ceeb\",sTb:\"6a5acd\",sTgr:\"708090\",snw:\"afa\",n:\"-ff7f\",stb:\"4682b4\",tn:\"d2b48c\",t:\"-8080\",thst:\"d8bfd8\",tmT:\"6347\",trqs:\"40e0d0\",vt:\"ee82ee\",whT:\"5deb3\",wht:\"\",hts:\"5f5f5\",w:\"-\",wgrn:\"9acd32\"};function pm(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:1;return(t>0?e.toFixed(t).replace(/0+$/,\"\").replace(/\\.$/,\"\"):e.toString())||\"0\"}var gm=function(){function e(t,i,n,r){hm(this,e);var s=this;if(void 0===t);else if(Array.isArray(t))this.rgba=t;else if(void 0===n){var o=t&&\"\"+t;o&&function(t){if(t.startsWith(\"hsl\")){var i=t.match(/([\\-\\d\\.e]+)/g).map(Number),n=um(i,4),r=n[0],o=n[1],a=n[2],c=n[3];void 0===c&&(c=1),r/=360,o/=100,a/=100,s.hsla=[r,o,a,c]}else if(t.startsWith(\"rgb\")){var l=t.match(/([\\-\\d\\.e]+)/g).map(Number),h=um(l,4),d=h[0],u=h[1],f=h[2],p=h[3];void 0===p&&(p=1),s.rgba=[d,u,f,p]}else t.startsWith(\"#\")?s.rgba=e.hexToRgb(t):s.rgba=e.nameToRgb(t)||e.hexToRgb(t)}(o.toLowerCase())}else this.rgba=[t,i,n,void 0===r?1:r]}return dm(e,[{key:\"printRGB\",value:function(e){var t=(e?this.rgba:this.rgba.slice(0,3)).map((function(e,t){return pm(e,3===t?3:0)}));return e?\"rgba(\"+t+\")\":\"rgb(\"+t+\")\"}},{key:\"printHSL\",value:function(e){var t=[360,100,100,1],i=[\"\",\"%\",\"%\",\"\"],n=(e?this.hsla:this.hsla.slice(0,3)).map((function(e,n){return pm(e*t[n],3===n?3:1)+i[n]}));return e?\"hsla(\"+n+\")\":\"hsl(\"+n+\")\"}},{key:\"printHex\",value:function(e){var t=this.hex;return e?t:t.substring(0,7)}},{key:\"rgba\",get:function(){if(this._rgba)return this._rgba;if(!this._hsla)throw new Error(\"No color is set\");return this._rgba=e.hslToRgb(this._hsla)},set:function(e){3===e.length&&(e[3]=1),this._rgba=e,this._hsla=null}},{key:\"rgbString\",get:function(){return this.printRGB()}},{key:\"rgbaString\",get:function(){return this.printRGB(!0)}},{key:\"hsla\",get:function(){if(this._hsla)return this._hsla;if(!this._rgba)throw new Error(\"No color is set\");return this._hsla=e.rgbToHsl(this._rgba)},set:function(e){3===e.length&&(e[3]=1),this._hsla=e,this._rgba=null}},{key:\"hslString\",get:function(){return this.printHSL()}},{key:\"hslaString\",get:function(){return this.printHSL(!0)}},{key:\"hex\",get:function(){var e=this.rgba.map((function(e,t){return t<3?e.toString(16):Math.round(255*e).toString(16)}));return\"#\"+e.map((function(e){return e.padStart(2,\"0\")})).join(\"\")},set:function(t){this.rgba=e.hexToRgb(t)}}],[{key:\"hexToRgb\",value:function(e){var t=(e.startsWith(\"#\")?e.slice(1):e).replace(/^(\\w{3})$/,\"$1F\").replace(/^(\\w)(\\w)(\\w)(\\w)$/,\"$1$1$2$2$3$3$4$4\").replace(/^(\\w{6})$/,\"$1FF\");if(!t.match(/^([0-9a-fA-F]{8})$/))throw new Error(\"Unknown hex color; \"+e);var i=t.match(/^(\\w\\w)(\\w\\w)(\\w\\w)(\\w\\w)$/).slice(1).map((function(e){return parseInt(e,16)}));return i[3]=i[3]/255,i}},{key:\"nameToRgb\",value:function(t){var i=t.toLowerCase().replace(\"at\",\"T\").replace(/[aeiouyldf]/g,\"\").replace(\"ght\",\"L\").replace(\"rk\",\"D\").slice(-5,4),n=fm[i];return void 0===n?n:e.hexToRgb(n.replace(/\\-/g,\"00\").padStart(6,\"f\"))}},{key:\"rgbToHsl\",value:function(e){var t=um(e,4),i=t[0],n=t[1],r=t[2],s=t[3];i/=255,n/=255,r/=255;var o=Math.max(i,n,r),a=Math.min(i,n,r),c=void 0,l=void 0,h=(o+a)/2;if(o===a)c=l=0;else{var d=o-a;switch(l=h>.5?d/(2-o-a):d/(o+a),o){case i:c=(n-r)/d+(n<r?6:0);break;case n:c=(r-i)/d+2;break;case r:c=(i-n)/d+4}c/=6}return[c,l,h,s]}},{key:\"hslToRgb\",value:function(e){var t=um(e,4),i=t[0],n=t[1],r=t[2],s=t[3],o=void 0,a=void 0,c=void 0;if(0===n)o=a=c=r;else{var l=function(e,t,i){return i<0&&(i+=1),i>1&&(i-=1),i<1/6?e+6*(t-e)*i:i<.5?t:i<2/3?e+(t-e)*(2/3-i)*6:e},h=r<.5?r*(1+n):r+n-r*n,d=2*r-h;o=l(d,h,i+1/3),a=l(d,h,i),c=l(d,h,i-1/3)}var u=[255*o,255*a,255*c].map(Math.round);return u[3]=s,u}}]),e}(),mm=function(){function e(){hm(this,e),this._events=[]}return dm(e,[{key:\"add\",value:function(e,t,i){e.addEventListener(t,i,!1),this._events.push({target:e,type:t,handler:i})}},{key:\"remove\",value:function(t,i,n){this._events=this._events.filter((function(r){var s=!0;return t&&t!==r.target&&(s=!1),i&&i!==r.type&&(s=!1),n&&n!==r.handler&&(s=!1),s&&e._doRemove(r.target,r.type,r.handler),!s}))}},{key:\"destroy\",value:function(){this._events.forEach((function(t){return e._doRemove(t.target,t.type,t.handler)})),this._events=[]}}],[{key:\"_doRemove\",value:function(e,t,i){e.removeEventListener(t,i,!1)}}]),e}();function wm(e,t,i){var n=!1;function r(e,t,i){return Math.max(t,Math.min(e,i))}function s(e,s,o){if(o&&(n=!0),n){e.preventDefault();var a=t.getBoundingClientRect(),c=a.width,l=a.height,h=s.clientX,d=s.clientY,u=r(h-a.left,0,c),f=r(d-a.top,0,l);i(u/c,f/l)}}function o(e,t){1===(void 0===e.buttons?e.which:e.buttons)?s(e,e,t):n=!1}function a(e,t){1===e.touches.length?s(e,e.touches[0],t):n=!1}e.add(t,\"mousedown\",(function(e){o(e,!0)})),e.add(t,\"touchstart\",(function(e){a(e,!0)})),e.add(window,\"mousemove\",o),e.add(t,\"touchmove\",a),e.add(window,\"mouseup\",(function(e){n=!1})),e.add(t,\"touchend\",(function(e){n=!1})),e.add(t,\"touchcancel\",(function(e){n=!1}))}var bm=\"keydown\",Fm=\"mousedown\",vm=\"focusin\";function ym(e,t){return(t||document).querySelector(e)}function Am(e){e.preventDefault(),e.stopPropagation()}function Cm(e,t,i,n,r){e.add(t,bm,(function(e){i.indexOf(e.key)>=0&&(r&&Am(e),n(e))}))}var _m=function(){function e(t){hm(this,e),this.settings={popup:\"right\",layout:\"default\",alpha:!0,editor:!0,editorFormat:\"hex\",cancelButton:!1,defaultColor:\"#0cf\"},this._events=new mm,this.onChange=null,this.onDone=null,this.onOpen=null,this.onClose=null,this.setOptions(t)}return dm(e,[{key:\"setOptions\",value:function(e){var t=this;if(e){var i=this.settings;if(e instanceof HTMLElement)i.parent=e;else{i.parent&&e.parent&&i.parent!==e.parent&&(this._events.remove(i.parent),this._popupInited=!1),function(e,t,i){for(var n in e)i&&i.indexOf(n)>=0||(t[n]=e[n])}(e,i),e.onChange&&(this.onChange=e.onChange),e.onDone&&(this.onDone=e.onDone),e.onOpen&&(this.onOpen=e.onOpen),e.onClose&&(this.onClose=e.onClose);var n=e.color||e.colour;n&&this._setColor(n)}var r=i.parent;if(r&&i.popup&&!this._popupInited){var s=function(e){return t.openHandler(e)};this._events.add(r,\"click\",s),Cm(this._events,r,[\" \",\"Spacebar\",\"Enter\"],s),this._popupInited=!0}else e.parent&&!i.popup&&this.show()}}},{key:\"openHandler\",value:function(e){if(this.show()){e&&e.preventDefault(),this.settings.parent.style.pointerEvents=\"none\";var t=e&&e.type===bm?this._domEdit:this.domElement;setTimeout((function(){return t.focus()}),100),this.onOpen&&this.onOpen(this.colour)}}},{key:\"closeHandler\",value:function(e){var t=e&&e.type,i=!1;if(e)if(t===Fm||t===vm){var n=(this.__containedEvent||0)+100;e.timeStamp>n&&(i=!0)}else Am(e),i=!0;else i=!0;i&&this.hide()&&(this.settings.parent.style.pointerEvents=\"\",t!==Fm&&this.settings.parent.focus(),this.onClose&&this.onClose(this.colour))}},{key:\"movePopup\",value:function(e,t){this.closeHandler(),this.setOptions(e),t&&this.openHandler()}},{key:\"setColor\",value:function(e,t){this._setColor(e,{silent:t})}},{key:\"_setColor\",value:function(e,t){if(\"string\"==typeof e&&(e=e.trim()),e){t=t||{};var i=void 0;try{i=new gm(e)}catch(e){if(t.failSilently)return;throw e}if(!this.settings.alpha){var n=i.hsla;n[3]=1,i.hsla=n}this.colour=this.color=i,this._setHSLA(null,null,null,null,t)}}},{key:\"setColour\",value:function(e,t){this.setColor(e,t)}},{key:\"show\",value:function(){if(!this.settings.parent)return!1;if(this.domElement){var e=this._toggleDOM(!0);return this._setPosition(),e}var t=function(e){var t=document.createElement(\"div\");return t.innerHTML=e,t.firstElementChild}(this.settings.template||'<div class=\"picker_wrapper\" tabindex=\"-1\"><div class=\"picker_arrow\"></div><div class=\"picker_hue picker_slider\"><div class=\"picker_selector\"></div></div><div class=\"picker_sl\"><div class=\"picker_selector\"></div></div><div class=\"picker_alpha picker_slider\"><div class=\"picker_selector\"></div></div><div class=\"picker_editor\"><input aria-label=\"Type a color name or hex value\"/></div><div class=\"picker_sample\"></div><div class=\"picker_done\"><button>Ok</button></div><div class=\"picker_cancel\"><button>Cancel</button></div></div>');return this.domElement=t,this._domH=ym(\".picker_hue\",t),this._domSL=ym(\".picker_sl\",t),this._domA=ym(\".picker_alpha\",t),this._domEdit=ym(\".picker_editor input\",t),this._domSample=ym(\".picker_sample\",t),this._domOkay=ym(\".picker_done button\",t),this._domCancel=ym(\".picker_cancel button\",t),t.classList.add(\"layout_\"+this.settings.layout),this.settings.alpha||t.classList.add(\"no_alpha\"),this.settings.editor||t.classList.add(\"no_editor\"),this.settings.cancelButton||t.classList.add(\"no_cancel\"),this._ifPopup((function(){return t.classList.add(\"popup\")})),this._setPosition(),this.colour?this._updateUI():this._setColor(this.settings.defaultColor),this._bindEvents(),!0}},{key:\"hide\",value:function(){return this._toggleDOM(!1)}},{key:\"destroy\",value:function(){this._events.destroy(),this.domElement&&this.settings.parent.removeChild(this.domElement)}},{key:\"_bindEvents\",value:function(){var e=this,t=this,i=this.domElement,n=this._events;function r(e,t,i){n.add(e,t,i)}r(i,\"click\",(function(e){return e.preventDefault()})),wm(n,this._domH,(function(e,i){return t._setHSLA(e)})),wm(n,this._domSL,(function(e,i){return t._setHSLA(null,e,1-i)})),this.settings.alpha&&wm(n,this._domA,(function(e,i){return t._setHSLA(null,null,null,1-i)}));var s=this._domEdit;r(s,\"input\",(function(e){t._setColor(this.value,{fromEditor:!0,failSilently:!0})})),r(s,\"focus\",(function(e){var t=this;t.selectionStart===t.selectionEnd&&t.select()})),this._ifPopup((function(){var t=function(t){return e.closeHandler(t)};r(window,Fm,t),r(window,vm,t),Cm(n,i,[\"Esc\",\"Escape\"],t);var s=function(t){e.__containedEvent=t.timeStamp};r(i,Fm,s),r(i,vm,s),r(e._domCancel,\"click\",t)}));var o=function(t){e._ifPopup((function(){return e.closeHandler(t)})),e.onDone&&e.onDone(e.colour)};r(this._domOkay,\"click\",o),Cm(n,i,[\"Enter\"],o)}},{key:\"_setPosition\",value:function(){var e=this.settings.parent,t=this.domElement;e!==t.parentNode&&e.appendChild(t),this._ifPopup((function(i){\"static\"===getComputedStyle(e).position&&(e.style.position=\"relative\");var n=!0===i?\"popup_right\":\"popup_\"+i;[\"popup_top\",\"popup_bottom\",\"popup_left\",\"popup_right\"].forEach((function(e){e===n?t.classList.add(e):t.classList.remove(e)})),t.classList.add(n)}))}},{key:\"_setHSLA\",value:function(e,t,i,n,r){r=r||{};var s=this.colour,o=s.hsla;[e,t,i,n].forEach((function(e,t){(e||0===e)&&(o[t]=e)})),s.hsla=o,this._updateUI(r),this.onChange&&!r.silent&&this.onChange(s)}},{key:\"_updateUI\",value:function(e){if(this.domElement){e=e||{};var t=this.colour,i=t.hsla,n=\"hsl(\"+360*i[0]+\", 100%, 50%)\",r=t.hslString,s=t.hslaString,o=this._domH,a=this._domSL,c=this._domA,l=ym(\".picker_selector\",o),h=ym(\".picker_selector\",a),d=ym(\".picker_selector\",c);b(0,l,i[0]),this._domSL.style.backgroundColor=this._domH.style.color=n,b(0,h,i[1]),F(0,h,1-i[2]),a.style.color=r,F(0,d,1-i[3]);var u=r,f=u.replace(\"hsl\",\"hsla\").replace(\")\",\", 0)\"),p=\"linear-gradient(\"+[u,f]+\")\";if(this._domA.style.background=p+\", linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0 / 2em 2em,\\n                   linear-gradient(45deg, lightgrey 25%,       white 25%,       white 75%, lightgrey 75%) 1em 1em / 2em 2em\",!e.fromEditor){var g=this.settings.editorFormat,m=this.settings.alpha,w=void 0;switch(g){case\"rgb\":w=t.printRGB(m);break;case\"hsl\":w=t.printHSL(m);break;default:w=t.printHex(m)}this._domEdit.value=w}this._domSample.style.color=s}function b(e,t,i){t.style.left=100*i+\"%\"}function F(e,t,i){t.style.top=100*i+\"%\"}}},{key:\"_ifPopup\",value:function(e,t){this.settings.parent&&this.settings.popup?e&&e(this.settings.popup):t&&t()}},{key:\"_toggleDOM\",value:function(e){var t=this.domElement;if(!t)return!1;var i=e?\"\":\"none\",n=t.style.display!==i;return n&&(t.style.display=i),n}}]),e}(),xm=document.createElement(\"style\");function km(e){if(Im[e])return Im[e];if(Im[\"chr\"+e]){const t=Im[\"chr\"+e];return Im[e]=t,t}{const r=(t=Math.round(255*Math.random()).toString(10),i=Math.round(255*Math.random()).toString(10),n=Math.round(255*Math.random()).toString(10),\"rgb(\"+t+\",\"+i+\",\"+n+\")\");return Im[e]=r,r}var t,i,n}xm.textContent='.picker_wrapper.no_alpha .picker_alpha{display:none}.picker_wrapper.no_editor .picker_editor{position:absolute;z-index:-1;opacity:0}.picker_wrapper.no_cancel .picker_cancel{display:none}.layout_default.picker_wrapper{display:flex;flex-flow:row wrap;justify-content:space-between;align-items:stretch;font-size:10px;width:25em;padding:.5em}.layout_default.picker_wrapper input,.layout_default.picker_wrapper button{font-size:1rem}.layout_default.picker_wrapper>*{margin:.5em}.layout_default.picker_wrapper::before{content:\"\";display:block;width:100%;height:0;order:1}.layout_default .picker_slider,.layout_default .picker_selector{padding:1em}.layout_default .picker_hue{width:100%}.layout_default .picker_sl{flex:1 1 auto}.layout_default .picker_sl::before{content:\"\";display:block;padding-bottom:100%}.layout_default .picker_editor{order:1;width:6.5rem}.layout_default .picker_editor input{width:100%;height:100%}.layout_default .picker_sample{order:1;flex:1 1 auto}.layout_default .picker_done,.layout_default .picker_cancel{order:1}.picker_wrapper{box-sizing:border-box;background:#f2f2f2;box-shadow:0 0 0 1px silver;cursor:default;font-family:sans-serif;color:#444;pointer-events:auto}.picker_wrapper:focus{outline:none}.picker_wrapper button,.picker_wrapper input{box-sizing:border-box;border:none;box-shadow:0 0 0 1px silver;outline:none}.picker_wrapper button:focus,.picker_wrapper button:active,.picker_wrapper input:focus,.picker_wrapper input:active{box-shadow:0 0 2px 1px #1e90ff}.picker_wrapper button{padding:.4em .6em;cursor:pointer;background-color:#f5f5f5;background-image:linear-gradient(0deg, gainsboro, transparent)}.picker_wrapper button:active{background-image:linear-gradient(0deg, transparent, gainsboro)}.picker_wrapper button:hover{background-color:#fff}.picker_selector{position:absolute;z-index:1;display:block;-webkit-transform:translate(-50%, -50%);transform:translate(-50%, -50%);border:2px solid #fff;border-radius:100%;box-shadow:0 0 3px 1px #67b9ff;background:currentColor;cursor:pointer}.picker_slider .picker_selector{border-radius:2px}.picker_hue{position:relative;background-image:linear-gradient(90deg, red, yellow, lime, cyan, blue, magenta, red);box-shadow:0 0 0 1px silver}.picker_sl{position:relative;box-shadow:0 0 0 1px silver;background-image:linear-gradient(180deg, white, rgba(255, 255, 255, 0) 50%),linear-gradient(0deg, black, rgba(0, 0, 0, 0) 50%),linear-gradient(90deg, #808080, rgba(128, 128, 128, 0))}.picker_alpha,.picker_sample{position:relative;background:linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0/2em 2em,linear-gradient(45deg, lightgrey 25%, white 25%, white 75%, lightgrey 75%) 1em 1em/2em 2em;box-shadow:0 0 0 1px silver}.picker_alpha .picker_selector,.picker_sample .picker_selector{background:none}.picker_editor input{font-family:monospace;padding:.2em .4em}.picker_sample::before{content:\"\";position:absolute;display:block;width:100%;height:100%;background:currentColor}.picker_arrow{position:absolute;z-index:-1}.picker_wrapper.popup{position:absolute;z-index:2;margin:1.5em}.picker_wrapper.popup,.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{background:#f2f2f2;box-shadow:0 0 10px 1px rgba(0,0,0,.4)}.picker_wrapper.popup .picker_arrow{width:3em;height:3em;margin:0}.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{content:\"\";display:block;position:absolute;top:0;left:0;z-index:-99}.picker_wrapper.popup .picker_arrow::before{width:100%;height:100%;-webkit-transform:skew(45deg);transform:skew(45deg);-webkit-transform-origin:0 100%;transform-origin:0 100%}.picker_wrapper.popup .picker_arrow::after{width:150%;height:150%;box-shadow:none}.popup.popup_top{bottom:100%;left:0}.popup.popup_top .picker_arrow{bottom:0;left:0;-webkit-transform:rotate(-90deg);transform:rotate(-90deg)}.popup.popup_bottom{top:100%;left:0}.popup.popup_bottom .picker_arrow{top:0;left:0;-webkit-transform:rotate(90deg) scale(1, -1);transform:rotate(90deg) scale(1, -1)}.popup.popup_left{top:0;right:100%}.popup.popup_left .picker_arrow{top:0;right:0;-webkit-transform:scale(-1, 1);transform:scale(-1, 1)}.popup.popup_right{top:0;left:100%}.popup.popup_right .picker_arrow{top:0;left:0}',document.documentElement.firstElementChild.appendChild(xm),_m.StyleElement=xm;const Im={chrX:\"rgb(204, 153, 0)\",chrY:\"rgb(153, 204, 0\",chrUn:\"rgb(50, 50, 50)\",chr1:\"rgb(80, 80, 255)\",chrI:\"rgb(139, 155, 187)\",chr2:\"rgb(206, 61, 50)\",chrII:\"rgb(206, 61, 50)\",chr2a:\"rgb(216, 71, 60)\",chr2b:\"rgb(226, 81, 70)\",chr3:\"rgb(116, 155, 88)\",chrIII:\"rgb(116, 155, 88)\",chr4:\"rgb(240, 230, 133)\",chrIV:\"rgb(240, 230, 133)\",chr5:\"rgb(70, 105, 131)\",chr6:\"rgb(186, 99, 56)\",chr7:\"rgb(93, 177, 221)\",chr8:\"rgb(128, 34, 104)\",chr9:\"rgb(107, 215, 107)\",chr10:\"rgb(213, 149, 167)\",chr11:\"rgb(146, 72, 34)\",chr12:\"rgb(131, 123, 141)\",chr13:\"rgb(199, 81, 39)\",chr14:\"rgb(213, 143, 92)\",chr15:\"rgb(122, 101, 165)\",chr16:\"rgb(228, 175, 105)\",chr17:\"rgb(59, 27, 83)\",chr18:\"rgb(205, 222, 183)\",chr19:\"rgb(97, 42, 121)\",chr20:\"rgb(174, 31, 99)\",chr21:\"rgb(231, 199, 111)\",chr22:\"rgb(90, 101, 94)\",chr23:\"rgb(204, 153, 0)\",chr24:\"rgb(153, 204, 0)\",chr25:\"rgb(51, 204, 0)\",chr26:\"rgb(0, 204, 51)\",chr27:\"rgb(0, 204, 153)\",chr28:\"rgb(0, 153, 204)\",chr29:\"rgb(10, 71, 255)\",chr30:\"rgb(71, 117, 255)\",chr31:\"rgb(255, 194, 10)\",chr32:\"rgb(255, 209, 71)\",chr33:\"rgb(153, 0, 51)\",chr34:\"rgb(153, 26, 0)\",chr35:\"rgb(153, 102, 0)\",chr36:\"rgb(128, 153, 0)\",chr37:\"rgb(51, 153, 0)\",chr38:\"rgb(0, 153, 26)\",chr39:\"rgb(0, 153, 102)\",chr40:\"rgb(0, 128, 153)\",chr41:\"rgb(0, 51, 153)\",chr42:\"rgb(26, 0, 153)\",chr43:\"rgb(102, 0, 153)\",chr44:\"rgb(153, 0, 128)\",chr45:\"rgb(214, 0, 71)\",chr46:\"rgb(255, 20, 99)\",chr47:\"rgb(0, 214, 143)\",chr48:\"rgb(20, 255, 177)\"};class Sm{constructor(e){this.tracks=[],this.chordSets=[]}addChordSet(e){this.chordSets=this.chordSets.filter((t=>t.name!==e.name)),this.chordSets.push(e);let t=this.tracks.find((t=>e.trackName===t.name));t&&(t.chordSets=t.chordSets.filter((t=>t.name!==e.name)),t.chordSets.push(e)),t||(t=new Em(e),this.tracks.push(t))}clearChords(){this.tracks=[],this.chordSets=[]}getTrack(e){return this.tracks.find((t=>e===t.name))}getChordSet(e){return this.chordSets.find((t=>e===t.name))}}class Em{constructor(e){this.name=e.trackName,this.color=e.trackColor,this.visible=!0,this.chordSets=[e],this.id=(\"0000\"+(Math.random()*Math.pow(36,4)|0).toString(36)).slice(-4)}get chords(){if(1===this.chordSets.length)return this.chordSets[0].chords;const e=[];for(let t of this.chordSets)for(let i of t.chords)e.push(i);return e}}const Nm=Math.exp(5);class Bm{static isInstalled(){return void 0!==window.JBrowseReactCircularGenomeView&&void 0!==window.React&&void 0!==window.ReactDOM}constructor(e,t){if(t=t||{},this.config=t,Bm.isInstalled()){this.parent=e,this.groupByTrack=!0===t.groupByTrack,this.chordManager=new Sm(t);const i=document.createElement(\"div\");i.className=\"igv-circview-container\",e.appendChild(i),this.createControls(i),this.resetControlPanel();const n=document.createElement(\"div\");n.className=\"igv-circview-circular-genome-view\",i.appendChild(n),this.container=n,t.assembly&&this.setAssembly(t.assembly),this.width=t.width||500,this.height=t.height||500,this.setSize(this.width,this.height)}else console.error(\"JBrowse circular view is not installed\")}createControls(e){const t=document.createElement(\"div\");t.className=\"igv-circview-toolbar\",e.appendChild(t),this.toolbar=t;const i=document.createElement(\"div\");i.className=\"igv-circview-track-panel\",e.appendChild(i),this.controlPanel=i,this.controlPanel.style.display=\"none\";const n=document.createElement(\"div\");n.className=\"igv-circview-toolbar-button-container\",this.toolbar.appendChild(n),this.showControlsButton=document.createElement(\"div\"),this.showControlsButton.className=\"igv-circview-button\",n.appendChild(this.showControlsButton),this.showControlsButton.innerText=\"none\"===this.controlPanel.style.display?\"Show Controls\":\"Hide Controls\",this.showControlsButton.addEventListener(\"click\",(e=>{this.controlPanel.querySelectorAll(\"div\").length>0&&(\"none\"===this.controlPanel.style.display?(this.controlPanel.style.display=\"flex\",e.target.innerText=\"Hide Controls\"):(this.controlPanel.style.display=\"none\",e.target.innerText=\"Show Controls\"))}));let r=document.createElement(\"div\");r.className=\"igv-circview-button\",n.appendChild(r),r.innerText=\"Clear All\",r.addEventListener(\"click\",(()=>{this.clearChords()})),!1!==this.config.showCloseButton&&(r=document.createElement(\"div\"),r.className=\"igv-circview-button\",n.appendChild(r),r.innerText=\"Close\",r.addEventListener(\"click\",(()=>{this.visible=!1})))}resetControlPanel(){this.controlPanel.innerHTML=\"\",this.controlPanel.appendChild(this.createGroupByCB());const e=this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets;for(let t of e)this.addToControlPanel(t)}createGroupByCB(){const e=document.createElement(\"input\");e.type=\"checkbox\",e.id=\"groupByCB\",e.style.width=\"1.4em\",e.style.height=\"1.4em\",e.checked=this.groupByTrack,e.onclick=e=>{this.groupByTrack=e.target.checked,this.resetControlPanel(),this.render()};const t=document.createElement(\"label\");t.for=\"groupByCB\",t.innerText=\"Group by track\",t.style.color=\"black\",t.style.paddingLeft=\"10px\";const i=document.createElement(\"div\");return i.style.width=\"100%\",i.style.paddingTop=\"5px\",i.style.paddingBottom=\"5px\",i.style.background=\"rgb(216, 230, 234)\",i.appendChild(e),i.appendChild(t),i}addToControlPanel(e){const t=document.createElement(\"div\");this.controlPanel.appendChild(t);const i=document.createElement(\"div\");i.className=\"igv-circview-button\",t.appendChild(i),i.innerText=!0===e.visible?\"Hide\":\"Show\",i.addEventListener(\"click\",(t=>{!0===e.visible?(this.hideChordSet(e.name),t.target.innerText=\"Show\"):(this.showChordSet(e.name),t.target.innerText=\"Hide\")}));const n=document.createElement(\"input\"),r=e=>200*Math.log(e*Nm),s=document.createElement(\"div\");s.className=\"igv-circview-button\",s.innerHTML=\"&nbsp;&nbsp;&nbsp;&nbsp;\",t.appendChild(s),s.style.backgroundColor=Mm(e.color,1);const o={parent:s,popup:\"right\",editorFormat:\"rgb\",color:e.color,onChange:({rgbaString:t})=>{s.style.backgroundColor=Mm(t,1),this.setColor(e.name,t),n.value=r(Rm(e.color))}},a=new _m(o);n.setAttribute(\"title\",\"Adjust transparency of arcs\"),n.type=\"range\",n.style.width=\"100px\",n.style.marginRight=\"10px\",n.setAttribute(\"class\",\"range\"),n.setAttribute(\"min\",\"0\"),n.setAttribute(\"max\",\"1000\"),n.value=r(Rm(e.color)),n.oninput=()=>{const t=(i=n.value,Math.exp(i/200)/Nm);var i;this.setColor(e.name,Mm(e.color,t)),a.setColor(e.color)},t.appendChild(n);const c=document.createElement(\"div\");c.style.color=\"black\",t.appendChild(c),c.innerText=c.title=e.name}setAssembly(e){const t=this.genomeId||Lm();if(this.genomeId===t)return;this.chordManager.clearChords(),this.genomeId=t,this.chrNames=new Set(e.chromosomes.map((e=>Dm(e.name))));const i=[],n=[];for(let t of e.chromosomes){const e=Dm(t.name);n.push(t.color||km(e)),i.push({refName:e,uniqueId:e,start:0,end:t.bpLength})}this.assembly={name:e.name,sequence:{trackId:t,type:\"ReferenceSequenceTrack\",adapter:{type:\"FromConfigSequenceAdapter\",features:i}},refNameColors:n},this.render()}addChords(e,t={}){const i=t.name||t.track||\"*\",n=i.split(\" \")[0].replaceAll(\"%20\",\" \"),r={name:i.replaceAll(\"%20\",\" \"),trackName:n,chords:e,color:t.color||\"black\",trackColor:t.trackColor||t.color||\"black\",visible:!0,id:t.id||Lm()};this.chordManager.addChordSet(r),this.resetControlPanel(),this.render()}setSize(e,t){if(t=t||e,this.width=e,this.height=t,this.viewState){const i=this.viewState.session.view;i.setWidth(e),i.setHeight(t),i.setBpPerPx(i.minBpPerPx)}}getSize(){return Math.min(this.width,this.height)}clearChords(){this.chordManager.clearChords(),this.resetControlPanel(),this.render()}clearSelection(){this.viewState.pluginManager.rootModel.session.clearSelection()}show(){this.parent.style.display=\"block\"}hide(){this.parent.style.display=\"none\"}get visible(){return\"none\"!==this.parent.style.display}set visible(e){this.parent.style.display=e?\"block\":\"none\"}hideChordSet(e){let t=this.getChordSet(e);t?(t.visible=!1,this.render()):console.warn(`No track with name: ${name}`)}showChordSet(e){let t=this.getChordSet(e);t?(t.visible=!0,this.render()):console.warn(`No track with name: ${e}`)}deleteTrack(e){let t=this.tracks.findIndex((t=>e===t.name));t>=0&&this.tracks.splice(t,1),this.render()}getChordSet(e){return this.groupByTrack?this.chordManager.getTrack(e):this.chordManager.getChordSet(e)}setColor(e,t){const i=this.getChordSet(e);if(i){i.color=t;const e=i.id;for(let i of this.viewState.config.tracks)if(e===i.trackId){i.displays[0].renderer.strokeColor.set(t);break}}}render(){const{createViewState:e,JBrowseCircularGenomeView:t}=JBrowseReactCircularGenomeView;ReactDOM.unmountComponentAtNode(this.container);const i=(this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets).filter((e=>e.visible)),n=[],r=[];for(let e of i)n.push({trackId:e.id,name:e.name,assemblyNames:[\"forIGV\"],type:\"VariantTrack\",adapter:{type:\"FromConfigAdapter\",features:e.chords}}),r.push(e.color);this.viewState=e({assembly:this.assembly,tracks:n});for(let e=0;e<i.length;e++)this.viewState.config.tracks[e].displays[0].renderer.strokeColor.set(r[e]);this.element=React.createElement(t,{viewState:this.viewState}),this.setSize(this.width,this.height),ReactDOM.render(this.element,this.container);const s=this.config.onChordClick||Tm;for(let e=0;e<i.length;e++)this.viewState.session.view.showTrack(this.viewState.config.tracks[e].trackId),s&&(this.viewState.pluginManager.jexl.addFunction(\"onChordClick\",s),this.viewState.config.tracks[e].displays[0].onChordClick.set(\"jexl:onChordClick(feature, track, pluginManager)\"))}}function Mm(e,t){const[i,n,r,s]=e.split(\",\");return`${i},${n},${r},${t})`}function Rm(e){return e.startsWith(\"rgba(\")?Number(e.split(\",\")[3].replace(\")\",\"\")):1}function Dm(e){return e.startsWith(\"chr\")?e.substring(3):e}function Tm(e,t,i){console.log(e)}function Lm(){return(\"0000\"+(Math.random()*Math.pow(36,4)|0).toString(36)).slice(-4)}if(\"undefined\"!=typeof document){function BA(e){for(let t of document.styleSheets)if(t=t.href?t.href.replace(/^.*[\\\\\\/]/,\"\"):\"\",t===e)return!0;return!1}BA(\"circular-view.css\")||function(){const e=document.createElement(\"style\");e.setAttribute(\"type\",\"text/css\"),e.innerHTML='.igv-circview-container {\\n  width: fit-content;\\n  height: fit-content;\\n  box-sizing: content-box;\\n  color: dimgray;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  background-color: white;\\n  border-color: dimgray;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-circview-toolbar {\\n  position: relative;\\n  width: 100%;\\n  height: 32px;\\n  background-color: lightgrey;\\n  border-bottom-style: solid;\\n  border-bottom-color: dimgray;\\n  border-bottom-width: thin;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n\\n.igv-circview-toolbar-button-container {\\n  height: 100%;\\n  width: fit-content;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-circview-toolbar-button-container > div {\\n  margin: 4px;\\n}\\n\\n.igv-circview-track-panel {\\n  z-index: 1024;\\n  position: absolute;\\n  top: 33px;\\n  left: 0;\\n  width: 100%;\\n  height: fit-content;\\n  border-bottom-style: solid;\\n  border-bottom-color: dimgray;\\n  border-bottom-width: thin;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n.igv-circview-track-panel > div {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-circview-track-panel > div > div {\\n  margin: 4px;\\n}\\n\\n.igv-circview-swatch-button {\\n  cursor: pointer;\\n  padding: 5px;\\n  width: 8px;\\n  height: 8px;\\n  border: 1px solid #8d8b8b;\\n  border-radius: 16px;\\n}\\n\\n.igv-circview-button {\\n  cursor: pointer;\\n  padding: 5px;\\n  color: #444;\\n  vertical-align: middle;\\n  text-align: center;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  border: 1px solid #8d8b8b;\\n  border-radius: 4px;\\n  background: #efefef;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.2);\\n}\\n\\n.igv-circview-button:hover {\\n  background: #efefef;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\\n}\\n\\n.igv-circview-button:active {\\n  color: #007bff;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\\n}\\n\\n/*# sourceMappingURL=circular-view.css.map */\\n',document.head.insertBefore(e,document.head.childNodes[document.head.childNodes.length-1])}()}const zm=e=>e.startsWith(\"chr\")?e.substring(3):e;function Hm(e){const t=[],i=[];if(e.wgChromosomeNames)for(let n of e.wgChromosomeNames){const r=e.getChromosome(n);i.push(Nu(r.name)),t.push({name:r.name,bpLength:r.bpLength})}return t}function Pm(e,t,i,n){const r=t.color||\"rgb(0,0,255)\",s=_s.addAlpha(\"all\"===i.chr?r:Nu(i.chr),n),o=_s.addAlpha(r,n),a=t.name.replaceAll(\" \",\"%20\"),c=\"all\"===i.chr?a:`${a}  ${i.chr}:${i.start}-${i.end}`;t.browser.circularView.addChords(e,{track:c,color:s,trackColor:o}),t.browser.circularViewVisible||(t.browser.circularViewVisible=!0)}class Om{constructor(e,{minTLENPercentile:t,maxTLENPercentile:i}){this.totalCount=0,this.frCount=0,this.rfCount=0,this.ffCount=0,this.sumF=0,this.sumF2=0,this.lp=void 0===t?.1:t,this.up=void 0===i?99.5:i,this.isizes=[],this.compute(e)}compute(e){for(let n of e)if(n.isProperPair()){var t=Math.abs(n.fragmentLength);this.sumF+=t,this.sumF2+=t*t,this.isizes.push(t);var i=n.pairOrientation;if(\"string\"==typeof i&&4===i.length)switch(\"\"+i.charAt(0)+i.charAt(2)){case\"FF\":case\"RR\":this.ffCount++;break;case\"FR\":this.frCount++;break;case\"RF\":this.rfCount++}this.totalCount++}this.ffCount/this.totalCount>.9?this.orienation=\"ff\":this.frCount/this.totalCount>.9?this.orienation=\"fr\":this.rfCount/this.totalCount>.9&&(this.orienation=\"rf\"),this.minTLEN=0===this.lp?0:Um(this.isizes,this.lp),this.maxTLEN=Um(this.isizes,this.up)}}function Um(e,t){if(0!==e.length){var i=Math.floor(e.length*(t/100));return e.sort((function(e,t){return e-t})),e[i]}}const qm=\"rgb(255,0,255)\",Qm=\"rgb(0,0,255)\",Vm=\"rgb(132, 178, 158)\",jm=new Map;jm.set(\"m\",\"rgb(255,0,0)\"),jm.set(\"h\",qm),jm.set(\"o\",\"rgb(111, 78, 129)\"),jm.set(\"f\",\"rgb(246, 200, 95)\"),jm.set(\"c\",\"rgb(157, 216, 102)\"),jm.set(\"g\",\"rgb(255, 160, 86)\"),jm.set(\"e\",\"rgb(141, 221, 208)\"),jm.set(\"b\",\"rgb(202, 71, 47)\"),jm.set(\"h\",qm),jm.set(\"a\",\"rgb(51,0,111)\"),jm.set(\"NONE_A\",Qm),jm.set(\"NONE_C\",Qm),jm.set(\"NONE_T\",Qm),jm.set(\"NONE_G\",Qm),jm.set(\"NONE_N\",Qm);const Wm=new Map;function Gm(e,t,i){let n=function(e,t){return jm.has(e)?jm.get(e):Vm}(e),r=Xf(t);if(r>255)return n;const s=e+r+i;if(r<0&&(r=0),!Wm.has(s)){const e=\"basemod2\"===i?Math.max(20,Math.min(255,r*r/50-4*r+200+20)):Math.max(20,Math.min(255,.006127*r*r)),[t,o,a]=_s.rgbComponents(n);Wm.set(s,`rgba(${t},${o},${a},${e/255})`)}return Wm.get(s)}class $m{constructor(e){this.alignmentTrack=e}updateContext(e){this.context=e}drawModifications(e,t,i,n,r,s){const{ctx:o,pixelEnd:a,bpStart:c,bpPerPixel:l}=n,h=e.getBaseModificationSets();if(h){let n;const d=r.split(\":\");2==d.length&&(r=d[0],n=d[1]);for(let d of e.blocks){if(\"S\"===d.type)continue;const e=t,u=i;let f=Math.max(1,1/l);for(let t=d.seqOffset;t<d.seqOffset+d.len;t++){let i=(d.start+(t-d.seqOffset)-c)/l;if(i>a)break;if(i+f<0)continue;let p,g=-1,m=255,w=0;for(let e of h)if((!n||e.modification===n)&&e.containsPosition(t)){const i=Xf(e.likelihoods.get(t));m-=i,(!p||i>g)&&(p=e.modification,w=e.canonicalBase,g=i)}if(p){const t=255*s;let n;m>g&&\"basemod2\"===r&&m>=t?n=Gm(\"NONE_\"+w,m,r):g>=t&&(n=Gm(p,g,r)),o.fillStyle=n,f<3&&(f=3,i--),o.fillRect(i,e,f,Math.max(1,u-2))}}}}}}const Km=new Set([\"firstOfPairStrand\"]);class Ym extends Hl{static defaults={viewAsPairs:!1,showSoftClips:!1,showAllBases:!1,showInsertions:!0,showMismatches:!0,colorBy:void 0,groupBy:void 0,displayMode:\"EXPANDED\",alignmentRowHeight:14,squishedRowHeight:3,negStrandColor:\"rgba(150, 150, 230, 0.75)\",posStrandColor:\"rgba(230, 150, 150, 0.75)\",baseModPosStrandColor:\"rgb(195, 195, 195)\",baseModNegStrandColor:\"rgb(195, 210, 195)\",insertionColor:\"rgb(138, 94, 161)\",insertionTextColor:\"white\",showInsertionText:!1,deletionColor:\"black\",deletionTextColor:\"black\",showDeletionText:!1,skippedColor:\"rgb(150, 170, 170)\",pairConnectorColor:void 0,smallTLENColor:\"rgb(0, 0, 150)\",largeTLENColor:\"rgb(200, 0, 0)\",expectedPairOrientation:\"fr\",rlColor:\"rgb(0, 150, 0)\",rrColor:\"rgb(20, 50, 200)\",llColor:\"rgb(0, 150, 150)\",bamColorTag:\"YC\",hideSmallIndels:!1,indelSizeThreshold:1,highlightColor:void 0,minTLEN:void 0,maxTLEN:void 0,tagColorPallete:\"Set1\"};_colorTables=new Map;_baseModifications=new Set;constructor(e,t){super(e,t),(e.colorTable||e.tagColorTable)&&(this.colorTable=new ao(e.tagColorTable)),e.largeFragmentLengthColor&&(this.largeTLENColor=e.largeFragmentLengthColor),e.pairOrienation&&(this.expectedPairOrientation=e.pairOrientation),e.smallFragmentLengthColor&&(this.smallTLENColor=e.smallFragmentLengthColor),e.largeFragmentLengthColor&&(this.largeTLENColor=e.largeFragmentLengthColor),e.minFragmentLength&&(this.minTLEN=e.minFragmentLength),e.maxFragmentLength&&(this.maxTLEN=e.maxFragmentLength),e.displayMode&&(this.displayMode=e.displayMode.toUpperCase()),e.colorBy&&e.colorByTag&&(this.colorBy=e.colorBy+\":\"+e.colorByTag),this.featureSource=this.parent.featureSource,this.top=0===e.coverageTrackHeight?0:e.coverageTrackHeight+5,this.pairColors={RL:this.rlColor,RR:this.rrColor,LL:this.llColor},e.highlightedReads&&this.setHighlightedReads(e.highlightedReads),this.hasPairs=!1,this.hasSupplemental=!1,this._groupByTags=[],this._groupByPositions=[],e.groupBy&&(this.groupBy=e.groupBy,e.groupBy.startsWith(\"base:\")&&this._groupByPositions.push(e.groupBy.substring(5)),e.groupBy.startsWith(\"tag:\")&&this._groupByTags.push(e.groupBy.substring(4))),this._locusChange=Zm.bind(this),this.browser.on(\"locuschange\",this._locusChange)}init(e){this.parent=e.parent,delete e.parent,super.init(e)}dispose(){this.browser.off(\"locuschage\",this._locusChange)}get baseModRenderer(){return this._baseModRenderer||(this._baseModRenderer=new $m(this)),this._baseModRenderer}get baseModificationThreshold(){return this.parent.baseModificationThreshold}setTop(e,t){this.top=0===e.height||!1===t?0:5+e.height}setHighlightedReads(e,t){if(!Array.isArray(e)||!e.every((e=>\"string\"==typeof e)))throw new Error(\"AlignmentTrack.setHighlightedReads() only accept array of strings\");t&&(this.highlightColor=t),this.highlightedReads=new Set(e)}computePixelHeight(e){if(e.packedGroups){let t=e.hasDownsampledIntervals()?15:0;const i=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;for(let n of e.packedGroups.values())t+=i*n.length+10;return t+5}return 0}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=r+s*n+1,a=this.showSoftClips,c=this.showAllBases,l=this.browser.nucleotideColors;i.save();for(let e of t.baseModificationKeys)this._baseModifications.add(e.modification);let h=t.sequence;h&&(h=h.toUpperCase());let d=0;this.colorBy||(this.colorBy=this.hasPairs?\"unexpectedPair\":\"none\");let u=e.pixelTop;this.top&&i.translate(0,this.top);const f=u+e.pixelHeight;t.hasDownsampledIntervals()?(d=15,t.downsampledIntervals.forEach((function(e){var t=(e.start-r)/n,s=(e.end-r)/n;s-t>5&&(t+=1,s-=1),xo.fillRect(i,t,2,s-t,8,{fillStyle:\"black\"})}))):d=0,this.alignmentsYOffset=d;const p=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight,g=t.packedGroups;if(g){let t=d;for(let n of g.keys()){const a=g.get(n),c=a.rows,l=c.length;a.pixelTop=t;for(let e=0;e<l;e++){const i=c[e],n=p<=4?p:p-2;if(t>f)break;if(t+n<u)t+=p;else{for(let e of i.alignments)if(this.browser.circularView&&(this.hasSupplemental=this.hasSupplemental||e.hasTag(\"SA\")),!(e.start+e.lengthOnRef<r)){if(e.start>o)break;!0!==e.hidden&&(e instanceof Qf?(m.call(this,e,t,n),w.call(this,e.firstAlignment,t,n),e.secondAlignment&&w.call(this,e.secondAlignment,t,n)):w.call(this,e,t,n))}t+=p}}if(a.pixelBottom=t,this.groupBy&&n){i.save(),i.font=\"400 12px sans-serif\";const r=i.measureText(n),o=r.width+10,c=-e.pixelShift+e.viewportWidth-o-10,l=r.actualBoundingBoxAscent+r.actualBoundingBoxDescent+10,h=Math.min(a.pixelTop+l-1,a.pixelBottom);i.textAlign=\"center\",i.fillStyle=\"white\",i.strokeStyle=\"lightGray\",xo.roundRect(i,c,h-r.actualBoundingBoxAscent-5,o,l,2,1,1),i.fillStyle=\"black\",i.fillText(n,c+o/2,h),xo.dashedLine(i,0,t,s,t),i.restore(),t+=10}}}function m(e,t,s){var a=this.getConnectorColor(e.firstAlignment),c=(e.connectingStart-r)/n,l=(e.connectingEnd-r)/n,h=t+s/2;e.connectingEnd<r||e.connectingStart>o||(e.mq<=0&&(a=_s.addAlpha(a,.15)),xo.setProperties(i,{fillStyle:a,strokeStyle:a}),xo.strokeLine(i,c,h,l,h))}function w(e,d,u){if(e.start+e.lengthOnRef<r||e.start>o)return;const f=a?e.blocks:e.blocks.filter((e=>\"S\"!==e.type));let g=this.getAlignmentColor(e);const m=g;e.mq<=0&&(g=_s.addAlpha(g,.15)),xo.setProperties(i,{fillStyle:g,strokeStyle:m});const w=[];for(let e=0;e<f.length;e++){const t=f[e];if(!(e!==f.length-1&&f[e+1].start<r)&&(w.push(...b.call(this,t,e)),t.start+t.len>o))break}if(e.gaps){const t=d+u/2;for(let s of e.gaps){const e=(s.start-r)/n,o=(s.start+s.len-r)/n,a=o-e,c=s.len.toString(),l=6*c.length,h=e+a/2,u=\"D\"===s.type?this.deletionColor:this.skippedColor;if(xo.strokeLine(i,e,t,o,t,{strokeStyle:u,lineWidth:2}),this.showDeletionText&&s.len>1&&a>=l+8){const e=h-l/2;xo.fillRect(i,e-1,d-1,l+2,12,{fillStyle:\"white\"}),xo.fillText(i,c,e,d+10,{font:\"normal 10px monospace\",fillStyle:this.deletionTextColor})}}}if(e.insertions&&this.showInsertions){let t=-1;for(let s of e.insertions){if(this.hideSmallIndels&&s.len<=this.indelSizeThreshold)continue;if(s.start<r)continue;if(s.start>o)break;const e=s.start-r,a=s.len.toString(),c=2+6*a.length,l=this.showInsertionText&&1!==s.len?Math.round(s.len/n):2,h=Math.max(Math.min(c,l),2),f=e/n-h/2;if(f-t>2){const e={fillStyle:this.insertionColor};xo.fillRect(i,f-2,d,h+4,2,e),xo.fillRect(i,f,d+2,h,u-4,e),xo.fillRect(i,f-2,d+u-2,h+4,2,e),this.showInsertionText&&s.len>1&&l>c&&xo.fillText(i,a,f+1,d+10,{font:\"normal 10px monospace\",fillStyle:this.insertionTextColor}),t=f}}}for(let{bbox:e,baseColor:t,readChar:r}of w){if(n<=.1&&e.height>=8){const n=Math.min(10,e.height);i.font=n+\"px sans-serif\";const s=e.x+e.width/2;xo.strokeText(i,r,s-i.measureText(r).width/2,n-1+e.y,{strokeStyle:t})}else xo.fillRect(i,e.x,e.y,e.width,e.height,{fillStyle:t})}if(this.colorBy&&this.colorBy.startsWith(\"basemod\")){const t={ctx:i,bpPerPixel:n,bpStart:r,bpEnd:o,pixelEnd:s};this.baseModRenderer.drawModifications(e,d,u,t,this.colorBy,this.baseModificationThreshold)}function b(o,a){const w=[],b=o.start-t.start,F=(o.start-r)/n,v=(o.start+o.len-r)/n,y=Math.max(1,v-F),A=100/n,C=Math.min(p/2,A/6),_=\"S\"===o.type,x=e.mq<=0||this.selectedReadName===e.readName||_||this.highlightedReads&&this.highlightedReads.has(e.readName);let k=m;this.selectedReadName===e.readName?k=\"red\":_?k=\"rgb(50,50,50)\":this.highlightedReads&&this.highlightedReads.has(e.readName)&&(k=this.highlightColor||\"#00ff00\");const I=!0===e.strand&&a===f.length-1,S=!1===e.strand&&0===a;if(I|S){let e,t;I?(e=[F,v,v+C,v,F,F],t=[d,d,d+u/2,d+u,d+u,d]):S&&(e=[v,F,F-C,F,v,v],t=[d,d,d+u/2,d+u,d+u,d]),xo.fillPolygon(i,e,t,{fillStyle:g}),x&&xo.strokePolygon(i,e,t,{strokeStyle:k})}else xo.fillRect(i,F,d,y,u,{fillStyle:g}),x&&(i.save(),i.strokeStyle=k,i.strokeRect(F,d,y,u),i.restore());if(_||c||this.showMismatches&&h&&e.seq&&\"*\"!==e.seq){const t=e.seq?e.seq.toUpperCase():void 0,i=e.qual,a=o.seqOffset,f=Math.max(1,1/n);for(let e=0,p=o.len;e<p;e++){const p=(o.start+e-r)/n;if(p+f<0)continue;if(p>s)break;let g=t?t.charAt(a+e):\"\";const m=b+e>=0?h.charAt(b+e):\"\";if(\"=\"===g&&(g=m),\"X\"===g||m!==g||_||c){let t=l[g]||\"rgb(0,0,0)\";if(!_&&void 0!==i&&i.length>a+e){t=Xm(i[a+e],t)}w.push({bbox:{x:p,y:d,width:f,height:u},baseColor:t,readChar:g})}}}return w}}i.restore()}popupData(e){const t=this.getClickedObject(e);return t?t.popupData(e.genomicLocation):void 0}menuItemList(){let e=[];e.push(\"<hr/>\");const t=Bt('<div class=\"igv-track-menu-category\">');t.text(\"Color by:\"),e.push({name:void 0,object:t,click:void 0,init:void 0});const i=[];i.push({key:\"none\",label:\"none\"}),i.push({key:\"strand\",label:\"read strand\"}),this.hasPairs&&(i.push({key:\"firstOfPairStrand\",label:\"first-of-pair strand\"}),i.push({key:\"pairOrientation\",label:\"pair orientation\"}),i.push({key:\"tlen\",label:\"insert size (TLEN)\"}),i.push({key:\"unexpectedPair\",label:\"pair orientation & insert size (TLEN)\"})),i.push({key:\"tag\",label:\"tag\"});for(let t of i){const i=void 0===this.colorBy&&\"none\"===t.key||this.colorBy===t.key;e.push(this.colorByCB(t,i))}const n=this._baseModifications.size;if(n>0){e.push('<hr style=\"border-top:1px dotted;border-bottom: none;\">');let t=1===n?\"base modification\":\"base modification (all)\";if(e.push(this.basemodColorByCB({key:\"basemod\",label:t})),n>1)for(let t of this._baseModifications)e.push(this.basemodColorByCB({key:\"basemod:\"+t,label:`base modification (${Kf(t)})`}));if(e.push('<hr style=\"border-top:1px dotted;border-bottom: none;\">'),t=1===n?\"base modification 2-color\":\"base modification 2-color (all)\",e.push(this.basemodColorByCB({key:\"basemod2\",label:t})),n>1)for(let t of this._baseModifications)e.push(this.basemodColorByCB({key:\"basemod2:\"+t,label:`base modification 2-color (${Kf(t)})`}))}e.push(\"<hr/>\");const r=Bt('<div class=\"igv-track-menu-category\">');r.text(\"Group by:\"),e.push({name:void 0,object:r,click:void 0,init:void 0});const s=[];s.push({key:\"none\",label:\"none\"}),s.push({key:\"strand\",label:\"read strand\"}),this.hasPairs&&(s.push({key:\"firstOfPairStrand\",label:\"first-of-pair strand\"}),s.push({key:\"pairOrientation\",label:\"pair orientation\"}),s.push({key:\"mateChr\",label:\"chromosome of mate\"})),s.push({key:\"chimeric\",label:\"chimeric\"}),s.push({key:\"supplementary\",label:\"supplementary flag\"}),s.push({key:\"readOrder\",label:\"read order\"});for(let e of this._groupByTags)s.push({key:`tag:${e}`,label:`tag:${e}`});for(let e of this._groupByPositions)s.push({key:`base:${e}`,label:`base:${e}`});s.push({key:\"tag\",label:\"tag...\"});for(let t of s){const i=void 0===this.groupBy&&\"none\"===t.key||this.groupBy===t.key;e.push(this.groupByCB(t,i))}e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"Show all bases\",this.showAllBases)),click:function(){this.alignmentTrack.showAllBases=!this.alignmentTrack.showAllBases,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show mismatches\",this.showMismatches)),click:function(){this.alignmentTrack.showMismatches=!this.alignmentTrack.showMismatches,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show insertions\",this.showInsertions)),click:function(){this.alignmentTrack.showInsertions=!this.alignmentTrack.showInsertions,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show soft clips\",this.showSoftClips)),click:function(){this.alignmentTrack.showSoftClips=!this.alignmentTrack.showSoftClips;const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this);this.trackView.repaintViews()}}),this.hasPairs&&(e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"View as pairs\",this.viewAsPairs)),click:function(){const e=!this.alignmentTrack.viewAsPairs;if(e&&this.groupBy&&!Km.has(this.groupBy))return void this.browser.alert.present(`'View as Pairs' is incompatible with 'Group By ${this.groupBy}'`);this.alignmentTrack.viewAsPairs=e;const t=this.getCachedAlignmentContainers();for(let e of t)e.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(e.push(\"<hr/>\"),this.hasPairs&&e.push({label:\"Add discordant pairs to circular view\",click:function(){for(let e of this.trackView.viewports)this.addPairedChordsForViewport(e)}}),this.hasSupplemental&&e.push({label:\"Add split reads to circular view\",click:function(){for(let e of this.trackView.viewports)this.addSplitChordsForViewport(e)}})),e.push(\"<hr/>\");const o=Bt('<div class=\"igv-track-menu-category\">');o.text(\"Display mode:\"),e.push({name:void 0,object:o,click:void 0,init:void 0});for(let t of[\"EXPANDED\",\"SQUISHED\",\"FULL\"])e.push({object:Bt(Dl(t.toLowerCase(),this.displayMode===t)),click:function(){this.alignmentTrack.setDisplayMode(t)}});return e}setDisplayMode(e){const t=\"FULL\"===this.displayMode||\"FULL\"===e;if(this.displayMode=e,t){const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this)}this.trackView.checkContentHeight(),this.trackView.repaintViews()}colorByCB(e,t){const i=Bt(Dl(e.label,t));if(\"tag\"!==e.key){function n(){this.alignmentTrack.colorBy=e.key,this.trackView.repaintViews()}return{name:void 0,object:i,click:n,init:void 0}}{function r(e){const t=this.alignmentTrack.colorBy.startsWith(\"tag:\")?this.alignmentTrack.colorBy.substring(4):\"\";this.browser.inputDialog.present({label:\"Tag Name\",value:t,callback:e=>{const t=this.alignmentTrack;e?(t.colorBy=\"tag:\"+e,t.colorTable||(t.colorTable=new oo(\"Set1\"))):t.colorBy=void 0,this.trackView.repaintViews()}},e)}return{name:void 0,object:i,dialog:r,init:void 0}}}basemodColorByCB(e){const t=this.colorBy===e.key;return{name:void 0,object:Bt(Dl(e.label,t)),click:function(){this.alignmentTrack.colorBy=e.key,this.trackView.repaintViews()},init:void 0}}groupByCB(e,t){return{name:void 0,object:Bt(Dl(e.label,t)),dialog:function(t){const i=()=>this.alignmentTrack.repackAlignments();if(\"tag\"===e.key){let e=\"\";this.alignmentTrack.groupBy&&this.alignmentTrack.groupBy.startsWith(\"tag:\")&&(e=this.alignmentTrack.groupBy.substring(4)),this.browser.inputDialog.present({label:\"Tag Name\",value:e,callback:e=>{e&&(this.alignmentTrack.groupBy=\"tag:\"+e,this.alignmentTrack._groupByTags.push(e),i())}},t)}else\"none\"===e.key?this.alignmentTrack.groupBy=void 0:this.alignmentTrack.groupBy=e.key,i()},init:void 0}}repackAlignments(){const e=this.getCachedAlignmentContainers();for(let t of e)\"function\"==typeof t.pack&&t.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}contextMenuItemList(e){const t=e.viewport,i=[],n=i=>{const n=this.sortObject,r=!n||n.position!==Math.floor(e.genomicLocation)||!n.direction,s={chr:t.referenceFrame.chr,position:Math.floor(e.genomicLocation),option:i,direction:r,sortAsPairs:t.trackView.track.viewAsPairs};this.sortObject=s,t.cachedFeatures.sortRows(s),t.repaint()};i.push(\"<b>Sort by...</b>\"),i.push({label:\"&nbsp; base\",click:()=>n(\"BASE\")}),i.push({label:\"&nbsp; read strand\",click:()=>n(\"strand\")}),i.push({label:\"&nbsp; start location\",click:()=>n(\"START\")}),i.push({label:\"&nbsp; insert size\",click:()=>n(\"INSERT_SIZE\")}),i.push({label:\"&nbsp; gap size\",click:()=>n(\"GAP_SIZE\")}),i.push({label:\"&nbsp; chromosome of mate\",click:()=>n(\"MATE_CHR\")}),i.push({label:\"&nbsp; mapping quality\",click:()=>n(\"MQ\")}),i.push({label:\"&nbsp; read name\",click:()=>n(\"READ_NAME\")}),i.push({label:\"&nbsp; aligned read length\",click:()=>n(\"ALIGNED_READ_LENGTH\")}),i.push({label:\"&nbsp; tag\",click:()=>{const i=this.sortObject,n=!i||i.position!==Math.floor(e.genomicLocation)||!i.direction,r={label:\"Tag Name\",value:this.sortByTag?this.sortByTag:\"\",callback:i=>{if(i){const r={chr:t.referenceFrame.chr,position:Math.floor(e.genomicLocation),option:\"TAG\",tag:i,direction:n};this.sortByTag=i,this.sortObject=r,t.cachedFeatures.sortRows(r),t.repaint()}}};this.browser.inputDialog.present(r,e.event)}}),i.push(\"<hr/>\");const r=`${t.referenceFrame.chr}:${Rt(Math.floor(e.genomicLocation)+1)}`;i.push({label:`Group by base @${r}`,click:()=>{this._groupByPositions.push(r),this.groupBy=`base:${r}`;const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),i.push(\"<hr/>\");const s=this.getClickedObject(e);if(s){const t=this.showSoftClips,n=\"function\"==typeof s.alignmentContaining?s.alignmentContaining(e.genomicLocation,t):s;if(n){n.isPaired()&&n.isMateMapped()&&i.push({label:\"View mate in split screen\",click:()=>{if(n.mate){const t=e.viewport.referenceFrame,i=this.browser.genome.getChromosome(n.mate.chr);if(i){this.selectedReadName=n.readName;const r=t.bpPerPixel*e.viewport.getWidth(),s=n.mate.position-r/2,o=n.mate.position+r/2;this.browser.addMultiLocusPanel(i.name,s,o,t)}else this.browser.alert.present(`Reference does not contain chromosome: ${n.mate.chr}`)}},init:void 0}),i.push({label:\"View read sequence\",click:()=>{const e=n.seq;e&&\"*\"!==e?this.browser.alert.present(e):this.browser.alert.present(\"Read sequence: *\")}}),Xa()&&i.push({label:\"Copy read sequence\",click:async()=>{const e=n.seq;try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}});const t=n.seq;if(t&&\"*\"!==t){t.length<Qd&&i.push({label:\"BLAT read sequence\",click:()=>{const e=n.isNegativeStrand()?cc(t):t,i=`${n.readName} - blat`,r=`${this.name} - ${i}`;jd({sequence:e,browser:this.browser,name:i,title:r})}});const e=n.softClippedBlocks();e.left&&e.left.len>20&&e.left.len<Qd&&i.push({label:\"BLAT left soft-clipped sequence\",click:()=>{const i=t.substr(e.left.seqOffset,e.left.len),r=n.isNegativeStrand()?cc(i):i,s=`${n.readName} - blat left clip`,o=`${this.name} - ${s}`;jd({sequence:r,browser:this.browser,name:s,title:o})}}),e.right&&e.right.len>20&&e.right.len<Qd&&i.push({label:\"BLAT right soft-clipped sequence\",click:()=>{const i=t.substr(e.right.seqOffset,e.right.len),r=n.isNegativeStrand()?cc(i):i,s=`${n.readName} - blat right clip`,o=`${this.name} - ${s}`;jd({sequence:r,browser:this.browser,name:s,title:o})}})}i.push(\"<hr/>\")}}return this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(this.hasPairs&&i.push({label:\"Add discordant pairs to circular view\",click:()=>{this.addPairedChordsForViewport(t)}}),this.hasSupplemental&&i.push({label:\"Add split reads to circular view\",click:()=>{this.addSplitChordsForViewport(t)}}),i.push(\"<hr/>\")),i}getClickedObject(e){let t=e.viewport.cachedFeatures;if(!t)return;const i=e.y-this.top,n=e.genomicLocation;if(t.packedGroups){let e=Number.MAX_VALUE;for(let r of t.packedGroups.values())if(e=Math.min(e,r.pixelTop),i>r.pixelTop&&i<=r.pixelBottom){const e=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;let t=Math.floor((i-r.pixelTop)/e);if(t>=0&&t<r.length){const e=r.rows[t].alignments.filter((e=>e.containsLocation(n,this.showSoftClips)));if(e.length>0)return e[0]}}}if(i<minGroupY&&t.downsampledIntervals)for(const e of t.downsampledIntervals)if(e.start<=n&&e.end>=n)return e}getConnectorColor(e){if(this.pairConnectorColor)return this.pairConnectorColor;let t=this.colorBy;switch(t&&t.startsWith(\"tag:\")&&(t.substring(4),t=\"tag\"),t){case\"strand\":case\"firstOfPairStrand\":case\"pairOrientation\":case\"tag\":return this.color?\"function\"==typeof this.color?this.color(e):this.color:\"rgb(200, 200, 200)\";default:return this.getAlignmentColor(e)}}getAlignmentColor(e){let t;t=this.color?\"function\"==typeof this.color?this.color(e):this.color:\"rgb(185, 185, 185)\";let i,n=this.colorBy;switch(n&&n.startsWith(\"tag:\")&&(i=n.substring(4),n=\"tag\"),n){case\"basemod\":case\"basemod2\":t=e.strand?this.baseModPosStrandColor:this.baseModNegStrandColor;break;case\"strand\":t=e.strand?this.posStrandColor:this.negStrandColor;break;case\"firstOfPairStrand\":const r=e.firstOfPairStrand;void 0!==r&&(t=r?this.posStrandColor:this.negStrandColor);break;case\"unexpectedPair\":case\"pairOrientation\":if(e.pairOrientation){const i=ep[this.expectedPairOrientation];if(i){const n=this.pairColors[i[e.pairOrientation]];if(n){t=n;break}}}if(\"pairOrientation\"===n)break;case\"tlen\":case\"fragmentLength\":e.mate&&e.isMateMapped()&&(e.mate.chr!==e.chr?t=Nu(e.mate.chr):this.minTemplateLength&&Math.abs(e.fragmentLength)<this.minTemplateLength?t=this.smallTLENColor:this.maxTemplateLength&&Math.abs(e.fragmentLength)>this.maxTemplateLength&&(t=this.largeTLENColor));break;case\"tag\":const s=e.tags()[i];void 0!==s&&(this.bamColorTag===i&&(t=_s.createColorStringSafe(s)),this.colorTable||(this.colorTable=new oo(this.tagColorPallete)),t=this.colorTable.getColor(s))}return t}get nucleotideColors(){return this.browser.nucleotideColors}get minTemplateLength(){return void 0!==this.minTLEN?this.minTLEN:this.parent._pairedEndStats?this.parent._pairedEndStats.minTLEN:0}get maxTemplateLength(){return void 0!==this.maxTLEN?this.maxTLEN:this.parent._pairedEndStats?this.parent._pairedEndStats.maxTLEN:1e3}getState(){const e=super.getState();return this.highlightedReads&&(e.highlightedReads=Array.from(this.highlightedReads)),e}get name(){return this.parent.name}set name(e){this.parent.name=e}get color(){return this.parent.color}set color(e){this.parent.color=e}get trackView(){return this.parent.trackView}get getCachedAlignmentContainers(){return this.parent.getCachedAlignmentContainers}get sortObject(){return this.parent.sortObject}set sortObject(e){this.parent.sortObject=e}addPairedChordsForViewport(e){return this.parent.addPairedChordsForViewport(e)}addSplitChordsForViewport(e){return this.parent.addSplitChordsForViewport(e)}}function Xm(e,t){let i;return i=e<5?.1:Math.max(.1,Math.min(1,.1+.9*(e-5)/15)),i=Math.round(10*i)/10,i<1&&(t=_s.addAlpha(t,i)),t}function Zm(){\"FULL\"!==this.displayMode||this.browser.isTrackPanning()||this.repackAlignments()}function Jm(e,t,i,n,r,s,o,a,c){const l=o.baseModCounts,h=o.coverageMap;if(l){let o;const d=a.split(\":\");2==d.length&&(a=d[0],o=d[1]);const u=Array.from(l.allModifications);u.sort(Vf.compare);const f=h.getTotalCount(s);if(!u.filter((e=>o?o===e.modification:!e.modification.startsWith(\"NONE_\"))).find((e=>l.getCount(s,e,0,!1)>0)))return;for(let d of u){if(d.modification.startsWith(\"NONE_\")&&\"basemod2\"!==a)continue;if(o&&o!==d.modification&&!d.modification.startsWith(\"NONE_\"))continue;const u=d.base,p=oc(u),g=h.getCount(s,u)+h.getCount(s,p),m=l.simplexModifications.has(d.modification)?h.getPosCount(s,u)+h.getNegCount(s,p):g;if(0==m)continue;const w=\"basemod2\"===a,b=l.getCount(s,d,c,w);if(0==b)continue;const F=g/f*(b/m),v=Math.round(F*r),y=l.getLikelihoodSum(s,d,c,w)/b,A=i-v,C=Gm(d.modification,y,a);e.fillStyle=C,e.fillRect(t,A,n,v),i=A}}}class ew{constructor(e,t){this.featureType=\"numeric\",this.parent=t,this.featureSource=t.featureSource,this.paintAxis=cd,this.top=0,this.autoscale=e.autoscale||void 0===e.max,e.coverageColor&&(this.color=e.coverageColor),this.autoscale||(this.dataRange={min:e.min||0,max:e.max})}get height(){return this.parent.coverageTrackHeight}draw(e){const t=e.pixelTop;e.pixelHeight;const i=this.parent.browser.nucleotideColors;if(t>this.height)return;const n=e.context,r=e.features,s=r.coverageMap;let o;s.refSeq&&(o=s.refSeq.toUpperCase());const a=e.bpPerPixel,c=e.bpStart,l=c+e.pixelWidth*a+1;let h;h=this.color?this.color:this.parent.color&&\"function\"!=typeof this.parent.color?_s.darkenLighten(this.parent.color,-35):\"rgb(150, 150, 150)\",xo.setProperties(n,{fillStyle:h,strokeStyle:h});const d=Math.max(1,1/a);for(let e=0,t=s.coverage.length;e<t;e++){const t=s.bpStart+e;if(t<c)continue;if(t>l)break;const i=s.coverage[e];if(!i)continue;const r=i.total/this.dataRange.max*this.height,o=this.height-r,h=(t-c)/a;xo.fillRect(n,h,o,d,r)}if(o)for(let e=0,t=s.coverage.length;e<t;e++){const t=s.bpStart+e;if(t<c)continue;if(t>l)break;const h=s.coverage[e];if(!h)continue;const u=h.total/this.dataRange.max*this.height;let f=this.height-u;const p=Math.floor((t-c)/a),g=o[e];if(this.parent.colorBy&&this.parent.colorBy.startsWith(\"basemod\"))Jm(n,p,this.height,d,u,t,r,this.parent.colorBy,this.parent.baseModificationThreshold);else if(h.isMismatch(g)){xo.setProperties(n,{fillStyle:i[g]}),xo.fillRect(n,p,f,d,u);let e=0;for(let t of[\"A\",\"C\",\"T\",\"G\"]){const r=(h[\"pos\"+t]+h[\"neg\"+t])/this.dataRange.max*this.height;f=this.height-r-e,e+=r,xo.setProperties(n,{fillStyle:i[t]}),xo.fillRect(n,p,f,d,r)}}}}getClickedObject(e){let t=e.viewport.cachedFeatures;if(!t||0===t.length)return;const i=Math.floor(e.genomicLocation),n=t.coverageMap,r=Math.floor(i-n.bpStart),s=n.coverage[r];return s?{coverage:s,baseModCounts:t.baseModCounts,hoverText:()=>n.coverage[r].hoverText()}:void 0}popupData(e){const t=[],{coverage:i,baseModCounts:n}=this.getClickedObject(e);if(i){const r=Math.floor(e.genomicLocation),s=e.viewport.referenceFrame;t.push(s.chr+\":\"+Rt(1+r)),t.push({name:\"Total Count\",value:i.total});let o=i.posA+i.negA;o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posA+\"+, \"+i.negA+\"- )\"),t.push({name:\"A\",value:o}),o=i.posC+i.negC,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posC+\"+, \"+i.negC+\"- )\"),t.push({name:\"C\",value:o}),o=i.posG+i.negG,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posG+\"+, \"+i.negG+\"- )\"),t.push({name:\"G\",value:o}),o=i.posT+i.negT,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posT+\"+, \"+i.negT+\"- )\"),t.push({name:\"T\",value:o}),o=i.posN+i.negN,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posN+\"+, \"+i.negN+\"- )\"),t.push({name:\"N\",value:o}),t.push(\"<HR/>\"),t.push({name:\"DEL\",value:i.del.toString()}),t.push({name:\"INS\",value:i.ins.toString()}),n&&(t.push(\"<hr/>\"),t.push(...n.popupData(r,this.parent.colorBy)))}return t}}class tw extends Hl{static defaults={alleleFreqThreshold:.2,visibilityWindow:3e4,showCoverage:!0,showAlignments:!0,height:300,coverageTrackHeight:50,baseModificationThreshold:0};constructor(e,t){super(e,t)}init(e){this.type=\"alignment\",this.featureSource=new cm(e,this.browser);const t=Object.assign({parent:this},e);this.coverageTrack=new ew(t,this);const i=Object.assign({parent:this},e);this.alignmentTrack=new Ym(i,this.browser),super.init(e),this.showAlignments||(this._height=this.coverageTrackHeight),e.sort&&(Array.isArray(e.sort)?this.assignSort(e.sort[0]):this.assignSort(e.sort))}dispose(){this.alignmentTrack.dispose()}setHighlightedReads(e,t){this.alignmentTrack.setHighlightedReads(e,t),this.updateViews()}get expectedPairOrientation(){return this.alignmentTrack.expectedPairOrientation}get viewAsPairs(){return this.alignmentTrack.viewAsPairs}get colorBy(){return this.alignmentTrack.colorBy}set height(e){this._height=e,this.showAlignments&&(this.alignmentTrack.height=this.showCoverage?e-this.coverageTrackHeight:e)}get height(){return this._height}sort(e){e=this.assignSort(e);for(let t of this.trackView.viewports)if(t.containsPosition(e.chr,e.position)){const i=t.cachedFeatures;i&&(i.sortRows(e),t.repaint())}}assignSort(e){if(e.locus){const t=function(e){const t=e.split(\":\"),i=t[1].split(\"-\"),n={chr:t[0],start:Number.parseInt(i[0].replace(/,/g,\"\"))-1};return i.length>1?n.end=Number.parseInt(i[1].replace(/,/g,\"\")):n.end=n.start+1,n}(e.locus);e.chr=t.chr,e.position=t.start}else e.position--;return e.direction=\"ASC\"===e.direction||!0===e.direction,e.chr=this.browser.genome.getChromosomeName(e.chr),this.sortObject=e,this.sortObject}async getFeatures(e,t,i,n,r){const s=await this.featureSource.getAlignments(e,t,i);if(s.viewport=r,s.hasPairs&&!this._pairedEndStats&&!this.config.maxFragmentLength){const e=new Om(s.allAlignments(),this.config);e.totalCount>99&&(this._pairedEndStats=e)}s.pack(this.alignmentTrack);const o=this.sortObject;return o&&o.chr===e&&o.position>=t&&o.position<=i&&s.sortRows(o),this.alignmentTrack.hasPairs=this.alignmentTrack.hasPairs||s.hasPairs,s}computePixelHeight(e){return(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.computePixelHeight(e):0)}draw(e){xo.fillRect(e.context,0,e.pixelTop,e.pixelWidth,e.pixelHeight,{fillStyle:\"rgb(255, 255, 255)\"}),!0===this.showCoverage&&this.coverageTrackHeight>0?(this.trackView.axisCanvas.style.display=\"block\",this.coverageTrack.draw(e)):this.trackView.axisCanvas.style.display=\"none\",!0===this.showAlignments&&(this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.alignmentTrack.draw(e))}paintAxis(e,t,i){this.coverageTrack.paintAxis(e,t,this.coverageTrackHeight)}contextMenuItemList(e){return this.alignmentTrack.contextMenuItemList(e)}popupData(e){return!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight?this.coverageTrack.popupData(e):this.alignmentTrack.popupData(e)}clickedFeatures(e){let t;return t=!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight?this.coverageTrack.getClickedObject(e):this.alignmentTrack.getClickedObject(e),t?[t]:void 0}hoverText(e){if(!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight){const t=this.coverageTrack.getClickedObject(e);if(t)return t.hoverText()}}menuItemList(){let e=[];e=e.concat(this.numericDataMenuItems()),e=e.concat(this.alignmentTrack.menuItemList());const t=()=>{if(!this.autoHeight){const e=(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.height:0);this.trackView.setTrackHeight(e)}};return e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"Show Coverage\",this.showCoverage)),click:function(){this.showCoverage=!this.showCoverage,t(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show Alignments\",this.showAlignments)),click:function(){this.showAlignments=!this.showAlignments,t(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),e}getState(){const e=super.getState();return this.sortObject&&(e.sort={chr:this.sortObject.chr,position:this.sortObject.position+1,option:this.sortObject.option,direction:this.sortObject.direction?\"ASC\":\"DESC\"}),Object.assign(e,this.alignmentTrack.getState()),e}getCachedAlignmentContainers(){return this.trackView.viewports.map((e=>e.cachedFeatures))}get dataRange(){return this.coverageTrack.dataRange}set dataRange(e){this.coverageTrack.dataRange=e}get logScale(){return this.coverageTrack.logScale}set logScale(e){this.coverageTrack.logScale=e}get autoscale(){return this.coverageTrack.autoscale}set autoscale(e){this.coverageTrack.autoscale=e}addPairedChordsForViewport(e){const t=this.maxTemplateLength,i=[],n=e.referenceFrame;for(let r of e.cachedFeatures.allAlignments())r.end>=n.start&&r.start<=n.end&&(r.paired?r.end-r.start>t&&i.push(r):r.mate&&r.mate.chr&&(r.mate.chr!==r.chr||Math.max(r.fragmentLength)>t)&&i.push(r));Pm((e=>{const t=[];for(let i of e)if(i.paired)i.firstAlignment&&i.secondAlignment&&t.push({uniqueId:i.readName,refName:zm(i.firstAlignment.chr),start:i.firstAlignment.start,end:i.firstAlignment.end,mate:{refName:zm(i.secondAlignment.chr),start:i.secondAlignment.start,end:i.secondAlignment.end}});else{const e=i.mate;e&&e.chr&&e.position&&t.push({uniqueId:i.readName,refName:zm(i.chr),start:i.start,end:i.end,mate:{refName:zm(e.chr),start:e.position-1,end:e.position}})}return t})(i),this,n,.02)}addSplitChordsForViewport(e){const t=[],i=e.referenceFrame;for(let n of e.cachedFeatures.allAlignments()){const e=n.hasTag(\"SA\");n.end>=i.start&&n.start<=i.end&&e&&t.push(n)}Pm((e=>{const t=e=>{const t=gp(e.tags().SA);let n=0;for(let r of t)r.start!==e.start&&i.push({uniqueId:`${e.readName}_${n++}`,refName:zm(e.chr),start:e.start,end:e.end,mate:{refName:zm(r.chr),start:r.start,end:r.start+r.lenOnRef}})},i=[];for(let i of e)i.paired?(t(i.firstAlignment),i.secondAlignment&&t(i.secondAlignment)):t(i);return i})(t),this,i,.02)}}class iw extends Hl{static defaults={height:250,theta:Math.PI/4,arcOrientation:\"UP\",showBlocks:!0,blockHeight:3,thickness:1,color:\"rgb(180,25,137)\",alpha:.02,logScale:!0};constructor(e,t){super(e,t)}init(e){super.init(e),!1===e.arcOrientation?this.arcOrientation=\"DOWN\":!0===e.arcOrientation?this.arcOrientation=\"UP\":e.arcOrientation?this.arcOrientation=e.arcOrientation.toUpperCase():this.arcOrientation=\"UP\",this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta),this.arcType=function(e){if(!e.arcType)return\"nested\";switch(e.arcType){case\"chiapet\":return\"inView\";case\"chiapetoutbound\":return\"partialInView\";default:return e.arcType}}(e),this.painter={flipAxis:\"DOWN\"===this.arcOrientation,dataRange:this.dataRange,paintAxis:cd},e.valueColumn?(this.valueColumn=e.valueColumn,this.hasValue=!0):e.useScore&&(this.hasValue=!0,this.valueColumn=\"score\"),e.max?(this.dataRange={min:e.min||0,max:e.max},this.autoscale=!1):this.autoscale=!0,e.featureSource?(this.featureSource=e.featureSource,delete e._featureSource):(this.featureSource=Ad(e,this.browser.genome),this.featureSource.getWGFeatures=aw)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow(),this.featureSource.visibilityWindow=this.visibilityWindow),this}get supportsWholeGenome(){return!0}async getFeatures(e,t,i){const n=this.visibilityWindow,r=await this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n});return void 0===this.hasValue&&r&&r.length>0&&(this.hasValue=void 0!==r[0].score),r}draw(e){\"proportional\"===this.arcType||\"inView\"===this.arcType||\"partialInView\"===this.arcType?this.drawProportional(e):this.drawNested(e)}drawNested(e){const t=e.context,i=e.pixelWidth,n=e.pixelHeight,r=e.viewportWidth,s=e.bpPerPixel,o=e.bpStart,a=s;xo.fillRect(t,0,e.pixelTop,i,n,{fillStyle:\"rgb(255, 255, 255)\"});const c=e.features;if(c){(function(){let e=0;for(let t of c){let n=(t.start-o)/a,r=(t.end-o)/a;n>=0&&r<=i&&(e=Math.max(e,r-n))}let t=Math.min(r,e)/2;if(e>0){let e=(n-10)/t;this.theta=function(e){let t,i=[.01570925532366355,.15838444032453644,.3249196962329063,.5095254494944288,.7265425280053609,.9999999999999999],n=[.031415926535897934,.3141592653589793,.6283185307179586,.9424777960769379,1.2566370614359172,1.5707963267948966];for(t=0;t<i.length&&!(i[t]>e);t++);let r=0===t?0:i[t-1],s=t<i.length?i[t]:1,o=(e-r)/(s-r),a=0===t?0:n[t-1],c=t<n.length?n[t]:Math.PI/2;return Math.min(Math.PI/2,a+o*(c-a))}(e),this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta)}}).call(this);const s=\"UP\"===this.arcOrientation,h=s?e.pixelHeight:0;t.font=\"8px sans-serif\",t.textAlign=\"center\";for(let e of c){let n;if(e.drawState=void 0,\"function\"==typeof this.color?n=this.color(e):(n=this.color||e.color||\"rgb(180,25,137)\",n&&this.config.useScore&&(n=ow(n,(l=e.score,Math.min(1,.11+l/779*.89).toString())))),t.lineWidth=e.thickness||this.thickness||1,e.chr1===e.chr2||\"all\"===e.chr){const{m1:c,m2:l}=nw(e,this.browser.genome);let d=Math.round((c-o)/a),u=Math.round((l-o)/a);if(u<0||d>i)continue;let f=u-d;f<3&&(f=3,d--);const p=f/2,g=p/this.sinTheta,m=this.cosTheta*g,w=d+p;let b,F,v;if(s?(b=this.height+m,F=Math.PI+Math.PI/2-this.theta,v=Math.PI+Math.PI/2+this.theta):(b=-m,F=Math.PI/2-this.theta,v=Math.PI/2+this.theta),this.showBlocks&&\"all\"!==e.chr){const i=(e.start1-o)/a,n=(e.end1-o)/a,r=(e.start2-o)/a,c=(e.end2-o)/a,l=s?-this.blockHeight:this.blockHeight;t.fillRect(i,h,n-i,l),t.fillRect(r,h,c-r,l)}n&&!this.config.useScore&&f>r&&(n=ow(n,this.alpha)),t.strokeStyle=n,t.fillStyle=n,t.beginPath(),t.arc(w,b,g,F,v,!1),t.stroke(),e.drawState={xc:w,yc:b,r:g}}else{let r=Math.round((e.start-o)/a),c=Math.round((e.end-o)/a);if(c<0||r>i)continue;let l=c-r;l<3&&(l=3,r--);const h=e.chr===e.chr1?e.chr2:e.chr1;t.strokeStyle=n,t.fillStyle=ow(Nu(h),.5),s?(t.fillRect(r,this.height/2,l,this.height/2),t.fillText(h,r+l/2,this.height/2-5),e.drawState={x:r,y:this.height/2,w:l,h:this.height/2}):(t.fillRect(r,0,l,this.height/2),t.fillText(h,r+l/2,this.height/2+13),e.drawState={x:r,y:0,w:l,h:this.height/2})}}}var l}getScaleFactor(e,t,i,n){return n?i/(Math.log10(t+1)-(e<=0?0:Math.log10(e+1))):i/(t-e)}drawProportional(e){const t=e.context,i=e.pixelWidth,n=e.pixelHeight,r=e.bpPerPixel,s=e.bpStart,o=r,a=e.referenceFrame.start,c=e.referenceFrame.end,l=\"UP\"===this.arcOrientation;xo.fillRect(t,0,e.pixelTop,i,n,{fillStyle:\"rgb(255, 255, 255)\"});const h=e.features;if(h&&h.length>0){const n=0,r=this.getScaleFactor(n,this.dataRange.max,e.pixelHeight-1,this.logScale),d=l?e.pixelHeight:0;for(let e of h){e.drawState=void 0;const n=this.valueColumn?e[this.valueColumn]:e.score;if(void 0===n||Number.isNaN(n))continue;const h=Math.round((this.logScale?Math.log10(n+1):n)*r);if(e.chr1===e.chr2||\"all\"===e.chr){const{m1:i,m2:r}=nw(e,this.browser.genome);let u=Math.round((i-s)/o),f=Math.round((r-s)/o)-u;if(f<3&&(f=3,u--),n<this.dataRange.min||n>this.dataRange.max)continue;if(\"proportional\"!==this.arcType){const e=\"partialInView\"===this.arcType,t=i>=a&&r<=c;let n=!1,s=!1;if(!t&&e&&(n=a<=i&&i<=c,n||(s=a<=r&&r<=c)),!(t||n||s))continue}const p=f/2,g=u+f/2;e.drawState={xc:g,yc:d,radiusX:p,radiusY:h};const m=l,w=e.color||this.color;if(t.strokeStyle=w,t.lineWidth=e.thickness||this.thickness||1,!0===t.isSVG?t.strokeEllipse(g,d,p,h,0,0,Math.PI,m):(t.beginPath(),t.ellipse(g,d,p,h,0,0,Math.PI,m),t.stroke()),this.alpha&&(t.fillStyle=ow(w,this.alpha),!0===t.isSVG?t.fillEllipse(g,d,p,h,0,0,Math.PI,m):t.fill()),this.showBlocks&&\"all\"!==e.chr){t.fillStyle=w;const i=(e.start1-s)/o,n=(e.end1-s)/o,r=(e.start2-s)/o,a=(e.end2-s)/o,c=l?-this.blockHeight:this.blockHeight;t.fillRect(i,d,n-i,c),t.fillRect(r,d,a-r,c)}}else{let r=Math.round((e.start-s)/o),a=Math.round((e.end-s)/o);if(a<0||r>i||n<this.dataRange.min||n>this.dataRange.max)continue;const c=Math.min(h,this.height-13);let d=a-r;d<3&&(d=3,r--);const u=e.chr===e.chr1?e.chr2:e.chr1;if(t.font=\"8px sans-serif\",t.textAlign=\"center\",t.fillStyle=ow(Nu(u),.5),l){const i=this.height-c;t.fillRect(r,i,d,c),t.fillText(u,r+d/2,i-5),e.drawState={x:r,y:i,w:d,h:c}}else t.fillRect(r,0,d,c),t.fillText(u,r+d/2,c+13),e.drawState={x:r,y:0,w:d,h:c}}}}}clearAxis(e,t,i){xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"})}paintAxis(e,t,i){const n={min:0,max:this.dataRange.max};\"proportional\"===this.arcType||\"inView\"===this.arcType||\"partialInView\"===this.arcType?(this.painter.flipAxis=\"DOWN\"===this.arcOrientation,this.painter.dataRange=n,this.painter.paintAxis(e,t,i)):this.clearAxis(e,t,i)}menuItemList(){let e=[];if(this.hasValue){e.push(\"<hr/>\");const t={nested:\"Nested\",proportional:\"Proportional - All\",inView:\"Proportional - Both Ends in View\",partialInView:\"Proportional - One End in View\"};e.push(\"<b>Arc Type</b>\");for(let i of[\"nested\",\"proportional\",\"inView\",\"partialInView\"])e.push({object:Bt(Dl(t[i],i===this.arcType)),click:function(){this.arcType=i,this.trackView.repaintViews()}})}return e.push(\"<hr/>\"),e.push({name:\"Toggle arc direction\",click:function(){this.arcOrientation=\"UP\"===this.arcOrientation?\"DOWN\":\"UP\",this.trackView.repaintViews()}}),e.push({name:this.showBlocks?\"Hide Blocks\":\"Show Blocks\",click:function(){this.showBlocks=!this.showBlocks,this.trackView.repaintViews()}}),\"proportional\"!==this.arcType&&\"inView\"!==this.arcType&&\"partialInView\"!==this.arcType||(e=e.concat(this.numericDataMenuItems())),this.browser.circularView&&(e.push(\"<hr/>\"),e.push({label:\"Add interactions to circular view\",click:function(){for(let e of this.trackView.viewports)this.addChordsForViewport(e.referenceFrame)}})),e}contextMenuItemList(e){if(this.browser.circularView){const t=e.viewport,i=[];return i.push({label:\"Add interactions to circular view\",click:()=>{const e=t.referenceFrame;this.addChordsForViewport(e)}}),i.push(\"<hr/>\"),i}}addChordsForViewport(e){let t;if(\"all\"===e.chr)t=Object.values(this.featureSource.getAllFeatures()).flat();else{t=this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end).filter((e=>e.drawState))}if(0===t.length)return;Pm(t.map((e=>{const t=e._f||e;return{uniqueId:`${t.chr1}:${t.start1}-${t.end1}_${t.chr2}:${t.start2}-${t.end2}`,refName:zm(t.chr1),start:t.start1,end:t.end1,mate:{refName:zm(t.chr2),start:t.start2,end:t.end2}}})),this,e,.5)}doAutoscale(e){let t=0;if(e)for(let i of e){const e=this.valueColumn?i[this.valueColumn]:i.score;Number.isNaN(e)||(t=Math.max(t,e))}return{min:0,max:t}}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){const t=e._||e;if(i.push({name:\"Region 1\",value:rw(t.chr1,t.start1,t.end1,t.strand1)}),i.push({name:\"Region 2\",value:rw(t.chr2,t.start2,t.end2,t.strand2)}),t.name&&i.push({name:\"Name\",value:t.name}),void 0!==t.value&&i.push({name:\"Value\",value:t.value}),void 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i})(s,r)},utf8border:(e,t)=>{(t=t||e.length)>e.length&&(t=e.length);let i=t-1;for(;i>=0&&128==(192&e[i]);)i--;return i<0||0===i?t:i+Kw[e[i]]>t?i:t}};var Xw=function(){this.input=null,this.next_in=0,this.avail_in=0,this.total_in=0,this.output=null,this.next_out=0,this.avail_out=0,this.total_out=0,this.msg=\"\",this.state=null,this.data_type=2,this.adler=0},Zw=function(e,t){let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_,x;const k=e.state;i=e.next_in,_=e.input,n=i+(e.avail_in-5),r=e.next_out,x=e.output,s=r-(t-e.avail_out),o=r+(e.avail_out-257),a=k.dmax,c=k.wsize,l=k.whave,h=k.wnext,d=k.window,u=k.hold,f=k.bits,p=k.lencode,g=k.distcode,m=(1<<k.lenbits)-1,w=(1<<k.distbits)-1;e:do{f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=p[u&m];t:for(;;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,0===F)x[r++]=65535&b;else{if(!(16&F)){if(64&F){if(32&F){k.mode=12;break e}e.msg=\"invalid literal/length code\",k.mode=30;break e}b=p[(65535&b)+(u&(1<<F)-1)];continue t}for(v=65535&b,F&=15,F&&(f<F&&(u+=_[i++]<<f,f+=8),v+=u&(1<<F)-1,u>>>=F,f-=F),f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=g[u&w];;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,16&F){if(y=65535&b,F&=15,f<F&&(u+=_[i++]<<f,f+=8,f<F&&(u+=_[i++]<<f,f+=8)),y+=u&(1<<F)-1,y>a){e.msg=\"invalid distance too far back\",k.mode=30;break e}if(u>>>=F,f-=F,F=r-s,y>F){if(F=y-F,F>l&&k.sane){e.msg=\"invalid distance too far back\",k.mode=30;break e}if(A=0,C=d,0===h){if(A+=c-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}else if(h<F){if(A+=c+h-F,F-=h,F<v){v-=F;do{x[r++]=d[A++]}while(--F);if(A=0,h<v){F=h,v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}}else if(A+=h-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}for(;v>2;)x[r++]=C[A++],x[r++]=C[A++],x[r++]=C[A++],v-=3;v&&(x[r++]=C[A++],v>1&&(x[r++]=C[A++]))}else{A=r-y;do{x[r++]=x[A++],x[r++]=x[A++],x[r++]=x[A++],v-=3}while(v>2);v&&(x[r++]=x[A++],v>1&&(x[r++]=x[A++]))}break}if(64&F){e.msg=\"invalid distance code\",k.mode=30;break 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0!==_&&(r[f+_]=g-y<<24|64<<16),a.bits=F,0},{Z_FINISH:sb,Z_BLOCK:ob,Z_TREES:ab,Z_OK:cb,Z_STREAM_END:lb,Z_NEED_DICT:hb,Z_STREAM_ERROR:db,Z_DATA_ERROR:ub,Z_MEM_ERROR:fb,Z_BUF_ERROR:pb,Z_DEFLATED:gb}=jw,mb=12,wb=30,bb=e=>(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24);function Fb(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new Uint16Array(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}var vb,yb,Ab=e=>{if(!e||!e.state)return db;const t=e.state;return e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=1,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new Int32Array(852),t.distcode=t.distdyn=new Int32Array(592),t.sane=1,t.back=-1,cb},Cb=e=>{if(!e||!e.state)return db;const t=e.state;return t.wsize=0,t.whave=0,t.wnext=0,Ab(e)},_b=(e,t)=>{let i;if(!e||!e.state)return db;const n=e.state;return t<0?(i=0,t=-t):(i=1+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?db:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,Cb(e))},xb=(e,t)=>{if(!e)return db;const i=new Fb;e.state=i,i.window=null;const n=_b(e,t);return n!==cb&&(e.state=null),n},kb=!0,Ib=e=>{if(kb){vb=new Int32Array(512),yb=new Int32Array(32);let t=0;for(;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(rb(1,e.lens,0,288,vb,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;rb(2,e.lens,0,32,yb,0,e.work,{bits:5}),kb=!1}e.lencode=vb,e.lenbits=9,e.distcode=yb,e.distbits=5},Sb=(e,t,i,n)=>{let r;const s=e.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new Uint8Array(s.wsize)),n>=s.wsize?(s.window.set(t.subarray(i-s.wsize,i),0),s.wnext=0,s.whave=s.wsize):(r=s.wsize-s.wnext,r>n&&(r=n),s.window.set(t.subarray(i-n,i-n+r),s.wnext),(n-=r)?(s.window.set(t.subarray(i-n,i),0),s.wnext=n,s.whave=s.wsize):(s.wnext+=r,s.wnext===s.wsize&&(s.wnext=0),s.whave<s.wsize&&(s.whave+=r))),0},Eb=(e,t)=>{let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_=0;const x=new Uint8Array(4);let k,I;const S=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(!e||!e.state||!e.output||!e.input&&0!==e.avail_in)return db;i=e.state,i.mode===mb&&(i.mode=13),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,d=a,u=c,C=cb;e:for(;;)switch(i.mode){case 1:if(0===i.wrap){i.mode=13;break}for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(2&i.wrap&&35615===l){i.check=0,x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0),l=0,h=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&l)<<8)+(l>>8))%31){e.msg=\"incorrect header check\",i.mode=wb;break}if((15&l)!==gb){e.msg=\"unknown compression method\",i.mode=wb;break}if(l>>>=4,h-=4,A=8+(15&l),0===i.wbits)i.wbits=A;else if(A>i.wbits){e.msg=\"invalid window size\",i.mode=wb;break}i.dmax=1<<i.wbits,e.adler=i.check=1,i.mode=512&l?10:mb,l=0,h=0;break;case 2:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.flags=l,(255&i.flags)!==gb){e.msg=\"unknown compression method\",i.mode=wb;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=wb;break}i.head&&(i.head.text=l>>8&1),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0,i.mode=3;case 3:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.time=l),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,x[2]=l>>>16&255,x[3]=l>>>24&255,i.check=Qw(i.check,x,4,0)),l=0,h=0,i.mode=4;case 4:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.xflags=255&l,i.head.os=l>>8),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0,i.mode=5;case 5:if(1024&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length=l,i.head&&(i.head.extra_len=l),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&(f=i.length,f>a&&(f=a),f&&(i.head&&(A=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Uint8Array(i.head.extra_len)),i.head.extra.set(n.subarray(s,s+f),A)),512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,i.length-=f),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.name+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.comment+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=wb;break}l=0,h=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=mb;break;case 10:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}e.adler=i.check=bb(l),l=0,h=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,hb;e.adler=i.check=1,i.mode=mb;case mb:if(t===ob||t===ab)break e;case 13:if(i.last){l>>>=7&h,h-=7&h,i.mode=27;break}for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}switch(i.last=1&l,l>>>=1,h-=1,3&l){case 0:i.mode=14;break;case 1:if(Ib(i),i.mode=20,t===ab){l>>>=2,h-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg=\"invalid block type\",i.mode=wb}l>>>=2,h-=2;break;case 14:for(l>>>=7&h,h-=7&h;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if((65535&l)!=(l>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=wb;break}if(i.length=65535&l,l=0,h=0,i.mode=15,t===ab)break e;case 15:i.mode=16;case 16:if(f=i.length,f){if(f>a&&(f=a),f>c&&(f=c),0===f)break e;r.set(n.subarray(s,s+f),o),a-=f,s+=f,c-=f,o+=f,i.length-=f;break}i.mode=mb;break;case 17:for(;h<14;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.nlen=257+(31&l),l>>>=5,h-=5,i.ndist=1+(31&l),l>>>=5,h-=5,i.ncode=4+(15&l),l>>>=4,h-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=wb;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.lens[S[i.have++]]=7&l,l>>>=3,h-=3}for(;i.have<19;)i.lens[S[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,k={bits:i.lenbits},C=rb(0,i.lens,0,19,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid code lengths set\",i.mode=wb;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(b<16)l>>>=m,h-=m,i.lens[i.have++]=b;else{if(16===b){for(I=m+2;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l>>>=m,h-=m,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=wb;break}A=i.lens[i.have-1],f=3+(3&l),l>>>=2,h-=2}else if(17===b){for(I=m+3;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=3+(7&l),l>>>=3,h-=3}else{for(I=m+7;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=11+(127&l),l>>>=7,h-=7}if(i.have+f>i.nlen+i.ndist){e.msg=\"invalid bit length repeat\",i.mode=wb;break}for(;f--;)i.lens[i.have++]=A}}if(i.mode===wb)break;if(0===i.lens[256]){e.msg=\"invalid code -- missing end-of-block\",i.mode=wb;break}if(i.lenbits=9,k={bits:i.lenbits},C=rb(1,i.lens,0,i.nlen,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid literal/lengths set\",i.mode=wb;break}if(i.distbits=6,i.distcode=i.distdyn,k={bits:i.distbits},C=rb(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,k),i.distbits=k.bits,C){e.msg=\"invalid distances set\",i.mode=wb;break}if(i.mode=20,t===ab)break e;case 20:i.mode=21;case 21:if(a>=6&&c>=258){e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,Zw(e,u),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,i.mode===mb&&(i.back=-1);break}for(i.back=0;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(w&&!(240&w)){for(F=m,v=w,y=b;_=i.lencode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,i.length=b,0===w){i.mode=26;break}if(32&w){i.back=-1,i.mode=mb;break}if(64&w){e.msg=\"invalid literal/length code\",i.mode=wb;break}i.extra=15&w,i.mode=22;case 22:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;_=i.distcode[l&(1<<i.distbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(!(240&w)){for(F=m,v=w,y=b;_=i.distcode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,64&w){e.msg=\"invalid distance code\",i.mode=wb;break}i.offset=b,i.extra=15&w,i.mode=24;case 24:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.offset+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=wb;break}i.mode=25;case 25:if(0===c)break e;if(f=u-c,i.offset>f){if(f=i.offset-f,f>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=wb;break}f>i.wnext?(f-=i.wnext,p=i.wsize-f):p=i.wnext-f,f>i.length&&(f=i.length),g=i.window}else g=r,p=o-i.offset,f=i.length;f>c&&(f=c),c-=f,i.length-=f;do{r[o++]=g[p++]}while(--f);0===i.length&&(i.mode=21);break;case 26:if(0===c)break e;r[o++]=i.length,c--,i.mode=21;break;case 27:if(i.wrap){for(;h<32;){if(0===a)break e;a--,l|=n[s++]<<h,h+=8}if(u-=c,e.total_out+=u,i.total+=u,u&&(e.adler=i.check=i.flags?Qw(i.check,r,u,o-u):Uw(i.check,r,u,o-u)),u=c,(i.flags?l:bb(l))!==i.check){e.msg=\"incorrect data check\",i.mode=wb;break}l=0,h=0}i.mode=28;case 28:if(i.wrap&&i.flags){for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=wb;break}l=0,h=0}i.mode=29;case 29:C=lb;break e;case wb:C=ub;break e;case 31:return fb;default:return db}return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,(i.wsize||u!==e.avail_out&&i.mode<wb&&(i.mode<27||t!==sb))&&Sb(e,e.output,e.next_out,u-e.avail_out),d-=e.avail_in,u-=e.avail_out,e.total_in+=d,e.total_out+=u,i.total+=u,i.wrap&&u&&(e.adler=i.check=i.flags?Qw(i.check,r,u,e.next_out-u):Uw(i.check,r,u,e.next_out-u)),e.data_type=i.bits+(i.last?64:0)+(i.mode===mb?128:0)+(20===i.mode||15===i.mode?256:0),(0===d&&0===u||t===sb)&&C===cb&&(C=pb),C},Nb={inflateReset:Cb,inflateReset2:_b,inflateResetKeep:Ab,inflateInit:e=>xb(e,15),inflateInit2:xb,inflate:Eb,inflateEnd:e=>{if(!e||!e.state)return db;let t=e.state;return t.window&&(t.window=null),e.state=null,cb},inflateGetHeader:(e,t)=>{if(!e||!e.state)return db;const i=e.state;return 2&i.wrap?(i.head=t,t.done=!1,cb):db},inflateSetDictionary:(e,t)=>{const i=t.length;let n,r,s;return e&&e.state?(n=e.state,0!==n.wrap&&11!==n.mode?db:11===n.mode&&(r=1,r=Uw(r,t,i,0),r!==n.check)?ub:(s=Sb(e,t,i,i),s?(n.mode=31,fb):(n.havedict=1,cb))):db},inflateInfo:\"pako inflate (from Nodeca project)\"};var Bb=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name=\"\",this.comment=\"\",this.hcrc=0,this.done=!1},Mb=Object.prototype.toString,{Z_NO_FLUSH:Rb,Z_FINISH:Db,Z_OK:Tb,Z_STREAM_END:Lb,Z_NEED_DICT:zb,Z_STREAM_ERROR:Hb,Z_DATA_ERROR:Pb,Z_MEM_ERROR:Ob}=jw;function Ub(e){this.options=Gw.assign({chunkSize:65536,windowBits:15,to:\"\"},e||{});const t=this.options;t.raw&&t.windowBits>=0&&t.windowBits<16&&(t.windowBits=-t.windowBits,0===t.windowBits&&(t.windowBits=-15)),!(t.windowBits>=0&&t.windowBits<16)||e&&e.windowBits||(t.windowBits+=32),t.windowBits>15&&t.windowBits<48&&(15&t.windowBits||(t.windowBits|=15)),this.err=0,this.msg=\"\",this.ended=!1,this.chunks=[],this.strm=new Xw,this.strm.avail_out=0;let i=Nb.inflateInit2(this.strm,t.windowBits);if(i!==Tb)throw new Error(Vw[i]);if(this.header=new Bb,Nb.inflateGetHeader(this.strm,this.header),t.dictionary&&(\"string\"==typeof t.dictionary?t.dictionary=Yw.string2buf(t.dictionary):\"[object ArrayBuffer]\"===Mb.call(t.dictionary)&&(t.dictionary=new Uint8Array(t.dictionary)),t.raw&&(i=Nb.inflateSetDictionary(this.strm,t.dictionary),i!==Tb)))throw new Error(Vw[i])}function qb(e,t){const i=new Ub(t);if(i.push(e),i.err)throw i.msg||Vw[i.err];return i.result}Ub.prototype.push=function(e,t){const i=this.strm,n=this.options.chunkSize,r=this.options.dictionary;let s,o,a;if(this.ended)return!1;for(o=t===~~t?t:!0===t?Db:Rb,\"[object ArrayBuffer]\"===Mb.call(e)?i.input=new Uint8Array(e):i.input=e,i.next_in=0,i.avail_in=i.input.length;;){for(0===i.avail_out&&(i.output=new Uint8Array(n),i.next_out=0,i.avail_out=n),s=Nb.inflate(i,o),s===zb&&r&&(s=Nb.inflateSetDictionary(i,r),s===Tb?s=Nb.inflate(i,o):s===Pb&&(s=zb));i.avail_in>0&&s===Lb&&i.state.wrap>0&&0!==e[i.next_in];)Nb.inflateReset(i),s=Nb.inflate(i,o);switch(s){case Hb:case Pb:case zb:case Ob:return this.onEnd(s),this.ended=!0,!1}if(a=i.avail_out,i.next_out&&(0===i.avail_out||s===Lb))if(\"string\"===this.options.to){let e=Yw.utf8border(i.output,i.next_out),t=i.next_out-e,r=Yw.buf2string(i.output,e);i.next_out=t,i.avail_out=n-t,t&&i.output.set(i.output.subarray(e,e+t),0),this.onData(r)}else this.onData(i.output.length===i.next_out?i.output:i.output.subarray(0,i.next_out));if(s!==Tb||0!==a){if(s===Lb)return s=Nb.inflateEnd(this.strm),this.onEnd(s),this.ended=!0,!0;if(0===i.avail_in)break}}return!0},Ub.prototype.onData=function(e){this.chunks.push(e)},Ub.prototype.onEnd=function(e){e===Tb&&(\"string\"===this.options.to?this.result=this.chunks.join(\"\"):this.result=Gw.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg};var Qb=function(e,t){return(t=t||{}).raw=!0,qb(e,t)},Vb={Inflate:Ub,inflate:qb,inflateRaw:Qb,ungzip:qb,constants:jw},{Inflate:jb,inflate:Wb,inflateRaw:Gb,ungzip:$b}=Vb,Kb=Wb,Yb=$b;var Xb=new Map([[1,function(e,t){let i=new Uint8Array(e);return Kb(i).buffer}],[2,function(e,t){let i=e.byteLength,n=new Uint8Array(i),r=Math.floor(i/t),s=new DataView(e);for(var o=0;o<t;o++)for(var a=0;a<r;a++)n[o+a*t]=s.getUint8(o*r+a);return n.buffer}],[3,function(e,t){return function(e){for(var t=e.byteLength%2!=0,i=e.byteLength-4,n=new DataView(e),r=0,s=0,o=0;o<i-1;o+=2){s=(s+(r=(r+n.getUint16(o,!0))%65535))%65535}if(t){s=(s+(r=(r+n.getUint8(i-1))%65535))%65535}var[a,c]=Aw.unpack_from(\">HH\",e,i);if(c%=65535,r!=(a%=65535)||s!=c)throw'ValueError(\"fletcher32 checksum invalid\")'}(e),e.slice(0,-4)}]]),Zb=class{constructor(e,t){this.fh=e,this.offset=t,this.depth=null}async init(){this.all_nodes=new Map,await this._read_root_node(),await this._read_children()}async _read_children(){let e=this.depth;for(;e>0;){for(var t of this.all_nodes.get(e))for(var i of t.get(\"addresses\"))this._add_node(await this._read_node(i,e-1));e--}}async _read_root_node(){let e=await this._read_node(this.offset,null);this._add_node(e),this.depth=e.get(\"node_level\")}_add_node(e){let t=e.get(\"node_level\");this.all_nodes.has(t)?this.all_nodes.get(t).push(e):this.all_nodes.set(t,[e])}async _read_node(e,t){let i=await this._read_node_header(e,t);return i.set(\"keys\",[]),i.set(\"addresses\",[]),i}async _read_node_header(e){throw\"NotImplementedError: must define _read_node_header in implementation class\"}},Jb=class extends Zb{constructor(){super(...arguments),pw(this,\"B_LINK_NODE\",new Map([[\"signature\",\"4s\"],[\"node_type\",\"B\"],[\"node_level\",\"B\"],[\"entries_used\",\"H\"],[\"left_sibling\",\"Q\"],[\"right_sibling\",\"Q\"]]))}async _read_node_header(e,t){let i=await gw(this.B_LINK_NODE,this.fh,e);if(null!=t&&i.get(\"node_level\")!=t)throw\"node level does not match\";return i}},eF=class extends Jb{constructor(e,t){super(e,t),pw(this,\"NODE_TYPE\",0),this.ready=this.init()}async _read_node(e,t){let i=await this._read_node_header(e,t);e+=bw(this.B_LINK_NODE);let n=[],r=[],s=i.get(\"entries_used\");for(var o=0;o<s;o++){let t=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8;let i=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8,n.push(t),r.push(i)}return n.push((await Aw.unpack_from_async(\"<Q\",this.fh,e))[0]),i.set(\"keys\",n),i.set(\"addresses\",r),i}symbol_table_addresses(){var e=[],t=this.all_nodes.get(0);for(var i of t)e=e.concat(i.get(\"addresses\"));return e}},tF=class extends Jb{constructor(e,t,i){super(e,t),pw(this,\"NODE_TYPE\",1),this.dims=i,this.ready=this.init()}async _read_node(e,t){let i=await this._read_node_header(e,t);e+=bw(this.B_LINK_NODE);var n=[],r=[];let s=i.get(\"entries_used\");for(var o=0;o<s;o++){let[t,i]=await Aw.unpack_from_async(\"<II\",this.fh,e);e+=8;let s=\"<\"+this.dims.toFixed()+\"Q\",o=Aw.calcsize(s),a=await Aw.unpack_from_async(s,this.fh,e);e+=o;let c=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8,n.push(new Map([[\"chunk_size\",t],[\"filter_mask\",i],[\"chunk_offset\",a]])),r.push(c)}return i.set(\"keys\",n),i.set(\"addresses\",r),i}async construct_data_from_chunks(e,t,i,n){var r,s,o;if(i instanceof Array){let e=i[0];if(\"REFERENCE\"==e){if(8!=i[1])throw\"NotImplementedError('Unsupported Reference type')\";i=\"<u8\",r=\"getUint64\",s=!1,o=8}else{if(\"VLEN_STRING\"!=e&&\"VLEN_SEQUENCE\"!=e)throw\"NotImplementedError('datatype not implemented')\";r=\"getVLENStruct\",s=!1,o=16}}else[r,s,o]=yw(i);var a=t.reduce((function(e,t){return e*t}),1),c=e.reduce((function(e,t){return e*t}),1);let l=t.length;var h=1;e.slice().map((function(e){let t=h;return h*=e,t}));h=1;var d=t.slice().reverse().map((function(e){let t=h;return h*=e,t})).reverse(),u=new Array(a);let f=c*o;for(var p of this.all_nodes.get(0)){let i=p.get(\"keys\"),a=p.get(\"addresses\"),h=i.length;for(var g=0;g<h;g++){let h=i[g],p=a[g];var m;if(null==n)m=await this.fh.slice(p,p+f);else{m=await this.fh.slice(p,p+h.get(\"chunk_size\"));let e=h.get(\"filter_mask\");m=this._filter_chunk(m,e,n,o)}for(var w=h.get(\"chunk_offset\").slice(),b=w.slice(),F=b.map((function(){return 0})),v=new Cw(m),y=0;y<c;y++){for(var A=l-1;A>=0&&F[A]>=e[A];A--)F[A]=0,b[A]=w[A],A>0&&(F[A-1]+=1,b[A-1]+=1);if(b.slice(0,-1).every((function(e,i){return e<t[i]}))){let e=y*o,t=v[r](e,!s,o),i=b.slice(0,-1).reduce((function(e,t,i){return t*d[i]+e}),0);u[i]=t}F[l-1]+=1,b[l-1]+=1}}}return u}_filter_chunk(e,t,i,n){let r=i.length,s=e.slice();for(var o=r-1;o>=0;o--){if(t&1<<o)continue;let e=i[o],r=e.get(\"filter_id\"),a=e.get(\"client_data\");if(!Xb.has(r))throw'NotImplementedError(\"Filter with id:'+r.toFixed()+' not supported\")';s=Xb.get(r)(s,n,a)}return s}},iF=class extends Zb{constructor(e,t){super(e,t),pw(this,\"B_TREE_HEADER\",new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"node_type\",\"B\"],[\"node_size\",\"I\"],[\"record_size\",\"H\"],[\"depth\",\"H\"],[\"split_percent\",\"B\"],[\"merge_percent\",\"B\"],[\"root_address\",\"Q\"],[\"root_nrecords\",\"H\"],[\"total_nrecords\",\"Q\"]])),pw(this,\"B_LINK_NODE\",new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"node_type\",\"B\"]])),this.ready=this.init()}async _read_root_node(){let e=await this._read_tree_header(this.offset);this.address_formats=this._calculate_address_formats(e),this.header=e,this.depth=e.get(\"depth\");let t=[e.get(\"root_address\"),e.get(\"root_nrecords\"),e.get(\"total_nrecords\")],i=await this._read_node(t,this.depth);this._add_node(i)}async _read_tree_header(e){return await gw(this.B_TREE_HEADER,this.fh,this.offset)}_calculate_address_formats(e){let t=e.get(\"node_size\"),i=e.get(\"record_size\"),n=0,r=0,s=new Map,o=e.get(\"depth\");for(var a=0;a<=o;a++){let e,c,l,h=\"\",d=\"\",u=\"\";if(0==a?(e=0,c=0,l=0):1==a?(e=8,h=\"<Q\",c=this._required_bytes(n),d=this._int_format(c),l=0):(e=8,h=\"<Q\",c=this._required_bytes(n),d=this._int_format(c),l=this._required_bytes(r),u=this._int_format(l)),s.set(a,[e,c,l,h,d,u]),a<o){let s=e+c+l;n=this._nrecords_max(t,i,s),r>0?r*=n:r=n}}return s}_nrecords_max(e,t,i){return Math.floor((e-10-i)/(t+i))}_required_bytes(e){return Math.ceil(_w(e)/8)}_int_format(e){return[\"<B\",\"<H\",\"<I\",\"<Q\"][e-1]}async _read_node(e,t){let[i,n,r]=e,s=this._read_node_header(i,t);i+=bw(this.B_LINK_NODE);let o=this.header.get(\"record_size\"),a=[];for(let e=0;e<n;e++){let e=await this._parse_record(this.fh,i,o);i+=o,a.push(e)}let c=[],l=this.address_formats.get(t);if(0!=t){let[e,t,r,s,o,a]=l;for(let l=0;l<=n;l++){let n=(await Aw.unpack_from_async(s,this.fh,i))[0];i+=e;let l=(await Aw.unpack_from_async(o,this.fh,i))[0];i+=t;let h=l;r>0&&(h=(await Aw.unpack_from_async(a,this.fh,i))[0],i+=r),c.push([n,l,h])}}return s.set(\"keys\",a),s.set(\"addresses\",c),s}async _read_node_header(e,t){let i=await gw(this.B_LINK_NODE,this.fh,e);return i.set(\"node_level\",t),i}*iter_records(){for(let e of this.all_nodes.values())for(let t of e)for(let e of t.get(\"keys\"))yield e}_parse_record(e){throw\"NotImplementedError\"}},nF=class extends iF{constructor(){super(...arguments),pw(this,\"NODE_TYPE\",5)}async _parse_record(e,t,i){let n=(await Aw.unpack_from_async(\"<I\",e,t))[0];t+=4;const r=await e.slice(t,t+7);return new Map([[\"namehash\",n],[\"heapid\",r]])}},rF=class extends iF{constructor(){super(...arguments),pw(this,\"NODE_TYPE\",6)}async _parse_record(e,t,i){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];t+=8;const r=await e.slice(t,t+7);return new Map([[\"creationorder\",n],[\"heapid\",r]])}},sF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await Aw.unpack_from_async(\"<B\",e,t+8);var n;if(0==i)n=await gw(uF,e,t),this._end_of_sblock=t+fF;else{if(2!=i&&3!=i)throw\"unsupported superblock version: \"+i.toFixed();n=await gw(pF,e,t),this._end_of_sblock=t+gF}if(n.get(\"format_signature\")!=hF)throw\"Incorrect file signature: \"+n.get(\"format_signature\");if(8!=n.get(\"offset_size\")||8!=n.get(\"length_size\"))throw\"File uses non-64-bit addressing\";this.version=n.get(\"superblock_version\"),this._contents=n,this._root_symbol_table=null,this._fh=e}async get_offset_to_dataobjects(){if(0==this.version){var e=new aF(this._fh,this._end_of_sblock,!0);return await e.ready,this._root_symbol_table=e,e.group_offset}if(2==this.version||3==this.version)return this._contents.get(\"root_group_address\");throw\"Not implemented version = \"+this.version.toFixed()}},oF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await gw(vF,e,t);ww(\"HEAP\"==i.get(\"signature\")),ww(0==i.get(\"version\"));let n=i.get(\"address_of_data_segment\"),r=await e.slice(n,n+i.get(\"data_segment_size\"));i.set(\"heap_data\",r),this._contents=i,this.data=r}get_object_name(e){let t=new Uint8Array(this.data).indexOf(0,e)-e;return Aw.unpack_from(\"<\"+t.toFixed()+\"s\",this.data,e)[0]}},aF=class{constructor(e,t,i=!1){this.ready=this.init(e,t,i)}async init(e,t,i){var n;if(i)n=new Map([[\"symbols\",1]]);else{if(\"SNOD\"!=(n=await gw(bF,e,t)).get(\"signature\"))throw\"incorrect node type\";t+=FF}for(var r=[],s=n.get(\"symbols\"),o=0;o<s;o++)r.push(await gw(mF,e,t)),t+=wF;return i&&(this.group_offset=r[0].get(\"object_header_address\")),this.entries=r,this._contents=n,this}assign_name(e){this.entries.forEach((function(t){let i=t.get(\"link_name_offset\"),n=e.get_object_name(i);t.set(\"link_name\",n)}))}get_links(e){var t={};return this.entries.forEach((function(i){let n=i.get(\"cache_type\"),r=i.get(\"link_name\");if(0==n||1==n)t[r]=i.get(\"object_header_address\");else if(2==n){let n=i.get(\"scratch\"),o=new ArrayBuffer(4),a=new Uint8Array(o);for(var s=0;s<4;s++)a[s]=n.charCodeAt(s);let c=Aw.unpack_from(\"<I\",o,0)[0];t[r]=e.get_object_name(c)}})),t}},cF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await gw(yF,e,t);t+=AF;let n=i.get(\"collection_size\")-AF,r=await e.slice(t,t+n);this.heap_data=r,this._header=i,this._objects=null}get objects(){if(null==this._objects){this._objects=new Map;for(var e=0;e<=this.heap_data.byteLength-_F;){let t=mw(CF,this.heap_data,e);if(0==t.get(\"object_index\"))break;e+=_F;let i=this.heap_data.slice(e,e+t.get(\"object_size\"));this._objects.set(t.get(\"object_index\"),i),e+=Fw(t.get(\"object_size\"))}}return this._objects}},lF=class{constructor(e,t){this.fh=e,this.ready=this.init(t)}async init(e){let t=await gw(xF,this.fh,e);if(e+=bw(xF),ww(\"FRHP\"==t.get(\"signature\")),ww(0==t.get(\"version\")),t.get(\"filter_info_size\")>0)throw\"Filter info size not supported on FractalHeap\";if(t.get(\"btree_address_huge_objects\")!=dF)throw\"Huge objects not implemented in FractalHeap\";t.set(\"btree_address_huge_objects\",null),t.get(\"root_block_address\")==dF&&t.set(\"root_block_address\",null);let i=t.get(\"log2_maximum_heap_size\"),n=this._min_size_nbits(i),r=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"heap_header_adddress\",\"Q\"],[\"block_offset\",`${n}B`]]);this.indirect_block_header=new Map(r),this.indirect_block_header_size=bw(r),2&~t.get(\"flags\")||r.set(\"checksum\",\"I\"),this.direct_block_header=r,this.direct_block_header_size=bw(r);let s=t.get(\"maximum_direct_block_size\");this._managed_object_offset_size=this._min_size_nbits(i);let o=Math.min(s,t.get(\"max_managed_object_size\"));this._managed_object_length_size=this._min_size_integer(o);let a=t.get(\"starting_block_size\"),c=t.get(\"table_width\");if(!(a>0))throw\"Starting block size == 0 not implemented\";let l=Number(Math.floor(Math.log2(s)));ww(1n<<BigInt(l)==s);let h=Number(Math.floor(Math.log2(a)));ww(1n<<BigInt(h)==a),this._max_direct_nrows=l-h+2;let d=Math.floor(Math.log2(c));ww(1<<d==c),this._indirect_nrows_sub=d+h-1,this.header=t,this.nobjects=t.get(\"managed_object_count\")+t.get(\"huge_object_count\")+t.get(\"tiny_object_count\");let u=[],f=t.get(\"root_block_address\"),p=0;if(null!=f&&(p=t.get(\"indirect_current_rows_count\")),p>0)for await(let e of this._iter_indirect_block(this.fh,f,p))u.push(e);else{let e=await this._read_direct_block(this.fh,f,a);u.push(e)}let g=u.reduce(((e,t)=>e+t.byteLength),0),m=new Uint8Array(g),w=0;u.forEach((e=>{m.set(new Uint8Array(e),w),w+=e.byteLength})),this.managed=m.buffer}async _read_direct_block(e,t,i){let n=await e.slice(t,t+i);return ww(\"FHDB\"==mw(this.direct_block_header,n).get(\"signature\")),n}get_data(e){let t=Aw.unpack_from(\"<B\",e,0)[0],i=t>>4&3,n=1;if(0==i){ww(0==t>>6);let i=this._managed_object_offset_size,r=xw(i,e,n);n+=i,i=this._managed_object_length_size;let s=xw(i,e,n);return this.managed.slice(r,r+s)}throw 1==i?\"tiny objectID not supported in FractalHeap\":2==i?\"huge objectID not supported in FractalHeap\":\"unknown objectID type in FractalHeap\"}_min_size_integer(e){return this._min_size_nbits(_w(e))}_min_size_nbits(e){return Math.ceil(e/8)}async*_iter_indirect_block(e,t,i){let n=await gw(this.indirect_block_header,e,t);t+=this.indirect_block_header_size,ww(\"FHIB\"==n.get(\"signature\"));let r=n.get(\"block_offset\").reduce(((e,t,i)=>e+(t<<8*i)),0);n.set(\"block_offset\",r);let[s,o]=this._indirect_info(i),a=[];for(let i=0;i<s;i++){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];if(t+=8,n==dF)break;let r=this._calc_block_size(i);a.push([n,r])}let c=[];for(let i=s;i<s+o;i++){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];if(t+=8,n==dF)break;let r=this._calc_block_size(i),s=this._iblock_nrows_from_block_size(r);c.push([n,s])}for(let[t,i]of a){let n=await this._read_direct_block(e,t,i);yield n}for(let[t,i]of c)for await(let n of this._iter_indirect_block(e,t,i))yield n}_calc_block_size(e){let t=Math.floor(e/this.header.get(\"table_width\"));return 2**Math.max(t-1,0)*this.header.get(\"starting_block_size\")}_iblock_nrows_from_block_size(e){let t=Math.floor(Math.log2(e));return ww(2**t==e),t-this._indirect_nrows_sub}_indirect_info(e){let t,i,n=this.header.get(\"table_width\"),r=e*n,s=this._max_direct_nrows*n;return e<=s?(t=r,i=0):(t=s,i=r-s),[t,i]}_int_format(e){return[\"B\",\"H\",\"I\",\"Q\"][e-1]}},hF=Aw.unpack_from(\"8s\",new Uint8Array([137,72,68,70,13,10,26,10]).buffer)[0],dF=Aw.unpack_from(\"<Q\",new Uint8Array([255,255,255,255,255,255,255,255]).buffer)[0],uF=new Map([[\"format_signature\",\"8s\"],[\"superblock_version\",\"B\"],[\"free_storage_version\",\"B\"],[\"root_group_version\",\"B\"],[\"reserved_0\",\"B\"],[\"shared_header_version\",\"B\"],[\"offset_size\",\"B\"],[\"length_size\",\"B\"],[\"reserved_1\",\"B\"],[\"group_leaf_node_k\",\"H\"],[\"group_internal_node_k\",\"H\"],[\"file_consistency_flags\",\"L\"],[\"base_address_lower\",\"Q\"],[\"free_space_address\",\"Q\"],[\"end_of_file_address\",\"Q\"],[\"driver_information_address\",\"Q\"]]),fF=bw(uF),pF=new Map([[\"format_signature\",\"8s\"],[\"superblock_version\",\"B\"],[\"offset_size\",\"B\"],[\"length_size\",\"B\"],[\"file_consistency_flags\",\"B\"],[\"base_address\",\"Q\"],[\"superblock_extension_address\",\"Q\"],[\"end_of_file_address\",\"Q\"],[\"root_group_address\",\"Q\"],[\"superblock_checksum\",\"I\"]]),gF=bw(pF),mF=new Map([[\"link_name_offset\",\"Q\"],[\"object_header_address\",\"Q\"],[\"cache_type\",\"I\"],[\"reserved\",\"I\"],[\"scratch\",\"16s\"]]),wF=bw(mF),bF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved_0\",\"B\"],[\"symbols\",\"H\"]]),FF=bw(bF),vF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved\",\"3s\"],[\"data_segment_size\",\"Q\"],[\"offset_to_free_list\",\"Q\"],[\"address_of_data_segment\",\"Q\"]]),yF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved\",\"3s\"],[\"collection_size\",\"Q\"]]),AF=bw(yF),CF=new Map([[\"object_index\",\"H\"],[\"reference_count\",\"H\"],[\"reserved\",\"I\"],[\"object_size\",\"Q\"]]),_F=bw(CF),xF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"object_index_size\",\"H\"],[\"filter_info_size\",\"H\"],[\"flags\",\"B\"],[\"max_managed_object_size\",\"I\"],[\"next_huge_object_index\",\"Q\"],[\"btree_address_huge_objects\",\"Q\"],[\"managed_freespace_size\",\"Q\"],[\"freespace_manager_address\",\"Q\"],[\"managed_space_size\",\"Q\"],[\"managed_alloc_size\",\"Q\"],[\"next_directblock_iterator_address\",\"Q\"],[\"managed_object_count\",\"Q\"],[\"huge_objects_total_size\",\"Q\"],[\"huge_object_count\",\"Q\"],[\"tiny_objects_total_size\",\"Q\"],[\"tiny_object_count\",\"Q\"],[\"table_width\",\"H\"],[\"starting_block_size\",\"Q\"],[\"maximum_direct_block_size\",\"Q\"],[\"log2_maximum_heap_size\",\"H\"],[\"indirect_starting_rows_count\",\"H\"],[\"root_block_address\",\"Q\"],[\"indirect_current_rows_count\",\"H\"]]),kF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];if(1==i)var[n,r,s]=await this._parse_v1_objects(e,t);else{if(i!=\"O\".charCodeAt(0))throw\"InvalidHDF5File('unknown Data Object Header')\";var[n,r,s]=await this._parse_v2_objects(e,t)}this.fh=e,this.msgs=n,this.msg_data=r,this.offset=t,this._global_heaps={},this._header=s,this._filter_pipeline=null,this._chunk_params_set=!1,this._chunks=null,this._chunk_dims=null,this._chunk_address=null}get dtype(){let e=this.find_msg_type(ev)[0].get(\"offset_to_message\");return new kw(this.fh,e).dtype}get chunks(){return this._get_chunk_params().then((()=>this._chunks))}get shape(){let e=this.find_msg_type(ZF)[0].get(\"offset_to_message\");return async function(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];var n;if(1==i)ww(1==(n=await gw(TF,e,t)).get(\"version\")),t+=LF;else{if(2!=i)throw\"InvalidHDF5File('unknown dataspace message version')\";ww(2==(n=await gw(zF,e,t)).get(\"version\")),t+=HF}let r=n.get(\"dimensionality\");return(await Aw.unpack_from_async(\"<\"+(2*r).toFixed()+\"I\",e,t)).filter((function(e,t){return t%2==0}))}(this.fh,e)}async get_filter_pipeline(){if(null!=this._filter_pipeline)return this._filter_pipeline;let e=this.find_msg_type(rv);if(!e.length)return this._filter_pipeline=null,this._filter_pipeline;var t=e[0].get(\"offset_to_message\");let[i,n]=await Aw.unpack_from_async(\"<BB\",this.fh,t);t+=Aw.calcsize(\"<BB\");var r=[];if(1==i){await Aw.unpack_from_async(\"<HI\",this.fh,t),t+=Aw.calcsize(\"<HI\");for(var s=0;s<n;s++){let e=await gw(YF,this.fh,t);t+=XF;let i=Fw(e.get(\"name_length\"),8),n=\"<\"+i.toFixed()+\"s\",s=(await Aw.unpack_from_async(n,this.fh,t))[0];e.set(\"filter_name\",s),t+=i,n=\"<\"+e.get(\"client_data_values\").toFixed()+\"I\";let o=await Aw.unpack_from_async(n,this.fh,t);e.set(\"client_data\",o),t+=4*e.get(\"client_data_values\"),e.get(\"client_data_values\")%2&&(t+=4),r.push(e)}}else{if(2!=i)throw`version ${i} is not supported`;for(let e=0;e<n;e++){let e=new Map,i=this.fh,n=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2,e.set(\"filter_id\",n);let s=0;n>255&&(s=(await Aw.unpack_from_async(\"<H\",i,t))[0],t+=2);let o=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2;let a=(1&o)>0;e.set(\"optional\",a);let c,l=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2,s>0&&(c=(await Aw.unpack_from_async(`${s}s`,i,t))[0],t+=s),e.set(\"name\",c);let h=await Aw.unpack_from_async(`<${l}i`,i,t);t+=4*l,e.set(\"client_data_values\",h),r.push(e)}}return this._filter_pipeline=r,this._filter_pipeline}find_msg_type(e){return this.msgs.filter((function(t){return t.get(\"type\")==e}))}async get_attributes(){let e={},t=this.find_msg_type(sv);for(let i of t){let t=i.get(\"offset_to_message\"),[n,r]=await this.unpack_attribute(t);e[n]=r}return e}async get_fillvalue(){var e,t=this.find_msg_type(tv)[0].get(\"offset_to_message\");let i=(await Aw.unpack_from_async(\"<B\",this.fh,t))[0];var n,r,s;if(1==i||2==i)n=await gw(WF,this.fh,t),t+=GF,e=n.get(\"fillvalue_defined\");else{if(3!=i)throw'InvalidHDF5File(\"Unknown fillvalue msg version: \"'+String(i);n=await gw($F,this.fh,t),t+=KF,e=32&n.get(\"flags\")}if(e?(r=(await Aw.unpack_from_async(\"<I\",this.fh,t))[0],t+=4):r=0,r){let[e,i,n]=yw(await this.dtype);s=new Cw(await this.fh.slice(t,t+n))[e](t,!i,n)}else s=0;return s}async unpack_attribute(e){let t=(await Aw.unpack_from_async(\"<B\",this.fh,e))[0];var i,n;if(1==t)ww(1==(i=await gw(EF,this.fh,e)).get(\"version\")),e+=NF,n=8;else{if(3!=t)throw\"unsupported attribute message version: \"+t;ww(3==(i=await gw(BF,this.fh,e)).get(\"version\")),e+=MF,n=1}let r=i.get(\"name_size\"),s=(await Aw.unpack_from_async(\"<\"+r.toFixed()+\"s\",this.fh,e))[0];var o;s=s.replace(/\\x00$/,\"\"),e+=Fw(r,n);try{o=await new kw(this.fh,e).dtype}catch(e){return console.warn(\"Attribute \"+s+\" type not implemented, set to null.\"),[s,null]}e+=Fw(i.get(\"datatype_size\"),n);let a=await this.determine_data_shape(this.fh,e),c=a.reduce((function(e,t){return e*t}),1);if(e+=Fw(i.get(\"dataspace_size\"),n),5===o.datatype_class)l=await this.fh.slice(e,e+o.size);else{var l=await this._attr_value(o,this.fh,c,e);0==a.length&&(l=l[0])}return[s,l]}async determine_data_shape(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];var n;if(1==i)ww(1==(n=await gw(TF,e,t)).get(\"version\")),t+=LF;else{if(2!=i)throw\"unknown dataspace message version\";ww(2==(n=await gw(zF,e,t)).get(\"version\")),t+=HF}let r=n.get(\"dimensionality\");return await Aw.unpack_from_async(\"<\"+r.toFixed()+\"Q\",e,t)}async _attr_value(e,t,i,n){var r=new Array(i);if(e instanceof Array){let l=e[0];for(var s=0;s<i;s++)if(\"VLEN_STRING\"==l){let i=e[2];var[o,a]=await this._vlen_size_and_data(t,n);const c=new TextDecoder(0==i?\"ascii\":\"utf-8\");r[s]=c.decode(a),n+=16}else if(\"REFERENCE\"==l){var c=await Aw.unpack_from_async(\"<Q\",t,n);r[s]=c,n+=8}else{if(\"VLEN_SEQUENCE\"!=l)throw\"NotImplementedError\";{let i=e[1];var[o,a]=this._vlen_size_and_data(t,n);r[s]=this._attr_value(i,a,o,0),n+=16}}}else{let[o,a,c]=yw(e);const l=await t.slice(n,n+i*c);let h=new Cw(l,0),d=0;for(s=0;s<i;s++)r[s]=h[o](d,!a,c),d+=c}return r}async _vlen_size_and_data(e,t){let i=(await Aw.unpack_from_async(\"<I\",e,t))[0],n=await gw(SF,e,t+4),r=n.get(\"collection_address\");var s;return ww(n.get(\"collection_address\")<Number.MAX_SAFE_INTEGER),r in this._global_heaps||(s=new cF(this.fh,r),await s.ready,this._global_heaps[r]=s),[i,(s=this._global_heaps[r]).objects.get(n.get(\"object_index\"))]}async _parse_v1_objects(e,t){let i=await gw(RF,e,t);ww(1==i.get(\"version\"));let n=i.get(\"total_header_messages\");for(var r=i.get(\"object_header_size\"),s=t+bw(RF),o=await e.slice(s,s+r),a=[[s,r]],c=0,l=0,h=new Array(n),d=0;d<n;d++){l>=r&&([s,r]=a[++c],l=0);let t=await gw(PF,e,s+l),i=s+l+OF;if(t.set(\"offset_to_message\",i),t.get(\"type\")==ov){var[u,f]=await Aw.unpack_from_async(\"<QQ\",e,i);a.push([u,f])}l+=OF+t.get(\"size\"),h[d]=t}return[h,o,i]}async _parse_v2_objects(e,t){var[i,n,r]=await this._parse_v2_header(e,t);t=r;for(var s=[],o=i.get(\"size_of_chunk_0\"),a=e.slice(t,t+=o),c=[[r,o]],l=0,h=0;;){if(h>=o-qF){let e=c[++l];if(null==e)break;[r,o]=e,h=0}let t=await gw(UF,e,r+h),i=r+h+qF+n;if(t.set(\"offset_to_message\",i),t.get(\"type\")==ov){var[d,u]=await Aw.unpack_from_async(\"<QQ\",e,i);c.push([d+4,u-4])}h+=qF+t.get(\"size\")+n,s.push(t)}return[s,a,i]}async _parse_v2_header(e,t){let i=await gw(DF,e,t);var n;if(t+=bw(DF),ww(2==i.get(\"version\")),n=4&i.get(\"flags\")?2:0,ww(!(16&i.get(\"flags\"))),32&i.get(\"flags\")){let n=await Aw.unpack_from_async(\"<4I\",e,t);t+=16,i.set(\"access_time\",n[0]),i.set(\"modification_time\",n[1]),i.set(\"change_time\",n[2]),i.set(\"birth_time\",n[3])}let r=[\"<B\",\"<H\",\"<I\",\"<Q\"][3&i.get(\"flags\")];return i.set(\"size_of_chunk_0\",(await Aw.unpack_from_async(r,e,t))[0]),[i,n,t+=Aw.calcsize(r)]}async find_link(e){if(this._links){for(link of this._links)if(e===link[0])return link}else{const t=[];for await(const i of this.iter_links()){if(e===i[0])return i;t.push(i)}this._links=t}}async get_links(){const e=[];for await(const t of this.iter_links())e.push(t);return Object.fromEntries(e)}async*iter_links(){for(let e of this.msgs)e.get(\"type\")==av?yield*this._iter_links_from_symbol_tables(e):e.get(\"type\")==iv?yield this._get_link_from_link_msg(e):e.get(\"type\")==JF&&(yield*this._iter_link_from_link_info_msg(e))}async*_iter_links_from_symbol_tables(e){ww(16==e.get(\"size\"));let t=await gw(QF,this.fh,e.get(\"offset_to_message\"));yield*this._iter_links_btree_v1(t.get(\"btree_address\"),t.get(\"heap_address\"))}async*_iter_links_btree_v1(e,t){let i=new eF(this.fh,e);await i.ready;let n=new oF(this.fh,t);await n.ready;for(let e of 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t=e.get(\"offset_to_message\"),i=await this._decode_link_info_msg(this.fh,t),n=i.get(\"heap_address\"),r=i.get(\"name_btree_address\"),s=i.get(\"order_btree_address\");null!=r&&(yield*this._iter_links_btree_v2(r,s,n))}async*_iter_links_btree_v2(e,t,i){let n,r=new lF(this.fh,i);await r.ready;const s=null!=t;s?(n=new rF(this.fh,t),await n.ready):(n=new nF(this.fh,e),await n.ready);let o=new Map;for(let e of n.iter_records()){let t=r.get_data(e.get(\"heapid\")),[i,n]=await this._decode_link_msg(t,0);const a=s?i:n[0];o.set(a,n)}let a=Array.from(o.keys()).sort();for(let e of a)yield o.get(e)}async _decode_link_info_msg(e,t){let[i,n]=await Aw.unpack_from_async(\"<BB\",e,t);ww(0==i),t+=2,(1&n)>0&&(t+=8);let r=(2&n)>0?jF:VF,s=await gw(r,e,t),o=new Map;for(let[e,t]of s.entries())o.set(e,t==IF?null:t);return o}get is_dataset(){return this.find_msg_type(ZF).length>0}async get_data(){let e=this.find_msg_type(nv)[0].get(\"offset_to_message\");var[t,i,n,r]=await 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wv(this.pytor_keys),n=i.get_rd_bins(),r=i.get_snp_bins();this.available_bins=[...new Set(n,r)],this.available_bins.includes(e)||(e=this.available_bins.at(-1));const s=await t.get(\"rd_chromosomes\");await s.dtype;let o=await s.value,a=await this.rd_stat(e);var c=[],l=[],h=[],d=[],u=[],f=[];for(let t of o){let i=new gv(t,e);var p=i.signals.raw_RD;let n=await this.get_chr_signal(t,e,p,a);c=c.concat(n);var g=i.signals.gc_RD;let r=await this.get_chr_signal(t,e,g,a);l=l.concat(r);let s=i.signals.gc_partition,o=await this.get_chr_signal(t,e,s,a);h=h.concat(o);let m=await this.rd_call_combined(t,e,a,i);d=d.concat(m);let w=i.signals.baf_i1,b=await this.get_baf_signals_v2(t,e,w);u=u.concat(b[0]),f=f.concat(b[1])}this.callers=[],0!=d.length&&this.callers.push(\"ReadDepth\"),0!=d.length&&this.callers.push(\"2D\");var m={},w={RD_Raw:c,RD_Raw_gc_coor:l,ReadDepth:h,\"2D\":d,BAF1:u,BAF2:f};return m[e]=w,m}decode_segments(e){let t=[],i=[];for(let n of e)4294967295==n?(t.push(i),i=[]):i.push(n);return t}async rd_call_combined(e,t,i,n){let r,s=[],o=n.signals.Mosaic_segments;if(this.pytor_keys.includes(o)){const e=await this.h5_obj.get(o);let t=await e.value;r=this.decode_segments(t)}let a=n.signals.Mosaic_calls;if(this.pytor_keys.includes(a)){const n=await this.h5_obj.get(a);let o=await n.to_array();r.forEach(((n,r)=>{n.forEach(((n,a)=>{s.push({chr:e,start:n*t,end:(n+1)*t,value:o[0][r]/i[4]*2})}))}))}return s}async rd_stat(e){let t,i=`rd_stat_${e}_auto`;if(this.pytor_keys.includes(i)){const e=await this.h5_obj.get(i);t=await e.value}return t}async get_chr_signal(e,t,i,n){let r=[];if(this.pytor_keys.includes(i)){const s=await this.h5_obj.get(i);(await s.value).forEach(((i,s)=>{r.push({chr:e,start:s*t,end:(s+1)*t,value:i/n[4]*2})}))}return r}async get_baf_signals(e,t,i,n=-1){let r=[],s=[];if(this.pytor_keys.includes(i)){let o=await this.h5_obj.get(i);(await o.to_array()).forEach(((i,o)=>{let a=Math.max(...i);const c=i.indexOf(a);let l=Math.max(c/200,1-c/200);r.push({chr:e,start:o*t,end:(o+1)*t,value:n*l}),.5!=l&&s.push({chr:e,start:o*t,end:(o+1)*t,value:n*(1-l)})}))}return[r,s]}async get_baf_signals_v2(e,t,i,n=-1){let r=[],s=[];if(this.pytor_keys.includes(i)){let o=await this.h5_obj.get(i);(await o.to_array()).forEach(((i,o)=>{isNaN(i)||(r.push({chr:e,start:o*t,end:(o+1)*t,value:n*(.5-i)}),.5!=i&&s.push({chr:e,start:o*t,end:(o+1)*t,value:n*(.5+i)}))}))}return[r,s]}}class wv{constructor(e){this.signals=e}get_rd_bins(){let e=[];this.signals.forEach((t=>{let i=t.match(/^his_rd_p_(.*)_(\\d+)$/);i&&e.push({chr:i[1],bin_size:i[2]})}));return[...new Set(e.map((e=>Number(e.bin_size))))]}get_snp_bins(){let e=[];this.signals.forEach((t=>{let i=t.match(/^snp_likelihood_(.*)_(\\d+)_mask$/);i&&e.push({chr:i[1],bin_size:i[2]})}));return[...new Set(e.map((e=>Number(e.bin_size))))]}}function bv(e){let t=function(e){if(e.length<4)return e;let t,i,n,r,s,o;return t=e.slice().sort(((e,t)=>e-t)),t.length/4%1==0?(i=.5*(t[t.length/4]+t[t.length/4+1]),n=.5*(t[t.length*(3/4)]+t[t.length*(3/4)+1])):(i=t[Math.floor(t.length/4+1)],n=t[Math.ceil(t.length*(3/4)+1)]),r=n-i,s=n+1.5*r,o=i-1.5*r,t.filter((e=>e>=o&&e<=s))}(e);const i=t.length,n=t.reduce(((e,t)=>e+t))/i,r=Math.sqrt(t.map((e=>Math.pow(e-n,2))).reduce(((e,t)=>e+t))/i);return[n,r]}var Fv={range_function:function(e,t,i){return Array(Math.ceil((t-e)/i)).fill(e).map(((e,t)=>e+t*i))},getDistParams:bv,linspace:function(e,t,i){if(void 0===i&&(i=Math.max(Math.round(t-e)+1,1)),i<2)return 1===i?[e]:[];var n=Array(i);for(let r=--i;r>=0;r--)n[r]=(r*t+(i-r)*e)/i;return n},GetFit:class{constructor(e){this.allBins=e}getValues(){return Object.values(this.allBins).reduce(((e,t)=>e.concat(t.filter((e=>e.binScore>0)).map((e=>e.binScore)))),[])}getMean(e){return e.reduce((function(e,t){return e+t}))/e.length}fit_data(){return bv(this.getValues())}histogram(e,t){const i=t[1]-t[0],n=[];e.forEach(((e,r)=>{t.forEach(((t,r)=>{if(n[t]||(n[t]={count:0}),t<=e&&e<t+i)return n[t].count++,!1}))}));const r=[];return n.forEach(((e,t)=>{r.push(e.count)})),r}}};function vv(e,t){return isNaN(e)||isNaN(t)||t<=0?NaN:0===e?.5:.5+.5*(yv(.5*t,.5,1)-yv(.5*t,.5,t/(t+e*e)))*Math.sign(e)}function yv(e,t,i){if(0==i)return 0;if(1==i)return 1;{let n=xv(e+t)-xv(e)-xv(t)+e*Math.log(i)+t*Math.log(1-i);return i<(e+1)/(e+t+2)?Math.exp(n)*Av(e,t,i)/e:1-Math.exp(n)*Av(t,e,1-i)/t}}function Av(e,t,i,n=1e3){let r=1,s=1,o=1,a=e+t,c=e+1,l=e-1,h=1-a*i/c;for(let d=0;d<=n;d++){let n=parseFloat(d+1),u=n+n,f=n*(t-n)*i/((l+u)*(e+u)),p=r+f*s,g=h+f*o;f=-(e+n)*(a+n)*i/((c+u)*(e+u));let m=g+f*h,w=r;if(s=p/m,o=g/m,r=(p+f*r)/m,h=1,Math.abs(r-w)<3e-7*Math.abs(r))return r}}function Cv(e){if(0==e||1==e)return 1;return e*Cv(e-1)}function _v(e){let t;var i=[75122.633153,80916.6278952,36308.2951477,8687.24529705,1168.92649479,83.8676043424,2.50662827511],n=0,r=1;if(0==e)t=1e99;else if(e%1==0)t=Cv(e-1);else{for(let t=0;t<i.length;t++)n+=i[t]*Math.pow(e,t),r*=e+t;t=n*Math.pow(e+5.5,e+.5)*Math.exp(-(e+5.5))/r}return t}function xv(e){return Math.log(_v(e))}var kv={TdistributionCDF:vv,gamma:_v,t_test_1_sample:function(e,t,i,n){0==i&&(i=1);var r=(e-t)/i*Math.sqrt(n);return 1-vv(Math.abs(r),n-1)},t_test_2_samples:function(e,t,i,n,r,s){0==t&&(t=1),0==r&&(r=1);var o=(e-n)/Math.sqrt(t**2/i+r**2/s),a=(t**2/i+r**2/s)**2*(i-1)*(s-1)/(t**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-vv(Math.abs(o),parseInt(a+.5))}};function Iv(e){return e.reduce((function(e,t){return e>t?e:t}))}function Sv(e,t,i,n){return t*Math.exp(-1*(e-i)**2/(2*n**2))/Math.sqrt(2*Math.PI)/n}function Ev(e,t,i,n){return Math.exp(-1*(e-i)**2/(t**2+n**2))}function Nv(e,t){let i;try{i=e.reduce(((e,i,n)=>e+Math.min(i,t[n])))}catch{return console.log(\"Failed to find likelihood overlap: \",e,t),0}return i}function Bv(e,t,i,n){return 0==t&&0==n?{nl:.5*(e+i),ne:0}:{nl:(e*n*n+i*t*t)/(t*t+n*n),ne:Math.sqrt(t*t*n*n/(t*t+n*n))}}function Mv(e,t){let i=parseInt(t*(e.length-1)),n=t*(e.length-1)-i;return i<e.length-1?e[i]*(1-n)+e[i+1]*n:e[i]}function Rv(e){const t=e.length,i=Math.max(...e);let n=e.indexOf(i);n>Math.floor(t/2)&&(n=t-1-n);const r=(t/2-n)/(t+1),s=Math.floor((t/2+n)/2),o=t-1-s;let a=e.slice(s,o+1).reduce(((e,t)=>e+t),0)/e.reduce(((e,t)=>e+t),0);return n===Math.floor(t/2)&&(a=1),{mean:r,p:a}}var Dv=class{constructor(e,t){this.wigFeatures=e,this.binSize=t}get_fit(){var e=new Fv.GetFit(this.wigFeatures),[t,i]=e.fit_data();return{globalMean:t,globalStd:i}}async call_2d(e=null,t=null,i=\"both\",n=.1,r=0,s=10,o=0){let a=this.get_fit();this.globalMean=a.globalMean,this.globalStd=a.globalStd;let c=null==e?.05*this.binSize/3e9:e,l=null==t?parseInt(this.binSize/1e4):t,h=[],d=[],u=[],f=[],p=[],g=[];for(const[e,t]of Object.entries(this.wigFeatures)){let e=[],i=[],s=[];t.forEach(((t,n)=>{t.hets_count>4&&t.dp_count>l&&(e.push([n]),i.push(t.binScore),s.push(t.likelihood_score),delete t.likelihood_score)}));let o=[];for(let e=1;e<i.length;e++)o.push(Math.abs(i[e]-i[e-1]));let a=[0];for(let e=1;e<o.length;e++)a.push(Math.min(o[e-1],o[e]));a.push(0);let g=i.map(((e,t)=>Math.sqrt(Math.sqrt(e)**2+this.globalStd**2+Math.pow(a[t]/2,2)))),m=[];for(let t=0;t<e.length-1;t++){let n=0;try{n=Nv(s[t],s[t+1])}catch{console.log(\"Overlap failed: \",t,s[t],e[t+1],s[t+1])}let r=Ev(i[t],g[t],i[t+1],g[t+1]);m.push(r*n)}for(;m.length>0;){m=m.filter((e=>\"number\"==typeof e));let t=Iv(m);if(isNaN(t)&&console.log(\"NaN value\",m),t<c)break;let n,r,o=m.indexOf(t),a=Bv(i[o],g[o],i[o+1],g[o+1]);try{n=s[o].map(((e,t)=>e*s[o+1][t])),r=n.reduce(((e,t)=>e+t))}catch{console.log(s),console.log(\"max_overlap:\",t,o,m.length),console.log(\"likelihood: \",o,s[o],s[o+1]),console.log(\"nlh: \",r)}if(i[o]=a.nl,g[o]=a.ne,s[o]=n.map((function(e){return e/r})),e[o].push(...e[o+1]),i.splice(o+1,1),g.splice(o+1,1),e.splice(o+1,1),s.splice(o+1,1),m.splice(o,1),o<m.length){let e=Ev(i[o],g[o],i[o+1],g[o+1])*Nv(s[o],s[o+1]);m[o]=e}if(o>0){let e=Ev(i[o-1],g[o-1],i[o],g[o])*Nv(s[o-1],s[o]);m[o-1]=e}}let w=-1;for(;;){m=[];for(let t=0;t<i.length;t++)for(let r=t;r<i.length;r++)e[r][0]-e[t].at(-1)<n*(e[t].length+e[r].length)&&m.push(Ev(i[t],g[t],i[r],g[r])*Nv(s[t],s[r]));if(0==m.length)break;let t=Iv(m);if(t<c)break;let r=0,o=1;for(;r<e.length-1;){let a=Ev(i[r],g[r],i[o],g[o])*Nv(s[r],s[o]);if(e[o][0]-e[r].at(-1)<n*(e[r].length+e[o].length)&&a==t){let t=Bv(i[r],g[r],i[r+1],g[r+1]);i[r]=t.nl,g[r]=t.ne;let n=s[r].map(((e,t)=>e*s[r+1][t])),a=n.reduce(((e,t)=>e+t));s[r]=n.map((function(e){return e/a})),e[r].push(...e[r+1]),e[r]=e[r].sort(((e,t)=>e-t)),i.splice(o,1),g.splice(o,1),e.splice(o,1),s.splice(o,1),o>=e.length&&(r+=1,o=r+1)}else o+=1,o>=e.length&&(r+=1,o=r+1)}if(w==e.length)break;w=e.length}e.forEach(((e,n)=>{let o=Rv(s[n]);e.length>1&&(e.forEach(((e,s)=>{d.push(t[e]),o.mean<=r&&h.push(t[e]),t[e].segment_score=i[n]})),u.push(i[n]),f.push(g[n]),p.push(s[n]))}))}let m=parseInt(1e3*(1-o));0==m&&(m=1);let w=Fv.linspace(o,1,m),b={},F={};for(let e=10;e>-1;e--)for(let t=0;t<e/2+1;t++){let n,r,s=e-t,o=w.map(((t,i)=>1-t+t*e/2)),a=e/2;e>0?(n=.5-t/(t+s),r=w.map(((e,i)=>.5-(1-e+e*t)/(2-2*e+(t+s)*e)))):(n=0,r=w.map(((e,t)=>0*e)));for(let i=0;i<u.length;i++){let c=Sv(a*this.globalMean,1,u[i],f[i])*Mv(p[i],.5+n);i in F?F[i].push([e,t,s,c,1]):F[i]=[e,t,s,c,1];let l=0,h=0,d=0;o.forEach(((e,t)=>{if(!isNaN(r[t])){let n=Sv(e*this.globalMean,1,u[i],f[i])*Mv(p[i],.5+r[t]);l+=n,n>h&&(h=n,d=w[t])}})),i in b?b[i].push([e,t,s,l/w.length,d]):b[i]=[e,t,s,l/w.length,d]}for(let e=0;e<u.length;e++)if(\"germline\"==i)b[e].sort(((e,t)=>e[3]-t[3]));else if(b[e].sort(((e,t)=>e[3]-t[3])),\"both\"==i&&(F[e].sort(((e,t)=>e[3]-t[3])),F[e][0][3]>b[e][0][3])){let t=b[e].filter((t=>t[0]!=F[e][0][0]&&t[1]<=F[e][0][1]));b[e]=[F[e][0]].push(...t)}for(let e=0;e<u.length;e++)b[e][0][0],b[e][0][0],u[e],this.globalMean,kv.t_test_1_sample(this.globalMean,u[e],f[e],g[e])}return{binScore:this.formatDataStructure(this.wigFeatures,\"binScore\",this.globalMean),segment_score:this.formatDataStructure(this.wigFeatures,\"segment_score\",this.globalMean)}}formatDataStructure(e,t,i=1){const n=[];for(const[r,s]of Object.entries(e))s.forEach((e=>{var r={...e};1!=i&&(r.value=e[t]/i*2),n.push(r)}));return n}formatDataStructure_BAF(e,t=-1){const i=[],n=[];for(const[r,s]of Object.entries(this.wigFeatures))s.forEach((r=>{var s={...r},o={...r};let a=r[e];.5!=a&&(o.value=t*(1-a),n.push(o)),s.value=t*a,i.push(s)}));return[i,n]}};const Tv=2871e6;function Lv(e){for(var t=1,i=1,n=1*e,r=1;r<50;r++)t*=r,n+=(i*=-1)*Math.pow(e,2*r+1)/(t*(2*r+1));return 2*n/Math.sqrt(3.14159265358979)}function zv(e,t,i,n,r){var s=new Ov(i.slice(n,r));return 0==s.std&&(s.std=t>0?t*s.mean/e:1),Uv(e,s.mean,s.std,r-n)/(r-n)}function Hv(e,t,i,n,r){var s=new Ov(i.slice(n,r));if(s.mean<e){var o=(s.max-s.mean)/(t*Math.sqrt(2));return Math.pow(.5*(1+Lv(o)),r-n)}o=(s.min-s.mean)/(t*Math.sqrt(2));return Math.pow(.5*(1-Lv(o)),r-n)}function Pv(e,t,i,n,r,s,o=1e3){for(var a=zv(e,t,i,n,r),c=0,l=!1;a>s&!l&c<o;){l=!0,c+=1;var[h,d,u,f]=[1e10,1e10,1e10,1e10];if(n>0&&(h=zv(e,t,i,n-1,r)),r-n>2)var d=zv(e,t,i,n+1,r),u=zv(e,t,i,n,r-1);if(r<i.length)var f=zv(e,t,i,n,r+1);Math.min[f]<a&&(l=!1,h==Math.min[f]&&(n-=1,a=h),elif(d==Math.min[f]),n+=1,a=d,elif(u==Math.min[f]),r-=1,a=u,elif(f==Math.min[f]),r+=1,a=f)}return a<=s?r:0}class Ov{constructor(e){this.data=e,this.mean=e.reduce(((e,t)=>e+t))/e.length,this.std=Math.sqrt(e.reduce(((e,t)=>(t-this.mean)**2))/e.length)}}function Uv(e,t,i,n){0==i&&(i=1);var r=(e-t)/i*Math.sqrt(n);return 1-kv.TdistributionCDF(Math.abs(r),n-1)}function qv(e,t,i,n,r,s){0==t&&(t=1),0==r&&(r=1);var o=(e-n)/Math.sqrt(t**2/i+r**2/s),a=(t**2/i+r**2/s)**2*(i-1)*(s-1)/(t**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-kv.TdistributionCDF(Math.abs(o),parseInt(a+.5))}var Qv=class{constructor(e,t,i){this.rd=e,this.mean=t,this.std=i,this.bin_bands=[2,3,4,5,6,7,8,10,12,14,16,20,24,28,32,40,48,56,64,80,96,112,128]}get_rd_signal_bandwidth(e){var t=[];return e.forEach(((e,i)=>{var n=0;n=e>this.mean/4?this.mean/(this.std**2*e):4/this.std**2,t.push(n)})),t}meanShiftCaller(e,t=3){var i={};return Object.entries(this.rd).forEach((([e,n])=>{var r=new Array(n.length).fill(!1),s=new Array(n.length);for(let e=0;e<n.length;e++)r[e]||(s[e]=n[e]);this.bin_bands.forEach(((e,i)=>{var o=r.map(((e,t)=>!e)),a=[];Object.entries(n).forEach((([e,t])=>{a.push(t.binScore)}));var c=[0],l=0;for(let e=0;e<r.length;e++)r[e]?l>0&&(c.push(c[c.length-1]+l-1),l=0):l+=1;c.shift();for(let i=0;i<t;i++){var h=this.get_rd_signal_bandwidth(a),d=new Array(a.length).fill(0);for(let t=0;t<a.length;t++)for(let i=t-3*e;i<=t+3*e+1;i++)if(!(i<0||i>=a.length||Math.abs(t-i)>=a.length)){var u=(i-t)*Math.exp(-.5*(i-t)**2/e**2)*Math.exp(-.5*(a[t]-a[i])**2*h[t]);d[t]+=u}for(var f=new Array,p=0;p<d.length-1;p++)d[p]<0&d[p+1]>=0&&f.push(p);f.push(d.length-1),f=f.concat(c).sort(((e,t)=>e-t)),f=Array.from(new Set(f));var g=0;for(p=0;p<f.length;p++){var m=a.slice(g,f[p]+1),w=m.reduce(((e,t)=>e+t))/m.length;a.fill(w,g,f[p]+1),g=f[p]+1}}p=0;for(var b=0;p<s.length;p++)o[p]&&(s[p]=a[b],b++);for(f=new Array,p=0;p<s.length-1;p++){Math.abs(s[p+1]-s[p])>.01&&f.push(p+1)}f.unshift(0),f.push(s.length),r=new Array(this.rd.length).fill(!1);for(p=1;p<f.length;p++){var F=[f[p-1],f[p]],v=[f[p-1],f[p-1]];if(!(p>1))continue;v[0]=f[p-2];var y=[f[p],f[p]];if(!(p<f.length-1))continue;y[1]=f[p+1];var A=F[1]-F[0],C=v[1]-v[0],_=y[1]-y[0];if(A<=1)continue;var x=new Ov(s.slice(F[0],F[1]));if(_<=15||C<=15||A<=15){var k=1.8*Math.sqrt(s[v[0]]/this.mean)*this.std;if(Math.abs(s[v[0]]-s[F[0]])<k)continue;if(k=1.8*Math.sqrt(s[y[0]]/this.mean)*this.std,Math.abs(s[y[0]]-s[F[0]])<k)continue}else{var I=s.slice(v[0],v[1]),S=new Ov(I),E=s.slice(y[0],y[1]),N=new Ov(E);if(qv(x.mean,x.std,x.data.length,S.mean,S.std,S.data.length)>.01/Tv*bin_size*(A+C))continue;if(qv(x.mean,x.std,x.data.length,N.mean,N.std,N.data.length)>.01/Tv*bin_size*(A+_))continue}if(Uv(this.mean,x.mean,x.std,x.data.length)>.05)continue;let e=a.slice(F[0],F[1]);var B=new Ov(e);r.fill(!0,F[0],F[1]),s.fill(B.mean,F[0],F[1])}})),i[e]=s})),i}call_mean_shift(e=3){for(var t=new Array(this.rd.length).fill(!1),i=new Array(this.rd.length),n=0;n<this.rd.length;n++)t[n]||(i[n]=this.rd[n]);return this.bin_bands.forEach(((n,r)=>{var s=t.map(((e,t)=>!e)),o=[];s.forEach(((e,t)=>{e&&o.push(this.rd[t])}));for(var a=[0],c=0,l=0;l<t.length;l++)t[l]?c>0&&(a.push(a[a.length-1]+c-1),c=0):c+=1;a.shift();for(var h=0;h<e;h++){var d=this.get_rd_signal_bandwidth(o),u=new Array(o.length).fill(0);for(l=0;l<o.length;l++)for(var f=l-3*n;f<=l+3*n+1;f++)if(!(f<0||f>=o.length||Math.abs(l-f)>=o.length)){var p=(f-l)*Math.exp(-.5*(f-l)**2/n**2)*Math.exp(-.5*(o[l]-o[f])**2*d[l]);u[l]+=p}var g=new Array;for(l=0;l<u.length-1;l++)u[l]<0&u[l+1]>=0&&g.push(l);g.push(u.length-1),g=g.concat(a).sort(((e,t)=>e-t)),g=Array.from(new Set(g));var m=0;for(l=0;l<g.length;l++){var w=o.slice(m,g[l]+1),b=w.reduce(((e,t)=>e+t))/w.length;o.fill(b,m,g[l]+1),m=g[l]+1}}for(l=0,f=0;l<i.length;l++)s[l]&&(i[l]=o[f],f++);for(g=new Array,l=0;l<i.length-1;l++){Math.abs(i[l+1]-i[l])>.01&&g.push(l+1)}g.unshift(0),g.push(i.length),t=new Array(this.rd.length).fill(!1);for(l=1;l<g.length;l++){var F=[g[l-1],g[l]],v=[g[l-1],g[l-1]];if(l>1){v[0]=g[l-2];var y=[g[l],g[l]];if(l<g.length-1){y[1]=g[l+1];var A=F[1]-F[0],C=v[1]-v[0],_=y[1]-y[0];if(!(A<=1)){var x=new Ov(i.slice(F[0],F[1]));if(_<=15||C<=15||A<=15){var k=1.8*Math.sqrt(i[v[0]]/this.mean)*this.std;if(Math.abs(i[v[0]]-i[F[0]])<k)continue;if(k=1.8*Math.sqrt(i[y[0]]/this.mean)*this.std,Math.abs(i[y[0]]-i[F[0]])<k)continue}else{var I=i.slice(v[0],v[1]),S=new Ov(I),E=i.slice(y[0],y[1]),N=new Ov(E);if(qv(x.mean,x.std,x.data.length,S.mean,S.std,S.data.length)>3.483106931382794e-9*(A+C))continue;if(qv(x.mean,x.std,x.data.length,N.mean,N.std,N.data.length)>3.483106931382794e-9*(A+_))continue}if(!(Uv(this.mean,x.mean,x.std,x.data.length)>.05)){var B=new Ov(this.rd.slice(F[0],F[1]));t.fill(!0,F[0],F[1]),i.fill(B.mean,F[0],F[1])}}}}}})),i}cnv_calling(e=1e5){var t=.25*this.mean,i=this.mean-t,n=this.mean+t,r=2971e6,s=this.meanShiftCaller(e),o={},a=[];return Object.entries(s).forEach((([c,l])=>{for(var h=!1;!h;){h=!0;var d=new Array(1).fill(0);for(let e=0;e<l.length-1;e++){Math.abs(l[e+1]-l[e])>.01&&d.push(e+1)}d.push(l.length);for(let e=0;e<d.length-2;e++){var u=Math.abs(l[d[e]]-l[d[e+1]]);if(u<t){var f=u+1,p=u+1;if(e>0&&(f=Math.abs(l[d[e]]-l[d[e-1]])),e<d.length-3&&(p=Math.abs(s[d[e+1]]-l[d[e+2]])),u<f&&u<p){h=!1;var g=new Ov(l.slice(d[e],d[e+2]));l.fill(g.mean,d[e],d[e+2]),d.splice(e+1,e+1)}}}}var m=[];Object.entries(this.rd[c]).forEach((([e,t])=>{m.push(t.binScore)}));for(var w,b=new Array(l.length).fill(\"\"),F=0,v=.05*e/r;F<l.length;){for(var y=F,A=F;F<l.length&l[F]<i;)F+=1;if((_=F)>A+1){var C=Pv(this.mean,this.std,m,A,_,v);if(C){var _=C;b.fill(\"D\",A,_)}}for(A=F;F<l.length&l[F]>n;)F+=1;(_=F)>A+1&&(C=Pv(this.mean,this.std,m,A,_,v))&&(_=C,b.fill(\"A\",A,_)),F==y&&(F+=1)}for(F=0;F<l.length;){for(;F<l.length&\"\"!=b[F];)F+=1;for(A=F;F<l.length&l[F]<i;)F+=1;(_=F)>A+1&&(Hv(this.mean,this.std,m,A,_)<1682935038707506e-26&&b.fill([\"d\"]*(_-A),A,_),F-=1),F+=1}(F=0)<l.length&&(w=b[F]),A=0;for(var x=[...m];F<l.length;){for(;b[F]==w&&!((F+=1)>=b.length););if(F>A){var k=new Ov(x.slice(A,F));x.fill(k.mean,A,F)}F<l.length&&(w=b[F]),A=F}for(o[c]=x,F=0;F<l.length;){if(\"\"==(w=b[F])){F+=1;continue}for(A=F;F<l.length&w==b[F];)F+=1;let t,i=new Ov(x.slice(A,F)).mean/this.mean;t=\"D\"==w?\"deletion\":\"duplication\";let n={chr:c,start:e*A+1,end:e*F,size:e*(F-A+1),value:2*i,event_type:t};a.push(n)}})),[o,a]}};class Vv{constructor(e,t){this.allVariants=e,this.rowBinSize=1e4,this.binSize=t,this.binFactor=parseInt(t/this.rowBinSize)}async read_rd_baf(e=\"ReadDepth\"){var t={};for(let e=this.allVariants.length-1;e>=0;e--){var i;let n=this.allVariants[e];this.allVariants.splice(e,1);let r=n.chr;i=Math.max(Math.floor(n.start/this.rowBinSize),0),t[r]||(t[r]=[]),t[r][i]||(t[r][i]={chr:r,start:i*this.rowBinSize,end:(i+1)*this.rowBinSize,dp_sum_score:0,dp_count:0,hets_count:0,hets:[]});const s=Object.values(n.calls);if(1!==s.length)throw Error(`Unexpected number of genotypes: ${s.length}.  CNVPytor expects 1 and only 1 genotype`);const o=s[0],a=o.info.DP;a&&(t[r][i].dp_sum_score+=Number.parseInt(a),t[r][i].dp_count++);let c=o.info.AD.split(\",\"),l=o.genotype;if(0==l[0]&&1==l[1]||1==l[0]&&0==l[1]){t[r][i].hets_count++;let e=parseInt(c[0]),n=parseInt(c[1]);t[r][i].hets.push({ref:e,alt:n})}}this.chromosomes=Object.keys(t);var n,r=this.adjust_bin_size(t);if(\"ReadDepth\"==e){n=new Wv(r,this.binSize).ReadDepth_caller();var s=this.formatDataStructure_BAF(r,\"max_likelihood\")}else if(\"2D\"==e){let e=new Dv(r,this.binSize),t=await e.call_2d();n=[t.binScore,[],t.segment_score];s=e.formatDataStructure_BAF(\"max_likelihood\",-1)}return[n,s]}formatDataStructure(e,t,i=1){const n=[];for(const[s,o]of Object.entries(e))for(let e of o){var r={...e};1!=i&&(r.value=e[t]/i*2),n.push(r)}return n}format_BAF_likelihood(e){const t=[];for(const[n,r]of Object.entries(e))for(let e of r){var i={...e};.5!=e.value&&(i.value=1-e.value,t.push(i))}return t}get_max_min_score(e){if(e.likelihood_score.length>0){const t=Math.max(...e.likelihood_score),i=e.likelihood_score.indexOf(t);e.value=Math.max(i/100,1-i/100),e.min_score=Math.min(i/100,1-i/100)}else e.score=0;return e}async getAllbins(){const e=await this.computeDepthFeatures();return new Fv.GetFit(e).fit_data(),e}formatDataStructure_BAF(e,t,i=-1){const n=[],r=[];for(const[a,c]of Object.entries(e))for(let e of c){var s={...e},o={...e};let a=e[t];.5!=a&&(o.value=i*(1-a),r.push(o)),s.value=i*a,n.push(s)}return[n,r]}adjust_bin_size(e){var t={};for(let r of this.chromosomes){t[r]||(t[r]=[]);for(let s=0;s<e[r].length/this.binFactor;s++){const o=s;t[r][s]||(t[r][s]={chr:r,start:o*this.binSize,end:(o+1)*this.binSize,dp_count:0,hets_count:0,binScore:0,likelihood_score:[],dp_sum_score:0});for(var i=s*this.binFactor;i<this.binFactor*s+this.binFactor;i++)if(e[r][i]&&(t[r][s].dp_sum_score+=e[r][i].dp_sum_score,t[r][s].dp_count+=e[r][i].dp_count,t[r][s].hets_count+=e[r][i].hets_count,0!=e[r][i].hets.length))for(let o of e[r][i].hets)if(0==t[r][s].likelihood_score.length)t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,t)=>jv(o.ref,o.alt,e)));else{var n=0;t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,i)=>{var a=t[r][s].likelihood_score[i]*jv(o.ref,o.alt,e);return n+=a,a})),t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,i)=>t[r][s].likelihood_score[i]/n))}t[r][s].binScore=100*parseInt(t[r][s].dp_sum_score/t[r][s].dp_count);const a=this.get_max_min_score(t[r][s]);t[r][s].max_likelihood=a.value}}return t}}function jv(e,t,i,n=!0){return Math.pow(i,e)*Math.pow(1-i,t)+Math.pow(i,t)*Math.pow(1-i,e)}class Wv{constructor(e,t){this.wigFeatures=e,this.binSize=t}ReadDepth_caller(){var e=new Fv.GetFit(this.wigFeatures),[t,i]=e.fit_data(),n=new Qv(this.wigFeatures,t,i),r=n.meanShiftCaller(this.binSize),s=n.cnv_calling();return Object.entries(this.wigFeatures).forEach((([e,t])=>{t.forEach(((t,i)=>{t.partition_level=parseInt(r[e][i]),t.partition_call=parseInt(s[0][e][i])}))})),[this.formatDataStructure(\"binScore\",t),this.formatDataStructure(\"partition_level\",t),this.formatDataStructure(\"partition_call\",t),s[1]]}formatDataStructure(e,t=1){const i=[];for(const[r,s]of Object.entries(this.wigFeatures))for(let r of s){var n={...r};1!=t&&(n.value=r[e]/t*2),i.push(n)}return i}}class Gv extends Hl{static DEFAULT_TRACK_HEIGHT=250;constructor(e,t){super(e,t)}init(e){this.featureType=\"numeric\",this.type=\"cnvpytor\",e.max||(this.defaultScale=!0,this.autoscale=!1),e.height||(e.height=Gv.DEFAULT_TRACK_HEIGHT),this.type=\"cnvpytor\",this.graphType=e.graphType||\"points\",this.bin_size=e.bin_size||1e5,this.signal_name=e.signal_name||\"rd_snp\",this.cnv_caller=e.cnv_caller||\"2D\",this.colors=e.colors||[\"gray\",\"black\",\"green\",\"blue\"],super.init(e)}get supportsWholeGenome(){return!0}get_signals(){let e=[];return\"rd_snp\"==this.signal_name?e=[\"RD_Raw\",\"RD_Raw_gc_coor\",this.cnv_caller,\"BAF1\",\"BAF2\"]:\"rd\"==this.signal_name?e=[\"RD_Raw\",\"RD_Raw_gc_coor\",this.cnv_caller]:\"snp\"==this.signal_name?e=[\"BAF1\",\"BAF2\"]:\"cnh\"==this.signal_name&&(e=[this.cnv_caller]),e}get_signal_colors(){return[{singal_name:\"RD_Raw\",color:this.colors[0]},{singal_name:\"RD_Raw_gc_coor\",color:this.colors[1]},{singal_name:\"ReadDepth\",color:this.colors[2]},{singal_name:\"2D\",color:this.colors[2]},{singal_name:\"BAF1\",color:this.colors[3]},{singal_name:\"BAF2\",color:this.colors[3]}]}async postInit(){if(\"vcf\"==this.config.format){let e;this.featureSource?e=Object.values(this.featureSource.getAllFeatures()).flat():(this.featureSource=this.featureSource||Ad(this.config,this.browser.genome),this.header=await this.getHeader(),e=this.featureSource.reader.features);const t=new Vv(e,this.bin_size);let i,n,r;this.wigFeatures_obj={},this.wigFeatures_obj[this.bin_size]={},\"2D\"==this.cnv_caller?(r=await t.read_rd_baf(\"2D\"),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size][\"2D\"]=i[2],this.available_callers=[\"2D\"]):(r=await t.read_rd_baf(),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size].ReadDepth=i[2],this.available_callers=[\"ReadDepth\"]),this.wigFeatures_obj[this.bin_size].RD_Raw=i[0],this.wigFeatures_obj[this.bin_size].RD_Raw_gc_coor=i[1],this.wigFeatures_obj[this.bin_size].BAF1=n[0],this.wigFeatures_obj[this.bin_size].BAF2=n[1],this.available_bins=[this.bin_size],this.set_available_callers()}else this.cnvpytor_obj=new mv(this.config.url,this.bin_size),this.wigFeatures_obj=await this.cnvpytor_obj.get_rd_signal(this.bin_size),this.available_bins=this.cnvpytor_obj.available_bins,this.available_callers=this.cnvpytor_obj.callers,this.set_available_callers();this.tracks=[];const e=[];this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(let t in this.wigFeatures_obj)for(const[i,n]of Object.entries(this.wigFeatures_obj[t]))if(this.signals.includes(i)){let t={type:\"wig\"};t.features=n,t.name=i,t.color=this.signal_colors.filter((e=>e.singal_name===i)).map((e=>e.color));const r=await this.browser.createTrack(t);r?(r.isMergedTrack=!0,r.autoscale=!1,this.tracks.push(r)):console.warn(\"Could not create track \"+t),\"function\"==typeof r.postInit&&e.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let e of this.tracks)e.autoscale=!1,e.dataRange=this.dataRange;return Promise.all(e)}set_available_callers(){this.available_callers.includes(this.cnv_caller)||(this.available_callers.length>0?this.cnv_caller=this.available_callers[0]:this.cnv_caller=null)}async getHeader(){if(!this.header){if(\"function\"==typeof this.featureSource.getHeader){const e=await this.featureSource.getHeader();e&&(this.callSets=e.callSets||[]),this.header=e}this.sampleKeys=this.callSets?this.callSets.map((e=>e.sample)):[],this.sampleNames=this.sampleKeys}return this.header}get height(){return this._height}set height(e){if(this._height=e,this.tracks)for(let t of this.tracks)t.height=e,t.config.height=e}menuItemList(){let e=[];void 0!==this.flipAxis&&e.push({label:\"Flip y-axis\",click:function(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),e=e.concat(this.numericDataMenuItems()),e.push(\"<hr/>\"),e.push(\"Bin Sizes\");for(let t of this.available_bins){const i=Dl(t,t===this.bin_size);e.push({object:Bt(i),click:async function(){this.bin_size=t,this.trackView.startSpinner(),await this.recreate_tracks(t),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}e.push(\"<hr/>\"),e.push(\"Signal Type\");let t={rd_snp:\"RD and BAF Likelihood\",rd:\"RD Signal\",snp:\"BAF Likelihood\"};for(let i in t){const n=Dl(t[i],i===this.signal_name);e.push({object:Bt(n),click:async function(){this.signal_name=i,await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}e.push(\"<hr/>\"),e.push(\"CNV caller\");for(let t of this.available_callers){const i=Dl(t,t===this.cnv_caller);e.push({object:Bt(i),click:async function(){this.cnv_caller=t,this.trackView.startSpinner(),await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}if(this.variantState){e.push(\"<hr/>\");for(let t of this.available_callers)e.push({label:\"Convert to variant track\",click:()=>{this.convertToVariant()}})}return e}async recreate_tracks(e){this.tracks=[];const t=[];e in this.wigFeatures_obj||(this.wigFeatures_obj={...this.wigFeatures_obj,...await this.cnvpytor_obj.get_rd_signal(e)}),this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(const[i,n]of Object.entries(this.wigFeatures_obj[e]))if(this.signals.includes(i)){let e={type:\"wig\"};e.features=n,e.name=i,e.color=this.signal_colors.filter((e=>e.singal_name===i)).map((e=>e.color));const r=await this.browser.createTrack(e);r?(r.isMergedTrack=!0,r.autoscale=!1,this.tracks.push(r)):console.warn(\"Could not create track \"+e),\"function\"==typeof r.postInit&&t.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let e of this.tracks)e.autoscale=!1,e.dataRange=this.dataRange;return Promise.all(t)}async getFeatures(e,t,i,n){if(this.tracks){const r=this.tracks.map((r=>r.getFeatures(e,t,i,n)));return Promise.all(r)}}getScaleFactor(e,t,i,n){return n?i/(Math.log10(t+1)-(e<=0?0:Math.log10(e+1))):i/(t-e)}computeYPixelValue(e,t){return(this.flipAxis?e-this.dataRange.min:this.dataRange.max-e)*t}computeYPixelValueInLogScale(e,t){let i=this.dataRange.max,n=this.dataRange.min;return i<=0?0:(n<=-1&&(n=0),n=n<=0?0:Math.log10(n+1),i=Math.log10(i+1),e=Math.log10(e+1),(this.flipAxis?e-n:i-e)*t)}draw(e){const t=e.features;if(!t)return;if(this.defaultScale&&(\"rd_snp\"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||-1,max:this.config.max||this.dataRange.max||5}:\"rd\"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||0,max:this.config.max||this.dataRange.max||5}:\"snp\"==this.signal_name&&(this.dataRange={min:this.config.min||this.dataRange.min||-1,max:this.config.max||this.dataRange.max||0})),this.autoscale&&(this.dataRange=function(e,t){let i=0,n=-Number.MAX_VALUE;for(let e of t)for(let t of e)void 0===t.value||Number.isNaN(t.value)||(i=Math.min(i,t.value),n=Math.max(n,t.value));return{min:i,max:n}}(e.referenceFrame.chr,t)),this.tracks)for(let i=0,n=this.tracks.length;i<n;i++){const n=Object.assign({},e);n.features=t[i],this.tracks[i].dataRange=this.dataRange,this.tracks[i].flipAxis=this.flipAxis,this.tracks[i].logScale=this.logScale,this.graphType&&(this.tracks[i].graphType=this.graphType),this.tracks[i].draw(n)}const i=this.getScaleFactor(this.dataRange.min,this.dataRange.max,e.pixelHeight,this.logScale),n=e=>this.logScale?this.computeYPixelValueInLogScale(e,i):this.computeYPixelValue(e,i);if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=n(t.y),r={strokeStyle:t.color,strokeWidth:1};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,r):xo.strokeLine(e.context,0,i,e.pixelWidth,i,r)}let r=n(2);xo.dashedLine(e.context,0,r,e.pixelWidth,r,5,{strokeStyle:\"lightgray\",strokeWidth:.5})}paintAxis(e,t,i){var n,r,s,o,a,c,l,h={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};if(void 0===this.dataRange||void 0===this.dataRange.max||void 0===this.dataRange.min)return;let d=void 0!==this.flipAxis&&this.flipAxis;function u(e){return e<0?Math.abs(e):0===e?\"0\":Math.abs(e)>=10||e%1==0?e.toFixed():Math.abs(e)>=1?e.toFixed(1):e.toFixed(2)}xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"}),n=(l=.95*t)-8,a={x:r=l,y:s=o=.01*i},xo.strokeLine(e,n,s,r,o,h),xo.fillText(e,u(d?this.dataRange.min:this.dataRange.max),n+4,s+12,h),c={x:r,y:s=o=.99*i},xo.strokeLine(e,n,s,r,o,h),xo.fillText(e,u(d?this.dataRange.max:this.dataRange.min),n+4,s-4,h),xo.strokeLine(e,a.x,a.y,c.x,c.y,h);const f=this.getScaleFactor(this.dataRange.min,this.dataRange.max,i,this.logScale),p=e=>this.logScale?this.computeYPixelValueInLogScale(e,f):this.computeYPixelValue(e,f),g=Math.ceil((this.dataRange.max-this.dataRange.min)/10);for(let t=Math.ceil(this.dataRange.min+1);t<Math.round(this.dataRange.max-.4);t+=g){const i=p(t);xo.strokeLine(e,45,i,50,i,h),xo.fillText(e,u(d?this.dataRange.max-t:t),44,i+4,h)}}popupData(e,t){const i=t||e.viewport.cachedFeatures;if(i&&i.length===this.tracks.length){const t=[];for(let n=0;n<this.tracks.length;n++){n>0&&t.push(\"<hr/>\"),t.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${this.tracks[n].name}</div>`);const r=this.tracks[n].popupData(e,i[n]);t.push(...r)}return t}}async convertToVariant(){this.variantState&&(Object.setPrototypeOf(this,Yv.prototype),this.init(this.variantState),await this.postInit(),this.trackView.clearCachedFeatures(),this.variantState.trackHeight&&this.trackView.setTrackHeight(this.variantState.trackHeight),this.trackView.checkContentHeight(),this.trackView.updateViews(),delete this.variantState)}}const $v=Mt,Kv=10;class Yv extends Hl{static defaults={displayMode:\"EXPANDED\",sortDirection:\"ASC\",showGenotypes:!0,expandedVariantHeight:10,squishedVariantHeight:2,squishedCallHeight:1,expandedCallHeight:10,expandedVGap:2,squishedVGap:1,expandedGroupGap:10,squishedGroupGap:5,featureHeight:14,noGenotypeColor:\"rgb(200,180,180)\",noCallColor:\"rgb(225, 225, 225)\",nonRefColor:\"rgb(200, 200, 215)\",mixedColor:\"rgb(200, 220, 200)\",homrefColor:\"rgb(200, 200, 200)\",homvarColor:\"rgb(17,248,254)\",hetvarColor:\"rgb(34,12,253)\",refColor:\"rgb(0,0,220)\",altColor:\"rgb(255,0,0)\",visibilityWindow:void 0,labelDisplayMode:void 0,type:\"variant\"};_sortDirections=new Map;constructor(e,t){super(e,t)}init(e){if(super.init(e),e.variantHeight&&(this.expandedVariantHeight=e.variantHeight),this.featureSource=Ad(e,this.browser.genome),this.colorTables=new Map,e.colorTable){const t=e.colorBy||\"*\";this.colorTables.set(t,new ao(e.colorTable))}if(this.strokecolor=e.strokecolor,this._context_hook=e.context_hook,e.color&&(this.colorBy=void 0),this.nVariantRows=1,e.samples)for(let t of e.samples)this.sampleKeys=e.samples;e.sort&&(this.initialSort=e.sort),this._colorByItems=new Map([[\"none\",\"None\"]])}async postInit(){if(this.header=await this.getHeader(),this.header.INFO){const e=new Set(Object.keys(this.header.INFO));this.config.colorBy?this.colorBy=this.config.colorBy:!this.config.color&&e.has(\"AF\")&&(this.colorBy=\"AF\"),e.has(\"AF\")&&this._colorByItems.set(\"AF\",\"Allele frequency\"),e.has(\"VT\")&&this._colorByItems.set(\"VT\",\"Variant Type\"),e.has(\"SVTYPE\")&&this._colorByItems.set(\"SVTYPE\",\"SV Type\")}if(this.config.colorBy&&!this._colorByItems.has(this.config.colorBy)&&this._colorByItems.set(this.config.colorBy,this.config.colorBy),!this.disposed){if(this.header&&!this.sampleKeys&&(this.sampleKeys=this.header.sampleNameMap?Array.from(this.header.sampleNameMap.keys()):[]),void 0===this.visibilityWindow&&!1!==this.config.indexed){const e=Ht(this.config.url)?this.config.url.name:this.config.url;$v(e)&&e.toLowerCase().includes(\"gnomad\")?this.visibilityWindow=1e3:\"function\"==typeof this.featureSource.defaultVisibilityWindow?this.visibilityWindow=await this.featureSource.defaultVisibilityWindow():this.visibilityWindow=1e6}return this}}get supportsWholeGenome(){return!this.config.indexURL||!0===this.config.supportsWholeGenome}get color(){return this._color||\"rgb(0,0,150)\"}set color(e){this._color=e,e&&(this.colorBy=void 0)}async getHeader(){return this.header||\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getSampleCount(){return this.sampleKeys?this.sampleKeys.length:0}async getFeatures(e,t,i,n){void 0===this.header&&(this.header=await this.getHeader());const r=await this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow});if(this.initialSort){const e=this.initialSort;if(void 0===e.option||\"GENOTYPE\"===e.option.toUpperCase())this.sortSamplesByGenotype(e,r);else if(\"ATTRIBUTE\"===e.option.toUpperCase()&&e.attribute){const t=\"ASC\"===e.direction?1:-1;this.sortByAttribute(e.attribute,t)}this.initialSort=void 0}return r}hasSamples(){return this.getSampleCount()>0}getSamples(){const e=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,i=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=t*((\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight)+e),r=Kv+t*(i+e);return{names:this.sampleKeys,yOffset:r,height:n}}computePixelHeight(e){if(!e||0===e.length)return Kv;const t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,i=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,n=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,r=\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s=!1===this.showGenotypes?0:this.getSampleCount()*t;return Kv+t*(n+i)+i+(s+1)*(r+i)}variantRowCount(e){this.nVariantRows=e}draw({context:e,pixelWidth:t,pixelHeight:i,bpPerPixel:n,bpStart:r,pixelTop:s,features:o}){xo.fillRect(e,0,s,t,i,{fillStyle:\"rgb(255, 255, 255)\"});const a=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,c=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,l=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=Kv+c*(l+a);let h=this.sampleColumns;const d=this.hasSamples();if(h&&d&&!1!==this.showGenotypes&&xo.strokeLine(e,0,this.variantBandHeight,t,this.variantBandHeight,{strokeStyle:\"rgb(224,224,224) \"}),o){const i=\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,a=r+t*n+1;for(let t of o){if(t.end<r)continue;if(t.start>a)break;const o=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,c=Kv+(\"COLLAPSED\"===this.displayMode?0:t.row*(o+s)),l=o;let h=(t.start-r)/n,u=(t.end-r)/n,f=Math.max(1,u-h);f<3?(f=3,h-=1):f>5&&(h+=1,f-=2);const p=t._f||t;let g;try{g=p.alleleFreq()}catch(e){console.log(e)}if(\"AF\"===this.colorBy&&g){const t=Math.min(1,g)*l,i=l-t;e.fillStyle=p.isFiltered()?this.refColorFiltered:this.refColor,e.fillRect(h,c,f,i),e.fillStyle=p.isFiltered()?this.altColorFiltered:this.altColor,e.fillRect(h,c+i,f,t)}else e.fillStyle=this.getColorForFeature(p),e.fillRect(h,c,f,l);let m=this.getVariantStrokecolor(p);if(m&&(e.strokeStyle=m,e.strokeRect(h,c,f,l)),this.callContextHook(p,e,h,c,f,l),d&&!1!==this.showGenotypes){const t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+s,this.sampleHeight=t*(i+s);let n=0;for(let t of this.sampleKeys){const r=this.header.sampleNameMap.get(t),o=p.calls[r];if(o){const t=\"COLLAPSED\"===this.displayMode?0:p.row,r=this.sampleYOffset+n*this.sampleHeight+t*(i+s);let a=!0,c=!0,l=!1;if(o.genotype)for(let e of o.genotype){if(\".\"===e){l=!0;break}0!==e&&(c=!1),0===e&&(a=!1)}o.genotype?e.fillStyle=l?this.noCallColor:c?this.homrefColor:a?this.homvarColor:this.hetvarColor:e.fillStyle=this.noGenotypeColor,e.fillRect(h,r,f,i)}n++}}}}else console.log(\"No feature list\")}get refColorFiltered(){return this._refColorFiltered||(this._refColorFiltered=_s.addAlpha(this.refColor,.2)),this._refColorFiltered}get altColorFiltered(){return this._altColorFiltered||(this._altColorFiltered=_s.addAlpha(this.altColor,.2)),this._altColorFiltered}getColorForFeature(e){const t=e._f||e;let i;if(this.colorBy&&\"none\"!==this.colorBy){const e=t.getAttributeValue(this.colorBy);i=void 0!==e?this.getVariantColorTable(this.colorBy).getColor(e):\"gray\"}else i=this.color?\"function\"==typeof this.color?this.color(e):this.color:\"NONVARIANT\"===t.type?this.nonRefColor:\"MIXED\"===t.type?this.mixedColor:this.color;return t.isFiltered()&&(i=_s.addAlpha(i,.2)),i}getVariantStrokecolor(e){const t=e._f||e;let i;return i=this.strokecolor?\"function\"==typeof this.strokecolor?this.strokecolor(t):this.strokecolor:void 0,i}callContextHook(e,t,i,n,r,s){if(this._context_hook&&\"function\"==typeof this._context_hook){const o=e._f||e;t.save(),this._context_hook(o,t,i,n,r,s),t.restore()}}clickedFeatures(e){let t=super.clickedFeatures(e);const i=\"EXPANDED\"===this.displayMode?this.expandedVGap:this.squishedVGap,n=i+(\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),r=e.y;if(r<=this.variantBandHeight){const e=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=Math.floor((r-Kv)/(e+i));\"COLLAPSED\"!==this.displayMode&&(t=t.filter((e=>e.row===n)))}else if(this.sampleKeys){const e=r-this.variantBandHeight,i=Math.floor(e/this.sampleHeight);if(i>=0&&i<this.sampleKeys.length){const r=Math.floor((e-i*this.sampleHeight)/n),s=\"COLLAPSED\"===this.displayMode?t:t.filter((e=>e.row===r)),o=this.sampleKeys[i],a=this.header.sampleNameMap.get(o);t=s.map((e=>{const t=e.calls[a];return t.genotypeString=function(e,t){if(e.genotype){let i=\"\";if(\".\"===t.alternateBases)i=\"No Call\";else{const n=t.alternateBases.split(\",\");for(let r of e.genotype)if(i.length>0&&(i+=\" | \"),\".\"===r)i+=\".\";else if(0===r)i+=t.referenceBases;else{i+=n[r-1].replace(\"<\",\"&lt;\")}}return i}}(t,e),t}))}}return t}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=this.browser.genome.id;let r=[];for(let e of t){const t=e._f||e;if(r.length>0&&r.push({html:'<hr style=\"border-top-width:2px ;border-color: #c9c3ba\" />'}),\"function\"==typeof t.popupData){const e=t.popupData(i,n);Array.prototype.push.apply(r,e)}}return r}menuItemList(){const e=[];if(this.header.INFO&&this.header.INFO){const t=this._colorByItems;e.push(\"<hr/>\");const i=Bt('<div class=\"igv-track-menu-category igv-track-menu-border-top\">');i.text(\"Color by:\"),e.push({name:void 0,object:i,click:void 0,init:void 0});for(let n of t.keys()){const r=this.colorBy===n;e.push(this.colorByCB({key:n,label:t.get(n)},r))}e.push(this.colorByCB({key:\"info\",label:\"Info field...\"}))}if(!0===Hf(this.browser.sampleInfo,this.sampleKeys)){e.push(\"<hr/>\"),e.push(\"Sort by attribute:\");for(const s of this.browser.sampleInfo.attributeNames)if(this.sampleKeys.some((e=>{const t=this.browser.sampleInfo.getAttributes(e);return t&&t[s]}))){const o=Bt(\"<div>\");function a(){const e=this._sortDirections.get(s)||1;this.sortByAttribute(s,e),this.config.sort={option:\"ATTRIBUTE\",attribute:s,direction:e>0?\"ASC\":\"DESC\"},this._sortDirections.set(s,-1*e)}o.html(`&nbsp;&nbsp;${s.split(Uu.emptySpaceReplacement).join(\" \")}`),e.push({object:o,click:a})}}e.push(\"<hr/>\"),this.getSampleCount()>0&&(e.push({object:Bt('<div class=\"igv-track-menu-border-top\">')}),e.push({object:Bt(Dl(\"Show Genotypes\",this.showGenotypes)),click:function(){this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.browser.sampleNameControl.performClickWithState(this.browser,this.showGenotypes),this.browser.sampleInfoControl.performClickWithState(this.browser,this.showGenotypes)}})),e.push({object:Bt('<div class=\"igv-track-menu-border-top\">')});for(let c of[\"COLLAPSED\",\"SQUISHED\",\"EXPANDED\"]){e.push({object:Bt(Dl({COLLAPSED:\"Collapse\",SQUISHED:\"Squish\",EXPANDED:\"Expand\"}[c],c===this.displayMode)),click:function(){this.displayMode=c,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return this.browser.circularView&&(e.push(\"<hr>\"),e.push({label:\"Add SVs to circular view\",click:function(){for(let e of this.trackView.viewports)this.sendChordsForViewport(e)}})),this.canCovertToPytor()&&(e.push(\"<hr>\"),e.push({label:\"Convert to CNVpytor track\",click:function(){this.convertToPytor()}})),e}contextMenuItemList(e){const t=[];if(this.hasSamples()&&this.showGenotypes){const i=e.viewport.referenceFrame,n=e.genomicLocation,r=i.toBP(2.5),s=this._sortDirections.get(\"genotype\")||1;this._sortDirections.set(\"genotype\",-1*s),t.push({label:\"Sort by genotype\",click:t=>{const i={direction:s,option:\"genotype\",chr:e.viewport.referenceFrame.chr,start:Math.floor(n-r),end:Math.ceil(n+r)},o=e.viewport.cachedFeatures;this.sortSamplesByGenotype(i,o),this.config.sort=i}}),t.push(\"<hr/>\")}if(this.browser.circularView){const i=e.viewport;t.push({label:\"Add SVs to Circular View\",click:()=>{this.sendChordsForViewport(i)}}),t.push(\"<hr/>\")}return t}async sortSamplesByGenotype({chr:e,position:t,start:i,end:n,direction:r},s){if(void 0===i&&(i=t-1),void 0===n&&(n=t),s||(s=await this.featureSource.getFeatures({chr:e,start:i,end:n})),!s)return;const o=new Map,a=\"ASC\"===r?1:-1;for(let e of s)if(!(e.end<i)){if(e.start>n)break;for(let t of e.calls){const e=t.sample,i=t.zygosityScore();o.set(e,o.has(e)?o.get(e)+i:i)}}this.sampleKeys.sort((function(e,t){let i=o.get(e)||0,n=o.get(t)||0;return a*(i-n)})),this.trackView.repaintViews()}sortByAttribute(e,t){this.config.sort={option:\"ATTRIBUTE\",attribute:e,direction:1===t?\"ASC\":\"DESC\"},this.sampleKeys=this.browser.sampleInfo.getSortedSampleKeysByAttribute(this.sampleKeys,e,t),this.trackView.repaintViews()}sendChordsForViewport(e){const t=e.referenceFrame;let i;if(\"all\"===t.chr){const e=this.featureSource.getAllFeatures(),t=Object.keys(e).map((t=>e[t]));i=[].concat(...t)}else i=this.featureSource.featureCache.queryFeatures(t.chr,t.start,t.end);Pm(i.filter((e=>{const t=e._f||e;return t.info&&t.info.CHR2&&t.info.END&&(t.info.CHR2!==t.chr||Math.abs(Number.parseInt(t.info.END)-t.pos)>1e6)})).map((e=>{const t=e._f||e,i=Number.parseInt(t.info.END),n=i-100,r=i+100;return{uniqueId:`${t.chr}:${t.start}-${t.end}_${t.info.CHR2}:${t.info.END}`,refName:zm(t.chr),start:t.start,end:t.end,mate:{refName:zm(t.info.CHR2),start:n,end:r}}})),this,t,.5)}colorByCB(e,t){const i=Bt(Dl(e.label,t));if(\"info\"!==e.key){function n(){const t=\"none\"===e.key?void 0:e.key;this.colorBy=t,this.config.colorBy=t,this.trackView.repaintViews()}return{name:void 0,object:i,click:n,init:void 0}}{function r(e){this.browser.inputDialog.present({label:\"Info field\",value:\"\",callback:e=>{e?(this.colorBy=e,this._colorByItems.set(e,e)):this.colorBy=void 0,this.trackView.repaintViews()}},e)}return{name:void 0,object:i,dialog:r,init:void 0}}}getState(){const e=super.getState();return this.color&&\"function\"!=typeof this.color&&(e.color=this.color),e}getVariantColorTable(e){if(this.colorTables.has(e))return this.colorTables.get(e);if(this.colorTables.has(\"*\"))return this.colorTables.get(\"*\");{let t;if(\"SVTYPE\"===e)t=Xv;else t=new oo(\"Set1\");return this.colorTables.set(e,t),t}}paintAxis(){}canCovertToPytor(){return!this.config.indexURL&&(!!this.header&&(1===Object.keys(this.sampleKeys).length&&this.header.FORMAT&&this.header.FORMAT.AD&&this.header.FORMAT.DP))}async convertToPytor(){this.variantState={...this.config,...this.getState()},this.variantState.trackHeight=this.height,this.trackView.startSpinner(),setTimeout((async()=>{try{const e=Object.assign({},this.config);Object.setPrototypeOf(this,Gv.prototype),this.init(e),await this.postInit(),this.trackView.clearCachedFeatures(),this.trackView.setTrackHeight(this.config.height||Gv.DEFAULT_TRACK_HEIGHT),this.trackView.checkContentHeight(),this.trackView.updateViews()}finally{this.trackView.stopSpinner()}}),100)}}const Xv=new ao({DEL:\"#ff2101\",INS:\"#001888\",DUP:\"#028401\",INV:\"#008688\",CNV:\"#8931ff\",BND:\"#891100\",\"*\":\"#002eff\"}),Zv={timeout:5e3,type:\"plain\",url:\"https://igv.org/genomes/locus.php?genome=$GENOME$&name=$FEATURE$\",coords:0};async function Jv(e,t){const i=e.searchConfig||Zv;let n;t=t.toUpperCase();const r=e.tracks.filter((e=>e.searchable));for(let e of r){const i=await e.search(t);if(i)return i}if(e.config&&!1!==e.config.search)try{return n=await async function(e,t,i){let n=i.url.replace(\"$FEATURE$\",t.toUpperCase());n.indexOf(\"$GENOME$\")>-1&&(n=n.replace(\"$GENOME$\",e.genome.id?e.genome.id:\"hg19\"));const r=i.timeout?{timeout:i.timeout}:void 0,s=await Qs.loadString(n,r);return function(e,t,i){let n;n=\"plain\"===i.type?function(e,t){const i=[],n=Dt(t);for(let t of n){const n=t.split(\"\\t\");if(n.length>=3){const t=n[1].split(\":\"),r=t[1].split(\"-\");i.push({chromosome:e.genome.getChromosomeName(t[0].trim()),start:parseInt(r[0].replace(/,/g,\"\")),end:parseInt(r[1].replace(/,/g,\"\")),name:n[0].toUpperCase()})}}return i}(e,t):JSON.parse(t);i.resultsField&&(n=n[i.resultsField]);if(n&&0!==n.length){const e=i.chromosomeField||\"chromosome\",t=i.startField||\"start\",r=i.endField||\"end\",s=i.coords||1;let o;o=Array.isArray(n)?n[0]:n,o.hasOwnProperty(e)&&o.hasOwnProperty(t)||console.error(\"Search service results must include chromosome and start fields: \"+o);const a=o[e];let c=o[t]-s,l=o[r];void 0===l&&(l=c+1);const h={chr:a,start:c,end:l};if(!o.type||o.type,i.geneField&&i.snpField){const e=o[i.geneField]||o[i.snpField];e&&(h.name=e.toUpperCase())}return h}return}(e,s,i)}(e,t,i),n}catch(e){console.log(\"Search service not available \"+e)}}function ey(e,t=!1){const i=e.split(\"\\t\");if(i.length>2)try{const e=i[0],t=parseInt(i[1].replace(/,/g,\"\"),10)-1,n=parseInt(i[2].replace(/,/g,\"\"),10);if(!isNaN(t)&&!isNaN(n))return{chr:e,start:t,end:n}}catch(e){}const n=e.split(\":\"),r={chr:n[0]};if(n.length>1){let e,i=n[1].split(\"-\");if(i.length>2){if(!n[1].startsWith(\"-\"))return;{const e=n[1].indexOf(\"-\",1);if(e>0){i=[n[1].substring(0,e),n[1].substring(e+1)]}}}if(e=i[0].replace(/,/g,\"\"),isNaN(e))return;if(r.start=parseInt(e,10)-1,r.end=r.start+1,1===i.length&&(r.start-=20,r.end+=20),2===i.length){if(e=i[1].replace(/,/g,\"\"),isNaN(e))return;if(r.end=parseInt(e,10),r.start<0&&!t){const e=-extent.start;r.start+=e,r.end+=e}}}return r}class ty extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"qtl\",this.name=e.name;const t=e.minLogP||e.min,i=e.maxLogP||e.max;this.dataRange={min:void 0!==t?t:3.5,max:i||25},this.autoscale=!i||e.autoscale,this.autoscalePercentile=void 0===e.autoscalePercentile?98:e.autoscalePercentile,this.background=e.background,this.divider=e.divider||\"rgb(225,225,225)\",this.dotSize=e.dotSize||2,this.height=e.height||100,this.disableButtons=e.disableButtons,this.featureSource=Ad(e,this.browser.genome)}paintAxis(e,t,i){const n=(this.dataRange.max-this.dataRange.min)/i,r={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"});const s=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let o=4;o<=this.dataRange.max;o+=s){const s=.85*t,a=s-5,c=s,l=i-(o-this.dataRange.min)/n;xo.strokeLine(e,a,l,c,l,r),l>8&&xo.fillText(e,o,a-1,l+2,r)}r.textAlign=\"center\",xo.fillText(e,\"-log10(pvalue)\",t/4,i/2,r,{rotate:{angle:-90}})}async getFeatures(e,t,i){const n=this.visibilityWindow;return await this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const{context:t,referenceFrame:i,pixelWidth:n,pixelHeight:r}=e;this.background&&xo.fillRect(t,0,0,n,r,{fillStyle:this.background}),xo.strokeLine(t,0,r-1,n,r-1,{strokeStyle:this.divider}),i.feature&&i.feature.match(/RS[0-9]+/);const s=i=>{const s=i?2*this.dotSize:this.dotSize,o=e.bpStart,a=(this.dataRange.max-this.dataRange.min)/r;for(let d of e.features){const u=(d.start-o+.5)/e.bpPerPixel;if(u<0)continue;if(u>n)break;const f=d.phenotype;let p;if(this.browser.qtlSelections.qtl?(l=this.browser.qtlSelections.qtl,h=d,p=l.chr===h.chr&&l.start===h.start&&l.pValue===h.pValue):p=this.browser.qtlSelections.snps.size>0?this.browser.qtlSelections.hasSnp(d.snp)&&this.browser.qtlSelections.hasPhenotype(f):this.browser.qtlSelections.hasPhenotype(f),!i||p){var c=-Math.log(d.pValue)/Math.LN10;if(c>=this.dataRange.min){let e;c>this.dataRange.max?(c=this.dataRange.max,e=!0):e=!1;const n=Math.max(0+s,r-Math.round((c-this.dataRange.min)/a));let o;d.px=u,d.py=n,d.radius=s,i&&p?(o=this.browser.qtlSelections.colorForGene(f),xo.setProperties(t,{fillStyle:o,strokeStyle:\"black\"})):(o=e?\"rgb(150, 150, 150)\":\"rgb(180, 180, 180)\",xo.setProperties(t,{fillStyle:o,strokeStyle:o})),xo.fillCircle(t,u,n,s),xo.strokeCircle(t,u,n,s)}}}var l,h};s(!1),s(!0)}popupData(e,t){if(void 0===t&&(t=e.viewport.cachedFeatures),!t||0===t.length)return[];const i=this.name,n=[];for(let r of this._clickedFeatures(e,t))n.length>0&&n.push(\"<hr/>\"),\"function\"==typeof r.popupData?n.push(...r.popupData(e)):n.push({name:\"snp id\",value:r.snp},{name:\"gene id\",value:r.gencodeId},{name:\"gene name\",value:r.geneSymbol},{name:\"p value\",value:r.pValue},{name:\"tissue\",value:i});return n}_clickedFeatures(e,t){const i=(e,t)=>Math.sqrt((e.px-t.canvasX)*(e.px-t.canvasX)+(e.py-t.canvasY)*(e.py-t.canvasY)),n=t.filter((t=>i(t,e)<6));if(n.length>1){n.sort(((t,n)=>i(t,e)-i(n,e)));const t=i(n[0],e);return n.filter((n=>i(n,e)<=t))}return n}contextMenuItemList(e){const t=[],i=e.viewport.cachedFeatures;if(i){const n=this._clickedFeatures(e,i);n.length>0&&(t.push({label:\"Highlight associated features\",click:async()=>{this.browser.qtlSelections.clear();for(let e of n)this.browser.qtlSelections.qtl=e,this.browser.qtlSelections.addPhenotype(e.phenotype);this.browser.repaintViews()}}),t.push(\"<hr>\"))}return t}menuItemList(){const e=[];return e.push(...this.numericDataMenuItems()),e.push(\"<hr/>\"),e.push({label:\"Search for...\",dialog:function(e){this.browser.inputDialog.present({label:\"Search for snp or phenotype\",value:\"\",callback:async e=>{if(e){e=e.trim().toUpperCase();const t=t=>((t.phenotype&&t.phenotype.toUpperCase())===e||t.snp&&t.snp.toUpperCase()===e)&&-Math.log(t.pValue)/Math.LN10>this.dataRange.min;let i,n,r,s=await this.featureSource.findFeatures(t);if(0==s.length){await this.browser.search(e)&&(s=await this.featureSource.findFeatures(t))}if(s.length>0){this.browser.qtlSelections.clear();const t=new Set;i=s[0].chr,n=s[0].start,r=s[0].end;for(let o of s)o.snp&&o.snp.toUpperCase()===e&&this.browser.qtlSelections.addSnp(o.snp),this.browser.qtlSelections.addPhenotype(o.phenotype),t.add(o.phenotype),o.chr===i&&(n=Math.min(n,o.start),r=Math.max(r,o.end));const o=this.browser.genome.getChromosomeName(i);for(let e of t){const t=await Jv(this.browser,e);t&&o===this.browser.genome.getChromosomeName(t.chr)&&(n=Math.min(n,t.start),r=Math.max(r,t.end))}const a=Math.floor(.1*(r-n));n=Math.max(0,n-a),r+=a,await this.browser.search(`${i}:${n}-${r}`)}}}},e)}}),e}doAutoscale(e){let t=this.config.max||25;if(e.length>0){const i=e.map((e=>-Math.log(e.pValue)/Math.LN10));i.sort(((e,t)=>e-t));t=i[Math.floor(i.length*(this.autoscalePercentile/100))]}return this.dataRange.max=Math.max(t,10),this.dataRange}}const iy={X:\"rgb(204, 153, 0)\",Y:\"rgb(153, 204, 0)\",Un:\"darkGray)\",1:\"rgb(80, 80, 255)\",2:\"rgb(206, 61, 50)\",\"2a\":\"rgb(210, 65, 55)\",\"2b\":\"rgb(215, 70, 60)\",3:\"rgb(116, 155, 88)\",4:\"rgb(240, 230, 133)\",5:\"rgb(70, 105, 131)\",6:\"rgb(186, 99, 56)\",7:\"rgb(93, 177, 221)\",8:\"rgb(128, 34, 104)\",9:\"rgb(107, 215, 107)\",10:\"rgb(213, 149, 167)\",11:\"rgb(146, 72, 34)\",12:\"rgb(131, 123, 141)\",13:\"rgb(199, 81, 39)\",14:\"rgb(213, 143, 92)\",15:\"rgb(122, 101, 165)\",16:\"rgb(228, 175, 105)\",17:\"rgb(59, 27, 83)\",18:\"rgb(205, 222, 183)\",19:\"rgb(97, 42, 121)\",20:\"rgb(174, 31, 99)\",21:\"rgb(231, 199, 111)\",22:\"rgb(90, 101, 94)\",23:\"rgb(204, 153, 0)\",24:\"rgb(153, 204, 0)\",25:\"rgb(51, 204, 0)\",26:\"rgb(0, 204, 51)\",27:\"rgb(0, 204, 153)\",28:\"rgb(0, 153, 204)\",29:\"rgb(10, 71, 255)\",30:\"rgb(71, 117, 255)\",31:\"rgb(255, 194, 10)\",32:\"rgb(255, 209, 71)\",33:\"rgb(153, 0, 51)\",34:\"rgb(153, 26, 0)\",35:\"rgb(153, 102, 0)\",36:\"rgb(128, 153, 0)\",37:\"rgb(51, 153, 0)\",38:\"rgb(0, 153, 26)\",39:\"rgb(0, 153, 102)\",40:\"rgb(0, 128, 153)\",41:\"rgb(0, 51, 153)\",42:\"rgb(26, 0, 153)\",43:\"rgb(102, 0, 153)\",44:\"rgb(153, 0, 128)\",45:\"rgb(214, 0, 71)\",46:\"rgb(255, 20, 99)\",47:\"rgb(0, 214, 143)\",48:\"rgb(20, 255, 177)\"};for(let DA of Object.keys(iy)){iy[\"chr\"+DA]=iy[DA]}for(let TA=1;TA<=48;TA++){if(10===TA)continue;const LA=ny(TA);iy[LA]=iy[TA.toString()]}function ny(e){if(!+e)return!1;for(var t=String(+e).split(\"\"),i=[\"\",\"C\",\"CC\",\"CCC\",\"CD\",\"D\",\"DC\",\"DCC\",\"DCCC\",\"CM\",\"\",\"X\",\"XX\",\"XXX\",\"XL\",\"L\",\"LX\",\"LXX\",\"LXXX\",\"XC\",\"\",\"I\",\"II\",\"III\",\"IV\",\"V\",\"VI\",\"VII\",\"VIII\",\"IX\"],n=\"\",r=3;r--;)n=(i[+t.pop()+10*r]||\"\")+n;return Array(+t.join(\"\")+1).join(\"M\")+n}class ry extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.useChrColors=void 0===e.useChrColors||e.useChrColors,this.trait=e.trait,this.posteriorProbability=e.posteriorProbability,this.valueProperty=\"bed\"===e.format?\"score\":\"value\",this.height=e.height||100,this.autoscale=e.autoscale,this.autoscalePercentile=void 0===e.autoscalePercentile?98:e.autoscalePercentile,this.background=e.background,this.divider=e.divider||\"rgb(225,225,225)\",this.dotSize=e.dotSize||3,this.popoverWindow=void 0===e.popoverWindow?1e8:e.popoverWindow,this.useChrColors?this.colorScale=new ao(e.colorTable||iy):e.color?this.colorScale=new ff(e.color):this.colorScale=new df(e.colorScale||{thresholds:[5e-8,5e-4,.5],colors:[\"rgb(255,50,50)\",\"rgb(251,100,100)\",\"rgb(251,170,170)\",\"rgb(227,238,249)\"]}),this.featureSource=Ad(e,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),this.autoscale||(this.posteriorProbability?this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?1:this.config.max}:this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?25:this.config.max}),this}get supportsWholeGenome(){return!0}async getFeatures(e,t,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const t=e.features,i=e.context,n=e.pixelWidth,r=e.pixelHeight;if(this.background&&xo.fillRect(i,0,0,n,r,{fillStyle:this.background}),xo.strokeLine(i,0,r-1,n,r-1,{strokeStyle:this.divider}),t){const s=e.bpPerPixel,o=e.bpStart,a=o+n*s+1;for(let e of t){const t=e.start;if(t<o)continue;if(t>a)break;let n;if(this.posteriorProbability)n=e[this.valueProperty];else{const t=e[this.valueProperty];if(!t)continue;n=-Math.log10(t)}const c=this.useChrColors?e._f?e._f.chr:e.chr:n,l=this.colorScale.getColor(c),h=(this.dataRange.max-this.dataRange.min)/r,d=Math.round((t-o)/s),u=Math.max(this.dotSize,r-Math.round((n-this.dataRange.min)/h));l&&xo.setProperties(i,{fillStyle:l,strokeStyle:\"black\"}),xo.fillCircle(i,d,u,this.dotSize),e.px=d,e.py=u}}}paintAxis(e,t,i){xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"});var n={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};const r=(this.dataRange.max-this.dataRange.min)/i;if(this.posteriorProbability){const t=.1;for(let s=this.dataRange.min;s<this.dataRange.max;s+=t){const t=i-Math.round((s-this.dataRange.min)/r);xo.strokeLine(e,45,t-2,50,t-2,n),xo.fillText(e,s.toFixed(1),44,t+2,n)}}else{const t=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let s=this.dataRange.min;s<this.dataRange.max;s+=t){const t=i-Math.round((s-this.dataRange.min)/r);xo.strokeLine(e,45,t,50,t,n),xo.fillText(e,Math.floor(s),44,t+4,n)}}n.textAlign=\"center\",this.posteriorProbability?xo.fillText(e,\"PPA\",t/2,i/2,n,{rotate:{angle:-90}}):xo.fillText(e,\"-log10(pvalue)\",t/2,i/2,n,{rotate:{angle:-90}})}popupData(e,t){void 0===t&&(t=e.viewport.cachedFeatures);let i=[];const n=e.viewport.trackView.track;if(t){let r=0;for(let s of t){const t=Math.abs(e.canvasX-s.px),o=Math.abs(e.canvasY-s.py);if(t<this.dotSize&&o<this.dotSize){if(r>0&&i.push(\"<HR/>\"),5==r){i.push(\"...\");break}if(s=s._f||s,\"function\"==typeof s.popupData)i=i.concat(s.popupData());else{const e=s[this.valueProperty],t=s.chr,r=Rt(s.start+1);i.push({name:\"chromosome\",value:t}),i.push({name:\"position\",value:r}),i.push({name:\"name\",value:s.name}),n.posteriorProbability?i.push({name:\"posterior probability\",value:e}):i.push({name:\"pValue\",value:e})}r++}}}return i}menuItemList(){return this.numericDataMenuItems()}doAutoscale(e){if(e.length>0){const t=this.valueProperty,i=this.posteriorProbability,n=e.map((function(e){const n=e[t];return{value:i?n:-Math.log(n)/Math.LN10}}));this.dataRange=qa(n)}else this.posteriorProbability?this.dataRange={min:this.config.min||0,max:this.config.max||1}:this.dataRange={min:this.config.max||25,max:this.config.min||0};return this.dataRange}}class sy extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.autoscale=e.autoscale||void 0===e.max,this.dataRange={min:e.min||0,max:e.max},this.windowFunction=e.windowFunction||\"mean\",this.paintAxis=cd,this.graphType=e.graphType||\"bar\",e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):this.featureSource=Ad(this.config,this.browser.genome),this.visibilityWindow=-1,this.featureSource.visibilityWindow=this.visibilityWindow}async postInit(){if(\"function\"==typeof this.featureSource.getHeader){if(this.header=await this.featureSource.getHeader(),this.disposed)return;if(this.sampleKeys=this.header.columnNames.slice(3),this.setTrackProperties(this.header),this.header.hasOwnProperty(\"clickToHighlight\")){let e=this.header.clickToHighlight;this.config.clickToHighlight=e,this.config.samplesClickedToHighlight={}}if(this.header.hasOwnProperty(\"highlight\")){this.config.highlightSamples={};let e=this.header.highlight;Array.isArray(e)||(e=[e]);for(let t of e){const e=t.split(\";\");2===e.length&&(this.config.highlightSamples[e[0]]=e[1])}}}}menuItemList(){return this.numericDataMenuItems()}async getFeatures(e,t,i){const n=await this.featureSource.getFeatures({chr:e,start:0,end:Number.MAX_SAFE_INTEGER,visibilityWindow:this.visibilityWindow});let r,s;for(let e=1;e<n.length-1;e++)if(void 0===r&&n[e].end>t&&(r=e-1),void 0===s&&n[e].start>i){s=e+1;break}return void 0===r&&(r=0),void 0===s&&(s=n.length),n.slice(r,s)}draw(e){const{features:t,context:i,bpPerPixel:n,bpStart:r,pixelWidth:s,pixelHeight:o}=e,a=e=>(this.dataRange.max-e)/(this.dataRange.max-this.dataRange.min)*o,c=function(e){let t=Math.floor((e-r)/n);return isNaN(t)&&console.warn(\"isNaN(x). feature start \"+Rt(e)+\" bp start \"+Rt(r)),t};if(t&&t.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const e=this.config.highlightSamples,n=this.config.onlyHandleClicksForHighlightedSamples,r=this.config.clickToHighlight;let s=-1,o={},l=[],h=[];this.clickDetectorCache={};for(let d of t){const t=c(d.start),u=c(d.end),f=s>=0?c(s):t;if(!isNaN(t)&&!isNaN(u)){this.clickDetectorCache[t]=[],this.clickDetectorCache[u]=[];for(let s=0;s<d.values.length;s++){const c=this.sampleKeys[s],p=d.values[s],g=a(p);if(t-f>=1){const s=o[c],h=a(s),d=e&&e[c];d?l.push([f,h,t,g,d]):r&&c in this.config.samplesClickedToHighlight?l.push([f,h,t,g,this.config.samplesClickedToHighlight[c]]):xo.strokeLine(i,f,h,t,g,{strokeStyle:\"#D9D9D9\"}),n&&!(c in e)||this.clickDetectorCache[t].push([f,h,t,g,c,d||\"gray\"])}if(u-t>=1){const s=e&&e[c];s?h.push([t,g,u,g,s]):r&&c in this.config.samplesClickedToHighlight?h.push([t,g,u,g,this.config.samplesClickedToHighlight[c]]):xo.strokeLine(i,t,g,u,g,{strokeStyle:\"gray\"}),n&&!(c in e)||this.clickDetectorCache[u].push([t,g,u,g,c,s||\"gray\"])}o[c]=p}s=d.end}}for(let e of l)xo.strokeLine(i,e[0],e[1],e[2],e[3],{strokeStyle:e[4],lineWidth:1.3});for(let e of h)xo.strokeLine(i,e[0],e[1],e[2],e[3],{strokeStyle:e[4],lineWidth:2})}(e=>{if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=a(t.y),n={strokeStyle:t.color,strokeWidth:2};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,n):xo.strokeLine(e.context,0,i,e.pixelWidth,i,n)}})(e)}doAutoscale(e){let t,i;return e.length>0?(t=Number.MAX_VALUE,i=-Number.MAX_VALUE,e.forEach((function(e){t=Math.min(t,...e.values),i=Math.max(i,...e.values)})),t-=.01,i+=.01):(t=0,i=100),{min:t,max:i}}clickedFeatures(e){const t=e.canvasX,i=e.canvasY;let n=null;for(n of Object.keys(this.clickDetectorCache))if(n=parseInt(n),n>=t)break;if(n){let e=Number.MAX_VALUE,o=[];const a=this.clickDetectorCache[n];for(let n of a){const r=n[0],s=n[2];if(t<r||t>s)return[];const a=n[1],c=n[3];if(i<Math.min(a,c)-10||i>Math.max(a,c)+10)continue;const l=oy(t,i,r,a,s,c);l<e&&(o=[{name:n[4],color:n[5]}],e=l)}if(e<5){if(this.config.clickToHighlight){if(o[0].name in this.config.samplesClickedToHighlight)delete this.config.samplesClickedToHighlight[o[0].name];else if(\"any\"===this.config.clickToHighlight){var r=[\"red\",\"darkblue\",\"green\",\"teal\",\"olivedrab\",\"orange\",\"maroon\",\"purple\",\"blue\",\"gold\"],s=r[Math.floor(Math.random()*(r.length+1))];this.config.samplesClickedToHighlight[o[0].name]=s}else this.config.samplesClickedToHighlight[o[0].name]=this.config.clickToHighlight;this.trackView.repaintViews()}return o}}return[]}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];return t.forEach((function(e){for(let t of Object.keys(e))Oa(e[t])&&i.push({name:t,value:e[t]})})),i}get supportsWholeGenome(){return!1}}function oy(e,t,i,n,r,s){const o=r-i,a=s-n,c=Math.abs(o*(n-t)-(i-e)*a),l=Math.sqrt(o*o+a*a);return l>0?c/l:0}class ay extends Hl{static defaults={height:300,theta:Math.PI/2,arcOrientation:\"UP\"};constructor(e,t){super(e,t),!1===e.arcOrientation?this.arcOrientation=\"DOWN\":!0===e.arcOrientation?this.arcOrientation=\"UP\":e.arcOrientation?this.arcOrientation=e.arcOrientation.toUpperCase():this.arcOrientation=\"UP\",\"bp\"===e.format?this.featureSource=new ly(e,t.genome):this.featureSource=new ud(e,t.genome)}async getFeatures(e,t,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const t=e.context,i=Math.PI/2,n=e.pixelWidth,r=e.pixelHeight;e.viewportWidth;const s=e.bpPerPixel,o=e.bpStart,a=s,c=\"UP\"===this.arcOrientation;xo.fillRect(t,0,e.pixelTop,n,r,{fillStyle:\"rgb(255, 255, 255)\"});const l=e.features;if(l){cy(l,1);for(let e of l)if(e.startLeft){let n=Math.round((e.startLeft-o)/a),r=Math.round((e.startRight-o)/a),s=Math.round((e.endLeft-o)/a),l=Math.round((e.endRight-o)/a);t.fillStyle=e.color,t.strokeStyle=e.color,t.beginPath();let h=(n+l)/2,d=(l-n)/2,u=this.height,f=Math.PI+(Math.PI/2-i),p=2*Math.PI-(Math.PI/2-i);c?(t.arc(h,u,d,f,p),t.lineTo(s,u)):(u=0,t.arc(h,u,d,p,f),t.lineTo(l,u));const g=(r+s)/2,m=(s-r)/2,w=u;c?(t.arc(g,w,m,p,f,!0),t.lineTo(n,w)):(t.arc(g,w,m,f,p,!0),t.lineTo(s,w)),t.stroke(),t.fill(),e.drawState={x1:h,y1:u,r1:d,x2:g,y2:w,r2:m,sa:f,ea:p}}else{let n=Math.round((e.start-o)/a),r=Math.round((e.end-o)/a);t.strokeStyle=e.color,t.beginPath();let s=(n+r)/2,l=(r-n)/2,h=this.height,d=Math.PI+(Math.PI/2-i),u=2*Math.PI-(Math.PI/2-i);c?t.arc(s,h,l,d,u):(h=0,t.arc(s,h,l,u,d)),t.stroke(),e.drawState={x1:s,y1:h,r1:l,sa:d,ea:u}}}}clickedFeatures(e){const t=super.clickedFeatures(e),i=[];cy(t,-1);for(let n of t){const t=n.drawState,r=e.canvasX-t.x1,s=e.canvasY-t.y1,o=Math.sqrt(r*r+s*s),a=t.r1+3;let c,l;if(void 0===t.x2)c=o,l=t.r1-3;else{const i=e.canvasX-t.x2,n=e.canvasY-t.y2;c=Math.sqrt(i*i+n*n),l=t.r2-3}if(o<a&&c>l){i.push(n);break}}return i}popupData(e,t){if(void 0===t&&(t=this.clickedFeatures(e)),t&&t.length>0)return this.extractPopupData(t[0],this.getGenomeId())}menuItemList(){return[{name:\"Toggle arc direction\",click:function(){this.arcOrientation=\"UP\"===this.arcOrientation?\"DOWN\":\"UP\",this.trackView.repaintViews()}}]}}function cy(e,t){e.sort((function(e,i){const n=void 0===e.score?-Number.MAX_VALUE:e.score,r=void 0===i.score?-Number.MAX_VALUE:i.score;return(void 0===t?1:t)*(n-r)}))}class ly{constructor(e,t){this.config=e,this.genome=t}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome;if(this.featureCache)return this.featureCache.queryFeatures(e,t,i);{const n=Ua(this.config),r=await Qs.loadByteArray(this.config.url,n);return this.featureCache=new Zs(function(e){if(!e)return null;const t=mh(e);let i,n=!0;const r=[],s=[],o=[];for(;void 0!==(i=t.nextLine());){const e=i.split(\"\\t\");if(n&&i.startsWith(\"color:\")){const t=\"rgb(\"+e[1]+\",\"+e[2]+\",\"+e[3]+\")\";r.push(t),e.length>4&&s.push(e[4])}else{n=!1;const t=e[0],i=Number.parseInt(e[1])-1,c=Number.parseInt(e[2])-1,l=Number.parseInt(e[3]),h=Number.parseInt(e[4]);var a=Number.parseInt(e[5]);const d=r[a];let u;u=i<=h?{chr:t,startLeft:Math.min(i,c),startRight:Math.max(i,c),endLeft:Math.min(l,h),endRight:Math.max(l,h),color:d,score:a}:{chr:t,startLeft:Math.min(l,h),startRight:Math.max(l,h),endLeft:Math.min(i,c),endRight:Math.max(i,c),color:d,score:a},u.start=u.startLeft,u.end=u.endRight,s.length>a&&(u.description=s[a]),o.push(u)}}return o}(r),s),this.featureCache.queryFeatures(e,t,i)}}}class hy{constructor(e){this.browser=e,this.type=\"ideogram\",this.height=16,this.order=Number.MIN_SAFE_INTEGER,this.disableButtons=!0,this.ignoreTrackMenu=!0}computePixelHeight(e){return this.height}draw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,features:r}){const s=t.chr,o=t.genome.getChromosome(s);if(void 0===o||i<=0||n<=0||\"all\"===s.toLowerCase())return;!function({ctx:e,chr:t,referenceFrame:i,genome:n,width:r,height:s,stainColors:o,features:a}){const c=1,l=.5*c,h=0;if(void 0===n)return;xo.fillRect(e,0,0,r,s,{fillStyle:_s.greyScale(255)});const d=a;if(d){const t=h+s/2,i=[],n=[];if(0===d.length)return;const a=r/d[d.length-1].end;e.beginPath(),xo.roundRect(e,l,l+h,r-2*l,s-2*l,(s-2*l)/2,0,1),e.clip();for(let r=0;r<d.length;r++){const l=d[r],u=a*l.start,f=a*l.end;\"c\"===l.type?(\"p\"===l.name.charAt(0)?(i[0]=u,n[0]=s+h,i[1]=u,n[1]=h,i[2]=f,n[2]=t):(i[0]=f,n[0]=s+h,i[1]=f,n[1]=h,i[2]=u,n[2]=t),e.fillStyle=\"rgb(150, 0, 0)\",e.strokeStyle=\"rgb(150, 0, 0)\",xo.polygon(e,i,n,1,0)):(e.fillStyle=dy(o,l),xo.fillRect(e,u,c+h,f-u,s-2*c))}}e.strokeStyle=_s.greyScale(41),xo.roundRect(e,l,l+h,r-2*l,s-2*l,(s-2*l)/2,0,1)}({ctx:e,features:r,chr:s,referenceFrame:t,genome:t.genome,width:i,height:n,stainColors:[]});const a=Math.round(t.bpPerPixel*i),c=t.start;let l=o.bpLength;const h=t.genome.getCytobands(s);if(h&&h.length>0&&h[h.length-1].end&&(l=Math.max(l,h[h.length-1].end),o.bpLength=l),a<l){const t=a/l,r=c/l;let s=Math.floor(r*i),o=Math.floor(t*i);s=Math.max(0,s),s=Math.min(i-o,s),e.save(),e.strokeStyle=\"red\",e.lineWidth=o<2?1:2;const h=s+e.lineWidth/2;o=o<2?1:o-e.lineWidth;const d=e.lineWidth/2,u=n-e.lineWidth;e.strokeRect(h,d,o,u),e.restore()}}dispose(){this.trackView=void 0}}function dy(e,t){if(\"c\"===t.type)return\"rgb(150, 10, 10)\";var i=t.stain,n=230;\"p\"===t.type&&(n=Math.floor(230-i/100*230));var r=e[n];return r||(r=\"rgb(\"+n+\",\"+n+\",\"+n+\")\",e[n]=r),r}let uy=new oo(\"Dark2\");[\"GT/AG\",\"CT/AC\",\"GC/AG\",\"CT/GC\",\"AT/AC\",\"GT/AT\",\"non-canonical\"].forEach((e=>{uy.getColor(e)}));class fy extends Hl{static defaults={margin:10,colorByNumReadsThreshold:5,height:100};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=e.type||\"junctions\",e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):this.featureSource=e.featureSource?e.featureSource:Ad(e,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get supportsWholeGenome(){return!1}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}computePixelHeight(e){return this.height}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=e.pixelHeight,a=r+s*n+1;if(this.isMergedTrack||xo.fillRect(i,0,e.pixelTop,s,o,{fillStyle:\"rgb(255, 255, 255)\"}),t){const s={};s.referenceFrame=e.viewport.referenceFrame,s.referenceFrameStart=s.referenceFrame.start,s.referenceFrameEnd=s.referenceFrameStart+s.referenceFrame.toBP(e.viewport.getWidth()),s.featureZoomOutTracker={};for(let e of t)if(!(e.end<r)){if(e.start>a)break;this.renderJunction(e,r,n,o,i,s)}}else console.log(\"No feature list\")}renderJunction(e,t,i,n,r,s){e.isVisible=!1;const o=Math.round((e.start-t)/i),a=Math.round((e.end-t)/i),c=(o+a)/2;if(a-o<=3){if(c in s.featureZoomOutTracker)return;s.featureZoomOutTracker[c]=!0}if(this.config.hideAnnotatedJunctions&&\"true\"===e.attributes.annotated_junction)return;if(this.config.hideUnannotatedJunctions&&\"false\"===e.attributes.annotated_junction)return;if(this.config.hideMotifs&&this.config.hideMotifs.includes(e.attributes.motif))return;if(this.config.hideStrand===e.strand)return;if(this.config.minJunctionEndsVisible){let t=0;if(e.start>=s.referenceFrameStart&&e.start<=s.referenceFrameEnd&&(t+=1),e.end>=s.referenceFrameStart&&e.end<=s.referenceFrameEnd&&(t+=1),t<this.config.minJunctionEndsVisible)return}let l,h,d,u;if(e.attributes.uniquely_mapped){if(l=parseInt(e.attributes.uniquely_mapped),l<this.config.minUniquelyMappedReads)return;if(h=parseInt(e.attributes.multi_mapped),d=l+h,d<this.config.minTotalReads)return;if(d>0&&h/d>this.config.maxFractionMultiMappedReads)return;if(e.attributes.maximum_spliced_alignment_overhang&&parseInt(e.attributes.maximum_spliced_alignment_overhang)<this.config.minSplicedAlignmentOverhang)return}if(e.attributes.num_samples_with_this_junction){if(u=parseInt(e.attributes.num_samples_with_this_junction),this.config.minSamplesWithThisJunction&&u<this.config.minSamplesWithThisJunction)return;if(this.config.maxSamplesWithThisJunction&&u>this.config.maxSamplesWithThisJunction)return;if(e.attributes.num_samples_total&&(e.attributes.percent_samples_with_this_junction=100*u/Number(e.attributes.num_samples_total),this.config.minPercentSamplesWithThisJunction&&(e.attributes.percent_samples_with_this_junction<this.config.minPercentSamplesWithThisJunction||e.attributes.percent_samples_with_this_junction>this.config.maxPercentSamplesWithThisJunction)))return}const f=this.margin,p=n,g=f+.5*p;let m=f;const w=f+p-10,b=(o+c)/2,F=(c+a)/2;let v,y,A=1;e.attributes.line_width?A=Number(e.attributes.line_width):(void 0===this.config.thicknessBasedOn||\"numUniqueReads\"===this.config.thicknessBasedOn?A=l:\"numReads\"===this.config.thicknessBasedOn?A=d:\"numSamplesWithThisJunction\"===this.config.thicknessBasedOn&&void 0!==u&&(A=u),A=1+Math.log(A+1)/Math.log(12)),void 0===this.config.bounceHeightBasedOn||\"random\"===this.config.bounceHeightBasedOn?v=(e.start+e.end)%7:\"distance\"===this.config.bounceHeightBasedOn?v=6*(e.end-e.start)/(s.referenceFrameEnd-s.referenceFrameStart):\"thickness\"===this.config.bounceHeightBasedOn&&(v=2*A),m+=p*Math.max(7-v,0)/10,y=e.attributes.color?e.attributes.color:void 0===this.config.colorBy||\"numUniqueReads\"===this.config.colorBy?l>this.config.colorByNumReadsThreshold?\"blue\":\"#AAAAAA\":\"numReads\"===this.config.colorBy?d>this.config.colorByNumReadsThreshold?\"blue\":\"#AAAAAA\":\"isAnnotatedJunction\"===this.config.colorBy?\"true\"===e.attributes.annotated_junction?\"#b0b0ec\":\"orange\":\"strand\"===this.config.colorBy?\"+\"===e.strand?\"#b0b0ec\":\"#ecb0b0\":\"motif\"===this.config.colorBy?uy.getColor(e.attributes.motif):\"#AAAAAA\";let C=\"\";e.attributes.label?C=e.attributes.label.replace(/_/g,\" \"):void 0===this.config.labelWith||\"uniqueReadCount\"===this.config.labelWith?C=l:\"totalReadCount\"===this.config.labelWith?C=d:\"numSamplesWithThisJunction\"===this.config.labelWith?void 0!==u&&(C=u):\"percentSamplesWithThisJunction\"===this.config.labelWith?void 0!==e.attributes.percent_samples_with_this_junction&&(C=e.attributes.percent_samples_with_this_junction.toFixed(0)+\"%\"):\"motif\"===this.config.labelWith&&void 0!==e.attributes.motif&&(C+=e.attributes.motif),\"uniqueReadCount\"===this.config.labelWithInParen?C+=\" (\"+l+\")\":\"totalReadCount\"===this.config.labelWithInParen?C+=\" (\"+d+\")\":\"multiMappedReadCount\"===this.config.labelWithInParen?h>0&&(C+=\" (+\"+h+\")\"):\"numSamplesWithThisJunction\"===this.config.labelWithInParen?void 0!==u&&(C+=\" (\"+u+\")\"):\"percentSamplesWithThisJunction\"===this.config.labelWithInParen?void 0!==e.attributes.percent_samples_with_this_junction&&(C+=\" (\"+e.attributes.percent_samples_with_this_junction.toFixed(0)+\"%)\"):\"motif\"===this.config.labelWithInParen&&void 0!==e.attributes.motif&&(C+=` ${e.attributes.motif}`),e.isVisible=!0,r.beginPath(),r.moveTo(o,w),r.bezierCurveTo(b,m,F,m,a,w),r.lineWidth=A,r.strokeStyle=y,r.stroke();const _=(e,t,i,n)=>{e.beginPath(),e.moveTo(t,i),e.lineTo(t-n/2,i-n),e.lineTo(t+n/2,i-n),e.lineTo(t,i),e.closePath(),e.fill()};if(e.attributes.left_shape||e.attributes.right_shape){r.fillStyle=y;const t=r.lineWidth>2?10:7;e.attributes.left_shape&&_(r,o,w,t),e.attributes.right_shape&&_(r,a,w,t)}r.fillText(C,c-r.measureText(C).width/2,(7*m+g)/8)}clickedFeatures(e){return super.clickedFeatures(e).filter((function(e){return e.isVisible&&e.attributes}))}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=[];for(let e of t){const t=\"function\"==typeof e.popupData?e.popupData(i):this.extractPopupData(e._f||e,this.getGenomeId());t&&(n.length>0&&n.push(\"<hr/><hr/>\"),Array.prototype.push.apply(n,t))}return n}dispose(){this.trackView=void 0}}const py={min:0,max:3e3,color:\"rgb(0,0,255)\"};class gy{constructor(e){e=e||py,this.max=e.max,this.min=e.min||0,this.cache=[],this.nbins=1e3,this.binsize=(this.max-this.min)/this.nbins,this.updateColor(e.color||\"rgb(0,0,255)\")}updateColor(e){const t=e.substring(4).replace(\")\",\"\").split(\",\");3===t.length&&(this.r=Number.parseInt(t[0].trim()),this.g=Number.parseInt(t[1].trim()),this.b=Number.parseInt(t[2].trim())),this.cache=[]}setMinMax(e,t){this.min=e,this.max=t,this.cache=[],this.binsize=(this.max-this.min)/this.nbins}getColor(e){if(e<this.min)return\"white\";const t=Math.floor((Math.min(this.max,e)-this.min)/this.binsize);if(void 0===this.cache[t]){const i=(ys.clamp(e,0,this.max)-0)/(this.max-0);this.cache[t]=`rgba(${this.r},${this.g},${this.b}, ${i})`}return this.cache[t]}toJson(){return{min:this.min,max:this.max,color:`rgb(${this.r},${this.g},${this.b})`}}static parse(e){const t=e.split(\",\"),i={min:Number.parseFloat(t[0]),max:Number.parseFloat(t[1]),color:`${t[2]},${t[3]},${t[4]}`};return new gy(i)}}class my extends Hl{static defaults={height:300,rowHeight:3,max:3e3,visibilityWindow:1e4};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"shoebox\",this.height=e.height||300,this.rowHeight=e.rowHeight||3,this.max=e.max||3e3,this.sampleKeys=[];for(let e=1;e<=100;e++)this.sampleKeys.push(e);const t=Object.assign({},this.config);t.format=\"shoebox\",this.featureSource=Ad(t,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))if(this.header&&this.setTrackProperties(this.header),this.config.colorScale&&this.config.colorScale.max&&this.config.colorScale.color)this.colorScale=new gy(this.config.colorScale);else{const e=this.dataRange.min,t=this.dataRange.max;this.colorScale=new gy({min:e,max:t,color:this.color})}}get color(){return this._color||\"rgb(0,0,255)\"}set color(e){this._color=e,this.colorScale&&this.colorScale.updateColor(e)}menuItemList(){const e=[];e.push(\"<hr/>\");let t=Bt(\"<div>\");return t.text(\"Set data range\"),e.push({object:t,dialog:function(){this.trackView.track.selected?this.browser.dataRangeDialog.configure(this.trackView.browser.getSelectedTrackViews()):this.browser.dataRangeDialog.configure(this.trackView),this.browser.dataRangeDialog.present(Bt(this.browser.columnContainer))}}),e}setDataRange({min:e,max:t}){this.dataRange.min=e,this.dataRange.max=t,this.colorScale.min=e,this.colorScale.max=t,this.trackView.repaintViews()}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys,height:this.rowHeight,yOffset:0}}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}draw({context:e,pixelTop:t,pixelWidth:i,pixelHeight:n,features:r,bpPerPixel:s,bpStart:o}){if(xo.fillRect(e,0,t,i,n,{fillStyle:\"rgb(255, 255, 255)\"}),r&&r.length>0){const a=this.rowHeight,c=t+n,l=o+i*s+1,h=a;for(let i of r){if(i.end<o||i.start>l)continue;const n=Math.round((i.start-o)/s),r=Math.round((i.end-o)/s),d=Math.max(1,r-n);let u=0;for(let r=i.values.length-1;r>=0;r--){const s=i.values[r],o=u*a;if(o+a<t||o>c)continue;const l=this.colorScale.getColor(s);e.fillStyle=l,e.fillRect(n,o,d,h),u++}}}}computePixelHeight(e){return e&&0!==e.length?e[0].values.length*this.rowHeight:0}clickedFeatures(e){const t=super.clickedFeatures(e),i=e.y;return t.filter((function(e){const t=e.pixelRect;return t&&i>=t.y&&i<=t.y+t.h}))}hoverText(e){const t=this.clickedFeatures(e);if(t&&t.length>0)return`${t[0].sample}: ${t[0].value}`}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){i.length>0&&(i.push(\"<hr/>\"),i.push(\"<hr/>\"));const t=e._f||e,n=\"function\"==typeof t.popupData?t.popupData(this.type,this.browser.genome.id):this.extractPopupData(t);Array.prototype.push.apply(i,n)}return i}get supportsWholeGenome(){return!1}getState(){const e=super.getState();return e.colorScale=this.colorScale.toJson(),e}}const wy=new Map([[\"ideogram\",(e,t)=>new hy(e,t)],[\"sequence\",(e,t)=>new Zd(e,t)],[\"feature\",(e,t)=>new Hd(e,t)],[\"seg\",(e,t)=>new Pf(e,t)],[\"mut\",(e,t)=>new Pf(e,t)],[\"maf\",(e,t)=>new Pf(e,t)],[\"shoebox\",(e,t)=>new my(e,t)],[\"wig\",(e,t)=>new ld(e,t)],[\"merged\",(e,t)=>new tf(e,t)],[\"alignment\",(e,t)=>new tw(e,t)],[\"interaction\",(e,t)=>new iw(e,t)],[\"interact\",(e,t)=>new iw(e,t)],[\"variant\",(e,t)=>new Yv(e,t)],[\"qtl\",(e,t)=>new ty(e,t)],[\"eqtl\",(e,t)=>new ty(e,t)],[\"gwas\",(e,t)=>new ry(e,t)],[\"arc\",(e,t)=>new ay(e,t)],[\"gcnv\",(e,t)=>new sy(e,t)],[\"junction\",(e,t)=>new fy(e,t)],[\"blat\",(e,t)=>new Vd(e,t)],[\"cnvpytor\",(e,t)=>new Gv(e,t)]]);class by{constructor(e,t){const i=(new DOMParser).parseFromString(e,\"text/xml\");this.processRootNode(i,t);const n=i.getElementsByTagName(\"Resource\"),r=i.getElementsByTagName(\"Track\"),s=r&&r.length>0,o=[];this.tracks=o;const a=new Map;Array.from(n).forEach((function(e,t){var i={url:e.getAttribute(\"path\"),indexURL:e.getAttribute(\"index\"),order:t};a.set(i.url,i),s||o.push(i)})),s&&Array.from(r).forEach((function(e){const t=e.getElementsByTagName(\"Track\");if(t&&t.length>0){const i={type:\"merged\",tracks:[]};Fy(e,i),o.push(i),Array.from(t).forEach((function(e){e.processed=!0;const t=e.getAttribute(\"id\"),n=a.get(t);n&&(i.tracks.push(n),Fy(e,n),n.autoscale=!1,i.height=n.height)}))}else if(!e.processed){const t=e.getAttribute(\"id\"),i=a.get(t);i&&(o.push(i),Fy(e,i))}}))}processRootNode(e,t){const i=e.getElementsByTagName(\"Session\");!i||i.length;const n=i.item(0),r=n.getAttribute(\"genome\"),s=n.getAttribute(\"locus\"),o=n.getAttribute(\"ucscID\");t&&t.hasOwnProperty(r)?this.genome=r:(this.reference={fastaURL:r},o&&(this.reference.id=o)),s&&(this.locus=s)}}function Fy(e,t){t.name=e.getAttribute(\"name\");const i=e.getAttribute(\"color\");i&&(t.color=\"rgb(\"+i+\")\");const n=e.getAttribute(\"altColor\");i&&(t.altColor=\"rgb(\"+n+\")\");const r=e.getAttribute(\"height\");r&&(t.height=parseInt(r));const s=e.getAttribute(\"autoScale\");s&&(t.autoscale=\"true\"===s);const o=e.getAttribute(\"autoscaleGroup\");o&&(t.autoscaleGroup=o);const a=e.getAttribute(\"windowFunction\");a&&(t.windowFunction=a);const c=e.getAttribute(\"visibilityWindow\")||e.getAttribute(\"featureVisibilityWindow\");c&&(t.visibilityWindow=c);const l=e.getAttribute(\"indexed\");l&&(t.indexed=\"true\"===l);const h=e.getAttribute(\"normalize\");h&&(t.normalize=\"true\"===h);const d=e.getElementsByTagName(\"DataRange\");if(d.length>0){const e=d.item(0);t.min=Number(e.getAttribute(\"minimum\")),t.max=Number(e.getAttribute(\"maximum\")),t.logScale=\"LOG\"===e.getAttribute(\"type\")}}class vy{constructor(e,t,i,n,r){this.genome=e,this.chr=t,this.start=i,this.end=n,this.bpPerPixel=r,this.id=s()}get center(){return(this.start+this.end)/2}get locusSearchString(){return`${this.chr}:${this.start+1}-${this.end}`}extend(e){const t=Math.min(e.start,this.start),i=Math.max(e.end,this.end),n=(i-t)/(this.end-this.start);this.start=t,this.end=i,this.bpPerPixel*=n}calculateEnd(e){return this.start+this.bpPerPixel*e}calculateCenter(e){return this.start+this.bpPerPixel*e/2}calculateBPP(e,t){return(e-this.start)/t}set(e){this.chr=e.chr,this.start=e.start,this.bpPerPixel=e.bpPerPixel}toPixels(e){return e/this.bpPerPixel}toBP(e){return this.bpPerPixel*e}shift(e){this.start+=e,this.end+=e}shiftPixels(e,t,i){const n=this.start,r=e*this.bpPerPixel;return this.start+=r,i&&this.clampStart(t),this.end=this.start+t*this.bpPerPixel,n!==this.start}clampStart(e){const t=this.genome.getChromosome(this.chr).bpStart||0;if(this.start=Math.max(t,this.start),e){const{bpLength:t}=this.genome.getChromosome(this.chr),i=t-e*this.bpPerPixel;this.start>i&&(this.start=i)}}async zoomWithScaleFactor(e,t,i,n){const r=void 0===n?this.start+this.toBP(i/2):n,s=this.start,o=this.bpPerPixel,a=this.getChromosome().bpLength,c=t<1?e.minimumBases()/i:a/i;this.bpPerPixel=t<1?Math.max(this.bpPerPixel*t,c):Math.min(this.bpPerPixel*t,c);const l=this.bpPerPixel*i;this.start=r-.5*l,this.clampStart(i),this.end=this.start+l;(s!==this.start||o!==this.bpPerPixel)&&await e.updateViews(!0)}getChromosome(){return this.genome.getChromosome(this.chr)}getMultiLocusLabelBPLengthOnly(e){const t=\"&nbsp\",i=Math.floor(this.start)+1,n=Math.round(this.start+this.bpPerPixel*e);return`${t}${this.chr}${t}${Wa(n-i)}${t}`}getMultiLocusLabelLocusOnly(e){const t=\"&nbsp\",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(e);return`${t}${i}:${n}-${r}${t}`}getMultiLocusLabel(e){const t=\"&nbsp\",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(e),s=Math.floor(this.start)+1;return`${t}${i}:${n}-${r}${t}${t}(${Wa(Math.round(this.start+this.bpPerPixel*e)-s)})${t}`}getPresentationLocusComponents(e){if(\"all\"===this.chr)return{chr:this.chr};{const t=Rt(Math.floor(this.start)+1),i=Rt(Math.round(this.start+this.bpPerPixel*e));return{chr:this.chr,start:t,end:i}}}getLocusString(){if(\"all\"===this.chr)return\"all\";return`${this.genome.getChromosomeDisplayName(this.chr)}:${Rt(Math.floor(this.start)+1)}-${Rt(Math.round(this.end))}`}description(e){console.log(` ${e||\"\"} referenceFrame - ${this.chr} bpp ${this.bpPerPixel.toFixed(3)} start ${Rt(Math.round(this.start))} end ${Rt(Math.round(this.end))} `)}overlaps(e){return this.chr===e.chr&&this.end>=e.start&&e.end>=this.start}}function yy(){return\"3.0.9\"}const Ay=\"Maximum sequence count exceeded\";class Cy{constructor(t,i){this.container=e({class:\"igv-chromosome-select-widget-container\"}),i.appendChild(this.container),this.select=document.createElement(\"select\"),this.select.setAttribute(\"name\",\"chromosome-select-widget\"),this.container.appendChild(this.select),this.select.addEventListener(\"change\",(()=>{this.select.blur(),\"\"!==this.select.value&&Ay!==this.select.value&&t.search(this.select.value)})),this.showAllChromosomes=!1!==t.config.showAllChromosomes,this.genome=t.genome}show(){this.container.style.display=\"flex\"}hide(){this.container.style.display=\"none\"}setValue(e){this.select.value=this.genome.getChromosomeDisplayName(e)}update(e){this.genome=e;const t=e.wgChromosomeNames.map((t=>e.getChromosomeDisplayName(t)))||[];if(this.showAllChromosomes&&e.chromosomeNames.length>1){const i=new Set(t);let n=0;for(let r of e.chromosomeNames){if(1e3==++n){t.push(Ay);break}i.has(r)||(r=e.getChromosomeDisplayName(r),t.push(r))}}this.select.innerHTML=\"\",e.showWholeGenomeView()&&t.unshift(\"all\");for(let i of t){const t=document.createElement(\"option\");t.setAttribute(\"value\",i),t.innerText=e.getChromosomeDisplayName(i),this.select.appendChild(t)}}}class _y{constructor(t,i){this.container=e({class:\"igv-windowsize-panel-container\"}),t.appendChild(this.container),i.on(\"locuschange\",(e=>{this.updatePanel(e)})),this.browser=i}show(){this.container.style.display=\"block\"}hide(){this.container.style.display=\"none\"}updatePanel(e){const t=this.browser.calculateViewportWidth(this.browser.referenceFrameList.length);this.container.innerText=1===e.length?Wa(Math.round(t*e[0].bpPerPixel)):\"\"}}class xy extends Ju{constructor(e,t,i,n){super(e,t,\"Select Tracks\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>multi select</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"multi-select\">\\n            <rect id=\"backdrop-copy-3\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-copy-3\" transform=\"translate(81, 427)\" fill=\"#737373\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy-2\" transform=\"translate(82, 277)\">\\n                <rect id=\"Rectangle\" fill-opacity=\"0.33\" fill=\"#CFCECE\" x=\"133\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke-opacity=\"0.32659528\" stroke=\"#CFCECE\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy\" transform=\"translate(81, 119)\" fill=\"#737373\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-17\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>multi select hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"multi-select-hover\">\\n            <rect id=\"backdrop-copy-4\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-copy-3\" transform=\"translate(81, 427)\" fill=\"#FFFFFF\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke=\"#FFFFFF\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy-2\" transform=\"translate(82, 277)\">\\n                <rect id=\"Rectangle\" fill-opacity=\"0.33\" fill=\"#CFCECE\" x=\"133\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke-opacity=\"0.33\" stroke=\"#CFCECE\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy\" transform=\"translate(81, 119)\" fill=\"#FFFFFF\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-17\" stroke=\"#FFFFFF\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n        </g>\\n    </g>\\n</svg>',!1),this.navbar=i,this.enableMultiTrackSelection=!1,this.button.addEventListener(\"mouseenter\",(e=>{!1===n&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(e=>{!1===n&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{this.setMultiTrackSelection(!this.enableMultiTrackSelection)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler)}setMultiTrackSelection(e){this.enableMultiTrackSelection=e,this.setState(this.enableMultiTrackSelection),!1===this.enableMultiTrackSelection&&this.navbar.overlayTrackButton.setVisibility(!1);for(const t of this.browser.trackViews)t.enableTrackSelection(e)}}class ky{constructor(t,i){this.browser=i,this.columnContainer=t,this.horizontalGuide=e({class:\"igv-cursor-guide-horizontal\"}),t.appendChild(this.horizontalGuide),this.verticalGuide=e({class:\"igv-cursor-guide-vertical\"}),t.appendChild(this.verticalGuide),this.addMouseHandler(i),this.setVisibility(i.config.showCursorGuide)}addMouseHandler(e){this.boundMouseMoveHandler=function(t){t.target.tagName;const{x:i,y:n}=a(t,this.columnContainer);if(this.horizontalGuide.style.top=`${n}px`,\"CANVAS\"===t.target.tagName){const n=function(e,t){for(;e.parentElement;){if(e.parentElement.classList.contains(t))return e.parentElement;e=e.parentElement}return}(t.target,\"igv-viewport\");if(n&&e.getRulerTrackView()){this.verticalGuide.style.left=`${i}px`;const r=e.root.querySelectorAll(\".igv-column\");let s;const o=n.parentElement;for(let e=0;e<r.length;e++)void 0===s&&o===r[e]&&(s=e);if(void 0!==s){const i=e.getRulerTrackView().viewports[s].mouseMove(t);if(i){const{start:e,bp:t,end:n}=i,r=(t-e)/(n-e);this.customMouseHandler&&this.customMouseHandler({start:e,bp:t,end:n,interpolant:r})}}}}}.bind(this),this.columnContainer.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandler(){this.columnContainer.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}setVisibility(e){!0===e?this.show():this.hide()}show(){this.verticalGuide.style.display=\"block\",this.horizontalGuide.style.display=\"block\"}hide(){if(this.verticalGuide.style.display=\"none\",this.horizontalGuide.style.display=\"none\",this.browser.getRulerTrackView())for(let e of this.browser.getRulerTrackView().viewports)e.$tooltip.hide()}}class Iy extends Ju{constructor(e,t){super(e,t,\"Crosshairs\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>cursor</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"cursor\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-3\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group\" transform=\"translate(5, 9)\" stroke-width=\"24\">\\n                <line x1=\"0.5\" y1=\"212.5\" x2=\"614.5\" y2=\"212.5\" id=\"Line\"></line>\\n                <line x1=\"-115.5\" y1=\"303.5\" x2=\"490.5\" y2=\"303.5\" id=\"Line-Copy\" transform=\"translate(187.5, 303.5) scale(-1, 1) rotate(90) translate(-187.5, -303.5)\"></line>\\n            </g>\\n            <circle id=\"Oval\" stroke-width=\"24\" cx=\"191.5\" cy=\"221.5\" r=\"88.5\"></circle>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>cursor hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"cursor-hover\">\\n            <rect id=\"Rectangle-Copy-5\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group-Copy-2\" transform=\"translate(5, 9)\" stroke=\"#FFFFFF\" stroke-width=\"24\">\\n                <line x1=\"0.5\" y1=\"212.5\" x2=\"614.5\" y2=\"212.5\" id=\"Line\"></line>\\n                <line x1=\"-115.5\" y1=\"303.5\" x2=\"490.5\" y2=\"303.5\" id=\"Line-Copy\" transform=\"translate(187.5, 303.5) scale(-1, 1) rotate(90) translate(-187.5, -303.5)\"></line>\\n            </g>\\n            <circle id=\"Oval\" stroke=\"#FFFFFF\" stroke-width=\"24\" cx=\"191.5\" cy=\"221.5\" r=\"88.5\"></circle>\\n        </g>\\n    </g>\\n</svg>',t.doShowCursorGuide),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowCursorGuide&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowCursorGuide&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowCursorGuide=!t.doShowCursorGuide,t.setCursorGuideVisibility(t.doShowCursorGuide),this.setState(t.doShowCursorGuide)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showCursorTrackingGuideButton)}}class Sy extends Ju{constructor(e,t){super(e,t,\"Center Line\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>centerline</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"centerline\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-2\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"6.5\" y1=\"312.5\" x2=\"618.5\" y2=\"312.5\" id=\"Line-Copy\" stroke-width=\"31\" transform=\"translate(312.5, 312.5) scale(-1, 1) rotate(90) translate(-312.5, -312.5)\"></line>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>centerline hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"centerline-hover\">\\n            <rect id=\"Rectangle-Copy-9\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"6.5\" y1=\"312.5\" x2=\"618.5\" y2=\"312.5\" id=\"Line-Copy\" stroke=\"#FFFFFF\" stroke-width=\"31\" transform=\"translate(312.5, 312.5) scale(-1, 1) rotate(90) translate(-312.5, -312.5)\"></line>\\n        </g>\\n    </g>\\n</svg>',t.config.showCenterGuide),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowCenterLine&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowCenterLine&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowCenterLine=!t.doShowCenterLine,t.setCenterLineVisibility(t.doShowCenterLine),this.setState(t.doShowCenterLine)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showCenterGuideButton)}}class Ey extends Ju{constructor(e,t){super(e,t,\"Track Labels\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>track labels</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"track-labels\" fill=\"#FFFFFF\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-27\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"group\" transform=\"translate(52.2778, 149.7248)\" stroke-width=\"24\">\\n                <path d=\"M448.444444,87.1189616 L448.444444,322.431462 L166.619398,322.431462 L19.2344421,204.775212 L166.619398,87.1189616 L448.444444,87.1189616 Z M244.028212,163.997434 C232.925565,163.997434 222.874656,168.493347 215.598982,175.760254 C208.318067,183.032394 203.815972,193.079106 203.815972,204.175675 C203.815972,215.272243 208.318067,225.318955 215.598982,232.591095 C222.874656,239.858002 232.925565,244.353915 244.028212,244.353915 C255.130858,244.353915 265.181767,239.858002 272.457442,232.591095 C279.738356,225.318955 284.240451,215.272243 284.240451,204.175675 C284.240451,193.079106 279.738356,183.032394 272.457442,175.760254 C265.181767,168.493347 255.130858,163.997434 244.028212,163.997434 Z\" id=\"backdrop\"></path>\\n                <path d=\"M495.232604,12 L495.232604,264.550423 L193.616935,264.550423 L35.4455183,138.275212 L193.616935,12 L495.232604,12 Z M168.133512,95.1660194 C156.441871,95.1660194 145.858581,99.8943121 138.197214,107.534302 C130.523695,115.18641 125.780417,125.758499 125.780417,137.434423 C125.780417,149.110347 130.523695,159.682435 138.197214,167.334543 C145.858581,174.974533 156.441871,179.702826 168.133512,179.702826 C179.825153,179.702826 190.408443,174.974533 198.06981,167.334543 C205.743329,159.682435 210.486607,149.110347 210.486607,137.434423 C210.486607,125.758499 205.743329,115.18641 198.06981,107.534302 C190.408443,99.8943121 179.825153,95.1660194 168.133512,95.1660194 Z\" id=\"hero\"></path>\\n            </g>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>track labels hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"track-labels-hover\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-29\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"group\" transform=\"translate(52.2778, 149.7248)\" fill=\"#FFFFFF\" stroke-width=\"24\">\\n                <path d=\"M448.444444,85.1189616 L448.444444,320.431462 L166.619398,320.431462 L19.2344421,202.775212 L166.619398,85.1189616 L448.444444,85.1189616 Z M244.028212,161.997434 C232.925565,161.997434 222.874656,166.493347 215.598982,173.760254 C208.318067,181.032394 203.815972,191.079106 203.815972,202.175675 C203.815972,213.272243 208.318067,223.318955 215.598982,230.591095 C222.874656,237.858002 232.925565,242.353915 244.028212,242.353915 C255.130858,242.353915 265.181767,237.858002 272.457442,230.591095 C279.738356,223.318955 284.240451,213.272243 284.240451,202.175675 C284.240451,191.079106 279.738356,181.032394 272.457442,173.760254 C265.181767,166.493347 255.130858,161.997434 244.028212,161.997434 Z\" id=\"backdrop\"></path>\\n                <path d=\"M495.232604,12 L495.232604,264.550423 L193.616935,264.550423 L35.4455183,138.275212 L193.616935,12 L495.232604,12 Z M168.133512,95.1660194 C156.441871,95.1660194 145.858581,99.8943121 138.197214,107.534302 C130.523695,115.18641 125.780417,125.758499 125.780417,137.434423 C125.780417,149.110347 130.523695,159.682435 138.197214,167.334543 C145.858581,174.974533 156.441871,179.702826 168.133512,179.702826 C179.825153,179.702826 190.408443,174.974533 198.06981,167.334543 C205.743329,159.682435 210.486607,149.110347 210.486607,137.434423 C210.486607,125.758499 205.743329,115.18641 198.06981,107.534302 C190.408443,99.8943121 179.825153,95.1660194 168.133512,95.1660194 Z\" id=\"hero\"></path>\\n            </g>\\n        </g>\\n    </g>\\n</svg>',t.config.showTrackLabels),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowTrackLabels&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowTrackLabels&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowTrackLabels=!t.doShowTrackLabels,t.setTrackLabelVisibility(t.doShowTrackLabels),this.setState(t.doShowTrackLabels)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showTrackLabelButton)}}class Ny extends Ju{constructor(e,t){super(e,t,[\"ROI\",\"Regions of Interest Table\"],ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>roi</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"roi\">\\n            <rect id=\"Rectangle-Copy-23\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <text id=\"ROI\" font-family=\"HelveticaNeue-Bold, Helvetica Neue\" font-size=\"258\" font-weight=\"bold\" fill=\"#737373\">\\n                <tspan x=\"81.445\" y=\"389\">ROI</tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>roi hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"roi-hover\">\\n            <rect id=\"Rectangle-Copy-24\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <text id=\"ROI\" font-family=\"HelveticaNeue-Bold, Helvetica Neue\" font-size=\"258\" font-weight=\"bold\" fill=\"#FFFFFF\">\\n                <tspan x=\"81.445\" y=\"389\">ROI</tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>',!1),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowROITable&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowROITable&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>this.buttonHandler(!t.doShowROITable))),this.setVisibility(!1)}buttonHandler(e){this.setState(e),this.browser.setROITableVisibility(e)}}class By extends Ju{constructor(e,t){super(e,t,\"Sample Info\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample info</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-info\">\\n            <rect id=\"Rectangle-Copy-6\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group-2\" transform=\"translate(8, 149)\">\\n                <rect id=\"Rectangle\" fill=\"#8DD3C7\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#FBB4AE\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#7FC97F\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#E41A1C\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#3F70AE\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"Group-2-Copy\" transform=\"translate(8, 251)\">\\n                <rect id=\"Rectangle\" fill=\"#E41A1C\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BC80BD\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#FFFFB3\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"Group-2-Copy-2\" transform=\"translate(314, 404) scale(-1, 1) translate(-314, -404)translate(8, 353)\">\\n                <rect id=\"Rectangle\" fill=\"#1B9E77\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BAD1E9\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#4DAF4A\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#CBF03E\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <rect id=\"Rectangle-Copy-10\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample info hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-info-hover\">\\n            <rect id=\"Rectangle-Copy-14\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-2\" transform=\"translate(314, 404) scale(-1, 1) translate(-314, -404)translate(8, 353)\">\\n                <rect id=\"Rectangle\" fill=\"#1B9E77\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BAD1E9\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#4DAF4A\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#CBF03E\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"row-1\" transform=\"translate(8, 251)\">\\n                <rect id=\"Rectangle\" fill=\"#E41A1C\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BC80BD\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#FFFFB3\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"row-0\" transform=\"translate(8, 149)\">\\n                <rect id=\"Rectangle\" fill=\"#8DD3C7\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#FBB4AE\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#7FC97F\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#E41A1C\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#3F70AE\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <rect id=\"Rectangle-Copy-15\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <rect id=\"scrim\" fill=\"#000000\" style=\"mix-blend-mode: hue;\" x=\"8\" y=\"149\" width=\"612\" height=\"306\"></rect>\\n        </g>\\n    </g>\\n</svg>',!1),this.showSampleInfo=!1,this.button.addEventListener(\"mouseenter\",(()=>{!1===this.showSampleInfo&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===this.showSampleInfo&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>{this.performClickWithState(t,void 0)}))}performClickWithState(e,t){this.showSampleInfo=void 0===t?!this.showSampleInfo:t;e.columnContainer.querySelector(\".igv-sample-info-column\").style.display=!1===this.showSampleInfo?\"none\":\"flex\",this.setState(this.showSampleInfo),e.layoutChange()}setButtonVisibility(e){this.showSampleInfo=e,this.setState(this.showSampleInfo),!0===this.showSampleInfo?this.show():this.hide()}}class My extends Ju{constructor(e,t){super(e,t,\"Sample Names\",'<svg width=\"90px\" height=\"20px\" viewBox=\"0 0 90 20\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"igv-navbar-button-group\">\\n            <rect id=\"Rectangle\" x=\"0.5\" y=\"0.5\" width=\"89\" height=\"18\" rx=\"6\"></rect>\\n            <text id=\"igv-text-button-label\" x=\"50%\" y=\"50%\" dy=\".1em\" font-family=\"Helvetica\" font-size=\"12\" font-weight=\"normal\" letter-spacing=\"-0.372\">\\n                <tspan id=\"igv-navbar-button-label\"></tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample names</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-names\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-13\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"80\" y1=\"465\" x2=\"541\" y2=\"464.5\" id=\"Line-3-Copy-3\" stroke-width=\"32\"></line>\\n            <line x1=\"80\" y1=\"312.5\" x2=\"542\" y2=\"313\" id=\"Line-3\" stroke-width=\"32\"></line>\\n            <line x1=\"80\" y1=\"158\" x2=\"541\" y2=\"158\" id=\"Line-3-Copy\" stroke-width=\"32\"></line>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample names hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-names-hover\">\\n            <rect id=\"Rectangle-Copy-18\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"80\" y1=\"465\" x2=\"541\" y2=\"464.5\" id=\"Line-3-Copy-3\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n            <line x1=\"80\" y1=\"312.5\" x2=\"542\" y2=\"313\" id=\"Line-3\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n            <line x1=\"80\" y1=\"158\" x2=\"541\" y2=\"158\" id=\"Line-3-Copy\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n        </g>\\n    </g>\\n</svg>',t.config.showSampleNames),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.showSampleNames&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.showSampleNames&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>{this.performClickWithState(t,void 0)})),!0===t.config.showSampleNameButton?this.show():this.hide()}performClickWithState(e,t){e.showSampleNames=void 0===t?!e.showSampleNames:t;e.columnContainer.querySelector(\".igv-sample-name-column\").style.display=!1===e.showSampleNames?\"none\":\"flex\",this.setState(e.showSampleNames),e.layoutChange()}}class Ry{constructor(t,i){this.parent=t,this.popover=e({class:\"igv-ui-dropdown\"}),t.appendChild(this.popover),this.popoverContent=e(),this.popover.appendChild(this.popoverContent),this.popover.style.display=\"none\",this.shim=i}configure(e){if(0===e.length)return;const t=nc(e,this.popover);for(const{object:e}of t)this.popoverContent.appendChild(e)}present(e){this.popover.style.display=\"block\";let{x:t,y:i}=a(e,this.parent);this.popover.style.left=`${t+this.shim.left}px`,this.popover.style.top=`${i+this.shim.top}px`}_present(e){this.popover.style.display=\"block\";let{x:t,y:i,width:n}=a(e,this.parent);t+=this.shim.left,i+=this.shim.top,this.popover.style.top=`${i}px`;const{width:r}=this.popover.getBoundingClientRect(),s=t+r,o=s-n;this.popover.style.left=`${s>n?t-o:t}px`}dismiss(){this.popover.style.display=\"none\"}}class Dy extends Ju{constructor(e,t){super(e,t,\"Save Image\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>save image</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"save-image\">\\n            <rect id=\"border\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"frame\" transform=\"translate(66, 66)\" fill=\"#737373\" fill-rule=\"nonzero\">\\n                <path d=\"M54.75,493 C39.69375,493 26.8046875,487.639062 16.0828125,476.917187 C5.3609375,466.195312 0,453.30625 0,438.25 L0,274 L54.75,274 L54.75,438.25 L219,438.25 L219,493 L54.75,493 Z\" id=\"Path\"></path>\\n                <path d=\"M274,493 L274,438.25 L438.25,438.25 L438.25,274 L493,274 L493,438.25 C493,453.30625 487.639062,466.195312 476.917187,476.917187 C466.195312,487.639062 453.30625,493 438.25,493 L274,493 Z\" id=\"Path\"></path>\\n                <path d=\"M0,219 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Hy(t,i,u.get(0)),!1===t.showNavigation&&this.$navigation.hide()}navbarDidResize(){const e=this.$navigation.width(),t=this.currentNavbarButtonClass();\"igv-navbar-text-button\"===t&&(this.textButtonContainerWidth=this.navbarRightContainer.getBoundingClientRect().width);const i=this.browser,n=i.isMultiLocusWholeGenomeView()||i.referenceFrameList&&mu.isWholeGenomeView(i.referenceFrameList[0].chr);n?this.windowSizePanel.hide():this.windowSizePanel.show();const{x:r,width:s}=this.navbarLeftContainer.getBoundingClientRect(),o=r+s,{x:a}=this.navbarRightContainer.getBoundingClientRect();let c;if(\"igv-navbar-text-button\"===t&&a-o<8)c=\"igv-navbar-icon-button\";else if(this.textButtonContainerWidth&&\"igv-navbar-icon-button\"===t){e-o-this.textButtonContainerWidth>8&&(c=\"igv-navbar-text-button\")}let l;c&&t!==c&&(this.currentClass=c,this.browser.fireEvent(\"navbar-resize\",[c])),l=n?\"igv-zoom-widget-hidden\":e>860?\"igv-zoom-widget\":\"igv-zoom-widget-900\",Bt(this.zoomWidget.zoomContainer).removeClass(),Bt(this.zoomWidget.zoomContainer).addClass(l)}setCenterLineButtonVisibility(e){e?this.centerLineButton.setVisibility(!e):this.centerLineButton.setVisibility(this.config.showCenterGuideButton)}setCursorGuideVisibility(e){e?this.cursorGuide.show():this.cursorGuide.hide()}updateGenome(e){let t=e.id&&e.id.length<20?e.id:`${e.id.substring(0,8)}...${e.id.substring(e.id.length-8)}`;this.$current_genome.text(t),this.$current_genome.attr(\"title\",e.description);!1!==this.config.showChromosomeWidget&&!1!==e.showChromosomeWidget&&e.chromosomeNames&&e.chromosomeNames.length>1?(this.chromosomeSelectWidget.update(e),this.chromosomeSelectWidget.show()):this.chromosomeSelectWidget.hide()}updateLocus(e,t){this.$searchInput&&this.$searchInput.val(e),this.chromosomeSelectWidget&&(this.chromosomeSelectWidget.select.value=t)}currentNavbarButtonClass(){return this.currentClass}setEnableTrackSelection(e){this.multiTrackSelectButton.setMultiTrackSelection(e)}getEnableTrackSelection(){return this.multiTrackSelectButton.enableMultiTrackSelection}hide(){this.$navigation.hide()}show(){this.$navigation.show()}}const Oy=(e,t)=>{const i=0===e?t.nextElementSibling:t.previousElementSibling;t.remove(),i.remove()},Uy=t=>{const i=e({class:\"igv-column-shim\"});Ya(i,t);const 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Vy=function(t,i){this.button=e({class:\"igv-navbar-button\"}),t.appendChild(this.button),this.button.textContent=\"circular view\",this.button.addEventListener(\"click\",(()=>{i.circularViewVisible=!i.circularViewVisible})),this.browser=i,this.setVisibility(i.config.showCircularViewButton),this.setState(i.circularViewVisible)};Vy.prototype.setVisibility=function(e){!0===e?this.show():this.hide()},Vy.prototype.setState=function(e){!0===e?this.button.classList.add(\"igv-navbar-button-clicked\"):this.button.classList.remove(\"igv-navbar-button-clicked\")},Vy.prototype.show=function(){this.button.style.display=\"block\",this.setState(this.browser.circularViewVisible)},Vy.prototype.hide=function(){this.button.style.display=\"none\"};class jy{constructor(t,i){this.browser=t,this.container=e({class:\"igv-roi-menu\"}),i.appendChild(this.container);const n=e();this.container.appendChild(n),u(n,(()=>this.container.style.display=\"none\")),this.body=e(),this.container.appendChild(this.body),this.container.style.display=\"none\"}async present(e,t,i,n,r,s){const o=this.menuItems(e,t,i,n,r,s);this.browser.menuPopup.presentTrackContextMenu(i,o)}menuItems(e,t,i,n,r,s){const o=e.name?[`<b>${e.name}</b><br/>`]:[];return\"name\"in t&&o.push(`<b>ROI Set: ${t.name}</b>`),o.length>0&&o.push(\"<hr/>\"),t.isUserDefined&&o.push({label:\"Set description ...\",click:()=>{const t={label:\"Description\",value:e.name||\"\",callback:()=>{const t=this.browser.inputDialog.value||\"\";e.name=t.trim(),this.browser.roiManager.repaintTable()}};this.browser.inputDialog.present(t,i)}}),Xa()&&e.end-e.start<1e6&&o.push({label:\"Copy reference sequence\",click:async()=>{this.container.style.display=\"none\";let t=await this.browser.genome.getSequence(e.chr,e.start,e.end);t||(t=\"Unknown sequence\");try{await navigator.clipboard.writeText(t)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),e.end-e.start<=25e3&&o.push({label:\"BLAT reference sequence\",click:async()=>{this.container.style.display=\"none\";const{chr:t,start:i,end:n}=e;let r=await this.browser.genome.getSequence(t,i,n);if(r){const e=`blat: ${t}:${i+1}-${n}`,s=`blat: ${t}:${i+1}-${n}`;jd({sequence:r,browser:this.browser,name:e,title:s})}}}),t.isUserDefined&&o.push(\"<hr/>\",{label:\"Delete\",click:async()=>{t.removeFeature(e);const i=await t.getAllFeatures();0===Object.keys(i).length&&n.deleteUserDefinedROISet(),n.deleteRegionWithKey(s.dataset.region,r),n.repaintTable()}}),o}dispose(){this.container.innerHTML=\"\"}}class Wy extends Pd{constructor(e){const t={browser:e,parent:e.columnContainer,headerTitle:\"Regions of 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n=e({class:\"igv-roi-table-button\"});this._footerDOM.appendChild(n),n.id=\"igv-roi-hide-show-button\",n.textContent=\"Hide all ROIs\",this.toggleROIButton=n,this.boundToggleDisplayButtonHandler=function(e){e.preventDefault(),e.stopPropagation(),this.browser.roiManager.toggleROIs()}.bind(this),this.toggleROIButton.addEventListener(\"click\",this.boundToggleDisplayButtonHandler)}setROIVisibility(e){const t=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let i=0;i<t.length;i++){const n=t[i];!1===e?$y(n,0):n.style.backgroundColor=n.dataset.color}this.toggleROIButton.textContent=!1===e?\"Show all ROIs\":\"Hide all ROIs\"}setTableRowSelectionState(e){super.setTableRowSelectionState(e);const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\");if(t.length>0&&t.length<2){const{locus:e}=Jy(t[0].dataset.region),{chr:i,start:n,end:r}=ey(e,this.browser.isSoftclipped());Gy(this.copySequenceButton,r-n<1e6)}else Gy(this.copySequenceButton,!1)}dispose(){document.removeEventListener(\"click\",this.boundGotoButtonHandler),document.removeEventListener(\"click\",this.boundCopySequenceButtonHandler),document.removeEventListener(\"click\",this.boundToggleDisplayButtonHandler),this.browser.roiTableControl.buttonHandler(!1),super.dispose()}static getColumnFormatConfiguration(e){return!0===e?[{label:\"Chr\",width:\"20%\"},{label:\"Start\",width:\"15%\"},{label:\"End\",width:\"15%\"},{label:\"Description\",width:\"30%\"},{label:\"ROI Set\",width:\"20%\"}]:[{label:\"Chr\",width:\"25%\"},{label:\"Start\",width:\"20%\"},{label:\"End\",width:\"20%\"},{label:\"Description\",width:\"35%\"}]}static gotoButtonHandler(e){e.stopPropagation();const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\"),i=[];for(let e of t){const{locus:t}=Jy(e.dataset.region);i.push(t)}for(let e of this.tableDOM.querySelectorAll(\".igv-roi-table-row\"))e.classList.remove(\"igv-roi-table-row-selected\");this.setTableRowSelectionState(!1),i.length>0&&this.browser.search(i.join(\" \"))}}function Gy(e,t){e.style.pointerEvents=t?\"auto\":\"none\",e.style.color=ro(t?\"licorice\":\"silver\"),e.style.borderColor=ro(t?\"licorice\":\"silver\")}function $y(e,t){const i=window.getComputedStyle(e).backgroundColor.match(/[\\d.]+/g);3===i.length&&i.push(1),i[3]=t,e.style.backgroundColor=`rgba(${i.join(\", \")})`}class Ky{constructor(e){this.browser=e,this.roiMenu=new jy(e,e.columnContainer),this.roiTable=new Wy(e,e.columnContainer),this.top=0,this.roiSets=[],this.boundLocusChangeHandler=Yy.bind(this),e.on(\"locuschange\",this.boundLocusChangeHandler);this.observer=new MutationObserver((()=>{const t=e.findTracks((e=>new Set([\"ideogram\",\"ruler\"]).has(e.type))),[i,n]=t.map((e=>e.trackView.viewports[0].$viewport.get(0))).map((e=>function(e){const t=window.getComputedStyle(e),i=parseInt(t.marginTop),n=parseInt(t.marginBottom),{top:r,bottom:s,height:o}=e.getBoundingClientRect();return{top:Math.floor(r)-i,bottom:Math.floor(s)+n,height:Math.floor(o)+i+n}}(e))),r=i?i.height:0,s=n?n.height:0,o=e.columnContainer.querySelectorAll(\".igv-roi-region\");if(o)for(const e of o)e.style.marginTop=`${r+s+-.5}px`})),this.observer.observe(e.columnContainer,{attributes:!0,childList:!0,subtree:!0})}async reset(){this.roiSets.length>0&&this.browser.roiTableControl.setVisibility(!0);const e=this.roiSets.map((e=>this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e})));e.length>0&&await Promise.all(e);const t=await this.getTableRecords();if(this.roiTable.renderTable(t),this.roiSets.length>0){const e=this.roiSets[0].isVisible;this.roiTable.setROIVisibility(e)}}async loadROI(e,t){const i=Array.isArray(e)?e:[e];for(let e of i)!e.name&&e.url&&(e.name=await ja(e.url)),e.url&&!e.format&&(e.format=await am(e)),this.roiSets.push(new ku(e,t));await this.reset()}clearROIs(){this.roiTable.clearTable();const e=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let t of e)t.remove();for(let e of this.roiSets)e.dispose();this.roiSets=[]}async getTableRecords(){const e=[];for(let t of this.roiSets){const i=t.name||\"\",n=await t.getAllFeatures();for(let t of Object.keys(n))for(let r of n[t])e.push({setName:i,feature:r})}return e}presentTable(){this.roiTable.present()}async repaintTable(){const e=await this.getTableRecords();this.roiTable.renderTable(e)}dismissTable(){this.roiTable.dismiss()}roiTableIsVisible(){return this.roiTable.isVisible()}async updateUserDefinedROISet(e){let t=await this.getUserDefinedROISet();void 0===t&&(t=this.initializeUserDefinedROISet()),t.addFeature(e),this.setROITableButtonVisibility(!0),await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t});const i=await this.getTableRecords();this.roiTable.renderTable(i)}setROITableButtonVisibility(e){this.browser.roiTableControl.setVisibility(e)}toggleROIs(){const e=!this.roiSets[0].isVisible;this.roiTable.setROIVisibility(e);for(const t of this.roiSets)t.isVisible=e}async renderAllROISets(){for(let e of this.roiSets)await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e})}async renderROISet({browser:e,pixelTop:t,roiSet:i}){const n=e.columnContainer.querySelectorAll(\".igv-column\");for(let r=0;r<n.length;r++){let{chr:s,start:o,end:a,bpPerPixel:c}=e.referenceFrameList[r];const l=n[r].querySelectorAll(\".igv-roi-region\");for(let e of l){const t=e.dataset.region,{chr:i,start:n,end:r}=Jy(t);(i!==s||r<o||n>a)&&e.remove()}const h=await i.getFeatures(s,o,a);if(h)for(let l of h){const h=Xy(s,l.start,l.end),{x:d,width:u}=Iu(Math.max(o,l.start),Math.min(a,l.end),o,c),f=n[r].querySelector(Zy(h));if(f)f.style.left=`${d}px`,f.style.width=`${u}px`;else{const s=this.createRegionElement(e.columnContainer,t,d,u,i,h,l);n[r].appendChild(s)}}}}createRegionElement(t,i,n,r,s,o,c){const l=e({class:\"igv-roi-region\"});l.style.top=`${i}px`,l.style.left=`${n}px`,l.style.width=`${r}px`,l.style.backgroundColor=s.color,l.dataset.color=s.color,l.dataset.region=o;const h=e();return l.appendChild(h),h.style.backgroundColor=s.headerColor,h.addEventListener(\"click\",(e=>{e.preventDefault(),e.stopPropagation(),a(e,t),this.roiMenu.present(c,s,e,this,t,l)})),l}renderSVGContext(e,t,{deltaX:i,deltaY:n}){for(const r of e.querySelectorAll(\".igv-roi-region\")){const{x:e,y:s,width:o,height:a}=r.getBoundingClientRect();t.fillStyle=r.style.backgroundColor,t.fillRect(e-i,s+n,o,a);const c=r.querySelector(\"div\"),{x:l,y:h,width:d,height:u}=c.getBoundingClientRect();t.fillStyle=c.style.backgroundColor,t.fillRect(l-i,h+n,d,u)}}getUserDefinedROISet(){return this.roiSets.find((e=>!0===e.isUserDefined))}deleteUserDefinedROISet(){this.roiSets=this.roiSets.filter((e=>!0!==e.isUserDefined))}initializeUserDefinedROISet(){const e=new ku({name:\"user defined\",isUserDefined:!0,features:[]},this.browser.genome);return this.roiSets.push(e),e}async deleteRegionWithKey(e,t){t.querySelectorAll(Zy(e)).forEach((e=>e.remove()));0===(await this.getTableRecords()).length&&(this.browser.roiTableControl.buttonHandler(!1),this.setROITableButtonVisibility(!1))}toJSON(){return this.roiSets.map((e=>e.toJSON()))}dispose(){this.browser.off(\"locuschange\",this.boundLocusChangeHandler);const e=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let t of e)t.remove();this.roiMenu&&this.roiMenu.dispose(),this.roiTable&&this.roiTable.dispose();for(let e of this.roiSets)e.dispose();for(let e of Object.keys(this))this[e]=void 0}}function Yy(){this.renderAllROISets()}function Xy(e,t,i){return`${e}-${t}-${i}`}function Zy(e){return`[data-region=\"${e}\"]`}function Jy(e){let t=e.split(\"-\"),i=parseInt(t.pop()),n=parseInt(t.pop()),r=t.join(\"-\");return{chr:r,start:n,end:i,locus:`${r}:${n}-${i}`,bedRecord:`${r}\\t${n}\\t${i}`}}class eA{constructor(e,t){this.name=e.name,this.featureSource=e.featureSource||Ad(e,t),this.color=e.color||_u}async getFeatures(e,t,i){return this.featureSource.getFeatures({chr:e,start:t,end:i})}draw(e){const{context:t,bpPerPixel:i,bpStart:n,pixelTop:r,pixelHeight:s,pixelWidth:o,features:a}=e;if(!a)return;const c=n+o*i+1;for(let{start:e,end:o}of a){if(o<n)continue;if(e>c)break;const{x:a,width:l}=Iu(e,o,n,i);xo.fillRect(t,a,r,l,s,{fillStyle:this.color})}}}class tA{aliasRecordCache=new Map;constructor(e,t,i){(t=t||{}).url=e,this.reader=new Zh(t,i)}async preload(e){await this.reader.preload();for(let t of e)await this.search(t)}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}async search(e){if(!this.aliasRecordCache.has(e)){const t=await this.reader.search(e);if(t)for(let e of Object.keys(t))\"start\"!==e&&\"end\"!==e&&this.aliasRecordCache.set(t[e],t)}return this.aliasRecordCache.get(e)}async getChromosomeNames(){return await this.reader.loadHeader(),Array.from(this.reader.chrNames)}}class iA{aliasRecordCache=new Map;constructor(e,t,i){this.aliasURL=e,this.config=t,this.genome=i}async preload(){return this.loadAliases()}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}async loadAliases(){const e=await Qs.loadString(this.aliasURL,Ua(this.config)),t=Dt(e),i=t[0];i.startsWith(\"#\")&&(this.headings=i.substring(1).split(\"\\t\").map((e=>e.trim())),this.altNameSets=this.headings.slice(1));const n=this.genome.chromosomeNames?new Set(this.genome.chromosomeNames):new Set;for(let e of t)if(!e.startsWith(\"#\")&&e.length>0){const t=e.split(\"\\t\");let i=t.find((e=>n.has(e)));i||(i=t[0]);const r={chr:i};for(let e=0;e<t.length;e++){r[this.headings?this.headings[e]:e]=t[e],this.aliasRecordCache.set(t[e],r)}this.aliasRecordCache.set(i.toLowerCase(),r),this.aliasRecordCache.set(i.toUpperCase(),r)}}async search(e){return 0===this.aliasRecordCache.size&&await this.loadAliases(),this.aliasRecordCache.get(e)}}class nA{constructor(e,t,i,n){this.start=e,this.end=t,this.name=i,this.stain=0,\"acen\"===n?this.type=\"c\":(this.type=n.charAt(1),\"p\"===this.type&&(this.stain=parseInt(n.substring(4))))}}class rA{cytobandMap=new Map;constructor(e,t,i){(t=t||{}).url=e,this.source=new od(t,i)}async getCytobands(e){if(this.cytobandMap.has(e))return this.cytobandMap.get(e);{let t=await this.#k(e);return t||(t=[]),this.cytobandMap.set(e,t),t}}async#k(e){return(await this.source.getFeatures({chr:e})).map((e=>new nA(e.start,e.end,e.name,e.gieStain)))}}class sA{cytobands=new Map;constructor(e,t){this.url=e,this.config=t}async getCytobands(e){return 0===this.cytobands.size&&await this.#I(),this.cytobands.get(e)}async#I(){let e,t;if(Ga(this.url)){const t=vs(this.url);e=\"\";const i=t.length;for(let n=0;n<i;n++)e+=String.fromCharCode(t[n])}else e=await Qs.loadString(this.url,Ua(this.config));let i=[];const n=Dt(e);for(let e of n){const n=e.split(\"\\t\"),r=n[0];if(t||(t=r),r!==t&&(this.cytobands.set(t,i),i=[],t=r),5===n.length){const e=parseInt(n[1]),t=parseInt(n[2]),r=n[3],s=n[4];i.push(new nA(e,t,r,s))}}}async getChromosomeNames(){return 0===this.cytobands.size&&await this.#I(),Array.from(this.cytobands.keys())}async getChromosomes(){0===this.cytobands.size&&await this.#I();const e=[];let t=0;for(let[i,n]of this.cytobands.entries())e.push(new lc(i,t++,n[n.length-1].end));return e}}class oA{aliasRecordCache=new Map;constructor(e,t){this.genomeID=e,this.update(e,t)}async preload(){}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}update(e,t){if(t){const i=[];for(let n of t){if(this.aliasRecordCache.has(n))continue;let t=!1;const r={chr:n};if(i.push(r),n.startsWith(\"gi|\")){const e=oA.getNCBIName(n);r[\"ncbi-gi-versioned\"]=e;const t=e.lastIndexOf(\".\");if(t>0){const e=e.substring(0,t);r[\"ncbi-gi\"]=e}}else{if(e.startsWith(\"hg\")||e.startsWith(\"GRCh\")||\"1kg_ref\"===e||\"b37\"===e)switch(n){case\"23\":r.ucsc=\"chrX\",t=!0;break;case\"24\":r.ucsc=\"chrY\",t=!0;break;case\"chrX\":r.ncbi=\"23\",t=!0;break;case\"chrY\":r.ncbi=\"24\",t=!0}else if(e.startsWith(\"mm\")||e.startsWith(\"GRCm\")||e.startsWith(\"rheMac\"))switch(n){case\"21\":r.ucsc=\"chrX\",t=!0;break;case\"22\":r.ucsc=\"chrY\",t=!0;break;case\"chrX\":r.ncbi=\"21\",t=!0;break;case\"chrY\":r.ncbi=\"22\",t=!0}if(t)continue;\"chrM\"===n?r.ncbi=\"MT\":\"MT\"===n?r.ucsc=\"chrM\":n.toLowerCase().startsWith(\"chr\")?r.ncbi=n.substring(3):Number.isInteger(Number(n))&&(r.ucsc=\"chr\"+n)}}for(let e of i){for(let t of Object.values(e))this.aliasRecordCache.set(t,e);this.aliasRecordCache.set(e.chr.toLowerCase(),e),this.aliasRecordCache.set(e.chr.toUpperCase(),e)}}}search(e){return this.aliasRecordCache.get(e)}static getNCBIName(e){const t=e.split(\"\\\\|\");return t[t.length-1]}}class aA{#S;static async createGenome(e,t){const i=new aA(e,t);return await i.init(),i}constructor(e,t){this.config=e,this.browser=t,this.id=e.id||function(e){return void 0!==e.id?e.id:e.fastaURL&&Mt(e.fastaURL)&&!e.fastaURL.startsWith(\"data:\")?e.fastaURL:e.fastaURL&&e.fastaURL.name?e.fastaURL.name:\"\"}(e),this.name=e.name,this.nameSet=e.nameSet}async init(){const e=this.config;if(this.sequence=await Nc(e,this.browser),e.chromSizesURL?this.chromosomes=await async function(e){const t=new Map;let i;if(Ga(e)){let t=vs(e);i=\"\";for(let e of t)i+=String.fromCharCode(e)}else i=await Qs.load(e,{});const n=Fc(i);let r=0;for(let e of n){const i=e.split(\"\\t\");if(i.length>1){const e=Number.parseInt(i[1]);t.set(i[0],new lc(i[0],r++,e))}}return t}(e.chromSizesURL):this.chromosomes=this.sequence.chromosomes||new Map,this.chromosomes.size>0&&(this.chromosomeNames=Array.from(this.chromosomes.keys())),e.chromAliasBbURL?(this.chromAlias=new tA(e.chromAliasBbURL,Object.assign({},e),this),this.chromosomeNames||(this.chromosomeNames=await this.chromAlias.getChromosomeNames())):e.aliasURL?this.chromAlias=new iA(e.aliasURL,Object.assign({},e),this):this.chromosomeNames&&(this.chromAlias=new oA(this.id,this.chromosomeNames)),e.cytobandBbURL)this.cytobandSource=new rA(e.cytobandBbURL,Object.assign({},e),this),this.chromosomeNames||(this.chromosomeNames=await this.cytobandSource.getChromosomeNames());else if(e.cytobandURL&&(this.cytobandSource=new sA(e.cytobandURL,Object.assign({},e)),this.chromosomeNames||(this.chromosomeNames=await this.cytobandSource.getChromosomeNames()),0===this.chromosomes.size)){const e=await this.cytobandSource.getChromosomes();for(let t of e)this.chromosomes.set(e.name,e)}if(!1!==e.wholeGenomeView&&this.chromosomes.size>0&&(e.chromosomeOrder?Array.isArray(e.chromosomeOrder)?this.#S=e.chromosomeOrder:this.#S=e.chromosomeOrder.split(\",\").map((e=>e.trim())):this.#S=function(e){const t=[];let i,n=1;for(let r of e.values()){if(i){if(r.bpLength<i/100)continue;i=((n-1)*i+r.bpLength)/n,t.push(r.name)}else i=r.bpLength,t.push(r.name);n++}return t}(this.chromosomes),await this.chromAlias.preload(this.#S)),this.wholeGenomeView=!1!==e.wholeGenomeView&&this.#S&&this.chromosomes.size>1,this.wholeGenomeView){const e=this.#S.reduce(((e,t)=>e+this.chromosomes.get(t).bpLength),0);this.chromosomes.set(\"all\",new lc(\"all\",0,e))}}get description(){return this.config.description||`${this.id}\\n${this.name}`}get infoURL(){return this.config.infoURL}showWholeGenomeView(){return this.wholeGenomeView}toJSON(){return Object.assign({},this.config,{tracks:void 0})}get initialLocus(){return this.config.locus?this.config.locus:this.getHomeChromosomeName()}getHomeChromosomeName(){return this.showWholeGenomeView()&&this.chromosomes.has(\"all\")?\"all\":this.chromosomeNames[0]}getChromosomeName(e){return this.chromAlias?this.chromAlias.getChromosomeName(e,this.chromosomes.keys()):e}getChromosomeDisplayName(e){return this.nameSet&&this.chromAlias&&this.chromAlias.getChromosomeAlias(e,this.nameSet)||e}getChromosome(e){return this.chromAlias&&(e=this.chromAlias.getChromosomeName(e)),this.chromosomes.get(e)}async loadChromosome(e){if(this.chromAlias){const t=await this.chromAlias.search(e);t&&(e=t.chr)}if(!this.chromosomes.has(e)){let t;const i=await this.sequence.getSequenceRecord(e);i&&(t=new lc(e,0,i.bpLength)),this.chromosomes.set(e,t)}return this.chromosomes.get(e)}async getAliasRecord(e){if(this.chromAlias)return this.chromAlias.search(e)}async getCytobands(e){if(this.cytobandSource){const t=this.getChromosomeName(e);return await this.cytobandSource.getCytobands(t)}}getChromosomes(){return this.chromosomes}get wgChromosomeNames(){return this.#S?this.#S.slice():void 0}get showChromosomeWidget(){return this.config.showChromosomeWidget}getGenomeCoordinate(e,t){var i=this.getCumulativeOffset(e);if(void 0!==i)return i+t}getChromosomeCoordinate(e){let t;void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=computeCumulativeOffsets.call(this));let i=0;for(let n of this.#S){const r=this.cumulativeOffsets[n];if(r>e){return{chr:t,position:e-i}}t=n,i=r}return{chr:this.#S[this.#S.length-1],position:0}}getCumulativeOffset(e){void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=function(){let e={},t=0;for(let i of this.#S){e[i]=Math.floor(t);t+=this.getChromosome(i).bpLength}return e}.call(this));const t=this.getChromosomeName(e);return this.cumulativeOffsets[t]}getGenomeLength(){if(!this.bpLength){let e=0;for(let t of this.#S){e+=this.chromosomes.get(t).bpLength}this.bpLength=e}return this.bpLength}async getSequence(e,t,i){return e=this.getChromosomeName(e),this.sequence.getSequence(e,t,i)}getSequenceInterval(e,t,i){return\"function\"==typeof this.sequence.getSequenceInterval?this.sequence.getSequenceInterval(e,t,i):void 0}}class cA{constructor(){this.clear()}clear(){this.phenotypeColors=new Map,this.snps=new Set,this.qtl=null}isEmpty(){return 0===this.phenotypeColors.size&&0===this.snps.size&&null===this.qtl}addSnp(e){e=e.toUpperCase(),this.snps.add(e)}addPhenotype(e){e=e.toUpperCase();const t=this.phenotypeColors.size;if(!this.phenotypeColors.has(e.toUpperCase())){const i=t<lA.length?lA[t]:_s.randomRGB(0,255);this.phenotypeColors.set(e.toUpperCase(),i)}}hasSnp(e){return e&&this.snps.has(e.toUpperCase())}hasPhenotype(e){return e&&this.phenotypeColors.has(e.toUpperCase())}hasQTL(e){return this.qtls.has(e)}colorForGene(e){return e?this.phenotypeColors.get(e.toUpperCase()):\"black\"}toJSON(){const e={};return this.phenotypeColors.size>0&&(e.phenotypes=Array.from(this.phenotypeColors.keys())),this.snps.size>0&&(e.snps=Array.from(this.snps)),this.qtl&&(e.qtl=this.qtl),e}static fromJSON(e){const t=new cA;if(e.phenotypes)for(let i of e.phenotypes)t.addPhenotype(i);if(e.snps)for(let i of e.snps)t.addSnp(i);return e.qtl&&(t.qtl=e.qtl),t}}const lA=[];lA.push(\"rgb(228,26,28)\"),lA.push(\"rgb(55,126,184)\"),lA.push(\"rgb(77,175,74)\"),lA.push(\"rgb(166,86,40)\"),lA.push(\"rgb(152,78,163)\"),lA.push(\"rgb(255,127,0)\"),lA.push(\"rgb(247,129,191)\"),lA.push(\"rgb(255,255,51)\"),lA.push(\"rgb(102,194,165)\"),lA.push(\"rgb(252,141,98)\"),lA.push(\"rgb(141, 160, 203)\"),lA.push(\"rgb(231, 138, 195)\"),lA.push(\"rgb(166, 216, 84)\"),lA.push(\"rgb(255, 217, 47)\"),lA.push(\"rgb(229, 196, 148)\"),lA.push(\"rgb( 141, 211, 199)\"),lA.push(\"rgb(255, 255, 179)\"),lA.push(\"rgb(190, 186, 218)\"),lA.push(\"rgb(251, 128, 114)\"),lA.push(\"rgb(128, 177, 211)\"),lA.push(\"rgb(253, 180, 98)\"),lA.push(\"rgb(179, 222, 105)\"),lA.push(\"rgb(252, 205, 229)\"),lA.push(\"rgb(188, 128, 189)\"),lA.push(\"rgb(204, 235, 197)\"),lA.push(\"rgb(255, 237, 111)\");class hA{constructor(t){this.parent=t,this.container=e({class:\"igv-ui-generic-dialog-container\"}),t.appendChild(this.container);const n=e({class:\"igv-ui-generic-dialog-header\"});this.container.appendChild(n),this.label=e({class:\"igv-ui-generic-dialog-one-liner\"}),this.container.appendChild(this.label),this.label.text=\"Unlabeled\",this.input_container=e({class:\"igv-ui-generic-dialog-input\"}),this.container.appendChild(this.input_container);let r='<input type=\"range\" id=\"igv-slider-dialog-input\" name=\"igv-slider-dialog-input\" />';this._input=document.createRange().createContextualFragment(r).firstChild,this.input_container.appendChild(this._input),r='<output id=\"igv-slider-dialog-output\" name=\"igv-slider-dialog-output\" for=\"igv-slider-dialog-input\"></output>',this._output=document.createRange().createContextualFragment(r).firstChild,this.input_container.appendChild(this._output);const s=e({class:\"igv-ui-generic-dialog-ok-cancel\"});this.container.appendChild(s),this.ok=e(),s.appendChild(this.ok),this.ok.textContent=\"OK\",this.cancel=e(),s.appendChild(this.cancel),this.cancel.textContent=\"Cancel\",i(this.container),this._input.addEventListener(\"input\",(()=>{const e=parseFloat(this._input.value)/this._scaleFactor;this.callback(e),this._output.value=`${e.toFixed(2)}`}),!1),this.ok.addEventListener(\"click\",(()=>{if(\"function\"==typeof this.callback){const e=parseFloat(this._input.value)/this._scaleFactor;this.callback(e),this.callback=void 0}this._input.value=void 0,i(this.container)}));const o=()=>{this._input.value=void 0,i(this.container)};this.cancel.addEventListener(\"click\",o),u(n,o),p(this.container,n)}get value(){return Ea.sanitize(this._input.value)}present(e,t){this.label.textContent=e.label,this._scaleFactor=e.scaleFactor;const[i,r,s]=[e.min,e.max,e.value].map((e=>Math.floor(this._scaleFactor*e).toString()));this._input.min=i,this._input.max=r,this._input.value=s;const o=parseFloat(s)/this._scaleFactor;this._output.value=`${o.toFixed(2)}`,this.callback=e.callback||e.click,n(this.container),this.clampLocation(t.clientX,t.clientY)}clampLocation(e,t){const{width:i,height:n}=this.container.getBoundingClientRect(),r=window.innerHeight,s=window.innerWidth,o=Math.min(r-n,t),a=Math.min(s-i,e);this.container.style.left=`${a}px`,this.container.style.top=`${o}px`}}class dA{qtlSelections=new cA;constructor(t,i){this.config=t,this.guid=s(),this.namespace=\".browser_\"+this.guid,this.parent=i;let n=i.shadowRoot;if(!n){n=i.attachShadow({mode:\"open\"});const e=new CSSStyleSheet;e.replaceSync('.igv-ui-dropdown {\\n  cursor: default;\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  z-index: 2048;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: 1px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div {\\n  overflow-y: auto;\\n  overflow-x: hidden;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div > div {\\n  padding: 4px;\\n  width: 100%;\\n  overflow-x: hidden;\\n  text-overflow: ellipsis;\\n  white-space: nowrap;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: 1px;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div > div:last-child {\\n  border-bottom-color: transparent;\\n  border-bottom-width: 0;\\n}\\n.igv-ui-dropdown > div > div:hover {\\n  cursor: pointer;\\n  background-color: rgba(0, 0, 0, 0.04);\\n}\\n\\n.igv-ui-popover {\\n  cursor: default;\\n  position: absolute;\\n  z-index: 2048;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: 1px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  background-color: white;\\n}\\n.igv-ui-popover > div:first-child {\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-width: 0;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-popover > div:first-child > div:first-child {\\n  margin-left: 4px;\\n}\\n.igv-ui-popover > div:first-child > div:last-child {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-popover > div:first-child > div:last-child:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-popover > div:last-child {\\n  user-select: text;\\n  overflow-y: auto;\\n  overflow-x: hidden;\\n  max-height: 400px;\\n  max-width: 800px;\\n  background-color: white;\\n  border-bottom-width: 0;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n}\\n.igv-ui-popover > div:last-child > div {\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  min-width: 220px;\\n  overflow-x: hidden;\\n  text-overflow: ellipsis;\\n  white-space: nowrap;\\n}\\n.igv-ui-popover > div:last-child > div > span {\\n  font-weight: bolder;\\n}\\n.igv-ui-popover > div:last-child hr {\\n  width: 100%;\\n}\\n\\n.igv-ui-alert-dialog-container {\\n  box-sizing: content-box;\\n  position: absolute;\\n  z-index: 2048;\\n  top: 50%;\\n  left: 50%;\\n  width: 400px;\\n  height: 200px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  outline: none;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 15px;\\n  font-weight: 400;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-ui-alert-dialog-container > div:first-child {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-alert-dialog-container > div:first-child div:first-child {\\n  padding-left: 8px;\\n}\\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body {\\n  -webkit-user-select: text;\\n  -moz-user-select: text;\\n  -ms-user-select: text;\\n  user-select: text;\\n  color: #373737;\\n  width: 100%;\\n  height: calc(100% - 24px - 64px);\\n  overflow-y: scroll;\\n}\\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body .igv-ui-alert-dialog-body-copy {\\n  margin: 16px;\\n  width: auto;\\n  height: auto;\\n  overflow-wrap: break-word;\\n  word-break: break-word;\\n  background-color: white;\\n  border: unset;\\n}\\n.igv-ui-alert-dialog-container > div:last-child {\\n  width: 100%;\\n  margin-bottom: 10px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-ui-alert-dialog-container > div:last-child div {\\n  margin: unset;\\n  width: 40px;\\n  height: 30px;\\n  line-height: 30px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  border-color: #2B81AF;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-ui-alert-dialog-container > div:last-child div:hover {\\n  cursor: pointer;\\n  border-color: #25597f;\\n  background-color: #25597f;\\n}\\n\\n.igv-ui-color-swatch {\\n  position: relative;\\n  box-sizing: content-box;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: wrap;\\n  justify-content: center;\\n  align-items: center;\\n  width: 32px;\\n  height: 32px;\\n  border-style: solid;\\n  border-width: 2px;\\n  border-color: white;\\n  border-radius: 4px;\\n}\\n\\n.igv-ui-color-swatch:hover {\\n  border-color: dimgray;\\n}\\n\\n.igv-ui-colorpicker-menu-close-button {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 32px;\\n  margin-top: 4px;\\n  margin-bottom: 4px;\\n  padding-right: 8px;\\n}\\n.igv-ui-colorpicker-menu-close-button i.fa {\\n  display: block;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  color: #5f5f5f;\\n}\\n.igv-ui-colorpicker-menu-close-button i.fa:hover,\\n.igv-ui-colorpicker-menu-close-button i.fa:focus,\\n.igv-ui-colorpicker-menu-close-button i.fa:active {\\n  cursor: pointer;\\n  color: #0f0f0f;\\n}\\n\\n.igv-ui-generic-dialog-container {\\n  box-sizing: content-box;\\n  position: fixed;\\n  top: 0;\\n  left: 0;\\n  width: 300px;\\n  height: fit-content;\\n  padding-bottom: 16px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  z-index: 2048;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-one-liner {\\n  color: #373737;\\n  width: 95%;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-top: 8px;\\n  padding-left: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input {\\n  margin-top: 8px;\\n  width: 95%;\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  padding-left: 8px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input > div {\\n  width: fit-content;\\n  height: 100%;\\n  font-size: 16px;\\n  text-align: right;\\n  padding-right: 8px;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\\n  width: 50%;\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input {\\n  margin-top: 8px;\\n  width: calc(100% - 16px);\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input[type=range] {\\n  width: 70%;\\n  -webkit-appearance: none;\\n  background: linear-gradient(90deg, white, black);\\n  outline: none;\\n  margin: 0;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input output {\\n  display: block;\\n  height: 100%;\\n  width: 20%;\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel {\\n  width: 100%;\\n  height: 28px;\\n  padding-top: 16px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div {\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:first-child {\\n  margin-left: 32px;\\n  margin-right: 0;\\n  background-color: #5ea4e0;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:last-child {\\n  margin-left: 0;\\n  margin-right: 32px;\\n  background-color: #c4c4c4;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n\\n.igv-ui-generic-container {\\n  box-sizing: content-box;\\n  position: absolute;\\n  z-index: 2048;\\n  background-color: white;\\n  cursor: pointer;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: wrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-container > div:first-child {\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  height: 24px;\\n  width: 100%;\\n  background-color: #dddddd;\\n}\\n.igv-ui-generic-container > div:first-child > div {\\n  display: block;\\n  color: #5f5f5f;\\n  cursor: pointer;\\n  width: 14px;\\n  height: 14px;\\n  margin-right: 8px;\\n  margin-bottom: 4px;\\n}\\n\\n.igv-ui-dialog {\\n  z-index: 2048;\\n  position: fixed;\\n  width: fit-content;\\n  height: fit-content;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  background-color: white;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-dialog .igv-ui-dialog-one-liner {\\n  width: 95%;\\n  height: 24px;\\n  line-height: 24px;\\n  text-align: left;\\n  margin: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n  font-weight: bold;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel {\\n  width: 100%;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div {\\n  margin: 16px;\\n  margin-top: 32px;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child {\\n  background-color: #5ea4e0;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child {\\n  background-color: #c4c4c4;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok {\\n  width: 100%;\\n  height: 36px;\\n  margin-top: 32px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok div {\\n  width: 98px;\\n  height: 36px;\\n  line-height: 36px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  border-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok div:hover {\\n  cursor: pointer;\\n  background-color: #25597f;\\n}\\n\\n.igv-ui-panel, .igv-ui-panel-row, .igv-ui-panel-column {\\n  z-index: 2048;\\n  background-color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  display: flex;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-ui-panel-column {\\n  display: flex;\\n  flex-direction: column;\\n}\\n\\n.igv-ui-panel-row {\\n  display: flex;\\n  flex-direction: row;\\n}\\n\\n.igv-ui-textbox {\\n  background-color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  display: flex;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-ui-table {\\n  background-color: white;\\n}\\n\\n.igv-ui-table thead {\\n  position: sticky;\\n  top: 0;\\n}\\n\\n.igv-ui-table th {\\n  text-align: left;\\n}\\n\\n.igv-ui-table td {\\n  padding-right: 20px;\\n}\\n\\n.igv-ui-table tr:hover {\\n  background-color: lightblue;\\n}\\n\\n.igv-ui-center-fixed {\\n  left: 50%;\\n  top: 50%;\\n  transform: translate(-50%, -50%);\\n}\\n\\n.igv-navbar {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  box-sizing: border-box;\\n  width: 100%;\\n  color: #444;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  line-height: 32px;\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  margin-top: 2px;\\n  margin-bottom: 6px;\\n  height: 32px;\\n  border-style: solid;\\n  border-radius: 3px;\\n  border-width: thin;\\n  border-color: #bfbfbf;\\n  background-color: #f3f3f3;\\n}\\n.igv-navbar .igv-navbar-left-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  height: 32px;\\n  line-height: 32px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-logo {\\n  width: 34px;\\n  height: 32px;\\n  margin-right: 8px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\\n  height: 32px;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  user-select: none;\\n  line-height: 32px;\\n  vertical-align: middle;\\n  text-align: center;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  height: 100%;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n  height: 100%;\\n  width: 125px;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\\n  display: block;\\n  cursor: pointer;\\n  width: 100px;\\n  height: 75%;\\n  outline: none;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  margin-left: 8px;\\n  height: 22px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 240px;\\n  height: 22px;\\n  line-height: 22px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\\n  cursor: text;\\n  width: 85%;\\n  height: 22px;\\n  line-height: 22px;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  text-align: left;\\n  padding-left: 8px;\\n  margin-right: 8px;\\n  outline: none;\\n  border-style: solid;\\n  border-radius: 3px;\\n  border-width: thin;\\n  border-color: #bfbfbf;\\n  background-color: white;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\\n  cursor: pointer;\\n  height: 16px;\\n  width: 16px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\\n  margin-left: 4px;\\n  user-select: none;\\n}\\n.igv-navbar .igv-navbar-right-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\\n  position: relative;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-hidden {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  height: 100%;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\\n  color: #737373;\\n  font-size: 18px;\\n  margin-left: 8px;\\n  user-select: none;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\\n  cursor: pointer;\\n  margin-left: unset;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: unset;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: 4px;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\\n  display: block;\\n  height: fit-content;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\\n  display: block;\\n  width: 125px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\\n  display: block;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\\n  color: #737373;\\n  font-size: 18px;\\n  height: 32px;\\n  line-height: 32px;\\n  margin-left: 8px;\\n  user-select: none;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\\n  cursor: pointer;\\n  margin-left: unset;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: unset;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: 4px;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\\n  width: 0;\\n  height: 0;\\n  display: none;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\\n  width: 0;\\n  height: 0;\\n  display: none;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\\n  display: block;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\\n  display: none;\\n}\\n\\n.igv-navbar-button {\\n  display: block;\\n  box-sizing: unset;\\n  padding-left: 6px;\\n  padding-right: 6px;\\n  height: 18px;\\n  text-transform: capitalize;\\n  user-select: none;\\n  line-height: 18px;\\n  text-align: center;\\n  vertical-align: middle;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 11px;\\n  font-weight: 200;\\n  color: #737373;\\n  background-color: #f3f3f3;\\n  border-color: #737373;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 6px;\\n}\\n\\n.igv-navbar-button:hover {\\n  cursor: pointer;\\n}\\n\\n.igv-navbar-button-clicked {\\n  color: white;\\n  background-color: #737373;\\n}\\n\\n.igv-navbar-icon-button {\\n  cursor: pointer;\\n  position: relative;\\n  width: 24px;\\n  height: 24px;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-icon-button > div:first-child {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: -18px;\\n  width: 24px;\\n  height: 24px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-icon-button > div:last-child {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 18px;\\n  width: 24px;\\n  height: 24px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n\\n.igv-navbar-text-button {\\n  cursor: pointer;\\n  position: relative;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  border: none;\\n  display: flex;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-navbar-text-button > div:nth-child(2) {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 0;\\n  width: 38px;\\n  height: 18px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-text-button > div:nth-child(3) {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 42px;\\n  width: 38px;\\n  height: 18px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n\\n#igv-text-button-label {\\n  text-anchor: middle;\\n  dominant-baseline: middle;\\n}\\n\\n.igv-navbar-text-button-svg-inactive rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n.igv-navbar-text-button-svg-inactive text {\\n  fill: #737373;\\n}\\n.igv-navbar-text-button-svg-inactive tspan {\\n  dominant-baseline: middle;\\n}\\n\\n.igv-navbar-text-button-svg-hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n.igv-navbar-text-button-svg-hover text {\\n  fill: white;\\n}\\n.igv-navbar-text-button-svg-hover tspan {\\n  dominant-baseline: middle;\\n}\\n\\n#igv-save-svg-group rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n#igv-save-svg-group text {\\n  fill: #737373;\\n}\\n\\n#igv-save-svg-group:hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n#igv-save-svg-group:hover text {\\n  fill: white;\\n}\\n\\n#igv-save-png-group rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n#igv-save-png-group text {\\n  fill: #737373;\\n}\\n\\n#igv-save-png-group:hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n#igv-save-png-group:hover text {\\n  fill: white;\\n}\\n\\n.igv-zoom-in-notice-container {\\n  z-index: 256;\\n  position: absolute;\\n  top: 8px;\\n  left: 50%;\\n  transform: translate(-50%, 0%);\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n  background-color: white;\\n}\\n.igv-zoom-in-notice-container > div {\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  padding-top: 2px;\\n  padding-bottom: 2px;\\n  width: 100%;\\n  height: 100%;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  color: #3f3f3f;\\n}\\n\\n.igv-zoom-in-notice {\\n  position: absolute;\\n  top: 10px;\\n  left: 50%;\\n}\\n.igv-zoom-in-notice div {\\n  position: relative;\\n  left: -50%;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #3f3f3f;\\n  background-color: rgba(255, 255, 255, 0.51);\\n  z-index: 64;\\n}\\n\\n.igv-container-spinner {\\n  position: absolute;\\n  top: 90%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  z-index: 1024;\\n  width: 24px;\\n  height: 24px;\\n  pointer-events: none;\\n  color: #737373;\\n}\\n\\n.igv-multi-locus-close-button {\\n  position: absolute;\\n  top: 2px;\\n  right: 0;\\n  padding-left: 2px;\\n  padding-right: 2px;\\n  width: 12px;\\n  height: 12px;\\n  color: #666666;\\n  background-color: white;\\n  z-index: 1000;\\n}\\n.igv-multi-locus-close-button > svg {\\n  vertical-align: top;\\n}\\n\\n.igv-multi-locus-close-button:hover {\\n  cursor: pointer;\\n  color: #434343;\\n}\\n\\n.igv-multi-locus-ruler-label {\\n  z-index: 64;\\n  position: absolute;\\n  top: 2px;\\n  left: 0;\\n  width: 100%;\\n  height: 12px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-multi-locus-ruler-label > div {\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  color: rgb(16, 16, 16);\\n  background-color: white;\\n}\\n.igv-multi-locus-ruler-label > div {\\n  cursor: pointer;\\n}\\n\\n.igv-multi-locus-ruler-label-square-dot {\\n  z-index: 64;\\n  position: absolute;\\n  left: 50%;\\n  top: 5%;\\n  transform: translate(-50%, 0%);\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\\n  width: 14px;\\n  height: 14px;\\n}\\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\\n  margin-left: 16px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  color: rgb(16, 16, 16);\\n}\\n\\n.igv-ruler-sweeper {\\n  display: none;\\n  pointer-events: none;\\n  position: absolute;\\n  top: 26px;\\n  bottom: 0;\\n  left: 0;\\n  width: 0;\\n  z-index: 99999;\\n  background-color: rgba(68, 134, 247, 0.25);\\n}\\n\\n.igv-ruler-tooltip {\\n  pointer-events: none;\\n  z-index: 128;\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: 1px;\\n  height: 32px;\\n  background-color: transparent;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ruler-tooltip > div {\\n  pointer-events: none;\\n  width: 128px;\\n  height: auto;\\n  padding: 1px;\\n  color: #373737;\\n  font-size: 10px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  background-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #373737;\\n}\\n\\n.igv-track-label {\\n  position: absolute;\\n  left: 8px;\\n  top: 8px;\\n  width: auto;\\n  height: auto;\\n  max-width: 50%;\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  text-align: center;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  border-color: #444;\\n  border-radius: 2px;\\n  border-style: solid;\\n  border-width: thin;\\n  background-color: white;\\n  z-index: 128;\\n  cursor: pointer;\\n}\\n\\n.igv-track-label:hover,\\n.igv-track-label:focus,\\n.igv-track-label:active {\\n  background-color: #e8e8e8;\\n}\\n\\n.igv-track-label-popup-shim {\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  padding-top: 4px;\\n}\\n\\n.igv-center-line {\\n  display: none;\\n  pointer-events: none;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  left: 50%;\\n  transform: translateX(-50%);\\n  z-index: 8;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  border-left-style: dashed;\\n  border-left-width: thin;\\n  border-right-style: dashed;\\n  border-right-width: thin;\\n}\\n\\n.igv-center-line-wide {\\n  background-color: rgba(0, 0, 0, 0);\\n  border-left-color: rgba(127, 127, 127, 0.51);\\n  border-right-color: rgba(127, 127, 127, 0.51);\\n}\\n\\n.igv-center-line-thin {\\n  background-color: rgba(0, 0, 0, 0);\\n  border-left-color: rgba(127, 127, 127, 0.51);\\n  border-right-color: rgba(0, 0, 0, 0);\\n}\\n\\n.igv-cursor-guide-horizontal {\\n  display: none;\\n  pointer-events: none;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  position: absolute;\\n  left: 0;\\n  right: 0;\\n  top: 50%;\\n  height: 1px;\\n  z-index: 32;\\n  margin-left: 50px;\\n  margin-right: 54px;\\n  border-top-style: dotted;\\n  border-top-width: thin;\\n  border-top-color: rgba(127, 127, 127, 0.76);\\n}\\n\\n.igv-cursor-guide-vertical {\\n  pointer-events: none;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  left: 50%;\\n  width: 1px;\\n  z-index: 32;\\n  border-left-style: dotted;\\n  border-left-width: thin;\\n  border-left-color: rgba(127, 127, 127, 0.76);\\n  display: none;\\n}\\n\\n.igv-user-feedback {\\n  position: fixed;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 512px;\\n  height: 360px;\\n  z-index: 2048;\\n  background-color: white;\\n  border-color: #a2a2a2;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #444;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-user-feedback div:first-child {\\n  position: relative;\\n  height: 24px;\\n  width: 100%;\\n  background-color: white;\\n  border-bottom-color: #a2a2a2;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-user-feedback div:first-child div {\\n  position: absolute;\\n  top: 2px;\\n  width: 16px;\\n  height: 16px;\\n  background-color: transparent;\\n}\\n.igv-user-feedback div:first-child div:first-child {\\n  left: 8px;\\n}\\n.igv-user-feedback div:first-child div:last-child {\\n  cursor: pointer;\\n  right: 8px;\\n}\\n.igv-user-feedback div:last-child {\\n  width: 100%;\\n  height: calc(100% - 24px);\\n  border-width: 0;\\n}\\n.igv-user-feedback div:last-child div {\\n  width: auto;\\n  height: auto;\\n  margin: 8px;\\n}\\n\\n.igv-generic-dialog-container {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: 300px;\\n  height: 200px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  z-index: 2048;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\\n  color: #373737;\\n  width: 95%;\\n  height: 24px;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-top: 8px;\\n  padding-left: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\\n  margin-top: 8px;\\n  width: 95%;\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  padding-left: 8px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\\n  width: 30%;\\n  height: 100%;\\n  font-size: 16px;\\n  text-align: right;\\n  padding-right: 8px;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\\n  width: 50%;\\n  font-size: 16px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input {\\n  margin-top: 8px;\\n  width: calc(100% - 16px);\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input input {\\n  font-size: 16px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\\n  width: 100%;\\n  height: 28px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\\n  margin-top: 32px;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\\n  margin-left: 32px;\\n  margin-right: 0;\\n  background-color: #5ea4e0;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\\n  margin-left: 0;\\n  margin-right: 32px;\\n  background-color: #c4c4c4;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok {\\n  width: 100%;\\n  height: 36px;\\n  margin-top: 32px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\\n  width: 98px;\\n  height: 36px;\\n  line-height: 36px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  border-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\\n  cursor: pointer;\\n  background-color: #25597f;\\n}\\n\\n.igv-generic-container {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  z-index: 2048;\\n  background-color: white;\\n  cursor: pointer;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: wrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-container div:first-child {\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  height: 24px;\\n  width: 100%;\\n  background-color: #dddddd;\\n}\\n.igv-generic-container div:first-child i {\\n  display: block;\\n  color: #5f5f5f;\\n  cursor: pointer;\\n  width: 14px;\\n  height: 14px;\\n  margin-right: 8px;\\n  margin-bottom: 4px;\\n}\\n\\n.igv-menu-popup {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: max-content;\\n  max-width: 400px;\\n  z-index: 512;\\n  cursor: pointer;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  color: #4b4b4b;\\n  background: white;\\n  border-radius: 4px;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-end;\\n  text-align: left;\\n}\\n.igv-menu-popup > div:not(:first-child) {\\n  width: 100%;\\n}\\n.igv-menu-popup > div:not(:first-child) > div {\\n  background: white;\\n}\\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\\n  padding-left: 4px;\\n  padding-right: 4px;\\n}\\n.igv-menu-popup > div:not(:first-child) > div:last-child {\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-color: transparent;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-menu-popup > div:not(:first-child) > div:hover {\\n  background: #efefef;\\n}\\n\\n.igv-menu-popup-shim {\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  padding-bottom: 1px;\\n  padding-top: 1px;\\n}\\n\\n.igv-menu-popup-header {\\n  position: relative;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-menu-popup-header div {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-menu-popup-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n\\n.igv-menu-popup-check-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 100%;\\n  height: 20px;\\n  margin-right: 4px;\\n  background-color: transparent;\\n}\\n.igv-menu-popup-check-container div {\\n  padding-top: 2px;\\n  padding-left: 8px;\\n}\\n.igv-menu-popup-check-container div:first-child {\\n  position: relative;\\n  width: 12px;\\n  height: 12px;\\n}\\n.igv-menu-popup-check-container div:first-child svg {\\n  position: absolute;\\n  width: 12px;\\n  height: 12px;\\n}\\n\\n.igv-user-feedback {\\n  position: fixed;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 512px;\\n  height: 360px;\\n  z-index: 2048;\\n  background-color: white;\\n  border-color: #a2a2a2;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #444;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-user-feedback div:first-child {\\n  position: relative;\\n  height: 24px;\\n  width: 100%;\\n  background-color: white;\\n  border-bottom-color: #a2a2a2;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-user-feedback div:first-child div {\\n  position: absolute;\\n  top: 2px;\\n  width: 16px;\\n  height: 16px;\\n  background-color: transparent;\\n}\\n.igv-user-feedback div:first-child div:first-child {\\n  left: 8px;\\n}\\n.igv-user-feedback div:first-child div:last-child {\\n  cursor: pointer;\\n  right: 8px;\\n}\\n.igv-user-feedback div:last-child {\\n  width: 100%;\\n  height: calc(100% - 24px);\\n  border-width: 0;\\n}\\n.igv-user-feedback div:last-child div {\\n  width: auto;\\n  height: auto;\\n  margin: 8px;\\n}\\n\\n.igv-loading-spinner-container {\\n  z-index: 1024;\\n  position: absolute;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 32px;\\n  height: 32px;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-loading-spinner-container > div {\\n  box-sizing: border-box;\\n  width: 100%;\\n  height: 100%;\\n  border-radius: 50%;\\n  border: 4px solid rgba(128, 128, 128, 0.5);\\n  border-top-color: rgb(255, 255, 255);\\n  animation: spin 1s ease-in-out infinite;\\n  -webkit-animation: spin 1s ease-in-out infinite;\\n}\\n\\n@keyframes spin {\\n  to {\\n    -webkit-transform: rotate(360deg);\\n    transform: rotate(360deg);\\n  }\\n}\\n@-webkit-keyframes spin {\\n  to {\\n    -webkit-transform: rotate(360deg);\\n    transform: rotate(360deg);\\n  }\\n}\\n.igv-roi-menu {\\n  position: absolute;\\n  z-index: 512;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  color: #4b4b4b;\\n  background-color: white;\\n  width: 192px;\\n  border-radius: 4px;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n}\\n.igv-roi-menu > div:first-child {\\n  height: 24px;\\n  border-top-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-roi-menu > div:first-child > div {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-roi-menu > div:first-child > div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-roi-menu > div:last-child {\\n  background-color: white;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-color: transparent;\\n  border-bottom-style: solid;\\n  border-bottom-width: 0;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  text-align: start;\\n  vertical-align: middle;\\n}\\n.igv-roi-menu > div:last-child > div {\\n  height: 24px;\\n  padding-left: 4px;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  border-bottom-color: #7f7f7f;\\n}\\n.igv-roi-menu > div:last-child > div:not(:first-child):hover {\\n  cursor: pointer;\\n  background-color: rgba(127, 127, 127, 0.1);\\n}\\n.igv-roi-menu > div:last-child div:first-child {\\n  font-style: italic;\\n  text-align: center;\\n  padding-right: 4px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n}\\n.igv-roi-menu > div:last-child > div:last-child {\\n  border-bottom-width: 0;\\n  border-bottom-color: transparent;\\n}\\n\\n.igv-roi-placeholder {\\n  font-style: normal;\\n  color: rgba(75, 75, 75, 0.6);\\n}\\n\\n.igv-roi-table {\\n  position: absolute;\\n  z-index: 1024;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  resize: both;\\n  overflow: hidden;\\n  width: min-content;\\n  max-width: 1600px;\\n  border-color: #7f7f7f;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  font-weight: 400;\\n  background-color: white;\\n  cursor: default;\\n}\\n.igv-roi-table > div {\\n  height: 24px;\\n  font-size: 14px;\\n  text-align: start;\\n  vertical-align: middle;\\n  line-height: 24px;\\n}\\n.igv-roi-table > div:first-child {\\n  border-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-top-width: 0;\\n  border-bottom-color: #7f7f7f;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-roi-table > div:first-child > div:first-child {\\n  text-align: center;\\n  white-space: nowrap;\\n  text-overflow: ellipsis;\\n  overflow: hidden;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  width: calc(100% - 4px - 12px);\\n}\\n.igv-roi-table > div:first-child > div:last-child {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7f7f7f;\\n}\\n.igv-roi-table > div:first-child > div:last-child > svg {\\n  display: block;\\n}\\n.igv-roi-table > div:first-child > div:last-child:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-roi-table > .igv-roi-table-description {\\n  padding: 4px;\\n  margin-left: 4px;\\n  word-break: break-all;\\n  overflow-y: auto;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-goto-explainer {\\n  margin-top: 5px;\\n  margin-left: 4px;\\n  color: #7F7F7F;\\n  font-style: italic;\\n  height: 24px;\\n  border-top: solid lightgray;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles {\\n  height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n  padding-right: 16px;\\n  background-color: white;\\n  border-top-color: #7f7f7f;\\n  border-top-style: solid;\\n  border-top-width: thin;\\n  border-bottom-color: #7f7f7f;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles > div {\\n  font-size: 14px;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-left: 4px;\\n  height: 24px;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  border-right-color: #7f7f7f;\\n  border-right-style: solid;\\n  border-right-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles > div:last-child {\\n  border-right: unset;\\n}\\n.igv-roi-table > .igv-roi-table-row-container {\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  overflow: auto;\\n  height: 360px;\\n  flex: 1 1 auto;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\\n  height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\\n  font-size: 14px;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-left: 4px;\\n  height: 24px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  border-right-color: transparent;\\n  border-right-style: solid;\\n  border-right-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:last-child {\\n  border-right: unset;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\\n  background-color: rgba(0, 0, 0, 0.04);\\n}\\n.igv-roi-table > div:last-child {\\n  min-height: 32px;\\n  height: 32px;\\n  line-height: 32px;\\n  border-top-color: #7f7f7f;\\n  border-top-style: solid;\\n  border-top-width: thin;\\n  border-bottom-color: transparent;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-width: 0;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n\\n.igv-roi-table-row-selected {\\n  background-color: rgba(0, 0, 0, 0.125);\\n}\\n\\n.igv-roi-table-button {\\n  cursor: pointer;\\n  height: 20px;\\n  user-select: none;\\n  line-height: 20px;\\n  text-align: center;\\n  vertical-align: middle;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 13px;\\n  font-weight: 400;\\n  color: black;\\n  padding-left: 6px;\\n  padding-right: 6px;\\n  background-color: rgb(239, 239, 239);\\n  border-color: black;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 3px;\\n}\\n\\n.igv-roi-table-button:hover {\\n  font-weight: 400;\\n  background-color: rgba(0, 0, 0, 0.13);\\n}\\n\\n.igv-roi-region {\\n  z-index: 64;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  pointer-events: none;\\n  overflow: visible;\\n  margin-top: 66px;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n}\\n.igv-roi-region > div {\\n  position: relative;\\n  width: 100%;\\n  height: 8px;\\n  pointer-events: auto;\\n}\\n\\n.igv-roi-menu-row {\\n  height: 24px;\\n  padding-left: 8px;\\n  font-size: small;\\n  text-align: start;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  background-color: white;\\n}\\n\\n.igv-roi-menu-row-edit-description {\\n  width: -webkit-fill-available;\\n  font-size: small;\\n  text-align: start;\\n  vertical-align: middle;\\n  background-color: white;\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  padding-bottom: 4px;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n}\\n.igv-roi-menu-row-edit-description > label {\\n  margin-left: 2px;\\n  margin-bottom: 0;\\n  display: block;\\n  width: -webkit-fill-available;\\n}\\n.igv-roi-menu-row-edit-description > input {\\n  display: block;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  margin-bottom: 1px;\\n  width: -webkit-fill-available;\\n}\\n\\n.igv-container {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  padding-top: 4px;\\n  user-select: none;\\n  -webkit-user-select: none;\\n  -ms-user-select: none;\\n  min-height: 160px;\\n}\\n\\n.igv-viewport {\\n  position: relative;\\n  margin-top: 5px;\\n  line-height: 1;\\n  overflow-x: hidden;\\n  overflow-y: hidden;\\n}\\n\\n.igv-viewport-content {\\n  position: relative;\\n  width: 100%;\\n}\\n.igv-viewport-content > canvas {\\n  position: relative;\\n  display: block;\\n}\\n\\n.igv-column-container {\\n  position: relative;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  width: 100%;\\n}\\n\\n.igv-column-shim {\\n  width: 1px;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  background-color: #545453;\\n}\\n\\n.igv-axis-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 50px;\\n}\\n.igv-axis-column > div {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 100%;\\n}\\n.igv-axis-column > div > div {\\n  z-index: 512;\\n  position: absolute;\\n  top: 8px;\\n  left: 8px;\\n  width: fit-content;\\n  height: fit-content;\\n  background-color: transparent;\\n  display: grid;\\n  align-items: start;\\n  justify-items: center;\\n}\\n.igv-axis-column > div > div > input {\\n  display: block;\\n  margin: unset;\\n  cursor: pointer;\\n}\\n\\n.igv-column {\\n  position: relative;\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-sample-info-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-sample-name-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-scrollbar-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 14px;\\n}\\n.igv-scrollbar-column > div {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 14px;\\n}\\n.igv-scrollbar-column > div > div {\\n  cursor: pointer;\\n  position: absolute;\\n  top: 0;\\n  left: 2px;\\n  width: 8px;\\n  border-width: 1px;\\n  border-style: solid;\\n  border-color: #c4c4c4;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n}\\n.igv-scrollbar-column > div > div:hover {\\n  background-color: #c4c4c4;\\n}\\n\\n.igv-track-drag-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 12px;\\n  background-color: white;\\n}\\n.igv-track-drag-column > .igv-track-drag-handle {\\n  z-index: 512;\\n  position: relative;\\n  cursor: pointer;\\n  margin-top: 5px;\\n  width: 100%;\\n  border-style: solid;\\n  border-width: 0;\\n  border-top-right-radius: 6px;\\n  border-bottom-right-radius: 6px;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-color {\\n  background-color: #c4c4c4;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-hover-color {\\n  background-color: #787878;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-selected-color {\\n  background-color: #0963fa;\\n}\\n.igv-track-drag-column > .igv-track-drag-shim {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 100%;\\n  border-style: solid;\\n  border-width: 0;\\n}\\n\\n.igv-gear-menu-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 28px;\\n}\\n.igv-gear-menu-column > div {\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  margin-top: 5px;\\n  width: 100%;\\n  background: white;\\n}\\n.igv-gear-menu-column > div > div {\\n  position: relative;\\n  margin-top: 4px;\\n  width: 16px;\\n  height: 16px;\\n  color: #7F7F7F;\\n}\\n.igv-gear-menu-column > div > div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n\\n/*# sourceMappingURL=igv.css.map */\\n'),n.adoptedStyleSheets=[e]}if(this.root=e({class:\"igv-container\"}),n.appendChild(this.root),this.spinner=e({class:\"igv-loading-spinner-container\"}),this.root.appendChild(this.spinner),this.spinner.appendChild(e()),this.spinner.style.width=\"64px\",this.spinner.style.height=\"64px\",this.stopSpinner(),this.alert=new La(this.root),this.columnContainer=e({class:\"igv-column-container\"}),this.root.appendChild(this.columnContainer),this.menuPopup=new Xu(this.columnContainer),this.menuUtils=new bo(this),this.initialize(t),this.trackViews=[],this.constants={dragThreshold:3,scrollThreshold:5,defaultColor:\"rgb(0,0,150)\",doubleClickDelay:t.doubleClickDelay||500},this.eventHandlers={},t.listeners)for(let e of Object.keys(t.listeners))this.on(e,t.listeners[e]);this.on(\"trackremoved\",(()=>{0===this.findTracks((e=>\"function\"==typeof e.getSamples)).length&&(this.sampleInfoControl.setButtonVisibility(!1),this.sampleNameViewportWidth=void 0,this.showSampleNames=!1,this.sampleNameControl.setState(this.showSampleNames),this.sampleNameControl.hide(),this.layoutChange())})),this.on(\"didchangecolumnlayout\",(()=>{if(yu.length>0){const e=yu.length;for(let t=0;t<e;t++)yu[t].dispose();yu.length=0}})),this.addEventHandlers(),this.sampleInfo=new Uu(this),this.createStandardControls(t),this.roiManager=new Ky(this)}get doShowROITable(){return this.roiManager.roiTableIsVisible()}startSpinner(){this.spinner.style.display=\"flex\"}stopSpinner(){this.spinner.style.display=\"none\"}initialize(e){this.flanking=e.flanking,this.crossDomainProxy=e.crossDomainProxy,this.formats=e.formats,this.trackDefaults=e.trackDefaults,this.nucleotideColors=e.nucleotideColors||Bc;for(let e of Object.keys(this.nucleotideColors))this.nucleotideColors[e.toLowerCase()]=this.nucleotideColors[e];this.doShowTrackLabels=e.showTrackLabels,this.doShowCenterLine=e.showCenterGuide,this.doShowCursorGuide=e.showCursorGuide,this.showSampleNames=e.showSampleNames,this.sampleNameViewportWidth=void 0,e.sampleNameViewportWidth&&(this.sampleNameViewportWidth=e.sampleNameViewportWidth),e.search&&(this.searchConfig={type:\"json\",url:e.search.url,coords:void 0===e.search.coords?1:e.search.coords,chromosomeField:e.search.chromosomeField||\"chromosome\",startField:e.search.startField||\"start\",endField:e.search.endField||\"end\",geneField:e.search.geneField||\"gene\",snpField:e.search.snpField||\"snp\",resultsField:e.search.resultsField})}createStandardControls(e){this.setTrackLabelVisibility(e.showTrackLabels),this.navbar=new Py(e,this),this.navbar.$navigation.insertBefore(Bt(this.columnContainer)),!1===e.showControls&&this.navbar.hide(),this.cursorGuide=new ky(this.columnContainer,this),this.inputDialog=new Na(this.root),this.inputDialog.container.id=`igv-input-dialog-${s()}`,this.dataRangeDialog=new _o(this,Bt(this.root)),this.dataRangeDialog.$container.get(0).id=`igv-data-range-dialog-${s()}`,this.genericColorPicker=new Ra({parent:this.columnContainer,width:432}),this.genericColorPicker.container.id=`igv-track-color-picker-${s()}`,this.sliderDialog=new hA(this.root),this.sliderDialog.container.id=`igv-slider-dialog-${s()}`}getSampleNameViewportWidth(){return void 0===this.sampleNameViewportWidth||!1===this.showSampleNames?0:this.sampleNameViewportWidth}getSampleInfoViewportWidth(){return this.getSampleInfoColumnWidth()}isMultiLocusMode(){return this.referenceFrameList&&this.referenceFrameList.length>1}isMultiLocusWholeGenomeView(){if(void 0===this.referenceFrameList||1===this.referenceFrameList.length)return!1;for(let e of this.referenceFrameList)if(\"all\"===e.chr.toLowerCase())return!0;return!1}currentLoci(){const e=e=>`${e.chr}:${e.start+1}-${e.end}`;return void 0===this.referenceFrameList||0===this.referenceFrameList.length?\"\":1===this.referenceFrameList.length?e(this.referenceFrameList[0]):this.referenceFrameList.map((t=>e(t)))}toSVG(){const{x:e,y:t,width:i,height:n}=this.columnContainer.getBoundingClientRect(),r=new lu({width:i,height:n,backdropColor:\"white\",multiLocusGap:0,viewbox:{x:0,y:0,width:i,height:n}}),s={deltaX:0,deltaY:-t};for(let e of this.trackViews)e.renderSVGContext(r,s);return s.deltaX=e,this.roiManager.renderSVGContext(this.columnContainer,r,s),r.getSerializedSvg(!0)}saveSVGtoFile(e,t){let i=this.toSVG();if(t){const e=document.createElement(\"svg\");e.innerHTML=i,t.append(e),t.appendChild(e)}const n=e||\"igvjs.svg\",r=URL.createObjectURL(new Blob([i],{type:\"application/octet-stream\"}));Pt(n,r),URL.revokeObjectURL(r)}savePNGtoFile(e){const t=this.toSVG(),i=new Blob([t],{type:\"image/svg+xml\"}),n=URL.createObjectURL(i),r=document.createElement(\"img\");r.addEventListener(\"load\",(()=>{const t=this.columnContainer.getBoundingClientRect(),i=window.devicePixelRatio,s=t.width*i,o=t.height*i,a=document.createElement(\"canvas\");a.width=s,a.height=o;const c=a.getContext(\"2d\");c.scale(i,i),c.drawImage(r,0,0);const l=a.toDataURL(\"image/png\");Pt(e=e||\"igvjs.png\",l),URL.revokeObjectURL(n)})),r.src=n}async loadSession(e){let t;return this.sampleInfo.initialize(),this.roiSets=[],t=e.url||e.file?await dA.loadSessionFile(e):e,this.loadSessionObject(t)}static async loadSessionFile(e){const t=e.url||e.file;let i;if(e.url&&Mt(e.url)&&(e.url.startsWith(\"blob:\")||e.url.startsWith(\"data:\"))){const t=dA.uncompressSession(e.url);i=JSON.parse(t)}else{let n=e.filename;if(n||(n=e.url?await ja(e.url):e.file.name),n.endsWith(\".xml\")){const e=mu.KNOWN_GENOMES,n=await Qs.loadString(t);i=new by(n,e)}else if(n.endsWith(\"hub.txt\")){i={reference:(await du.loadHub(t,e)).getGenomeConfig()}}else{if(!n.endsWith(\".json\"))throw Error(\"Unrecognized session file format:\"+n);i=await Qs.loadJson(t)}}return bA(i)}async loadSessionObject(e){this.cleanHouseForSession(),this.config=e,e.browsers&&(e=await async function(e){const t=e.browsers[0],i={},n=new Mf({url:t.url});await n.readHeaderAndFooter(),i.sampleNameViewportWidth=20,i.genome=\"hg38\";const r=t.state.split(\",\"),s=n.bpResolutions[Number.parseInt(r[2])],o=Number.parseInt(r[0]),a=Math.floor(Number.parseFloat(r[3])*s),c=a+Math.floor(1700*s);return i.locus=`${n.chromosomes[o].name}:${a}-${c}`,i.tracks=(t.tracks||[]).filter((e=>!(\"refgene\"===e.format||\"cellType\"===e.name))),i.tracks.push({type:\"shoebox\",url:t.url,name:t.name,colorScale:t.colorScale,_hicFile:n}),i}(e)),this.navbar.sampleInfoControl.setButtonVisibility(!1),this.showSampleNames=e.showSampleNames||!1,this.navbar.sampleNameControl.setState(!0===this.showSampleNames),e.sampleNameViewportWidth&&(this.sampleNameViewportWidth=e.sampleNameViewportWidth),$a(this.columnContainer,\"igv-axis-column\"),$a(this.columnContainer,\"igv-sample-info-column\"),$a(this.columnContainer,\"igv-sample-name-column\"),$a(this.columnContainer,\"igv-scrollbar-column\"),$a(this.columnContainer,\"igv-track-drag-column\"),$a(this.columnContainer,\"igv-gear-menu-column\");const t=e.reference||e.genome;if(!t)return void console.warn(\"No genome or reference object specified\");const i=Mt(t)?await mu.expandReference(this.alert,t):t;if(await this.loadReference(i,i.locus||e.locus),this.centerLineList=this.createCenterLineList(this.columnContainer),!1!==e.showIdeogram){const e=new hy(this);e.id=\"ideogram\";const t=new hf(this,this.columnContainer,e);this.trackViews.push(t)}if(!1!==e.showRuler){const e=new hf(this,this.columnContainer,new Wu(this));this.trackViews.push(e)}e.qtlSelections&&(this.qtlSelections=cA.fromJSON(e.qtlSelections)),this.roiManager.clearROIs(),e.roi?this.roiManager.loadROI(e.roi):await this.roiManager.reset();const n=[];if(e.sampleinfo)for(const t of e.sampleinfo)t.file?n.push(t.file):this.loadSampleInfo(t);const r=i.tracks||[],s=e.tracks?r.concat(e.tracks):r;0===s.filter((e=>\"sequence\"===e.type&&!e.url&&!e.fastaURL)).length&&s.push({type:\"sequence\",order:Wd,removable:!1});const o=s.filter((e=>void 0!==e.file)).map((({file:e})=>e)),a=s.filter((e=>void 0!==e.indexFile)).map((({indexFile:e})=>e));a.length>0&&o.push(...a),n.length>0&&o.push(...n),o.length>0&&alert(`Local files cannot be loaded automatically.\\nThis session contains references to these local files:\\n${o.map((e=>`    ${e}`)).join(\"\\n\")}`);const c=s.filter((e=>void 0===e.file));let l=1;for(let e of c)void 0===e.order&&(e.order=l++);await this.loadTrackList(c);for(let e of this.trackViews.filter((e=>\"ruler\"===e.track.type||\"ideogram\"===e.track.type)))await e.updateViews();return this.trackViews.some((e=>e.track.selected))&&this.navbar.setEnableTrackSelection(!0),this.updateUIWithReferenceFrameList(),this.updateLocusSearchWidget(),s}cleanHouseForSession(){for(let e of this.trackViews)e.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(\".igv-axis-column, .igv-column-shim, .igv-column, .igv-sample-info-column, .igv-sample-name-column, .igv-scrollbar-column, .igv-track-drag-column, .igv-gear-menu-column\").forEach((e=>e.remove())),this.trackViews=[],this.circularView&&this.circularView.clearChords()}async loadReference(e,t){let i;this.removeAllTracks(),this.roiManager.clearROIs(),this.navbar.setEnableTrackSelection(!1),i=e.gbkURL?await wd(e.gbkURL):await aA.createGenome(e,this);const n=void 0===this.genome||this.genome.id!==i.id;this.genome=i,this.navbar.updateGenome(i);let r=t||i.initialLocus;Array.isArray(r)&&(r=r.join(\" \"));if(!await this.search(r,!0))throw new Error(`Cannot set initial locus ${r}`);if(n){let t;if(e.hubURL){t=(await du.loadHub(e.hubURL)).getGroupedTrackConfigurations()}this.fireEvent(\"genomechange\",[{genome:i,trackConfigurations:t}]),this.circularView&&this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Hm(this.genome)})}}async loadGenome(e){let t;e.genarkAccession&&(e.url=hu(e.genarkAccession)),e.url&&(Mt(e.url)&&e.url.endsWith(\"/hub.txt\")?(e.hubURL=e.url,delete e.url):\"gbk\"===function(e){let t;if(e instanceof File)t=e.name;else{if(\"string\"!=typeof e)throw new Error(\"Input must be a File object or a URL string\");t=e}const i=t.split(\".\").pop();return i.split(\"?\")[0]}(e.url)&&(e.gbkURL=e.url,delete e.url));if(e.hubURL||e.url&&Mt(e.url)&&e.url.endsWith(\"/hub.txt\")){t=(await du.loadHub(e.hubURL||e.url,e)).getGenomeConfig()}else t=Mt(e)||!(e.url||e.fastaURL||e.twoBitURL||e.gbkURL)?await mu.expandReference(this.alert,e):e;let i;await this.loadReference(t),i=t.gbkURL||\"gbk\"===t.format?[{name:\"Annotations\",format:\"gbk\",url:t.gbkURL}]:t.tracks||[];return 0===i.filter((e=>\"sequence\"===e.type)).length&&i.push({type:\"sequence\",order:Wd}),await this.loadTrackList(i),await this.updateViews(),this.genome}async loadTrackHub(e){const t=bA((await du.loadHub(e.url,e)).getGenomeConfig());return this.loadGenome(t)}updateUIWithReferenceFrameList(){const e=this.referenceFrameList;this.isMultiLocusWholeGenomeView()||mu.isWholeGenomeView(e[0].chr),this.navbar.navbarDidResize(),mA(this.trackViews,this.doShowTrackLabels),this.doShowCenterLine&&mu.isWholeGenomeView(e[0].chr)&&this.navbar.centerLineButton.boundMouseClickHandler(),this.doShowCursorGuide&&mu.isWholeGenomeView(e[0].chr)&&this.navbar.cursorGuideButton.boundMouseClickHandler(),this.setCenterLineAndCenterLineButtonVisibility(mu.isWholeGenomeView(e[0].chr))}setCenterLineAndCenterLineButtonVisibility(e){e?this.navbar.centerLineButton.setVisibility(!1):this.navbar.centerLineButton.setVisibility(this.config.showCenterGuideButton);for(let t of this.centerLineList)e?this.setCenterLineVisibility(!e):this.setCenterLineVisibility(this.doShowCenterLine)}setTrackLabelVisibility(e){mA(this.trackViews,e)}setROITableVisibility(e){!0===e?this.roiManager.presentTable():this.roiManager.dismissTable()}setCursorGuideVisibility(e){e?this.cursorGuide.show():this.cursorGuide.hide()}setCustomCursorGuideMouseHandler(e){this.cursorGuide.customMouseHandler=e}setCenterLineVisibility(e){for(let t of this.centerLineList)!0===e?(t.show(),t.repaint()):t.hide()}async loadTrackList(e){let t=0;for(let i of e)void 0===i.order&&(i.order=t++);const i=[];for(let t of e)i.push(this._loadTrack(t));const n=await Promise.all(i);return this.trackViews.filter((function(e){return e.track.autoscaleGroup})).length>0&&this.updateViews(),n}async loadTrack(e){e.sync=!1!==e.sync;const t=this._loadTrack(e);return t&&e.autoscaleGroup&&(await t,this.updateViews()),t}async _loadTrack(e){Mt(e)&&(e=JSON.parse(e));try{if(e.hidden){const t=Ad(e,this.genome);return void await t.getFeatures({chr:\"1\",start:0,end:Number.MAX_SAFE_INTEGER})}const t=await this.createTrack(e);if(\"sampleinfo\"===e.type)return void this.layoutChange();if(void 0===t)return;return this.addTrack(e,t)}catch(t){let i=t.message||t.error||t.toString();const n={401:\"Access unauthorized\",403:\"Access forbidden\",404:\"Not found\"};n.hasOwnProperty(i)&&(i=n[i]),i=`${i} : ${Ht(e.url)?e.url.name:e.url}`;const r=new Error(i);throw console.error(r),r}}async addTrack(e,t){void 0===t.order&&(t.order=this.trackViews.length);const i=new hf(this,this.columnContainer,t);if(this.trackViews.push(i),mA(this.trackViews,this.doShowTrackLabels),\"function\"==typeof t.postInit)try{i.startSpinner(),await t.postInit()}finally{i.stopSpinner()}return t.autoscaleGroup||(e.sync?await i.updateViews():i.updateViews()),\"function\"==typeof t.hasSamples&&t.hasSamples()&&(this.sampleInfo.hasAttributes()&&this.sampleInfoControl.setButtonVisibility(!0),!1!==this.config.showSampleNameButton&&this.sampleNameControl.show()),this.reorderTracks(),this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()]),t.trackView.enableTrackSelection(this.navbar.getEnableTrackSelection()),t}async loadROI(e){return this.roiManager.loadROI(e,this.genome)}clearROIs(){this.roiManager.clearROIs()}async getUserDefinedROIs(){if(this.roiManager){const e=this.roiManager.getUserDefinedROISet();if(void 0===e)return[];const t=await e.getAllFeatures(),i=[];for(let e of Object.values(t))i.push(...e);return i}return[]}getRulerTrackView(){const e=this.trackViews.filter((({track:e})=>\"ruler\"===e.id));return e.length>0?e[0]:void 0}async createTrack(e){let t=await async function(e){return\"function\"==typeof e?e():e}\n",
-       "/*! pako 2.1.0 https://github.com/nodeca/pako @license (MIT AND Zlib) */(e.url||e.fastaURL);if(Mt(t)&&(t=t.trim()),t)if(e.format)e.format=e.format.toLowerCase();else if(e.fastaURL)e.format=\"fasta\";else if(e.sourceType)\"htsget\"===e.sourceType&&await Rh.inferFormat(e);else{const t=await am(e);t&&(e.format=t)}e.type&&Ha(e);let i=e.type?e.type.toLowerCase():void 0;if(!i){if(!e.format)throw Error(`Unrecognized track:  ${JSON.stringify(e)}`);if(\"hic\"===e.format){const t=new Mf(e);if(await t.readHeaderAndFooter(),!t.chromosomeIndexMap.celltype)throw Error(\"'.hic' files not supported\");i=\"shoebox\",e._hicFile=t}else if(i=za(e.format),\"bedtype\"===i){const t=Ad(e,this.genome);e._featureSource=t;const n=await t.trackType();i=n||\"annotation\"}e.type=i}if(this.trackDefaults&&i){const t=this.trackDefaults[i];if(t)for(let i in t)t.hasOwnProperty(i)&&void 0===e[i]&&(e[i]=t[i])}const n=function(e,t,i){let n;switch(e){case\"annotation\":case\"genes\":case\"fusionjuncspan\":case\"snp\":n=\"feature\";break;case\"seg\":case\"maf\":case\"mut\":n=\"seg\";break;case\"junctions\":case\"splicejunctions\":n=\"junction\";break;default:n=e}return wy.has(n)?wy.get(n)(t,i):void 0}(i,e,this);if(void 0!==n)return e.roi&&e.roi.length>0&&(n.roiSets=e.roi.map((e=>new eA(e,this.genome)))),n;this.alert.present(new Error(`Error creating track.  Could not determine track type for file: ${e.url||e}`),void 0)}reorderTracks(){this.trackViews.sort((function(e,t){const i=e=>\"ideogram\"===e.track.id?1:\"ruler\"===e.track.id?2:3,n=i(e),r=i(t);if(n===r){return(e.track.order||0)-(t.track.order||0)}return n-r}));for(let{axis:e,viewports:t,sampleInfoViewport:i,sampleNameViewport:n,outerScroll:r,dragHandle:s,gearContainer:o}of this.trackViews){e.remove();for(let{$viewport:e}of t)e.detach();i.viewport.remove(),n.viewport.remove(),r.remove(),s.remove(),o.remove()}const e=this.columnContainer.querySelectorAll(\".igv-column\");for(let{axis:t,viewports:i,sampleInfoViewport:n,sampleNameViewport:r,outerScroll:s,dragHandle:o,gearContainer:a}of this.trackViews){this.columnContainer.querySelector(\".igv-axis-column\").appendChild(t);for(let t=0;t<e.length;t++){const{$viewport:n}=i[t];e[t].appendChild(n.get(0))}this.columnContainer.querySelector(\".igv-sample-info-column\").appendChild(n.viewport),this.columnContainer.querySelector(\".igv-sample-name-column\").appendChild(r.viewport),this.columnContainer.querySelector(\".igv-scrollbar-column\").appendChild(s),this.columnContainer.querySelector(\".igv-track-drag-column\").appendChild(o),this.columnContainer.querySelector(\".igv-gear-menu-column\").appendChild(a)}}getTrackOrder(){return this.trackViews.filter((e=>e.track&&e.track.name)).map((e=>e.track.name))}getSelectedTrackViews(){return this.trackViews.filter((e=>!0===e.track.selected))}removeTrackByName(e){const t=this.trackViews.slice();for(let i of t)e===i.track.name&&this.removeTrack(i.track)}removeTrack(e){for(let t of this.trackViews)if(e===t.track){this._removeTrack(t.track);break}}_removeTrack(e){e.disposed||(this.trackViews.splice(this.trackViews.indexOf(e.trackView),1),this.fireEvent(\"trackremoved\",[e]),this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()]),e.trackView&&e.trackView.dispose())}removeAllTracks(){const e=this.trackViews;this.trackViews=[];for(let t of e)\"ruler\"!==t.track.id&&\"ideogram\"!==t.track.id?(this.fireEvent(\"trackremoved\",[t.track]),t.dispose()):this.trackViews.push(t)}get ideogramTrackView(){return this.trackViews[0]}get rulerTrackView(){return this.trackViews[1]}findTracks(e,t){let i=\"function\"==typeof e?t=>e(t.track):i=>t===i.track[e];return this.trackViews.filter(i).map((e=>e.track))}get tracks(){return this.trackViews.map((e=>e.track)).filter((e=>void 0!==e))}setTrackHeight(e){this.trackHeight=e,this.trackViews.forEach((function(t){t.setTrackHeight(e)}))}async visibilityChange(){this.layoutChange()}async layoutChange(){if(this.referenceFrameList.find((e=>e.bpPerPixel<0))){const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel=(t.end-t.start)/e}this.referenceFrameList&&this.navbar.navbarDidResize(),uA.call(this),await this.updateViews()}async updateViews(){const e=this.trackViews;this.updateLocusSearchWidget();for(let e of this.referenceFrameList)e.bpPerPixel<=10&&await this.genome.getSequence(e.chr,e.start,e.start+1);for(let e of this.centerLineList)e.repaint();if(this.dragObject)for(let t of e)await t.updateViews();else{const t={},i=[];for(const n of e)if(n.track.autoscaleGroup){const e=n.track.autoscaleGroup;t[e]||(t[e]=[]),t[e].push(n)}else i.push(n);if(Object.entries(t).length>0)for(const[e,i]of Object.entries(t)){const e=await Promise.all(i.map((e=>e.getInViewFeatures()))),t=qa(e.flat());for(const e of i)e.track.dataRange=Object.assign({},t),e.track.autoscale=!1;await Promise.all(i.map((e=>e.updateViews())))}await Promise.all(i.map((e=>e.updateViews())))}}repaintViews(){for(let e of this.trackViews)e.repaintViews()}updateLocusSearchWidget(){if(!this.referenceFrameList)return;const e=this.referenceFrameList,t=this.calculateViewportWidth(this.referenceFrameList.length);for(let i of e)i.end=i.start+i.bpPerPixel*t;const i=1===e.length?this.referenceFrameList[0].chr:\"\",n=this.referenceFrameList.map((e=>e.getLocusString())).join(\" \");this.navbar.updateLocus(n,i),this.fireEvent(\"locuschange\",[this.referenceFrameList])}calculateViewportWidth(e){let{width:t}=this.columnContainer.getBoundingClientRect();return t-=50+this.getSampleInfoViewportWidth()+this.getSampleNameViewportWidth()+14+12+28,t-=5*(e-1),Math.floor(t/e)}minimumBases(){return this.config.minimumBases}zoomIn(){this.zoomWithScaleFactor(.5)}zoomOut(){this.zoomWithScaleFactor(2)}async zoomWithScaleFactor(e,t,i){if(!this.referenceFrameList)return;const n=this.calculateViewportWidth(this.referenceFrameList.length);let r=i?[i]:this.referenceFrameList;for(let i of r)i.zoomWithScaleFactor(this,e,n,t)}async addMultiLocusPanel(e,t,i,n){if(!this.referenceFrameList)return;const r=this.calculateViewportWidth(1+this.referenceFrameList.length),s=this.calculateViewportWidth(this.referenceFrameList.length)/this.calculateViewportWidth(1+this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel*=s;const o=(i-t)/r,a=new vy(this.genome,e,t,i,o),c=n?this.referenceFrameList.indexOf(n):this.referenceFrameList.length-1,l=1+c,{$viewport:h}=this.trackViews[0].viewports[c],d=Uy(h.get(0).parentElement);if(this.fireEvent(\"didchangecolumnlayout\"),l===this.referenceFrameList.length){this.referenceFrameList.push(a);for(let e of this.trackViews){const t=zu(e,d,a);e.viewports.push(t)}}else{this.referenceFrameList.splice(l,0,a);for(let e of this.trackViews){const t=zu(e,d,a);e.viewports.splice(l,0,t)}}this.centerLineList=this.createCenterLineList(this.columnContainer),uA.call(this),await this.updateViews(!0)}createCenterLineList(e){const t=e.querySelectorAll(\".igv-center-line\");for(let e=0;e<t.length;e++)t[e].remove();const i=[],n=e.querySelectorAll(\".igv-column\");for(let e=0;e<n.length;e++)i.push(new Qy(this,this.referenceFrameList[e],n[e]));return i}async removeMultiLocusPanel(e){const t=this.referenceFrameList.indexOf(e),{$viewport:i}=this.trackViews[0].viewports[t];Oy(t,i.parent().get(0)),this.fireEvent(\"didchangecolumnlayout\");for(let{viewports:e}of this.trackViews)e[t].dispose(),e.splice(t,1);if(this.referenceFrameList.splice(t,1),1===this.referenceFrameList.length&&this.getRulerTrackView())for(let e of this.getRulerTrackView().viewports)e.dismissLocusLabel();const n=this.calculateViewportWidth(1+this.referenceFrameList.length)/this.calculateViewportWidth(this.referenceFrameList.length);await this.rescaleForMultiLocus(n)}async gotoMultilocusPanel(e){const t=this.referenceFrameList.indexOf(e);this.columnContainer.querySelectorAll(\".igv-column\").forEach(((e,i)=>{i===t||e.remove()})),this.columnContainer.querySelectorAll(\".igv-column-shim\").forEach((e=>e.remove()));for(let e of this.trackViews){const i=e.viewports[t];e.viewports.filter(((e,i)=>i!==t)).forEach((e=>e.dispose())),e.viewports=[i]}const i=this.calculateViewportWidth(1);e.bpPerPixel=(e.end-e.start)/i,this.referenceFrameList=[e],this.trackViews.forEach((({viewports:e})=>e.forEach((e=>e.setWidth(i))))),this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}async rescaleForMultiLocus(e){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel*=e;for(let{viewports:e}of this.trackViews)for(let i of e)i.setWidth(t);this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews()}async goto(e,t,i){await this.search(e+\":\"+t+\"-\"+i)}async doSearch(e,t){const i=await this.search(e,t);return i||this.alert.present(new Error(`Unrecognized locus: <b> ${e} </b>`)),i}async search(e,t){const i=await async function(e,t){if(void 0===t||\"\"===t.trim())return;const i=t.split(\" \");let n=[];const r=async t=>{if(\"all\"===t.trim().toLowerCase()||\"*\"===t)return e.genome.wholeGenomeView?{chr:\"all\",start:0,end:e.genome.getChromosome(\"all\").bpLength}:void 0;let i,n;if(t.includes(\":\")&&(i=ey(t,e.isSoftclipped()),i&&(n=await e.genome.loadChromosome(i.chr))),!n){i=void 0;const r=await Jv(e,t);r&&(i={chr:r.chr,start:r.start,end:r.end,name:(r.name||t).toUpperCase()}),i||(n=await e.genome.loadChromosome(t),n&&(i={chr:n.name}))}return i&&(n=n||await e.genome.loadChromosome(i.chr),i.chr=n.name,void 0===i.start&&void 0===i.end&&(i.start=0,i.end=n.bpLength)),i};for(let e of i){const t=await r(e);t&&n.push(t)}if(0===n.length){const e=await r(t.replaceAll(\" \",\"+\"));e&&n.push(e)}return 0===n.length?void 0:n}(this,e);if(i&&i.length>0){this.referenceFrameList=function(e,t,i,n,r,s){return e.map((e=>{const o=Object.assign({},e);if(i&&o.name&&(o.start=Math.max(0,o.start-i),o.end+=i),!s){const e=t.getChromosome(o.chr);Qa(e.bpLength,o,n)}return new vy(t,o.chr,o.start,o.end,(o.end-o.start)/r)}))}(i,this.genome,this.flanking,this.minimumBases(),this.calculateViewportWidth(i.length),this.isSoftclipped());for(let e of this.trackViews)e.removeViewportsFromColumnContainer();this.columnContainer.querySelectorAll(\".igv-column-shim, .igv-column\").forEach((e=>e.remove())),qy(this.columnContainer.querySelector(\".igv-sample-info-column\"),this.referenceFrameList.length),this.fireEvent(\"didchangecolumnlayout\");for(let e of this.trackViews)e.createViewports(this,this.columnContainer,this.referenceFrameList);return this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),t||await this.updateViews(),!0}return!1}async loadSampleInfo(e){await this.sampleInfo.loadSampleInfoFile(e.url);for(const{sampleInfoViewport:e}of this.trackViews)e.setWidth(this.getSampleInfoColumnWidth());this.findTracks((e=>\"function\"==typeof e.getSamples)).length>0&&(this.sampleInfoControl.performClickWithState(this,!0),this.sampleInfoControl.setButtonVisibility(!0));for(const{sampleInfoViewport:e}of this.trackViews)e.repaint()}getSampleInfoColumnWidth(){if(this.sampleInfo.attributeCount){const e=this.findTracks((e=>\"function\"==typeof e.getSamples)).length>0,t=this.sampleInfo.hasAttributes(),i=this.sampleInfoControl.showSampleInfo;return e&&t&&i?this.sampleInfo.attributeCount*Vu+8:0}return 0}on(e,t){this.eventHandlers[e]||(this.eventHandlers[e]=[]),this.eventHandlers[e].push(t)}un(e,t){this.off(e,t)}off(e,t){if(e)if(t){const i=this.eventHandlers[e];if(i&&0!==i.length){const n=i.indexOf(t);-1!==n&&this.eventHandlers[e].splice(n,1)}else console.warn(\"No handlers to remove for event: \"+e)}else this.eventHandlers[e]=[];else this.eventHandlers={}}fireEvent(e,t,i){const n=this.eventHandlers[e];if(void 0===n||0===n.length)return;const r=i||window;return n.map((function(e){return e.apply(r,t)}))[0]}dispose(){this.removeEventHandlers();for(let e of this.trackViews)e.dispose();this.roiManager&&this.roiManager.dispose()}toJSON(){const e={version:\"3.0.9\"};if(void 0!==this.showSampleNames&&(e.showSampleNames=this.showSampleNames),this.sampleNameViewportWidth&&(e.sampleNameViewportWidth=this.sampleNameViewportWidth),e.reference=this.genome.toJSON(),e.reference.fastaURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.fastaURL.name}.`);if(e.reference.indexURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.indexURL.name}.`);const t=[];let i=this.trackViews[0];for(let{referenceFrame:e}of i.viewports){const i=e.getLocusString();t.push(i)}e.locus=1===t.length?t[0]:t,e.roi=this.roiManager.toJSON(),this.qtlSelections.isEmpty()||(e.qtlSelections=this.qtlSelections.toJSON());const n=[],r=[];for(const{track:e}of this.trackViews)try{let t;\"function\"==typeof e.getState?t=Hl.localFileInspection(e.getState()):e.config&&(t=Hl.localFileInspection(e.config)),t&&(t.browser&&delete t.browser,t.order=e.order,n.push(t))}catch(t){const i=`Track: ${e.name}: ${t}`;console.error(i),r.push(i)}if(r.length>0){let e=1,t=\"Errors encountered saving session: </br>\";for(let i of r)t+=` (${e++}) ${i.toString()} <br/>`;throw Error(t)}e.tracks=n;const s=[];for(const e of n)for(const t of Object.keys(e))\"file\"!==t&&\"indexFile\"!==t||s.push(e[t]);const o=[];if(this.sampleInfo.sampleInfoFiles.length>0){const t=this.sampleInfo.toJSON();t.length>0&&(e.sampleinfo=t);for(const e of this.sampleInfo.sampleInfoFiles){const t=Hl.localFileInspection({url:e});t.file&&o.push(t.file)}o.length>0&&s.push(...o)}return s.length>0&&alert(`This session includes reference(s) to local file(s):\\n${s.map((e=>`    ${e}`)).join(\"\\n\")}\\nLocal files cannot be loaded automatically when a saved session is restored.`),e}compressedSession(){return function(e){const t=new Uint8Array(e.length);for(var i=0;i<e.length;i++)t[i]=e.charCodeAt(i);const n=new cs(t),r=String.fromCharCode.apply(null,n);return btoa(r).replace(/\\+/g,\".\").replace(/\\//g,\"_\").replace(/=/g,\"-\")}(JSON.stringify(this.toJSON()))}sessionURL(){const e=window.location.href.slice(),t=e.indexOf(\"?\");return(t>0?e.substring(0,t):e)+\"?sessionURL=blob:\"+this.compressedSession()}mouseDownOnViewport(e,t){var i;i=r(e),this.vpMouseDown={viewport:t,lastMouseX:i.x,mouseDownX:i.x,lastMouseY:i.y,mouseDownY:i.y,referenceFrame:t.referenceFrame}}cancelTrackPan(){const e=this.dragObject;this.dragObject=void 0,this.isScrolling=!1,this.vpMouseDown=void 0,e&&e.viewport.referenceFrame.start!==e.start&&(this.updateViews(),this.fireEvent(\"trackdragend\",[e.viewport]))}isTrackPanning(){return this.dragObject}isSoftclipped(){return void 0!==this.trackViews.find((e=>!0===e.track.showSoftClips))}startTrackDrag(e){this.dragTrack=e}updateTrackDrag(e){if(e&&this.dragTrack){const t=this.dragTrack,i=this.trackViews.indexOf(e),n=this.trackViews.indexOf(t),r=this.trackViews;r[i]=t,r[n]=e;const s=this.trackViews[i].track.order;this.trackViews[n].track.order=s;const o=r.length;let a=s;if(i<n)for(let e=i+1;e<o;e++){const t=r[e].track;if(!(t.order<=a))break;t.order=Math.min(Number.MAX_SAFE_INTEGER,a+1),a=t.order}else for(let e=i-1;e>0;e--){const t=r[e].track;if(!(t.order>=a))break;t.order=Math.max(-Number.MAX_SAFE_INTEGER,a-1),a=t.order}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()])):this.dragTrack=void 0}addEventHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers(),this.addKeyboardHandler()}removeEventHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers(),this.removeKeyboardHandler()}addWindowResizeHandler(){this.boundWindowResizeHandler=uA.bind(this),window.addEventListener(\"resize\",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener(\"resize\",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=pA.bind(this),this.root.addEventListener(\"mouseup\",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener(\"mouseup\",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=pA.bind(this),this.root.addEventListener(\"mouseleave\",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener(\"mouseleave\",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=fA.bind(this),this.boundColumnContainerTouchMoveHandler=fA.bind(this),this.boundColumnContainerMouseLeaveHandler=pA.bind(this),this.boundColumnContainerMouseUpHandler=pA.bind(this),this.boundColumnContainerTouchEndHandler=pA.bind(this),this.columnContainer.addEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener(\"touchmove\",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener(\"mouseleave\",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener(\"touchend\",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener(\"touchmove\",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener(\"mouseleave\",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener(\"touchend\",this.boundColumnContainerTouchEndHandler)}addKeyboardHandler(){this.keyUpHandler=gA.bind(this),document.addEventListener(\"keyup\",this.keyUpHandler)}removeKeyboardHandler(){console.log(\"Remove handler\"),document.addEventListener(\"keyup\",this.keyUpHandler)}static uncompressSession(e){let t;if(e.indexOf(\"/gzip;base64\")>0){t=vs(e);let i=\"\";for(let e of t)i+=String.fromCharCode(e);return i}return function(e){e=e.replace(/\\./g,\"+\").replace(/_/g,\"/\").replace(/-/g,\"=\");const t=atob(e),i=[];for(let e=0;e<t.length;e++)i.push(t.charCodeAt(e));const n=hs(i);let r=\"\";for(let e of n)r+=String.fromCharCode(e);return r}(e.substring(5))}createCircularView(e,t){var i;return t=!0===t,this.circularView=(i=this,new Bm(e,{onChordClick:(e,t,n)=>{const r=e.data,s=r.mate;function o(e){e.chr=i.genome.getChromosomeName(e.refName);let t=!1;for(let n of i.referenceFrameList){const i=lm.fromLocusString(n.getLocusString());if(i.contains(e)){t=!0;break}if(i.overlaps(e)){n.extend(e),t=!0;break}}if(!t){const t=2e3,n=(e.start+e.end)/2;i.addMultiLocusPanel(e.chr,n-t,n+t)}}o(r),o(s)}})),this.circularViewControl=new Vy(this.navbar.toggle_button_container,this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Hm(this.genome)}),this.circularViewVisible=t,this.circularView}get circularViewVisible(){return void 0!==this.circularView&&this.circularView.visible}set circularViewVisible(e){this.circularView&&(this.circularView.visible=e,this.circularViewControl.setState(e))}get sampleInfoControl(){return this.navbar.sampleInfoControl}get overlayTrackButton(){return this.navbar.overlayTrackButton}get roiTableControl(){return this.navbar.roiTableControl}get sampleInfoControl(){return this.navbar.sampleInfoControl}get sampleNameControl(){return this.navbar.sampleNameControl}}async function uA(){if(!this.referenceFrameList)return;const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList){const i=this.referenceFrameList.indexOf(t),{chr:n,genome:r}=t,{bpLength:s}=r.getChromosome(t.chr),o=t.toBP(e);mu.isWholeGenomeView(n)||o>s?t.bpPerPixel=s/e:t.end=t.start+t.toBP(e);for(let{viewports:t}of this.trackViews)t[i].setWidth(e)}this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}function fA(e){e.preventDefault();const{x:t,y:i}=r(e);if(this.vpMouseDown){const{viewport:e,referenceFrame:n}=this.vpMouseDown,r=Math.abs(t-this.vpMouseDown.mouseDownX)>Math.abs(i-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling)if(r)this.vpMouseDown.mouseDownX&&Math.abs(t-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:e,start:n.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(i-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const t=e.$viewport.height(),i=e.trackView.maxViewportContentHeight();this.vpMouseDown.r=t/i}if(this.dragObject){const i=!this.isSoftclipped();let r=this.vpMouseDown.lastMouseX-t;n.shiftPixels(r,e.$viewport.width(),i)&&this.updateViews(),this.fireEvent(\"trackdrag\")}if(this.isScrolling){const t=this.vpMouseDown.r*(this.vpMouseDown.lastMouseY-i);e.trackView.moveScroller(t)}this.vpMouseDown.lastMouseX=t,this.vpMouseDown.lastMouseY=i}}function pA(e){this.cancelTrackPan(),this.endTrackDrag()}async function gA(e){if(this.referenceFrameList&&!(this.referenceFrameList.length>1)&&(\"KeyF\"===e.code||\"KeyB\"===e.code)){const t=this.getSelectedTrackViews();if(t.length>0){const i=t[0].track;if(\"function\"==typeof i.nextFeatureAfter){const t=this.referenceFrameList[0],n=t.viewport?t.viewport.getWidth():this.calculateViewportWidth(this.referenceFrameList.length),r=\"all\"===t.chr.toLowerCase(),s=i.visibilityWindow;if(r||s&&s>0&&t.bpPerPixel*n>s)return;const o=\"KeyF\"===e.code,a=t.chr,c=t.center,l=await i.nextFeatureAfter(a,c,o);if(l){const i=await this.genome.getChromosomeName(l.chr);if(a===i){const i=(l.start+l.end)/2;if(e.shiftKey){const e=this.config.minimumBases||40,r=Math.max(e,1.1*(l.end-l.start));t.start=Math.max(0,i-r/2),t.end=i+r/2,t.bpPerPixel=(t.end-t.start)/n}else t.shift(i-c);this.updateViews()}else{t.chr=i;const r=(l.start+l.end)/2;if(e.shiftKey){const e=this.config.minimumBases||40,i=Math.max(e,1.1*(l.end-l.start));t.start=Math.max(0,r-i/2),t.end=t.start+i,t.bpPerPixel=(t.end-t.start)/n}else t.start=r-n*t.bpPerPixel/2,t.end=t.start+n*t.bpPerPixel;this.updateViews()}}}}}}function mA(e,t){for(let{viewports:i}of e)for(let e of i)e.$trackLabel&&(0===i.indexOf(e)&&!0===t?e.$trackLabel.show():e.$trackLabel.hide())}let wA=[];function bA(e){return void 0===e.minimumBases&&(e.minimumBases=40),void 0===e.showIdeogram&&(e.showIdeogram=!0),void 0===e.showCircularView&&(e.showCircularView=!1),void 0===e.showCircularViewButton&&(e.showCircularViewButton=!1),void 0===e.showTrackLabelButton&&(e.showTrackLabelButton=!0),void 0===e.showTrackLabels&&(e.showTrackLabels=!0),void 0===e.showCursorTrackingGuideButton&&(e.showCursorTrackingGuideButton=!0),void 0===e.showCursorGuide&&(e.showCursorGuide=e.showCursorTrackingGuide||!1),void 0===e.showCenterGuideButton&&(e.showCenterGuideButton=!0),void 0===e.showCenterGuide&&(e.showCenterGuide=!1),void 0===e.showSampleNames&&(e.showSampleNames=!1),void 0===e.showSVGButton&&(e.showSVGButton=!0),void 0===e.showControls&&(e.showControls=!0),void 0===e.showNavigation&&(e.showNavigation=!0),void 0===e.showRuler&&(e.showRuler=!0),void 0===e.flanking&&(e.flanking=1e3),void 0===e.pairsSupported&&(e.pairsSupported=!0),e.tracks||(e.tracks=[]),e}const FA=Qs.setApiKey;const vA=Qs.oauth;var yA={TrackUtils:Pa,IGVGraphics:xo,MenuUtils:bo,DataRangeDialog:_o,createTrack:async function(e,t){return await dA.prototype.createTrack.call(t,e)},createBrowser:async function(e,t){void 0===t&&(t={}),mu.KNOWN_GENOMES||await mu.initializeGenomes(t),bA(t),t.queryParametersSupported&&function(e){var t,i,n,r,s,o,a,c,l;let h,d,u;if(a=window.location.href,s={},t=a.indexOf(\"?\"),i=a.lastIndexOf(\"#\"),t>=0)for(i<0&&(i=a.length),n=t+1;n<i;)(r=a.indexOf(\"&\",n))<0&&(r=i),2===(o=a.substring(n,r).split(\"=\",2)).length?(c=o[0],l=decodeURIComponent(o[1]),\"file\"===c?h=l.split(\",\"):\"index\"===c?d=l.split(\",\"):\"name\"===c?u=l.split(\",\"):\"genome\"===c?!l.startsWith(\"https://\")&&!l.startsWith(\"http://\")||l.endsWith(\".json\")?(e[c]=l,e.reference=void 0):e.reference={fastaURL:l,indexURL:l+\".fai\"}:(\"reference\"===c&&(e.genome=void 0),e[c]=l),n=r+1):n++;if(h){e.tracks||(e.tracks=[]);for(let t=0;t<h.length;t++){if(h[t].endsWith(\".xml\")||h[t].endsWith(\".json\")){e.sessionURL=h[t];break}const i={url:h[t]};d&&d.length>t&&(i.indexURL=d[t]),u&&u.length>t&&(i.name=u[t]),e.tracks.push(i)}}}(t),t.apiKey&&Qs.setApiKey(t.apiKey),t.oauthToken&&Qs.setOauthToken(t.oauthToken),t.clientId&&!Ts()&&await async function(e){if(!google.accounts.oauth2.initTokenClient)throw new Error(\"Google accounts token client not loaded (https://accounts.google.com/gsi/client)\");if(Ts())throw new Error(\"Google client is already initialized\");const t={client_id:e.client_id||e.clientId,scope:e.scope||\"https://www.googleapis.com/auth/userinfo.profile\",state:e.state||\"igv\",error:e=>{throw new Error(e.type)},hint:e.hint,hosted_domain:e.hosted_domain},i=google.accounts.oauth2.initTokenClient(t);google.igv={tokenClient:i,apiKey:e.apiKey}}({client_id:t.clientId,apiKey:t.apiKey,scope:\"https://www.googleapis.com/auth/userinfo.profile\"});const i=new dA(t,e);wA.push(i),i.startSpinner();const n=t.sessionURL||t.session||t.hubURL;return n?await i.loadSession({url:n}):await i.loadSessionObject(t),i.stopSpinner(),i.navbar.navbarDidResize(),i},removeBrowser:function(e){e.dispose(),e.root.remove(),wA=wA.filter((t=>t!==e))},removeAllBrowsers:function(){for(let e of wA)e.dispose(),e.root.remove();wA=[]},visibilityChange:async function(){for(let e of wA)await e.visibilityChange()},setGoogleOauthToken:function(e){return Qs.setOauthToken(e)},setOauthToken:function(e,t){return Qs.setOauthToken(e,t)},oauth:vA,version:yy,setApiKey:FA,TrackBase:Hl,registerTrackClass:function(e,t){wy.set(e,((e,i)=>new t(e,i)))},registerTrackCreatorFunction:function(e,t){wy.set(e,t)},registerFileFormats:function(e,t){Sl[e]={fields:t}},loadSessionFile:dA.loadSessionFile};return yA}();\n",
-       "//# sourceMappingURL=igv.iife.js.map\n"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "/**\n",
-       " * Global handler for igv.js messages.  Messages have the form\n",
-       " * {\n",
-       " *     command  -- the command to execute\n",
-       " *     id -- the id of the igv.js browser, if applicable\n",
-       " *     data -- any data needed for the command\n",
-       " * }\n",
-       " */\n",
-       "\n",
-       "// Use a self-evaluating function to keep variables in this file scope, with the execption of the global handler\n",
-       "\n",
-       "(function () {\n",
-       "\n",
-       "    const isColab = window.google !== undefined && window.google.colab\n",
-       "    const isNotebook = !isColab && window.Jupyter !== undefined\n",
-       "\n",
-       "    let svgComm\n",
-       "    if (isNotebook) {\n",
-       "        svgComm = Jupyter.notebook.kernel.comm_manager.new_comm('svg', {})\n",
-       "    }\n",
-       "\n",
-       "    async function toSVG(displayID, locus, svg) {\n",
-       "        //console.log(isNotebook + \" \" + locus)\n",
-       "        if (isNotebook) {\n",
-       "            svgComm.send({\n",
-       "                \"display_id\": displayID,\n",
-       "                \"locus\": locus,\n",
-       "                \"svg\": svg\n",
-       "            })\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    console.log(\"Installing IGVMessageHandler\")\n",
-       "\n",
-       "    function convertUrlsAndPaths(session) {\n",
-       "        if (session.reference) {\n",
-       "            for (let pre of [\"fasta\", \"index\", \"cytoband\", \"cytobandBb\", \"compressedIndex\", \"alias\", \"aliasBb\",\n",
-       "            \"twoBit\", \"twoBitBpt\", \"chromAliasBb\", \"chromSizes\", \"trix\"]) {\n",
-       "                convert(session.reference, pre)\n",
-       "            }\n",
-       "            if (session.reference.tracks) {\n",
-       "                for (let t of session.reference.tracks) {\n",
-       "                    convert(t)\n",
-       "                    convert(t, \"index\")\n",
-       "                    if (!t.indexURL) {\n",
-       "                        t.indexed = false\n",
-       "                    }\n",
-       "                }\n",
-       "            }\n",
-       "        }\n",
-       "\n",
-       "        if (session.tracks) {\n",
-       "            for (let t of session.tracks) {\n",
-       "                convert(t)\n",
-       "                convert(t, \"index\")\n",
-       "                if (!t.indexURL) {\n",
-       "                    t.indexed = false\n",
-       "                }\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Return true if the sessionJson object contains only absolute URLs to resources\n",
-       "     */\n",
-       "    function safeToWeblink(sessionJson) {\n",
-       "        const unsafe = (url) => typeof url.startsWith != 'function' || !url.startsWith(\"http\")\n",
-       "        if (sessionJson.reference) {\n",
-       "            if (unsafe(sessionJson.reference.fastaURL)) return false\n",
-       "        }\n",
-       "        if (sessionJson.tracks) {\n",
-       "            const urls = sessionJson.tracks.filter(t => t.url).map(t => t.url)\n",
-       "            if (urls.some(unsafe)) return false\n",
-       "        }\n",
-       "        return true\n",
-       "    }\n",
-       "\n",
-       "    class MessageHandler {\n",
-       "\n",
-       "        constructor() {\n",
-       "            this.browserCache = new Map()\n",
-       "            this.messageQueue = new Queue()\n",
-       "        }\n",
-       "\n",
-       "        on(msg) {\n",
-       "            this.messageQueue.enqueue(msg)\n",
-       "            this.processQueue()\n",
-       "        }\n",
-       "\n",
-       "        async processQueue() {\n",
-       "\n",
-       "            const convertTrackData = (data) => {\n",
-       "                convert(data)\n",
-       "                convert(data, \"index\")\n",
-       "                if (!data.indexURL) {\n",
-       "                    data.indexed = false\n",
-       "                }\n",
-       "            }\n",
-       "\n",
-       "            if (!this.processing) {\n",
-       "                this.processing = true\n",
-       "                while (!this.messageQueue.isEmpty()) {\n",
-       "                    const msg = this.messageQueue.dequeue()\n",
-       "                    const command = msg.command\n",
-       "                    const browserID = msg.id\n",
-       "                    const data = msg.data\n",
-       "                    const browser = this.browserCache.get(browserID)\n",
-       "                    try {\n",
-       "                        switch (command) {\n",
-       "                            case \"createBrowser\":\n",
-       "\n",
-       "                                // custom button bar\n",
-       "                                const button_container = document.getElementById(`${browserID}_buttons`) // <= created from python\n",
-       "                                const customButtonDiv = document.createElement('div')\n",
-       "                                customButtonDiv.style = `background: #f3f3f3;padding: 5px;border-color: #bfbfbf;border-style: solid;border-width: thin;border-radius: 3px;`\n",
-       "                                button_container.appendChild(customButtonDiv)\n",
-       "\n",
-       "                                data.sync = true\n",
-       "                                convertUrlsAndPaths(data)\n",
-       "\n",
-       "                                const container = document.getElementById(`${browserID}_igvcontainer`)  // <= created from python\n",
-       "                                const newBrowser = await igv.createBrowser(container, data)\n",
-       "                                this.browserCache.set(browserID, newBrowser)\n",
-       "\n",
-       "                                // Add igv-notebook button bar\n",
-       "                                const toJsonButton = document.createElement('button')\n",
-       "                                toJsonButton.innerText = \"Save Session\"\n",
-       "                                toJsonButton.style = \"margin-right:5px\"\n",
-       "                                toJsonButton.addEventListener('click', (evt) => {\n",
-       "                                    let fn\n",
-       "                                    if (isNotebook) {\n",
-       "                                        fn = prompt(\"Filename:\", \"session.json\")\n",
-       "                                    } else {\n",
-       "                                        fn = \"session.json\"\n",
-       "                                    }\n",
-       "                                    if (fn) {\n",
-       "                                        const json = newBrowser.toJSON()\n",
-       "                                        const jsonString = JSON.stringify(json, null, '\\t')\n",
-       "                                        download(fn, jsonString)\n",
-       "                                    }\n",
-       "                                })\n",
-       "                                customButtonDiv.appendChild(toJsonButton)\n",
-       "\n",
-       "                                const webLinkNode = document.createElement('a')\n",
-       "                                webLinkNode.target = \"igvWeb\"\n",
-       "                                webLinkNode.innerText = \"Link to IGV-Web\"\n",
-       "                                webLinkNode.style.display = \"none\"\n",
-       "\n",
-       "                                const shareButton = document.createElement('button')\n",
-       "                                shareButton.innerText = \"Show IGV-Web Link\"\n",
-       "                                shareButton.style = \"margin-right:5px\"\n",
-       "                                shareButton.addEventListener('click', async (evt) => {\n",
-       "\n",
-       "                                    if (safeToWeblink(newBrowser.toJSON())) {\n",
-       "                                        const sessionURL = `https://igv.org/app?sessionURL=blob:${newBrowser.compressedSession()}`\n",
-       "                                        const shortURL = await shortenURL(sessionURL)\n",
-       "                                        webLinkNode.innerText = \"Link to IGV-Web\"\n",
-       "                                        webLinkNode.setAttribute(\"href\", shortURL)\n",
-       "                                        webLinkNode.style.display = \"inline-block\"\n",
-       "                                        shareButton.innerText = \"Update IGV-Web Link\"\n",
-       "                                    } else {\n",
-       "                                        webLinkNode.innerText = \"Cannot link -- non URL resources used\"\n",
-       "                                        webLinkNode.style.display = \"inline-block\"\n",
-       "                                    }\n",
-       "                                })\n",
-       "                                customButtonDiv.appendChild(shareButton)\n",
-       "                                customButtonDiv.appendChild(webLinkNode)\n",
-       "\n",
-       "                                if (isNotebook) {\n",
-       "                                    const toSVGButton = document.createElement('button')\n",
-       "                                    toSVGButton.innerText = \"To SVG\"\n",
-       "                                    toSVGButton.style = \"float:right\"\n",
-       "                                    toSVGButton.addEventListener('click', (evt) => {\n",
-       "                                        const locus = newBrowser.referenceFrameList.map(rf => rf.getLocusString()).join(' ')\n",
-       "                                        const svg = newBrowser.toSVG()\n",
-       "                                        toSVG(browserID, locus, svg)\n",
-       "                                    })\n",
-       "                                    customButtonDiv.appendChild(toSVGButton)\n",
-       "                                }\n",
-       "\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadSession\":\n",
-       "                                convertUrlsAndPaths(data)\n",
-       "                                browser.loadSessionObject(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadTrack\":\n",
-       "                                convertTrackData(data)\n",
-       "                                await browser.loadTrack(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadROI\":\n",
-       "                                if (Array.isArray(data)) {\n",
-       "                                    data.map(convertTrackData)\n",
-       "                                } else {\n",
-       "                                    convertTrackData(data)\n",
-       "                                }\n",
-       "                                await browser.loadROI(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"clearROIs\":\n",
-       "                                await browser.clearROIs()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"search\":\n",
-       "                                browser.search(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"zoomIn\":\n",
-       "                                browser.zoomIn()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"zoomOut\":\n",
-       "                                browser.zoomOut()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"remove\":\n",
-       "                                this.browserCache.delete(browserID)\n",
-       "                                document.getElementById(browserID).parentNode.removeChild(container)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"toSVG\":\n",
-       "                                const displayId = data\n",
-       "                                const svg = browser.toSVG()\n",
-       "                                const locus = browser.referenceFrameList.map(rf => rf.getLocusString()).join(' ')\n",
-       "                                toSVG(displayId, locus, svg)\n",
-       "                                break\n",
-       "\n",
-       "                            default:\n",
-       "                                console.error(\"Unrecognized method: \" + msg.command)\n",
-       "                        }\n",
-       "                    } catch (e) {\n",
-       "                        console.error(e)\n",
-       "                    }\n",
-       "                }\n",
-       "                this.processing = false\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Potentially convert a path to a local File-like object.\n",
-       "     * @param path\n",
-       "     * @returns {*}\n",
-       "     */\n",
-       "    function createNotebookFile(path) {\n",
-       "        if (!path ||\n",
-       "            path.startsWith(\"https://\") || path.startsWith(\"http://\") || path.startsWith(\"gs://\") || path.startsWith(\"data:\")) {\n",
-       "            return path\n",
-       "        } else {\n",
-       "            // Try to create a notebook file.  If no notebook file implementation is available for the kernel in\n",
-       "            // use (e.g. Jupyter Lab) treat as a URL.\n",
-       "            const nbFile = igv.createNotebookLocalFile({path})\n",
-       "            if (nbFile != null) {\n",
-       "                return nbFile\n",
-       "            } else {\n",
-       "                // Try to treat as relative URL.  This may or may not work\n",
-       "                return convertURL(path)\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Convert relative URLs to absolute.  Primarily for Jupyter Lab, not generally needed for Jupyter Notebook\n",
-       "     * @param url\n",
-       "     * @returns {*}\n",
-       "     */\n",
-       "    function convertURL(url) {\n",
-       "\n",
-       "        const pageURL = window.location.href\n",
-       "\n",
-       "        if (!url ||\n",
-       "            url.startsWith(\"https://\") ||\n",
-       "            url.startsWith(\"http://\") ||\n",
-       "            url.startsWith(\"gs://\") ||\n",
-       "            url.startsWith(\"data:\")) {\n",
-       "            return url\n",
-       "        } else if (isColab) {\n",
-       "            // Interpret relative url as a path.\n",
-       "            igv.createNotebookLocalFile({path: url})\n",
-       "        } else if (isNotebook) {\n",
-       "            // Jupyter Notebook\n",
-       "            //\n",
-       "            // Examples\n",
-       "            // https://hub-binder.mybinder.ovh/user/igvteam-igv-notebook-tnlb45ie/notebooks/examples/BamFiles-Jupyter.ipynb\n",
-       "            //   => https://hub-binder.mybinder.ovh/user/igvteam-igv-notebook-tnlb45ie/files/examples/data/gstt1_sample.bam\",\n",
-       "\n",
-       "            const baseURL = document.querySelector('body').getAttribute('data-base-url')\n",
-       "            const notebookPath = document.querySelector('body').getAttribute('data-notebook-path')\n",
-       "            const notebookName = document.querySelector('body').getAttribute('data-notebook-name')\n",
-       "            const notebookDir = notebookPath.slice(0, -1 * notebookName.length)\n",
-       "\n",
-       "            //`${location.origin}${base_path}files/${nb_dir}${url}`\n",
-       "            if (url.startsWith(\"/\")) {\n",
-       "                url = `files${url}`\n",
-       "                return encodeURI(`${location.origin}${baseURL}${url}`)\n",
-       "            } else {\n",
-       "                // URL is relative to notebook\n",
-       "                return encodeURI(`${location.origin}${baseURL}files/${notebookDir}${url}`)\n",
-       "            }\n",
-       "        } else if (pageURL.includes(\"/lab\")) {\n",
-       "\n",
-       "            console.log(\"Jupyter lab\")\n",
-       "            // Jupyter Lab\n",
-       "\n",
-       "            // Examples\n",
-       "            // http://localhost:8888/lab/workspaces/auto-N/tree/examples/BamFiles.ipynb\n",
-       "            //     =>  http://localhost:8888/files/examples/data/gstt1_sample.bam\n",
-       "            //\n",
-       "            // https://hub.gke2.mybinder.org/user/igvteam-igv-notebook-5ivkyktt/lab/tree/examples/BamFiles.ipynb\n",
-       "            //    => https://hub.gke2.mybinder.org/user/igvteam-igv-notebook-5ivkyktt/files/examples/data/gstt1_sample.bam\n",
-       "\n",
-       "            const baseIndex = pageURL.indexOf(\"/lab\")\n",
-       "            const baseURL = pageURL.substring(0, baseIndex)\n",
-       "\n",
-       "            if (url.startsWith(\"/\")) {\n",
-       "                return encodeURI(`${baseURL}/files${url}`)\n",
-       "            } else if (pageURL.includes(\"/tree/\")) {\n",
-       "                // Interpret URL as relative to notebook location.  This is not reliable, '/tree/' is not always in the page URL\n",
-       "                const treeIndex = pageURL.indexOf(\"/tree/\") + 6\n",
-       "                const lastSlashIndex = pageURL.lastIndexOf(\"/\")\n",
-       "                const notebookDir = pageURL.substring(treeIndex, lastSlashIndex)\n",
-       "                return encodeURI(`${baseURL}/files/${notebookDir}/${url}`)\n",
-       "            } else {\n",
-       "                // We don't know how to determine the notebook path\n",
-       "                console.warn(\"Page url missing '/tree/'.  Can't determine notebook path.\")\n",
-       "                return encodeURI(`${baseURL}/files/${url}`)\n",
-       "            }\n",
-       "        } else {\n",
-       "            // We should never get here,\n",
-       "            return encodeURI(url)\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    function convert(config, prefix) {\n",
-       "        const urlProp = prefix ? prefix + \"URL\" : \"url\"\n",
-       "        const pathProp = prefix ? prefix + \"Path\" : \"path\"\n",
-       "        if (config[pathProp]) {\n",
-       "            config[urlProp] = createNotebookFile(config[pathProp])\n",
-       "        } else if (config[urlProp]) {\n",
-       "            config[urlProp] = convertURL(config[urlProp])\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    class Queue {\n",
-       "        constructor() {\n",
-       "            this.elements = []\n",
-       "        }\n",
-       "\n",
-       "        enqueue(e) {\n",
-       "            this.elements.push(e)\n",
-       "        }\n",
-       "\n",
-       "        dequeue() {\n",
-       "            return this.elements.shift()\n",
-       "        }\n",
-       "\n",
-       "        isEmpty() {\n",
-       "            return this.elements.length == 0\n",
-       "        }\n",
-       "\n",
-       "        peek() {\n",
-       "            return !this.isEmpty() ? this.elements[0] : undefined\n",
-       "        }\n",
-       "\n",
-       "        length() {\n",
-       "            return this.elements.length\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    window.igv.MessageHandler = new MessageHandler()\n",
-       "\n",
-       "    function download(filename, text) {\n",
-       "\n",
-       "        const data = URL.createObjectURL(new Blob([text], {type: \"application/octet-stream\"}))\n",
-       "        const element = document.createElement('a')\n",
-       "        element.setAttribute('href', data)\n",
-       "        element.setAttribute('download', filename)\n",
-       "        element.style.display = 'none'\n",
-       "        document.body.appendChild(element)\n",
-       "        element.click()\n",
-       "        document.body.removeChild(element)\n",
-       "    }\n",
-       "\n",
-       "    async function shortenURL(url) {\n",
-       "        const endpoint = \"https://2et6uxfezb.execute-api.us-east-1.amazonaws.com/dev/tinyurl/\"\n",
-       "        const enc = encodeURIComponent(url)\n",
-       "        const response = await fetch(`${endpoint}${enc}`)\n",
-       "        if (response.ok) {\n",
-       "            return response.text()\n",
-       "        } else {\n",
-       "            throw new Error(response.statusText)\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    console.log(\"igv.MessageHandler installed\")\n",
-       "\n",
-       "})()"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "/**\n",
-       " * Mock objects to emulate the browser \"File\" class for use with Jupyter and Colab notebooks.  These objects delegate\n",
-       " * actual file reading to python.\n",
-       " */\n",
-       "\n",
-       "// Use a self-evaluating function to keep variables in this file scope\n",
-       "\n",
-       "(function () {\n",
-       "\n",
-       "    const isColab =  window.google !== undefined && window.google.colab\n",
-       "    const isNotebook =  !isColab &&  window.Jupyter !== undefined\n",
-       "\n",
-       "    igv.createNotebookLocalFile = function (options) {\n",
-       "        if (isColab) {\n",
-       "            return new ColabLocalFile(options)\n",
-       "        } else if (isNotebook) {\n",
-       "            return new JupyterLocalFile(options)\n",
-       "        } else {\n",
-       "            return undefined;  //TODO -- throw error?\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    // Start up a Comm object if in a Jupyter Notebook environment (i.e. not Colab or JupyterLab).\n",
-       "    let comm\n",
-       "    const pendingRequests = new Map()\n",
-       "    if (isNotebook) {\n",
-       "        console.log('registering comm')\n",
-       "        comm = Jupyter.notebook.kernel.comm_manager.new_comm('file_request', {})\n",
-       "        // Register a handler\n",
-       "        comm.on_msg(function (msg) {\n",
-       "            const id = msg.content.data.id\n",
-       "            const data = msg.content.data.data\n",
-       "            pendingRequests.set(id, data)\n",
-       "        })\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Emulates a browser \"File\" for Jupyter notebooks.  File reading is delegated to python via Comms messaging.\n",
-       "     * Polling is used to synchronize the async message passing.\n",
-       "     *\n",
-       "     * NOTE: This will not work for JupyterLab\n",
-       "     */\n",
-       "    class JupyterLocalFile {\n",
-       "\n",
-       "        constructor({path, name, start, end}) {\n",
-       "            this.type = 'JupyterLocalFile'\n",
-       "            this.path = path\n",
-       "            this.name = name || path\n",
-       "            this.start = start\n",
-       "            this.end = end\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a new Blob object containing the data in the specified range of bytes of the blob on which it's called.\n",
-       "         * @param start An index into the Blob indicating the first byte to include in the new Blob\n",
-       "         * @param end  An index into the Blob indicating the first byte that will *not* be included in the new Blob\n",
-       "         * @param contentType\n",
-       "         * @returns {*}\n",
-       "         */\n",
-       "        slice(start, end) {\n",
-       "            return new JupyterLocalFile({path: this.path, name: this.name, start, end})\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with an ArrayBuffer containing the entire contents of the Blob as binary data.\n",
-       "         *\n",
-       "         * @returns {Promise<*>}\n",
-       "         */\n",
-       "        async arrayBuffer() {\n",
-       "\n",
-       "            const id = uniqueID()\n",
-       "            const path = this.path\n",
-       "            const promise = new Promise((resolve, reject) => {\n",
-       "                let count = 0\n",
-       "\n",
-       "                function poll() {\n",
-       "\n",
-       "                    if (count > 100) {\n",
-       "                        console.error(`error reading ${path}: timed out`)\n",
-       "                        reject(`error reading ${path}: timed out`)\n",
-       "                    }\n",
-       "\n",
-       "                    count++\n",
-       "                    if (pendingRequests.has(id)) {\n",
-       "                        const data = pendingRequests.get(id)\n",
-       "                        const dataString = atob(data)\n",
-       "                        const bytes = new Uint8Array(dataString.length)\n",
-       "                        for (var i = 0; i < dataString.length; i++) {\n",
-       "                            bytes[i] = dataString.charCodeAt(i)\n",
-       "                        }\n",
-       "                        pendingRequests.delete(id)\n",
-       "                        resolve(bytes.buffer)\n",
-       "                    } else {\n",
-       "                        setTimeout(poll, 100)\n",
-       "                    }\n",
-       "                }\n",
-       "\n",
-       "                poll()\n",
-       "            })\n",
-       "\n",
-       "            const msg = (this.start === undefined) ?\n",
-       "                {id: id, 'path': this.path, 'method': 'arrayBuffer'} :\n",
-       "                {id: id, 'path': this.path, 'method': 'arrayBuffer', 'start': this.start, 'end': this.end}\n",
-       "\n",
-       "            comm.send(msg)\n",
-       "\n",
-       "            return promise\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with a USVString containing the entire contents of the Blob interpreted as UTF-8 text.\n",
-       "         *\n",
-       "         * @returns {Promise<string>}\n",
-       "         */\n",
-       "        async text() {\n",
-       "            throw Error(\"text not implemented\")\n",
-       "        }\n",
-       "\n",
-       "        stream() {\n",
-       "            throw Error(\"stream not implemented\")\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Emulates a browser \"File\" for Colab environments.\n",
-       "     */\n",
-       "    class ColabLocalFile {\n",
-       "\n",
-       "        constructor({path, name, start, end}) {\n",
-       "            this.type = 'ColabLocalFile'\n",
-       "            this.path = path\n",
-       "            this.name = name || path\n",
-       "            this.start = start\n",
-       "            this.end = end\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a new Blob object containing the data in the specified range of bytes of the blob on which it's called.\n",
-       "         * @param start An index into the Blob indicating the first byte to include in the new Blob\n",
-       "         * @param end  An index into the Blob indicating the first byte that will *not* be included in the new Blob\n",
-       "         * @param contentType\n",
-       "         * @returns {*}\n",
-       "         */\n",
-       "        slice(start, end) {\n",
-       "            return new ColabLocalFile({path: this.path, name: this.name, start, end})\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with an ArrayBuffer containing the entire contents of the Blob as\n",
-       "         * binary data.\n",
-       "         */\n",
-       "        async arrayBuffer() {\n",
-       "\n",
-       "            const args = (this.start === undefined) ?\n",
-       "                [this.path] :\n",
-       "                [this.path, this.start.toString(), this.end.toString()]\n",
-       "\n",
-       "            const result = await google.colab.kernel.invokeFunction(\n",
-       "                'ReadFile', // The callback name.\n",
-       "                args, // The arguments.\n",
-       "                {}) // kwargs\n",
-       "            const data = result.data[\"text/plain\"]\n",
-       "            const dataString = atob(data.substring(2, data.length - 1))\n",
-       "            const bytes = new Uint8Array(dataString.length)\n",
-       "            for (var i = 0; i < dataString.length; i++) {\n",
-       "                bytes[i] = dataString.charCodeAt(i)\n",
-       "            }\n",
-       "            return bytes.buffer\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with a USVString containing the entire contents of the Blob interpreted as UTF-8 text.\n",
-       "         *\n",
-       "         * @returns {Promise<string>}\n",
-       "         */\n",
-       "        async text() {\n",
-       "            throw Error(\"text not implemented\")\n",
-       "        }\n",
-       "\n",
-       "        stream() {\n",
-       "            throw Error(\"stream not implemented\")\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    let counter = 0\n",
-       "\n",
-       "    function uniqueID() {\n",
-       "        return `${Math.random()}-${counter++}`\n",
-       "    }\n",
-       "\n",
-       "})()"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/html": [
-       "<div id=\"jb_423544_buttons\"></div><div id=\"jb_423544_igvcontainer\"></div>"
-      ],
-      "text/plain": [
-       "<IPython.core.display.HTML object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "window.igv.MessageHandler.on({\"id\": \"jb_423544\", \"command\": \"createBrowser\", \"data\": {\"reference\": {\"id\": \"AgamP4\", \"name\": \"Anopheles gambiae (PEST)\", \"fastaURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai\", \"tracks\": [{\"name\": \"Genes\", \"type\": \"annotation\", \"format\": \"gff3\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz\", \"indexed\": false}]}, \"locus\": \"2L:2,422,600-2,422,700\", \"tracks\": [{\"name\": \"Filters - gamb_colu_arab\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/gamb_colu_arab/2L_sitefilters.vcf.gz\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/gamb_colu_arab/2L_sitefilters.vcf.gz.tbi\", \"format\": \"vcf\", \"type\": \"variant\", \"visibilityWindow\": 20000, \"height\": 30, \"colorBy\": \"FILTER\", \"colorTable\": {\"PASS\": \"#00cc96\", \"*\": \"#ef553b\"}}, {\"name\": \"Filters - gamb_colu\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/gamb_colu/2L_sitefilters.vcf.gz\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/gamb_colu/2L_sitefilters.vcf.gz.tbi\", \"format\": \"vcf\", \"type\": \"variant\", \"visibilityWindow\": 20000, \"height\": 30, \"colorBy\": \"FILTER\", \"colorTable\": {\"PASS\": \"#00cc96\", \"*\": \"#ef553b\"}}, {\"name\": \"Filters - arab\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/arab/2L_sitefilters.vcf.gz\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/arab/2L_sitefilters.vcf.gz.tbi\", \"format\": \"vcf\", \"type\": \"variant\", \"visibilityWindow\": 20000, \"height\": 30, \"colorBy\": \"FILTER\", \"colorTable\": {\"PASS\": \"#00cc96\", \"*\": \"#ef553b\"}}, {\"name\": \"SNPs\", \"url\": \"https://vo_agam_output.cog.sanger.ac.uk/AR0002-C.vcf.gz\", \"indexURL\": \"https://vo_agam_output.cog.sanger.ac.uk/AR0002-C.vcf.gz.tbi\", \"format\": \"vcf\", \"type\": \"variant\", \"visibilityWindow\": 20000, \"height\": 50}, {\"name\": \"Alignments\", \"url\": \"https://vo_agam_output.cog.sanger.ac.uk/AR0002-C.bam\", \"indexURL\": \"https://vo_agam_output.cog.sanger.ac.uk/AR0002-C.bam.bai\", \"format\": \"bam\", \"type\": \"alignment\", \"visibilityWindow\": 20000, \"height\": 500}], \"id\": \"jb_423544\"}})"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "ag3.view_alignments(sample=\"AR0002-C\", region=\"2L:2,422,600-2,422,700\")"
    ]
@@ -1893,7 +44,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f6ff2c51",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1903,7 +54,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3e64cfeb",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1912,728 +63,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
-   "id": "08571777",
+   "execution_count": null,
+   "id": "6",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "                                     \r"
-     ]
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "window.igv=function(){\"use strict\";function e(e){return t(\"div\",e)}function t(e,t){const i=document.createElement(e);return t&&(t.class&&i.classList.add(t.class),t.id&&(i.id=t.id),t.style&&function(e,t){for(let i of Object.keys(t))e.style[i]=t[i]}(i,t.style)),i}function i(e){const t=getComputedStyle(e);\"none\"!==t.display&&(e._initialDisplay=t.display),e.style.display=\"none\"}function n(e){if(\"none\"===getComputedStyle(e).display){const t=e._initialDisplay||\"block\";e.style.display=t}}function r(e){if(e.type.startsWith(\"touch\")){const t=e.touches[0];return{x:t.pageX,y:t.pageY}}return{x:e.pageX,y:e.pageY}}function s(){return(\"0000\"+(Math.random()*Math.pow(36,4)|0).toString(36)).slice(-4)}let o=(e,{clientX:t,clientY:i})=>{const{left:n,top:r,width:s,height:o}=e.getBoundingClientRect(),a=t-n,c=i-r;return{x:a,y:c,xNormalized:a/s,yNormalized:c/o,width:s,height:o}};function a(e,t){const{clientX:i,clientY:n}=e;return o(t,{clientX:i,clientY:n})}class 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r;for(hi(e,t-257,5),hi(e,i-1,5),hi(e,n-4,4),r=0;r<n;r++)hi(e,e.bl_tree[2*Yt[r]+1],3);yi(e,e.dyn_ltree,t-1),yi(e,e.dyn_dtree,i-1)})(e,e.l_desc.max_code+1,e.d_desc.max_code+1,o+1),bi(e,e.dyn_ltree,e.dyn_dtree)),pi(e),n&&gi(e)},ki={_tr_init:_i,_tr_stored_block:Ci,_tr_flush_block:xi,_tr_tally:(e,t,i)=>(e.pending_buf[e.sym_buf+e.sym_next++]=t,e.pending_buf[e.sym_buf+e.sym_next++]=t>>8,e.pending_buf[e.sym_buf+e.sym_next++]=i,0===t?e.dyn_ltree[2*i]++:(e.matches++,t--,e.dyn_ltree[2*(ei[i]+Qt+1)]++,e.dyn_dtree[2*ci(t)]++),e.sym_next===e.sym_end),_tr_align:e=>{hi(e,2,3),di(e,256,Xt),(e=>{16===e.bi_valid?(li(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=255&e.bi_buf,e.bi_buf>>=8,e.bi_valid-=8)})(e)}};var Ii=(e,t,i,n)=>{let r=65535&e,s=e>>>16&65535,o=0;for(;0!==i;){o=i>2e3?2e3:i,i-=o;do{r=r+t[n++]|0,s=s+r|0}while(--o);r%=65521,s%=65521}return r|s<<16};const Si=new Uint32Array((()=>{let e,t=[];for(var i=0;i<256;i++){e=i;for(var n=0;n<8;n++)e=1&e?3988292384^e>>>1:e>>>1;t[i]=e}return t})());var Ei=(e,t,i,n)=>{const r=Si,s=n+i;e^=-1;for(let i=n;i<s;i++)e=e>>>8^r[255&(e^t[i])];return~e},Ni={2:\"need dictionary\",1:\"stream end\",0:\"\",\"-1\":\"file error\",\"-2\":\"stream error\",\"-3\":\"data error\",\"-4\":\"insufficient memory\",\"-5\":\"buffer error\",\"-6\":\"incompatible version\"},Bi={Z_NO_FLUSH:0,Z_PARTIAL_FLUSH:1,Z_SYNC_FLUSH:2,Z_FULL_FLUSH:3,Z_FINISH:4,Z_BLOCK:5,Z_TREES:6,Z_OK:0,Z_STREAM_END:1,Z_NEED_DICT:2,Z_ERRNO:-1,Z_STREAM_ERROR:-2,Z_DATA_ERROR:-3,Z_MEM_ERROR:-4,Z_BUF_ERROR:-5,Z_NO_COMPRESSION:0,Z_BEST_SPEED:1,Z_BEST_COMPRESSION:9,Z_DEFAULT_COMPRESSION:-1,Z_FILTERED:1,Z_HUFFMAN_ONLY:2,Z_RLE:3,Z_FIXED:4,Z_DEFAULT_STRATEGY:0,Z_BINARY:0,Z_TEXT:1,Z_UNKNOWN:2,Z_DEFLATED:8};const{_tr_init:Mi,_tr_stored_block:Ri,_tr_flush_block:Di,_tr_tally:Ti,_tr_align:Li}=ki,{Z_NO_FLUSH:zi,Z_PARTIAL_FLUSH:Hi,Z_FULL_FLUSH:Pi,Z_FINISH:Oi,Z_BLOCK:Ui,Z_OK:qi,Z_STREAM_END:Qi,Z_STREAM_ERROR:Vi,Z_DATA_ERROR:ji,Z_BUF_ERROR:Wi,Z_DEFAULT_COMPRESSION:Gi,Z_FILTERED:$i,Z_HUFFMAN_ONLY:Ki,Z_RLE:Yi,Z_FIXED:Xi,Z_DEFAULT_STRATEGY:Zi,Z_UNKNOWN:Ji,Z_DEFLATED:en}=Bi,tn=258,nn=262,rn=42,sn=113,on=666,an=(e,t)=>(e.msg=Ni[t],t),cn=e=>2*e-(e>4?9:0),ln=e=>{let t=e.length;for(;--t>=0;)e[t]=0},hn=e=>{let t,i,n,r=e.w_size;t=e.hash_size,n=t;do{i=e.head[--n],e.head[n]=i>=r?i-r:0}while(--t);t=r,n=t;do{i=e.prev[--n],e.prev[n]=i>=r?i-r:0}while(--t)};let dn=(e,t,i)=>(t<<e.hash_shift^i)&e.hash_mask;const un=e=>{const t=e.state;let i=t.pending;i>e.avail_out&&(i=e.avail_out),0!==i&&(e.output.set(t.pending_buf.subarray(t.pending_out,t.pending_out+i),e.next_out),e.next_out+=i,t.pending_out+=i,e.total_out+=i,e.avail_out-=i,t.pending-=i,0===t.pending&&(t.pending_out=0))},fn=(e,t)=>{Di(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,un(e.strm)},pn=(e,t)=>{e.pending_buf[e.pending++]=t},gn=(e,t)=>{e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=255&t},mn=(e,t,i,n)=>{let r=e.avail_in;return r>n&&(r=n),0===r?0:(e.avail_in-=r,t.set(e.input.subarray(e.next_in,e.next_in+r),i),1===e.state.wrap?e.adler=Ii(e.adler,t,r,i):2===e.state.wrap&&(e.adler=Ei(e.adler,t,r,i)),e.next_in+=r,e.total_in+=r,r)},wn=(e,t)=>{let i,n,r=e.max_chain_length,s=e.strstart,o=e.prev_length,a=e.nice_match;const c=e.strstart>e.w_size-nn?e.strstart-(e.w_size-nn):0,l=e.window,h=e.w_mask,d=e.prev,u=e.strstart+tn;let f=l[s+o-1],p=l[s+o];e.prev_length>=e.good_match&&(r>>=2),a>e.lookahead&&(a=e.lookahead);do{if(i=t,l[i+o]===p&&l[i+o-1]===f&&l[i]===l[s]&&l[++i]===l[s+1]){s+=2,i++;do{}while(l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&s<u);if(n=tn-(u-s),s=u-tn,n>o){if(e.match_start=t,o=n,n>=a)break;f=l[s+o-1],p=l[s+o]}}}while((t=d[t&h])>c&&0!=--r);return o<=e.lookahead?o:e.lookahead},bn=e=>{const t=e.w_size;let i,n,r;do{if(n=e.window_size-e.lookahead-e.strstart,e.strstart>=t+(t-nn)&&(e.window.set(e.window.subarray(t,t+t-n),0),e.match_start-=t,e.strstart-=t,e.block_start-=t,e.insert>e.strstart&&(e.insert=e.strstart),hn(e),n+=t),0===e.strm.avail_in)break;if(i=mn(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=i,e.lookahead+e.insert>=3)for(r=e.strstart-e.insert,e.ins_h=e.window[r],e.ins_h=dn(e,e.ins_h,e.window[r+1]);e.insert&&(e.ins_h=dn(e,e.ins_h,e.window[r+3-1]),e.prev[r&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=r,r++,e.insert--,!(e.lookahead+e.insert<3)););}while(e.lookahead<nn&&0!==e.strm.avail_in)},Fn=(e,t)=>{let i,n,r,s=e.pending_buf_size-5>e.w_size?e.w_size:e.pending_buf_size-5,o=0,a=e.strm.avail_in;do{if(i=65535,r=e.bi_valid+42>>3,e.strm.avail_out<r)break;if(r=e.strm.avail_out-r,n=e.strstart-e.block_start,i>n+e.strm.avail_in&&(i=n+e.strm.avail_in),i>r&&(i=r),i<s&&(0===i&&t!==Oi||t===zi||i!==n+e.strm.avail_in))break;o=t===Oi&&i===n+e.strm.avail_in?1:0,Ri(e,0,0,o),e.pending_buf[e.pending-4]=i,e.pending_buf[e.pending-3]=i>>8,e.pending_buf[e.pending-2]=~i,e.pending_buf[e.pending-1]=~i>>8,un(e.strm),n&&(n>i&&(n=i),e.strm.output.set(e.window.subarray(e.block_start,e.block_start+n),e.strm.next_out),e.strm.next_out+=n,e.strm.avail_out-=n,e.strm.total_out+=n,e.block_start+=n,i-=n),i&&(mn(e.strm,e.strm.output,e.strm.next_out,i),e.strm.next_out+=i,e.strm.avail_out-=i,e.strm.total_out+=i)}while(0===o);return a-=e.strm.avail_in,a&&(a>=e.w_size?(e.matches=2,e.window.set(e.strm.input.subarray(e.strm.next_in-e.w_size,e.strm.next_in),0),e.strstart=e.w_size,e.insert=e.strstart):(e.window_size-e.strstart<=a&&(e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,e.insert>e.strstart&&(e.insert=e.strstart)),e.window.set(e.strm.input.subarray(e.strm.next_in-a,e.strm.next_in),e.strstart),e.strstart+=a,e.insert+=a>e.w_size-e.insert?e.w_size-e.insert:a),e.block_start=e.strstart),e.high_water<e.strstart&&(e.high_water=e.strstart),o?4:t!==zi&&t!==Oi&&0===e.strm.avail_in&&e.strstart===e.block_start?2:(r=e.window_size-e.strstart,e.strm.avail_in>r&&e.block_start>=e.w_size&&(e.block_start-=e.w_size,e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,r+=e.w_size,e.insert>e.strstart&&(e.insert=e.strstart)),r>e.strm.avail_in&&(r=e.strm.avail_in),r&&(mn(e.strm,e.window,e.strstart,r),e.strstart+=r,e.insert+=r>e.w_size-e.insert?e.w_size-e.insert:r),e.high_water<e.strstart&&(e.high_water=e.strstart),r=e.bi_valid+42>>3,r=e.pending_buf_size-r>65535?65535:e.pending_buf_size-r,s=r>e.w_size?e.w_size:r,n=e.strstart-e.block_start,(n>=s||(n||t===Oi)&&t!==zi&&0===e.strm.avail_in&&n<=r)&&(i=n>r?r:n,o=t===Oi&&0===e.strm.avail_in&&i===n?1:0,Ri(e,e.block_start,i,o),e.block_start+=i,un(e.strm)),o?3:1)},vn=(e,t)=>{let i,n;for(;;){if(e.lookahead<nn){if(bn(e),e.lookahead<nn&&t===zi)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),0!==i&&e.strstart-i<=e.w_size-nn&&(e.match_length=wn(e,i)),e.match_length>=3)if(n=Ti(e,e.strstart-e.match_start,e.match_length-3),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=3){e.match_length--;do{e.strstart++,e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart}while(0!=--e.match_length);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=dn(e,e.ins_h,e.window[e.strstart+1]);else n=Ti(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(fn(e,!1),0===e.strm.avail_out))return 1}return e.insert=e.strstart<2?e.strstart:2,t===Oi?(fn(e,!0),0===e.strm.avail_out?3:4):e.sym_next&&(fn(e,!1),0===e.strm.avail_out)?1:2},yn=(e,t)=>{let i,n,r;for(;;){if(e.lookahead<nn){if(bn(e),e.lookahead<nn&&t===zi)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),e.prev_length=e.match_length,e.prev_match=e.match_start,e.match_length=2,0!==i&&e.prev_length<e.max_lazy_match&&e.strstart-i<=e.w_size-nn&&(e.match_length=wn(e,i),e.match_length<=5&&(e.strategy===$i||3===e.match_length&&e.strstart-e.match_start>4096)&&(e.match_length=2)),e.prev_length>=3&&e.match_length<=e.prev_length){r=e.strstart+e.lookahead-3,n=Ti(e,e.strstart-1-e.prev_match,e.prev_length-3),e.lookahead-=e.prev_length-1,e.prev_length-=2;do{++e.strstart<=r&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart)}while(0!=--e.prev_length);if(e.match_available=0,e.match_length=2,e.strstart++,n&&(fn(e,!1),0===e.strm.avail_out))return 1}else if(e.match_available){if(n=Ti(e,0,e.window[e.strstart-1]),n&&fn(e,!1),e.strstart++,e.lookahead--,0===e.strm.avail_out)return 1}else e.match_available=1,e.strstart++,e.lookahead--}return e.match_available&&(n=Ti(e,0,e.window[e.strstart-1]),e.match_available=0),e.insert=e.strstart<2?e.strstart:2,t===Oi?(fn(e,!0),0===e.strm.avail_out?3:4):e.sym_next&&(fn(e,!1),0===e.strm.avail_out)?1:2};function An(e,t,i,n,r){this.good_length=e,this.max_lazy=t,this.nice_length=i,this.max_chain=n,this.func=r}const Cn=[new An(0,0,0,0,Fn),new An(4,4,8,4,vn),new An(4,5,16,8,vn),new An(4,6,32,32,vn),new An(4,4,16,16,yn),new An(8,16,32,32,yn),new An(8,16,128,128,yn),new An(8,32,128,256,yn),new An(32,128,258,1024,yn),new An(32,258,258,4096,yn)];function _n(){this.strm=null,this.status=0,this.pending_buf=null,this.pending_buf_size=0,this.pending_out=0,this.pending=0,this.wrap=0,this.gzhead=null,this.gzindex=0,this.method=en,this.last_flush=-1,this.w_size=0,this.w_bits=0,this.w_mask=0,this.window=null,this.window_size=0,this.prev=null,this.head=null,this.ins_h=0,this.hash_size=0,this.hash_bits=0,this.hash_mask=0,this.hash_shift=0,this.block_start=0,this.match_length=0,this.prev_match=0,this.match_available=0,this.strstart=0,this.match_start=0,this.lookahead=0,this.prev_length=0,this.max_chain_length=0,this.max_lazy_match=0,this.level=0,this.strategy=0,this.good_match=0,this.nice_match=0,this.dyn_ltree=new Uint16Array(1146),this.dyn_dtree=new Uint16Array(122),this.bl_tree=new Uint16Array(78),ln(this.dyn_ltree),ln(this.dyn_dtree),ln(this.bl_tree),this.l_desc=null,this.d_desc=null,this.bl_desc=null,this.bl_count=new Uint16Array(16),this.heap=new Uint16Array(573),ln(this.heap),this.heap_len=0,this.heap_max=0,this.depth=new Uint16Array(573),ln(this.depth),this.sym_buf=0,this.lit_bufsize=0,this.sym_next=0,this.sym_end=0,this.opt_len=0,this.static_len=0,this.matches=0,this.insert=0,this.bi_buf=0,this.bi_valid=0}const xn=e=>{if(!e)return 1;const t=e.state;return!t||t.strm!==e||t.status!==rn&&57!==t.status&&69!==t.status&&73!==t.status&&91!==t.status&&103!==t.status&&t.status!==sn&&t.status!==on?1:0},kn=e=>{if(xn(e))return an(e,Vi);e.total_in=e.total_out=0,e.data_type=Ji;const t=e.state;return t.pending=0,t.pending_out=0,t.wrap<0&&(t.wrap=-t.wrap),t.status=2===t.wrap?57:t.wrap?rn:sn,e.adler=2===t.wrap?0:1,t.last_flush=-2,Mi(t),qi},In=e=>{const t=kn(e);var i;return t===qi&&((i=e.state).window_size=2*i.w_size,ln(i.head),i.max_lazy_match=Cn[i.level].max_lazy,i.good_match=Cn[i.level].good_length,i.nice_match=Cn[i.level].nice_length,i.max_chain_length=Cn[i.level].max_chain,i.strstart=0,i.block_start=0,i.lookahead=0,i.insert=0,i.match_length=i.prev_length=2,i.match_available=0,i.ins_h=0),t},Sn=(e,t,i,n,r,s)=>{if(!e)return Vi;let o=1;if(t===Gi&&(t=6),n<0?(o=0,n=-n):n>15&&(o=2,n-=16),r<1||r>9||i!==en||n<8||n>15||t<0||t>9||s<0||s>Xi||8===n&&1!==o)return an(e,Vi);8===n&&(n=9);const a=new _n;return e.state=a,a.strm=e,a.status=rn,a.wrap=o,a.gzhead=null,a.w_bits=n,a.w_size=1<<a.w_bits,a.w_mask=a.w_size-1,a.hash_bits=r+7,a.hash_size=1<<a.hash_bits,a.hash_mask=a.hash_size-1,a.hash_shift=~~((a.hash_bits+3-1)/3),a.window=new Uint8Array(2*a.w_size),a.head=new Uint16Array(a.hash_size),a.prev=new Uint16Array(a.w_size),a.lit_bufsize=1<<r+6,a.pending_buf_size=4*a.lit_bufsize,a.pending_buf=new 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t}for(v=65535&b,F&=15,F&&(f<F&&(u+=_[i++]<<f,f+=8),v+=u&(1<<F)-1,u>>>=F,f-=F),f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=g[u&w];;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,16&F){if(y=65535&b,F&=15,f<F&&(u+=_[i++]<<f,f+=8,f<F&&(u+=_[i++]<<f,f+=8)),y+=u&(1<<F)-1,y>a){e.msg=\"invalid distance too far back\",k.mode=Zn;break e}if(u>>>=F,f-=F,F=r-s,y>F){if(F=y-F,F>l&&k.sane){e.msg=\"invalid distance too far back\",k.mode=Zn;break e}if(A=0,C=d,0===h){if(A+=c-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}else if(h<F){if(A+=c+h-F,F-=h,F<v){v-=F;do{x[r++]=d[A++]}while(--F);if(A=0,h<v){F=h,v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}}else if(A+=h-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}for(;v>2;)x[r++]=C[A++],x[r++]=C[A++],x[r++]=C[A++],v-=3;v&&(x[r++]=C[A++],v>1&&(x[r++]=C[A++]))}else{A=r-y;do{x[r++]=x[A++],x[r++]=x[A++],x[r++]=x[A++],v-=3}while(v>2);v&&(x[r++]=x[A++],v>1&&(x[r++]=x[A++]))}break}if(64&F){e.msg=\"invalid distance code\",k.mode=Zn;break e}b=g[(65535&b)+(u&(1<<F)-1)]}}break}}while(i<n&&r<o);v=f>>3,i-=v,f-=v<<3,u&=(1<<f)-1,e.next_in=i,e.next_out=r,e.avail_in=i<n?n-i+5:5-(i-n),e.avail_out=r<o?o-r+257:257-(r-o),k.hold=u,k.bits=f};const er=15,tr=new Uint16Array([3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0]),ir=new Uint8Array([16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78]),nr=new Uint16Array([1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0]),rr=new Uint8Array([16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64]);var sr=(e,t,i,n,r,s,o,a)=>{const c=a.bits;let l,h,d,u,f,p,g=0,m=0,w=0,b=0,F=0,v=0,y=0,A=0,C=0,_=0,x=null;const k=new Uint16Array(16),I=new Uint16Array(16);let S,E,N,B=null;for(g=0;g<=er;g++)k[g]=0;for(m=0;m<n;m++)k[t[i+m]]++;for(F=c,b=er;b>=1&&0===k[b];b--);if(F>b&&(F=b),0===b)return r[s++]=20971520,r[s++]=20971520,a.bits=1,0;for(w=1;w<b&&0===k[w];w++);for(F<w&&(F=w),A=1,g=1;g<=er;g++)if(A<<=1,A-=k[g],A<0)return-1;if(A>0&&(0===e||1!==b))return-1;for(I[1]=0,g=1;g<er;g++)I[g+1]=I[g]+k[g];for(m=0;m<n;m++)0!==t[i+m]&&(o[I[t[i+m]]++]=m);if(0===e?(x=B=o,p=20):1===e?(x=tr,B=ir,p=257):(x=nr,B=rr,p=0),_=0,m=0,g=w,f=s,v=F,y=0,d=-1,C=1<<F,u=C-1,1===e&&C>852||2===e&&C>592)return 1;for(;;){S=g-y,o[m]+1<p?(E=0,N=o[m]):o[m]>=p?(E=B[o[m]-p],N=x[o[m]-p]):(E=96,N=0),l=1<<g-y,h=1<<v,w=h;do{h-=l,r[f+(_>>y)+h]=S<<24|E<<16|N}while(0!==h);for(l=1<<g-1;_&l;)l>>=1;if(0!==l?(_&=l-1,_+=l):_=0,m++,0==--k[g]){if(g===b)break;g=t[i+o[m]]}if(g>F&&(_&u)!==d){for(0===y&&(y=F),f+=w,v=g-y,A=1<<v;v+y<b&&(A-=k[v+y],!(A<=0));)v++,A<<=1;if(C+=1<<v,1===e&&C>852||2===e&&C>592)return 1;d=_&u,r[d]=F<<24|v<<16|f-s}}return 0!==_&&(r[f+_]=g-y<<24|64<<16),a.bits=F,0};const{Z_FINISH:or,Z_BLOCK:ar,Z_TREES:cr,Z_OK:lr,Z_STREAM_END:hr,Z_NEED_DICT:dr,Z_STREAM_ERROR:ur,Z_DATA_ERROR:fr,Z_MEM_ERROR:pr,Z_BUF_ERROR:gr,Z_DEFLATED:mr}=Bi,wr=16180,br=16190,Fr=16191,vr=16192,yr=16194,Ar=16199,Cr=16200,_r=16206,xr=16209,kr=e=>(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24);function Ir(){this.strm=null,this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new Uint16Array(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}const Sr=e=>{if(!e)return 1;const t=e.state;return!t||t.strm!==e||t.mode<wr||t.mode>16211?1:0},Er=e=>{if(Sr(e))return ur;const t=e.state;return e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=wr,t.last=0,t.havedict=0,t.flags=-1,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new Int32Array(852),t.distcode=t.distdyn=new Int32Array(592),t.sane=1,t.back=-1,lr},Nr=e=>{if(Sr(e))return ur;const t=e.state;return t.wsize=0,t.whave=0,t.wnext=0,Er(e)},Br=(e,t)=>{let i;if(Sr(e))return ur;const n=e.state;return t<0?(i=0,t=-t):(i=5+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?ur:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,Nr(e))},Mr=(e,t)=>{if(!e)return ur;const i=new Ir;e.state=i,i.strm=e,i.window=null,i.mode=wr;const n=Br(e,t);return n!==lr&&(e.state=null),n};let Rr,Dr,Tr=!0;const Lr=e=>{if(Tr){Rr=new Int32Array(512),Dr=new Int32Array(32);let t=0;for(;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(sr(1,e.lens,0,288,Rr,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;sr(2,e.lens,0,32,Dr,0,e.work,{bits:5}),Tr=!1}e.lencode=Rr,e.lenbits=9,e.distcode=Dr,e.distbits=5},zr=(e,t,i,n)=>{let r;const s=e.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new Uint8Array(s.wsize)),n>=s.wsize?(s.window.set(t.subarray(i-s.wsize,i),0),s.wnext=0,s.whave=s.wsize):(r=s.wsize-s.wnext,r>n&&(r=n),s.window.set(t.subarray(i-n,i-n+r),s.wnext),(n-=r)?(s.window.set(t.subarray(i-n,i),0),s.wnext=n,s.whave=s.wsize):(s.wnext+=r,s.wnext===s.wsize&&(s.wnext=0),s.whave<s.wsize&&(s.whave+=r))),0};var Hr=(e,t)=>{let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_=0;const x=new Uint8Array(4);let k,I;const S=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(Sr(e)||!e.output||!e.input&&0!==e.avail_in)return ur;i=e.state,i.mode===Fr&&(i.mode=vr),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,d=a,u=c,C=lr;e:for(;;)switch(i.mode){case wr:if(0===i.wrap){i.mode=vr;break}for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(2&i.wrap&&35615===l){0===i.wbits&&(i.wbits=15),i.check=0,x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0),l=0,h=0,i.mode=16181;break}if(i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&l)<<8)+(l>>8))%31){e.msg=\"incorrect header check\",i.mode=xr;break}if((15&l)!==mr){e.msg=\"unknown compression method\",i.mode=xr;break}if(l>>>=4,h-=4,A=8+(15&l),0===i.wbits&&(i.wbits=A),A>15||A>i.wbits){e.msg=\"invalid window size\",i.mode=xr;break}i.dmax=1<<i.wbits,i.flags=0,e.adler=i.check=1,i.mode=512&l?16189:Fr,l=0,h=0;break;case 16181:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.flags=l,(255&i.flags)!==mr){e.msg=\"unknown compression method\",i.mode=xr;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=xr;break}i.head&&(i.head.text=l>>8&1),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0,i.mode=16182;case 16182:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.time=l),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,x[2]=l>>>16&255,x[3]=l>>>24&255,i.check=Ei(i.check,x,4,0)),l=0,h=0,i.mode=16183;case 16183:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.xflags=255&l,i.head.os=l>>8),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0,i.mode=16184;case 16184:if(1024&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length=l,i.head&&(i.head.extra_len=l),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0}else i.head&&(i.head.extra=null);i.mode=16185;case 16185:if(1024&i.flags&&(f=i.length,f>a&&(f=a),f&&(i.head&&(A=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Uint8Array(i.head.extra_len)),i.head.extra.set(n.subarray(s,s+f),A)),512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,i.length-=f),i.length))break e;i.length=0,i.mode=16186;case 16186:if(2048&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.name+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=16187;case 16187:if(4096&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.comment+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.comment=null);i.mode=16188;case 16188:if(512&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(4&i.wrap&&l!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=xr;break}l=0,h=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=Fr;break;case 16189:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}e.adler=i.check=kr(l),l=0,h=0,i.mode=br;case br:if(0===i.havedict)return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,dr;e.adler=i.check=1,i.mode=Fr;case Fr:if(t===ar||t===cr)break e;case vr:if(i.last){l>>>=7&h,h-=7&h,i.mode=_r;break}for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}switch(i.last=1&l,l>>>=1,h-=1,3&l){case 0:i.mode=16193;break;case 1:if(Lr(i),i.mode=Ar,t===cr){l>>>=2,h-=2;break e}break;case 2:i.mode=16196;break;case 3:e.msg=\"invalid block type\",i.mode=xr}l>>>=2,h-=2;break;case 16193:for(l>>>=7&h,h-=7&h;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if((65535&l)!=(l>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=xr;break}if(i.length=65535&l,l=0,h=0,i.mode=yr,t===cr)break e;case yr:i.mode=16195;case 16195:if(f=i.length,f){if(f>a&&(f=a),f>c&&(f=c),0===f)break e;r.set(n.subarray(s,s+f),o),a-=f,s+=f,c-=f,o+=f,i.length-=f;break}i.mode=Fr;break;case 16196:for(;h<14;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.nlen=257+(31&l),l>>>=5,h-=5,i.ndist=1+(31&l),l>>>=5,h-=5,i.ncode=4+(15&l),l>>>=4,h-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=xr;break}i.have=0,i.mode=16197;case 16197:for(;i.have<i.ncode;){for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.lens[S[i.have++]]=7&l,l>>>=3,h-=3}for(;i.have<19;)i.lens[S[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,k={bits:i.lenbits},C=sr(0,i.lens,0,19,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid code lengths set\",i.mode=xr;break}i.have=0,i.mode=16198;case 16198:for(;i.have<i.nlen+i.ndist;){for(;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(b<16)l>>>=m,h-=m,i.lens[i.have++]=b;else{if(16===b){for(I=m+2;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l>>>=m,h-=m,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=xr;break}A=i.lens[i.have-1],f=3+(3&l),l>>>=2,h-=2}else if(17===b){for(I=m+3;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=3+(7&l),l>>>=3,h-=3}else{for(I=m+7;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=11+(127&l),l>>>=7,h-=7}if(i.have+f>i.nlen+i.ndist){e.msg=\"invalid bit length repeat\",i.mode=xr;break}for(;f--;)i.lens[i.have++]=A}}if(i.mode===xr)break;if(0===i.lens[256]){e.msg=\"invalid code -- missing end-of-block\",i.mode=xr;break}if(i.lenbits=9,k={bits:i.lenbits},C=sr(1,i.lens,0,i.nlen,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid literal/lengths set\",i.mode=xr;break}if(i.distbits=6,i.distcode=i.distdyn,k={bits:i.distbits},C=sr(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,k),i.distbits=k.bits,C){e.msg=\"invalid distances set\",i.mode=xr;break}if(i.mode=Ar,t===cr)break e;case Ar:i.mode=Cr;case Cr:if(a>=6&&c>=258){e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,Jn(e,u),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,i.mode===Fr&&(i.back=-1);break}for(i.back=0;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(w&&!(240&w)){for(F=m,v=w,y=b;_=i.lencode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,i.length=b,0===w){i.mode=16205;break}if(32&w){i.back=-1,i.mode=Fr;break}if(64&w){e.msg=\"invalid literal/length code\",i.mode=xr;break}i.extra=15&w,i.mode=16201;case 16201:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=16202;case 16202:for(;_=i.distcode[l&(1<<i.distbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(!(240&w)){for(F=m,v=w,y=b;_=i.distcode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,64&w){e.msg=\"invalid distance code\",i.mode=xr;break}i.offset=b,i.extra=15&w,i.mode=16203;case 16203:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.offset+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=xr;break}i.mode=16204;case 16204:if(0===c)break e;if(f=u-c,i.offset>f){if(f=i.offset-f,f>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=xr;break}f>i.wnext?(f-=i.wnext,p=i.wsize-f):p=i.wnext-f,f>i.length&&(f=i.length),g=i.window}else g=r,p=o-i.offset,f=i.length;f>c&&(f=c),c-=f,i.length-=f;do{r[o++]=g[p++]}while(--f);0===i.length&&(i.mode=Cr);break;case 16205:if(0===c)break e;r[o++]=i.length,c--,i.mode=Cr;break;case _r:if(i.wrap){for(;h<32;){if(0===a)break e;a--,l|=n[s++]<<h,h+=8}if(u-=c,e.total_out+=u,i.total+=u,4&i.wrap&&u&&(e.adler=i.check=i.flags?Ei(i.check,r,u,o-u):Ii(i.check,r,u,o-u)),u=c,4&i.wrap&&(i.flags?l:kr(l))!==i.check){e.msg=\"incorrect data check\",i.mode=xr;break}l=0,h=0}i.mode=16207;case 16207:if(i.wrap&&i.flags){for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(4&i.wrap&&l!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=xr;break}l=0,h=0}i.mode=16208;case 16208:C=hr;break e;case xr:C=fr;break e;case 16210:return pr;default:return ur}return 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Object.values(this.allFeatures))for(let n of i)e(n)&&t.push(n);return t}queryFeatures(e,t,i){const n=this.treeMap[e];if(!n)return[];const r=n.findOverlapping(t,i);if(0===r.length)return[];{const n=[],s=this.allFeatures[e];if(s){for(let e of r){const r=e.value;for(let e=r.start;e<r.end;e++){let r=s[e];if(r.start>i)break;r.end>=t&&n.push(r)}}n.sort((function(e,t){return e.start-t.start}))}return n}}getAllFeatures(){return this.allFeatures}buildTreeMap(e,t){const i={},n=[];if(this.allFeatures={},e){for(let i of e){let e=i.chr;t&&(e=t.getChromosomeName(e));let r=this.allFeatures[e];r||(n.push(e),r=[],this.allFeatures[e]=r),r.push(i)}for(let e of n){const t=this.allFeatures[e];t.sort((function(e,t){return e.start===t.start?0:e.start>t.start?1:-1})),i[e]=Js(t)}}return i}}function Js(e){const t=new js,i=e.length,n=Math.max(10,Math.round(i/10));for(let r=0;r<i;r+=n){const s=Math.min(i,r+n),o=new eo(r,s),a=e[r].start;let c=a;for(let t=r;t<s;t++)c=Math.max(c,e[t].end);t.insert(a,c,o)}return t}class eo{constructor(e,t){this.start=e,this.end=t}}const to=function(e,t,i){if(e&&0!==e.length){const n=function(e){const t=new js,i=e.length,n=Math.max(10,Math.round(i/100));e.sort((function(e,t){return e.start===t.start?0:e.start>t.start?1:-1}));for(let r=0;r<i;r+=n){const s=Math.min(i,r+n),o=e.slice(r,s),a=o[0].start;let c=a;o.forEach((function(e){c=Math.max(c,e.end)})),t.insert(a,c,o)}return t}(e),r=n.findOverlapping(t,i);return 0===r.length?[]:(e=[],r.forEach((function(n){const r=n.value,s=r.length;for(let n=0;n<s;n++){const s=r[n];if(s.start>i)break;s.end>t&&e.push(s)}})),e.sort((function(e,t){return e.start-t.start})),e)}return[]};function io(e){if(3===(e=e.replace(/^#/,\"\")).length&&(e=e.split(\"\").map((e=>e+e)).join(\"\")),6!==e.length)throw new Error(\"Invalid HEX color.\");let t=parseInt(e,16);return`rgb(${t>>16&255}, ${t>>8&255}, ${255&t})`}const no={cantaloupe:{r:255,g:206,b:110},honeydew:{r:206,g:250,b:110},spindrift:{r:104,g:251,b:208},sky:{r:106,g:207,b:255},lavender:{r:210,g:120,b:255},carnation:{r:255,g:127,b:211},licorice:{r:0,g:0,b:0},snow:{r:255,g:255,b:255},salmon:{r:255,g:114,b:110},banana:{r:255,g:251,b:109},flora:{r:104,g:249,b:110},ice:{r:104,g:253,b:255},orchid:{r:110,g:118,b:255},bubblegum:{r:255,g:122,b:255},lead:{r:30,g:30,b:30},mercury:{r:232,g:232,b:232},tangerine:{r:255,g:136,b:2},lime:{r:131,g:249,b:2},sea_foam:{r:3,g:249,b:135},aqua:{r:0,g:140,b:255},grape:{r:137,g:49,b:255},strawberry:{r:255,g:41,b:135},tungsten:{r:58,g:58,b:58},silver:{r:208,g:208,b:208},maraschino:{r:255,g:33,b:1},lemon:{r:255,g:250,b:3},spring:{r:5,g:248,b:2},turquoise:{r:0,g:253,b:255},blueberry:{r:0,g:46,b:255},magenta:{r:255,g:57,b:255},iron:{r:84,g:84,b:83},magnesium:{r:184,g:184,b:184},mocha:{r:137,g:72,b:0},fern:{r:69,g:132,b:1},moss:{r:1,g:132,b:72},ocean:{r:0,g:74,b:136},eggplant:{r:73,g:26,b:136},maroon:{r:137,g:22,b:72},steel:{r:110,g:110,b:110},aluminum:{r:160,g:159,b:160},cayenne:{r:137,g:17,b:0},aspargus:{r:136,g:133,b:1},clover:{r:2,g:132,b:1},teal:{r:0,g:134,b:136},midnight:{r:0,g:24,b:136},plum:{r:137,g:30,b:136},tin:{r:135,g:134,b:135},nickel:{r:136,g:135,b:135}};function ro(e){const{r:t,g:i,b:n}=no[e];return`rgb(${t},${i},${n})`}const so={Set1:[\"rgb(228,26,28)\",\"rgb(55,126,184)\",\"rgb(77,175,74)\",\"rgb(166,86,40)\",\"rgb(152,78,163)\",\"rgb(255,127,0)\",\"rgb(247,129,191)\",\"rgb(153,153,153)\",\"rgb(255,255,51)\"],Dark2:[\"rgb(27,158,119)\",\"rgb(217,95,2)\",\"rgb(117,112,179)\",\"rgb(231,41,138)\",\"rgb(102,166,30)\",\"rgb(230,171,2)\",\"rgb(166,118,29)\",\"rgb(102,102,102)\"],Set2:[\"rgb(102, 194,165)\",\"rgb(252,141,98)\",\"rgb(141,160,203)\",\"rgb(231,138,195)\",\"rgb(166,216,84)\",\"rgb(255,217,47)\",\"rgb(229,196,148)\",\"rgb(179,179,179)\"],Set3:[\"rgb(141,211,199)\",\"rgb(255,255,179)\",\"rgb(190,186,218)\",\"rgb(251,128,114)\",\"rgb(128,177,211)\",\"rgb(253,180,98)\",\"rgb(179,222,105)\",\"rgb(252,205,229)\",\"rgb(217,217,217)\",\"rgb(188,128,189)\",\"rgb(204,235,197)\",\"rgb(255,237,111)\"],Pastel1:[\"rgb(251,180,174)\",\"rgb(179,205,227)\",\"rgb(204,235,197)\",\"rgb(222,203,228)\",\"rgb(254,217,166)\",\"rgb(255,255,204)\",\"rgb(229,216,189)\",\"rgb(253,218,236)\"],Pastel2:[\"rgb(173,226,207)\",\"rgb(253,205,172)\",\"rgb(203,213,232)\",\"rgb(244,202,228)\",\"rgb(230,245,201)\",\"rgb(255,242,174)\",\"rgb(243,225,206)\"],Accent:[\"rgb(127,201,127)\",\"rgb(190,174,212)\",\"rgb(253,192,134)\",\"rgb(255,255,153)\",\"rgb(56,108,176)\",\"rgb(240,2,127)\",\"rgb(191,91,23)\"]};class oo{constructor(e){this.colors=so[e],Array.isArray(this.colors)||(this.colors=[]),this.colorTable=new Map,this.nextIdx=0,this.colorGenerator=new co}getColor(e){return this.colorTable.has(e)||(this.nextIdx<this.colors.length?this.colorTable.set(e,this.colors[this.nextIdx]):this.colorTable.set(e,this.colorGenerator.get()),this.nextIdx++),this.colorTable.get(e)}}class ao{constructor(e){this.colorTable=e||{},this.nextIdx=0,this.colorGenerator=new co}getColor(e){if(!this.colorTable.hasOwnProperty(e)){if(this.colorTable.hasOwnProperty(\"*\"))return this.colorTable[\"*\"];this.colorTable[e]=this.colorGenerator.get()}return this.colorTable[e]}}function co(){this.hue=Math.random(),this.goldenRatio=.618033988749895,this.hexwidth=2}function lo(e,t,i,n){return`rgba(${e=ys.clamp(e,0,255)}, ${t=ys.clamp(t,0,255)}, ${i=ys.clamp(i,0,255)}, ${n=ys.clamp(n,0,1)})`}function ho(e,t){e=ys.clamp(e,0,255),t=ys.clamp(t,0,255);return`rgb(${Math.round(Math.random()*(t-e)+e).toString(10)},${Math.round(Math.random()*(t-e)+e).toString(10)},${Math.round(Math.random()*(t-e)+e).toString(10)})`}function uo(e){if(e.startsWith(\"rgb(\")){const[t,i]=e.split(\"(\"),[n]=i.split(\")\");return n.split(\",\").map((e=>parseInt(e)))}}co.prototype.hsvToRgb=function(e,t,i){var n=Math.floor(6*e),r=6*e-n,s=i*(1-t),o=i*(1-r*t),a=i*(1-(1-r)*t),c=255,l=255,h=255;switch(n){case 0:c=i,l=a,h=s;break;case 1:c=o,l=i,h=s;break;case 2:c=s,l=i,h=a;break;case 3:c=s,l=o,h=i;break;case 4:c=a,l=s,h=i;break;case 5:c=i,l=s,h=o}return[Math.floor(256*c),Math.floor(256*l),Math.floor(256*h)]},co.prototype.padHex=function(e){return e.length>this.hexwidth?e:new Array(this.hexwidth-e.length+1).join(\"0\")+e},co.prototype.get=function(e,t){this.hue+=this.goldenRatio,this.hue%=1,\"number\"!=typeof e&&(e=.5),\"number\"!=typeof t&&(t=.95);var i=this.hsvToRgb(this.hue,e,t);return\"#\"+this.padHex(i[0].toString(16))+this.padHex(i[1].toString(16))+this.padHex(i[2].toString(16))},new co;function fo(e,t,i){if(i<.005)return e;if(i>.995)return t;{let n,r,s,o,a,c;i<.5?(i/=.5,[n,r,s]=uo(e),[o,a,c]=uo(ro(\"snow\"))):(i=(i-.5)/.5,[n,r,s]=uo(ro(\"snow\")),[o,a,c]=uo(t));const[l,h,d]=[Math.floor(ys.lerp(n,o,i)),Math.floor(ys.lerp(r,a,i)),Math.floor(ys.lerp(s,c,i))];return function(e,t,i){return`rgb(${e=ys.clamp(e,0,255)}, ${t=ys.clamp(t,0,255)}, ${i=ys.clamp(i,0,255)})`}(l,h,d)}}const po=new Set([\"bedtype\",\"alignment\",\"annotation\",\"variant\",\"wig\",\"interact\",\"shoebox\"]),go=new Set([\"alignment\",\"annotation\",\"variant\",\"eqtl\",\"qtl\",\"snp\",\"shoebox\",\"wig\"]),mo=new Set([\"sequence\",\"ruler\",\"ideogram\"]),wo={};class bo{constructor(e){this.browser=e,this.initialize()}initialize(){const e=new c;e.add(\"...\");const t={parent:this.browser.root,content:e};this.dialog=new w(t),this.browser.root.appendChild(this.dialog.elem),i(this.dialog.elem)}trackMenuItemList(e){const t=[];return\"sequence\"!==e.track.config.type&&t.push(function(){const e=Bt(\"<div>\");function t(e){const t=()=>{const e=parseInt(this.browser.inputDialog.value,10);if(void 0!==e){const t=[];this.trackView.track.selected?t.push(...this.trackView.browser.getSelectedTrackViews().map((({track:e})=>e))):t.push(this);for(const i of t)i.trackView.autoHeight=!1,void 0!==i.minHeight&&i.minHeight>e&&(i.minHeight=e),void 0!==i.maxHeight&&i.maxHeight<e&&(i.minHeight=e),i.trackView.setTrackHeight(e,!0),i.trackView.checkContentHeight(),i.trackView.repaintViews()}},i={label:\"Track Height\",value:this.height,callback:t};this.browser.inputDialog.present(i,e)}return e.text(\"Set track height\"),{object:e,dialog:t}}()),!0===function(e){const t=e.browser.getSelectedTrackViews();return t&&t.length>1&&new Set(t).has(e)}(e)?t.push(...this.multiSelectMenuItems(e)):(\"sequence\"!==e.track.config.type&&t.push(function(){const e=Bt(\"<div>\");function t(e){const t=()=>{let e=this.browser.inputDialog.value;e=\"\"===e||void 0===e?\"untitled\":e.trim(),this.name=e},i={label:\"Track Name\",value:Ao(this)||\"unnamed\",callback:t};this.browser.inputDialog.present(i,e)}return e.text(\"Set track name\"),{object:e,click:t}}()),t.push(...this.defaultMenuItems(e))),!1!==e.track.removable&&(t.push(\"<hr/>\"),t.push(function(e){const t=e.track.selected?\"Remove tracks\":\"Remove track\",i=Bt(\"<div>\");function n(e){this.trackView.browser._removeTrack(this)}return i.text(t),{object:i,click:n,menuItemType:\"removeTrack\"}}(e))),t}defaultMenuItems(e){const t=[];return Co(e.track)&&(t.push(\"<hr/>\"),t.push(Fo({trackView:e,label:\"Set track color\",option:\"color\"})),t.push(vo({trackView:e,label:\"Unset track color\"})),\"wig\"!==e.track.config.type&&\"annotation\"!==e.track.config.type||(t.push(Fo({trackView:e,label:\"Set alt color\",option:\"altColor\"})),t.push(yo({trackView:e,label:\"Unset alt color\"})))),e.track.menuItemList&&t.push(...e.track.menuItemList()),function(e){const t=e.track;return t&&t.config&&void 0!==t.config.visibilityWindow||t&&go.has(t.type)}(e)&&(t.push(\"<hr/>\"),t.push(function(e){const t=Bt(\"<div>\");function i(t){const i=()=>{let e=this.browser.inputDialog.value;e=\"\"===e||void 0===e?-1:e.trim(),this.visibilityWindow=Number.parseInt(e),this.config.visibilityWindow=Number.parseInt(e),this.trackView.updateViews()},n={label:\"wig\"===e?\"Visibility window (bp). Enter 0 for whole chromosome, -1 for whole genome.\":\"Visibility window (bp). Enter 0 for whole chromosome.\",value:this.visibilityWindow,callback:i};this.browser.inputDialog.present(n,t)}return t.text(\"Set visibility window\"),{object:t,click:i}}(e.track.type))),t}multiSelectMenuItems(e){const t=[],i=e.browser.getSelectedTrackViews();var n;return!0===(n=i.map((({track:e})=>e.type)),1===[...new Set(n)].length)?(t.push(...this.defaultMenuItems(e)),\"wig\"===e.track.type&&(t.push(\"<hr/>\"),t.push(function(){const e=Bt(\"<div>\");function t(e){const t=so.Dark2,i=Math.floor(Math.random()*t.length),n=`auto-scale-group-${s()}`;wo[n]=t[i];const r=this.browser.getSelectedTrackViews();for(const{track:e}of r)e.autoscaleGroup=n;this.browser.updateViews()}return e.text(\"Group autoscale\"),{object:e,doAllMultiSelectedTracks:!0,click:t}}()))):Co(e.track)&&(t.push(\"<hr/>\"),t.push(Fo({trackView:e,label:\"Set track color\",option:\"color\"})),t.push(vo({trackView:e,label:\"Unset track color\"})),\"wig\"!==e.track.config.type&&\"annotation\"!==e.track.config.type||(t.push(Fo({trackView:e,label:\"Set alt color\",option:\"altColor\"})),t.push(yo({trackView:e,label:\"Unset alt color\"})))),t}}function Fo({trackView:e,label:t,option:i}){const n=Bt(\"<div>\");return n.text(t),{object:n,click:()=>e.presentColorPicker(i)}}function vo({trackView:e,label:t}){const i=Bt(\"<div>\");return i.text(t),{object:i,click:()=>{e.track.color=void 0,e.repaintViews()}}}function yo({trackView:e,label:t}){const i=Bt(\"<div>\");return i.text(t),{object:i,click:()=>{e.track.altColor=void 0,e.repaintViews()}}}function Ao(e){return e.name}function Co(e){return void 0===e.type||po.has(e.type)}class _o{constructor(e,t){this.browser=e,this.$container=Bt(\"<div>\",{class:\"igv-generic-dialog-container\"}),t.append(this.$container),this.$container.offset({left:0,top:0});const i=Bt(\"<div>\",{class:\"igv-generic-dialog-header\"});this.$container.append(i),u(i[0],(()=>{this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\"),this.$container.offset({left:0,top:0}),this.$container.hide()})),this.$minimum=Bt(\"<div>\",{class:\"igv-generic-dialog-label-input\"}),this.$container.append(this.$minimum);const n=Bt(\"<div>\");n.text(\"Minimum\"),this.$minimum.append(n),this.$minimum_input=Bt(\"<input>\"),this.$minimum.append(this.$minimum_input),this.$maximum=Bt(\"<div>\",{class:\"igv-generic-dialog-label-input\"}),this.$container.append(this.$maximum);const r=Bt(\"<div>\");r.text(\"Maximum\"),this.$maximum.append(r),this.$maximum_input=Bt(\"<input>\"),this.$maximum.append(this.$maximum_input);const s=Bt(\"<div>\",{class:\"igv-generic-dialog-ok-cancel\"});this.$container.append(s),this.$ok=Bt(\"<div>\"),s.append(this.$ok),this.$ok.text(\"OK\"),this.$cancel=Bt(\"<div>\"),s.append(this.$cancel),this.$cancel.text(\"Cancel\"),this.$cancel.on(\"click\",(()=>{this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\"),this.$container.offset({left:0,top:0}),this.$container.hide()})),p(this.$container.get(0),i.get(0)),this.$container.hide()}configure(e){let t;if(Array.isArray(e)){t={min:Number.MAX_SAFE_INTEGER,max:-Number.MAX_SAFE_INTEGER};for(const i of e)i.track.dataRange&&(t.min=Math.min(i.track.dataRange.min,t.min),t.max=Math.max(i.track.dataRange.max,t.max))}else t=e.track.dataRange;t&&(this.$minimum_input.val(t.min),this.$maximum_input.val(t.max)),this.$minimum_input.unbind(),this.$minimum_input.on(\"keyup\",(t=>{13===t.keyCode&&this.processResults(e),t.stopImmediatePropagation()})),this.$maximum_input.unbind(),this.$maximum_input.on(\"keyup\",(t=>{13===t.keyCode&&(t.stopImmediatePropagation(),this.processResults(e))})),this.$ok.unbind(),this.$ok.on(\"click\",(t=>{this.processResults(e)}))}processResults(e){if(\"\"!==this.$minimum_input.val()&&\"\"!==this.$maximum_input.val()){const t=Number(this.$minimum_input.val()),i=Number(this.$maximum_input.val());if(isNaN(t)||isNaN(i))this.browser.alert.present(new Error(\"Must input numeric values\"),void 0);else{const n=Array.isArray(e)?e:[e];for(const e of n)e.track.setDataRange({min:t,max:i})}this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\")}this.$container.offset({left:0,top:0}),this.$container.hide()}present(e){const t=e.offset().top,i=Bt(\"body\").scrollTop();this.$container.offset({left:e.width()-this.$container.width(),top:t+i}),this.$container.show()}}const xo={configureHighDPICanvas:function(e,t,i){const n=window.devicePixelRatio;e.canvas.style.width=`${t}px`,e.canvas.width=Math.floor(n*t),e.canvas.style.height=`${i}px`,e.canvas.height=Math.floor(n*i),e.scale(n,n)},setProperties:function(e,t){for(var i in t)if(t.hasOwnProperty(i)){var 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a=e=>{o.show(),i(n),e.preventDefault(),e.stopPropagation()};s.addEventListener(\"click\",a),s.addEventListener(\"touchend\",a),s.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}else s=e(),\"string\"==typeof t.label&&(s.innerHTML=t.label);if(t.click&&\"color\"!==t.type){function c(e){t.click(),i(n),e.preventDefault(),e.stopPropagation()}s.addEventListener(\"click\",c),s.addEventListener(\"touchend\",c),s.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}}return{object:s,init:t.init}}));return r}const rc=[[\"A\",\"T\"],[\"G\",\"C\"],[\"Y\",\"R\"],[\"W\",\"S\"],[\"K\",\"M\"],[\"D\",\"H\"],[\"B\",\"V\"]],sc=new Map;for(let _A of rc){const xA=_A[0],kA=_A[1];sc.set(xA,kA),sc.set(kA,xA),sc.set(xA.toLowerCase(),kA.toLowerCase()),sc.set(kA.toLowerCase(),xA.toLowerCase())}function oc(e){return sc.has(e)?sc.get(e):e}function ac(e){let t=\"\";for(let i of e)t+=sc.has(i)?sc.get(i):i;return t}function cc(e){let t=\"\",i=e.length;for(;i-- >0;){const n=e[i];t+=sc.has(n)?sc.get(n):n}return t}class lc{constructor(e,t,i,n){this.name=e,this.order=t,this.bpLength=i,this.altNames=n}getAltName(e){return this.altNames&&this.altNames.has(e)?this.altNames.get(e):this.name}}class hc{constructor(e,t,i,n){this.chr=e,this.start=t,this.end=i,this.features=n}contains(e,t,i){return this.chr===e&&this.start<=t&&this.end>=i}containsRange(e){return this.chr===e.chr&&this.start<=e.start&&this.end>=e.end}get locusString(){return`${this.chr}:${this.start+1}-${this.end}`}}class dc extends hc{constructor(e,t,i,n){super(e,t,i,n)}getSequence(e,t){if(e<this.start||t>this.end)return null;const i=e-this.start,n=t-e;return this.features?this.features.substring(i,i+n):null}hasSequence(e,t){return e>=this.start&&t<=this.end}}const uc=Dt,fc=new Set([\"fastaURL\",\"indexURL\",\"cytobandURL\",\"indexed\"]);class pc{#e;chromosomes=new Map;sequences=new Map;constructor(e){this.fastaURL=e.fastaURL,this.withCredentials=e.withCredentials;const t={};for(let i in e)e.hasOwnProperty(i)&&!fc.has(i)&&(t[i]=e[i]);this.config=t}async init(){return this.loadAll()}getSequenceRecord(e){return this.chromosomes.get(e)}get chromosomeNames(){return this.#e||(this.#e=Array.from(this.chromosomes.keys())),this.#e}getFirstChromosomeName(){return this.chromosomeNames[0]}async getSequence(e,t,i){if(0===this.sequences.size&&await this.loadAll(),!this.sequences.has(e))return;let n=this.sequences.get(e).find((e=>e.contains(t,i)));if(!n&&(n=this.sequences.get(e).find((e=>e.overlaps(t,i))),!n))return;t-=n.offset,i-=n.offset;let r=\"\";if(t<0)for(let e=t;e<Math.min(i,0);e++)r+=\"*\";if(i<=0)return r;const s=n.sequence,o=Math.min(i,s.length);return r+s.substring(t,o)}async loadAll(){let e;if(Ga(this.fastaURL)){let t=vs(this.fastaURL);e=\"\";for(let i of t)e+=String.fromCharCode(i)}else e=await Qs.load(this.fastaURL,Ua(this.config));const t=new Set,i=uc(e),n=i.length;let r,s=0,o=0,a={};for(;s<n;){if(r=i[s++].trim(),r.startsWith(\"#\")||0===r.length);else if(r.startsWith(\">\")){a&&a.seq&&c.call(this,a,o++);const e=r.substr(1).split(/\\s+/),t=e[0].split(\":\");if(a.chr=t[0],a.seq=\"\",a.offset=0,t.length>1&&t[1].indexOf(\"-\")>0){const i=t[1].split(\"-\");2===i.length&&/^[0-9]+$/.test(i[0])&&/^[0-9]+$/.test(i[1]);const n=Number.parseInt(i[0]);if(Number.parseInt(i[1])>n&&(a.offset=n-1),e.length>1&&e[1].startsWith(\"@len=\"))try{a.length=parseInt(e[1].trim().substring(5))}catch(e){a.length=void 0,console.error(`Error parsing sequence length for ${r}`)}else a.length=void 0}}else a.seq+=r;a&&a.seq&&c.call(this,a,o)}function c(e,i){const n=e.length||e.offset+e.seq.length;if(t.has(e.chr)){const t=this.chromosomes.get(e.chr);t.bpLength=Math.max(t.bpLength,n)}else this.sequences.set(e.chr,[]),this.chromosomes.set(e.chr,new lc(e.chr,i,n)),t.add(e.chr);this.sequences.get(e.chr).push(new gc(e.offset,e.seq))}}getSequenceInterval(e,t,i){const n=this.sequences.get(e);if(n)for(let r of n){const n=r.sequence,s=r.offset,o=s+n.length;if(s<=t&&o>=i)return new dc(e,s,o,n)}}}class gc{constructor(e,t){this.offset=e,this.sequence=t}contains(e,t){return this.offset<=e&&this.end>=t}overlaps(e,t){return this.offset<t&&this.end>e}get end(){return this.offset+this.sequence.length}}const mc=Dt,wc=new Set([\"fastaURL\",\"indexURL\",\"compressedIndexURL\",\"cytobandURL\",\"indexed\"]);class bc{#e;chromosomes=new Map;constructor(e){this.file=e.fastaURL,this.indexFile=e.indexURL,this.compressedIndexFile=e.compressedIndexURL,this.withCredentials=e.withCredentials;const t={};for(let i in e)e.hasOwnProperty(i)&&!wc.has(i)&&(t[i]=e[i]);this.config=t}getSequenceRecord(e){return this.chromosomes.get(e)}async init(){return this.getIndex()}get chromosomeNames(){return this.#e||(this.#e=Array.from(this.chromosomes.keys())),this.#e}getFirstChromosomeName(){return this.chromosomeNames[0]}async getIndex(){if(this.index)return this.index;{const e=await Qs.load(this.indexFile,Ua(this.config)),t=mc(e),i=t.length;let n=0,r=0;for(this.index={};n<i;){const e=t[n++].split(\"\\t\");if(5===e.length){const t=e[0],i=parseInt(e[1]),n={size:i,position:parseInt(e[2]),basesPerLine:parseInt(e[3]),bytesPerLine:parseInt(e[4])};this.index[t]=n,this.chromosomes.set(t,new lc(t,r++,i))}}return this.index}}async getCompressedIndex(){if(this.compressedIndex)return this.compressedIndex;if(!this.compressedIndexFile)return this.compressedIndex=[],this.compressedIndex;this.compressedIndex=[];const e=await Qs.loadArrayBuffer(this.compressedIndexFile,Ua(this.config)),t=e.byteLength;if(t<8)return console.log(\"Cannot parse GZI index file: length (\"+t+\" bytes) is insufficient to determine content of index.\"),this.compressedIndex;const i=e.slice(0,8),n=Number(new DataView(i).getBigUint64(0,!0)),r=8+2*n*8;if(t!=r)return console.log(\"Incorrect file size of reference genome index. Expected : \"+r+\". Received : \"+t),this.compressedIndex;this.compressedIndex.push([0,0]);for(let t=0;t<n;t++){const i=8+2*t*8,n=8+2*t*8+16,r=e.slice(i,n),s=new DataView(r),o=Number(s.getBigUint64(0,!0)),a=Number(s.getBigUint64(8,!0));this.compressedIndex.push([o,a])}return this.compressedIndex}async getRelevantCompressedBlockNumbers(e,t){if(e<0||t<0||t<e)return console.log(\"Incompatible query positions for reference-genome. Start:\"+e+\" | End:\"+t),[];await this.getCompressedIndex();let i=[];const n=this.compressedIndex.length-1;if(0==this.compressedIndex.length)return console.log(\"Compressed index does not contain any content\"),[];if(e>this.compressedIndex[n][1])return[n];let r=0,s=n,o=Math.floor(this.compressedIndex.length/2),a=this.compressedIndex.length+1,c=!1;for(let t=0;t<a;t++){const t=this.compressedIndex[o][1],i=o<this.compressedIndex.length-1?this.compressedIndex[o+1][1]:1/0;if(t<=e&&i>e){c=!0;break}t<e?r=o+1:s=o-1,o=Math.ceil((s-r)/2)+r}if(!c)return console.log(\"No blocks within compressed index found that correspond with query positions \"+e+\",\"+t),console.log(this.compressedIndex),[];i.push(o);for(let e=o+1;e<this.compressedIndex.length;e++){i.push(e);if(this.compressedIndex[e][1]>=t)break}const l=i[i.length-1];return l===this.compressedIndex.length-1&&this.compressedIndex[l][1]<t&&i.push(-1),i}async loadAndUncompressBlocks(e,t){if(await this.getCompressedIndex(),0==e.length)return\"\";let i=Array(e.length-1);for(let t=0;t<e.length-1;t++){const n=e[t],r=this.compressedIndex[n][0],s=e[t+1];let o=[];if(-1!=s){const e=this.compressedIndex[s][0]-r;o=await Qs.loadArrayBuffer(this.file,Ua(this.config,{range:{start:r,size:e}}))}else o=await Qs.loadArrayBuffer(this.file,Ua(this.config,{range:{start:r}}));const a=await gs(o);i[t]=a}let n=\"\";for(let e=0;e<i.length;e++)for(let t=0;t<i[e].length;t++){n+=String.fromCharCode(i[e][t])}const r=t-this.compressedIndex[e[0]][1];return n=n.substring(r),n}async readSequence(e,t,i){await this.getIndex(),await this.getCompressedIndex();const n=this.index[e];if(!n)return console.log(\"No index entry for chr: \"+e),this.index[e]=null,null;const r=Math.max(0,t),s=Math.min(n.size,i),o=n.bytesPerLine,a=n.basesPerLine,c=n.position,l=o-a,h=Math.floor(r/a),d=Math.floor(s/a),u=r-h*a,f=c+h*o+u,p=c+d*o+(s-d*a)-1,g=p-f+1;if(g<=0)return console.error(\"No sequence for \"+e+\":\"+t+\"-\"+i),null;let m;if(this.compressedIndexFile){let e=await this.getRelevantCompressedBlockNumbers(f,p);if(0===e.length)return console.log(\"No blocks in the compressed index that correspond with the requested byte positions (\"+f+\",\"+p+\")\"),null;m=await this.loadAndUncompressBlocks(e,f)}else m=await Qs.load(this.file,Ua(this.config,{range:{start:f,size:g}}));if(!m)return null;let w,b=\"\",F=0,v=m.length;for(u>0&&(w=Math.min(s-r,a-u),b+=m.substr(F,w),F+=w+l);F<v;)w=Math.min(a,v-F),b+=m.substr(F,w),F+=w+l;return b}}const Fc=Dt;class vc{#e;chromosomes=new Map;constructor(e){this.url=e}async init(){return this.loadAll()}getSequenceRecord(e){return this.chromosomes.get(e)}get chromosomeNames(){this.#e||(this.#e=Array.from(this.chromosomes.keys()))}async getSequence(e,t,i){return null}async loadAll(){let e;if(Ga(this.url)){let t=vs(this.fastaURL);e=\"\";for(let i of t)e+=String.fromCharCode(i)}else e=await Qs.load(this.url,{});const t=Fc(e);let i=0;for(let e of t){const t=e.split(\"\\t\");if(t.length>1){const e=Number.parseInt(t[1]),n=new lc(t[0],i++,e);this.chromosomes.set(t[0],n)}}}}class yc{constructor(e,t=!0){this.littleEndian=t,this.position=0,this.view=e,this.length=e.byteLength}dumpBytes(e=100){const t=this.position,i=[];for(let t=0;t<=e;t++)i.push(this.getByte());console.log(i.join(\" \")),this.setPosition(t)}setPosition(e){this.position=e}available(){return this.length-this.position}remLength(){return this.length-this.position}hasNext(){return this.position<this.length-1}getByte(){const e=this.view.getUint8(this.position,this.littleEndian);return this.position++,e}getShort(){const e=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,e}getUShort(){const e=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,e}getInt(){const e=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,e}getUInt(){const e=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,e}getLong(){var e=[];e[0]=this.view.getUint8(this.position),e[1]=this.view.getUint8(this.position+1),e[2]=this.view.getUint8(this.position+2),e[3]=this.view.getUint8(this.position+3),e[4]=this.view.getUint8(this.position+4),e[5]=this.view.getUint8(this.position+5),e[6]=this.view.getUint8(this.position+6),e[7]=this.view.getUint8(this.position+7);let t=0;if(this.littleEndian)for(let i=e.length-1;i>=0;i--)t=256*t+e[i];else for(let i=0;i<e.length;i++)t=256*t+e[i];return this.position+=8,t}getString(e){let t,i=\"\";for(;0!==(t=this.view.getUint8(this.position++))&&(i+=String.fromCharCode(t),!e||i.length!==e););return i}getFixedLengthString(e){let t=\"\";for(let i=0;i<e;i++){const e=this.view.getUint8(this.position++);e>0&&(t+=String.fromCharCode(e))}return t}getFloat(){var e=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,e}getDouble(){var e=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,e}skip(e){return this.position+=e,this.position}getVPointer(){var e=this.position,t=this.view.getUint8(e+1)<<8|this.view.getUint8(e),i=4294967296*(255&this.view.getUint8(e+6))+16777216*(255&this.view.getUint8(e+5))+65536*(255&this.view.getUint8(e+4))+256*(255&this.view.getUint8(e+3))+(255&this.view.getUint8(e+2));return this.position+=8,new Ac(i,t)}}class Ac{constructor(e,t){this.block=e,this.offset=t}isLessThan(e){return this.block<e.block||this.block===e.block&&this.offset<e.offset}isGreaterThan(e){return this.block>e.block||this.block===e.block&&this.offset>e.offset}isEqualTo(e){return this.block===e.block&&this.offset===e.offset}print(){return this.block+\":\"+this.offset}}class Cc{static magic=2026540177;littleEndian=!0;nodeCache=new Map;static async loadBpTree(e,t,i){return new Cc(e,t,i).init()}constructor(e,t,i){this.path=e,this.config=t,this.startOffset=i}async init(){const e=await this.#t(this.startOffset,32);let t=e.getInt();if(t!==Cc.magic&&(e.setPosition(0),this.littleEndian=!this.littleEndian,e.littleEndian=this.littleEndian,t=e.getInt(),t!==Cc.magic))throw Error(`Bad magic number ${t}`);const i=e.getInt(),n=e.getInt(),r=e.getInt(),s=e.getLong(),o=e.getLong(),a=this.startOffset+32;return this.header={magic:t,blockSize:i,keySize:n,valSize:r,itemCount:s,reserved:o,nodeOffset:a},this}async search(e){this.header||await this.init();const{keySize:t,valSize:i}=this.header;if(16!==i&&8!==i)throw Error(`Unexpected valSize ${i}`);const n=async e=>{if(this.nodeCache.has(e))return this.nodeCache.get(e);{let n=await this.#t(e,4);const r=n.getByte();n.getByte();const s=n.getUShort(),o=[];if(1===r){const r=s*(t+i);n=await this.#t(e+4,r);for(let e=0;e<s;e++){const e=n.getFixedLengthString(t),r=n.getLong();let s;if(16===i){const e=n.getInt();n.getInt(),s={offset:r,length:e}}else s={offset:r};o.push({key:e,value:s})}}else{const i=s*(t+8);n=await this.#t(e+4,i);for(let e=0;e<s;e++){const e=n.getFixedLengthString(t),i=n.getLong();o.push({key:e,offset:i})}}const a={type:r,count:s,items:o};return this.nodeCache.set(e,a),a}},r=async t=>{const i=await n(t);if(1!==i.type){let t=i.items[0].offset;for(let n=1;n<i.items.length;n++){const r=i.items[n].key;if(e.localeCompare(r)<0)break;t=i.items[n].offset}return r(t)}for(let t of i.items)if(e===t.key)return t.value};return r(this.header.nodeOffset)}async#t(e,t){const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:t}}));return new yc(new DataView(i),this.littleEndian)}}\n",
-       "/**\n",
-       "     * Note: Some portions of this code adapated from the GMOD two-bit.js project, @Copyright (c) 2017 Robert Buels\n",
-       "     * * https://github.com/GMOD/twobit-js/blob/master/src/twoBitFile.ts*\n",
-       "     */const _c=[\"T\",\"C\",\"A\",\"G\"],xc=[];for(let IA=0;IA<256;IA++)xc.push(_c[IA>>6&3]+_c[IA>>4&3]+_c[IA>>2&3]+_c[3&IA]);const kc=xc.map((e=>e.toLowerCase()));class Ic{littleEndian;metaIndex=new Map;constructor(e){this.url=e.twoBitURL||e.fastaURL,this.config=e,e.twoBitBptURL&&(this.bptURL=e.twoBitBptURL)}async init(){if(this.bptURL)this.index=await Cc.loadBpTree(this.bptURL,this.config,0);else{const e=await this._readIndex();this.index={search:async t=>e.has(t)?{offset:e.get(t)}:void 0}}}async readSequence(e,t,i){this.index||await this.init();const n=await this.getSequenceRecord(e);if(!n)return null;if(t<0)throw new TypeError(\"regionStart cannot be less than 0\");(void 0===i||i>n.dnaSize)&&(i=n.dnaSize);const r=this._getOverlappingBlocks(t,i,n.nBlocks),s=this._getOverlappingBlocks(t,i,n.maskBlocks),o=Math.floor(t/4),a=n.packedPos+o,c=Math.floor(i/4)-o+1,l=await Qs.loadArrayBuffer(this.url,{range:{start:a,size:c}}),h=new Uint8Array(l);let d=\"\";for(let e=t;e<i;e+=1){for(;s.length&&s[0].end<=e;)s.shift();const t=s[0]&&s[0].start<=e&&s[0].end>e;if(r[0]&&e>=r[0].start&&e<r[0].end){const t=r.shift();for(;e<t.end&&e<i;)d+=\"N\",e++;e--}else{const i=e%4,n=h[Math.floor(e/4)-o];d+=t?kc[n][i]:xc[n][i]}}return d}async _readIndex(){const e=new Map;let t=await Qs.loadArrayBuffer(this.url,{range:{start:0,size:64}}),i=new DataView(t),n=0;const r=i.getUint32(n,!0),s=i.getUint32(n,!1);n+=4;const o=440477507;if(r===o)this.littleEndian=!0;else{if(s!==o)throw Error(`Bad magic number ${o}`);this.littleEndian=!1}let a,c;this.version=i.getUint32(n,this.littleEndian),n+=4,this.sequenceCount=i.getUint32(n,this.littleEndian),n+=4,this.reserved=i.getUint32(n,this.littleEndian),n+=4;let l=20;for(let t=0;t<this.sequenceCount;t++){(!c||c.available()<1)&&(a=(this.sequenceCount-t)*l,c=await this._loadBinaryBuffer(n,a));const i=c.getByte();n+=1,c.available()<i+5&&(a=(this.sequenceCount-t)*l+100,c=await this._loadBinaryBuffer(n,a));const r=c.getString(i),s=c.getUInt();n+=i+4,e.set(r,s),l=Math.floor(l*(t/(t+1))+r.length/(t+1))}return e}async getSequenceRecord(e){if(!this.metaIndex.has(e)){if(!this.index)throw Error(\"TwobitSequence object must be initialized before accessing sequence\");let t=await this.index.search(e);if(!t)return;let i=t.offset,n=8,r=await this._loadBinaryBuffer(i,n);const s=r.getUInt(),o=r.getUInt();i+=n,n=8*o+4,r=await this._loadBinaryBuffer(i,n);const a=[];for(let e=0;e<o;e++)a.push(r.getUInt());const c=[];for(let e=0;e<o;e++)c.push(r.getUInt());const l=r.getUInt();i+=n,n=8*l+4,r=await this._loadBinaryBuffer(i,n);const h=[];for(let e=0;e<l;e++)h.push(r.getUInt());const d=[];for(let e=0;e<l;e++)d.push(r.getUInt());const u=[];for(let e=0;e<o;e++)u.push(new Sc(a[e],c[e]));const f=[];for(let e=0;e<l;e++)f.push(new Sc(h[e],d[e]));if(0!=r.getUInt())throw Error(\"Bad 2-bit file\");i+=n;const p={dnaSize:s,nBlocks:u,maskBlocks:f,packedPos:i,bpLength:s};this.metaIndex.set(e,p)}return this.metaIndex.get(e)}_getOverlappingBlocks(e,t,i){const n=[];for(let r of i){if(r.start>t)break;r.end<e||n.push(r)}return n}async _loadBinaryBuffer(e,t){const i=await Qs.loadArrayBuffer(this.url,{range:{start:e,size:t}});return new yc(new DataView(i),this.littleEndian)}}class Sc{constructor(e,t){this.start=e,this.size=t}get end(){return this.start+this.size}}class Ec{static#i=1e5;#n;#r=[];#s=10;constructor(e,t){this.sequenceReader=e,this.browser=t}get chromosomes(){return this.sequenceReader.chromosomes}async getSequenceRecord(e){return this.sequenceReader.getSequenceRecord(e)}async getSequence(e,t,i){let n=this.#r.find((n=>n.contains(e,t,i)));if(n||(n=await this.#o(e,t,i),this.#a(n),this.#r.push(n)),n){const e=t-n.start,r=i-t;return n.features?n.features.substring(e,e+r):null}}#a(e){this.#r=this.#r.filter((t=>!e.contains(t))),this.#r.length===this.#s&&this.#r.shift(),this.browser&&this.browser.referenceFrameList.length<100&&(this.#r=this.#r.filter((e=>void 0!==this.browser.referenceFrameList.find((t=>t.overlaps(e))))))}getSequenceInterval(e,t,i){return this.#r.find((n=>n.contains(e,t,i)))}async#o(e,t,i){let n=t,r=i;if(i-t<Ec.#i){const e=i-t,s=Math.round(t+e/2);n=Math.max(0,s-Ec.#i/2),r=n+Ec.#i}const s=new dc(e,n,r);if(this.#n&&this.#n[0].contains(e,t,i))return this.#n[1];{const t=new Promise((async(t,i)=>{s.features=await this.sequenceReader.readSequence(e,n,r),t(s)}));return this.#n=[s,t],t}}async init(){return this.sequenceReader.init()}get chromosomeNames(){return this.sequenceReader.chromosomeNames}getFirstChromosomeName(){return\"function\"==typeof this.sequenceReader.getFirstChromosomeName?this.sequenceReader.getFirstChromosomeName():void 0}#c(e){this.browser.referenceFrameList}}async function Nc(e,t){let i;return\"chromsizes\"===e.format?i=new vc(e.fastaURL||e.url):\"2bit\"===e.format||e.twoBitURL?i=new Ec(new Ic(e),t):Ga(e.fastaURL)||!e.indexURL?i=new pc(e):\"gbk\"===e.format||e.gbkURL||(i=new Ec(new bc(e),t)),await i.init(),i}const Bc={A:\"rgb(  0, 200,   0)\",C:\"rgb(  0,0,200)\",T:\"rgb(255,0,0)\",G:\"rgb(209,113,  5)\",N:\"rgb(80,80,80)\"};function Mc(e,t){if(e.length<6)return void console.log(\"Skipping line: \"+e.join(\" \"));var i={chr1:e[0],start1:Number.parseInt(e[1]),end1:Number.parseInt(e[2]),chr2:e[3],start2:Number.parseInt(e[4]),end2:Number.parseInt(e[5])};if(isNaN(i.start1)||isNaN(i.end1)||isNaN(i.start2)||isNaN(i.end2))return;t&&void 0===t.hiccups&&(t.hiccups=!!t.columnNames&&Dc(t.columnNames));const n=t&&t.hiccups,r=n?6:10;if(n||(e.length>6&&\".\"!==e[6]&&(i.name=e[6]),e.length>7&&\".\"!==e[7]&&(i.score=Number(e[7])),e.length>8&&\".\"!==e[8]&&(i.strand1=e[8]),e.length>9&&\".\"!==e[9]&&(i.strand2=e[9])),t){const n=t.colorColumn;n&&n<e.length&&(i.color=_s.createColorString(e[n]));const s=t.thicknessColumn;s&&s<e.length&&(i.thickness=e[s]),e.length>r&&t.columnNames&&t.columnNames.length===e.length&&(i.extras=e.slice(r))}return i.chr1===i.chr2&&(i.chr=i.chr1,i.start=Math.min(i.start1,i.start2),i.end=Math.max(i.end1,i.end2)),i}function Rc(e,t){if(!(e.length<8))return{chr:e[0],start:Number.parseInt(e[1]),end:Number.parseInt(e[2]),color:_s.createColorString(e[6]),value:Number(e[7])}}function Dc(e){return e&&(e.includes(\"fdrDonut\")||e.includes(\"fdr_donut\"))}function Tc(e,t){if(!(e.length<6))return{chr:e[0],start:Number.parseInt(e[1]),end:Number.parseInt(e[2]),chr1:e[8],start1:Number.parseInt(e[9]),end1:Number.parseInt(e[10]),chr2:e[13],start2:Number.parseInt(e[14]),end2:Number.parseInt(e[15]),name:e[3],score:Number(e[4]),value:Number(e[5]),color:\".\"===e[7]?void 0:\"0\"===e[7]?\"rgb(0,0,0)\":e[7]};console.log(\"Skipping line: \"+e.join(\" \"))}class Lc{constructor(e){this.message=e}}const zc=new Map([[\"%09\",\"\\t\"],[\"%0A\",\"\\n\"],[\"%0D\",\"\\r\"],[\"%25\",\"%\"],[\"%3B\",\";\"],[\"%3D\",\"=\"],[\"%26\",\"&\"],[\"%2C\",\",\"]]);function Hc(e){if(!e.includes(\"%\"))return e;let t=\"\";for(let i=0;i<e.length;i++)if(37===e.charCodeAt(i)&&i<e.length-2){const n=e.substring(i,i+3);zc.has(n)?t+=zc.get(n):t+=n,i+=2}else t+=e.charAt(i);return t}function Pc(e,t=\"=\"){const i=\"=\"===t;var n=[];for(let r of e.split(\";\")){r=r.trim();const e=r.indexOf(t);if(e>0&&e<r.length-1){let t=Hc(r.substring(0,e).trim()),s=Hc(r.substring(e+1).trim());i||(t=Oc(t),s=Oc(s)),n.push([t,s])}}return n}function Oc(e){return e.startsWith('\"')&&e.endsWith('\"')&&(e=e.substr(1,e.length-2)),e}function Uc(e,t,i=Number.MAX_SAFE_INTEGER){if(e.length<3)return;t&&t.gffTags;const n=e[0],r=parseInt(e[1]),s=e.length>2?parseInt(e[2]):r+1;if(isNaN(r)||isNaN(s))return new Lc(\"Unparsable bed record.\");const o=new nl({chr:n,start:r,end:s,score:1e3});let a=3;try{if(e.length>3&&a++<i){if(e[3].indexOf(\";\")>0&&e[3].indexOf(\"=\")>0){const i=Pc(e[3],\"=\");o.attributes={};for(let e of i)o.attributes[e[0]]=e[1],null!=t.nameField&&e[0]===t.nameField&&(o.name=e[1])}o.name||(o.name=\".\"===e[3]?\"\":e[3])}if(e.length>4&&a++<i&&(o.score=\".\"===e[4]?0:Number(e[4]),isNaN(o.score)))return o;if(e.length>5&&a++<i&&(o.strand=e[5],\".\"!==o.strand&&\"+\"!==o.strand&&\"-\"!==o.strand))return o;if(e.length>6&&a++<i&&(o.cdStart=parseInt(e[6]),isNaN(o.cdStart)))return o;if(e.length>7&&a++<i&&(o.cdEnd=parseInt(e[7]),isNaN(o.cdEnd)))return o;if(e.length>8&&a++<i&&\".\"!==e[8]&&\"0\"!==e[8]&&(o.color=_s.createColorString(e[8])),e.length>11&&a++<i){const t=parseInt(e[9]);if(t>1e3)return o;const i=e[10].replace(/,$/,\"\").split(\",\"),n=e[11].replace(/,$/,\"\").split(\",\");if(i.length!==n.length||t!==i.length)return o;const s=[];for(let e=0;e<t;e++){const t=r+parseInt(n[e]),o=t+parseInt(i[e]);s.push({start:t,end:o})}s.length>0&&(Yc(s,o.cdStart,o.cdEnd),o.exons=s)}if(t){let i=t.thicknessColumn,n=t.colorColumn;n&&n<e.length&&(o.color=_s.createColorString(e[n])),i&&i<e.length&&(o.thickness=e[i])}}catch(e){}return o}function qc(e,t){const i=Uc(e,t);return i&&e.length>14&&(i.signal=Number(e[12]),i.pValue=Number(e[13]),i.qValue=Number(e[14])),i}function Qc(e,t){const i=Uc(e,t,9);if(i){const t=[\"Coverage\",\"% Showing Methylation\",\"N-mod\",\"N-canonical\",\"N-other mod\",\"N-delete\",\"N-fail\",\"N-dff\",\"N-nocall\"];for(let n=9;n<e.length;n++){i[t[n-9]]=e[n]}}return i}function Vc(e,t){if(e.length<=15)return;return{swScore:Number.parseInt(e[1]),milliDiv:Number.parseInt(e[2]),milliDel:Number.parseInt(e[3]),milliIns:Number.parseInt(e[4]),chr:e[5],start:Number.parseInt(e[6]),end:Number.parseInt(e[7]),strand:e[9],repName:e[10],repClass:e[11],repFamily:e[12],repStart:Number.parseInt(e[13]),repEnd:Number.parseInt(e[14]),repLeft:Number.parseInt(e[15])}}function jc(e,t){var i=void 0===t.shift?0:1;if(e.length<=9+i)return;const n=parseInt(e[5+i]),r=parseInt(e[6+i]);var s={name:e[0+i],chr:e[1+i],strand:e[2+i],start:parseInt(e[3+i]),end:parseInt(e[4+i]),cdStart:n,cdEnd:r,id:e[0+i]};const o=Kc(parseInt(e[7+i]),e[8+i],e[9+i]);return Yc(o,n,r),s.exons=o,s}function Wc(e,t){var i=void 0===t.shift?0:1;if(e.length<=11+i)return;const n=parseInt(e[5+i]),r=parseInt(e[6+i]),s={name:e[11+i],chr:e[1+i],strand:e[2+i],start:parseInt(e[3+i]),end:parseInt(e[4+i]),cdStart:n,cdEnd:r,id:e[0+i]},o=Kc(parseInt(e[7+i]),e[8+i],e[9+i],e[14+i]);return Yc(o,n,r),s.exons=o,s}function Gc(e,t){var i=void 0===t.shift?0:1;if(e.length<=10+i)return;const n=parseInt(e[6+i]),r=parseInt(e[7+i]);var s={name:e[0+i],id:e[1+i],chr:e[2+i],strand:e[3+i],start:parseInt(e[4+i]),end:parseInt(e[5+i]),cdStart:n,cdEnd:r};const o=Kc(parseInt(e[8+i]),e[9+i],e[10+i]);return Yc(o,n,r),s.exons=o,s}function $c(e,t){if(e.length<21)return;const i=e[13],n=parseInt(e[15]),r=parseInt(e[16]),s=e[8].charAt(0),o=parseInt(e[17]),a=[],c=e[20].replace(/,$/,\"\").split(\",\"),l=e[18].replace(/,$/,\"\").split(\",\");for(let e=0;e<o;e++){const t=parseInt(c[e]),i=t+parseInt(l[e]);a.push({start:t,end:i})}return new rl({chr:i,start:n,end:r,strand:s,exons:a,tokens:e})}function Kc(e,t,i,n){const r=t.replace(/,$/,\"\").split(\",\"),s=i.replace(/,$/,\"\").split(\",\"),o=n?n.replace(/,$/,\"\").split(\",\"):void 0,a=[];for(let t=0;t<e;t++){const e={start:parseInt(r[t]),end:parseInt(s[t])};if(o){const i=parseInt(o[t]);-1!=i&&(e.readingFrame=i)}a.push(e)}return a}function Yc(e,t,i){for(let n of e){const e=n.end,r=n.start;e<t||r>i?n.utr=!0:(t>=r&&t<=e&&(n.cdStart=t),i>=r&&i<=e&&(n.cdEnd=i))}}function Xc(e,t){var i,n,r,s,o,a,c;if(!(e.length<9))return i=e[0],n=parseInt(e[1]),r=parseInt(e[2]),o=e[3],a=Number(e[4]),s=e[5].trim(),c=Number(e[6]),0===a&&(a=c),{chr:i,start:n,end:r,name:o,score:a,strand:s,signal:c,pValue:Number(e[7]),qValue:Number(e[8])}}function Zc(e,t){const i=Xc(e);return e.length>9&&(i.peak=Number(e[9])),i}function Jc(e,t){if(e.length<=3)return;const i={chr:e[0],start:parseInt(e[1]),end:parseInt(e[2]),value:Number(e[3])};if(t){let n=t.colorColumn;n&&n<e.length&&(i.color=_s.createColorString(e[n]))}return i}function el(e,t){const i=t.wig;if(i&&\"fixedStep\"===i.format){const t=i.index*i.step+i.start,n=t+i.span,r=Number(e[0]);return++i.index,isNaN(r)?null:{chr:i.chrom,start:t,end:n,value:r}}if(i&&\"variableStep\"===i.format){if(e.length<2)return null;const t=parseInt(e[0],10)-1,n=t+i.span,r=Number(e[1]);return isNaN(r)?null:{chr:i.chrom,start:t,end:n,value:r}}return Jc(e)}function tl(e,t){if(e.length<6)return;const i=[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"refNCBI\",\"refUCSC\",\"observed\",\"molType\",\"class\",\"valid\",\"avHet\",\"avHetSE\",\"func\",\"locType\",\"weight\",\"exceptions\",\"submitterCount\",\"submitters\",\"alleleFreqCount\",\"alleles\",\"alleleNs\",\"alleleFreqs\",\"bitfields\"],n={chr:e[1],start:Number.parseInt(e[2]),end:Number.parseInt(e[3]),name:e[4],score:Number.parseInt(e[5])},r=Math.min(e.length,i.length);for(let t=6;t<r;t++)n[i[t]]=e[t];return n}function il(e,t,i=Number.MAX_SAFE_INTEGER){if(e.length<4)return;const n=e[0],r=parseInt(e[1]),s=e.length>2?parseInt(e[2]):r+1;if(isNaN(r)||isNaN(s))return new Lc(\"Unparsable bed record.\");const o=new nl({chr:n,start:r,end:s,score:1e3}),a=[];for(let t=3;t<e.length;t++)a.push(Number.parseInt(e[t]));return o.values=a,o}class nl{constructor(e){Object.assign(this,e)}getAttributeValue(e){return this.hasOwnProperty(e)?this[e]:this.attributes?this.attributes[e]:void 0}}class rl{constructor(e){Object.assign(this,e)}get score(){const e=this.tokens,t=parseInt(e[0]),i=parseInt(e[2]),n=parseInt(e[1]),r=parseInt(e[4]),s=parseInt(e[6]),o=parseInt(e[10]);return Math.floor(1e3*(t+i-n-r-s)/o)}get matches(){return this.tokens[0]}get misMatches(){return this.tokens[1]}get repMatches(){return this.tokens[2]}get nCount(){return this.tokens[3]}get qNumInsert(){return this.tokens[4]}get qBaseInsert(){return this.tokens[5]}get tNumInsert(){return this.tokens[6]}get tBaseInsert(){return this.tokens[7]}popupData(){return[{name:\"chr\",value:this.chr},{name:\"start\",value:this.start+1},{name:\"end\",value:this.end},{name:\"strand\",value:this.strand},{name:\"score\",value:this.score},{name:\"match\",value:this.matches},{name:\"mis-match\",value:this.misMatches},{name:\"rep. match\",value:this.repMatches},{name:\"N's\",value:this.nCount},{name:\"Q gap count\",value:this.qNumInsert},{name:\"Q gap bases\",value:this.qBaseInsert},{name:\"T gap count\",value:this.tNumInsert},{name:\"T gap bases\",value:this.tBaseInsert}]}}const sl=new Set([\"transcript\",\"primary_transcript\",\"processed_transcript\",\"mRNA\",\"mrna\",\"lnc_RNA\",\"miRNA\",\"ncRNA\",\"rRNA\",\"scRNA\",\"snRNA\",\"snoRNA\",\"tRNA\"]),ol=new Set([\"CDS\",\"cds\"]),al=new Set([\"start_codon\",\"stop_codon\"]),cl=new Set([\"5UTR\",\"3UTR\",\"UTR\",\"five_prime_UTR\",\"three_prime_UTR\",\"3'-UTR\",\"5'-UTR\"]),ll=new Set([\"exon\",\"coding-exon\"]),hl=new Set;for(let SA of[ol,al,cl,ll])for(let EA of SA)hl.add(EA);function dl(e){return e.includes(\"intron\")}function ul(e){return ol.has(e)||al.has(e)}function fl(e){return cl.has(e)}function pl(e){return sl.has(e)||e.endsWith(\"RNA\")||e.endsWith(\"transcript\")}function gl(e){return hl.has(e)||e.endsWith(\"RNA\")||dl(e)}const ml=new Set([\"id\",\"parent\",\"name\"]);class wl{constructor(e){Object.assign(this,e),void 0!==e.phase&&\".\"!==e.phase&&(this.readingFrame=(3-parseInt(e.phase))%3)}popupData(e){const t=this.geneObject?this.geneObject.popupData():[];if(this.geneObject&&t.push(\"<hr/>\"),this.name&&t.push({name:\"Name\",value:this.name}),t.push({name:\"Type\",value:this.type}),t.push({name:\"Source\",value:this.source}),void 0!==this.score&&t.push({name:\"Score\",value:this.score}),t.push({name:\"Phase\",value:this.phase}),this.attributeString){const e=Pc(this.attributeString,this.delim);for(let[i,n]of e)void 0!==n&&n.length>0&&!ml.has(i.toLowerCase())&&t.push({name:i+\":\",value:n})}return t.push({name:\"Location\",value:`${this.chr}:${Rt(this.start+1)}-${Rt(this.end)}`}),t}getAttributeValue(e){if(this.hasOwnProperty(e))return this[e];if(this._attributeCache||(this._attributeCache=new Map),this._attributeCache.has(e))return this._attributeCache.get(e);{const t=Pc(this.attributeString,this.delim);let i;for(let[n,r]of t)if(n===e){i=r;break}return this._attributeCache.set(e,i),i}}}class bl extends wl{constructor(e){super(e),this.exons=[],this.parts=[]}addExon(e){this.exons.push(e),this.start=Math.min(this.start,e.start),this.end=Math.max(this.end,e.end)}addPart(e){this.parts.push(e)}assembleParts(){if(0===this.parts.length)return;this.parts.sort((function(e,t){return e.start-t.start}));let e=this.parts[0].start,t=this.parts[0].end;for(let i=1;i<this.parts.length;i++){const n=this.parts[i];if(!dl(n.type))if(n.start<=t)t=Math.max(t,n.end);else{this.findExonContaining({start:e,end:t})||this.exons.push({start:e,end:t,psuedo:!0}),e=n.start,t=n.end}}this.findExonContaining({start:e,end:t})||(this.exons.push({start:e,end:t,psuedo:!0}),this.start=Math.min(this.start,e),this.end=Math.max(this.end,t));for(let e of this.parts){const t=e.type;ul(t)?this.addCDS(e):fl(t)&&this.addUTR(e)}}findExonContaining({start:e,end:t}){for(let i of this.exons)if(i.end>=t&&i.start<=e)return i}addCDS(e){let t;const i=this.exons;for(let n of i)if(n.start<=e.start&&n.end>=e.end){t=n;break}t?(t.cdStart=t.cdStart?Math.min(e.start,t.cdStart):e.start,t.cdEnd=t.cdEnd?Math.max(e.end,t.cdEnd):e.end,t.readingFrame=e.readingFrame):console.error(\"No exon found spanning \"+e.start+\"-\"+e.end),this.cdStart=this.cdStart?Math.min(e.start,this.cdStart):e.start,this.cdEnd=this.cdEnd?Math.max(e.end,this.cdEnd):e.end}addUTR(e){let t;const i=this.exons;for(let n=0;n<i.length;n++)if(i[n].start<=e.start&&i[n].end>=e.end){t=i[n];break}t?e.start===t.start&&e.end===t.end?t.utr=!0:(e.end<t.end&&(t.cdStart=e.end),e.start>t.start&&(t.cdEnd=e.start)):console.error(\"No exon found spanning \"+cds.start+\"-\"+cds.end)}finish(){this.assembleParts();var e=this.cdStart,t=this.cdEnd;this.exons.sort((function(e,t){return e.start-t.start})),e&&this.exons.forEach((function(i){(i.end<e||i.start>t)&&(i.utr=!0)}))}popupData(e){const t=super.popupData(e);for(let i of this.exons)if(!i.pseudo&&e>=i.start&&e<i.end&&\"function\"==typeof i.popupData){t.push(\"<hr/>\");const n=i.popupData(e);for(let e of n)t.push(e)}for(let i of this.parts)if(e>=i.start&&e<i.end&&\"function\"==typeof i.popupData){t.push(\"<hr/>\");const n=i.popupData(e);for(let e of n)t.push(e)}return t}}function Fl(e,t){const i=t.format;if(e.length<9)return;const n=\"gff3\"===i?\"=\":\" \";return new wl({source:Hc(e[1]),type:e[2],chr:e[0],start:parseInt(e[3])-1,end:parseInt(e[4]),score:\".\"===e[5]?void 0:Number(e[5]),strand:e[6],phase:\".\"===e[7]?\".\":parseInt(e[7]),attributeString:e[8],delim:n})}function vl(e,t){const i=Fl(e,t);if(!i)return;const n=Pc(i.attributeString,i.delim);for(let[e,t]of n){const n=e.toLowerCase();\"color\"===n||\"colour\"===n?i.color=_s.createColorString(t):\"ID\"===e?i.id=t:\"Parent\"===e&&(i.parent=t)}return i}function yl(e,t){const i=Fl(e,t);if(!i)return;const n=Pc(i.attributeString,i.delim);let r,s;switch(i.type){case\"gene\":r=\"gene_id\";break;case\"transcript\":r=\"transcript_id\",s=\"gene_id\";break;default:s=\"transcript_id\"}for(let[e,t]of n){const n=e.toLowerCase();\"color\"===n||\"colour\"===n?i.color=_s.createColorString(t):e===r?i.id=t:e===s&&(i.parent=t)}return i}function Al(e,t){if(!(e.length<7)){var i=e[0],n=e[1],r=parseInt(e[2]),s=parseInt(e[3]),o=parseInt(e[4]),a=parseInt(e[5]),c=e[6],l={chr:i,name:n,junction_left:r,junction_right:s,num_junction_reads:o,num_spanning_frags:a,spanning_frag_coords:[],start:-1,end:-1},h=r,d=s;if(a>0)for(var u=c.split(\",\"),f=0;f<u.length;f++){var p=u[f].split(\"-\"),g=p[0],m=p[1];g<h&&(h=g),m>d&&(d=m),l.spanning_frag_coords.push({left:g,right:m})}return l.start=h,l.end=d,l}}function Cl(e,t){if(e.length<7)return null;const i={chr:e[0],start:parseInt(e[1])-1,end:parseInt(e[2]),\"Strongest SNP-risk allele\":e[3],\"Disease/Phenotype\":e[4],\"P-value\":e[5],\"Odds ratio or beta\":e[6]};return e.length>6&&(i.PUBMEDID=`<a target = \"blank\" href = \"https://www.ncbi.nlm.nih.gov/pubmed/${e[7]}\">${e[7]}</a>`),i}function _l(e,t){const i=t.customFormat;if(e.length<i.fields.length)return;const n=i.coords||0,r=e[i.chr],s=parseInt(e[i.start])-n,o={chr:r,start:s,end:void 0!==i.end?parseInt(e[i.end]):s+1};return i.fields&&i.fields.forEach((function(t,n){n!==i.chr&&n!==i.start&&n!==i.end&&(o[t]=e[n])})),o}function xl(e,t){const i=t.columnNames;if(!i)throw Error(\"Sample names are not defined.   Missing column headers?\");const n=i.length-3,r=e[0],s=parseInt(e[1]),o=parseInt(e[2]),a=e.slice(3).map(Number);return a.length==n?{chr:r,start:s,end:o,values:a}:void console.warn(`${r}:${s}-${o} row contains ${a.length} sample columns instead of the expected ${n} columns. Skipping...`)}const kl=[\"Name\",\"transcript_id\",\"gene_name\",\"gene\",\"gene_id\",\"alias\",\"locus\",\"name\"];class Il{constructor(e){this.format=e.format,this.nameField=e.nameField,this.filterTypes=void 0===e.filterTypes?new Set([\"chromosome\"]):new Set(e.filterTypes)}combineFeatures(e,t){let i;const n=this.filterTypes;if(e=e.filter((e=>void 0===n||!n.has(e.type))),\"gff3\"===this.format){const t=this.combineFeaturesById(e);i=this.combineFeaturesByType(t)}else i=this.combineFeaturesByType(e);return this.numberExons(i,t),this.nameFeatures(i),i}combineFeaturesById(e){const t=new Map,i=[];for(let n of e)if(gl(n.type)||pl(n.type)||!n.id)i.push(n);else{let e=t.get(n.chr);e||(e=new Map,t.set(n.chr,e));let i=e.get(n.id);i?i.push(n):e.set(n.id,[n])}for(let e of t.values())for(let t of e.values())if(t.length>1){const e=t[0];e.exons=[];for(let i of t)e.start=Math.min(e.start,i.start),e.end=Math.max(e.end,i.end),e.exons.push({start:i.start,end:i.end});i.push(e)}else i.push(t[0]);return i}combineFeaturesByType(e){const t=e.filter((e=>\"gene\"===e.type||e.type.endsWith(\"_gene\"))),i=Object.create(null);for(let e of t)i[e.id]=e;const n=Object.create(null),r=[],s=new Set,o=this.filterTypes;e=e.filter((e=>void 0===o||!o.has(e.type)));for(let t of e)if(pl(t.type)){const e=t.id;if(void 0!==e){const o=new bl(t);n[e]=o,r.push(o),s.add(t);const a=i[t.parent];a&&(o.geneObject=a,s.add(a))}}for(let t of e)if(gl(t.type)){const e=l(t);if(e)for(let i of e){let o=n[i];if(!o&&\"gtf\"===this.format){const e=Object.assign({},t);e.type=\"transcript\",o=new bl(e),n[i]=o,r.push(o)}if(void 0!==o){if(a=t.type,ll.has(a))if(e.length>1){const e=new wl(t);o.addExon(e)}else o.addExon(t);else o.addPart(t);s.add(t)}}}var a;r.forEach((function(e){\"function\"==typeof e.finish&&e.finish()}));const c=e.filter((e=>!s.has(e)));for(let e of c)r.push(e);return r;function l(e){return e.parent&&\"\"!==e.parent.trim()?e.parent.trim().split(\",\"):null}}numberExons(e,t){for(let i of e)if(i.exons&&(!t||i.end<=t.end&&i.start>t.start))for(let e=0;e<i.exons.length;e++){i.exons[e].number=\"-\"===i.strand?i.exons.length-e:e+1}}nameFeatures(e){for(let t of e)if(\"function\"==typeof t.getAttributeValue)if(this.nameField)t.name=t.getAttributeValue(this.nameField);else for(let e of kl){const i=t.getAttributeValue(e);if(i){t.name=i;break}}}}const Sl={gwascatalog:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"pubMedID\",\"author\",\"pubDate\",\"journal\",\"title\",\"trait\",\"initSample\",\"replSample\",\"region\",\"genes\",\"riskAllele\",\"riskAlFreq\",\"pValue\",\"pValueDesc\",\"orOrBeta\",\"ci95\",\"platform\",\"cnv\"]},wgrna:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"thickStart\",\"thickEnd\",\"type\"]},cpgislandext:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"length\",\"cpgNum\",\"gcNum\",\"perCpg\",\"perGc\",\"obsExp\"]},clinVarMain:{fields:[\"chr1\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"thickStart\",\"thickEnd\",\"reserved\",\"blockCount\",\"blockSizes\",\"chromStarts\",\"origName\",\"clinSign\",\"reviewStatus\",\"type\",\"geneId\",\"snpId\",\"nsvId\",\"rcvAcc\",\"testedInGtr\",\"phenotypeList\",\"phenotype\",\"origin\",\"assembly\",\"cytogenetic\",\"hgvsCod\",\"hgvsProt\",\"numSubmit\",\"lastEval\",\"guidelines\",\"otherIds\"]}};class El{constructor(e){this.config=e,this.header={},e.nameField&&(this.header.nameField=e.nameField),this.skipRows=0,e.decode?(this.decode=e.decode,this.delimiter=e.delimiter||\"\\t\"):e.format&&(this.header.format=e.format.toLowerCase(),this.setDecoder(this.header.format)),this.delimiter||(this.delimiter=\"\\t\")}async parseHeader(e){let t,i,n=this.header;for(;void 0!==(i=await e.nextLine());)if(i.startsWith(\"track\")||i.startsWith(\"#track\")){let e=Nl(i);Object.assign(n,e)}else if(i.startsWith(\"browser\"));else if(i.startsWith(\"#columns\")){let e=Bl(i);Object.assign(n,e)}else if(i.startsWith(\"##gff-version 3\"))n.format=\"gff3\";else if(i.startsWith(\"#gffTags\"))n.gffTags=!0;else{if(i.startsWith(\"fixedStep\")||i.startsWith(\"variableStep\"))break;if(i.startsWith(\"#\")){const e=i.split(this.delimiter||\"\\t\");e.length>1&&(t=e)}else{this.setDecoder(n.format);const e=i.split(this.delimiter||\"\\t\");try{const i=Object.assign({columnNames:t},n);if(this.decode(e,i))break;e.length>1&&(t=e)}catch(i){e.length>1&&(t=e)}}}if(t){n.columnNames=t;for(let e=0;e<t.length;e++)\"color\"===t[e]||\"colour\"===t[e]?n.colorColumn=e:\"thickness\"===t[e]&&(n.thicknessColumn=e)}return this.header=n,n}async parseFeatures(e){const t=[],i=this.decode,n=this.header.format,r=this.delimiter||\"\\t\";let s,o=0,a=0;for(;void 0!==(s=await e.nextLine());){if(o++,o<=this.skipRows)continue;if(!s||s.startsWith(\"track\")||s.startsWith(\"#\")||s.startsWith(\"browser\"))continue;if(\"wig\"===n&&s.startsWith(\"fixedStep\")){this.header.wig=Ml(s);continue}if(\"wig\"===n&&s.startsWith(\"variableStep\")){this.header.wig=Rl(s);continue}const e=s.split(r);if(e.length<1)continue;const c=i(e,this.header);c instanceof Lc?(a++,a>0&&console.error(`Error parsing line '${s}': ${c.message}`)):c&&t.push(c)}return i===Mc&&function(e){if(0==e.length)return;const t=e[0];if(void 0===t.score&&void 0!==t.name){for(let t of e)if(!Va(t.name)&&\".\"!==t.name)return;for(let t of e)t.score=Number(t.name),delete t.name}const i=e.filter((e=>e.chr1!==e.chr2));for(let t of i){const i=Object.assign({},t);i.dup=!0,e.push(i),t.chr=t.chr1,t.start=t.start1,t.end=t.end1,i.chr=i.chr2,i.start=i.start2,i.end=i.end2}}(t),\"gtf\"!==this.config.format&&\"gff3\"!==this.config.format&&\"gff\"!==this.config.format||!1===this.config.assembleGFF?t:new Il(this.config).combineFeatures(t)}setDecoder(e){switch(e){case\"broadpeak\":case\"regionpeak\":case\"peaks\":this.decode=Xc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"narrowpeak\":this.decode=Zc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedgraph\":this.decode=Jc,this.delimiter=/\\s+/;break;case\"wig\":this.decode=el,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gff3\":case\"gff\":this.decode=vl,this.delimiter=\"\\t\";break;case\"gtf\":this.decode=yl,this.delimiter=\"\\t\";break;case\"fusionjuncspan\":this.decode=Al,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gtexgwas\":this.skipRows=1,this.decode=Cl,this.delimiter=\"\\t\";break;case\"refflat\":this.decode=Gc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"genepred\":this.decode=jc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"genepredext\":this.decode=Wc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"ensgene\":this.decode=jc,this.header.shift=1,this.delimiter=this.config.delimiter||/\\s+/;break;case\"refgene\":this.decode=Wc,this.delimiter=this.config.delimiter||/\\s+/,this.header.shift=1;break;case\"bed\":this.decode=Uc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gappedpeak\":this.decode=qc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedmethyl\":this.decode=Qc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedpe\":case\"hiccups\":this.decode=Mc,this.delimiter=this.config.delimiter||\"\\t\";break;case\"bedpe-domain\":this.decode=Rc,this.headerLine=!0,this.delimiter=this.config.delimiter||\"\\t\";break;case\"bedpe-loop\":this.decode=Mc,this.delimiter=this.config.delimiter||\"\\t\",this.header={colorColumn:7};break;case\"interact\":this.decode=Tc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"snp\":this.decode=tl,this.delimiter=\"\\t\";break;case\"rmsk\":this.decode=Vc,this.delimiter=\"\\t\";break;case\"gcnv\":this.decode=xl,this.delimiter=\"\\t\";break;case\"shoebox\":this.decode=il,this.delimiter=\"\\t\";break;default:const t=function(e){return Sl&&Sl[e]?function(e){const t=e.fields,i=[\"chr\",\"start\",\"end\"];for(let n=0;n<t.length;n++)for(let r of i)r===t[n]&&(e[r]=n);return e}(Sl[e]):void 0}(e);void 0!==t?(this.decode=_l,this.header.customFormat=t,this.delimiter=t.delimiter||\"\\t\"):(this.decode=Uc,this.delimiter=this.config.delimiter||/\\s+/)}}}function Nl(e){const t={},i=e.split(/(?:\")([^\"]+)(?:\")|([^\\s\"]+)(?=\\s+|$)/g);let n;const r=[];for(let e of i)e&&0!==e.trim().length&&(e.endsWith(\"=\")?n=e:n?(r.push(n+e),n=void 0):r.push(e));for(let e of r){if(!e)return;var s=e.split(\"=\",2);if(2===s.length){const e=s[0].trim(),i=s[1].trim();if(t.hasOwnProperty(e)){let n=t[e];Array.isArray(n)?n.push(i):t[e]=[n,i]}else t[e]=i}}return\"interact\"==t.type?t.format=\"interact\":\"gcnv\"===t.type&&(t.format=\"gcnv\"),t}function Bl(e){let t={},i=e.split(/\\s+/);if(2===i.length){i[1].split(\";\").forEach((function(e){let i=e.split(\"=\");\"color\"===i[0]?t.colorColumn=Number.parseInt(i[1])-1:\"thickness\"===i[0]&&(t.thicknessColumn=Number.parseInt(i[1])-1)}))}return t}function Ml(e){const t=e.split(/\\s+/);return{format:\"fixedStep\",chrom:t[1].split(\"=\")[1],start:parseInt(t[2].split(\"=\")[1],10)-1,step:parseInt(t[3].split(\"=\")[1],10),span:t.length>4?parseInt(t[4].split(\"=\")[1],10):1,index:0}}function Rl(e){const t=e.split(/\\s+/);return{format:\"variableStep\",chrom:t[1].split(\"=\")[1],span:t.length>2?parseInt(t[2].split(\"=\")[1],10):1}}function Dl(t,i){const n=e({class:\"igv-menu-popup-check-container\"}),r=e();n.appendChild(r);const s=l(\"check\",!0===i?\"#444\":\"transparent\");r.appendChild(s);const o=e();return o.innerText=t,n.appendChild(o),n}function Tl(e,t){t=t||Number.MAX_SAFE_INTEGER;const i=[];e.sort((function(e,t){return e.start-t.start})),i.push(-1e3);for(let n of e){let e=0;const r=Math.min(i.length,t);for(e=0;e<r;e++)if(n.start>=i[e]){n.row=e,i[e]=n.end;break}n.row=e,i[e]=n.end}}async function Ll(e,t,i){const n=e=>{const i=Object.assign({},e);return i.chr=\"all\",i.start=t.getGenomeCoordinate(e.chr,e.start),i.end=t.getGenomeCoordinate(e.chr,e.end),i._f=e,i.exons&&delete i.exons,i},r=new Set(t.wgChromosomeNames),s=[];let o=0;for(let a of t.wgChromosomeNames){if(Array.isArray(e)){const i={};for(let n of e){const e=t.getChromosomeName(n.chr);i.hasOwnProperty(e)||(i[e]=[]),i[e].push(n)}e=i}const c=e[a];if(c){const e=i||1e4;for(let i of c){let a=t.getChromosomeName(i.chr);if(r.has(a))if(s.length<e)s.push(n(i));else{const t=e/(o+1);if(Math.random()<t){s[Math.floor(Math.random()*(e-1))]=n(i)}}o++}}}return s.sort((function(e,t){return e.start-t.start})),s}function zl(e,t){if(t=t||1e3,null==e||0===e.length)return;const i={},n=[];for(let t of e){const e=t.chr;let r=i[e];r||(r=[],i[e]=r,n.push(e)),r.push(t)}for(let e of n)Tl(i[e],t)}class Hl{static defaults={height:50,autoHeight:!1,visibilityWindow:void 0,color:void 0,altColor:void 0,supportHiDPI:!0,selected:!1};constructor(e,t){this.browser=t,this.init(e)}init(e){this.config=e,e.displayMode&&(e.displayMode=e.displayMode.toUpperCase());const t=Object.assign({},Hl.defaults);if(this.constructor.defaults)for(let e of Object.keys(this.constructor.defaults))t[e]=this.constructor.defaults[e];for(let n of Object.keys(t))this[n]=e.hasOwnProperty(n)?e[n]:t[n],\"color\"!==n&&\"altColor\"!==n||!this[n]||(this[n]=Mt(i=this[n])&&i.indexOf(\",\")>0&&!i.startsWith(\"rgb(\")&&!i.startsWith(\"rgba(\")?`rgb(${i})`:i);var i;e.name||e.label?this.name=e.name||e.label:Ht(e.url)?this.name=e.url.name:Mt(e.url)&&!e.url.startsWith(\"data:\")&&(this.name=zt(e.url)),this.url=e.url,this.config.type&&(this.type=this.config.type),this.id=void 0===this.config.id?this.name:this.config.id,this.order=e.order,this.autoscaleGroup=e.autoscaleGroup,this.removable=void 0===e.removable||e.removable,this.minHeight=e.minHeight||Math.min(25,this.height),this.maxHeight=e.maxHeight||Math.max(1e3,this.height),e.onclick&&(this.onclick=e.onclick,e.onclick=void 0),e.description&&(\"function\"==typeof e.description?this.description=e.description:this.description=()=>e.description),e.hoverTextFields?this.hoverText=Pl.bind(this):\"function\"==typeof this.config.hoverText&&(this.hoverText=this.config.hoverText)}get name(){return this._name}set name(e){this._name=e,this.trackView&&this.trackView.setTrackLabelName(e)}clearCachedFeatures(){this.trackView&&this.trackView.clearCachedFeatures()}updateViews(){this.trackView&&this.trackView.updateViews()}repaintViews(){this.trackView&&this.trackView.repaintViews()}getState(){const e={},t=Object.keys(this.config).filter((e=>{return!(void 0===(t=this.config[e])||\"function\"==typeof t||t instanceof Promise);var t}));for(const i of t)i.startsWith(\"_\")||(e[i]=this.config[i]);for(let t of Object.keys(e)){if(t.startsWith(\"_\"))continue;const i=this[t];void 0===i||!Oa(i)&&\"boolean\"!=typeof i&&\"metadata\"!==t||(e[t]=i)}const i=Object.assign({},Hl.defaults);if(this.constructor.defaults)for(let e of Object.keys(this.constructor.defaults))i[e]=this.constructor.defaults[e];for(let t of Object.keys(i))void 0!==this[t]&&i[t]!==this[t]&&(e[t]=this[t]);return!this.autoscale&&this.dataRange&&(e.min=this.dataRange.min,e.max=this.dataRange.max),this.autoscaleGroup&&(e.autoscaleGroup=this.autoscaleGroup),e}get supportsWholeGenome(){return!0===this.config.supportsWholeGenome}hasSamples(){return!1}getGenomeId(){return this.browser.genome?this.browser.genome.id:void 0}setTrackProperties(e){if(this.disposed)return;const t={};let i;for(let n of Object.keys(e))switch(n.toLowerCase()){case\"usescore\":t.useScore=1===e[n]||\"1\"===e[n]||\"on\"===e[n]||!0===e[n];break;case\"visibility\":switch(e[n]){case\"2\":case\"3\":case\"pack\":case\"full\":t.displayMode=\"EXPANDED\";break;case\"4\":case\"squish\":t.displayMode=\"SQUISHED\";break;case\"1\":case\"dense\":t.displayMode=\"COLLAPSED\"}break;case\"color\":case\"altcolor\":t[n]=e[n].startsWith(\"rgb(\")?e[n]:\"rgb(\"+e[n]+\")\";break;case\"featurevisiblitywindow\":case\"visibilitywindow\":t.visibilityWindow=Number.parseInt(e[n]);break;case\"maxheightpixels\":i=e[n].split(\":\"),3===i.length&&(t.minHeight=Number.parseInt(i[2]),t.height=Number.parseInt(i[1]),t.maxHeight=Number.parseInt(i[0]));break;case\"viewlimits\":if(!this.config.autoscale){i=e[n].split(\":\");let r,s=0;1==i.length?r=Number(i[0]):2==i.length&&(s=Number(i[0]),r=Number(i[1])),Number.isNaN(r)||Number.isNaN(s)?console.warn(`Unexpected viewLimits value in track line: ${e.viewLimits}`):(t.autoscale=!1,t.dataRange={min:s,max:r},this.viewLimitMin=s,this.viewLimitMax=r)}case\"name\":t[n]=e[n];break;case\"url\":t.infoURL=e[n];break;case\"type\":const r=e[n];Ol.has(r)?t[n]=Ol.get(r):t[n]=r;break;case\"graphtype\":t.graphType=e[n];break;default:t[n]=e[n]}for(let e of Object.keys(t))if(!this.config.hasOwnProperty(e)||\"name\"===e&&this.config._derivedName){let i=t[e];if(\"true\"===i&&(i=!0),\"false\"===i&&(i=!1),this[e]=i,\"height\"===e&&this.trackView)try{const e=Number.parseInt(i);this.trackView.setTrackHeight(e)}catch(e){console.error(e)}}}clickedFeatures(e){const t=e.viewport.cachedFeatures;if(!t||!Array.isArray(t)||0===t.length)return[];const i=e.genomicLocation,n=e.referenceFrame.bpPerPixel>.2?3*e.referenceFrame.bpPerPixel:.2;return to(t,i-n,i+n)}extractPopupData(e,t){const i=new Set([\"row\",\"color\",\"chr\",\"start\",\"end\",\"cdStart\",\"cdEnd\",\"strand\",\"alpha\"]),n=[];let r,s;for(let t in e)if(e.hasOwnProperty(t)&&!i.has(t)&&Oa(e[t])){let i=e[t];n.push({name:Lt(t),value:i}),\"alleles\"===t?r=e[t]:\"alleleFreqs\"===t&&(s=e[t])}if(r&&s){r.endsWith(\",\")&&(r=r.substr(0,r.length-1)),s.endsWith(\",\")&&(s=s.substr(0,s.length-1));let i=r.split(\",\"),o=s.split(\",\");if(o.length>1){let r=[];for(let e=0;e<o.length;e++)r.push({a:i[e],af:Number(o[e])});r.sort((function(e,t){return e.af-t.af}));let s=r[r.length-1].a;if(1===s.length)for(let i=r.length-2;i>=0;i--){let o=r[i].a;if(1===o.length){t||(t=this.getGenomeId());const i=Hl.getCravatLink(e.chr,e.start+1,s,o,t);console.log(i),i&&(n.push(\"<hr/>\"),n.push({html:i}),n.push(\"<hr/>\"))}}}}if(e.attributes)for(let t of Object.keys(e.attributes))n.push({name:t,value:e.attributes[t]});let o=`${e.chr}:${Rt(e.start+1)}-${Rt(e.end)}`;return e.strand&&(o+=` (${e.strand})`),n.push({name:\"Location\",value:o}),n}description(){const e=(e,t)=>`<div class=\"igv-track-label-popup-shim\"><b>${e}: </b>${t}</div>`;let t='<div class=\"igv-track-label-popup\">';if(this.url?Ht(this.url)?t+=e(\"Filename\",this.url.name):t+=e(\"URL\",this.url):t=this.name,this.config){if(this.config.metadata)for(let i of Object.keys(this.config.metadata)){t+=e(i,this.config.metadata[i])}for(let i of Object.keys(this.config)){if(i.startsWith(\"_\"))continue;let n=i.substr(0,1);if(n!==n.toLowerCase()){const n=this.config[i];n&&Oa(n)&&(t+=e(i,n))}}}return t+=\"</div>\",t}getColorForFeature(e){return\"function\"==typeof this.color?this.color(feature):this.color}numericDataMenuItems(){const e=[];e.push(\"<hr/>\");let t=Bt(\"<div>\");if(t.text(\"Set data range\"),e.push({object:t,dialog:function(){this.trackView.track.selected?this.browser.dataRangeDialog.configure(this.trackView.browser.getSelectedTrackViews()):this.browser.dataRangeDialog.configure(this.trackView),this.browser.dataRangeDialog.present(Bt(this.browser.columnContainer))}}),void 0!==this.logScale){function i(){this.logScale=!this.logScale,this.trackView.repaintViews()}t=Bt(Dl(\"Log scale\",this.logScale)),e.push({object:t,click:i})}return t=Bt(Dl(\"Autoscale\",this.autoscale)),e.push({object:t,click:function(){this.autoscaleGroup=void 0,this.autoscale=!this.autoscale,this.browser.updateViews()}}),e}setDataRange({min:e,max:t}){this.dataRange={min:e,max:t},this.autoscale=!1,this.autoscaleGroup=void 0,this.trackView.repaintViews()}async nextFeatureAfter(e,t,i){let n=this.trackView.viewports[0].cachedFeatures;if(n&&Array.isArray(n)&&n.length>0){if(this.browser.genome.getChromosomeName(n[0].chr)===e){const e=function(e,t,i=!0){const n=e=>(e.start+e.end)/2,r=i?(e,t)=>e.start-t.start+e.end-t.end:(e,t)=>t.start-e.start+t.end-e.end,s=Array.from(e);s.sort(r);let o=0,a=s.length;for(;o<a;){let e=Math.floor((o+a)/2);i?n(s[e])<=t?o=e+1:a=e:n(s[e])>=t?o=e+1:a=e}return s[o]}(n,t,i);if(e)return e}}if(\"function\"==typeof this.featureSource.nextFeature)return this.featureSource.nextFeature(e,t,i,this.visibilityWindow)}dispose(){this.disposed=!0;for(let e of Object.keys(this))this[e]=void 0}static getCravatLink(e,t,i,n,r){if(\"hg38\"===r||\"GRCh38\"===r){return`<a target=\"_blank\" href=\"https://run.opencravat.org/result/nocache/variant.html?chrom=${e.startsWith(\"chr\")?e:\"chr\"+e}&pos=${t}&ref_base=${i}&alt_base=${n}\"><b>Cravat ${i}->${n}</b></a>`}}static localFileInspection(e){const t=Object.assign({},e),i={url:\"file\",indexURL:\"indexFile\"};for(const e of[\"url\",\"indexURL\"])t[e]&&t[e]instanceof File&&(t[i[e]]=t[e].name,delete t[e]);return t}}function Pl(e){if(!this.hoverTextFields)return;const t=this.clickedFeatures(e);if(t&&t.length>0){let e=\"\";for(let i=0;i<t.length;i++){if(10===i){e+=\"; ...\";break}if(!t[i])continue;const n=t[i]._f||t[i];e.length>0&&(e+=\"\\n\"),e=\"\";for(let t of this.hoverTextFields)e.length>0&&(e+=\"\\n\"),n.hasOwnProperty(t)?e+=n[t]:\"function\"==typeof n.getAttribute&&(e+=n.getAttribute(t))}return e}}const Ol=new Map([[\"wiggle_0\",\"wig\"],[\"bed\",\"bed\"],[\"bigBed\",\"bigBed\"],[\"bigWig\",\"bigWig\"]]);class Ul{constructor(e){switch(this.type=e||\"seg\",this.type){case\"mut\":this.sampleColumn=3,this.chrColumn=0,this.startColumn=1,this.endColumn=2,this.dataColumn=4;break;case\"maf\":this.sampleColumn=15,this.chrColumn=4,this.startColumn=5,this.endColumn=6,this.dataColumn=8;break;default:this.sampleColumn=0,this.chrColumn=1,this.startColumn=2,this.endColumn=3}}async parseHeader(e){let t;for(;void 0!==(t=await e.nextLine());)if(!t.startsWith(\"#\")){const e=t.split(\"\\t\");this.header={headings:e};break}return this.header}async parseFeatures(e){const t=[];let i;this.header||(this.header=await this.parseHeader(e)),\"seg\"===this.type&&(this.dataColumn=this.header.headings.length-1),this.header.headings.length>5&&(i=this.extractExtraColumns(this.header.headings));const n=this.header.headings[this.dataColumn];let r;for(;void 0!==(r=await e.nextLine());){const e=r.split(\"\\t\"),s=\"seg\"===this.type?Number(e[this.dataColumn]):e[this.dataColumn];if(e.length>this.dataColumn){const r=new ql({sample:e[this.sampleColumn],chr:e[this.chrColumn],start:parseInt(e[this.startColumn])-1,end:parseInt(e[this.endColumn]),value:s,valueColumnName:n});if(i){const t=this.extractExtraColumns(e);r.setAttributes({names:i,values:t})}t.push(r)}}return t}extractExtraColumns(e){const t=[];for(let i=0;i<e.length;i++)i!==this.chrColumn&&i!==this.startColumn&&i!==this.endColumn&&i!==this.sampleColumn&&t.push(e[i]);return t}}class ql{constructor({sample:e,chr:t,start:i,end:n,value:r,valueColumnName:s}){this.sample=e,this.chr=t,this.start=i,this.end=n,this.value=r,this.valueColumnName=s}setAttributes({names:e,values:t}){this.attributeNames=e,this.attributeValues=t}getAttribute(e){if(this.attributeNames){const t=this.attributeNames.indexOf(e);if(t>=0)return this.attributeValues[t]}}popupData(e,t){const i=new Set([\"chr\",\"start\",\"end\",\"sample\",\"value\",\"row\",\"color\",\"sampleKey\",\"uniqueSampleKey\",\"sampleId\",\"chromosome\",\"uniquePatientKey\"]),n=this.chr+\":\"+Rt(this.start+1)+\"-\"+Rt(this.end),r=[{name:\"Sample\",value:this.sample},{name:\"Location\",value:n},{name:this.valueColumnName?Lt(this.valueColumnName):\"Value\",value:this.value}];if(\"mut\"===e&&\"hg38\"===t){const e=this.extractCravatLink(t);e&&(r.push(\"<hr/>\"),r.push({html:e}),r.push(\"<hr/>\"))}if(this.attributeNames&&this.attributeNames.length>0)for(let e=0;e<this.attributeNames.length;e++)!i.has(this.attributeNames[e])&this.valueColumnName!==this.attributeNames[e]&&r.push({name:Lt(this.attributeNames[e]),value:this.attributeValues[e]});return r}extractCravatLink(e){let t,i;if(this.attributeNames&&this.attributeNames.length>0)for(let n=0;n<this.attributeNames.length;n++)if(t||\"Reference_Allele\"!==this.attributeNames[n]||(t=this.attributeValues[n]),!i&&this.attributeNames[n].startsWith(\"Tumor_Seq_Allele\")&&this.attributeValues[n]!==t&&(i=this.attributeValues[n]),t&&i)return Hl.getCravatLink(this.chr,this.start+1,t,i,e)}}const Ql=new Map([[\"REF\",\"referenceBases\"],[\"ALT\",\"alternateBases\"],[\"QUAL\",\"quality\"],[\"FILTER\",\"filter\"]]);class Vl{constructor(e){this.chr=e[0],this.pos=parseInt(e[1]),this.names=e[2],this.referenceBases=e[3],this.alternateBases=e[4],this.quality=e[5],this.filter=e[6],this.info={};const t=e[7];if(t&&\".\"!==t)for(let e of t.split(\";\")){var i=e.split(\"=\");this.info[i[0]]=i[1]}this.init()}getAttributeValue(e){return Ql.has(e)&&(e=Ql.get(e)),this.hasOwnProperty(e)?this[e]:this.info[e]}init(){const e=this.referenceBases,t=this.alternateBases;if(this.info&&(this.info.VT?this.type=this.info.VT:this.info.SVTYPE?this.type=\"SV\":this.info.PERIOD&&(this.type=\"STR\")),void 0===this.type&&(this.type=function(e,t){const i=e.length;if(void 0===t)return\"UNKNOWN\";if(0===t.trim().length||\"<NON_REF>\"===t||\"<*>\"===t||\".\"===t)return\"NONVARIANT\";{const e=t.split(\",\").map((function(e){return 1===i&&1===e.length?\"SNP\":\"<NON_REF>\"===e?\"NONVARIANT\":e.length>i&&$l(e)?\"INSERTION\":e.length<i&&$l(e)?\"DELETION\":\"OTHER\"}));let n=e[0];for(let t of e)if(t!==n)return\"MIXED\";return n}}(e,t)),this.info.END)this.start=this.pos-1,this.info.CHR2&&this.info.CHR2!==this.chr?this.end=this.start+1:this.end=Number.parseInt(this.info.END);else if(\"NONVARIANT\"===this.type)this.start=this.pos-1,this.end=this.start+e.length;else{const i=t.split(\",\").filter((e=>e.length>0));this.alleles=[],this.start=void 0,this.end=void 0;for(let t of i)if(this.alleles.push(t),\"SV\"!==this.type&&$l(t)){let i=t.length,n=e.length;const r=Math.min(i,n);let s=0;for(;s<r&&e.charCodeAt(s)===t.charCodeAt(s);)s++,i--,n--;for(;i>0&&n>0;){const r=s+i-1,o=s+n-1;if(t.charCodeAt(r)!==e.charCodeAt(o))break;i--,n--}for(;i>0&&n>0;){const r=s,o=s;if(t.charCodeAt(r)!==e.charCodeAt(o))break;s++,i--,n--}const o=this.pos+s-1,a=o+n;this.start=void 0===this.start?o:Math.min(this.start,o),this.end=void 0===this.end?a:Math.max(this.end,a)}void 0===this.start&&(this.start=this.pos-1,this.end=this.pos),this.start===this.end&&(this.start-=.5,this.end+=.5)}}popupData(e,t){const i=`${Rt(this.pos)}`,n=this.start===this.end?`${Rt(this.start)} | ${Rt(this.start+1)}`:`${Rt(this.start+1)}-${Rt(this.end)}`,r=[{name:\"Chr\",value:this.chr},{name:\"Pos\",value:i},{name:\"Loc\",value:n},{name:\"ID\",value:this.names?this.names:\"\"},{name:\"Ref\",value:this.referenceBases},{name:\"Alt\",value:this.alternateBases.replace(\"<\",\"&lt;\")},{name:\"Qual\",value:this.quality},{name:\"Filter\",value:this.filter}];if(this.type&&r.push({name:\"Type\",value:this.type}),\"SNP\"===this.type){let e=this.referenceBases;if(1===e.length){let i=this.alternateBases.split(\",\");for(let n of i)if(1===n.length){let i=Hl.getCravatLink(this.chr,this.pos,e,n,t);i&&(r.push(\"<hr/>\"),r.push({html:i}))}}}const s=Object.keys(this.info);if(this.info&&s.length>0){r.push({html:'<hr style=\"border-top: dotted 1px;border-color: #c9c3ba\" />'});for(let e of s)r.push({name:e,value:Kl(decodeURIComponent(this.info[e]))})}return r}getInfo(e){return this.info?this.info[e]:void 0}isRefBlock(){return\"NONVARIANT\"===this.type}isFiltered(){return!(\".\"===this.filter||\"PASS\"===this.filter)}alleleFreq(){return this.info?this.info.AF:void 0}}class jl{constructor(e){this.mate=e,this.chr=e.info.CHR2,this.pos=Number.parseInt(e.info.END),this.start=this.pos-1,this.end=this.pos}get info(){return this.mate.info}get names(){return this.mate.names}get referenceBases(){return this.mate.referenceBases}get alternateBases(){return this.mate.alternateBases}get quality(){return this.mate.quality}get filter(){return this.mate.filter}get calls(){return this.mate.calls}getAttributeValue(e){return this.mate.getAttributeValue(e)}getInfo(e){this.mate.getInfo(e)}isFiltered(){return this.mate.isFiltered()}alleleFreq(){return this.mate.alleleFreq()}popupData(e,t){const i=[];return i.push(\"SV Breakpoint\"),i.push({name:\"Chr\",value:this.chr}),i.push({name:\"Pos\",value:`${Rt(this.pos)}`}),i.push({html:'<hr style=\"border-top: dotted 1px;border-color: #c9c3ba\" />'}),i.push(\"SV\"),i.push(...this.mate.popupData(e,t)),i}}class Wl{constructor({formatFields:e,sample:t,token:i}){this.info={},this.sample=t;const n=i.split(\":\");for(let t=0;t<n.length;t++){const i=n[t];if(t==e.genotypeIndex){this.genotype=[];for(let e of i.split(/[\\|\\/]/))this.genotype.push(\".\"===e?e:parseInt(e))}else this.info[e.fields[t]]=i}}get zygosity(){if(!this._zygosity)if(this.genotype){let e=!0,t=!0,i=!1;for(let n of this.genotype){if(\".\"===n){i=!0;break}0!==n&&(t=!1),0===n&&(e=!1)}this._zygosity=i?\"nocall\":t?\"homref\":e?\"homvar\":\"hetvar\"}else this._zygosity=\"unknown\";return this._zygosity}zygosityScore(){switch(this.zygosity){case\"homvar\":return 4;case\"hetvar\":return 3;case\"homref\":return 2;case\"nocall\":return 1;default:return 0}}#l(){switch(this.zygosity){case\"homref\":return\"Homozygous reference\";case\"homvar\":return\"Homozygous variant\";case\"hetvar\":return\"Heterozygous\";default:return\"\"}}popupData(e,t){const i=[];void 0!==this.sample&&i.push({name:\"Sample\",value:this.sample}),this.genotypeString&&i.push({name:\"Genotype\",value:this.genotypeString});const n=this.#l();n&&i.push({name:\"Zygosity\",value:n});var r=Object.keys(this.info);r.length&&i.push(\"<hr/>\");for(let e of r)i.push({name:e,value:decodeURIComponent(this.info[e])});return i}}const Gl=new Set([\"A\",\"C\",\"T\",\"G\"].map((e=>e.charCodeAt(0))));function $l(e){for(let t=0;t<e.length;t++)if(!Gl.has(e.charCodeAt(t)))return!1;return!0}function Kl(e,t){return void 0===t&&(t=\",\"),Array.isArray(e)?e.join(t):e}class Yl{construtor(){}async parseHeader(e,t){const i={};i.chrAliasTable=new Map;let n=await e.nextLine();if(!n.startsWith(\"##fileformat\"))throw new Error(\"Invalid VCF file: missing fileformat line\");for(i.version=n.substr(13);void 0!==(n=await e.nextLine())&&n.startsWith(\"#\");){let e;const s={};if(n.startsWith(\"##\")){if(n.startsWith(\"##INFO\")||n.startsWith(\"##FILTER\")||n.startsWith(\"##FORMAT\")){const t=n.indexOf(\"<\"),o=n.lastIndexOf(\">\");if(!(t>2&&o>0)){console.log(\"Malformed VCF header line: \"+n);continue}const a=n.substring(2,t-1);i[a]||(i[a]={});const c=Tt(n.substring(t+1,o-1),\",\");for(let t of c){var r=t.split(\"=\");r.length>1&&(\"ID\"===r[0]?e=r[1]:s[r[0]]=r[1])}e&&(i[a][e]=s)}else if(n.startsWith(\"##contig\")&&t){const e=n.indexOf(\"<ID=\");let r=n.indexOf(\",\",e);-1==r&&(r=n.indexOf(\">\",e));const s=n.substring(e+4,r),o=t.getChromosomeName(s);i.chrAliasTable.set(o,s)}}else if(n.startsWith(\"#CHROM\")){const e=n.split(\"\\t\");if(e.length>8){i.sampleNameMap=new Map;for(let t=9;t<e.length;t++)i.sampleNameMap.set(e[t],t-9)}}}return this.header=i,i}async parseFeatures(e){const t=[],i=this.header.sampleNameMap?Array.from(this.header.sampleNameMap.keys()):void 0,n=8+(i?i.length+1:0);let r;for(;void 0!==(r=await e.nextLine());)if(r&&!r.startsWith(\"#\")){const e=r.split(\"\\t\");if(e.length===n){const n=new Vl(e);if(n.header=this.header,t.push(n),e.length>9){const r=Xl(e[8].split(\":\"));n.calls=[];for(let t=9;t<e.length;t++){const s=i[t-9],o=e[t],a=new Wl({formatFields:r,sample:s,token:o});n.calls.push(a)}n.info&&n.info.CHR2&&n.info.END&&t.push(new jl(n))}}}return t}}function Xl(e){const t={genotypeIndex:-1,fields:e};for(let i=0;i<e.length;i++)\"GT\"===e[i]&&(t.genotypeIndex=i);return t}const Zl=Math.log10(Number.MIN_VALUE);class Jl{constructor(e){if(this.config=e,e.columns){if(void 0===e.columns.chromosome||void 0===e.columns.position||void 0===e.columns.value)throw Error(\"columns property must define chrCol, posCol, and valueCol\");this.posCol=e.columns.position-1,this.chrCol=e.columns.chromosome-1,this.valueCol=e.columns.value-1}else this.posCol=2,this.chrCol=1,this.valueCol=3}async parseHeader(e){const t=await e.nextLine();return this.parseHeaderLine(t)}parseHeaderLine(e){if(this.columns=e.split(/\\t/),!this.config.columns)for(let e=0;e<this.columns.length;e++){switch(this.columns[e].toLowerCase()){case\"chr\":case\"chromosome\":case\"chr_id\":this.chrCol=e;break;case\"bp\":case\"pos\":case\"position\":case\"chr_pos\":this.posCol=e;break;case\"p\":case\"pval\":case\"pvalue\":case\"p-value\":case\"p.value\":this.valueCol=e}}return this.columns}async parseFeatures(e){const t=[],i=e.nextLine();let n;this.columns||this.parseHeaderLine(i);const r=e=>{const t=e.indexOf(\"E\");if(t>0){if(Number.parseInt(e.substring(t+1))<Zl)return Number.MIN_VALUE}return Number(e)};for(;void 0!==(n=e.nextLine());){const e=n.split(/\\t/);if(e.length===this.columns.length){const i=e[this.posCol];if(i.indexOf(\";\")>0||0==i.length||i.indexOf(\"x\")>0)continue;const s=e[this.chrCol],o=r(e[this.valueCol]),a=parseInt(i)-1,c=a+1;t.push(new eh({chr:s,start:a,end:c,value:o,line:n,columns:this.columns}))}}return t}static isGWAS(e){const t=e.split(\"\\t\");if(t.length<5)return!1;const i=[[\"chr\",\"chromosome\",\"chr_id\",\"chrom\"],[\"bp\",\"pos\",\"position\",\"chr_pos\",\"chromEnd\"],[\"p\",\"pval\",\"p-value\",\"p.value\"]];for(let e of i)if(!t.some((t=>e.includes(t.toLowerCase()))))return!1;return!0}}class eh{constructor({chr:e,start:t,end:i,value:n,line:r,columns:s}){this.chr=e,this.start=t,this.end=i,this.value=n,this.line=r,this.columns=s}popupData(){const e=this.line.split(/\\t/);return this.columns.map((function(t,i){return{name:t,value:e[i]}}))}getAttribute(e){const t=this.line.split(/\\t/);for(let i=0;i<this.columns.length;i++)if(this.columns[i]===e)return t[i]}}var th=new RegExp(\"([^:]*)\\\\(([^)]*)\\\\)\"),ih=new RegExp(\"([^:]*):([^(]*)\\\\(([^)]*)\\\\)\");class nh{constructor(e){const t=e?e.decode:void 0;this.nameField=e?e.nameField:void 0,this.skipRows=0,this.decode=t||lh,this.delimiter=\"\\t\"}async parseHeader(e){let t,i;for(;(t=await e.nextLine())&&(t.startsWith(\"track\")||t.startsWith(\"#\")||t.startsWith(\"browser\"));)if(t.startsWith(\"track\")||t.startsWith(\"#track\")){let e=oh(t);i?Object.assign(i,e):i=e}else if(t.startsWith(\"#columns\")){let e=ah(t);i?Object.assign(i,e):i=e}else t.startsWith(\"##gff-version 3\")&&(this.format=\"gff3\",i||(i={}),i.format=\"gff3\");return this.header=i,i}async parseFeatures(e){const t=[],i=this.decode,n=this.delimiter||\"\\t\";let r,s=0;for(;void 0!==(r=e.nextLine());){if(s++,s<=this.skipRows||r.startsWith(\"track\")||r.startsWith(\"#\")||r.startsWith(\"browser\"))continue;let e=o();if(e.length<1)continue;if(!this.aed){this.aed=sh(e);continue}const n=i.call(this,e,undefined);n&&t.push(n)}return t;function o(){for(var e,t,i=[],s=\"\",o=!1;r||\"\"===r;){for(e=0;e<r.length;e++)(t=r.charAt(e))===n?o?s+=t:(i.push(s),s=\"\"):'\"'===t?e+1<r.length&&'\"'===r.charAt(e+1)?(o&&(s+='\"'),e++):o=!o:s+=t;if(!o)break;s+=\"\\n\",r=nextLine()}return i.push(s),i}}}function rh(e){var t=ih.exec(e);if(t)return{namespace:t[1],name:t[2],type:t[3]};if(t=th.exec(e))return{namespace:\"?\",name:t[1],type:t[2]};throw new Error(\"Error parsing the header row of AED file - column not in ns:name(ns:type) format\")}function sh(e){var t,i,n;for(t={columns:[],metadata:{}},i=0;i<e.length;i++)n=rh(e[i]),t.columns.push(n);return t}function oh(e){const t={},i=e.split(/(?:\")([^\"]+)(?:\")|([^\\s\"]+)(?=\\s+|$)/g);let n;const r=[];for(let e of i)e&&0!==e.trim().length&&(e.endsWith(\"=\")>0?n=e:n?(r.push(n+e),n=void 0):r.push(e));for(let e of r){if(!e)return;var s=e.split(\"=\",2);if(2===s.length){const e=s[0].trim(),i=s[1].trim();t[e]=i}}return t}function ah(e){let t={},i=e.split(/\\s+/);if(2===i.length){i[1].split(\";\").forEach((function(e){let i=e.split(\"=\");\"color\"===i[0]?t.colorColumn=Number.parseInt(i[1])-1:\"thickness\"===i[0]&&(t.thicknessColumn=Number.parseInt(i[1])-1)}))}return t}function ch(e,t){var i,n,r=e.columns;this.aed=e,this.allColumns=t,this.chr=null,this.start=null,this.end=null,this.score=1e3,this.strand=\".\",this.cdStart=null,this.cdEnd=null,this.name=null,this.color=null;for(let e=0;e<t.length;e++)if(i=t[e]){\"aed:Integer\"===(n=r[e]).type&&(i=parseInt(i));var s=[];if(n.namespace.length>0)for(let e=0;e<n.namespace.length;e++)s.push(n.namespace.charCodeAt(e));\"bio\"===n.namespace.trim()?\"sequence\"===n.name?this.chr=i:\"start\"===n.name?this.start=i:\"end\"===n.name?this.end=i:\"cdsMin\"===n.name?this.cdStart=i:\"cdsMax\"===n.name?this.cdEnd=i:\"strand\"===n.name&&(this.strand=i):\"aed\"===n.namespace?\"name\"===n.name&&(this.name=i):\"style\"===n.namespace&&\"color\"===n.name&&(this.color=_s.createColorString(i))}}function lh(e,t){var i,n,r,s,o,a,c=0,l=this.aed.columns;if(e.length===l.length){for(a=0;a<e.length;a++)s=l[a],\"\"!==(r=e[a])&&c++,\"name\"===s.name&&\"aed\"===s.namespace?i=r:\"value\"===s.name&&\"aed\"===s.namespace&&(n=r);if(2===c&&i&&n)return o=rh(i),this.aed.metadata[o.namespace]||(this.aed.metadata[o.namespace]={}),void(this.aed.metadata[o.namespace][o.name]||(this.aed.metadata[o.namespace][o.name]={type:o.type,value:n}));var h=new ch(this.aed,e);if(h.chr&&(h.start||0===h.start)&&h.end)return h;console.log(\"Cannot parse feature: \"+e.join(\",\"))}else console.log(\"Corrupted AED file row: \"+e.join(\",\"))}function hh(e,t){if(0===e.length)return e;if(e.sort((function(e,t){const i=e.minv.block-t.minv.block;return 0!==i?i:e.minv.offset-t.minv.offset})),e.length<=1)return e;t&&(e=e.filter((e=>e.maxv.isGreaterThan(t))));const i=[];let n;for(let t of e)n&&dh(n,t)?t.maxv.isGreaterThan(n.maxv)&&(n.maxv=t.maxv):(i.push(t),n=t);return i}function dh(e,t){const i=t.minv.block-e.maxv.block;return t.maxv.block-e.minv.block<5e6&&i<65e3}ch.prototype.popupData=function(){for(var e=[],t=this.aed,i=0;i<this.allColumns.length;i++){var n=this.allColumns[i],r=t.columns[i].name;\"sequence\"!==r&&\"color\"!==r&&n&&e.push({name:r,value:n})}return e};class uh{constructor(){this.tabix=!0}parse(e){const t=new yc(new DataView(e)),i=t.getInt();if(21582659!==i)throw 38359875===i?Error(\"CSI version 2 is not supported.  Please enter an issue at https://github.com/igvteam/igv.js\"):Error(\"Not a CSI index\");this.indices=[],this.blockMin=Number.MAX_SAFE_INTEGER,this.lastBlockPosition=[],this.sequenceIndexMap={},this.minShift=t.getInt(),this.depth=t.getInt();const n=[];let r=0;if(t.getInt()>=28){t.getInt(),t.getInt(),t.getInt(),t.getInt(),t.getInt(),t.getInt();const e=t.getInt(),i=t.position+e;let r=0;for(;t.position<i;){let e=t.getString();this.sequenceIndexMap[e]=r,n[r]=e,r++}}const s=this.bin_limit()+1,o=t.getInt();for(let e=0;e<o;e++){const i=[],n=[],o=t.getInt();for(let e=0;e<o;e++){const e=t.getInt();if(n[e]=t.getVPointer(),e>s)t.getInt(),t.getVPointer(),t.getVPointer(),t.getLong(),t.getLong();else{i[e]=[];const n=t.getInt();for(let s=0;s<n;s++){const n=t.getVPointer(),s=t.getVPointer();n&&s&&(n.block<this.blockMin&&(this.blockMin=n.block),s.block>r&&(r=s.block),i[e].push([n,s]))}}}o>0&&(this.indices[e]={binIndex:i,loffset:n})}this.lastBlockPosition=r}get sequenceNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(e,t,i){const n=this.indices[e];if(n){const e=this.reg2bins(t,i);if(0==e.length)return[];const r=[];for(let t of e)for(let e=t[0];e<=t[1];e++)if(n.binIndex[e]){const t=n.binIndex[e];for(let i of t){const t=i[0],n=i[1];r.push({minv:t,maxv:n,bin:e})}}let s=e[this.depth][0];do{if(n.binIndex[s])break;s>1+(this.getParentBin(s)<<3)?s--:s=this.getParentBin(s)}while(0!=s);return hh(r,n.loffset[s])}return[]}getParentBin(e){return 0==e?0:e-1>>3}reg2bins(e,t){(e-=1)<1&&(e=1),t>2**34&&(t=2**34),t-=1;let i=0,n=0,r=this.minShift+3*this.depth;const s=[];for(;i<=this.depth;r-=3,n+=1<<3*i,i+=1){const i=n+(e>>r),o=n+(t>>r);s.push([i,o])}return s}bin_limit(){return((1<<3*(this.depth+1))-1)/7}}class fh{constructor(){}async parse(e,t){const i=[];let n=Number.MAX_SAFE_INTEGER,r=0;const s=new yc(new DataView(e)),o=s.getInt(),a={};if(!(21578050===o||t&&21578324===o))throw new Error(indexURL+\" is not a \"+(t?\"tabix\":\"bai\")+\" file\");{const e=s.getInt();if(t){s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt();for(let t=0;t<e;t++){a[s.getString()]=t}}for(let t=0;t<e;t++){const e={},o=[],a=s.getInt();for(let t=0;t<a;t++){const t=s.getInt();if(37450===t)s.getInt(),s.getVPointer(),s.getVPointer(),s.getLong(),s.getLong();else{e[t]=[];const i=s.getInt();for(let o=0;o<i;o++){const i=s.getVPointer(),o=s.getVPointer();i&&o&&(i.block<n&&(n=i.block),o.block>r&&(r=o.block),e[t].push([i,o]))}}}const c=s.getInt();for(let e=0;e<c;e++){const e=s.getVPointer();o.push(e)}a>0&&(i[t]={binIndex:e,linearIndex:o})}this.firstBlockPosition=n,this.lastBlockPosition=r,this.indices=i,this.sequenceIndexMap=a,this.tabix=t}}get sequenceNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(e,t,i){const n=this.indices[e];if(n){const e=function(e,t){const i=[];t>=1<<29&&(t=1<<29);return--t,i.push([0,0]),i.push([1+(e>>26),1+(t>>26)]),i.push([9+(e>>23),9+(t>>23)]),i.push([73+(e>>20),73+(t>>20)]),i.push([585+(e>>17),585+(t>>17)]),i.push([4681+(e>>14),4681+(t>>14)]),i}(t,i),r=[];for(let t of e)for(let e=t[0];e<=t[1];e++)if(n.binIndex[e]){const t=n.binIndex[e];for(let e of t){const t=e[0],i=e[1];r.push({minv:t,maxv:i})}}const s=n.linearIndex.length;let o;const a=Math.min(t>>14,s-1),c=Math.min(i>>14,s-1);for(let e=a;e<=c;e++){const t=n.linearIndex[e];if(t){o=t;break}}return hh(r,o)}return[]}}class ph{constructor(){this.tribble=!0}async parse(e){let t=0;this.chrIndex={},this.lastBlockPosition=[];const i=new yc(new DataView(e));!function(e){e.getInt(),e.getInt();const t=e.getInt();if(e.getString(),e.getLong(),e.getLong(),e.getString(),e.getInt(),t>=3){let t=e.getInt();for(;t-- >0;)e.getString(),e.getString()}}(i);let n=i.getInt();for(;n-- >0;){let e=i.getString();const n=i.getInt(),r=i.getInt(),s=i.getInt();i.getInt(),i.getInt();let o=i.getLong();const a=[];for(let e=0;e<r;e++){const e=i.getLong();a.push({min:o,max:e}),o=e,e>t&&(t=e)}this.chrIndex[e]={chr:e,blocks:a,longestFeature:s,binWidth:n}}this.lastBlockPosition=t}get sequenceNames(){return Object.keys(this.chrIndex)}chunksForRange(e,t,i){const n=this.chrIndex[e];if(n){const e=n.blocks,r=n.longestFeature,s=n.binWidth,o=Math.max(t-r,0),a=Math.floor(o/s);if(a>=e.length)return[];{const t=Math.min(Math.floor((i-1)/s),e.length-1),n=e[a].min,r=e[t].max;if(0===r-n)return[];return[{minv:{block:n,offset:0},maxv:{block:r,offset:0}}]}}}}async function gh(e,t){let i=await Qs.loadArrayBuffer(e,Ua(t)),n=new DataView(i);if(31===n.getUint8(0)&&139===n.getUint8(1)){i=gs(i).buffer,n=new DataView(i)}switch(n.getInt32(0,!0)){case 21578050:return async function(e){const t=new fh;return await t.parse(e,!1),t}(i);case 21578324:return async function(e){const t=new fh;return await t.parse(e,!0),t}(i);case 21582659:return async function(e){const t=new uh;return t.parse(e),t}(i);case 1480870228:return async function(e){const t=new ph;return t.parse(e),t}(i);case 38359875:throw Error(\"CSI version 2 is not supported.\");default:throw Error(`Unrecognized index type: ${e}`)}}function mh(e){return\"string\"==typeof e||e instanceof String?new wh(e):new bh(e)}class wh{constructor(e){this.data=e,this.ptr=0}nextLine(){var e=this.ptr,t=this.data.indexOf(\"\\n\",e),i=this.data;if(t>0)return this.ptr=t+1,t>e&&\"\\r\"===i.charAt(t-1)?i.substring(e,t-1):i.substring(e,t);var n=i.length;return this.ptr=n,e>=n?void 0:i.substring(e)}}class bh{constructor(e){this.data=e,this.length=this.data.length,this.ptr=0}nextLine(){if(this.ptr>=this.data.length)return;let e=this.ptr;const t=this.data;let i=\"\",n=!1;for(;e<t.length;){var r=t[e],s=0,o=0;if(r<=127?(s=0,o=255&r):r<=223?(s=1,o=31&r):r<=239?(s=2,o=15&r):r<=244&&(s=3,o=7&r),t.length-e-s>0)for(var a=0;a<s;)o=o<<6|63&(r=t[e+a+1]),a+=1;else o=65533,s=t.length-e;e+=s+1;const c=String.fromCodePoint(o);if(\"\\r\"===c)n=!0;else{if(\"\\n\"===c)break;n&&(i+=\"\\r\",n=!1),i+=c}}return this.ptr=e,i}}class Fh{constructor(e){this.config=e,this.filePtr=0,this.bufferPtr=0,this.buffer}async nextLine(){let e;try{for(;;){const t=this.buffer?this.buffer.length:0;for(;this.bufferPtr<t;){const t=String.fromCharCode(this.buffer[this.bufferPtr++]);if(\"\\r\"!==t){if(\"\\n\"===t)return e;e=e?e+t:t}}if(this.eof)return e;await this.readNextBlock()}}catch(t){return console.warn(t),this.eof=!0,e}}async readNextBlock(){const e=Ua(this.config,{range:{start:this.filePtr,size:26}}),t=ms(await Qs.loadArrayBuffer(this.config.url,e));if(0===t)this.eof=!0,this.buffer=void 0;else{const e=Ua(this.config,{range:{start:this.filePtr,size:t}}),i=await Qs.loadArrayBuffer(this.config.url,e);i.byteLength<t&&(this.eof=!0),this.buffer=gs(i),0==this.buffer.byteLength&&(this.eof=!0),this.bufferPtr=0,this.filePtr+=i.byteLength}}}const vh=e=>{const t=ArrayBuffer.isView(e)?e:new Uint8Array(e);return 1+(t[17]<<8|t[16])};class yh{constructor(e){this.config=e,this.cacheBlocks=0!=e.cacheBlocks,this.cache=void 0}async getData(e,t){const i=e.block,n=t.block,r=0===t.offset,s=await this.getInflatedBlocks(i,n,r);if(1===s.length)return s[0];let o=0;for(const e of s)o+=e.byteLength;const a=new Uint8Array(o);let c=0;for(const e of s)a.set(e,c),c+=e.byteLength;return a}async getInflatedBlocks(e,t,i){if(this.cacheBlocks){const n=this.cache;if(n&&n.startBlock<=e&&(n.endBlock>=t||i&&n.nextEndBlock===t)){const i=e-n.startBlock,r=t-n.startBlock;return Ch(n.buffer,i,r)}{let r;if(!n||n.startBlock>t||n.endBlock<e)r=await this.loadBLockData(e,t,{skipEnd:i});else{const s=[];if(e<n.startBlock){const t=await this.loadBLockData(e,n.startBlock,{skipEnd:!0});s.push(t)}let o;if(e<=n.startBlock&&t>=n.endBlock)o=n.buffer;else{const i=Math.max(0,e-n.startBlock);let r;if(t>=n.endBlock)r=n.buffer.byteLength;else{const e=Ah(n.buffer);for(let i=0;i<e.length-1;i++)if(n.startBlock+e[i]===t){r=e[i+1];break}}o=n.buffer.slice(i,r)}if(s.push(o),t>n.endBlock){const e=await this.loadBLockData(n.endBlock,t,{skipStart:!0,skipEnd:i});s.push(e)}r=function(e){if(1===e.length)return e[0];let t=0;for(const i of e)t+=i.byteLength;const i=new Uint8Array(t);let n=0;for(const t of e)i.set(new Uint8Array(t),n),n+=t.byteLength;return i.buffer}(s)}let s=t;if(i){const e=Ah(r);t=e[e.length-1]}return this.cache={startBlock:e,endBlock:t,nextEndBlock:s,buffer:r},Ch(r)}}return Ch(await this.loadBLockData(e,t,{skipEnd:i}))}async loadBLockData(e,t,i){const n=this.config,r=i&&i.skipStart;let s=0;if(!(i&&i.skipEnd)){const e=Ua(n,{range:{start:t,size:26}}),i=await Qs.loadArrayBuffer(n.url,e);s=vh(i)}if(r){const t=Ua(n,{range:{start:e,size:26}}),i=await Qs.loadArrayBuffer(n.url,t);e+=vh(i)}const o=Ua(n,{range:{start:e,size:t+s-e}});return Qs.loadArrayBuffer(n.url,o)}}function Ah(e){const t=e.byteLength;let i=0;const n=[0];for(;i<t;){const r=new Uint8Array(e,i);i+=1+(r[17]<<8|r[16]),i<t&&n.push(i)}return n}function Ch(e,t,i){const n=[];let r=t=t||0;const s=e.byteLength-18;for(;r<s;)try{const t=new Uint8Array(e,r,18),s=t[11]<<8|t[10],o=t[17]<<8|t[16],a=12+s+r,c=e.byteLength-a,l=o-s-18;if(c<l||l<=0)break;const h=new Uint8Array(e,a,l),d=hs(h);if(n.push(d),i===r)break;r+=o+1}catch(e){console.error(e);break}return n}const _h=Math.log10(Number.MIN_VALUE);class xh{chrCol=-1;snpCol=-1;posCol=-1;pValueCol=-1;phenotypeColumn=-1;delimiter=\"\\t\";constructor(e){this.config=e}async parseHeader(e){const t=this.config;t.delimiter&&(this.delimiter=t.delimiter);const i=await e.nextLine(),n=this.parseHeaderLine(i);return t.chrColumn&&(this.chrColumn=t.chrColumn-1),t.snpColumn&&(this.snpColumn=t.snpColumn-1),t.posColumn&&(this.posColumn=t.posColumn-1),t.pValueColumn&&(this.pValueColumn=t.pValueColumn-1),t.phenotypeColumn&&(this.phenotypeColumn=t.phenotypeColumn-1),n}parseHeaderLine(e){this.columns=e.split(this.delimiter);for(let e=0;e<this.columns.length;e++){switch(this.columns[e].toLowerCase()){case\"chr\":case\"chromosome\":case\"chr_id\":case\"chrom\":this.chrColumn=e;break;case\"bp\":case\"pos\":case\"position\":case\"chr_pos\":case\"chromEnd\":this.posColumn=e;break;case\"p\":case\"pval\":case\"pvalue\":case\"p-value\":case\"p.value\":this.pValueColumn=e;break;case\"rsid\":case\"variant\":case\"snp\":this.snpColumn=e;break;case\"phenotype\":case\"gene\":case\"gene_id\":case\"molecular_trait_id\":this.phenotypeColumn=e}}return this.columns}async parseFeatures(e){const t=[],i=e.nextLine();let n;this.columns||this.parseHeaderLine(i);const r=e=>{const t=e.indexOf(\"E\");if(t>0){if(Number.parseInt(e.substring(t+1))<_h)return Number.MIN_VALUE}return Number(e)};for(;void 0!==(n=e.nextLine());){const e=n.split(this.delimiter);if(e.length===this.columns.length){const i=e[this.posColumn];if(i.indexOf(\";\")>0||0==i.length||i.indexOf(\"x\")>0)continue;const n=e[this.chrColumn],s=r(e[this.pValueColumn]),o=parseInt(i)-1,a=o+1,c=e[this.snpColumn],l=e[this.phenotypeColumn],h=new kh({chr:n,start:o,end:a,pValue:s,snp:c,phenotype:l},this.columns,e);t.push(h)}}return t}static isQTL(e){const t=e.split(\"\\t\");if(t.length<5)return!1;const i=[[\"chr\",\"chromosome\",\"chr_id\",\"chrom\"],[\"bp\",\"pos\",\"position\",\"chr_pos\",\"chromEnd\"],[\"p\",\"pval\",\"p-value\",\"p.value\"],[\"rsid\",\"variant\",\"snp\"],[\"phenotype\",\"gene\",\"gene_id\",\"molecular_trait_id\"]];for(let e of i)if(!t.some((t=>e.includes(t.toLowerCase()))))return!1;return!0}}class kh{constructor({chr:e,start:t,end:i,pValue:n,snp:r,phenotype:s},o,a){this.chr=e,this.start=t,this.end=i,this.pValue=n,this.snp=r,this.phenotype=s,this.headers=o,this.tokens=a}popupData(){const e=[];for(let t=0;t<this.headers.length;t++)e.push({name:this.headers[t],value:this.tokens[t]});return e}}class Ih{sequenceNames;constructor(e,t){if(this.config=e||{},this.genome=t,this.indexURL=e.indexURL,this.indexed=e.indexed||void 0!==this.indexURL,this.queryable=this.indexed,Ht(this.config.url))this.filename=this.config.url.name;else if(Ga(this.config.url))this.indexed=!1,this.dataURI=e.url;else{const t=Ot(this.config.url);this.filename=e.filename||t.file}this.parser=this.getParser(this.config),\"vcf\"!==this.config.format||this.config.indexURL||console.warn(\"Warning: index file not specified.  The entire vcf file will be loaded.\")}async defaultVisibilityWindow(){if(this.config.indexURL){const e=await this.getIndex();if(e&&e.lastBlockPosition){let t=0;const i=1e4;for(let i of e.sequenceNames){const e=this.genome.getChromosome(i);e&&(t+=e.bpLength)}return Math.round(t/e.lastBlockPosition*i)}}}async readFeatures(e,t,i){let n;this.dataURI||this.header||await this.readHeader();return await this.getIndex()?(this.indexed=!0,n=await this.loadFeaturesWithIndex(e,t,i)):this.dataURI?(this.indexed=!1,n=await this.loadFeaturesFromDataURI()):\"service\"===this.config.sourceType?n=await this.loadFeaturesFromService(e,t,i):(this.indexed=!1,n=await this.loadFeaturesNoIndex()),n.sort((function(e,t){return e.chr===t.chr?e.start-t.start:e.chr.localeCompare(t.chr)})),n}async readHeader(){if(this.dataURI)return await this.loadFeaturesFromDataURI(this.dataURI),this.header;if(this.config.indexURL){const e=await this.getIndex();if(!e)throw new Error(\"Unable to load index: \"+this.config.indexURL);let t;if(this.sequenceNames=new Set(e.sequenceNames),e.tabix)this._blockLoader=new yh(this.config),t=new Fh(this.config);else{const i=Object.values(e.chrIndex).flatMap((e=>e.blocks)).map((e=>e.max)).reduce(((e,t)=>Math.min(e,t)),Number.MAX_SAFE_INTEGER),n=Ua(this.config,{bgz:e.tabix,range:{start:0,size:i}});t=mh(await Qs.loadString(this.config.url,n))}return this.header=await this.parser.parseHeader(t),this.header}if(\"service\"!==this.config.sourceType){let e;if(this.config._filecontents)e=this.config._filecontents,delete this.config._filecontents;else{const t=Ua(this.config);e=await Qs.loadByteArray(this.config.url,t)}e.length<5e8&&(e=(new TextDecoder).decode(e));let t=mh(e);this.header=await this.parser.parseHeader(t),t=mh(e),this.features=await this.parser.parseFeatures(t),this.sequenceNames=new Set;for(let e of this.features)this.sequenceNames.add(e.chr);return this.header}if(this.config.seqnamesURL){const e=Ua(this.config,{}),t=await Qs.loadString(this.config.seqnamesURL,e);t&&(this.sequenceNames=new Set(t.split(\",\").map((e=>e.trim())).filter((e=>e))))}if(this.config.headerURL){const e=Ua(this.config,{}),t=mh(await Qs.loadString(this.config.headerURL,e));return this.header=await this.parser.parseHeader(t),this.header}}getParser(e){switch(e.format){case\"vcf\":return new Yl(e);case\"seg\":return new Ul(\"seg\");case\"mut\":return new Ul(\"mut\");case\"maf\":return new Ul(\"maf\");case\"gwas\":return new Jl(e);case\"qtl\":return new xh(e);case\"aed\":return new nh(e);default:return new El(e)}}async loadFeaturesNoIndex(){if(this.features){const e=this.features;return delete this.features,e}{const e=Ua(this.config),t=await Qs.loadByteArray(this.config.url,e);if(!this.header){const e=mh(t);this.header=await this.parser.parseHeader(e)}const i=mh(t),n=[];return await this._parse(n,i),n}}async loadFeaturesWithIndex(e,t,i){const n=this.config;this.parser;const r=this.index.tabix,s=r?this.index.sequenceIndexMap[e]:e;if(void 0===s)return[];const o=this.index.chunksForRange(s,t,i);if(o&&0!==o.length){const s=[];for(let a of o){let o;if(r)o=await this._blockLoader.getData(a.minv,a.maxv);else{const e=Ua(n,{range:{start:a.minv.block,size:a.maxv.block-a.minv.block+1}});o=await Qs.loadString(n.url,e)}const c=mh(a.minv.offset?o.slice(a.minv.offset):o);await this._parse(s,c,e,i,t)}return s}return[]}async loadFeaturesFromService(e,t,i){let n;n=\"function\"==typeof this.config.url?this.config.url({chr:e,start:t,end:i}):this.config.url.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i);const r=Ua(this.config),s=mh(await Qs.loadString(n,r)),o=[];return await this._parse(o,s),o}async _parse(e,t,i,n,r){let s=await this.parser.parseFeatures(t);if(s.sort((function(e,t){return e.chr===t.chr?e.start-t.start:e.chr.localeCompare(t.chr)})),void 0===i)for(let t of s)e.push(t);else{let t=!1;for(let o=0;o<s.length;o++){const a=s[o];if(a.chr===i){if(a.start>n){e.push(a);break}a.end>=r&&a.start<=n&&(t||(t=!0,o>0&&e.push(s[o-1])),e.push(a))}}}}async getIndex(){return this.index?this.index:this.config.indexURL?(this.index=await this.loadIndex(),this.index):void 0}async loadIndex(){return gh(this.config.indexURL,this.config)}async loadFeaturesFromDataURI(){if(this.features){const e=this.features;return delete this.features,e}{const e=vs(this.dataURI);let t=mh(e);this.header=await this.parser.parseHeader(t),this.header instanceof String&&this.header.startsWith(\"##gff-version 3\")&&(this.format=\"gff3\"),t=mh(e);const i=[];return await this._parse(i,t),i}}}const Sh=Mt;class Eh{constructor(e){this.config=e}async readFeatures(e,t,i){let n;n=\"function\"==typeof this.config.url?this.config.url({chr:e,start:t,end:i}):this.config.url.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i);let r,s=Object.assign({},this.config);void 0!==this.config.body&&(\"function\"==typeof this.config.body?s.body=this.config.body({chr:e,start:t,end:i}):s.body=this.config.body.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i));const o=await Qs.load(n,s);if(o&&(r=\"function\"==typeof this.config.parser?this.config.parser(o):Sh(o)?JSON.parse(o):o),this.config.mappings){let e=Object.keys(this.config.mappings);for(let t of r)for(let i of e)t[i]=t[this.config.mappings[i]]}return r}}const Nh=function(e,t){this.config=e,this.genome=t,this.expandQueryInterval=!1};Nh.prototype.readFeatures=function(e,t,i){const n=Math.max(0,Math.floor(t));let r=Math.ceil(i);if(this.genome){const t=this.genome.getChromosome(e);t&&r>t.bpLength&&(r=t.bpLength)}const s=this.config.url+\"?db=\"+this.config.db+\"&table=\"+this.config.tableName+\"&chr=\"+e+\"&start=\"+n+\"&end=\"+r;return Qs.loadJson(s,this.config).then((function(e){return e?(e.forEach((function(e){e.hasOwnProperty(\"exonStarts\")&&e.hasOwnProperty(\"exonEnds\")&&e.hasOwnProperty(\"exonCount\")&&e.hasOwnProperty(\"cdsStart\")&&e.hasOwnProperty(\"cdsEnd\")&&function(e){var t,i,n,r,s,o;t=e.exonCount,i=e.exonStarts.split(\",\"),n=e.exonEnds.split(\",\"),r=[];for(var a=0;a<t;a++){var c={start:s=parseInt(i[a]),end:o=parseInt(n[a])};(e.cdsStart>o||e.cdsEnd<e.cdsStart)&&(c.utr=!0),e.cdsStart>=s&&e.cdsStart<=o&&(c.cdStart=e.cdsStart),e.cdsEnd>=s&&e.cdsEnd<=o&&(c.cdEnd=e.cdsEnd),r.push(c)}e.exons=r}(e)})),e):null}))};class Bh{featureCaches=[];gtexChrs=new Set([\"chr1\",\"chr10\",\"chr11\",\"chr12\",\"chr13\",\"chr14\",\"chr15\",\"chr16\",\"chr17\",\"chr18\",\"chr19\",\"chr2\",\"chr20\",\"chr21\",\"chr22\",\"chr3\",\"chr4\",\"chr5\",\"chr6\",\"chr7\",\"chr8\",\"chr9\",\"chrM\",\"chrX\",\"chrY\"]);constructor(e){this.config=e,this.url=e.url,this.tissueId=e.tissueSiteDetailId,this.datasetId=e.datasetId||\"gtex_v8\"}async readFeatures(e,t,i){const n=e.startsWith(\"chr\")?e:\"MT\"===e?\"chrM\":\"chr\"+e;if(!this.gtexChrs.has(n))return[];const r=Math.floor(t),s=Math.ceil(i),o=this.datasetId,a=this.url+\"?chromosome=\"+n+\"&start=\"+r+\"&end=\"+s+\"&tissueSiteDetailId=\"+this.tissueId+\"&datasetId=\"+o,c=await Qs.loadJson(a,{withCredentials:this.config.withCredentials});return c&&c.singleTissueEqtl?c.singleTissueEqtl.map((e=>new Mh(e))):[]}}class Mh{constructor(e){this.chr=e.chromosome,this.start=e.pos-1,this.end=this.start+1,this.snp=e.snpId,this.phenotype=e.geneSymbol,this.pValue=e.pValue,this.json=e}popupData(){return Object.keys(this.json).map((e=>({name:e,value:this.json[e]})))}}class Rh{constructor(e,t){if(this.config=e,this.genome=t,!e.format)throw Error('Format is required, and must be either \"bam\" or \"cram\"');if(this.format=e.format.toUpperCase(),\"BAM\"!==this.format&&\"VCF\"!==this.format)throw Error(`htsget format ${e.format} is not supported`)}async readHeaderData(){const e=`${Dh(this.config)}?class=header&format=${this.format}`,t=await Qs.loadJson(e,Ua(this.config));return await this.loadUrls(t.htsget.urls)}async readData(e,t,i){const n=`${Dh(this.config)}?format=${this.format}&referenceName=${e}&start=${Math.floor(t)}&end=${Math.ceil(i)}`,r=await Qs.loadJson(n,Ua(this.config));return this.loadUrls(r.htsget.urls)}async loadUrls(e){const t=[];for(let i of e)if(i.url.startsWith(\"data:\"))t.push(Promise.resolve(Th(i.url)));else{const e=Ua(this.config||{});i.headers&&(e.headers=Object.assign(e.headers||{},i.headers)),t.push(Qs.loadArrayBuffer(i.url,e))}return function(e){let t=0;for(let i of e)t+=i.byteLength;let i=0;const n=new Uint8Array(t);for(let t of e){const e=new Uint8Array(t);n.set(e,i),i+=e.length}return n}(await Promise.all(t))}static async inferFormat(e){try{const t=Dh(e),i=`${t}${t.includes(\"?\")?\"&\":\"?\"}class=header`,n=await Qs.loadJson(i,Ua(e));if(n.htsget){const t=n.htsget.format;if(\"BAM\"!==t&&\"VCF\"!==t)throw Error(`htsget format ${t} is not supported`);e.format=t.toLowerCase(),e.sourceType=\"htsget\",e.name||(e.name=await ja(e.url))}}catch(e){}}}function Dh(e){if(e.url&&e.endpoint&&e.id)return e.url+e.endpoint+e.id;if(e.endpoint&&e.id)return e.endpoint+e.id;if(e.url)return e.url.startsWith(\"htsget://\")?e.url.replace(\"htsget://\",\"https://\"):e.url;throw Error(\"Must specify either 'url', or 'endpoint' and 'id\")}function Th(e){const t=e.split(\",\"),i=t[0].split(\":\")[1];let n=t[1];n=i.indexOf(\"base64\")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s<n.length;s++)r[s]=n.charCodeAt(s);return r}class Lh extends Rh{constructor(e,t){super(e,t),this.parser=new Yl}async readHeader(){if(!this.header){let e=await this.readHeaderData();fs(e)&&(e=ps(e));const t=mh(e);this.header=await this.parser.parseHeader(t,this.genome),this.chrAliasTable=this.header.chrAliasTable}return this.header}async readFeatures(e,t,i){if(this.config.format&&\"VCF\"!==this.config.format.toUpperCase())throw Error(`htsget format ${this.config.format} is not supported`);this.chrAliasTable||await this.readHeader();let n=this.chrAliasTable.has(e)?this.chrAliasTable.get(e):e,r=await this.readData(n,t,i);fs(r)&&(r=ps(r));const s=mh(r);return this.parser.parseFeatures(s)}}class zh{chrAliasTable=new Map;constructor(e,t){this.sequenceNames=new Set(e),this.genome=t}async getAliasName(e){if(!this.genome)return e;if(!this.chrAliasTable.has(e)){const t=await this.genome.getAliasRecord(e);if(t){let i;const n=Object.keys(t).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>t[e])).filter((e=>this.sequenceNames.has(e)));n.length>0&&(i=n[0]),this.chrAliasTable.set(e,i)}else this.chrAliasTable.set(e,void 0)}return this.chrAliasTable.get(e)}}class Hh{constructor(e){this.genome=e}async nextFeature(e,t,i,n){let r=this.genome.chromosomeNames||[e],s=r.indexOf(e);if(s<0)return;const o=Math.min(1e4,n||1e4);let a=i?t:Math.max(t-o,0);for(;s<r.length&&s>=0;){e=r[s];const c=this.genome.getChromosome(e).bpLength;for(;a<c&&a>=0;){let r=i?a+o:Math.min(t,a+o);const s=await this.getFeatures({chr:e,start:a,end:r,visibilityWindow:n});if(s){const e=(e,t)=>e.start-t.start+e.end-t.end,n=Array.from(s);n.sort(e);let r=i?0:n.length-1;for(;r>=0&&r<n.length;){const e=n[r],s=(e.start+e.end)/2;if(i){if(s>t)return e;r++}else{if(s<t)return e;r--}}}a=i?r:a-o}if(i)s++,a=0,t=0;else{if(s--,s<0)break;a=(t=this.genome.getChromosome(r[s]).bpLength)-o}}}async previousFeature(e,t,i,n){let r=this.genome.chromosomeNames||[e],s=r.indexOf(e);if(s<0)return;const o=Math.min(1e4,n||1e4);let a=i?t:Math.max(t-o,0);for(;s<r.length&&s>=0;){e=r[s];const c=this.genome.getChromosome(e).bpLength;for(;a<c&&a>=0;){let r=Math.min(t,a+o);const s=await this.getFeatures({chr:e,start:a,end:r,visibilityWindow:n});if(s){const e=(e,t)=>e.start-t.start+e.end-t.end,n=Array.from(s);n.sort(e);let r=i?0:n.length-1;for(;r>=0&&r<n.length;){const e=n[r],s=(e.start+e.end)/2;if(i){if(s>t)return e;r++}else{if(s<t)return e;r--}}}a=i?r:a-o}if(i)s++,a=0,t=0;else{if(s--,s<0)break;a=(t=this.genome.getChromosome(r[s]).bpLength)-o}}}}class Ph{constructor(e,t){this.config=e,this.genome=t,this.path=e.url,this.groupCache={},this.datasetCache={}}async readHeader(){if(void 0!==this.magic)return this;let e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:0,size:64e3}})),t=new yc(new DataView(e));if(this.magic=t.getInt(),this.version=t.getInt(),this.indexPos=t.getLong(),this.indexSize=t.getInt(),t.getInt(),this.version>=2){let e=t.getInt();for(this.windowFunctions=[];e-- >0;)this.windowFunctions.push(t.getString())}this.trackType=t.getString(),this.trackLine=t.getString();let i=t.getInt();for(this.trackNames=[];i-- >0;)this.trackNames.push(t.getString());this.genomeID=t.getString(),this.flags=t.getInt(),this.compressed=!!(1&this.flags),e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:this.indexPos,size:this.indexSize}})),t=new yc(new DataView(e)),this.datasetIndex={};let n=t.getInt();for(;n-- >0;){const e=t.getString(),i=t.getLong(),n=t.getInt();this.datasetIndex[e]={position:i,size:n}}for(this.groupIndex={},n=t.getInt();n-- >0;){const e=t.getString(),i=t.getLong(),n=t.getInt();this.groupIndex[e]={position:i,size:n}}return this}async readDataset(e,t,i){const n=e+\"_\"+t+\"_\"+i;if(this.datasetCache[n])return this.datasetCache[n];{await this.readHeader();const r=this.version<2?\"\":\"/\"+t,s=\"all\"===e.toLowerCase()||void 0===i?\"0\":i.toString();let o;o=\"raw\"===t?\"/\"+e+\"/raw\":\"/\"+e+\"/z\"+s+r;const a=this.datasetIndex[o];if(void 0===a)return;const c=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:a.position,size:a.size}}));if(!c)return;const l=new yc(new DataView(c));let h=l.getInt();const d={};for(;h-- >0;)d[l.getString()]=l.getString();const u=l.getString(),f=l.getFloat();let p=l.getInt();const g=[];for(;p-- >0;)g.push({position:l.getLong(),size:l.getInt()});const m={name:o,attributes:d,dataType:u,tileWidth:f,tiles:g};return this.datasetCache[n]=m,m}}async readRootGroup(){const e=this.genome,t=this.groupCache[\"/\"];if(t)return t;{const t=await this.readGroup(\"/\"),i=t.chromosomes,n=t.maxZoom;n&&(this.maxZoom=Number(n));const r=t.totalCount;r&&(t.totalCount=Number(r));const s={};return i&&i.split(\",\").forEach((function(t){const i=e.getChromosomeName(t);s[i]=t})),this.chrAliasTable=s,this.groupCache[\"/\"]=t,t}}async readGroup(e){const t=this.groupCache[e];if(t)return t;{await this.readHeader();const t=this.groupIndex[e];if(void 0===t)return;const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:t.position,size:t.size}}));if(!i)return;const n=new yc(new DataView(i)),r={name:e};let s=n.getInt();for(;s-- >0;){const e=n.getString(),t=n.getString();r[e]=t}return this.groupCache[e]=r,r}}async readTiles(e,t){if(e.sort((function(e,t){return e.position-t.position})),0===(e=e.filter((function(e){return e.size>0}))).length)return[];const i=[];for(let n of e){const e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:n.position,size:n.size}}));let r;try{r=this.compressed?ls(e).buffer:e}catch(e){console.error(e);continue}const s=new yc(new DataView(r)),o=s.getString();let a;switch(o){case\"fixedStep\":a=Oh(s,t);break;case\"variableStep\":a=Uh(s,t);break;case\"bed\":case\"bedWithName\":a=qh(s,t,o);break;default:throw\"Unknown tile type: \"+o}i.push(a)}return i}async readTile(e,t){let i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e.position,size:e.size}}));if(this.compressed){i=ls(i).buffer}const n=new yc(new DataView(i)),r=n.getString();switch(r){case\"fixedStep\":return Oh(n,t);case\"variableStep\":return Uh(n,t);case\"bed\":case\"bedWithName\":return qh(n,t,r);default:throw\"Unknown tile type: \"+r}}}function Oh(e,t){const i=e.getInt(),n=e.getInt(),r=e.getFloat(),s=[];let o=t;for(;o-- >0;){let t=i;const n=[];for(;t-- >0;)n.push(e.getFloat());s.push(n)}return{type:\"fixedStep\",start:n,span:r,data:s,nTracks:t,nPositions:i}}function Uh(e,t){const i=e.getInt(),n=e.getFloat(),r=e.getInt(),s=[];let o=r;for(;o-- >0;)s.push(e.getInt());e.getInt();const a=[];let c=t;for(;c-- >0;){o=r;const t=[];for(;o-- >0;)t.push(e.getFloat());a.push(t)}return{type:\"variableStep\",tileStart:i,span:n,start:s,data:a,nTracks:t,nPositions:r}}function qh(e,t,i){const n=e.getInt();let r=n;const s=[];for(;r-- >0;)s.push(e.getInt());r=n;const o=[];for(;r-- >0;)o.push(e.getInt());e.getInt();const a=[];let c=t;for(;c-- >0;){let t=n;const i=[];for(;t-- >0;)i.push(e.getFloat());a.push(i)}if(\"bedWithName\"===i){r=n;const t=[];for(;r-- >0;)t.push(e.getString())}return{type:i,start:s,end:o,data:a,nTracks:t,nPositions:n}}class Qh extends Hh{#h={};searchable=!1;constructor(e,t){super(t),this.genome=t,this.reader=new Ph(e,t),this.queryable=!0}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,windowFunction:r=\"mean\"}){return\"all\"===e.toLowerCase()?this.getWGValues(r,n):this._getFeatures(e,t,i,n,r)}async _getFeatures(e,t,i,n,r){const s=new hc(e,t,i),o=this.genome;if(!this.rootGroup&&(this.rootGroup=await this.reader.readRootGroup(),!this.normalizationFactor)){const e=this.rootGroup.totalCount;e&&(this.normalizationFactor=1e6/e)}s.bpPerPixel=n;const a=function(e,t,i){var n=i.getChromosome(e).bpLength;return Math.ceil(Math.log(Math.max(0,n/(700*t)))/Gh)}(e,n,o);let c=this.reader.chrAliasTable[e],l=this.reader.maxZoom;void 0===c&&(c=e),void 0===l&&(l=-1);const h=a>l?\"raw\":r,d=await this.reader.readDataset(c,h,a);if(null==d)return[];const u=d.tileWidth,f=Math.floor(t/u),p=Math.floor(i/u),g=await this.reader.readTiles(d.tiles.slice(f,p+1),1),m=[];for(let r of g)switch(r.type){case\"bed\":Vh(r,e,t,i,n,m);break;case\"variableStep\":jh(r,e,t,i,n,m);break;case\"fixedStep\":Wh(r,e,t,i,n,m);break;default:throw\"Unknown tile type: \"+r.type}return m.sort((function(e,t){return e.start-t.start})),m}get supportsWholeGenome(){return!0}get windowFunctions(){return this.reader.windowFunctions}async getWGValues(e,t){const i=this.#h[e];if(i&&i.bpPerPixel>.8*t&&i.bpPerPixel<1.2*t)return i.values;{const i=[],n=this.genome;if(this.genome.wgChromosomeNames)for(let r of n.wgChromosomeNames){const s=n.getChromosome(r).bpLength;t=s/1e3;const o=await this._getFeatures(r,0,s,t,e);if(o)for(let e of o){const t=Object.assign({},e);t.chr=\"all\",t.start=n.getGenomeCoordinate(e.chr,e.start),t.end=n.getGenomeCoordinate(e.chr,e.end),t._f=e,i.push(t)}}return this.#h[e]={values:i,bpPerPixel:t},i}}}function Vh(e,t,i,n,r,s){const o=e.nPositions,a=e.start,c=e.end,l=e.data[0];for(let e=0;e<o;e++){const r=a[e],o=c[e];if(!(o<i)){if(r>n)break;s.push({chr:t,start:r,end:o,value:l[e]})}}}function jh(e,t,i,n,r,s){const o=e.nPositions,a=e.start,c=e.span,l=e.data[0];for(let e=0;e<o;e++){const r=a[e],o=r+c;if(!(o<i)){if(r>n)break;s.push({chr:t,start:r,end:o,value:l[e]})}}}function Wh(e,t,i,n,r,s){const o=e.nPositions;let a=e.start;const c=e.span,l=e.data[0];for(let e=0;e<o;e++){const r=a+c;if(a>n)break;r>=i&&(Number.isNaN(l[e])||s.push({chr:t,start:a,end:r,value:l[e]})),a=r}}var Gh=Math.log(2);class $h{constructor(e,t,i,n){this.header=e,this.nameToId=t,this.idToName=i,this.sumLengths=n}static parseTree(e,t,i=!1){{const n=e.getInt(),r=e.getInt(),s=e.getInt(),o=e.getInt(),a=e.getLong(),c=e.getLong(),l={magic:n,blockSize:r,keySize:s,valSize:o,itemCount:a,reserved:c},h=new Map,d=[];let u=0;const f=n=>{n>=0&&(e.position=n);const r=e.getByte();e.getByte();const a=e.getUShort();if(1===r)for(let t=0;t<a;t++){let t,n=e.getFixedLengthString(s);if(8!==o)throw Error(`Unexpected \"valSize\" value in chromosome tree.  Expected 8, actual value is ${o}`);{t=e.getInt();const r=e.getInt();u+=r,i&&(n=i.getChromosomeName(n)),h.set(n,t),d[t]=n}}else for(let i=0;i<a;i++){e.getFixedLengthString(s);const i=e.getLong()-t,n=e.position;f(i),e.position=n}};return f(-1),new $h(l,h,d,u)}}}class Kh{static magic=610839776;littleEndian=!0;nodeCache=new Map;constructor(e,t,i){this.path=e,this.config=t,this.startOffset=i}async init(){const e=await this.#t(this.startOffset,48);let t=e.getInt();if(t!==Kh.magic&&(e.setPosition(0),this.littleEndian=!this.littleEndian,e.littleEndian=this.littleEndian,t=e.getInt(),t!==Kh.magic))throw Error(`Bad magic number ${t}`);const i=e.getUInt(),n=e.getLong(),r=e.getUInt(),s=e.getUInt(),o=e.getUInt(),a=e.getUInt(),c=e.getLong(),l=e.getUInt(),h=e.getUInt(),d=this.startOffset+48;return this.header={magic:t,blockSize:i,itemCount:n,startChromIx:r,startBase:s,endChromIx:o,endBase:a,endFileOffset:c,itemsPerSlot:l,reserved:h,rootNodeOffset:d},this}async#t(e,t){const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:t}}));return new yc(new DataView(i),this.littleEndian)}async findLeafItemsOverlapping(e,t,i,n){const r=[],s=async o=>{const a=await this.readNode(o);for(let o of a.items)Yh(o,e,t,i,n)&&(1===a.type?r.push(o):await s(o.childOffset))};return await s(this.header.rootNodeOffset),r}async readNode(e){const t=e;if(this.nodeCache.has(t))return this.nodeCache.get(t);let i=await this.#t(e,4);const n=i.getByte(),r=1===n;i.getByte();const s=i.getUShort();let o=s*(r?32:24);i=await this.#t(e+4,o);const a=[];for(let e=0;e<s;e++){let e={isLeaf:r,startChrom:i.getInt(),startBase:i.getInt(),endChrom:i.getInt(),endBase:i.getInt(),childOffset:i.getLong()};r&&(e.dataSize=i.getLong(),e.dataOffset=e.childOffset),a.push(e)}const c={type:n,items:a};return this.nodeCache.set(t,c),c}}function Yh(e,t,i,n,r){return e?(n>e.startChrom||n===e.startChrom&&r>=e.startBase)&&(t<e.endChrom||t===e.endChrom&&i<=e.endBase):(console.log(\"null item for \"+t+\" \"+i+\" \"+r),!1)}class Xh{ixFile;ixxFile;bufferCache=new Map;constructor(e,t){this.ixFile=t,this.ixxFile=e}async search(e,t){const i=e.split(\" \")[0].toLowerCase(),n=await this._getBuffer(i,t);if(!n)return;const r=n.slice(0,n.lastIndexOf(\"\\n\")).split(\"\\n\").filter((e=>!!e)),s=[];for(let e of r){const t=e.split(\" \")[0];if(t.startsWith(i)&&s.push(e),t.slice(0,i.length)>i)break}if(0!==s.length){const e=new Map;for(let t of s){const[i,...n]=t.split(\" \");e.set(i,n.map((e=>e.split(\",\")[0])))}return e}}async getIndex(e){return this.index||(this.index=await this._readIndex()),this.index}async _readIndex(e){return(await Qs.loadString(this.ixxFile)).split(\"\\n\").filter((e=>!!e)).map((e=>{const t=e.length-10,i=e.slice(0,t),n=e.slice(t);return[i,Number.parseInt(n,16)]}))}async _getBuffer(e,t){let i=0,n=65536;const r=await this.getIndex(t);for(let t=0;t<r.length;t++){const[s,o]=r[t],a=Math.min(s.length,e.length);s.slice(0,a)<e&&(i=o,n=o+65536)}const s=n-i;if(!(s<0)){if(this.bufferCache.has(i))return this.bufferCache.get(i);{const e=await Qs.loadString(this.ixFile,{range:{start:i,size:s}});return this.bufferCache.set(i,e),e}}}}class Zh{chrAliasTable=new Map;rpTreeCache=new Map;constructor(e,t){this.path=e.url,this.format=e.format||\"bigwig\",this.genome=t,this.config=e,this.bufferSize=512e3,this.loader=Ga(this.path)?new sd(vs(this.path).buffer):Qs;const i=e.trixURL||e.searchTrix;i&&(this._trix=new Xh(`${i}x`,i))}async preload(){const e=await Qs.loadArrayBuffer(this.path);this.loader=new sd(e)}async readWGFeatures(e,t){await this.loadHeader();const i=this.chromTree.idToName.length-1,n=this.chromTree.idToName[0],r=this.chromTree.idToName[i];return this.readFeatures(n,0,r,Number.MAX_VALUE,e,t)}async readFeatures(e,t,i,n,r,s=\"mean\"){t||(t=0),n||(n=Number.MAX_SAFE_INTEGER),await this.loadHeader();let o,a,c=await this.#d(e),l=await this.#d(i);if(void 0===c||void 0===l)return[];if(\"bigwig\"===this.type){const e=await this.getZoomHeaders();let t=r?function(e,t){let i;for(let n=0;n<t.length;n++){const r=t[n];if(r.reductionLevel<e){i=r;break}}return i}(r,e):void 0;t&&\"none\"!=s?(o=t.indexOffset,a=rd):(o=this.header.fullIndexOffset,a=id)}else o=this.header.fullIndexOffset,a=nd.call(this);const h=await this.loadRPTree(o),d=await h.findLeafItemsOverlapping(c,t,l,n);if(d&&0!==d.length){let e=Number.MAX_VALUE,i=0;for(let t of d)e=Math.min(e,t.dataOffset),i=Math.max(i,t.dataOffset+t.dataSize);const r=i-e,o=await this.loader.loadArrayBuffer(this.config.url,Ua(this.config,{range:{start:e,size:r}})),h=[];for(let i of d){const r=new Uint8Array(o,i.dataOffset-e,i.dataSize);let d;d=this.header.uncompressBuffSize>0?ls(r):r,a.call(this,new DataView(d.buffer),c,t,l,n,h,this.chromTree.idToName,s,this.littleEndian)}return h.sort((function(e,t){return e.start-t.start})),h}return[]}async#d(e){if(this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.chromTree.nameToId.get(e);if(void 0===t&&this.genome){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>this.chromTree.nameToId.has(e)));e.length>0&&(n=e[0],t=this.chromTree.nameToId.get(e[0]))}this.chrAliasTable.set(e,n)}return t}get searchable(){return\"bigbed\"===this.type}async search(e){if(this.header||await this.loadHeader(),!this.header||!this.header.extraIndexCount)return;const t=await this._searchForRegions(e);if(t){const i=await this._loadFeaturesForRange(t.offset,t.length);if(i){const t=i.filter((t=>{for(let i of Object.keys(t)){const n=t[i];if(Mt(n)&&n.toLowerCase()===e.toLowerCase())return!0}return!1}));return t.length>0?t.reduce(((e,t)=>e.end-e.start>t.end-t.start?e:t),i[0]):void 0}}}async _searchForRegions(e){const t=await this.#u();if(t){if(this._trix){const t=e.toLowerCase(),i=await this._trix.search(t);i&&i.has(t)&&(e=i.get(t)[0])}for(let i of t){const t=await i.search(e);if(t)return t}}}async#u(){if(void 0===this._searchTrees&&this.header.extraIndexOffsets&&this.header.extraIndexOffsets.length>0){this._searchTrees=[];for(let e of this.header.extraIndexOffsets){const t=await Cc.loadBpTree(this.path,this.config,e);this._searchTrees.push(t)}}return this._searchTrees}async getZoomHeaders(){return this.zoomLevelHeaders||await this.loadHeader(),this.zoomLevelHeaders}async loadHeader(){if(this.header)return this.header;{let e,t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:0,size:64}}));this.littleEndian=!0;const i=new yc(new DataView(t),this.littleEndian);let n=i.getUInt();if(2291137574===n)this.type=\"bigwig\";else if(2273964779===n)this.type=\"bigbed\";else{this.littleEndian=!1,i.littleEndian=!1,i.position=0;let e=i.getUInt();654085990===e?this.type=\"bigwig\":3958540679===e&&(this.type=\"bigbed\")}e={bwVersion:i.getUShort(),nZoomLevels:i.getUShort(),chromTreeOffset:i.getLong(),fullDataOffset:i.getLong(),fullIndexOffset:i.getLong(),fieldCount:i.getUShort(),definedFieldCount:i.getUShort(),autoSqlOffset:i.getLong(),totalSummaryOffset:i.getLong(),uncompressBuffSize:i.getInt(),extensionOffset:i.getLong()};const r=64;let s={start:r,size:e.totalSummaryOffset>0?e.totalSummaryOffset-r+40:Math.min(e.fullDataOffset,e.chromTreeOffset)-r};t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:s}));const o=new yc(new DataView(t),this.littleEndian),a=e.nZoomLevels;this.zoomLevelHeaders=[],this.firstZoomDataOffset=Number.MAX_SAFE_INTEGER;for(let e=1;e<=a;e++){const t=a-e,i=new Jh(t,o);this.firstZoomDataOffset=Math.min(i.dataOffset,this.firstZoomDataOffset),this.zoomLevelHeaders[t]=i}if(e.autoSqlOffset>0){o.position=e.autoSqlOffset-r;const t=o.getString();t&&(this.autoSql=function(e){let t;const i=[];let n=!1;const r=e.trim().split(/\\s*[\\r\\n]+\\s*/g);for(let e of r)if(e=e.trim(),e.length>0){if(e.startsWith(\"#\"))continue;if(e.startsWith(\"table\"))t=e.split(/\\s+/)[1].trim();else if(e.startsWith(\"(\"))n=!0;else if(e.startsWith(\")\"));else if(n){const t=e.indexOf(\";\");if(t>0){const n=e.substr(0,t).split(/\\s+/),r=e.substr(t+1).replace(/\"/g,\"\").trim();i.push({type:n[0],name:n[1],description:r})}}}return{table:t,fields:i}}(t))}e.totalSummaryOffset>0&&(o.position=e.totalSummaryOffset-r,this.totalSummary=new ed(o));const c=Math.min(2e5,Math.max(1e4,e.fullDataOffset-e.chromTreeOffset));if(this.chromTree=await this.#f(e.chromTreeOffset,c),this.chrNames=new Set(this.chromTree.idToName),\"bigbed\"===this.type){const t=await this.#p(e.fullDataOffset);this.featureDensity=t/this.chromTree.sumLengths}return this.header=e,e.extensionOffset>0&&await this.loadExtendedHeader(e.extensionOffset),this.header}}async#p(e){const t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:4}}));return new yc(new DataView(t),this.littleEndian).getInt()}async#f(e,t){let i=t;const n=async()=>{const t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:i}})),n=new yc(new DataView(t),this.littleEndian);return $h.parseTree(n,e,this.genome)};let r;for(;i<1e6;)try{return await n()}catch(e){r=e,i*=2}throw r}async loadExtendedHeader(e){let t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:64}})),i=new yc(new DataView(t),this.littleEndian);i.getUShort();const n=i.getUShort(),r=i.getLong();if(0===n)return;let s=56*n;t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:r,size:s}})),i=new yc(new DataView(t),this.littleEndian);const o=[],a=[],c=[];for(let e=0;e<n;e++){o.push(i.getUShort());const e=i.getUShort();c.push(i.getLong()),a.push(i.getInt());for(let t=0;t<e;t++)i.getUShort(),a.push(i.getUShort())}this.header.extraIndexCount=n,this.header.extraIndexOffsets=c}async loadRPTree(e){let t=this.rpTreeCache.get(e);return t||(t=new Kh(this.path,this.config,e),await t.init(),this.rpTreeCache.set(e,t),t)}async getType(){return await this.loadHeader(),this.type}async getTrackType(){return await this.loadHeader(),\"bigwig\"===this.type?\"wig\":this.autoSql&&\"chromatinInteract\"===this.autoSql.table?\"interact\":\"annotation\"}async _loadFeaturesForRange(e,t){const i=await this.loader.loadArrayBuffer(this.config.url,Ua(this.config,{range:{start:e,size:t}})),n=new Uint8Array(i),r=this.header.uncompressBuffSize>0?ls(n):n,s=[];return nd.call(this).call(this,new DataView(r.buffer),0,0,Number.MAX_SAFE_INTEGER,Number.MAX_SAFE_INTEGER,s,this.chromTree.idToName),s}}class Jh{constructor(e,t){this.index=e,this.reductionLevel=t.getInt(),this.reserved=t.getInt(),this.dataOffset=t.getLong(),this.indexOffset=t.getLong()}}class ed{constructor(e){e?(this.basesCovered=e.getLong(),this.minVal=e.getDouble(),this.maxVal=e.getDouble(),this.sumData=e.getDouble(),this.sumSquares=e.getDouble(),td.call(this)):(this.basesCovered=0,this.minVal=0,this.maxVal=0,this.sumData=0,this.sumSquares=0,this.mean=0,this.stddev=0)}}function td(){let e=this.basesCovered;if(e>0){this.mean=this.sumData/e,this.stddev=Math.sqrt(this.sumSquares/(e-1));let t=this.minVal<0?this.mean-2*this.stddev:0,i=this.maxVal>0?this.mean+2*this.stddev:0;this.defaultRange={min:t,max:i}}}function id(e,t,i,n,r,s,o,a,c){const l=new yc(e,c),h=l.getInt(),d=l.getInt();let u=d,f=l.getInt();const p=l.getInt(),g=l.getInt(),m=l.getByte();l.getByte();let w=l.getUShort();if(h>=t&&h<=n){let e=0;for(;w-- >0;){let a;switch(m){case 1:u=l.getInt(),f=l.getInt(),a=l.getFloat();break;case 2:u=l.getInt(),a=l.getFloat(),f=u+g;break;case 3:a=l.getFloat(),u=d+e*p,f=u+g,e++}if(!(h<t||h===t&&f<i)){if(h>n||h===n&&u>=r)break;if(Number.isFinite(a)){const e=o[h];s.push({chr:e,start:u,end:f,value:a})}}}}}function nd(){const e=function(e,t,i,n){if(\"biginteract\"===n||i&&(\"chromatinInteract\"===i.table||\"interact\"===i.table))return function(e,t){return e.chr1=t[5],e.start1=Number.parseInt(t[6]),e.end1=Number.parseInt(t[7]),e.chr2=t[10],e.start2=Number.parseInt(t[11]),e.end2=Number.parseInt(t[12]),e.name=t[0],e.score=Number(t[1]),e.value=Number(t[2]),e.color=\".\"===t[4]?void 0:\"0\"===t[4]?\"rgb(0,0,0)\":t[4],e};{const n=e-3;return function(r,s){if(n>0&&(r.name=s[0]),n>1&&(r.score=Number(s[1])),n>2&&(r.strand=s[2]),n>3&&(r.cdStart=parseInt(s[3])),n>4&&(r.cdEnd=parseInt(s[4])),n>5&&\".\"!==s[5]&&\"0\"!==s[5]&&\"-1\"!==s[5]){const e=_s.createColorString(s[5]);r.color=e.startsWith(\"rgb\")?e:void 0}if(n>8){const e=parseInt(s[6]),t=s[7].split(\",\"),i=s[8].split(\",\"),n=[];for(let s=0;s<e;s++){const e=r.start+parseInt(i[s]),o=e+parseInt(t[s]);n.push({start:e,end:o})}!function(e,t,i){for(let n of e){const e=n.end,r=n.start;e<t||r>i?n.utr=!0:(t>=r&&t<=e&&(n.cdStart=t),i>=r&&i<=e&&(n.cdEnd=i))}}(n,r.cdStart,r.cdEnd),r.exons=n}if(i)for(let n=e;n<t;n++)if(n<i.fields.length){const e=i.fields[n].name,t=s[n-3];r[e]=t}}}}(this.header.definedFieldCount,this.header.fieldCount,this.autoSql,this.format);return function(t,i,n,r,s,o,a,c,l){const h=new yc(t,l);for(;h.remLength()>=13;){const t=h.getInt(),c=a[t],l=h.getInt(),d=h.getInt(),u=h.getString();if(!(t<i||t===i&&d<n)){if(t>r||t===r&&l>=s)break;if(d>0){const t={chr:c,start:l,end:d};o.push(t);const i=u.split(\"\\t\");e(t,i)}}}}}function rd(e,t,i,n,r,s,o,a,c){const l=new yc(e,c);for(;l.remLength()>=32;){const e=l.getInt(),c=l.getInt(),h=l.getInt(),d=l.getInt(),u=l.getFloat(),f=l.getFloat(),p=l.getFloat();let g;switch(l.getFloat(),a){case\"min\":g=u;break;case\"max\":g=f;break;default:g=0===d?0:p/d}if(!(e<t||e===t&&h<i)){if(e>n||e===n&&c>=r)break;if(Number.isFinite(g)){const t=o[e];s.push({chr:t,start:c,end:h,value:g})}}}}class sd{constructor(e){this.data=e}loadArrayBuffer(e,t){const i=t.range;return i?this.data.slice(i.start,i.start+i.size):this.data}async dataViewForRange(e,t){const i=Math.min(this.data.byteLength-e.start,e.size);return t?new Uint8Array(this.data,e.start,i):new DataView(this.data,e.start,i)}}class od extends Hh{queryable=!0;#h={};windowFunctions=[\"mean\",\"min\",\"max\",\"none\"];constructor(e,t){super(t),this.reader=new Zh(e,t),this.genome=t,this.format=e.format||\"bigwig\"}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,windowFunction:r}){await this.reader.loadHeader();const s=\"bigwig\"===this.reader.type;let o;return o=\"all\"===e.toLowerCase()?s?await this.getWGValues(r,n):[]:await this.reader.readFeatures(e,t,e,i,n,r),s||Tl(o),o}async getHeader(){return this.reader.loadHeader()}async defaultVisibilityWindow(){return\"bigwig\"===this.reader.type?-1:this.reader.featureDensity?Math.floor(1e4/this.reader.featureDensity):-1}async getWGValues(e,t){const i=this.genome,n=this.#h[e];if(n&&n.bpPerPixel>.8*t&&n.bpPerPixel<1.2*t)return n.values;{const n=await this.reader.readWGFeatures(t,e);let r=[];for(let e of n){const t=e.chr,n=i.getCumulativeOffset(t);if(void 0===n)continue;const s=Object.assign({},e);s.chr=\"all\",s.start=n+e.start,s.end=n+e.end,s._f=e,r.push(s)}return r.sort(((e,t)=>e.start-t.start)),this.#h[e]={values:r,bpPerPixel:t},r}}supportsWholeGenome(){return\"bigwig\"===this.reader.type}async trackType(){return this.reader.getTrackType()}get searchable(){return this.reader.searchable}async search(e){return this.reader.search(e)}}const ad=.01;function cd(e,t,i,n){if(void 0===this.dataRange||void 0===this.dataRange.max||void 0===this.dataRange.min)return;xo.fillRect(e,0,0,t,i,{fillStyle:\"white\"}),n&&xo.fillRect(e,t-4-2,0,4,i,{fillStyle:n});const r=void 0!==this.flipAxis&&this.flipAxis,s=.95*t-8-5,o=.95*t-5,a={font:\"normal 10px Arial\",textAlign:\"right\",fillStyle:\"black\",strokeStyle:\"black\"};xo.strokeLine(e,s,ad*i,o,ad*i,a),xo.fillText(e,l(r?this.dataRange.min:this.dataRange.max),s+4,ad*i+12,a);const c=.99*i;function l(e){return 0===e?\"0\":Math.abs(e)>=10?e.toFixed():Math.abs(e)>=1?e.toFixed(1):Math.abs(e)>=.1?e.toFixed(2):e.toExponential(1)}xo.strokeLine(e,s,c,o,c,a),xo.fillText(e,l(r?this.dataRange.max:this.dataRange.min),s+4,c-4,a),xo.strokeLine(e,o,ad*i,o,c,a)}class ld extends Hl{static defaults={height:50,flipAxis:!1,logScale:!1,windowFunction:\"mean\",graphType:\"bar\",normalize:void 0,scaleFactor:void 0,overflowColor:\"rgb(255, 32, 255)\",baselineColor:\"lightGray\",summarize:!0,visibilityWindow:void 0};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"wig\",this.featureType=\"numeric\",this.resolutionAware=!0,this.paintAxis=cd;const t=e.format?e.format.toLowerCase():e.format;e.featureSource?(this.featureSource=e.featureSource,delete e.featureSource):this.featureSource=\"bigwig\"===t?new od(e,this.browser.genome):\"tdf\"===t?new Qh(e,this.browser.genome):Ad(e,this.browser.genome),void 0===e.max||!0===e.autoscale?this.autoscale=!0:this.dataRange={min:e.min||0,max:e.max}}async postInit(){const e=await this.getHeader();this.disposed||e&&this.setTrackProperties(e)}supportsWholeGenome(){return void 0===this.visibilityWindow||this.visibilityWindow<0}async getFeatures(e,t,i,n){const r=this.windowFunction,s=await this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow,windowFunction:r});if(this.normalize&&this.featureSource.normalizationFactor){const e=this.featureSource.normalizationFactor;for(let t of s)t.value*=e}if(this.scaleFactor){const e=this.scaleFactor;for(let t of s)t.value*=e}return!this.summarize||\"mean\"!==r&&\"min\"!==r&&\"max\"!==r?s:hd(s,t,n,r)}menuItemList(){const e=[];if(void 0!==this.flipAxis){function t(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}e.push(\"<hr>\"),e.push({label:\"Flip y-axis\",click:t})}return this.featureSource.windowFunctions&&e.push(...this.wigSummarizationItems()),e.push(...this.numericDataMenuItems()),e}wigSummarizationItems(){const e=this.featureSource.windowFunctions,t=[];t.push(\"<hr/>\"),t.push(\"<div>Windowing function</div>\");for(const i of e){const n=Bt(Dl(i,this.windowFunction===i));function r(){this.windowFunction=i,this.trackView.updateViews()}t.push({object:n,click:r})}return t}async getHeader(){return\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getScaleFactor(e,t,i,n){const r=!0===n?e<0?-Math.log10(Math.abs(e)+1):Math.log10(Math.abs(e)+1):e;return i/((!0===n?Math.log10(Math.abs(t)+1):t)-r)}computeYPixelValue(e,t){return(this.flipAxis?e-this.dataRange.min:this.dataRange.max-e)*t}computeYPixelValueInLogScale(e,t){let i=this.dataRange.max,n=this.dataRange.min;return n=n<0?-Math.log10(Math.abs(n)+1):Math.log10(Math.abs(n)+1),i=i<0?-Math.log10(Math.abs(i)+1):Math.log10(Math.abs(i)+1),e=e<0?-Math.log10(Math.abs(e)+1):Math.log10(e+1),(this.flipAxis?e-n:i-e)*t}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=e.pixelHeight-1,a=r+s*n+1,c=this.getScaleFactor(this.dataRange.min,this.dataRange.max,o,this.logScale),l=e=>this.logScale?this.computeYPixelValueInLogScale(e,c):this.computeYPixelValue(e,c);if(t&&t.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){let s,c=-1;const h=l(0);for(let d of t){if(d.end<r)continue;if(d.start>a)break;const t=(d.start-r)/n;if(isNaN(t))continue;let u=l(d.value);const f=(d.end-r)/n-t,p=e.alpha?_s.addAlpha(this.getColorForFeature(d),e.alpha):this.getColorForFeature(d);if(\"line\"===this.graphType)void 0!==s&&xo.strokeLine(i,c,s,t,u,{fillStyle:p,strokeStyle:p}),xo.strokeLine(i,t,u,t+f,u,{fillStyle:p,strokeStyle:p});else if(\"points\"===this.graphType){const e=this.config.pointSize||3,n=t+f/2;xo.fillCircle(i,n,u,e/2,{fillStyle:p,strokeStyle:p}),d.value>this.dataRange.max?xo.fillCircle(i,n,e/2,e/2,3,{fillStyle:this.overflowColor}):d.value<this.dataRange.min&&xo.fillCircle(i,n,o-e/2,e/2,3,{fillStyle:this.overflowColor})}else{const e=Math.min(o,u-h);xo.fillRect(i,t,h,f,e,{fillStyle:p}),d.value>this.dataRange.max?xo.fillRect(i,t,0,f,3,{fillStyle:this.overflowColor}):d.value<this.dataRange.min&&xo.fillRect(i,t,o-2,f,3,{fillStyle:this.overflowColor})}c=t+f,s=u}if(this.dataRange.min<0){let t=this.dataRange.max,n=this.dataRange.min;n=!0===this.logScale?n<0?-Math.log10(Math.abs(n)+1):Math.log10(Math.abs(n)+1):n,t=!0===this.logScale?t<0?-Math.log10(Math.abs(t)+1):Math.log10(Math.abs(t)+1):t;const r=t/(t-n),s=this.flipAxis?(1-r)*o:r*o;xo.strokeLine(i,0,s,e.pixelWidth,s,{strokeStyle:this.baselineColor})}}if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=l(t.y),n={strokeStyle:t.color,strokeWidth:2};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,n):xo.strokeLine(e.context,0,i,e.pixelWidth,i,n)}}popupData(e,t){if(void 0===t&&(t=this.clickedFeatures(e)),t&&t.length>0){const i=e.genomicLocation,n=[];t.sort((function(e,t){return Math.abs((e.start+e.end)/2-i)-Math.abs((t.start+t.end)/2-i)}));const r=t.length>10?t.slice(0,10):t;r.sort((function(e,t){return e.start-t.start}));for(let e of r)if(e){n.length>0&&n.push(\"<hr/>\");let t=e.end-e.start==1?Rt(Math.floor(e.start)+1):Rt(Math.floor(e.start)+1)+\"-\"+Rt(Math.floor(e.end));n.push({name:\"Position:\",value:t}),n.push({name:\"Value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\",value:Rt(e.value.toFixed(4))})}return r.length<t.length&&n.push(\"<hr/>...\"),n}return[]}get supportsWholeGenome(){return!this.config.indexURL&&!1!==this.config.supportsWholeGenome}getColorForFeature(e){let t=e.value<0&&this.altColor?this.altColor:this.color||\"rgb(150, 150, 150)\";return\"function\"==typeof t?t(e.value):t}dispose(){this.trackView=void 0}}function hd(e,t,i,n=\"mean\"){if(i<=1||!e||0===e.length)return e;const r=e[0].chr,s=i,o=[],a=e=>{const i=t+e.bin*s,a=i+s;let c;switch(n){case\"mean\":c=e.sumData/e.count;break;case\"max\":c=e.max;break;case\"min\":c=e.min;break;default:throw Error(`Unknown window function: ${n}`)}const l=`${n} of ${e.count} values`;o.push({chr:r,start:i,end:a,value:c,description:l})};let c;for(let i of e){let e=Math.floor((i.start-t)/s);const n=Math.floor((i.end-t)/s);if(c&&e===c.bin&&(c.add(i),e++),!c||n>c.bin){if(c&&a(c),n>e){const e=t+n*s;o.push({chr:r,start:i.start,end:e,value:i.value})}c=new dd(n,i)}}c&&a(c);const l=[];let h=o[0];for(let e of o)h.value===e.value&&e.start<=h.end?h.end=e.end:(l.push(h),h=e);return l.push(h),l}class dd{constructor(e,t){this.bin=e,this.sumData=t.value,this.count=1,this.min=t.value,this.max=t.value}add(e){this.sumData+=e.value,this.max=Math.max(e.value,this.max),this.min=Math.min(e.value,this.min),this.count++}get mean(){return this.sumData/this.count}}class ud extends Hh{constructor(e,t){super(t),this.config=e||{},this.genome=t,this.sourceType=void 0===e.sourceType?\"file\":e.sourceType,this.maxWGCount=e.maxWGCount||1e4,this.windowFunctions=[\"mean\",\"min\",\"max\",\"none\"];const i=new Set([\"bigwig\",\"bw\",\"bigbed\",\"bb\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\",\"tdf\"]);if(this.queryable=e.indexURL||!0===e.queryable,e.reader)this.reader=e.reader,this.queryable=!1!==e.queryable;else{if(\"ga4gh\"===e.sourceType)throw Error(\"Unsupported source type 'ga4gh'\");\"eqtl\"!==e.type&&\"qtl\"!==e.type||\"gtex-ws\"!==e.sourceType?\"htsget\"===e.sourceType?(this.reader=new Lh(e,t),this.queryable=!0):\"ucscservice\"===e.sourceType?(this.reader=new Nh(e.source),this.queryable=!0):\"custom\"===e.sourceType?(this.reader=new Eh(e.source),this.queryable=!1!==e.source.queryable):\"service\"===e.sourceType?(this.reader=new Ih(e,t),this.queryable=!0):(this.reader=new Ih(e,t),void 0!==e.queryable?this.queryable=e.queryable:(i.has(e.format)||this.reader.indexed)&&(this.queryable=!0)):(this.reader=new Bh(e),this.queryable=!0)}this.searchable=!1!==e.searchable}async defaultVisibilityWindow(){if(this.reader&&\"function\"==typeof this.reader.defaultVisibilityWindow)return this.reader.defaultVisibilityWindow()}async trackType(){const e=await this.getHeader();return e?e.type:void 0}async getHeader(){if(!this.header)if(this.reader&&\"function\"==typeof this.reader.readHeader){const e=await this.reader.readHeader();e?(this.header=e,e.format&&(this.config.format=e.format)):this.header={}}else this.header={};return this.header}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r,windowFunction:s}){const o=\"all\"===e.toLowerCase();if(t=t||0,i=i||Number.MAX_SAFE_INTEGER,(o&&!this.wgFeatures&&this.supportsWholeGenome()||this.config.disableCache||!this.featureCache||!this.featureCache.containsRange(new hc(e,t,i)))&&await this.loadFeatures(e,t,i,r),o){if(!this.wgFeatures)if(this.supportsWholeGenome())if(\"wig\"===this.config.type){const e=await Ll(this.featureCache.getAllFeatures(),this.genome,1e6);this.wgFeatures=hd(e,0,n,s)}else this.wgFeatures=await Ll(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount);else this.wgFeatures=[];return this.wgFeatures}return this.featureCache.queryFeatures(e,t,i)}async findFeatures(e){return this.featureCache?this.featureCache.findFeatures(e):[]}supportsWholeGenome(){return!this.queryable}getAllFeatures(){return this.queryable||!this.featureCache?[]:this.featureCache.getAllFeatures()}async loadFeatures(e,t,i,n){await this.getHeader();const r=this.reader;let s=t,o=i,a=e;if(!this.chrAliasManager&&this.reader&&this.reader.sequenceNames&&(this.chrAliasManager=new zh(this.reader.sequenceNames,this.genome)),this.chrAliasManager&&(a=await this.chrAliasManager.getAliasName(e)),(!n||n<=0)&&!1!==this.config.expandQuery){const e=this.genome?this.genome.getChromosome(a):void 0;s=0,o=Math.max(e?e.bpLength:Number.MAX_SAFE_INTEGER,i)}else if(n>i-t&&!1!==this.config.expandQuery){let e=Math.min(4.1*(i-t),n);this.config.minQuerySize&&e<this.config.minQuerySize&&(e=this.config.minQuerySize),s=Math.max(0,(t+i-e)/2),o=s+e}let c=await r.readFeatures(a,s,o);void 0===this.queryable&&(this.queryable=r.indexed);const l=this.queryable?new hc(e,s,o):void 0;if(c){if(\"wig\"!==this.config.format&&\"junctions\"!==this.config.type){zl(c,this.config.maxRows||Number.MAX_SAFE_INTEGER)}this.featureCache=new Zs(c,this.genome,l),this.searchable&&this.addFeaturesToDB(c,this.config)}else this.featureCache=new Zs([],l)}addFeaturesToDB(e,t){this.featureMap||(this.featureMap=new Map);const i=t.searchableFields||[\"name\",\"transcript_id\",\"gene_id\",\"gene_name\",\"id\"];for(let t of e)for(let e of i){let i;if(t.hasOwnProperty(e)?i=t[e]:\"function\"==typeof t.getAttributeValue&&(i=t.getAttributeValue(e)),i){if(i=i.replaceAll(\" \",\"+\").toUpperCase(),this.featureMap.has(i)){const e=this.featureMap.get(i);if(t.end-t.start<e.end-e.start)continue}this.featureMap.set(i,t)}}}search(e){if(this.featureMap)return this.featureMap.get(e.toUpperCase())}}class fd extends Hh{constructor(e,t){super(t),this.config=e,this.genome=t,this.queryable=!1,this.searchable=!1!==e.searchable,this.updateFeatures(e.features)}updateFeatures(e){zl(e=function(e,t){if(t)for(let i of e)i.chr=t.getChromosomeName(i.chr);return e}(e,this.genome)),this.config.mappings&&function(e,t){let i=Object.keys(t);e.forEach((function(e){i.forEach((function(i){e[i]=e[t[i]]}))}))}(e,this.config.mappings),this.featureCache=new Zs(e,this.genome),(this.searchable||this.config.searchableFields)&&this.addFeaturesToDB(e,this.config)}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome,o=s?s.getChromosomeName(e):e;return\"all\"===o.toLowerCase()?Ll(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.featureCache.queryFeatures(o,t,i)}getAllFeatures(){return this.featureCache.getAllFeatures()}supportsWholeGenome(){return!0}addFeaturesToDB(e,t){this.featureMap||(this.featureMap=new Map);const i=t.searchableFields||[\"name\"];for(let t of e)for(let e of i){let i;if(\"function\"==typeof t.getAttributeValue&&(i=t.getAttributeValue(e)),i||(i=t[e]),i){i=i.replaceAll(\" \",\"+\");const e=this.featureMap.get(i.toUpperCase());if(e&&e.end-e.start>t.end-t.start)continue;this.featureMap.set(i.toUpperCase(),t)}}}search(e){if(this.featureMap)return this.featureMap.get(e.toUpperCase())}}class pd{constructor({chr:e,locus:t,accession:i,aliases:n,features:r,sequence:s}){this.chr=e,this.locus=t,this.accession=i,this.aliases=n,this.features=r,this.sequence=s,this.bpLength=s.length}toJSON(){return{gbkURL:this.url}}getSequenceRecord(e){return{chr:this.chr,bpLength:this.bpLength}}get chromosomeNames(){return[this.chr]}getFirstChromosomeName(){return this.chr}get id(){return this.accession}get name(){return this.locus}get initialLocus(){return this.chr}get description(){return this.locus}get infoURL(){return this.url}showWholeGenomeView(){return!1}getHomeChromosomeName(){return this.chr}getChromosomeName(e){return e}getChromosomeDisplayName(e){return this.chr}getChromosome(e){if(e===this.chr)return{name:this.chr,bpLength:this.bpLength}}async loadChromosome(e){return this.getChromosome(e)}async getAliasRecord(e){}getCytobands(e){return[]}getChromosomes(){return[this.getChromosome(this.chr)]}get wgChromosomeNames(){}getGenomeCoordinate(e,t){if(e===this.chr)return t}getChromosomeCoordinate(e){return{chr:this.chr,position:e}}getCumulativeOffset(e){return 0}getGenomeLength(){return this.bpLength}async getSequence(e,t,i){return e===this.chr?this.sequence.substring(t,i):void 0}getSequenceInterval(e,t,i){return e===this.chr?new dc(this.chr,0,this.sequence.length,this.sequence):void 0}}const gd=/\\s+/,md=new Map;async function wd(e){let t=md.get(e);if(!t){t=function(e){if(!e)return null;const t=mh(e);let i=t.nextLine();const n=i.split(/\\s+/);if(\"LOCUS\"!==n[0].toUpperCase())throw Error(\"Expected `LOCUS` line.  Found: \"+i);const r=n[1].trim();let s,o;do{if(i=t.nextLine(),i.startsWith(\"ACCESSION\")){const e=i.split(gd);if(e.length<2)throw Error(\"Genbank file missing ACCESSION number.\");s=e[1].trim()}else if(i.startsWith(\"ALIASES\")){const e=i.split(gd);e.length>1&&(o=e[1].split(\",\"))}}while(i&&!i.startsWith(\"FEATURES\"));const a=s||r,c=function(e,t){const i=[];let n,r,s,o=0;for(;;)if(r=t.nextLine(),\"\"!==r){if(!r||r.startsWith(\"ORIGIN\"))break;if(r.length<6)o<10&&console(\"Unexpected line in genbank file (skipping): \"+r),o++;else if(\" \"!==r.charAt(5)){let t=r.substring(5,21).trim();s={chr:e,type:t,attributes:{},getAttributeValue:function(e){return this.attributes[e]}},n=r.substring(21),\"source\"!==t.toLowerCase()&&i.push(s)}else{let t=r.substring(21).trim();if(t.length>0)if(47===t.charCodeAt(0)){if(47===n.charCodeAt(0)){let e=n.split(\"=\",2);if(e.length>1){let t=e[0].length>1?e[0].substring(1):\"\",i=Fd(e[1]);s.attributes[t]=i}}else{const t=n.includes(\"complement\")?\"-\":\"+\";s.strand=t;let i=n.replace(\"join\",\"\").replace(\"order\",\"\").replace(\"complement\",\"\").replace(\"(\",\"\").replace(\")\",\"\");if(i.includes(\"..\")){i=i.replace(\"<\",\"\").replace(\">\",\"\");const n=bd(i,e,t),r=n[0];s.start=r.start;const o=n[n.length-1];s.end=o.end,n.length>1&&(s.exons=n)}else s.start=parseInt(i)-1,s.end=s.start+1}n=t}else n+=t}}return i}(a,t),l=function(e){let t,i=\"\";for(;(t=e.nextLine())&&!t.startsWith(\"//\");){t=t.trim();const e=t.split(/\\s+/);for(let t=1;t<e.length;t++)i+=e[t]}return i}(t);return new pd({chr:a,locus:r,accession:s,aliases:o,features:c,sequence:l})}(await Qs.loadString(e,{})),t.url=e,md.set(e,t)}return t}function bd(e,t,i){const n=e.split(\",\"),r=[];e.includes(\"complement\");for(const e of n){const n=e.split(\"..\");let s=0;try{s=parseInt(n[0])-1}catch(e){console.error(e)}let o=s+1;n.length>1&&(o=parseInt(n[1])),r.push({chr:t,start:s,end:o,strand:i})}return r.sort((function(e,t){return e.start-t.start})),r}function Fd(e){return e.startsWith('\"')&&e.endsWith('\"')&&(e=e.substring(1,e.length-2)),e}class vd extends Hh{constructor(e,t){super(t),this.config=e,this.searchable=!0}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){if(!this.featureSource){const e=await wd(this.config.url);this.featureSource=new fd({genome:this.config.genome,features:e.features,searchableFields:[\"gene\",\"db_xref\",\"locus_tag\",\"transcript_id\"]})}return this.featureSource.getFeatures({chr:e,start:t,end:i})}supportsWholeGenome(){return!1}search(e){return this.featureSource.search(e)}}const yd=new Set([\"bigwig\",\"bw\",\"bigbed\",\"bb\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\"]);function Ad(e,t){const i=e.format?e.format.toLowerCase():void 0;return e.features?new fd(e,t):yd.has(i)?new od(e,t):\"tdf\"===i?new Qh(e,t):\"gbk\"===i?new vd(e,t):new ud(e,t)}function Cd(e){return(3-e.readingFrame)%3}function _d(e){return e.cdStart||e.start}function xd(e){return e.cdEnd||e.end}const kd=.25;function Id(e,t,i){let n=(e.start-t)/i,r=(e.end-t)/i,s=r-n;return s<3&&(s=3,n-=1.5),{px:n,px1:r,pw:s}}function Sd(e,t,i,n,r,s){try{r.save(),r.fillStyle=this.color,r.strokeStyle=this.color;const n=this.getColorForFeature(e);let o,a;r.fillStyle=n,r.strokeStyle=n,\"SQUISHED\"===this.displayMode&&void 0!==e.row?(o=this.featureHeight/2,a=this.margin+this.squishedRowHeight*e.row):\"EXPANDED\"===this.displayMode&&void 0!==e.row?(o=this.featureHeight,a=this.margin+this.expandedRowHeight*e.row):(o=this.featureHeight,a=this.margin);const c=s.pixelWidth,l=a+o/2,h=o/2,d=l-h/2,u=e.exons?e.exons.length:0,f=Id(e,t,i),p=this.arrowSpacing,g=\"+\"===e.strand?1:\"-\"===e.strand?-1:0;if(0===u){const e=Math.max(0,f.px),t=Math.min(c,f.px1),i=t-e;if(r.fillRect(e,a,i,o),0!==g){r.fillStyle=\"white\",r.strokeStyle=\"white\";for(let i=e+p/2;i<t;i+=p)xo.strokeLine(r,i-2*g,l-2,i,l),xo.strokeLine(r,i-2*g,l+2,i,l);r.fillStyle=n,r.strokeStyle=n}}else{xo.strokeLine(r,f.px+1,l,f.px1-1,l);const u=Math.max(0,f.px)+p/2,m=Math.min(c,f.px1);for(let e=u;e<m;e+=p)xo.strokeLine(r,e-2*g,l-2,e,l),xo.strokeLine(r,e-2*g,l+2,e,l);for(let u=0;u<e.exons.length;u++){const f=e.exons[u];let m,w=Math.round((f.start-t)/i),b=Math.round((f.end-t)/i),F=Math.max(1,b-w);if(!(w+F<0)){if(w>c)break;if(f.utr)r.fillRect(w,d,F,h);else{if(f.cdStart&&(m=Math.round((f.cdStart-t)/i),r.fillRect(w,d,m-w,h),F-=m-w,w=m),f.cdEnd&&(m=Math.round((f.cdEnd-t)/i),r.fillRect(m,d,b-m,h),F-=b-m,b=m),F=Math.max(F,1),r.fillRect(w,a,F,o),void 0!==f.readingFrame&&s.bpPerPixel<kd&&s.sequenceInterval){const i=u>0&&void 0!==e.exons[u-1].readingFrame?e.exons[u-1]:void 0,n=u<e.exons.length-1&&void 0!==e.exons[u+1].readingFrame?e.exons[u+1]:void 0;Ed.call(this,r,e.strand,i,f,n,t,s.bpPerPixel,a,o,s.sequenceInterval)}if(F>p+5&&0!==g&&s.bpPerPixel>kd){r.fillStyle=\"white\",r.strokeStyle=\"white\";for(let e=w+p/2;e<b;e+=p)xo.strokeLine(r,e-2*g,l-2,e,l),xo.strokeLine(r,e-2*g,l+2,e,l);r.fillStyle=n,r.strokeStyle=n}}}}}s.drawLabel&&\"SQUISHED\"!==this.displayMode&&Nd.call(this,r,e,f.px,f.px1,a,s.referenceFrame,s)}finally{r.restore()}}function Ed(e,t,i,n,r,s,o,a,c,l){const h=[\"rgb(124,124,204)\",\"rgb(12, 12, 120)\"];e.save();const d=(t,i,n,r,d,u)=>{const f=Math.round((i-s)/o),p=Math.round((n-s)/o)-f;let g;if(void 0===r){if(l.hasSequence(i,n)){const e=l.getSequence(i,n);if(e&&3===e.length){const i=\"+\"===t?e:ac(e.split(\"\").reverse().join(\"\"));g=Gd[i]}}}else g=r;e.fillStyle=\"M\"===r||\"M\"===g&&0===u?\"#83f902\":\"STOP\"===g?\"#ff2101\":h[d],e.fillRect(f,a,p,c),g&&(e.save(),((t,i,n,r,s)=>{\"STOP\"===s&&(s=\"*\");const o=e.measureText(s).width;xo.fillText(e,s,n+(i-o)/2,r-4,{fillStyle:\"#ffffff\"})})(0,p,f,a+c,g),e.restore());const m=n-i;return m>0&&m<3?{start:i,end:n}:void 0},u=Cd(n);let f,p,g,m,w,b=_d(n),F=xd(n),v=1;if(\"+\"===t){for(u>0&&(b+=u),v=1,w=0,f=b;f<F;w++,f+=3)m=v%2,p=Math.min(F,f+3),g=d(t,f,p,void 0,v%2,w),++v;if(u>0||g){const e=u>0?Bd.call(this,t,u,b-u,b,g,i,n,r,l):Bd.call(this,t,void 0,void 0,void 0,g,i,n,r,l);if(e){const{left:i,rite:n}=e;i&&d(t,b-u,b,i.aminoAcidLetter,0,void 0),n&&d(t,g.start,g.end,n.aminoAcidLetter,m,void 0)}}}else{for(u>0&&(F-=u),v=1,w=0,w=0,p=F;p>b;w++,p-=3)m=v%2,f=Math.max(b,p-3),g=d(t,f,p,void 0,v%2,w),++v;if(u>0||g){const e=u>0?Bd.call(this,t,u,F,F+u,g,i,n,r,l):Bd.call(this,t,void 0,void 0,void 0,g,i,n,r,l);if(e){const{left:i,rite:n}=e;n&&d(t,F,F+u,n.aminoAcidLetter,0,void 0),i&&d(t,g.start,g.end,i.aminoAcidLetter,m,void 0)}}}e.restore()}function Nd(e,t,i,n,r,s,o){try{e.save();let s=t.name;if(void 0===s&&t.gene&&(s=t.gene.name),void 0===s&&(s=t.id||t.ID),!s||\".\"===s)return;let a=o.pixelXOffset||0;const c=Math.max(i,-a);let l,h=(c+Math.min(n,-a+o.viewportWidth))/2;\"COLLAPSED\"===this.displayMode&&\"SLANT\"===this.labelDisplayMode&&(l={rotate:{angle:45}});const d=function(e,t){return t?e+20:e+25}(r,l);let u=this.getColorForFeature(t),f=this.browser.qtlSelections.hasPhenotype(t.name);const p={textAlign:\"SLANT\"===this.labelDisplayMode?void 0:\"center\",fillStyle:u,strokeStyle:u},g=e.measureText(s),m=h-g.width/2,w=h+g.width/2,b=o.rowLastLabelX[t.row]||-Number.MAX_SAFE_INTEGER;(o.labelAllFeatures||m>b||f)&&(o.rowLastLabelX[t.row]=w,\"y\"===o.axis?(e.save(),xo.labelTransformWithContext(e,h),xo.fillText(e,s,h,d,p,l),e.restore()):(e.clearRect(h-g.width/2-1,d-g.actualBoundingBoxAscent-1,g.width+2,g.actualBoundingBoxAscent+g.actualBoundingBoxDescent+2),xo.fillText(e,s,h,d,p,l)))}finally{e.restore()}}function Bd(e,t,i,n,r,s,o,a,c){let l,h,d=\"\",u=\"\",f=\"\";const p={left:void 0,rite:void 0};if(\"+\"===e){if(t){if(u=c.getSequence(i,n),!u)return;if([l,h]=[xd(s)-(3-t),xd(s)],d=c.getSequence(l,h),!d)return;f=d+u,p.left={triplet:f,aminoAcidLetter:Gd[f]}}if(r){if(d=c.getSequence(r.start,r.end),!d)return;const e=Cd(a),t=_d(a);if(u=c.getSequence(t,t+e),!u)return;f=d+u,p.rite={triplet:f,aminoAcidLetter:Gd[f]}}}else{if(t){if(d=c.getSequence(i,n),void 0===d)return;if([l,h]=[_d(a),_d(a)+(3-t)],u=c.getSequence(l,h),void 0===u)return;f=d+u,f=ac(f.split(\"\").reverse().join(\"\")),p.rite={triplet:f,aminoAcidLetter:Gd[f]}}if(r){if(u=c.getSequence(r.start,r.end),void 0===u)return;const e=Cd(s),t=xd(s);if(d=c.getSequence(t-e,t),void 0===d)return;f=d+u,f=ac(f.split(\"\").reverse().join(\"\")),p.left={triplet:f,aminoAcidLetter:Gd[f]}}}return p}const Md=new Set([\"nonsense\",\"missense\",\"stop-loss\",\"frameshift\",\"cds-indel\"]),Rd=new Set([\"coding-synon\"]),Dd=new Set([\"splice-3\",\"splice-5\"]),Td=new Set([\"untranslated-5\",\"untranslated-3\"]);function Ld(e,t,i,n,r){var s,o,a,c,l,h,d=Id(e,t,i),u=this.margin,f=this.snpColors.length;switch(s=\"squished\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight,this.colorBy){case\"function\":c=e.func,h=c.split(\",\"),l=h.map((function(e){return Md.has(e)||Dd.has(e)?f-1:Rd.has(e)?f-2:Td.has(e)?f-3:0})),o=l.reduce((function(e,t){return Math.max(e,t)}));break;case\"class\":o=\"deletion\"===(a=e.class)?f-1:\"mnp\"===a?f-2:\"microsatellite\"===a||\"named\"===a?f-3:0}r.fillStyle=this.snpColors[o],r.fillRect(d.px,u,d.pw,s)}function zd(e,t,i,n,r){const s=\"EXPANDED\"===this.displayMode?this.expandedRowHeight:this.squishedRowHeight;let o=this.margin;\"COLLAPSED\"!==this.displayMode&&void 0!==e.row&&(o+=e.row*s);const a=o+.5*s,c=a-.5*s,l=a+.5*s,h=Math.round((e.junction_left-t)/i),d=Math.round((e.junction_right-t)/i);r.beginPath(),r.moveTo(h,a),r.bezierCurveTo(h,c,d,c,d,a),r.lineWidth=1+Math.log(e.num_junction_reads)/Math.log(2),r.strokeStyle=\"blue\",r.stroke();const u=e.spanning_frag_coords;for(let e=0;e<u.length;e++){const n=u[e],s=Math.round((n.left-t)/i),o=Math.round((n.right-t)/i);r.beginPath(),r.moveTo(s,a),r.bezierCurveTo(s,l,o,l,o,a),r.lineWidth=1,r.strokeStyle=\"purple\",r.stroke()}}class Hd extends Hl{static defaults={type:\"annotation\",maxRows:1e3,displayMode:\"EXPANDED\",margin:10,featureHeight:14,useScore:!1};constructor(e,t){super(e,t)}init(e){super.init(e),this.labelDisplayMode=e.labelDisplayMode,e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):\"blat\"!==e.type&&(this.featureSource=e.featureSource?e.featureSource:Ad(e,this.browser.genome)),\"FusionJuncSpan\"===e.type?(this.render=e.render||zd,this.squishedRowHeight=e.squishedRowHeight||50,this.expandedRowHeight=e.expandedRowHeight||50,this.height=e.height||this.margin+2*this.expandedRowHeight):\"snp\"===e.type?(this.render=e.render||Ld,this.snpColors=[\"rgb(0,0,0)\",\"rgb(0,0,255)\",\"rgb(0,255,0)\",\"rgb(255,0,0)\"],this.colorBy=\"function\",this.expandedRowHeight=e.expandedRowHeight||10,this.squishedRowHeight=e.squishedRowHeight||5,this.height=e.height||30):(this.render=e.render||Sd,this.arrowSpacing=30,function(e){e.browser.on&&(e.browser.on(\"trackdragend\",t),e.browser.on(\"trackremoved\",i));function t(){e.trackView&&\"SQUISHED\"!==e.displayMode&&e.trackView.repaintViews()}function i(n){e.browser.un&&e===n&&(e.browser.un(\"trackdragend\",t),e.browser.un(\"trackremoved\",i))}}(this),this.squishedRowHeight=e.squishedRowHeight||15,this.expandedRowHeight=e.expandedRowHeight||30,this.height=e.height||this.margin+2*this.expandedRowHeight,e.colorBy&&(e.colorBy.field&&(e.colorTable=e.colorBy.pallete||e.colorBy.palette,e.colorBy=e.colorBy.field),this.colorBy=e.colorBy,e.colorTable?this.colorTable=new ao(e.colorTable):this.colorTable=new oo(\"Set1\")))}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get searchable(){return this.featureSource.searchable}async search(e){return this.featureSource&&this.featureSource.searchable?this.featureSource.search(e):void 0}get supportsWholeGenome(){return void 0!==this.config.supportsWholeGenome?this.config.supportsWholeGenome:this.featureSource&&\"function\"==typeof this.featureSource.supportsWholeGenome?this.featureSource.supportsWholeGenome():!(void 0!==this.visibilityWindow||!1!==this.config.indexed&&this.config.indexURL)||void 0}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}computePixelHeight(e){if(\"COLLAPSED\"===this.displayMode)return this.margin+this.expandedRowHeight;{let t=0;if(e&&\"function\"==typeof e.forEach)for(let i of e)i.row&&i.row>t&&(t=i.row);return this.margin+(t+1)*(\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight)}}draw(e){const{features:t,context:i,bpPerPixel:n,bpStart:r,bpEnd:s,pixelWidth:o,pixelHeight:a,referenceFrame:c}=e;if(n<kd&&(e.sequenceInterval=this.browser.genome.getSequenceInterval(c.chr,r,s)),this.isMergedTrack||xo.fillRect(i,0,e.pixelTop,o,a,{fillStyle:\"rgb(255, 255, 255)\"}),t){const c=[];e.rowLastX=[],e.rowLastLabelX=[];for(let i of t)if(i.start>r&&i.end<s){const t=\"COLLAPSED\"===this.displayMode?0:i.row||0;c[t]?c[t]++:c[t]=1,e.rowLastX[t]=-Number.MAX_SAFE_INTEGER,e.rowLastLabelX[t]=-Number.MAX_SAFE_INTEGER}const l=o/Math.max(1,Math.max(...c.filter((e=>!isNaN(e)))));let h=[];const d=[];for(let o of t){if(o.end<r)continue;if(o.start>s)break;\"COLLAPSED\"===this.displayMode&&this.browser.qtlSelections.hasPhenotype(o.name)&&d.push(o);const t=\"COLLAPSED\"===this.displayMode?0:o.row;e.drawLabel=e.labelAllFeatures||l>10;const c=Math.ceil((o.end-r)/n),u=h[t];if(!u||c>u){this.render.call(this,o,r,n,a,i,e);const s=Math.floor((o.start-r)/n);u&&s-u<=0&&(i.globalAlpha=.5,xo.strokeLine(i,s,0,s,a,{strokeStyle:\"rgb(255, 255, 255)\"}),i.globalAlpha=1),h[t]=c}}for(let t of d)e.drawLabel=!0,this.render.call(this,t,r,n,a,i,e)}else console.log(\"No feature list\")}clickedFeatures(e){const t=e.y-this.margin,i=super.clickedFeatures(e);let n;switch(this.displayMode){case\"SQUISHED\":n=Math.floor(t/this.squishedRowHeight);break;case\"EXPANDED\":n=Math.floor(t/this.expandedRowHeight);break;default:n=void 0}return i.filter((function(e){return void 0===n||void 0===e.row||n===e.row}))}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=[];for(let e of t){const t=e._f||e,r=\"function\"==typeof t.popupData?t.popupData(i):this.extractPopupData(t);if(r){n.length>0&&n.push(\"<hr/><hr/>\");const s=this.infoURL||this.config.infoURL;for(let t of r)if(n.push(t),s&&t.name&&\"name\"===t.name.toLowerCase()&&t.value&&Mt(t.value)&&!t.value.startsWith(\"<\")){const i=s.replace(\"$$\",e.name);t.value=`<a target=_blank href=${i}>${t.value}</a>`}const o=\"gff\"===this.config.format||\"gff3\"===this.config.format||\"gtf\"===this.config.format;if(t.exons&&t.exons.length>1)for(let e=0;e<t.exons.length;e++){const r=t.exons[e];if(i>=r.start&&i<=r.end){const i=o?r.number:\"-\"===t.strand?t.exons.length-e:e+1;i&&(n.push(\"<hr/>\"),n.push({name:\"Exon Number\",value:i}));break}}}}return n}menuItemList(){const e=[];if(this.render===Ld){e.push(\"<hr/>\");for(const i of[\"function\",\"class\"]){const n=Bt(Dl(`Color by ${i}`,i===this.colorBy));function r(){this.colorBy=i,this.trackView.repaintViews()}e.push({object:n,click:r})}}e.push(\"<hr/>\");const t={COLLAPSED:\"Collapse\",SQUISHED:\"Squish\",EXPANDED:\"Expand\"};for(const s of[\"COLLAPSED\",\"SQUISHED\",\"EXPANDED\"]){const o=Bt(Dl(t[s],s===this.displayMode));function a(){this.displayMode=s,this.config.displayMode=s,this.trackView.checkContentHeight(),this.trackView.repaintViews()}e.push({object:o,click:a})}return e}contextMenuItemList(e){const t=this.clickedFeatures(e);if(void 0===t||0===t.length)return;t.length>1&&t.sort(((e,t)=>t.end-t.start-(e.end-e.start)));const i=t[0];if(i.end-i.start<=1e6){const e=[{label:\"View feature sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i.chr,i.start,i.end);e?\"-\"===i.strand&&(e=cc(e)):e=\"Unknown sequence\",this.browser.alert.present(e)}}];return Xa()&&void 0!==navigator.clipboard&&e.push({label:\"Copy feature sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i.chr,i.start,i.end);e?\"-\"===i.strand&&(e=cc(e)):e=\"Unknown sequence\";try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),e.push(\"<hr/>\"),e}}description(){if(Ld===this.render){let e=\"<html>\"+this.name+\"<hr/>\";return e+=\"<em>Color By Function:</em><br>\",e+='<span style=\"color:red\">Red</span>: Coding-Non-Synonymous, Splice Site<br>',e+='<span style=\"color:green\">Green</span>: Coding-Synonymous<br>',e+='<span style=\"color:blue\">Blue</span>: Untranslated<br>',e+='<span style=\"color:black\">Black</span>: Intron, Locus, Unknown<br><br>',e+=\"<em>Color By Class:</em><br>\",e+='<span style=\"color:red\">Red</span>: Deletion<br>',e+='<span style=\"color:green\">Green</span>: MNP<br>',e+='<span style=\"color:blue\">Blue</span>: Microsatellite, Named<br>',e+='<span style=\"color:black\">Black</span>: Indel, Insertion, SNP',e+=\"</html>\",e}return super.description()}getColorForFeature(e){const t=e._f||e;let i;if(e.name&&this.browser.qtlSelections.hasPhenotype(e.name))i=this.browser.qtlSelections.colorForGene(e.name);else if(this.altColor&&\"-\"===t.strand)i=\"function\"==typeof this.altColor?this.altColor(t):this.altColor;else if(this.color)i=\"function\"==typeof this.color?this.color(t):this.color;else if(this.colorBy){const e=t.getAttributeValue?t.getAttributeValue(this.colorBy):t[this.colorBy];i=this.colorTable.getColor(e)}else t.color&&(i=t.color);if(i||(i=\"rgb(0, 0, 150)\"),t.alpha&&1!==t.alpha)i=_s.addAlpha(i,t.alpha);else if(this.useScore&&t.score&&!Number.isNaN(t.score)){const e=function(e,t,i){const n=(t-e)/9,r=Math.floor((i-e)/n);return Math.min(1,.2+.8*r/9)}(this.config.min?this.config.min:this.viewLimitMin?this.viewLimitMin:0,this.config.max?this.config.max:this.viewLimitMax?this.viewLimitMax:1e3,t.score);t.alpha=e,i=_s.addAlpha(i,e)}return i}dispose(){this.trackView=void 0}}class Pd{constructor(t){if(this.config=t,this.browser=t.browser,this.columnFormat=t.columnFormat,this.tableRowSelectionList=[],this.tableDOM=e({class:\"igv-roi-table\"}),t.width){let[e]=t.width.split(\"px\");e=parseInt(e,10),this.tableDOM.style.width=`${Math.min(e,1600)}px`}t.parent.appendChild(this.tableDOM),this.headerDOM=t,this.tableColumnTitles=this.tableDOM,this.tableRowContainer=this.tableDOM,this.footerDOM=t.gotoButtonHandler}set headerDOM({browser:t,parent:i,headerTitle:n,dismissHandler:r}){const s=e();this.tableDOM.appendChild(s);const o=e();s.appendChild(o),o.innerHTML=n;const a=e();s.appendChild(a),a.appendChild(l(\"times\")),this.boundDismissHandler=function(e){e.stopPropagation(),r()}.bind(this),a.addEventListener(\"click\",this.boundDismissHandler);const{y:c}=t.root.getBoundingClientRect(),{y:h}=i.getBoundingClientRect(),d=-(h-c);p(this.tableDOM,s,{minX:0,minY:d}),this.tableDOM.style.display=\"none\",this._headerDOM=s}set tableColumnTitles(t){const i=e({class:\"igv-roi-table-column-titles\"});t.appendChild(i);for(const{label:t,width:n}of this.columnFormat){const r=e();i.appendChild(r),r.style.width=n,r.innerText=t}this._tableColumnTitlesDOM=i}get tableColumnTitles(){return this._tableColumnTitlesDOM}set tableRowContainer(t){const i=e({class:\"igv-roi-table-row-container\"});t.appendChild(i),this._tableRowContainerDOM=i}get tableRowContainer(){return this._tableRowContainerDOM}set footerDOM(t){const i=e();this.tableDOM.appendChild(i);const n=e({class:\"igv-roi-table-button\"});i.appendChild(n),n.id=\"igv-roi-table-view-button\",n.textContent=\"Go To\",n.style.pointerEvents=\"none\",this._footerDOM=i,this.gotoButton=n,this.boundGotoButtonHandler=t.bind(this),this.gotoButton.addEventListener(\"click\",this.boundGotoButtonHandler)}tableRowDOMHelper(e){e.addEventListener(\"mousedown\",(t=>{t.stopPropagation(),e.classList.toggle(\"igv-roi-table-row-selected\"),e.classList.contains(\"igv-roi-table-row-selected\")?e.classList.remove(\"igv-roi-table-row-hover\"):e.classList.add(\"igv-roi-table-row-hover\"),this.setTableRowSelectionState(e.classList.contains(\"igv-roi-table-row-selected\"))})),e.addEventListener(\"mouseover\",(t=>{e.classList.contains(\"igv-roi-table-row-selected\")?e.classList.remove(\"igv-roi-table-row-hover\"):e.classList.add(\"igv-roi-table-row-hover\")})),e.addEventListener(\"mouseout\",(t=>{e.classList.remove(\"igv-roi-table-row-hover\")}))}clearTable(){const e=this.tableRowContainer.querySelectorAll(\".igv-roi-table-row\");for(let t of e)t.remove()}setTableRowSelectionState(e){e?this.tableRowSelectionList.push(1):this.tableRowSelectionList.pop(),this.gotoButton.style.pointerEvents=this.tableRowSelectionList.length>0?\"auto\":\"none\"}present(){this.tableDOM.style.left=\"0px\";const{y:e}=this.browser.root.getBoundingClientRect(),{y:t}=this.config.parent.getBoundingClientRect();this.tableDOM.style.top=e-t+\"px\",this.tableDOM.style.display=\"flex\"}dismiss(){this.tableDOM.style.display=\"none\"}isVisible(){return\"none\"!==this.tableDOM.style.display}dispose(){this.tableDOM.innerHTML=\"\",this.tableDOM.remove();for(const e of Object.keys(this))this[e]=void 0;document.removeEventListener(\"click\",this.boundDismissHandler)}}class Od extends Pd{constructor(e){super(Object.assign({width:\"1024px\"},e)),this.descriptionDOM=e}set descriptionDOM(t){if(t.description){let i;i=e({class:\"igv-roi-table-description\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.style.height=\"auto\",i.innerHTML=\"BLAT result for query sequence:\",i=e({class:\"igv-roi-table-description\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.style.height=\"auto\",i.style.maxHeight=\"128px\",i.innerHTML=t.description,i=e({class:\"igv-roi-table-goto-explainer\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.innerHTML=\"Select one or more rows and click Go To to view the regions\"}}tableRowDOM(t){const i=e({class:\"igv-roi-table-row\"}),n=t.map((e=>isFinite(e)?Rt(e):e));for(let t=0;t<n.length;t++){const r=e();i.appendChild(r);const s=this.columnFormat[t];r.style.width=s.width||\"fit-content\",r.innerText=n[t]}return this.tableRowDOMHelper(i),i}renderTable(e){if(Array.from(this.tableRowContainer.querySelectorAll(\".igv-roi-table-row\")).forEach((e=>e.remove())),e.length>0)for(let t of e){const e=this.tableRowDOM(t);this.tableRowContainer.appendChild(e)}}static getColumnFormatConfiguration(){return[{label:\"chr\",width:\"7%\"},{label:\"start\",width:\"12%\"},{label:\"end\",width:\"12%\"},{label:\"strand\",width:\"5%\"},{label:\"score\",width:\"5%\"},{label:\"match\",width:\"5%\"},{label:\"mis-match\",width:\"7%\"},{label:\"rep. match\",width:\"7%\"},{label:\"N's\",width:\"3%\"},{label:\"Q gap count\",width:\"9%\"},{label:\"Q gap bases\",width:\"9%\"},{label:\"T gap count\",width:\"9%\"},{label:\"T gap bases\",width:\"9%\"}]}static gotoButtonHandler(e){e.stopPropagation();const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\"),i=[];for(const e of t){const t=[];e.querySelectorAll(\"div\").forEach((e=>t.push(e.innerText)));const[n,r,s]=t;i.push(`${n}:${r}-${s}`)}for(const e of this.tableDOM.querySelectorAll(\".igv-roi-table-row\"))e.classList.remove(\"igv-roi-table-row-selected\");this.setTableRowSelectionState(!1),this.browser.search(i.join(\" \"))}}const Ud=\"https://igv.org/services/blatUCSC.php\";async function qd({url:e,userSeq:t,db:i}){if(e=e||Ud,!i)throw Error(\"Blat database is not defined\");const n=await async function(e=\"\",t,i){const n=new URLSearchParams;n.append(\"userSeq\",t),n.append(\"db\",i);const r=await fetch(e,{method:\"post\",body:n});return r.json()}(e,t,i);n.fields;return n.blat.map($c)}const Qd=25e3;class Vd extends Hd{constructor(e,t){super(e,t),this.name||(this.name=\"Blat Results\"),this.sequence=e.sequence,this.table=void 0,e.features&&(this._features=e.features,this.featureSource=new fd({features:e.features},this.browser.genome),delete e.features)}async postInit(){if(!this.featureSource){const e=this.browser.genome.id,t=this.browser.config.blatServerURL,i=await qd({url:t,userSeq:this.sequence,db:e});this._features=i,this.featureSource=new fd({features:i},this.browser.genome)}}openTableView(){if(void 0===this.table){const e=this._features.map((e=>[e.chr,e.start+1,e.end,e.strand,e.score,e.matches,e.misMatches,e.repMatches,e.nCount,e.qNumInsert,e.qBaseInsert,e.tNumInsert,e.tBaseInsert])),t={browser:this.browser,parent:this.browser.columnContainer,headerTitle:this.config.title,description:this.sequence,dismissHandler:()=>{this.table.dismiss(),this.table.dispose(),this.table=void 0},columnFormat:Od.getColumnFormatConfiguration(),gotoButtonHandler:Od.gotoButtonHandler};this.table=new Od(t),this.table.renderTable(e)}this.table.present()}menuItemList(){const e=super.menuItemList();return e.push(\"<hr/>\"),e.push({label:\"Open table view\",click:function(){this.openTableView()}}),e}dispose(){super.dispose(),this.table&&this.table.popover.parentElement.removeChild(this.table.popover)}}async function jd({sequence:e,browser:t,name:i,title:n}){if(e.length>Qd)t.alert.present(`Sequence size exceeds maximum allowed length (${e.length} > 25000)`);else try{const r=t.genome.id,s=t.config.blatServerURL||\"https://igv.org/services/blatUCSC.php\",o={type:\"blat\",name:i||\"blat results\",title:n||\"blat results\",sequence:e,altColor:\"rgb(176, 176, 236)\",color:\"rgb(236, 176, 176)\",searchable:!1,features:await qd({url:s,userSeq:e,db:r})};(await t.loadTrack(o)).openTableView()}catch(e){t.alert.present(`Error performing blat search:  ${e}`)}}const Wd=Number.MIN_SAFE_INTEGER,Gd={TTT:\"F\",TTC:\"F\",TTA:\"L\",TTG:\"L\",CTT:\"L\",CTC:\"L\",CTA:\"L\",CTG:\"L\",ATT:\"I\",ATC:\"I\",ATA:\"I\",ATG:\"M\",GTT:\"V\",GTC:\"V\",GTA:\"V\",GTG:\"V\",TCT:\"S\",TCC:\"S\",TCA:\"S\",TCG:\"S\",CCT:\"P\",CCC:\"P\",CCA:\"P\",CCG:\"P\",ACT:\"T\",ACC:\"T\",ACA:\"T\",ACG:\"T\",GCT:\"A\",GCC:\"A\",GCA:\"A\",GCG:\"A\",TAT:\"Y\",TAC:\"Y\",TAA:\"STOP\",TAG:\"STOP\",CAT:\"H\",CAC:\"H\",CAA:\"Q\",CAG:\"Q\",AAT:\"N\",AAC:\"N\",AAA:\"K\",AAG:\"K\",GAT:\"D\",GAC:\"D\",GAA:\"E\",GAG:\"E\",TGT:\"C\",TGC:\"C\",TGA:\"STOP\",TGG:\"W\",CGT:\"R\",CGC:\"R\",CGA:\"R\",CGG:\"R\",AGT:\"S\",AGC:\"S\",AGA:\"R\",AGG:\"R\",GGT:\"G\",GGC:\"G\",GGA:\"G\",GGG:\"G\"},$d={},Kd=[\"A\",\"G\",\"C\",\"T\",\"Y\",\"R\",\"W\",\"S\",\"K\",\"M\",\"D\",\"V\",\"H\",\"B\",\"N\",\"X\"],Yd=[\"T\",\"C\",\"G\",\"A\",\"R\",\"Y\",\"W\",\"S\",\"M\",\"K\",\"H\",\"B\",\"D\",\"V\",\"N\",\"X\"];for(let NA=0;NA<Kd.length;NA++)$d[Kd[NA]]=Yd[NA],$d[Kd[NA].toLowerCase()]=Yd[NA].toLowerCase();const Xd=115;class Zd{constructor(e,t){this.config=e,this.browser=t,this.type=\"sequence\",this.removable=!0===e.removable,this.name=e.name,this.id=e.id,this.sequenceType=e.sequenceType||\"dna\",this.disableButtons=!1,this.order=e.order||Wd,this.ignoreTrackMenu=!1,this.reversed=!0===e.reversed,this.frameTranslate=!0===e.frameTranslate,this.height=this.frameTranslate?Xd:25,e.url&&(e.fastaURL=e.url),e.fastaURL||(this.id=e.id||\"sequence\")}menuItemList(){return[{name:this.reversed?\"Forward\":\"Reverse\",click:()=>{this.reversed=!this.reversed,this.trackView.repaintViews()}},{name:this.frameTranslate?\"Close Translation\":\"Three-frame Translate\",click:()=>{if(this.frameTranslate=!this.frameTranslate,this.frameTranslate){for(let e of this.trackView.viewports)e.setContentHeight(Xd);this.trackView.setTrackHeight(Xd)}else{for(let e of this.trackView.viewports)e.setContentHeight(25);this.trackView.setTrackHeight(25)}this.trackView.repaintViews()}}]}contextMenuItemList(e){const t=e.viewport;if(t.referenceFrame.bpPerPixel<=1){const e=t.getWidth()*t.referenceFrame.bpPerPixel,i=t.referenceFrame.chr,n=Math.floor(t.referenceFrame.start),r=Math.ceil(n+e),s=[{label:this.reversed?\"View visible sequence (reversed)...\":\"View visible sequence...\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);e?this.reversed&&(e=cc(e)):e=\"Unknown sequence\",this.browser.alert.present(e)}}];return Xa()&&s.push({label:\"Copy visible sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);e?this.reversed&&(e=cc(e)):e=\"Unknown sequence\";try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),s.push({label:\"BLAT read sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);if(e){this.reversed&&(e=cc(e));const t=`blat: ${i}:${n+1}-${r}`,s=`blat: ${i}:${n+1}-${r}`;jd({sequence:e,browser:this.browser,name:t,title:s})}}}),s.push(\"<hr/>\"),s}}translateSequence(e){const t=[[],[],[]];for(let i of[0,1,2]){let n=i;for(;e.length-n>=3;){let r=e.slice(n,n+3);this.reversed&&(r=r.split(\"\").reverse().join(\"\"));const s=Gd[r.toUpperCase()]||\"\";t[i].push({codons:r,aminoA:s}),n+=3}}return t}async getSequenceSource(){return this.config.fastaURL?(this.fasta||(this.fasta=new Jd(this.config,this.browser.genome),await this.fasta.init()),this.fasta):this.browser.genome}async getFeatures(e,t,i,n){if(t=Math.floor(t),i=Math.floor(i),n&&n>10)return null;{const n=await this.getSequenceSource();return{bpStart:t,sequence:await n.getSequence(e,t,i)}}}draw(e){const t=e.context;if(e.features){let i=e.features.sequence;if(!i)return;this.reversed&&(i=i.split(\"\").map((function(e){return $d[e]})).join(\"\"));const n=e.features.bpStart,r=1+e.bpStart+e.pixelWidth*e.bpPerPixel;for(let s=Math.floor(e.bpStart);s<=r;s++){const r=Math.floor(s-n);if(r>=0&&r<i.length){const n=(s-e.bpStart)/e.bpPerPixel,o=1/e.bpPerPixel,a=i[r],c=this.fillColor(a.toUpperCase());if(e.bpPerPixel>.1)xo.fillRect(t,n,5,o,10,{fillStyle:c});else{const i=n+.5*(o-t.measureText(a).width);\"y\"===e.axis?(t.save(),xo.labelTransformWithContext(t,i),xo.strokeText(t,a,i,15,{strokeStyle:c}),t.restore()):xo.strokeText(t,a,i,15,{strokeStyle:c})}}}if(this.frameTranslate){let r=25;const s=this.translateSequence(i);for(let i=0;i<s.length;i++){const o=s[i];for(let s=0;s<o.length;s++){let a=0==s%2?\"rgb(160,160,160)\":\"rgb(224,224,224)\";const c=o[s],l=n+i+3*s-e.bpStart,h=Math.floor(l/e.bpPerPixel),d=Math.floor((l+3)/e.bpPerPixel),u=Math.round((h+d)/2);if(d<0)continue;if(h>e.pixelWidth)break;let f=c.aminoA;c.aminoA.indexOf(\"STOP\")>-1?(a=\"rgb(255, 0, 0)\",f=\"STOP\"):\"M\"===c.aminoA&&(a=\"rgb(0, 153, 0)\",f=\"START\"),xo.fillRect(t,h,r,d-h,25,{fillStyle:a}),e.bpPerPixel<=.1&&xo.strokeText(t,f,u-t.measureText(f).width/2,r+15)}r+=30}}}}get supportsWholeGenome(){return!1}computePixelHeight(e){return this.height=this.frameTranslate?Xd:25,this.height}fillColor(e){return this.color?this.color:\"dna\"===this.sequenceType?this.browser.nucleotideColors[e]||\"gray\":\"rgb(0, 0, 150)\"}getState(){const e={type:\"sequence\"};return this.order!==Wd&&(e.order=this.order),this.reversed&&(e.revealed=!0),e}}class Jd{constructor(e,t){this.config=e,this.genome=t}async init(){this.fasta=await Nc(this.config),this.chrNameMap=new Map;for(let e of this.fasta.chromosomeNames)this.chrNameMap.set(this.genome.getChromosomeName(e),e)}async getSequence(e,t,i){const n=this.chrNameMap.has(e)?this.chrNameMap.get(e):e;return this.fasta.getSequence(n,t,i)}}class eu{constructor(e,t,i,n){this.guid=s(),this.trackView=e,this.referenceFrame=i,this.browser=e.browser,this.$viewport=Bt('<div class=\"igv-viewport\">'),t.appendChild(this.$viewport.get(0)),e.track.height&&(this.$viewport.get(0).style.height=`${e.track.height}px`),e.track instanceof Zd&&(this.alert=new Ta(this.$viewport.get(0))),this.contentTop=0,this.contentHeight=this.$viewport.height(),this.$viewport.width(n),this.initializationHelper()}initializationHelper(){}showMessage(e){this.messageDiv||(this.messageDiv=document.createElement(\"div\"),this.messageDiv.className=\"igv-viewport-message\",this.$viewport.append(Bt(this.messageDiv))),this.messageDiv.textContent=e,this.messageDiv.style.display=\"inline-block\"}hideMessage(e){this.messageDiv&&(this.messageDiv.style.display=\"none\")}setTrackLabel(e){}startSpinner(){}stopSpinner(){}checkZoomIn(){return!0}shift(){}setTop(e){this.contentTop=e,this.$viewport.height()}async loadFeatures(){}clearCache(){}repaint(){}draw(e,t,i){console.log(\"Viewport - draw(drawConfiguration, features, roiFeatures)\")}checkContentHeight(e){let t=this.trackView.track;if(e=e||this.cachedFeatures,\"FILL\"===t.displayMode)this.setContentHeight(this.$viewport.height());else if(\"function\"==typeof t.computePixelHeight&&e&&e.length>0){let i=t.computePixelHeight(e);i!==this.contentHeight&&this.setContentHeight(i)}}getContentHeight(){return this.contentHeight}setContentHeight(e){this.contentHeight=e}isLoading(){return!1}saveSVG(){}isVisible(){return this.$viewport.width()}setWidth(e){this.$viewport.width(e)}getWidth(){return this.$viewport.width()}getContentTop(){return this.contentTop}containsPosition(e,t){console.log(\"Viewport - containsPosition(chr, position)\")}addMouseHandlers(){}removeMouseHandlers(){}dispose(){this.$viewport.get(0).remove();for(let e of Object.keys(this))this[e]=void 0}}\n",
-       "/*!!\n",
-       "     *  Canvas 2 Svg v1.0.19\n",
-       "     *  A low level canvas to SVG converter. Uses a mock canvas context to build an SVG document.\n",
-       "     *\n",
-       "     *  Licensed under the MIT license:\n",
-       "     *  http://www.opensource.org/licenses/mit-license.php\n",
-       "     *\n",
-       "     *  Author:\n",
-       "     *  Kerry Liu\n",
-       "     *\n",
-       "     *  Copyright (c) 2014 Gliffy Inc.\n",
-       "     */function tu(e,t){var i,n=Object.keys(t);for(i=0;i<n.length;i++)e=e.replace(new RegExp(\"\\\\{\"+n[i]+\"\\\\}\",\"gi\"),t[n[i]]);return e}function iu(e){var t,i,n;if(!e)throw new Error(\"cannot create a random attribute name for an undefined object\");t=\"ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz\",i=\"\";do{for(i=\"\",n=0;n<12;n++)i+=t[Math.floor(51*Math.random())]}while(e[i]);return i}function nu(e){var t={alphabetic:\"alphabetic\",hanging:\"hanging\",top:\"text-before-edge\",bottom:\"text-after-edge\",middle:\"central\"};return t[e]||t.alphabetic}function ru(e){var t=Math.sqrt(e[0]*e[0]+e[1]*e[1]);return[e[0]/t,e[1]/t]}const su=function(e,t){var i,n,r,s={};for(e=e.split(\",\"),t=t||10,i=0;i<e.length;i+=2)n=\"&\"+e[i+1]+\";\",r=parseInt(e[i],t),s[n]=\"&#\"+r+\";\";return 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stroke\"},font:{canvas:\"10px sans-serif\"},shadowColor:{canvas:\"#000000\"},shadowOffsetX:{canvas:0},shadowOffsetY:{canvas:0},shadowBlur:{canvas:0},textAlign:{canvas:\"start\"},textBaseline:{canvas:\"alphabetic\"},lineDash:{svgAttr:\"stroke-dasharray\",canvas:[],svg:null,apply:\"stroke\"}};class au{constructor(e,t){this.__root=e,this.__ctx=t}addColorStop(e,t){var i,n=this.__ctx.__createElement(\"stop\");n.setAttribute(\"offset\",e),t&&-1!==t.indexOf(\"rgba\")?(i=/rgba\\(\\s*(\\d+)\\s*,\\s*(\\d+)\\s*,\\s*(\\d+)\\s*,\\s*(\\d?\\.?\\d*)\\s*\\)/gi.exec(t),n.setAttribute(\"stop-color\",tu(\"rgb({r},{g},{b})\",{r:i[1],g:i[2],b:i[3]})),n.setAttribute(\"stop-opacity\",i[4])):n.setAttribute(\"stop-color\",t),this.__root.appendChild(n)}}class cu{constructor(e,t){this.__root=e,this.__ctx=t}}class lu{constructor(e){if(!(this instanceof lu))return new 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e,t,i=Object.keys(ou);for(e=0;e<i.length;e++)this[t=i[e]]=ou[t].canvas}__applyStyleState(e){var t,i,n=Object.keys(e);for(t=0;t<n.length;t++)this[i=n[t]]=e[i]}__getStyleState(){var e,t,i={},n=Object.keys(ou);for(e=0;e<n.length;e++)i[t=n[e]]=this[t];return i}__applyStyleToCurrentElement(e){var t=this.__currentElement,i=this.__currentElementsToStyle;i&&(t.setAttribute(e,\"\"),t=i.element,i.children.forEach((function(t){t.setAttribute(e,\"\")})));var n,r,s,o,a,c=Object.keys(ou);for(n=0;n<c.length;n++)if(r=ou[c[n]],s=this[c[n]],r.apply)if(s instanceof cu){if(s.__ctx)for(;s.__ctx.__defs.childNodes.length;)o=s.__ctx.__defs.childNodes[0].getAttribute(\"id\"),this.__ids[o]=o,this.__defs.appendChild(s.__ctx.__defs.childNodes[0]);t.setAttribute(r.apply,tu(\"url(#{id})\",{id:s.__root.getAttribute(\"id\")}))}else if(s instanceof au)t.setAttribute(r.apply,tu(\"url(#{id})\",{id:s.__root.getAttribute(\"id\")}));else 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\"+w:w,l.setAttribute(\"transform\",b),o.appendChild(l)}}}else\"CANVAS\"!==p.nodeName&&\"IMG\"!==p.nodeName||((h=this.__createElement(\"image\")).setAttribute(\"width\",i),h.setAttribute(\"height\",n),h.setAttribute(\"preserveAspectRatio\",\"none\"),(g||m||r!==p.width||s!==p.height)&&((d=this.__document.createElement(\"canvas\")).width=i,d.height=n,d.getContext(\"2d\").drawImage(p,g,m,r,s,0,0,i,n),p=d),h.setAttribute(\"transform\",w),h.setAttributeNS(\"http://www.w3.org/1999/xlink\",\"xlink:href\",\"CANVAS\"===p.nodeName?p.toDataURL():p.getAttribute(\"src\")),o.appendChild(h))}createPattern(e,t){let i,n=this.__document.__createElement(\"pattern\"),r=iu(this.__ids);return n.setAttribute(\"id\",r),n.setAttribute(\"width\",e.width),n.setAttribute(\"height\",e.height),\"CANVAS\"===e.nodeName||\"IMG\"===e.nodeName?(i=this.__createElement(\"image\"),i.setAttribute(\"width\",e.width),i.setAttribute(\"height\",e.height),i.setAttributeNS(\"http://www.w3.org/1999/xlink\",\"xlink:href\",\"CANVAS\"===e.nodeName?e.toDataURL():e.getAttribute(\"src\")),n.appendChild(i),this.__defs.appendChild(n)):e instanceof lu&&(n.appendChild(e.__root.childNodes[1]),this.__defs.appendChild(n)),new cu(n,this)}setLineDash(e){e&&e.length>0?this.lineDash=e.join(\",\"):this.lineDash=null}drawFocusRing(){}createImageData(){}getImageData(){}putImageData(){}globalCompositeOperation(){}setTransform(){}}function hu(e){if(e.startsWith(\"GCF\")||e.startsWith(\"GCA\")&&e.length>=13){return\"https://hgdownload.soe.ucsc.edu/hubs/\"+e.substring(0,3)+\"/\"+e.substring(4,7)+\"/\"+e.substring(7,10)+\"/\"+e.substring(10,13)+\"/\"+e+\"/hub.txt\"}}class du{static supportedTypes=new Set([\"bigBed\",\"bigWig\",\"bigGenePred\",\"vcfTabix\"]);static filterTracks=new Set([\"cytoBandIdeo\",\"assembly\",\"gap\",\"gapOverlap\",\"allGaps\",\"cpgIslandExtUnmasked\",\"windowMasker\"]);static async loadHub(e){const t=e.lastIndexOf(\"/\"),i=e.substring(0,t+1),n=await pu(e);let r;if(\"genome\"===n[1].type){const e=n[1];if(e.hasProperty(\"groups\")){const t=i+e.getProperty(\"groups\");r=await pu(t)}if(e.hasProperty(\"chromSizes\")){const t=i+e.getProperty(\"chromSizes\"),n=await async function(e){try{const t=(await fetch(e,{method:\"HEAD\"})).headers;return t.has(\"content-length\")?t.get(\"content-length\"):null}catch(e){return null}}(t);null!==n&&Number.parseInt(n)<1e6&&e.setProperty(\"chromSizesURL\",t)}}return new du(e,n,r)}constructor(e,t,i){this.url=e;const n=e.lastIndexOf(\"/\");if(this.baseURL=e.substring(0,n+1),\"hub\"!==t[0].type)throw Error(\"Unexpected hub.txt file -- does the first line start with 'hub'?\");if(this.hubStanza=t[0],\"on\"!==this.hubStanza.getProperty(\"useOneFile\"))throw Error(\"Only 'useOneFile' hubs are currently supported\");if(t.length<2)throw Error(\"Expected at least 2 stanzas, hub and genome\");if(\"genome\"!==t[1].type)throw Error(`Unexpected hub file -- expected \"genome\" stanza but found \"${t[1].type}\"`);this.genomeStanza=t[1],this.trackStanzas=[];for(let e=2;e<t.length;e++)\"track\"===t[e].type&&this.trackStanzas.push(t[e]);if(i){this.groupStanzas=i,this.groupPriorityMap=new Map;for(let e of i)e.hasProperty(\"priority\")&&this.groupPriorityMap.set(e.getProperty(\"name\"),10*Number.parseInt(e.getProperty(\"priority\")))}}getDefaultPosition(){return this.genomeStanza.getProperty(\"defaultPos\")}getGenomeConfig(e={}){const t=this.genomeStanza.getProperty(\"genome\"),i=this.hubStanza.getProperty(\"shortLabel\")||this.genomeStanza.getProperty(\"scientificName\")||this.genomeStanza.getProperty(\"organism\")||this.genomeStanza.getProperty(\"description\"),n=i+(i?` (${t})`:` ${t}`),r={hubURL:this.url,id:t,name:n,twoBitURL:this.baseURL+this.genomeStanza.getProperty(\"twoBitPath\"),nameSet:\"ucsc\"};if(this.genomeStanza.hasProperty(\"chromSizesURL\")?r.chromSizesURL=this.genomeStanza.getProperty(\"chromSizesURL\"):(r.wholeGenomeView=!1,r.showChromosomeWidget=!1),this.genomeStanza.hasProperty(\"defaultPos\")){const e=this.genomeStanza.getProperty(\"defaultPos\");if(e){const t=e.lastIndexOf(\":\");r.locus=t>0?e.substring(0,t):e}}this.genomeStanza.hasProperty(\"blat\")&&(r.blat=this.baseURL+this.genomeStanza.getProperty(\"blat\")),this.genomeStanza.hasProperty(\"chromAliasBb\")&&(r.chromAliasBbURL=this.baseURL+this.genomeStanza.getProperty(\"chromAliasBb\")),this.genomeStanza.hasProperty(\"chromAlias\")&&(r.aliasURL=this.baseURL+this.genomeStanza.getProperty(\"chromAlias\")),this.genomeStanza.hasProperty(\"twoBitBptURL\")&&(r.twoBitBptURL=this.baseURL+this.genomeStanza.getProperty(\"twoBitBptURL\")),this.genomeStanza.hasProperty(\"twoBitBptUrl\")&&(r.twoBitBptURL=this.baseURL+this.genomeStanza.getProperty(\"twoBitBptUrl\")),e.includeChromSizes&&this.genomeStanza.hasProperty(\"chromSizes\")&&(r.chromSizesURL=this.baseURL+this.genomeStanza.getProperty(\"chromSizes\")),this.hubStanza.hasProperty(\"longLabel\")?r.description=this.hubStanza.getProperty(\"longLabel\").replace(\"/\",\"\\n\"):(r.description=r.id,this.genomeStanza.hasProperty(\"description\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"description\")}`),this.genomeStanza.hasProperty(\"organism\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"organism\")}`),this.genomeStanza.hasProperty(\"scientificName\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"scientificName\")}`),this.genomeStanza.hasProperty(\"htmlPath\")&&(r.infoURL=this.baseURL+this.genomeStanza.getProperty(\"htmlPath\")));const s=this.trackStanzas.filter((e=>\"cytoBandIdeo\"===e.name&&e.hasProperty(\"bigDataUrl\")));s.length>0&&(r.cytobandBbURL=this.baseURL+s[0].getProperty(\"bigDataUrl\"));return r.tracks=this.#g((e=>!du.filterTracks.has(e.name)&&\"hide\"!==e.getProperty(\"visibility\"))),r}getGroupedTrackConfigurations(){const e=new Map;for(let t of this.#g()){if(\"cytoBandIdeo\"===t.name)continue;const i=t.group||\"other\";e.has(i)?e.get(i).push(t):e.set(i,[t])}const t=this.groupStanzas?new Map(this.groupStanzas.map((e=>[e.getProperty(\"name\"),e]))):new Map;return Array.from(e.keys()).map((i=>({label:t.has(i)?t.get(i).getProperty(\"label\"):i,tracks:e.get(i)})))}#g(e){return this.trackStanzas.filter((t=>du.supportedTypes.has(t.format)&&t.hasProperty(\"bigDataUrl\")&&(!e||e(t)))).map((e=>this.#m(e)))}#m(e){const t=e.format,i={id:e.getProperty(\"track\"),name:e.getProperty(\"shortLabel\"),format:t,url:this.baseURL+e.getProperty(\"bigDataUrl\"),displayMode:e.displayMode};if(\"vcfTabix\"===t&&(i.indexURL=i.url+\".tbi\"),e.hasProperty(\"longLabel\")&&e.hasProperty(\"html\")?(i.description&&(i.description+=\"<br/>\"),i.description=`<a target=\"_blank\" href=\"${this.baseURL+e.getProperty(\"html\")}\">${e.getProperty(\"longLabel\")}</a>`):e.hasProperty(\"longLabel\")&&(i.description=e.getProperty(\"longLabel\")),e.hasProperty(\"autoScale\")&&(i.autoscale=\"on\"===e.getProperty(\"autoScale\").toLowerCase()),e.hasProperty(\"maxHeightPixels\")){const t=e.getProperty(\"maxHeightPixels\").split(\":\");i.maxHeight=Number.parseInt(t[0]),i.height=Number.parseInt(t[1]),i.minHeight=Number.parseInt(t[2])}if(e.hasProperty(\"color\")){const t=e.getProperty(\"color\");i.color=t.indexOf(\",\")>0?`rgb(${t})`:t}if(e.hasProperty(\"altColor\")){const t=e.getProperty(\"altColor\");i.altColor=t.indexOf(\",\")>0?`rgb(${t})`:t}if(e.hasProperty(\"viewLimits\")){const t=e.getProperty(\"viewLimits\").split(\":\");let n,r;t.length>1&&(n=Number.parseInt(t[0]),r=Number.parseInt(t[1])),Number.isNaN(r)||Number.isNaN(n)?console.warn(`Unexpected viewLimits value in track line: ${properties.viewLimits}`):(i.min=n,i.max=r)}if(e.hasProperty(\"itemRgb\"),\"hide\"===e.getProperty(\"visibility\")&&(i.visible=!1),e.hasProperty(\"url\")&&(i.infoURL=e.getProperty(\"url\")),e.hasProperty(\"searchIndex\")&&(i.searchIndex=e.getProperty(\"searchIndex\")),e.hasProperty(\"searchTrix\")&&(i.trixURL=this.baseURL+e.getProperty(\"searchTrix\")),e.hasProperty(\"group\")&&(i.group=e.getProperty(\"group\"),this.groupPriorityMap&&this.groupPriorityMap.has(i.group))){const e=this.groupPriorityMap.get(i.group)+1;i.order=e,this.groupPriorityMap.set(i.group,e)}return i}}function uu(e){const t=e.indexOf(\" \");return t>0?e.substring(0,t):e}class fu{properties=new Map;constructor(e,t){this.type=e,this.name=t}setProperty(e,t){this.properties.set(e,t)}getProperty(e){return this.properties.has(e)?this.properties.get(e):this.parent?this.parent.getProperty(e):void 0}hasProperty(e){return!!this.properties.has(e)||!!this.parent&&this.parent.hasProperty(e)}get format(){const e=this.getProperty(\"type\");if(e)return uu(e)}get displayMode(){let e=this.getProperty(\"visibility\");if(!e)return\"COLLAPSED\";switch(e=e.toLowerCase(),e){case\"dense\":default:return\"COLLAPSED\";case\"pack\":return\"EXPANDED\";case\"squish\":return\"SQUISHED\"}}}async function pu(e){const t=await fetch(e),i=(await t.text()).split(/\\n|\\r\\n|\\r/g),n=[];let r,s=!0;for(let e of i){const t=gu(e),i=e.indexOf(\" \",t);if(i<0)s=!0;else{const o=e.substring(t,i).trim();if(o.startsWith(\"#\"))continue;const a=e.substring(i+1).trim();if(s){const e=new fu(o,a);n.push(e),r=e,s=!1}r.setProperty(o,a)}}return function(e){const t=new Map;for(let i of e)t.set(i.name,i);for(let i of e)if(i.properties.has(\"parent\")){const e=uu(i.properties.get(\"parent\"));i.parent=t.get(e)}return e}(n)}function gu(e){let t=0;for(t=0;t<e.length;t++){const i=e.charAt(t);if(\" \"!==i&&\"\\t\"!==i)break}return t}const mu={initializeGenomes:async function(e){if(!mu.KNOWN_GENOMES){const t={};if(!1!==e.loadDefaultGenomes){const r=\"https://igv.org/genomes/genomes.json\";n(await Qs.loadJson(r,{timeout:5e3}))}const i=e.genomeList||e.genomes;if(i)if(\"string\"==typeof i){n(await Qs.loadJson(i,{}))}else n(i);function n(e){return e.forEach((function(e){t[e.id]=e})),t}mu.KNOWN_GENOMES=t}},isWholeGenomeView:function(e){return\"all\"===e.toLowerCase()},expandReference:async function(e,t){if(Mt(t)&&t.startsWith(\"{\"))try{t=JSON.parse(t)}catch(e){}let i;if(Mt(t)?i=t:t.genome?i=t.genome:void 0===t.id||t.fastaURL||t.twobitURL||(i=t.id),i){let t=mu.KNOWN_GENOMES[i];if(!t){if((i.startsWith(\"GCA_\")||i.startsWith(\"GCF_\"))&&i.length>=13)try{const e=hu(i);t=(await du.loadHub(e)).getGenomeConfig()}catch(e){console.error(e)}t||e.present(new Error(`Unknown genome id: ${i}`),void 0)}return t}return t}};let wu,bu,Fu=0,vu=0,yu=[];class Au extends eu{constructor(e,t,i,n){super(e,t,i,n)}initializationHelper(){this.$spinner=Bt(\"<div>\",{class:\"igv-loading-spinner-container\"}),this.$viewport.append(this.$spinner),this.$spinner.append(Bt(\"<div>\"));const e=this.trackView.track;\"sequence\"!==e.type&&(this.$zoomInNotice=this.createZoomInNotice(this.$viewport)),\"sequence\"!==e.id&&(this.$trackLabel=Bt('<div class=\"igv-track-label\">'),this.$viewport.append(this.$trackLabel),this.setTrackLabel(e.name||\"\"),!1===this.browser.doShowTrackLabels&&this.$trackLabel.hide()),this.stopSpinner(),this.addMouseHandlers()}setContentHeight(e){super.setContentHeight(e),this.featureCache&&(this.featureCache.redraw=!0)}setTrackLabel(e){this.$trackLabel.empty(),this.$trackLabel.html(e);const t=this.$trackLabel.text();this.$trackLabel.attr(\"title\",t)}startSpinner(){this.$spinner.show()}stopSpinner(){this.$spinner&&this.$spinner.hide()}checkZoomIn(){if(this.trackView.track&&\"sequence\"===this.trackView.track.type&&this.referenceFrame.bpPerPixel>10)return Bt(this.canvas).remove(),this.canvas=void 0,!1;if(!this.viewIsReady())return!1;if((()=>{if(\"all\"!==this.referenceFrame.chr.toLowerCase()||this.trackView.track.supportsWholeGenome){const e=this.trackView.track.visibilityWindow;return void 0!==e&&e>0&&this.referenceFrame.bpPerPixel*this.$viewport.width()>e}return!0})()){if(this.canvas&&(Bt(this.canvas).remove(),this.canvas=void 0),this.trackView.track.autoHeight){const e=this.trackView.minHeight||0;this.setContentHeight(e)}return this.$zoomInNotice&&this.$zoomInNotice.show(),!1}return this.$zoomInNotice&&this.$zoomInNotice.hide(),!0}shift(){const e=this.referenceFrame;this.canvas&&this.canvas._data&&this.canvas._data.referenceFrame.chr===this.referenceFrame.chr&&this.canvas._data.bpPerPixel===e.bpPerPixel&&(this.canvas._data.pixelShift=Math.round((this.canvas._data.bpStart-e.start)/e.bpPerPixel),this.canvas.style.left=this.canvas._data.pixelShift+\"px\")}genomicRange(){return{start:this.referenceFrame.start,end:this.referenceFrame.start+this.referenceFrame.bpPerPixel*this.$viewport.width()}}setTop(e){if(super.setTop(e),this.canvas){const t=this.$viewport.height(),i=e+this.canvas._data.pixelTop,n=i+this.canvas._data.pixelHeight;(i>0||n<t)&&this.repaint()}else this.repaint();if(this.canvas&&this.canvas._data){let t=e+this.canvas._data.pixelTop;this.canvas.style.top=`${t}px`}}async loadFeatures(){const e=this.referenceFrame,t=e.chr,i=await this.browser.genome.loadChromosome(t),n=i?i.bpLength:Number.MAX_SAFE_INTEGER,r=this.$viewport.width()*e.bpPerPixel,s=Math.floor(Math.max(0,e.start-r)),o=Math.ceil(Math.min(n,e.start+r+r));if(!this.loading||this.loading.start!==s||this.loading.end!==o){this.loading={start:s,end:o},this.startSpinner();try{const i=this.trackView.track,n=await this.getFeatures(i,t,s,o,e.bpPerPixel);if(n){let r=[];if(i.roiSets&&i.roiSets.length>0)for(let n of i.roiSets){const i=await n.getFeatures(t,s,o,e.bpPerPixel);r.push({track:n,features:i})}const a=i&&i.resolutionAware,c=this.windowFunction;return this.featureCache=new Cu(t,s,o,e.bpPerPixel,n,r,a,c),this.loading=!1,this.hideMessage(),this.stopSpinner(),this.featureCache}}catch(e){this.trackView&&!0!==this.trackView.disposed&&(this.showMessage(\"Error loading track data\"),this.browser.alert.present(e),console.error(e))}finally{this.loading=!1,this.stopSpinner()}}}get track(){return this.trackView.track}get windowFunction(){return this.track?this.track.windowFunction:void 0}repaintDimensions(){const e=mu.isWholeGenomeView(this.referenceFrame.chr),t=e?this.$viewport.width():3*this.$viewport.width(),i=this.referenceFrame.bpPerPixel;return{bpStart:this.referenceFrame.start-(e?0:this.$viewport.width()*i),bpEnd:e?Number.MAX_SAFE_INTEGER:this.referenceFrame.start+2*this.$viewport.width()*i+1,pixelWidth:t}}repaint(){if(void 0===this.featureCache)return;const{features:e,roiFeatures:t}=this.featureCache,{bpStart:i,bpEnd:n,pixelWidth:r}=this.repaintDimensions(),s=this.$viewport.height(),o=this.getContentHeight(),a=t?Math.max(o,s):o,c=Math.min(a,3*s);if(0===r||0===c)return void(this.canvas&&Bt(this.canvas).remove());const l=Math.max(0,-this.contentTop-Math.floor(c/3)),h=this.referenceFrame.bpPerPixel,d=Math.round((i-this.referenceFrame.start)/h),u=(this.contentTop||0)+l,f=document.createElement(\"canvas\");f.style.position=\"relative\",f.style.display=\"block\",f.style.width=r+\"px\",f.style.height=c+\"px\",f.style.left=d+\"px\",f.style.top=u+\"px\";const p=\"FILL\"===this.trackView.track.displayMode||!1!==this.trackView.track.supportHiDPI?window.devicePixelRatio:1;f.width=p*r,f.height=p*c;const g=f.getContext(\"2d\");g.scale(p,p),g.translate(0,-l);const m={context:g,pixelXOffset:d,pixelWidth:r,pixelHeight:c,pixelTop:l,bpStart:i,bpEnd:n,bpPerPixel:h,pixelShift:d,windowFunction:this.windowFunction,referenceFrame:this.referenceFrame,selection:this.selection,viewport:this,viewportWidth:this.$viewport.width()};this.draw(m,e,t),this.canvas&&Bt(this.canvas).remove(),f._data=m,this.canvas=f,this.$viewport.append(Bt(f))}refresh(){if(!this.canvas||!this.featureCache)return;const e=this.canvas._data;e.context.clearRect(0,0,this.canvas.width,this.canvas.height);const{features:t,roiFeatures:i}=this.featureCache;this.draw(e,t,i)}draw(e,t,i){if(t&&(e.features=t,this.trackView.track.draw(e)),i&&i.length>0)for(let t of i)e.features=t.features,t.track.draw(e)}containsPosition(e,t){return this.referenceFrame.chr===e&&t>=this.referenceFrame.start&&t<=this.referenceFrame.calculateEnd(this.getWidth())}isLoading(){return this.loading}savePNG(){if(!this.canvas)return;const e=this.canvas._data,t=e?e.pixelTop:0,i=window.devicePixelRatio,n=this.$viewport.width()*i,r=this.$viewport.height()*i,s=-Bt(this.canvas).position().left*i,o=(-this.contentTop-t)*i,a=this.canvas.getContext(\"2d\").getImageData(s,o,n,r),c=document.createElement(\"canvas\"),l=c.getContext(\"2d\");c.width=a.width,c.height=a.height,l.putImageData(a,0,0);Pt((this.$trackLabel.text()?this.$trackLabel.text():\"image\")+\".png\",c.toDataURL(\"image/png\"))}saveSVG(){let{width:e,height:t}=this.browser.columnContainer.getBoundingClientRect();const i=new lu({width:e,height:8e3,backdropColor:\"white\",multiLocusGap:0,viewbox:{x:0,y:0,width:e,height:8e3}}),n={deltaX:32,deltaY:32};this.renderSVGContext(i,n,!1),i.setHeight(t);const r=(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\"),o=this.browser.referenceFrameList.indexOf(this.referenceFrame),a=i.getSerializedSvg(!0),c=URL.createObjectURL(new Blob([a],{type:\"application/octet-stream\"}));Pt(`${`${r}_referenceFrame_${o}_guid_${s()}`}.svg`,c)}renderSVGContext(e,{deltaX:t,deltaY:i},n=!0){if(!(this.$zoomInNotice&&this.$zoomInNotice.is(\":visible\"))){const{width:n,height:r}=this.$viewport.get(0).getBoundingClientRect(),o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${s()}`,a=t,c=i+this.contentTop,l=-this.contentTop;e.saveWithTranslationAndClipRect(o,a,c,n,r,l);const{start:h,bpPerPixel:d}=this.referenceFrame,u=Math.round((h-this.referenceFrame.start)/d),f={context:e,viewport:this,referenceFrame:this.referenceFrame,top:l,pixelTop:l,pixelWidth:n,pixelHeight:r,pixelXOffset:u,pixelShift:u,bpStart:h,bpEnd:h+n*d,bpPerPixel:d,viewportWidth:n,selection:this.selection},p=this.featureCache?this.featureCache.features:void 0,g=this.featureCache?this.featureCache.roiFeatures:void 0;this.draw(f,p,g),e.restore()}if(n&&this.$trackLabel&&this.browser.doShowTrackLabels){const{x:n,y:r,width:s,height:o}=((e,t)=>{const{x:i,y:n,width:r,height:s}=e.getBoundingClientRect(),{x:o,y:a,width:c,height:l}=t.getBoundingClientRect();return{x:o-i,y:a-n,width:c,height:l}})(this.$viewport.get(0),this.$trackLabel.get(0));this.renderTrackLabelSVG(e,t+n,i+r,s,o)}}renderTrackLabelSVG(e,t,i,n,r){const o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_track_label_guid_${s()}`;e.saveWithTranslationAndClipRect(o,t,i,n,r,0),e.fillStyle=\"white\",e.fillRect(0,0,n,r),e.font=\"12px Arial\",e.fillStyle=\"rgb(68, 68, 68)\";const{width:a}=e.measureText(this.$trackLabel.text()),c=.25*(n-a),l=.7*(r-12);e.fillText(this.$trackLabel.text(),c,r-l),e.strokeStyle=\"rgb(68, 68, 68)\",e.strokeRect(0,0,n,r),e.restore()}get cachedFeatures(){return this.featureCache?this.featureCache.features:[]}clearCache(){this.featureCache=void 0,this.canvas&&(this.canvas._data=void 0)}async getFeatures(e,t,i,n,r){if(this.featureCache&&this.featureCache.containsRange(t,i,n,r,this.windowFunction))return this.featureCache.features;if(\"function\"==typeof e.getFeatures){const s=await e.getFeatures(t,i,n,r,this);return this.checkContentHeight(s),s}}needsRepaint(){if(!this.canvas)return!0;const e=this.canvas._data;return!e||this.referenceFrame.start<e.bpStart||this.referenceFrame.end>e.bpEnd||this.referenceFrame.chr!==e.referenceFrame.chr||this.referenceFrame.bpPerPixel!=e.bpPerPixel||this.windowFunction!=e.windowFunction}needsReload(){if(!this.featureCache)return!0;const{chr:e,bpPerPixel:t}=this.referenceFrame,{bpStart:i,bpEnd:n}=this.repaintDimensions();return!this.featureCache.containsRange(e,i,n,t,this.windowFunction)}createZoomInNotice(e){const t=Bt(\"<div>\",{class:\"igv-zoom-in-notice-container\"});e.append(t);const i=Bt(\"<div>\");return t.append(i),i.text(\"Zoom in to see features\"),t.hide(),t}viewIsReady(){return this.browser&&this.browser.referenceFrameList&&this.referenceFrame}addMouseHandlers(){const e=this.$viewport.get(0);this.addViewportContextMenuHandler(e);const t=e=>{this.enableClick=!0,this.browser.mouseDownOnViewport(e,this),r(e)};e.addEventListener(\"mousedown\",t),e.addEventListener(\"touchstart\",t);const i=e=>{this.browser.dragObject||this.browser.isScrolling?(this.browser.cancelTrackPan(),this.enableClick=!1):(this.browser.cancelTrackPan(),this.browser.endTrackDrag())};e.addEventListener(\"mouseup\",i),e.addEventListener(\"touchend\",i),\"function\"==typeof this.trackView.track.hoverText&&e.addEventListener(\"mousemove\",(e=>{if(0===e.buttons&&Date.now()-vu>100){vu=Date.now();const t=this.createClickState(e);if(t){const e=this.trackView.track.hoverText(t);e?this.$viewport[0].setAttribute(\"title\",e):this.$viewport[0].removeAttribute(\"title\")}}})),this.addViewportClickHandler(this.$viewport.get(0)),this.trackView.track.name&&\"sequence\"!==this.trackView.track.config.type&&this.addTrackLabelClickHandler(this.$trackLabel.get(0))}addViewportContextMenuHandler(e){e.addEventListener(\"contextmenu\",(e=>{if(this.browser.dragObject)return!1;const t=this.createClickState(e);if(void 0===t)return!1;e.preventDefault();let i=[];if(\"function\"==typeof this.trackView.track.contextMenuItemList){const e=this.trackView.track.contextMenuItemList(t);e&&(i=e)}i.length>0&&i.push({label:Bt(\"<HR>\")}),i.push({label:\"Save Image (PNG)\",click:()=>this.savePNG()}),i.push({label:\"Save Image (SVG)\",click:()=>this.saveSVG()}),this.browser.menuPopup.presentTrackContextMenu(e,i)}))}addViewportClickHandler(e){e.addEventListener(\"click\",(e=>{if(this.enableClick&&this.canvas){if(3===e.which||e.ctrlKey)return;if(this.browser.dragObject||this.browser.isScrolling)return;e.preventDefault();const t=a(e,this.$viewport.get(0)).x,i=a(e,this.canvas).x,n=this.referenceFrame;Math.floor(n.start+n.toBP(i));const r=Date.now();if(r-Fu<this.browser.constants.doubleClickDelay){wu&&(window.clearTimeout(wu),wu=void 0);const e=Math.round(n.start+n.toBP(t));let i;if(\"all\"===this.referenceFrame.chr.toLowerCase()){const t=this.browser.genome.getChromosomeCoordinate(e).chr;if(1===this.browser.referenceFrameList.length)i=t;else{const e=this.browser.referenceFrameList.map((({locusSearchString:e})=>e));e[this.browser.referenceFrameList.indexOf(this.referenceFrame)]=t,i=e.join(\" \")}this.browser.search(i)}else this.browser.zoomWithScaleFactor(.5,e,this.referenceFrame)}else\"function\"==typeof this.trackView.track.popupData&&(wu=setTimeout((()=>{const t=this.getPopupContent(e);if(t)if(!1===e.shiftKey){if(bu&&bu.dispose(),yu.length>0){for(const e of yu)e.dispose();yu.length=0}bu=new tc(this.$viewport.get(0).parentElement,!0,void 0,(()=>{bu.dispose()})),bu.presentContentWithEvent(e,t)}else{let i=new tc(this.$viewport.get(0).parentElement,!0,void 0,(()=>{const e=yu.indexOf(i);yu.splice(e,1),i.dispose()}));yu.push(i),i.presentContentWithEvent(e,t)}window.clearTimeout(wu),wu=void 0}),this.browser.constants.doubleClickDelay));Fu=r}}))}addTrackLabelClickHandler(e){e.addEventListener(\"click\",(e=>{e.stopPropagation();const{track:t}=this.trackView;let i;\"function\"==typeof t.description?i=t.description():t.description&&(i=`<div>${t.description}</div>`),i&&(void 0===this.popover&&(this.popover=new tc(this.browser.columnContainer,!0,t.name||\"\",void 0)),this.popover.presentContentWithEvent(e,i))}))}createClickState(e){if(!this.canvas)return;const t=this.referenceFrame,i=a(e,this.$viewport.get(0)),n=a(e,this.canvas),r=t.start+t.toBP(i.x);return{event:e,viewport:this,referenceFrame:t,genomicLocation:r,y:i.y-this.contentTop,canvasX:n.x,canvasY:n.y}}getPopupContent(e){const t=this.createClickState(e);if(void 0===t)return;let i=this.trackView.track;const n=i.popupData(t),r=this.browser.fireEvent(\"trackclick\",[i,n]);let s;return void 0===r||!0===r?n&&n.length>0&&(s=n.map((e=>{if(e.name){const t=`<span>${e.name}</span>&nbsp&nbsp&nbsp${e.value}`;return`<div title=\"${e.value}\">${t}</div>`}return\"<hr>\"===e?e:e.html?e.html:`<div title=\"${e}\">${e}</div>`})).join(\"\")):\"string\"==typeof r&&(s=r),s}dispose(){this.popover&&this.popover.dispose(),super.dispose()}}class Cu{constructor(e,t,i,n,r,s,o,a){this.chr=e,this.bpStart=t,this.bpEnd=i,this.bpPerPixel=n,this.features=r,this.roiFeatures=s,this.multiresolution=o,this.windowFunction=a}containsRange(e,t,i,n,r){if(r&&r!==this.windowFunction)return!1;const s=this.multiresolution?this.bpPerPixel/n:1;return t>=this.bpStart&&i<=this.bpEnd&&e===this.chr&&s>.5&&s<2}overlapsRange(e,t,i){return this.chr===e&&i>=this.bpStart&&t<=this.bpEnd}}const _u=function(e,t){const{r:i,g:n,b:r}=no[e];return`rgba(${i},${n},${r},${t})`}(\"nickel\",2/16),xu=_u;class ku{constructor(e,t){if(this.url=e.url,e.name&&(this.name=e.name),this.isUserDefined=e.isUserDefined,e.featureSource)this.featureSource=e.featureSource;else if(e.features)this.featureSource=new Su(e.features,t);else{if(!e.format)throw Error(\"ROI configuration must define either features or file format\");this.featureSource=Ad(e,t)}!0===this.isUserDefined?(this.color=e.color||xu,this.headerColor=\"rgba(155,185,129)\"):(this.color=e.color||_u,this.headerColor=\"rgb(190,190,190)\"),this.isVisible=void 0===e.isVisible||e.isVisible}async getFeatures(e,t,i){return this.featureSource.getFeatures({chr:e,start:t,end:i})}async getAllFeatures(){return\"function\"==typeof this.featureSource.getAllFeatures?await this.featureSource.getAllFeatures():{}}addFeature(e){this.featureSource.addFeature(e)}removeFeature(e){this.featureSource.removeFeature(e)}toJSON(){if(this.url)return{name:this.name,color:this.color,url:this.url,isUserDefined:this.isUserDefined,isVisible:this.isVisible};{const e=this.featureSource.getAllFeatures(),t=[];for(let i of Object.keys(e))for(let n of e[i])t.push(n);return{name:this.name,color:this.color,features:t,isUserDefined:this.isUserDefined,isVisible:this.isVisible}}}dispose(){for(let e of Object.keys(this))this[e]=void 0}}function Iu(e,t,i,n){let r=Math.round((e-i)/n);let s=Math.round((t-i)/n)-r;return s<3&&(s=3,r-=1),{x:r,width:s}}class Su{constructor(e,t){this.featureMap={},this.genome=t;for(let i of e){const e=t?t.getChromosomeName(i.chr):i.chr;let n=this.featureMap[e];n||(n=[],this.featureMap[e]=n),n.push(i)}for(let e of Object.keys(this.featureMap))this.featureMap[e].sort(((e,t)=>e.start-t.start))}async getFeatures({chr:e,start:t,end:i}){if(\"all\"===e.toLowerCase())return Ll(this.featureMap,this.genome);{const n=this.featureMap[e];return n?n.filter((e=>e.end>t&&e.start<i)):[]}}getAllFeatures(){return this.featureMap}supportsWholeGenome(){return!0}addFeature(e){let t=this.featureMap[e.chr];t||(t=[],this.featureMap[e.chr]=t),t.push(e),t.sort(((e,t)=>e.start-t.start))}removeFeature({chr:e,start:t,end:i}){if(this.featureMap[e]){const n=`${e}-${t}-${i}`;this.featureMap[e]=this.featureMap[e].filter((e=>n!==`${e.chr}-${e.start}-${e.end}`)),0===this.featureMap[e].length&&delete this.featureMap[e]}}}class Eu{constructor(t,i,n,r){this.rulerViewport=t,this.rulerSweeper=e({class:\"igv-ruler-sweeper\"}),i.appendChild(this.rulerSweeper),this.browser=n,this.referenceFrame=r,this.isMouseHandlers=void 0,this.addBrowserObserver()}addBrowserObserver(){this.boundObserverHandler=(()=>{this.referenceFrame&&(mu.isWholeGenomeView(this.referenceFrame.chr)?this.removeMouseHandlers():this.addMouseHandlers())}).bind(this),this.browser.on(\"locuschange\",this.boundObserverHandler)}removeBrowserObserver(){this.browser.off(\"locuschange\",this.boundObserverHandler)}addMouseHandlers(){if(!0===this.isMouseHandlers)return;let e,t,i,n,r,s;this.boundContentMouseDownHandler=function(s){e=!0,t=!0;const{x:o}=a(s,this.rulerViewport.contentDiv);n=i=o,r=1,this.rulerSweeper.style.display=\"block\",this.rulerSweeper.style.backgroundColor=!0===s.shiftKey?xu:\"rgba(68, 134, 247, 0.25)\",this.rulerSweeper.style.left=`${n}px`,this.rulerSweeper.style.width=`${r}px`}.bind(this),this.rulerViewport.contentDiv.addEventListener(\"mousedown\",this.boundContentMouseDownHandler),this.boundDocumentMouseMoveHandler=function(o){let c;if(e&&t){const{x:e}=a(o,this.rulerViewport.contentDiv);c=Math.max(Math.min(e,this.rulerViewport.contentDiv.clientWidth),0),s=c-i,r=Math.abs(s),this.rulerSweeper.style.width=`${r}px`,s<0&&(n=i+s,this.rulerSweeper.style.left=`${n}px`)}}.bind(this),document.addEventListener(\"mousemove\",this.boundDocumentMouseMoveHandler),this.boundDocumentMouseUpHandler=function(i){let s;if(!0===e&&!0===t&&(e=t=void 0,this.rulerSweeper.style.display=\"none\",r>1)){s={start:Math.floor(this.referenceFrame.calculateEnd(n)),end:Math.floor(this.referenceFrame.calculateEnd(n+r))};!0===i.shiftKey?this.browser.roiManager.updateUserDefinedROISet(Object.assign({chr:this.referenceFrame.chr},s)):(Qa(this.browser.genome.getChromosome(this.referenceFrame.chr).bpLength,s,this.browser.minimumBases()),function(e,t,i){e.start=Math.round(t.start),e.end=Math.round(t.end),e.bpPerPixel=(e.end-e.start)/i}(this.referenceFrame,s,this.rulerViewport.contentDiv.clientWidth),this.browser.updateViews(this.referenceFrame))}}.bind(this),document.addEventListener(\"mouseup\",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!0}removeMouseHandlers(){this.rulerViewport.contentDiv.removeEventListener(\"mousedown\",this.boundContentMouseDownHandler),document.removeEventListener(\"mousemove\",this.boundDocumentMouseMoveHandler),document.removeEventListener(\"mouseup\",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!1}dispose(){this.removeBrowserObserver(),this.removeMouseHandlers(),this.rulerSweeper.remove()}}function Nu(e){if(Bu[e])return Bu[e];if(Bu[\"chr\"+e]){const t=Bu[\"chr\"+e];return Bu[e]=t,t}{const t=_s.randomRGB(0,255);return Bu[e]=t,t}}const Bu={chrX:\"rgb(204, 153, 0)\",chrY:\"rgb(153, 204, 0)\",chrUn:\"rgb(50, 50, 50)\",chr1:\"rgb(80, 80, 255)\",chrI:\"rgb(139, 155, 187)\",chr2:\"rgb(206, 61, 50)\",chrII:\"rgb(206, 61, 50)\",chr2a:\"rgb(216, 71, 60)\",chr2b:\"rgb(226, 81, 70)\",chr3:\"rgb(116, 155, 88)\",chrIII:\"rgb(116, 155, 88)\",chr4:\"rgb(240, 230, 133)\",chrIV:\"rgb(240, 230, 133)\",chr5:\"rgb(70, 105, 131)\",chr6:\"rgb(186, 99, 56)\",chr7:\"rgb(93, 177, 221)\",chr8:\"rgb(128, 34, 104)\",chr9:\"rgb(107, 215, 107)\",chr10:\"rgb(213, 149, 167)\",chr11:\"rgb(146, 72, 34)\",chr12:\"rgb(131, 123, 141)\",chr13:\"rgb(199, 81, 39)\",chr14:\"rgb(213, 143, 92)\",chr15:\"rgb(122, 101, 165)\",chr16:\"rgb(228, 175, 105)\",chr17:\"rgb(59, 27, 83)\",chr18:\"rgb(205, 222, 183)\",chr19:\"rgb(97, 42, 121)\",chr20:\"rgb(174, 31, 99)\",chr21:\"rgb(231, 199, 111)\",chr22:\"rgb(90, 101, 94)\",chr23:\"rgb(204, 153, 0)\",chr24:\"rgb(153, 204, 0)\",chr25:\"rgb(51, 204, 0)\",chr26:\"rgb(0, 204, 51)\",chr27:\"rgb(0, 204, 153)\",chr28:\"rgb(0, 153, 204)\",chr29:\"rgb(10, 71, 255)\",chr30:\"rgb(71, 117, 255)\",chr31:\"rgb(255, 194, 10)\",chr32:\"rgb(255, 209, 71)\",chr33:\"rgb(153, 0, 51)\",chr34:\"rgb(153, 26, 0)\",chr35:\"rgb(153, 102, 0)\",chr36:\"rgb(128, 153, 0)\",chr37:\"rgb(51, 153, 0)\",chr38:\"rgb(0, 153, 26)\",chr39:\"rgb(0, 153, 102)\",chr40:\"rgb(0, 128, 153)\",chr41:\"rgb(0, 51, 153)\",chr42:\"rgb(26, 0, 153)\",chr43:\"rgb(102, 0, 153)\",chr44:\"rgb(153, 0, 128)\",chr45:\"rgb(214, 0, 71)\",chr46:\"rgb(255, 20, 99)\",chr47:\"rgb(0, 214, 143)\",chr48:\"rgb(20, 255, 177)\"};let Mu,Ru;class Du extends Au{constructor(e,t,i,n){super(e,t,i,n)}get contentDiv(){return this.$viewport.get(0)}initializationHelper(){let e;this.$multiLocusCloseButton=Bt(\"<div>\",{class:\"igv-multi-locus-close-button\"}),this.$viewport.append(this.$multiLocusCloseButton),this.$multiLocusCloseButton.get(0).appendChild(l(\"times-circle\")),this.$multiLocusCloseButton.click((()=>{this.browser.removeMultiLocusPanel(this.referenceFrame)})),this.$rulerLabel=Bt(\"<div>\",{class:\"igv-multi-locus-ruler-label\"}),this.$viewport.append(this.$rulerLabel),e=document.createElement(\"div\"),this.$rulerLabel.append(Bt(e)),this.$rulerLabel.get(0).addEventListener(\"click\",(async e=>{e.stopPropagation(),await this.browser.gotoMultilocusPanel(this.referenceFrame)})),this.$tooltip=Bt(\"<div>\",{class:\"igv-ruler-tooltip\"}),this.$tooltip.height(this.$viewport.height()),this.$viewport.append(this.$tooltip),this.$tooltipContent=Bt(\"<div>\"),this.$tooltip.append(this.$tooltipContent),this.rulerSweeper=new Eu(this,this.$viewport.get(0).parentElement,this.browser,this.referenceFrame),this.attachMouseHandlers(mu.isWholeGenomeView(this.referenceFrame.chr)),this.$tooltip.hide(),this.dismissLocusLabel()}presentLocusLabel(e){this.$multiLocusCloseButton.show(),this.$rulerLabel.show(),this.$rulerLabel.get(0).style.backgroundColor=Nu(this.referenceFrame.chr);const t=this.$rulerLabel.get(0).querySelector(\"div\"),{width:i}=this.$rulerLabel.get(0).getBoundingClientRect();t.innerHTML=`${this.referenceFrame.getMultiLocusLabel(e)}`;const{width:n}=t.getBoundingClientRect();n/i>.5&&(t.innerHTML=`${this.referenceFrame.getMultiLocusLabelBPLengthOnly(e)}`)}dismissLocusLabel(){this.$rulerLabel.hide(),this.$multiLocusCloseButton.hide()}attachMouseHandlers(e){if(this.namespace=`.ruler_track_viewport_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}`,this.$viewport.off(this.namespace),!0===e){const e=this.browser.referenceFrameList.indexOf(this.referenceFrame),t=`click${this.namespace}`;this.$viewport.on(t,(t=>{const{x:i}=a(t,this.$viewport.get(0)),n=Math.round(this.referenceFrame.start+this.referenceFrame.toBP(i));let r;const{chr:s}=this.browser.genome.getChromosomeCoordinate(n);if(1===this.browser.referenceFrameList.length)r=s;else{let t=this.browser.referenceFrameList.map((({locusSearchString:e})=>e));t[e]=s,r=t.join(\" \")}this.browser.search(r)})),this.$viewport.get(0).style.cursor=\"pointer\"}else this.$viewport.get(0).style.cursor=\"default\"}mouseMove(e){if(!0===this.browser.doShowCursorGuide){void 0===Ru?(Ru=this,this.$tooltip.show()):Ru.guid!==this.guid?(Ru.$tooltip&&Ru.$tooltip.hide(),this.$tooltip.show(),Ru=this):this.$tooltip.show();if(this.browser.isMultiLocusWholeGenomeView()||mu.isWholeGenomeView(this.referenceFrame.chr))return void this.$tooltip.hide();const{x:t}=a(e,this.$viewport.get(0)),{start:i,end:n,bpPerPixel:r}=this.referenceFrame,s=Math.round(.5+i+Math.max(0,t)*r);this.$tooltipContent.text(Rt(s));const{width:o}=this.$tooltipContent.get(0).getBoundingClientRect(),{width:c}=this.$viewport.get(0).getBoundingClientRect();return this.$tooltip.css({left:`${ys.clamp(t,0,c-o)}px`}),clearTimeout(Mu),Mu=setTimeout((()=>{this.$tooltip&&this.$tooltip.hide()}),1e4),{start:i,bp:s,end:n}}}startSpinner(){}stopSpinner(){}dispose(){this.rulerSweeper.dispose(),super.dispose()}}class Tu extends Au{featureCache=new Lu;constructor(e,t,i,n){super(e,t,i,n)}initializationHelper(){this.canvas=document.createElement(\"canvas\"),this.canvas.className=\"igv-ideogram-canvas\",this.$viewport.append(Bt(this.canvas)),this.ideogram_ctx=this.canvas.getContext(\"2d\"),this.addMouseHandlers()}async getFeatures(e,t,i,n){return this.featureCache.containsRange(e)?this.featureCache.get(e):this.loadFeatures()}async loadFeatures(){const e=this.referenceFrame.chr,t=await this.referenceFrame.genome.getCytobands(e);return this.featureCache.set(e,t),t}repaint(){if(void 0===this.featureCache)return;const{width:e,height:t}=this.$viewport[0].getBoundingClientRect();xo.configureHighDPICanvas(this.ideogram_ctx,e,t);const i=this.referenceFrame.chr,n=this.featureCache.get(i),r={context:this.ideogram_ctx,pixelWidth:e,pixelHeight:t,referenceFrame:this.referenceFrame,features:n};this.trackView.track.draw(r)}addMouseHandlers(){this.addViewportClickHandler(this.$viewport.get(0))}addViewportClickHandler(e){this.boundClickHandler=function(e){const{xNormalized:t,width:i}=a(e,this.ideogram_ctx.canvas),{bpLength:n}=this.browser.genome.getChromosome(this.referenceFrame.chr),r=this.referenceFrame.bpPerPixel*i/n;let s=t;s-r/2<0&&(s=r/2);s+r/2>1&&(s=1-r/2);const o=Math.round((s-r/2)*n),c=Math.round((s+r/2)*n);this.referenceFrame.start=o,this.referenceFrame.end=c,this.referenceFrame.bpPerPixel=(c-o)/i,this.browser.updateViews(this.referenceFrame,this.browser.trackViews,!0)}.bind(this),e.addEventListener(\"click\",this.boundClickHandler)}setWidth(e){this.$viewport.width(e)}renderSVGContext(e,{deltaX:t,deltaY:i},n=!0){const{width:r,height:o}=this.$viewport.get(0).getBoundingClientRect(),a=`ideogram_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${s()}`,c=t,l=i+this.contentTop,h=-this.contentTop;e.saveWithTranslationAndClipRect(a,c,l,r,o,h),this.trackView.track.draw({context:e,pixelWidth:r,pixelHeight:o,referenceFrame:this.referenceFrame,features:this.featureCache.get(this.referenceFrame.chr)}),e.restore()}startSpinner(){}stopSpinner(){}}class Lu{features=new Map;containsRange(e){return this.features.has(e)}set(e,t){this.features.set(e,t)}get(e){return this.features.get(e)}}function zu(e,t,i,n){if(\"ruler\"===e.track.type)return new Du(e,t,i,n);if(\"ideogram\"===e.track.id)return new Tu(e,t,i,n);{const r=new Au(e,t,i,n);return i.viewport=r,r}}const Hu=[\"rgb(255, 0, 0)\",\"rgb(0, 255, 0)\",\"rgb(0, 0, 255)\",\"rgb(255, 0, 255)\",\"rgb(0, 255, 255)\",\"rgb(128, 0, 128)\",\"rgb(255, 165, 0)\",\"rgb(255, 105, 180)\",\"rgb(255, 127, 80)\",\"rgb(220, 20, 60)\",\"rgb(255, 99, 71)\",\"rgb(173, 216, 230)\",\"rgb(144, 238, 144)\",\"rgb(224, 255, 255)\",\"rgb(250, 250, 210)\",\"rgb(152, 251, 152)\",\"rgb(70, 130, 180)\",\"rgb(102, 205, 170)\"].map((e=>{const[t,i,n]=e.split(\",\"),[r,s]=t.split(\"(\"),[o,a]=n.split(\")\");return[s,i,o]})),Pu=ro(\"magnesium\"),Ou=[\"#sampleTable\",\"#sampleMapping\",\"#colors\"];class Uu{static emptySpaceReplacement=\"|\";sampleDictionary={};attributeNames=[];sampleMappingDictionary={};colorDictionary={};attributeRangeLUT={};constructor(e){e.tracks.some((e=>\"function\"==typeof e.getSamples)).length>0&&e.sampleInfoControl.setButtonVisibility(!0),this.initialize()}initialize(){this.sampleInfoFiles=[],this.attributeNames=[],this.sampleDictionary={},this.sampleMappingDictionary={},this.colorDictionary={},this.attributeRangeLUT={},this.initialized=!1}get attributeCount(){return this.attributeNames?this.attributeNames.length:0}isInitialized(){return this.initialized}hasAttributes(){return this.attributeCount>0}getAttributes(e){const t=0===Object.keys(this.sampleMappingDictionary)?e:this.sampleMappingDictionary[e]||e;return this.sampleDictionary[t]}async loadSampleInfoFile(e){try{const t=await Qs.loadString(e);this.#w(t),this.sampleInfoFiles.push(e)}catch(e){console.error(e.message)}}#w(e){const t=function(e){const t={},i=e.split(/\\r?\\n|\\r/).map((e=>e.trim())).filter((e=>\"\"!==e));let n;Ou.includes(i[0])||(n=\"#sampleTable\",t[n]=[]);for(const e of i)Ou.includes(e)?(n=e,t[n]=[]):n&&!1===e.startsWith(\"#\")&&t[n].push(e);return t}(e);for(const[e,i]of Object.entries(t))switch(e){case\"#sampleTable\":this.#b(i);break;case\"#sampleMapping\":this.#F(i);break;case\"#colors\":this.#v(i)}this.initialized=!0}getAttributeColor(e,t){let i;if(\"-\"===t)i=ro(\"snow\");else if(\"string\"==typeof t&&this.colorDictionary[t])i=this.colorDictionary[t]();else if(this.colorDictionary[e])i=this.colorDictionary[e](t);else if(\"string\"==typeof t)i=\"NA\"===t?Pu:function(e){let t=0;for(let i=0;i<e.length;i++)t=e.charCodeAt(i)+((t<<5)-t);let i=[];for(let e=0;e<3;e++){const n=t>>8*e&255;i.push(n)}return`rgb(${i.join(\", \")})`}(t);else{const[n,r]=this.attributeRangeLUT[e],s=.2,o=Math.max((t-n)/(r-n),s),[a,c,l]=Hu[Object.keys(this.attributeRangeLUT).indexOf(e)];i=`rgba(${a},${c},${l},${o})`}return i}getSortedSampleKeysByAttribute(e,t,i){i=i||1;const n=e.filter((e=>\"number\"==typeof this.getAttributes(e)[t])),r=e.filter((e=>\"string\"==typeof this.getAttributes(e)[t])),s=(e,n)=>{const r=this.getAttributes(e)[t],s=this.getAttributes(n)[t];return\"string\"==typeof r&&\"string\"==typeof s?i*r.localeCompare(s):\"number\"==typeof r&&\"number\"==typeof s?i*(r-s):void 0};return n.sort(s),r.sort(s),-1===i?[...n,...r]:[...r,...n]}toJSON(){const e=[];for(const t of this.sampleInfoFiles){const i={url:t},n=Hl.localFileInspection(i);e.push(n)}return e}#b(e){const t=e.shift().split(\"\\t\").filter((e=>e.length>0));t.shift();const i=t.map((e=>e.split(\" \").join(Uu.emptySpaceReplacement))),n=e.filter((e=>e.length>0));let r;for(const e of n){const t=e.split(\"\\t\"),n=t.shift();void 0===r&&(r={}),r[n]={};for(let e=0;e<t.length;e++){const s={};\"\"===t[e]?s[i[e]]=\"-\":s[i[e]]=t[e],Object.assign(r[n],s)}}for(const[e,t]of Object.entries(r))r[e]=Qu(t);const s=function(e,t){const i={};for(const n of Object.values(t))for(const t of e){let e=n[t];void 0===i[t]&&(i[t]=[]),i[t].push(e)}const n=e=>\"number\"==typeof e,r=e=>\"string\"==typeof e;for(const e of Object.keys(i)){const t=i[e],s=new Set(t),o=Array.from(s);if(!0===o.some(r)&&!0===o.some(n)?i[e]=o.filter((e=>!r(e))):i[e]=o,!i[e].some(r)){const t=i[e].slice();i[e]=[Math.min(...t),Math.max(...t)]}}return i}(i,r);qu(this.attributeRangeLUT,s);const o=new Set(this.attributeNames);for(const e of i)o.has(e)||this.attributeNames.push(e);qu(this.sampleDictionary,r)}#F(e){for(const t of e){const[e,i]=t.split(\"\\t\");this.sampleMappingDictionary[e]=i}}#v(e){const t=(e,t,i)=>{let n;switch(t){case 0:n=e.split(\" \").join(Uu.emptySpaceReplacement);break;case 1:n=e.includes(\":\")?e.split(\":\").map((e=>parseFloat(e))):e;break;case 2:case 3:n=`rgb(${e})`}return n},i=e.map((e=>e.split(\"\\t\").map(t))),n=i.filter((e=>3===e.length&&!e.includes(\"*\"))).filter((([e,t,i])=>!Array.isArray(t))),r={};for(const e of n){const[t,i,n]=e;void 0===r[t]&&(r[t]={}),r[t][i.toUpperCase()]=n}for(const[e,t]of Object.entries(r)){const i=Object.assign({},t);this.colorDictionary[e]=e=>{const t=e.toUpperCase();return i[t]||ro(\"snow\")}}const s=i.filter((e=>Array.isArray(e[1])));for(const e of s){const[t,i]=e[1],n=e[0];if(3===e.length){const[r,s,o]=uo(e[2]);this.colorDictionary[n]=e=>{e=ys.clamp(e,t,i);return lo(r,s,o,(e-t)/(i-t))}}else if(4===e.length){const[t,i]=e[1],[n,r,s,o]=e;this.colorDictionary[n]=e=>{e=ys.clamp(e,t,i);return fo(s,o,(e-t)/(i-t))}}}const o=i.filter((e=>3===e.length&&e.includes(\"*\")));for(const e of o)if(\"*\"===e[1]){const[t,i,n]=e;this.colorDictionary[t]=e=>{if(\"NA\"===e)return Pu;{const[i,r]=this.attributeRangeLUT[t],s=(e-i)/(r-i),[o,a,c]=uo(n);return lo(o,a,c,s)}}}else if(\"*\"===e[0]){const[t,i,n]=e;this.colorDictionary[i]=()=>n}}}function qu(e,t){for(const[i,n]of Object.entries(t))i in e&&e[i]===n||(e[i]=n)}function Qu(e){const t=Object.assign({},e);for(const[e,i]of Object.entries(t))\"string\"!=typeof i||isNaN(i)||(t[e]=Number(i));return t}const Vu=16,ju=Rt;class Wu{constructor(e){this.browser=e,this.height=40,this.name=\"\",this.id=\"ruler\",this.disableButtons=!0,this.ignoreTrackMenu=!0,this.order=.01*Number.MIN_SAFE_INTEGER,this.removable=!1,this.type=\"ruler\"}async getFeatures(e,t,i){return[]}computePixelHeight(e){return this.height}draw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpPerPixel:r,bpStart:s}){mu.isWholeGenomeView(t.chr)?this.drawWholeGenome({context:e,pixelWidth:i,pixelHeight:n,bpPerPixel:r}):this.doDraw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpStart:s})}drawWholeGenome({context:e,pixelWidth:t,pixelHeight:i,bpPerPixel:n}){e.save(),xo.fillRect(e,0,0,t,i,{fillStyle:\"white\"});for(let t of this.browser.genome.wgChromosomeNames){let r=this.browser.genome.getCumulativeOffset(t),s=this.browser.genome.getChromosome(t).bpLength,o=Math.round(r/n),a=Math.round(s/n);this.renderChromosomeRect(e,o,0,a,i,t)}e.restore()}doDraw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpStart:r}){e.clearRect(0,0,i,n);const s=function(e,t){if(e<10)return new Gu(1,\"bp\",1);const i=Math.floor(Math.log10(e));let n=\"bp\",r=1;i>9?(n=\"gb\",r=1e9):i>6?(n=\"mb\",r=1e6):i>3&&(n=\"kb\",r=1e3);const s=Math.pow(10,i-1),o=e/s,a=75,c=Math.pow(10,i-1),l=Math.pow(10,i)/2;return new Gu(o<a&&!0!==t?c:l,n,r)}(Math.floor(t.toBP(i)),e.isSVG);let o=Math.floor(r/s.majorTick)-1;const{tickDelta:a,labelLength:c}=function(e,t,i,n,r){const s=l(t,c(1+n,r),i)-l(t,c(n,r),i),o=`${Rt(Math.floor(c(n,r)/r.unitMultiplier))} ${r.majorUnit}`,a=Math.floor(e.measureText(o).width);return{tickDelta:s,labelLength:a};function c(e,t){return Math.floor(e*t.majorTick)}function l(e,t,i){return Math.round(e.toPixels(t-1-i+.5))}}(e,t,r,o,s);let l,h;this.browser.referenceFrameList.indexOf(t);let d=a;const u=.25*c;do{h=Math.floor(o*s.majorTick);const i=`${Rt(Math.floor(h/s.unitMultiplier))} ${s.majorUnit}`;l=Math.round(t.toPixels(h-1-r+.5));const n=Math.round(l-e.measureText(i).width/2);n>0&&u+c<=d&&(xo.fillText(e,i,n,this.height-8),d=0),l>0&&xo.strokeLine(e,l,this.height-6,l,this.height-2),h=Math.floor((1+o)*s.majorTick);let f=l+(Math.round(t.toPixels(h-1-r+.5))-l)/2;f>0&&xo.strokeLine(e,f,this.height-6,f,this.height-2),++o,d+=a}while(l<i);xo.strokeLine(e,0,this.height-2,i,this.height-2)}renderChromosomeRect(e,t,i,n,r,s){e.textAlign=\"center\",e.textBaseline=\"middle\",e.font=\"12px sans-serif\",xo.strokeLine(e,t+n,i,t+n,i+r,{strokeStyle:_s.greyScale(191)});const o=(s=this.browser.genome.getChromosomeDisplayName(s)).startsWith(\"chr\")?s.substring(3):s;n>e.measureText(o).width&&xo.fillText(e,o,t+n/2,i+r/2,{fillStyle:_s.greyScale(68)})}get supportsWholeGenome(){return!0}dispose(){}}class Gu{constructor(e,t,i){this.majorTick=e,this.minorTick=e/10,this.majorUnit=t,this.unitMultiplier=i}description(e){console.log((e||\"\")+\" tick \"+ju(this.majorTick)+\" label width \"+ju(this.labelWidthBP)+\" multiplier \"+this.unitMultiplier)}}class $u{constructor(t,i,n){this.guid=s(),this.trackView=t,this.browser=t.browser,this.viewport=e({class:\"igv-viewport\"}),i.appendChild(this.viewport),this.viewport.style.height=`${t.track.height}px`,null===this.viewport.previousElementSibling&&(this.viewport.style.zIndex=16,this.viewport.style.overflow=\"visible\"),this.canvas=document.createElement(\"canvas\"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext(\"2d\"),this.ctx.font=\"10px verdana\",this.contentTop=0,this.hitList=void 0,this.sortDirection=1,this.setWidth(n),this.addMouseHandlers()}resizeCanvas(){const e=window.devicePixelRatio,t=this.browser.getSampleInfoViewportWidth();let i;if(this.browser.trackViews.length>1&&null===this.viewport.previousElementSibling){const[e,t]=[this.browser.ideogramTrackView.track,this.browser.rulerTrackView.track];i=e.height+t.height}else i=this.viewport.clientHeight;if(this.canvas.width!==t*e||this.canvas.height!==i*e){const n=this.canvas;n.width=t*e,n.height=i*e,n.style.width=`${t}px`,n.style.height=`${i}px`,this.ctx=this.canvas.getContext(\"2d\"),this.ctx.scale(e,e),null===this.viewport.previousElementSibling&&xo.fillRect(this.ctx,0,0,this.ctx.canvas.width,this.ctx.canvas.height,{fillStyle:ro(\"snow\")})}}setTop(e){\"function\"==typeof this.trackView.track.getSamples&&(this.contentTop=e,this.repaint())}setWidth(e){this.viewport.innerWidth=e,this.resizeCanvas()}setHeight(e){const t=this.browser.getSampleInfoViewportWidth();this.viewport.style.width=`${t}px`,this.viewport.style.height=`${e}px`;const i=window.devicePixelRatio;this.canvas.width=t*i,this.canvas.height=e*i,this.canvas.style.width=`${t}px`,this.canvas.style.height=`${e}px`,this.ctx=this.canvas.getContext(\"2d\"),this.ctx.scale(i,i),null===this.viewport.previousElementSibling&&xo.fillRect(this.ctx,0,0,this.ctx.canvas.width,this.ctx.canvas.height,{fillStyle:ro(\"snow\")})}async repaint(){if(this.resizeCanvas(),\"function\"==typeof this.trackView.track.getSamples){const e=this.trackView.track.getSamples();e.names&&e.names.length>0&&this.draw({context:this.ctx,samples:e})}else null===this.viewport.previousElementSibling&&(this.browser.rulerTrackView&&this.browser.rulerTrackView.setTrackHeight(!0===this.browser.sampleInfoControl.showSampleInfo?this.calculateSampleInfoColumnHeight():40,!0),this.renderSampleInfoColumns(this.ctx))}calculateSampleInfoColumnHeight(){const e=this.browser.sampleInfo.attributeNames.map((e=>this.ctx.measureText(e).width));return 4+Math.min(Math.max(...e),128)}draw({context:e,samples:t}){if(e.clearRect(0,0,e.canvas.width,e.canvas.height),e.fillStyle=ro(\"snow\"),e.fillRect(0,0,e.canvas.width,e.canvas.height),t&&t.names.length>0){const i=this.browser.sampleInfo.attributeNames,n=this.viewport.getBoundingClientRect().height;let r=1;const s=t.height;r=s-2*r<=1?0:1;let o=this.contentTop+t.yOffset;this.hitList={};for(const a of t.names){if(o>n)break;if(o+s>0){const t=this.browser.sampleInfo.getAttributes(a);if(t){const n=Object.entries(t);for(const t of n){const[n,a]=t;e.fillStyle=this.browser.sampleInfo.getAttributeColor(n,a);const c=8+i.indexOf(n)*Vu,l=o+r,h=s-2*r;e.fillRect(c,l,15,h);const d=`${Math.floor(c)}#${Math.floor(l)}#16#${Math.ceil(h)}`;this.hitList[d]=`${n}#${a}`}}}o+=s}}}renderSampleInfoColumns(e){const t=(e,t,i,n,r,s)=>{e.save(),e.font=\"10px verdana\",e.translate(i+r/2,n+s),e.rotate(-Math.PI/2),e.textAlign=\"left\",e.fillStyle=ro(\"lead\"),e.fillText(t,2,2),e.restore()},i=this.browser.sampleInfo.attributeNames;this.hitList={};for(let n=0;n<i.length;n++){const r=8+n*Vu,s=15,o=Math.round(e.canvas.height/window.devicePixelRatio);xo.fillRect(e,r,0,s,o,{fillStyle:ro(\"snow\")}),t(e,i[n],r,0,s,o);const a=`${Math.floor(r)}#0#${s}#${Math.ceil(o)}`;this.hitList[a]=`${i[n]}`}}renderSVGContext(e,{deltaX:t,deltaY:i}){if(\"function\"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:o,height:a}=this.viewport.getBoundingClientRect(),c=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_sample_names_guid_${s()}`;e.saveWithTranslationAndClipRect(c,t,i+r,o,a,-r),this.draw({context:e,samples:n}),e.restore()}}addMouseHandlers(){this.addMouseMoveHandler()}addMouseMoveHandler(){this.boundMouseMoveHandler=function(e){if(this.hitList){const t=Object.entries(this.hitList);if(null===this.viewport.previousElementSibling){const i=(t,i)=>{const{marginTop:n}=window.getComputedStyle(i),{x:r,y:s}=a(e,this.browser.columnContainer.querySelector(\".igv-sample-info-column\"));return{x:Math.floor(r),y:Math.floor(s-parseInt(n,10))}},n=this.browser.columnContainer.querySelector(\".igv-sample-info-column\"),{x:r,y:s}=i(n,this.viewport);n.setAttribute(\"title\",\"\");for(const[e,i]of t){const[t,o,a,c]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(r<t||r>t+a||s<o||s>o+c)){n.setAttribute(\"title\",`${i}`);break}}}else{const{x:i,y:n}=a(e,this.viewport);this.viewport.setAttribute(\"title\",\"\");for(const[e,r]of t){const[t,s,o,a]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(i<t||i>t+o||n<s||n>s+a)){const[e,t]=r.split(\"#\");this.viewport.setAttribute(\"title\",`${e.split(Uu.emptySpaceReplacement).join(\" \")}: ${\"-\"===t?\"\":t}`);break}}}}}.bind(this),this.viewport.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandlers(){this.viewport.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}show(){this.viewport.style.display=\"block\"}hide(){this.viewport.style.display=\"none\"}}class Ku{constructor(t,i,n,r){this.guid=s(),this.trackView=t,this.browser=t.browser,this.viewport=e({class:\"igv-viewport\"}),i.appendChild(this.viewport),t.track.height&&(this.viewport.style.height=`${t.track.height}px`),this.canvas=document.createElement(\"canvas\"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext(\"2d\"),this.trackScrollDelta=0,this.contentTop=0,this.hitList=void 0,this.sortDirection=1,this.setWidth(r),this.addMouseHandlers()}checkCanvas(){const e=this.browser.sampleNameViewportWidth||0;this.ctx.canvas.width=e*window.devicePixelRatio,this.ctx.canvas.style.width=`${e}px`,this.ctx.canvas.height=this.viewport.clientHeight*window.devicePixelRatio,this.ctx.canvas.style.height=`${this.viewport.clientHeight}px`,this.ctx.scale(window.devicePixelRatio,window.devicePixelRatio)}setTop(e){if(\"function\"==typeof this.trackView.track.getSamples){this.contentTop=e;const t=this.trackView.track.getSamples();this.repaint(t)}}setWidth(e){this.viewport.innerWidth=e,this.checkCanvas()}async repaint(e){if(e.names.length>0&&!0===this.browser.showSampleNames&&(this.checkCanvas(),this.draw({context:this.ctx,samples:e}),void 0===this.browser.sampleNameViewportWidth)){const t=e.names.map((e=>this.ctx.measureText(e).width));this.browser.sampleNameViewportWidth=Math.min(200,4+Math.ceil(Math.max(...t))),this.browser.layoutChange()}}draw({context:e,samples:t}){if(xo.fillRect(e,0,0,e.canvas.width,t.height,{fillStyle:ro(\"snow\")}),t&&t.names.length>0){const i=this.viewport.getBoundingClientRect().height,n=t.height,r=n-2<=1?0:1;let s=this.contentTop+t.yOffset;this.hitList={};for(const o of t.names){if(s>i)break;if(s+n>0){const t=n-2*r;Yu(e,o,0+2,s+r,e.canvas.width,t)}s+=n}}}renderSVGContext(e,{deltaX:t,deltaY:i}){if(\"function\"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:o,height:a}=this.viewport.getBoundingClientRect(),c=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_sample_names_guid_${s()}`;e.saveWithTranslationAndClipRect(c,t,i+r,o,a,-r),this.draw({context:e,samples:n}),e.restore()}}addMouseHandlers(){this.boundClickHandler=function(e){e.preventDefault();const t={label:\"Name Panel Width\",value:this.browser.sampleNameViewportWidth,callback:e=>{this.browser.sampleNameViewportWidth=parseInt(e),this.browser.layoutChange()}};this.browser.inputDialog.present(t,e)}.bind(this),this.viewport.addEventListener(\"contextmenu\",this.boundClickHandler),this.boundMouseMoveHandler=function(e){if(this.hitList){const t=Object.entries(this.hitList),{x:i,y:n}=a(e,this.viewport);this.viewport.setAttribute(\"title\",\"\");for(const[e,r]of t){const[t,s,o,a]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(i<t||i>t+o||n<s||n>s+a)){this.viewport.setAttribute(\"title\",`${r}`);break}}}}.bind(this),this.viewport.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandlers(){this.viewport.removeEventListener(\"contextmenu\",this.boundClickHandler),this.viewport.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}}function Yu(e,t,i,n,r,s){const o=Math.min(s,10);e.font=`${o}px sans-serif`,e.textAlign=\"start\",e.fillStyle=ro(\"lead\");const a=i,c=e.measureText(t),l=n+s/2+(c.actualBoundingBoxAscent+c.actualBoundingBoxDescent)/2;e.fillText(t,a,l)}class Xu{constructor(t){this.popover=e({class:\"igv-menu-popup\"}),t.appendChild(this.popover),this.parent=t;const i=e({class:\"igv-menu-popup-header\"});this.popover.appendChild(i),u(i,(()=>this.popover.style.display=\"none\")),this.popoverContent=e(),this.popover.appendChild(this.popoverContent),p(this.popover,i),i.addEventListener(\"click\",(e=>{e.stopPropagation(),e.preventDefault()})),this.popover.style.display=\"none\"}presentMenuList(e,t){if(Zu(this.parent),t.length>0){this.popoverContent.innerHTML=\"\";const i=this.parseMenuList(e,t);for(let e of i){e.init&&e.init();let t=e.object;0===i.indexOf(e)&&t.removeClass(\"igv-track-menu-border-top\"),t.hasClass(\"igv-track-menu-border-top\")||t.hasClass(\"igv-menu-popup-check-container\")||t.is(\"div\")&&t.addClass(\"igv-menu-popup-shim\"),this.popoverContent.appendChild(t.get(0))}this.popover.style.display=\"flex\";const{width:n}=this.popover.getBoundingClientRect();this.popover.style.left=-n+\"px\",this.popover.style.top=\"0px\"}}parseMenuList(e,t){return t.map(((t,i)=>{let n;if(t.name?(n=Bt(\"<div>\"),n.text(t.name)):t.object?n=t.object:\"string\"==typeof t.label?(n=Bt(\"<div>\"),n.html(t.label)):\"string\"==typeof t&&(n=t.startsWith(\"<\")?Bt(t):Bt(\"<div>\"+t+\"</div>\")),0===i&&n.addClass(\"igv-track-menu-border-top\"),t.click||t.dialog){const i=i=>{if(i.preventDefault(),i.stopPropagation(),t.click)if(e.track.selected){const n=e.browser.getSelectedTrackViews();if(!0===t.doAllMultiSelectedTracks)t.click.call(e.track,i);else if(\"removeTrack\"===t.menuItemType){const r=()=>{e.browser.overlayTrackButton.setVisibility(!1);for(const{track:e}of n)t.click.call(e,i)},s={html:`Are you sure you want to delete ${n.length} tracks?`,callback:r};e.browser.menuUtils.dialog.present(s,i)}else for(const{track:e}of n)t.click.call(e,i)}else t.click.call(e.track,i);else t.dialog&&t.dialog.call(e.track,i);this.popover.style.display=\"none\"};n.on(\"click\",i),n.on(\"touchend\",(e=>i(e))),n.on(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}return{object:n,init:t.init||void 0}}))}presentTrackContextMenu(t,n){this.popoverContent.innerHTML=\"\";const r=function(t,n){return t.map((t=>{let r;if(\"string\"==typeof t&&\"<hr/>\"===t)r=document.createElement(\"hr\");else if(\"string\"==typeof t)r=e({class:\"context-menu\"}),r.innerHTML=t;else if(\"Node\"==typeof t)r=t;else{if(\"function\"==typeof t.init&&t.init(),\"checkbox\"===t.type)r=Dl(\"Show all bases\",t.value);else if(\"color\"===t.type){const s=new Ra(n.parentElement);s.configure({color:\"grey\"}),r=e({class:\"context-menu\"}),\"string\"==typeof t.label&&(r.innerHTML=t.label);const o=e=>{s.show(),i(n),e.preventDefault(),e.stopPropagation()};r.addEventListener(\"click\",o),r.addEventListener(\"touchend\",o),r.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}else r=e({class:\"context-menu\"}),\"string\"==typeof t.label&&(r.innerHTML=t.label);if(t.click&&\"color\"!==t.type){function a(e){t.click(),i(n),e.preventDefault(),e.stopPropagation()}r.addEventListener(\"click\",a),r.addEventListener(\"touchend\",a),r.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}}return{el:r,init:t.init}}))}(n,this.popover);for(let{el:e}of r)this.popoverContent.appendChild(e);!function(e,t){t.style.display=\"flex\";const{x:i,y:n}=a(e,t.parentNode),{width:r}=t.getBoundingClientRect(),s=i+r,{width:o}=t.parentNode.getBoundingClientRect();t.style.left=`${s>o?i-(s-o):i}px`,t.style.top=`${n}px`}(t,this.popover)}hide(){this.popover.style.display=\"none\"}dispose(){this.popoverContent.innerHTML=\"\",this.popover.innerHTML=\"\",Object.keys(this).forEach((function(e){this[e]=void 0}))}}const Zu=e=>{const t=e.querySelectorAll(\".igv-menu-popup\");for(const e of t)e.style.display=\"none\"};class Ju{constructor(t,i,n,r,s,o,a){this.browser=i,this.button=e({class:\"igv-navbar-text-button\"}),t.appendChild(this.button),Array.isArray(n)?(this.textContent=n[0],this.title=n[1]):this.textContent=this.title=n,this.buttonLabel=r,this.imageDictionary={image:`url(\"data:image/svg+xml,${encodeURIComponent(s)}\")`,imageHover:`url(\"data:image/svg+xml,${encodeURIComponent(o)}\")`},this.responsiveKey=\"text\",this.configureButton(this.textContent,this.title),this.setState(a),i.on(\"navbar-resize\",(e=>{this.navbarResizeHandler(e)}))}navbarResizeHandler(e){const t=\"igv-navbar-icon-button\"===e?\"image\":\"text\";t!==this.responsiveKey&&(this.responsiveKey=t,this.configureButton(this.textContent,this.title),this.setState(void 0))}configureButton(e,t){this.groupElement=void 0,this.button.title=t,this.button.innerHTML=\"\",this.button.style.backgroundImage=\"none\",this.button.classList.remove(\"igv-navbar-icon-button\"),this.button.classList.remove(\"igv-navbar-text-button\"),\"text\"===this.responsiveKey?this.configureTextButton(e):this.configureIconButton()}configureTextButton(e){console.log(`text ${this.title}`),this.button.classList.add(\"igv-navbar-text-button\");const t=document.createElement(\"div\");t.innerHTML=this.buttonLabel;const i=t.firstChild;this.button.appendChild(i),this.groupElement=i.querySelector(\"#igv-navbar-button-group\");i.querySelector(\"#igv-navbar-button-label\").textContent=e}configureIconButton(){console.log(`icon ${this.title}`),this.button.classList.add(\"igv-navbar-icon-button\")}setState(e){void 0!==e&&(this.doHover=e),\"text\"===this.responsiveKey?this.setTextButtonState(this.doHover):this.setIconButtonState(this.doHover)}setTextButtonState(e){this.groupElement.classList.remove(...this.groupElement.classList);const t=!0===e?\"igv-navbar-text-button-svg-hover\":\"igv-navbar-text-button-svg-inactive\";this.groupElement.classList.add(t)}setIconButtonState(e){this.button.style.backgroundImage=!0===e?this.imageDictionary.imageHover:this.imageDictionary.image}show(){this.button.style.display=\"flex\"}hide(){this.button.style.display=\"none\"}setVisibility(e){!0===e?this.show():this.hide()}}const ef='<svg width=\"80px\" height=\"18px\" viewBox=\"0 0 80 18\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"igv-navbar-button-group\">\\n            <rect id=\"Rectangle\" x=\"0.5\" y=\"0.5\" width=\"79\" height=\"17\" rx=\"6\"></rect>\\n            <text id=\"igv-text-button-label\" x=\"50%\" y=\"50%\" dy=\".1em\" font-family=\"Helvetica\" font-size=\"12\" font-weight=\"normal\" letter-spacing=\"-0.372\">\\n                <tspan id=\"igv-navbar-button-label\"></tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>';class tf extends Hl{static defaults={autoscale:void 0,alpha:.5,height:50};constructor(e,t,i){super(e,t),this.type=\"merged\",this.paintAxis=cd,this.graphType=e.graphType,this.tracks=i||[]}async postInit(){if(this.config.tracks){for(let e of this.config.tracks){const t=await this.browser.createTrack(e);t?this.tracks.push(t):console.warn(\"Could not create track \"+e),\"function\"==typeof t.postInit&&await t.postInit()}this.config.tracks.every((e=>void 0!==e.autoscale||void 0!==e.max))||(this.config.autoscale=void 0===this.config.max)}for(let e of this.tracks)e.isMergedTrack=!0;if(this.config.autoscale?this.autoscale=this.config.autoscale:void 0!==this.config.max&&this.setDataRange({min:this.config.min||0,max:this.config.max}),void 0!==this.config.flipAxis)for(let e of this.tracks)e.flipAxis=this.config.flipAxis;if(void 0!==this.config.logScale)for(let e of this.tracks)e.logScale=this.config.logScale;this.resolutionAware=this.tracks.some((e=>e.resolutionAware))}set flipAxis(e){this.config.flipAxis=e;for(let t of rf(this.tracks))t.flipAxis=e}get flipAxis(){return rf(this.tracks).every((e=>e.flipAxis))}set logScale(e){this.config.logScale=e;for(let t of rf(this.tracks))t.logScale=e}get logScale(){return rf(this.tracks).every((e=>e.logScale))}get height(){return this._height}set height(e){if(this.config.height=e,this._height=e,this.tracks)for(let t of this.tracks)t.height=e,t.config.height=e}set autoscale(e){if(this._autoscale=e,!1===e&&this.tracks)for(let e of this.tracks)e.autoscale=!1}get autoscale(){return this._autoscale}set autoscaleGroup(e){if(this.tracks)for(let t of this.tracks)t.autoscaleGroup=e}get autoscaleGroup(){if(this.tracks&&this.tracks.length>0){const e=this.tracks[0].autoscaleGroup;return this.tracks.some((t=>e!==t.autoscaleGroup))?void 0:e}}setDataRange({min:e,max:t}){this.autoscale=!1;for(const i of rf(this.tracks))i.dataRange={min:e,max:t},i.autoscale=!1,i.autoscaleGroup=!1}set dataRange({min:e,max:t}){for(const i of rf(this.tracks))i.dataRange={min:e,max:t}}get dataRange(){if(this.tracks){const e=rf(this.tracks);if(e.length>0){const t=e[0].dataRange;if(e.every((e=>e.dataRange&&e.dataRange.min===t.min&&e.dataRange.max===t.max)))return t}}}menuItemList(){const e=[];return rf(this.tracks).length>0&&(void 0!==this.flipAxis&&e.push({label:\"Flip y-axis\",click:function(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),e.push(...this.numericDataMenuItems())),e.push(\"<hr/>\"),e.push(this.overlayTrackAlphaAdjustmentMenuItem()),e.push(this.trackSeparationMenuItem()),e}async getFeatures(e,t,i,n){const r=this.tracks.map((r=>r.getFeatures(e,t,i,n))),s=await Promise.all(r);if(s.every((e=>0===e.length)))return new nf([],[]);{const e=this.tracks.map((e=>e.name));return new nf(s,e)}}draw(e){const t=e.features;for(let i=0,n=this.tracks.length;i<n;i++){const n=Object.assign({},e);n.features=t.featureArrays[i],n.alpha=this.alpha,this.graphType&&(this.tracks[i].graphType=this.graphType),this.tracks[i].draw(n)}}popupData(e){const t=this.clickedFeatures(e);if(t&&t.length===this.tracks.length){const i=[];let n=!0;for(let r=0;r<t.length;r++)if(r>0&&i.push(\"<hr/>\"),i.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${t[r].trackName}</div>`),t[r].features.length>0){n=!1;const s=this.tracks[r].popupData(e,t[r].features);i.push(...s)}else i.push(\"Missing or 0 value(s)\");return!0===n?[]:i}}clickedFeatures(e){const t=e.viewport.cachedFeatures;if(!t||!t.featureArrays||!Array.isArray(t.featureArrays)||0===t.featureArrays.length)return[];const i=e.genomicLocation,n=[],r=e.referenceFrame.bpPerPixel>.2?3*e.referenceFrame.bpPerPixel:.2,s=i-r,o=i+r;for(let e=0;e<t.featureArrays.length;e++){const i=to(t.featureArrays[e],s,o);n.push({trackName:t.trackNames[e],features:i})}return n}get supportsWholeGenome(){return this.tracks.every((e=>e.supportsWholeGenome))}getState(){const e=super.getState(),t=[];for(let e of this.tracks)t.push(e.getState());return e.tracks=t,e}updateScales(e){let t;if(this.autoscale){t=!0;let i=[];for(let t of e){if(t.featureCache&&t.featureCache.features){const e=t.referenceFrame,n=e.start,r=n+e.toBP(t.getWidth()),s=t.featureCache.features;this.autoscale&&(i.push({value:s.getMax(n,r)}),i.push({value:s.getMin(n,r)}))}const e=qa(i);for(const t of rf(this.tracks))t.dataRange=e}}else{let i=-1;for(let n of this.tracks)if(++i,n.autoscale){t=!0;let r=[];for(let t of e)if(t.featureCache&&t.featureCache.features){const e=t.referenceFrame,n=e.start,s=n+e.toBP(t.getWidth()),o=t.featureCache.features.featureArrays[i];if(o)for(let e of o)if(!(e.end<n)){if(e.start>s)break;r.push(e)}}n.dataRange=qa(r)}}return t}overlayTrackAlphaAdjustmentMenuItem(){const t=e();return t.innerText=\"Set transparency\",{object:Bt(t),dialog:function(e){const t={label:\"Transparency\",value:this.alpha,min:0,max:1,scaleFactor:1e3,callback:e=>{this.alpha=Math.max(.001,e),this.repaintViews()}};this.browser.sliderDialog.present(t,e)}}}trackSeparationMenuItem(){const e=Bt(\"<div>\");return e.text(\"Separate tracks\"),{object:e,click:function(e){const t=this.autoscale,i=this.name,n=this.tracks,r=this.browser,s=this.order;r.removeTrack(this);for(let e of n)e.order=s,t&&(e.autoscaleGroup=i),e.isMergedTrack=!1,r.addTrack(e.config,e);r.updateViews()}}}}class nf{constructor(e,t){this.featureArrays=e,this.trackNames=t}getMax(e,t){let i=-Number.MAX_VALUE;for(let n of this.featureArrays)if(Array.isArray(n))for(let r of n)if(!(void 0===r.value||Number.isNaN(r.value)||r.end<e)){if(r.start>t)break;i=Math.max(i,r.value)}return i!==-Number.MAX_VALUE?i:100}getMin(e,t){let i=0;for(let n of this.featureArrays)if(Array.isArray(n))for(let r of n)if(void 0!==r.value&&!Number.isNaN(r.value)){if(r.end<e)continue;if(r.start>t)break;i=Math.min(i,r.value)}return i}}const rf=e=>e?e.filter((e=>void 0!==e.dataRange||void 0!==e.autoscale||void 0!==e.autoscaleGroup)):[];class sf extends Ju{constructor(e,t){super(e,t,\"Overlay Tracks\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>Overlay Tracks</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"Overlay-Tracks\">\\n            <rect id=\"backdrop\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"layer-group\" transform=\"translate(3, 127)\">\\n                <rect id=\"a\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#A1A1A1\" x=\"12\" y=\"12\" width=\"332\" height=\"139\"></rect>\\n                <rect id=\"a---hold-out\" fill=\"#A1A1A1\" x=\"9\" y=\"25\" width=\"324\" height=\"115\"></rect>\\n                <rect id=\"b\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#C9C9C9\" x=\"81\" y=\"103\" width=\"474\" height=\"139\"></rect>\\n                <rect id=\"c\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#ECECEC\" x=\"238\" y=\"214\" width=\"372\" height=\"139\"></rect>\\n                <rect id=\"c---hold-out\" fill=\"#ECECEC\" x=\"250\" y=\"226\" width=\"372\" height=\"115\"></rect>\\n            </g>\\n            <rect id=\"over-border\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>Overlay Tracks Hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"Overlay-Tracks-Hover\">\\n            <rect id=\"backdrop-copy\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"layer-group\" transform=\"translate(3, 127)\">\\n                <rect id=\"a\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#A1A1A1\" x=\"12\" y=\"12\" width=\"332\" height=\"139\"></rect>\\n                <rect id=\"a---hold-out\" fill=\"#A1A1A1\" x=\"9\" y=\"25\" width=\"324\" height=\"115\"></rect>\\n                <rect id=\"b\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#C9C9C9\" x=\"81\" y=\"103\" width=\"474\" height=\"139\"></rect>\\n                <rect id=\"c\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#ECECEC\" x=\"238\" y=\"214\" width=\"372\" height=\"139\"></rect>\\n                <rect id=\"c---hold-out\" fill=\"#ECECEC\" x=\"250\" y=\"226\" width=\"372\" height=\"115\"></rect>\\n            </g>\\n            <rect id=\"over-border-copy\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>',!1),this.button.addEventListener(\"mouseenter\",(()=>this.setState(!0))),this.button.addEventListener(\"mouseleave\",(()=>this.setState(!1)));this.boundMouseClickHandler=(()=>{this.setVisibility(!1),of.call(this)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(!0)}}function of(e){if(!0===af(this.browser)){const e=this.browser.getSelectedTrackViews().map((({track:e})=>e));for(const t of e)t.selected=!1;const t=[];for(let i of e)\"merged\"===i.type?t.push(...i.tracks):t.push(i);const i={name:\"Overlay\",type:\"merged\",autoscale:!1,alpha:.5,height:Math.max(...e.map((({height:e})=>e))),order:Math.min(...e.map((({order:e})=>e)))},n=new tf(i,this.browser,t);for(const t of e){const e=this.browser.trackViews.indexOf(t.trackView);this.browser.trackViews.splice(e,1),t.trackView.dispose()}this.browser.addTrack(i,n),n.trackView.updateViews()}}function af(e){const t=e.getSelectedTrackViews();if(t&&t.length>1){const e=new Set([\"wig\",\"merged\"]);return t.filter((({track:t})=>e.has(t.type))).length>1}return!1}const cf=new Set([\"sequence\",\"ruler\",\"ideogram\"]),lf=new Set([\"ruler\",\"sequence\",\"ideogram\"]);class hf{constructor(e,t,i){this.namespace=`trackview-${s()}`,this.browser=e,this.track=i,i.trackView=this,this.addDOMToColumnContainer(e,t,e.referenceFrameList)}startSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].startSpinner()}stopSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].stopSpinner()}addDOMToColumnContainer(e,t,i){this.axis=this.createAxis(e,this.track),this.createViewports(e,t,i),this.sampleInfoViewport=new $u(this,e.columnContainer.querySelector(\".igv-sample-info-column\"),e.getSampleInfoViewportWidth()),this.sampleNameViewport=new Ku(this,e.columnContainer.querySelector(\".igv-sample-name-column\"),void 0,e.getSampleNameViewportWidth()),this.createTrackScrollbar(e),this.createTrackDragHandle(e),this.createTrackGearPopup(e)}createViewports(e,t,i){this.viewports=[];const n=e.calculateViewportWidth(i.length),r=t.querySelectorAll(\".igv-column\");for(let e=0;e<r.length;e++){const t=zu(this,r[e],i[e],n);this.viewports.push(t)}}createAxis(t,i){const n=e();if(this.axis=n,t.columnContainer.querySelector(\".igv-axis-column\").appendChild(n),n.dataset.tracktype=i.type,n.style.height=`${i.height}px`,\"function\"==typeof i.paintAxis){const{width:e,height:t}=n.getBoundingClientRect();this.axisCanvas=document.createElement(\"canvas\"),this.axisCanvas.style.width=`${e}px`,this.axisCanvas.style.height=`${t}px`,n.appendChild(this.axisCanvas)}if(!1===mo.has(this.track.type)){this.trackSelectionContainer=e(),n.appendChild(this.trackSelectionContainer);const t='<input type=\"checkbox\" name=\"track-select\">',i=document.createRange().createContextualFragment(t).firstChild;this.trackSelectionContainer.appendChild(i),i.checked=this.track.selected||!1,i.addEventListener(\"change\",(e=>{e.preventDefault(),e.stopPropagation(),this.track.selected=e.target.checked,this.setDragHandleSelectionState(e.target.checked),this.browser.overlayTrackButton.setVisibility(af(this.browser))})),this.enableTrackSelection(!1)}return n}resizeAxisCanvas(e,t){this.axis.style.width=`${e}px`,this.axis.style.height=`${t}px`,\"function\"==typeof this.track.paintAxis&&(this.axisCanvas.style.width=`${e}px`,this.axisCanvas.style.height=`${t}px`)}renderSVGContext(e,{deltaX:t,deltaY:i}){!function(e,t,i,n,r){if(\"function\"==typeof t.paintAxis){const{y:o,width:a,height:c}=i.getBoundingClientRect(),l=`${(t.name||t.id).replace(/\\W/g,\"\")}_axis_guid_${s()}`;e.saveWithTranslationAndClipRect(l,n,o+r,a,c,0),t.paintAxis(e,a,c),e.restore()}}(e,this.track,this.axisCanvas,t,i);const{width:n}=this.axis.getBoundingClientRect(),{y:r}=this.viewports[0].$viewport.get(0).getBoundingClientRect();let o={deltaX:n+t,deltaY:r+i};for(let t of this.viewports){t.renderSVGContext(e,o);const{width:i}=t.$viewport.get(0).getBoundingClientRect();o.deltaX+=i}if(!0===this.browser.sampleInfo.isInitialized()&&!0===this.browser.sampleInfoControl.showSampleInfo){this.sampleInfoViewport.renderSVGContext(e,o);const{width:t}=this.sampleInfoViewport.viewport.getBoundingClientRect();o.deltaX+=t}!0===this.browser.showSampleNames&&this.sampleNameViewport.renderSVGContext(e,o)}presentColorPicker(e){if(!1===lf.has(this.track.type)){const t=[],i=this.track.color||this.track.defaultColor;Mt(i)&&t.push(i),this.track.altColor&&Mt(this.track.altColor)&&t.push(this.track.altColor);let n=t.map((e=>e.startsWith(\"#\")?e:e.startsWith(\"rgb(\")?_s.rgbToHex(e):_s.colorNameToHex(e))),r={color:e=>{this.track.color=io(e),this.repaintViews()},altColor:e=>{this.track.altColor=io(e),this.repaintViews()}};const s=this.browser.getSelectedTrackViews();s.length>0&&new Set(s).has(this)?(r={color:e=>{for(let t of s)t.track.color=e,t.repaintViews()}},this.browser.genericColorPicker.configure(n,r)):this.browser.genericColorPicker.configure(n,r),this.browser.genericColorPicker.setActiveColorHandler(e),this.browser.genericColorPicker.show()}}setTrackHeight(e,t){t||(this.track.minHeight&&(e=Math.max(this.track.minHeight,e)),this.track.maxHeight&&(e=Math.min(this.track.maxHeight,e))),this.track.height=e,this.resizeAxisCanvas(this.axis.clientWidth,this.track.height),\"function\"==typeof this.track.paintAxis&&this.paintAxis();for(let{$viewport:t}of this.viewports)t.height(e);if(this.sampleInfoViewport.setHeight(e),this.sampleNameViewport.viewport.style.height=`${e}px`,\"function\"!=typeof this.track.computePixelHeight)for(let t of this.viewports)t.setContentHeight(e);this.repaintViews(),this.updateScrollbar(),this.dragHandle.style.height=`${e}px`,this.gearContainer.style.height=`${e}px`}updateScrollbar(){const e=this.viewports[0].$viewport.height();if(this.outerScroll.style.height=`${e}px`,!1===cf.has(this.track.type)){const t=this.maxViewportContentHeight(),i=Math.round(e/t*e);t>e?(this.innerScroll.style.display=\"block\",this.innerScroll.style.height=`${i}px`):this.innerScroll.style.display=\"none\"}}moveScroller(e){const t=Bt(this.innerScroll).position().top+e,i=Math.min(Math.max(0,t),this.outerScroll.clientHeight-this.innerScroll.clientHeight);Bt(this.innerScroll).css(\"top\",`${i}px`);const n=this.maxViewportContentHeight(),r=-Math.round(i*(n/this.viewports[0].$viewport.height()));for(let e of this.viewports)e.setTop(r);this.sampleInfoViewport.setTop(r),this.sampleNameViewport.trackScrollDelta=e,this.sampleNameViewport.setTop(r)}isLoading(){for(let e of this.viewports)if(e.isLoading())return!0}repaintViews(){for(let e of this.viewports)e.isVisible()&&e.repaint();\"function\"==typeof this.track.paintAxis&&this.paintAxis(),this.repaintSampleInfo(),this.repaintSamples()}repaintSampleInfo(){this.sampleInfoViewport.repaint()}repaintSamples(){if(\"function\"==typeof this.track.getSamples){const e=this.track.getSamples();e.names&&e.names.length>0&&this.sampleNameViewport.repaint(e)}}setTrackLabelName(e){this.viewports.forEach((t=>t.setTrackLabel(e)))}resize(e){for(let t of this.viewports)t.setWidth(e)}async updateViews(){if(!this.browser||!this.browser.referenceFrameList)return;const e=this.viewports.filter((e=>e.isVisible()));if(e.forEach((e=>e.shift())),this.browser.dragObject)return;const t=e.filter((e=>e.needsRepaint())).filter((e=>e.checkZoomIn())),i=e.filter((e=>e.checkZoomIn())).filter((e=>e.needsReload()));for(let e of i)await e.loadFeatures();if(this.disposed)return;if(this.track&&\"function\"==typeof this.track.variantRowCount&&i.length>0){let e=0;for(let t of this.viewports)t.featureCache&&t.featureCache.features&&(e=Math.max(e,t.featureCache.features.reduce(((e,t)=>Math.max(e,t.row||0)),0)));if(this.track.nVariantRows!==e+1){this.track.variantRowCount(e+1);for(let e of this.viewports)e.checkContentHeight()}}let n;if(\"merged\"===this.track.type)n=this.track.updateScales(e);else if(this.track.autoscale){let t=[];for(let i of e){const e=i.referenceFrame,n=e.start,r=n+e.toBP(i.getWidth());if(i.featureCache&&i.featureCache.features)if(\"function\"==typeof i.featureCache.features.getMax){const e=i.featureCache.features.getMax(n,r);if(t.push({value:e}),\"function\"==typeof i.featureCache.features.getMin){const e=i.featureCache.features.getMin(n,r);t.push({value:e})}}else{const e=to(i.featureCache.features,n,r);for(let i of e)t.push(i)}}\"function\"==typeof this.track.doAutoscale?this.track.dataRange=this.track.doAutoscale(t):this.track.dataRange=qa(t)}const r=this.track.autoscale||this.track.autoscaleGroup||\"ruler\"===this.track.type||n||this.track.groupBy;for(let i of e)t.includes(i)?i.repaint():r&&i.refresh();this.adjustTrackHeight(),this.repaintSampleInfo(),this.repaintSamples(),this.updateRulerViewportLabels()}clearCachedFeatures(){for(let e of this.viewports)e.clearCache()}updateRulerViewportLabels(){const e=this.browser.calculateViewportWidth(this.viewports.length);for(let t of this.viewports)\"ruler\"===this.track.type&&(this.viewports.length>1?t.presentLocusLabel(e):t.dismissLocusLabel())}async getInViewFeatures(){if(!this.browser||!this.browser.referenceFrameList)return[];let e=[];const t=this.viewports.filter((e=>e.isVisible()));for(let i of t){const t=i.referenceFrame,{chr:n,start:r,bpPerPixel:s}=i.referenceFrame,o=r+t.toBP(i.getWidth());if((!i.featureCache||!i.featureCache.containsRange(n,r,o,s))&&await i.loadFeatures(),i.featureCache&&i.featureCache.features)if(\"function\"==typeof i.featureCache.features.getMax){const t=i.featureCache.features.getMax(r,o);e.push({value:t})}else{const t=\"function\"==typeof i.featureCache.queryFeatures?i.featureCache.queryFeatures(n,r,o):to(i.featureCache.features,r,o);e=e.concat(t)}}return e}checkContentHeight(){for(let e of this.viewports)e.checkContentHeight();this.adjustTrackHeight()}adjustTrackHeight(){var e=this.maxViewportContentHeight();if(this.track.autoHeight?this.setTrackHeight(e,!1):this.track.paintAxis&&this.paintAxis(),!1===cf.has(this.track.type)){const t=this.viewports[0].getContentTop(),i=this.viewports[0].$viewport.height(),n=Math.min(0,i-e);if(t<n)for(let e of this.viewports)e.setTop(n);this.updateScrollbar()}}viewportsToReload(e){return this.viewports.filter((t=>{if(!t.isVisible())return!1;if(t.checkZoomIn()){const i=t.referenceFrame,n=t.referenceFrame.chr,r=i.start,s=r+i.toBP(Bt(t.contentDiv).width()),o=i.bpPerPixel;return e||!t.tile||t.tile.invalidate||!t.tile.containsRange(n,r,s,o)}return!1}))}createTrackScrollbar(t){const i=e();if(t.columnContainer.querySelector(\".igv-scrollbar-column\").appendChild(i),i.style.height=`${this.track.height}px`,this.outerScroll=i,!1===cf.has(this.track.type)){const n=e();i.appendChild(n),this.innerScroll=n,this.addTrackScrollMouseHandlers(t)}}createTrackDragHandle(t){\"sequence\"!==this.track.type&&!0===mo.has(this.track.type)?this.dragHandle=e({class:\"igv-track-drag-shim\"}):(this.dragHandle=e({class:\"igv-track-drag-handle\"}),this.dragHandle.classList.add(\"igv-track-drag-handle-color\")),t.columnContainer.querySelector(\".igv-track-drag-column\").appendChild(this.dragHandle),this.dragHandle.style.height=`${this.track.height}px`,this.addTrackDragMouseHandlers(t)}createTrackGearPopup(t){if(this.gearContainer=e(),t.columnContainer.querySelector(\".igv-gear-menu-column\").appendChild(this.gearContainer),this.gearContainer.style.height=`${this.track.height}px`,!0===this.track.ignoreTrackMenu);else{function i(e){if(e.preventDefault(),e.stopPropagation(),\"none\"===this.trackGearPopup.popover.style.display){for(const e of t.trackViews.filter((e=>e!==this&&void 0!==e.trackGearPopup)))e.trackGearPopup.popover.style.display=\"none\";this.trackGearPopup.presentMenuList(this,t.menuUtils.trackMenuItemList(this))}else this.trackGearPopup.popover.style.display=\"none\"}this.gear=e(),this.gearContainer.appendChild(this.gear),this.gear.appendChild(l(\"cog\")),this.trackGearPopup=new Xu(this.gear),this.boundTrackGearClickHandler=i.bind(this),this.gear.addEventListener(\"click\",this.boundTrackGearClickHandler)}}addTrackScrollMouseHandlers(e){this.boundTrackScrollMouseDownHandler=function(t){t.stopPropagation();const{y:i}=r(t);Bt(this.innerScroll).data(\"yDown\",i.toString()),this.boundColumnContainerMouseMoveHandler=function(e){e.stopPropagation();const{y:t}=r(e);this.moveScroller(t-parseInt(Bt(this.innerScroll).data(\"yDown\"))),Bt(this.innerScroll).data(\"yDown\",t.toString())}.bind(this),e.columnContainer.addEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler)}.bind(this),this.innerScroll.addEventListener(\"mousedown\",this.boundTrackScrollMouseDownHandler),this.boundColumnContainerMouseUpHandler=function(t){e.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler)}.bind(this),e.columnContainer.addEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),e.columnContainer.addEventListener(\"mouseleave\",this.boundColumnContainerMouseUpHandler)}removeTrackScrollMouseHandlers(){!1===cf.has(this.track.type)&&(this.innerScroll.removeEventListener(\"mousedown\",this.boundTrackScrollMouseDownHandler),this.browser.columnContainer.removeEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.browser.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.browser.columnContainer.removeEventListener(\"mouseleave\",this.boundColumnContainerMouseMoveHandler))}addTrackDragMouseHandlers(e){if(\"sequence\"===this.track.type||!1===mo.has(this.track.type)){let t;function i(i){i.preventDefault(),t=i.target,!1===this.track.selected&&(t.classList.remove(\"igv-track-drag-handle-color\"),t.classList.add(\"igv-track-drag-handle-hover-color\")),e.startTrackDrag(this)}function n(i){e.endTrackDrag(),t&&i.target!==t&&!1===this.track.selected&&(t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.add(\"igv-track-drag-handle-color\")),t=void 0}function r(i){i.preventDefault(),void 0===t&&!1===this.track.selected&&(i.target.classList.remove(\"igv-track-drag-handle-color\"),i.target.classList.add(\"igv-track-drag-handle-hover-color\")),e.updateTrackDrag(this)}function s(e){e.preventDefault(),void 0===t&&!1===this.track.selected&&(e.target.classList.remove(\"igv-track-drag-handle-hover-color\"),e.target.classList.add(\"igv-track-drag-handle-color\"))}this.boundTrackDragMouseDownHandler=i.bind(this),this.dragHandle.addEventListener(\"mousedown\",this.boundTrackDragMouseDownHandler),this.boundDocumentTrackDragMouseUpHandler=n.bind(this),document.addEventListener(\"mouseup\",this.boundDocumentTrackDragMouseUpHandler),this.boundTrackDragMouseEnterHandler=r.bind(this),this.dragHandle.addEventListener(\"mouseenter\",this.boundTrackDragMouseEnterHandler),this.dragHandle.addEventListener(\"mouseout\",(e=>{e.preventDefault(),void 0===t&&!1===this.track.selected&&(e.target.classList.remove(\"igv-track-drag-handle-hover-color\"),e.target.classList.add(\"igv-track-drag-handle-color\"))})),this.boundTrackDragMouseOutHandler=s.bind(this),this.dragHandle.addEventListener(\"mouseout\",this.boundTrackDragMouseOutHandler)}}removeTrackDragMouseHandlers(){\"ideogram\"===this.track.type||\"ruler\"===this.track.type||(this.dragHandle.removeEventListener(\"mousedown\",this.boundTrackDragMouseDownHandler),document.removeEventListener(\"mouseup\",this.boundDocumentTrackDragMouseUpHandler),this.dragHandle.removeEventListener(\"mouseup\",this.boundTrackDragMouseEnterHandler),this.dragHandle.removeEventListener(\"mouseout\",this.boundTrackDragMouseOutHandler))}removeTrackGearMouseHandlers(){!0===this.track.ignoreTrackMenu||this.gear.removeEventListener(\"click\",this.boundTrackGearClickHandler)}removeDOMFromColumnContainer(){this.axis.remove(),this.removeViewportsFromColumnContainer(),this.sampleInfoViewport.dispose(),this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove()}removeViewportsFromColumnContainer(){for(let e of this.viewports)e.$viewport.remove()}dispose(){this.axis.remove();for(let e of this.viewports)e.dispose();this.sampleInfoViewport.dispose(),this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove(),\"function\"==typeof this.track.dispose&&this.track.dispose();for(let e of Object.keys(this))this[e]=void 0;this.alert&&this.alert.container.remove(),this.disposed=!0}paintAxis(){if(\"function\"==typeof this.track.paintAxis){const{width:e,height:t}=this.axisCanvas.getBoundingClientRect(),i=window.devicePixelRatio||1;this.axisCanvas.height=i*t,this.axisCanvas.width=i*e;const n=this.axisCanvas.getContext(\"2d\");if(n.scale(i,i),this.track.autoscaleGroup){if(void 0===wo[this.track.autoscaleGroup]){const e=so.Dark2,t=Math.floor(Math.random()*so.Dark2.length);wo[this.track.autoscaleGroup]=e[t]}const i=_s.addAlpha(wo[this.track.autoscaleGroup],.75);this.track.paintAxis(n,e,t,i)}else this.track.paintAxis(n,e,t,void 0)}}maxViewportContentHeight(){return Math.max(...this.viewports.map((e=>e.getContentHeight())))}enableTrackSelection(e){const t=this.trackSelectionContainer;if(t&&!mo.has(this.track.type))if(!1!==e)t.style.display=\"grid\";else{this.track.selected=!1;t.querySelector(\"[name=track-select]\").checked=this.track.selected,this.dragHandle&&this.setDragHandleSelectionState(!1),t.style.display=\"none\"}}setDragHandleSelectionState(e){const t=this.dragHandle;e?(t.classList.remove(\"igv-track-drag-handle-color\"),t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.add(\"igv-track-drag-handle-selected-color\")):(t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.remove(\"igv-track-drag-handle-selected-color\"),t.classList.add(\"igv-track-drag-handle-color\"))}}function df(e){this.thresholds=e.thresholds,this.colors=e.colors}function uf(e){this.scale=e,this.lowColor=\"rgb(\"+e.lowR+\",\"+e.lowG+\",\"+e.lowB+\")\",this.highColor=\"rgb(\"+e.highR+\",\"+e.highG+\",\"+e.highB+\")\",this.diff=e.high-e.low}df.prototype.getColor=function(e){for(let t of this.thresholds)if(e<t)return this.colors[this.thresholds.indexOf(t)];return this.colors[this.colors.length-1]},uf.prototype.getColor=function(e){var t,i=this.scale;return e<=i.low?this.lowColor:e>=i.high?this.highColor:(t=(e-i.low)/this.diff,\"rgb(\"+Math.floor(i.lowR+t*(i.highR-i.lowR))+\",\"+Math.floor(i.lowG+t*(i.highG-i.lowG))+\",\"+Math.floor(i.lowB+t*(i.highB-i.lowB))+\")\")};class ff{constructor(e){this.color=e}getColor(){return this.color}}const pf={threshold:2e3,r:0,g:0,b:255};class gf{constructor(e){e=e||pf,this.threshold=e.threshold,this.r=e.r,this.g=e.g,this.b=e.b,this.cache=[],this.nbins=2e3,this.binsize=this.threshold/this.nbins}setThreshold(e){this.threshold=e,this.cache=[],this.binsize=this.threshold/this.nbins}getThreshold(){return this.threshold}setColorComponents(e){this.r=e.r,this.g=e.g,this.b=e.b,this.cache=[]}getColorComponents(){return{r:this.r,g:this.g,b:this.b}}equals(e){return JSON.stringify(this)===JSON.stringify(e)}getColor(e){const t=Math.floor(Math.min(this.threshold,e)/this.binsize);if(void 0===this.cache[t]){const i=(ys.clamp(e,0,this.threshold)-0)/(this.threshold-0);this.cache[t]=`rgba(${this.r},${this.g},${this.b}, ${i})`}return this.cache[t]}stringify(){return this.threshold+\",\"+this.r+\",\"+this.g+\",\"+this.b}static parse(e){var t,i;return e.startsWith(\"R:\")?(t=e.substring(2).split(\":\"),(i=new RatioColorScale(Number.parseFloat(t[0]))).positiveScale=n(t[1]),i.negativeScale=n(t[2]),i):n(e);function n(e){var t,i;return t={threshold:(i=e.split(\",\"))[0],r:i[1],g:i[2],b:i[3]},new gf(t)}}}class mf{constructor(e){this.config=e,this.url=e.path||e.url}async read(e,t){const i={start:e,size:t};return Qs.loadArrayBuffer(this.url,{range:i})}}class wf{constructor(e){this.file=e}async read(e,t){const i=this.file;return void 0!==e?i.slice(e,e+t).arrayBuffer():i.arrayBuffer()}}class bf{constructor(e,t){this.file=e,this.rateLimiter=t}async read(e,t){const i=this.file,n=this.rateLimiter;return new Promise((function(r,s){n.limiter((async function(i){try{const n=await i.read(e,t);r(n)}catch(e){s(e)}}))(i)}))}}class Ff{constructor(e){this.file=e.file,this.size=e.size||64e3,this.position=0,this.bufferStart=0,this.bufferLength=0,this.buffer=void 0}async read(e,t){const i=e,n=e+t,r=this.bufferStart,s=this.bufferStart+this.bufferLength;if(t>this.size)return this.buffer=void 0,this.bufferStart=0,this.bufferLength=0,this.file.read(e,t);if(i>=r&&n<=s){const e=i-r,n=e+t;return this.buffer.slice(e,n)}if(i<r&&n>r){const n=r-i,s=await this.file.read(e,n),o=t-n;if(o>0){const e=this.buffer.slice(0,o);return vf(s,e)}return s}if(!(i<s&&n>s))return this.buffer=await this.file.read(e,this.size),this.bufferStart=e,this.bufferLength=this.buffer.byteLength,this.buffer.slice(0,t);{const e=s-i,n=this.bufferLength-e,r=this.buffer.slice(n,this.bufferLength),o=t-e;if(!(o>0))return r;try{this.buffer=await this.file.read(s,this.size),this.bufferStart=s,this.bufferLength=this.buffer.byteLength;const e=this.buffer.slice(0,o);return vf(r,e)}catch(e){if(e.code&&416===e.code)return r;throw e}}}}var vf=function(e,t){var i=new Uint8Array(e.byteLength+t.byteLength);return i.set(new Uint8Array(e),0),i.set(new Uint8Array(t),e.byteLength),i.buffer};const yf=function(e,t){this.littleEndian=void 0===t||t,this.position=0,this.view=e,this.length=e.byteLength};function Af(e,t){this.block=e,this.offset=t}yf.prototype.available=function(){return this.length-this.position},yf.prototype.remLength=function(){return this.length-this.position},yf.prototype.hasNext=function(){return this.position<this.length-1},yf.prototype.getByte=function(){var e=this.view.getUint8(this.position,this.littleEndian);return this.position++,e},yf.prototype.getShort=function(){var e=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,e},yf.prototype.getUShort=function(){var e=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,e},yf.prototype.getInt=function(){var e=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getUInt=function(){var e=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getLong=function(){var e=[];e[0]=this.view.getUint8(this.position),e[1]=this.view.getUint8(this.position+1),e[2]=this.view.getUint8(this.position+2),e[3]=this.view.getUint8(this.position+3),e[4]=this.view.getUint8(this.position+4),e[5]=this.view.getUint8(this.position+5),e[6]=this.view.getUint8(this.position+6),e[7]=this.view.getUint8(this.position+7);var t=0;if(this.littleEndian)for(var i=e.length-1;i>=0;i--)t=256*t+e[i];else for(i=0;i<e.length;i++)t=256*t+e[i];return this.position+=8,t},yf.prototype.getString=function(e){for(var t,i=\"\";0!=(t=this.view.getUint8(this.position++))&&(i+=String.fromCharCode(t),!e||i.length!=e););return i},yf.prototype.getFixedLengthString=function(e){var t,i,n=\"\";for(t=0;t<e;t++)(i=this.view.getUint8(this.position++))>0&&(n+=String.fromCharCode(i));return n},yf.prototype.getFixedLengthTrimmedString=function(e){var t,i,n=\"\";for(t=0;t<e;t++)(i=this.view.getUint8(this.position++))>32&&(n+=String.fromCharCode(i));return n},yf.prototype.getFloat=function(){var e=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getDouble=function(){var e=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,e},yf.prototype.skip=function(e){return this.position+=e,this.position},yf.prototype.getVPointer=function(){var e=this.position,t=this.view.getUint8(e+1)<<8|this.view.getUint8(e),i=4294967296*(255&this.view.getUint8(e+6))+16777216*(255&this.view.getUint8(e+5))+65536*(255&this.view.getUint8(e+4))+256*(255&this.view.getUint8(e+3))+(255&this.view.getUint8(e+2));return this.position+=8,new Af(i,t)},Af.prototype.isLessThan=function(e){return this.block<e.block||this.block===e.block&&this.offset<e.offset},Af.prototype.isGreaterThan=function(e){return this.block>e.block||this.block===e.block&&this.offset>e.offset},Af.prototype.print=function(){return this.block+\":\"+this.offset};class Cf{constructor(e,t){this.chr1=e,this.chr2=t}getKey(){return this.chr1.name+\"_\"+this.chr2.name+\"_\"+this.zoom.unit+\"_\"+this.zoom.binSize}getBlockNumbers(e,t,i){if(e.chr==this.chr2&&t.chr===this.chr1){const i=e;e=t,t=i}const n=this.chr1===this.chr2,r=this.zoom.binSize,s=this.blockBinCount,o=this.blockColumnCount;return i<9||!n?function(){const i=e.start/r,a=e.end/r,c=t.start/r,l=t.end/r,h=Math.floor(i/s),d=Math.floor((a-1)/s),u=Math.floor(c/s),f=Math.floor((l-1)/s),p=[];for(let e=u;e<=f;e++)for(let t=h;t<=d;t++){let i;i=n&&e<t?t*o+e:e*o+t,p.includes(i)||p.push(i)}return p}():function(){const i=e.start/r,n=e.end/r,a=t.start/r,c=t.end/r,l=Math.floor((i+a)/2/s),h=Math.floor((n+c)/2/s),d=Math.floor(Math.log2(1+Math.abs(i-c)/Math.sqrt(2)/s)),u=Math.floor(Math.log2(1+Math.abs(n-a)/Math.sqrt(2)/s)),f=(n-a)*(i-c)<0?0:Math.min(d,u),p=Math.max(d,u),g=[];for(let e=f;e<=p;e++)for(let t=l;t<=h;t++){const i=e*o+t;g.push(i)}return g}()}static parseMatrixZoomData(e,t,i){const n=new Cf(e,t),r=i.getString(),s=i.getInt(),o=i.getFloat(),a=i.getFloat(),c=i.getFloat(),l=i.getFloat(),h=i.getInt();n.blockBinCount=i.getInt(),n.blockColumnCount=i.getInt();const d=i.getInt();n.zoom={index:s,unit:r,binSize:h},n.blockIndex=new _f(d,i);const u=o/(e.size/h)/(t.size/h);return n.averageCount=u,n.sumCounts=o,n.stdDev=c,n.occupiedCellCount=a,n.percent95=l,n}}class _f{constructor(e,t){for(this.blockIndex={};e-- >0;){const e=t.getInt(),i=t.getLong(),n=t.getInt();this.blockIndex[e]={filePosition:i,size:n}}}getBlockIndexEntry(e){return this.blockIndex[e]}}class xf{constructor(e,t,i){this.chr1=e,this.chr2=t,this.bpZoomData=[],this.fragZoomData=[];for(let e of i)\"BP\"===e.zoom.unit?this.bpZoomData.push(e):this.fragZoomData.push(e)}findZoomForResolution(e,t){const i=\"FRAG\"===t?this.fragZoomData:this.bpZoomData;for(let t=1;t<i.length;t++){if(i[t].zoom.binSize<e)return t-1}return i.length-1}getZoomData(e,t){const i=\"BP\"===(t=t||\"BP\")?this.bpZoomData:this.fragZoomData;for(let t=0;t<i.length;t++){var n=i[t];if(e===n.zoom.binSize)return n}}getZoomDataByIndex(e,t){return(\"FRAG\"===t?this.fragZoomData:this.bpZoomData)[e]}static getKey(e,t){if(e>t){const i=e;e=t,t=i}return`${e}_${t}`}static parseMatrix(e,t){const i=new yf(new DataView(e)),n=i.getInt(),r=i.getInt(),s=t[n],o=t[r];let a=i.getInt();const c=[];for(;a-- >0;){const e=Cf.parseMatrixZoomData(s,o,i);c.push(e)}return new xf(n,r,c)}}class kf{constructor(e,t,i){this.bin1=e,this.bin2=t,this.counts=i}getKey(){return this.bin1+\"_\"+this.bin2}}class If{constructor(e=10){this.max=e,this.map=new Map}get(e){let t=this.map.get(e);return t&&(this.map.delete(e),this.map.set(e,t)),t}set(e,t){this.map.has(e)?this.map.delete(e):this.map.size===this.max&&this.map.delete(this.first()),this.map.set(e,t)}has(e){return this.map.has(e)}clear(){this.map.clear()}first(){return this.map.keys().next().value}}class Sf{constructor(e,t,i,n){this.file=e,this.filePosition=t,this.nValues=i,this.dataType=n,this.cache=void 0}async getValues(e,t){if(!this.cache||e<this.cache.start||t>this.cache.end){const i=Math.max(0,e-1e3),n=Math.min(this.nValues,t+1e3),r=this.filePosition+i*this.dataType,s=n-i,o=s*this.dataType,a=await this.file.read(r,o);if(!a)return;const c=new yf(new DataView(a)),l=[];for(let e=0;e<s;e++)l[e]=8===this.dataType?c.getDouble():c.getFloat();this.cache={start:i,end:n,values:l}}const i=e-this.cache.start,n=i+(t-e);return this.cache.values.slice(i,n)}getKey(){return Sf.getKey(this.type,this.chrIdx,this.unit,this.resolution)}static getNormalizationVectorKey(e,t,i,n){return e+\"_\"+t+\"_\"+i+\"_\"+n}}var 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mf(e);(t=this.url).indexOf(\"drive.google.com\")>=0||t.indexOf(\"www.googleapis.com/drive\")>0?this.file=new bf(i,Bf):this.file=i}}var t}async init(){this.initialized||(await this.readHeaderAndFooter(),this.initialized=!0)}async getVersion(){if(void 0===this.version){const e=await this.file.read(0,128);if(!e)return;const t=new yf(new DataView(e));return this.magic=t.getString(),this.version=t.getInt(),this.version}return this.version}async getMetaData(){return await this.init(),this.meta}async readHeaderAndFooter(){let e=await this.file.read(0,16);if(!e||0===e.byteLength)throw Error(\"File content is empty\");let t=new yf(new DataView(e));if(this.magic=t.getString(),this.version=t.getInt(),this.version<5)throw Error(\"Unsupported hic version: \"+this.version);this.footerPosition=t.getLong(),await this.readFooter();const i=Object.values(this.masterIndex).reduce(((e,t)=>Math.min(e,t.start)),Number.MAX_VALUE)-16;e=await this.file.read(16,i),t=new yf(new DataView(e)),this.genomeId=t.getString(),this.version>=9&&(this.normVectorIndexPosition=t.getLong(),this.normVectorIndexSize=t.getLong()),this.attributes={};let n=t.getInt();for(;n-- >0;)this.attributes[t.getString()]=t.getString();this.chromosomes=[],this.chromosomeIndexMap={};let r=t.getInt(),s=0;for(;r-- >0;){const e={index:s,name:t.getString(),size:this.version<9?t.getInt():t.getLong()};\"all\"===e.name.toLowerCase()&&(this.wholeGenomeChromosome=e,this.wholeGenomeResolution=Math.round(2*e.size)),this.chromosomes.push(e),this.chromosomeIndexMap[e.name]=e.index,s++}this.bpResolutions=[];let o=t.getInt();for(;o-- >0;)this.bpResolutions.push(t.getInt());if(this.loadFragData){this.fragResolutions=[];let e=t.getInt();if(e>0)for(;e-- >0;)this.fragResolutions.push(t.getInt())}this.chrAliasTable={};for(let e of Object.keys(this.chromosomeIndexMap))e.startsWith(\"chr\")?this.chrAliasTable[e.substr(3)]=e:\"MT\"===e?this.chrAliasTable.chrM=e:this.chrAliasTable[\"chr\"+e]=e;this.meta={version:this.version,genome:this.genomeId,chromosomes:this.chromosomes,resolutions:this.bpResolutions}}async readFooter(){const e=this.version<9?8:12;let t=await this.file.read(this.footerPosition,e);if(!t)return null;let i=new yf(new DataView(t));const n=this.version<9?i.getInt():i.getLong();let r=i.getInt();const s=196*r;for(t=await this.file.read(this.footerPosition+e,Math.min(s,n)),i=new yf(new DataView(t)),this.masterIndex={};r-- >0;){const e=i.getString(),t=i.getLong(),n=i.getInt();this.masterIndex[e]={start:t,size:n}}if(this.expectedValueVectors={},this.version>5){const e=this.version<9?4:8;this.normExpectedValueVectorsPosition=this.footerPosition+e+n}return this}async printIndexStats(){let e,t=0,i=0;await await this.init();for(let n of Object.keys(this.masterIndex)){const r=this.masterIndex[n];t+=r.size,r.size>i&&(i=r.size,e=n)}console.log(`${i}  ${e}  ${this.config.url}`)}async getMatrix(e,t){const i=xf.getKey(e,t);if(this.matrixCache.has(i))return this.matrixCache.get(i);{const n=await this.readMatrix(e,t);return this.matrixCache.set(i,n),n}}async readMatrix(e,t){if(await this.init(),e>t){const i=e;e=t,t=i}const i=xf.getKey(e,t),n=this.masterIndex[i];if(!n)return;const r=await this.file.read(n.start,n.size);return r?xf.parseMatrix(r,this.chromosomes):void 0}async getContactRecords(e,t,i,n,r,s=!1){await this.init();const o=this.chromosomeIndexMap[this.getFileChrName(t.chr)],a=this.chromosomeIndexMap[this.getFileChrName(i.chr)];if(o>a||o===a&&t.start>=i.end){const e=t;t=i,i=e}const c=await this.getBlocks(t,i,n,r);if(!c||0===c.length)return[];const l=[],h=t.start/r,d=t.end/r,u=i.start/r,f=i.end/r,p=Math.floor(h),g=Math.ceil(d),m=Math.floor(u),w=Math.ceil(f);for(let o of c)if(o){let a,c,b=e&&\"NONE\"!==e;const F=this.getFileChrName(t.chr),v=this.getFileChrName(i.chr);if(b){const t=await this.getNormalizationVector(e,F,n,r),i=F===v?t:await this.getNormalizationVector(e,v,n,r);t&&i?(a=await t.getValues(p,g),c=await i.getValues(m,w)):b=!1}for(let e of o.records)if(s||e.bin1>=h&&e.bin1<d&&e.bin2>=u&&e.bin2<f)if(b){const t=e.bin1,i=e.bin2,n=a[t-p]*c[i-m];if(0!==n&&!isNaN(n)){const r=e.counts/n;l.push(new kf(t,i,r))}}else l.push(e);void 0===this.percentile95&&o.records.length>10&&(this.percentile95=Lf(o.records,95))}return l}async getBlocks(e,t,i,n){const r=(e,t)=>`${t.getKey()}_${e}`;await this.init();const s=this.getFileChrName(e.chr),o=this.getFileChrName(t.chr),a=this.chromosomeIndexMap[s],c=this.chromosomeIndexMap[o];if(void 0===a)return console.log(\"No chromosome named: \"+e.chr),[];if(void 0===c)return console.log(\"No chromosome named: \"+t.chr),[];const l=await this.getMatrix(a,c);if(!l)return console.log(\"No matrix for \"+e.chr+\"-\"+t.chr),[];const h=l.getZoomData(n,i);if(!h){let i=`No data avalailble for resolution: ${n}  for map ${e.chr}-${t.chr}`;throw new Error(i)}const d=h.getBlockNumbers(e,t,this.version),u=[],f=[];for(let e of d){const t=r(e,h);this.blockCache.has(n,t)?u.push(this.blockCache.get(n,t)):f.push(e)}const p=f.map((e=>this.readBlock(e,h))),g=await Promise.all(p);for(let e of g)e&&this.blockCache.set(n,r(e.blockNumber,h),e);return u.concat(g)}async readBlock(e,t){const i=await t.blockIndex.getBlockIndexEntry(e);if(i){let n=await this.file.read(i.filePosition,i.size);if(!n)return;n=new ls(new Uint8Array(n)).buffer;const r=new yf(new DataView(n)),s=r.getInt(),o=[];if(this.version<7)for(let e=0;e<s;e++){const e=r.getInt(),t=r.getInt(),i=r.getFloat();o.push(new kf(e,t,i))}else{const e=r.getInt(),t=r.getInt(),i=1===r.getByte(),n=!(this.version<9)&&1==r.getByte(),s=!(this.version<9)&&1==r.getByte(),a=r.getByte();if(1===a){const a=s?r.getInt():r.getShort();for(let c=0;c<a;c++){const a=t+(s?r.getInt():r.getShort()),c=n?r.getInt():r.getShort();for(let t=0;t<c;t++){const t=e+(n?r.getInt():r.getShort()),s=i?r.getFloat():r.getShort();o.push(new kf(t,a,s))}}}else{if(2!=a)throw new Error(\"Unknown block type: \"+a);{const n=r.getInt(),s=r.getShort();for(let a=0;a<n;a++){const n=Math.floor(a/s),c=e+(a-n*s),l=t+n;if(i){const e=r.getFloat();isNaN(e)||o.push(new kf(c,l,e))}else{const e=r.getShort();-32768!=e&&o.push(new kf(c,l,e))}}}}}return new Df(e,t,o,i)}}async hasNormalizationVector(e,t,i,n){let r;if(await this.init(),Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}const s=Rf(e,r,i.toString(),n),o=await this.getNormVectorIndex();return o&&o[s]}async isNormalizationValueAvailableAtResolution(e,t,i,n){let r;if(Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}return void 0!==(await this.getNormVectorIndex())[Rf(e,r,i.toString(),n)]}async getNormalizationVector(e,t,i,n){let r;if(await this.init(),Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}const s=Rf(e,r,i.toString(),n);if(this.normVectorCache.has(s))return this.normVectorCache.get(s);const o=await this.getNormVectorIndex();if(!o)return void console.log(\"Normalization vectors not present in this file\");if(!1===await this.isNormalizationValueAvailableAtResolution(e,t,i,n)){const t=`Normalization option ${e} not available at resolution ${n}. Will use NONE.`;return console.log(t),void(this.alert&&this.alert(t))}const a=o[s],c=await this.file.read(a.filePosition,8);if(!c)return;const l=new yf(new DataView(c)),h=this.version<9?l.getInt():l.getLong(),d=this.version<9?8:4,u=this.version<9?a.filePosition+4:a.filePosition+8,f=new Sf(this.file,u,h,d);return this.normVectorCache.set(s,f),f}async getNormVectorIndex(){if(!(this.version<6)){if(!this.normVectorIndex){if(!this.config.nvi&&this.remote&&this.url){const e=new URL(this.url),t=encodeURIComponent(e.hostname+e.pathname);Ef.hasOwnProperty(t)&&(this.config.nvi=Ef[t])}if(this.config.nvi){const e=decodeURIComponent(this.config.nvi).split(\",\"),t={start:parseInt(e[0]),size:parseInt(e[1])};return this.readNormVectorIndex(t)}try{return await this.readNormExpectedValuesAndNormVectorIndex(),this.normVectorIndex}catch(e){\"416\"===e.code||416===e.code?this.normExpectedValueVectorsPosition=void 0:console.error(e)}}return this.normVectorIndex}}async getNormalizationOptions(){return await this.getNormVectorIndex(),this.normalizationTypes}async readNormVectorIndex(e){await this.init(),this.normalizationVectorIndexRange=e;const t=await this.file.read(e.start,e.size),i=new yf(new DataView(t));this.normVectorIndex={};let n=i.getInt();for(;n-- >0;)this.parseNormVectorEntry(i);return this.normVectorIndex}async readNormExpectedValuesAndNormVectorIndex(){if(await this.init(),void 0===this.normExpectedValueVectorsPosition)return;const e=await this.skipExpectedValues(this.normExpectedValueVectorsPosition);let t=4,i=await this.file.read(e,4);if(0===i.byteLength)return;const n=new yf(new DataView(i)).getInt(),r={start:e+t,size:30*n};i=await this.file.read(r.start,r.size),this.normalizedExpectedValueVectors={},this.normVectorIndex={},await async function i(n,r){const s=new yf(new DataView(r));for(;n-- >0;){if(s.available()<100){n++,t+=s.position;const r=Math.max(1e3,30*n),o={start:e+t,size:r},a=await this.file.read(o.start,o.size);return i.call(this,n,a)}this.parseNormVectorEntry(s)}t+=s.position}.call(this,n,i),this.config.nvi=e.toString()+\",\"+t}async skipExpectedValues(e){const t=this.version,i=new Ff({file:this.file,size:256e3}),n={start:e,size:4},r=await i.read(n.start,n.size),s=new yf(new DataView(r)).getInt();return 0===s?e+4:async function e(n,r){let s={start:n,size:500},o=0,a=n,c=await i.read(s.start,s.size),l=new yf(new DataView(c));l.getString(),l.getString(),l.getInt();const h=t<9?l.getInt():l.getLong();o+=l.position+h*(t<9?8:4),s={start:n+o,size:4},c=await i.read(s.start,s.size),l=new yf(new DataView(c));const d=l.getInt();return o+=4+d*(4+(t<9?8:4)),r--,0===r?a+o:e(a+o,r)}(e+4,s)}getZoomIndexForBinSize(e,t){let i;if(\"BP\"===(t=t||\"BP\"))i=this.bpResolutions;else{if(\"FRAG\"!==t)throw new Error(\"Invalid unit: \"+t);i=this.fragResolutions}for(let t=0;t<i.length;t++)if(i[t]===e)return t;return-1}parseNormVectorEntry(e){const t=e.getString(),i=e.getInt(),n=e.getString(),r=e.getInt(),s=e.getLong(),o=this.version<9?e.getInt():e.getLong(),a=t+\"_\"+i+\"_\"+n+\"_\"+r;this.normalizationTypes.includes(t)||this.normalizationTypes.push(t),this.normVectorIndex[a]={filePosition:s,size:o}}getFileChrName(e){return this.chrAliasTable.hasOwnProperty(e)?this.chrAliasTable[e]:e}}function Rf(e,t,i,n){return e+\"_\"+t+\"_\"+i+\"_\"+n}class Df{constructor(e,t,i,n){this.blockNumber=e,this.zoomData=t,this.records=i,this.idx=n}}class Tf{constructor(){this.resolution=void 0,this.map=new If(6)}set(e,t,i){this.resolution!==e&&this.map.clear(),this.resolution=e,this.map.set(t,i)}get(e,t){return this.resolution===e?this.map.get(t):void 0}has(e,t){return this.resolution===e&&this.map.has(t)}}function Lf(e,t){const i=e.map((e=>e.counts));i.sort((function(e,t){return e-t}));return i[Math.floor(t/100*e.length)]}class zf{constructor(e,t){this.config=e,this.genome=t,this.hicFile=e._hicFile?e._hicFile:new Mf(e),e._hicFile=void 0}async getHeader(){return await this.hicFile.init(),this.hicFile}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){this.hicFile.initialized||await this.hicFile.init();const s=this.hicFile.bpResolutions,o=s[s.length-1];return(await this.hicFile.getContactRecords(void 0,{chr:e,start:t,end:i},{chr:\"celltype\",start:0,end:1e8},\"BP\",o)).map((t=>{const i=t.bin1*o;return{chr:e,start:i,end:i+o,value:t.counts,sample:t.bin2.toString()}}))}supportsWholeGenome(){return!1}}function Hf(e,t){const i=new Set(e.attributeNames),n=t[0];if(void 0===e.getAttributes(n))return!1;{const t=Object.keys(e.getAttributes(n));for(const e of t)if(!1===i.has(e))return!1}return!0}class Pf extends Hl{#y=new Map;constructor(e,t){super(e,t)}init(e){if(super.init(e),this.type=e.type||\"seg\",\"maf\"===this.type&&(this.type=\"mut\"),this.isLog=e.isLog,this.displayMode=e.displayMode||\"EXPANDED\",this.height=e.height||300,this.maxHeight=e.maxHeight||500,this.squishedRowHeight=e.sampleSquishHeight||e.squishedRowHeight||2,this.expandedRowHeight=e.sampleExpandHeight||e.expandedRowHeight||13,this.sampleHeight=this.squishedRowHeight,this.sampleKeys=[],e.samples){for(let t of e.samples)this.sampleKeys.push(t);this.explicitSamples=!0}if(e.color)this.color=e.color;else if(e.colorTable)this.colorTable=new ao(e.colorTable);else switch(this.type){case\"mut\":this.colorTable=new ao(qf);break;case\"shoebox\":e.colorScale&&(this.sbColorScale=gf.parse(e.colorScale));break;default:this.posColorScale=new uf(e.posColorScale||Of),this.negColorScale=new uf(e.negColorScale||Uf)}const t=Object.assign({},this.config);t.maxWGCount=t.maxWGCount||Number.MAX_SAFE_INTEGER,\"shoebox\"===this.type?(this.featureSource=new zf(t,this.browser.genome),this.height=e.height||500,this.maxHeight=e.maxHeight||800,this.isLog=!1,this.squishedRowHeight=e.squishedRowHeight||1,this.displayMode=e.displayMode||\"SQUISHED\",this.visibilityWindow=void 0===e.visibilityWindow?1e6:e.visibilityWindow):this.featureSource=Ad(t,this.browser.genome),this.initialSort=e.sort}async postInit(){\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader(),this.disposed)||this.header&&this.setTrackProperties(this.header)}menuItemList(){const e=[];if(!0===Hf(this.browser.sampleInfo,this.sampleKeys)){e.push(\"<hr/>\"),e.push(\"Sort by attribute:\");for(const n of this.browser.sampleInfo.attributeNames){if(this.sampleKeys.some((e=>{const t=this.browser.sampleInfo.getAttributes(e);return t&&t[n]}))){const r=Bt(\"<div>\");function s(){const e=this.#y.get(n)||1;this.sortByAttribute(n,e),this.#y.set(n,-1*e),this.config.sort={option:\"ATTRIBUTE\",attribute:n,direction:1===e?\"ASC\":\"DESC\"}}r.html(`&nbsp;&nbsp;${n.split(Uu.emptySpaceReplacement).join(\" \")}`),e.push({object:r,click:s})}}}const t={SQUISHED:\"Squish\",EXPANDED:\"Expand\",FILL:\"Fill\"};if(\"shoebox\"===this.type&&this.sbColorScale){function o(e){this.browser.inputDialog.present({label:\"Color Scale Threshold\",value:this.sbColorScale.threshold,callback:()=>{const e=Number(this.browser.inputDialog.value,10);e&&(this.sbColorScale.setThreshold(e),this.trackView.repaintViews())}},e)}e.push(\"<hr/>\"),e.push({object:Bt(\"<div>Set color scale threshold</div>\"),dialog:o})}e.push(\"<hr/>\"),e.push(\"DisplayMode:\");const i=\"seg\"===this.type||\"shoebox\"===this.type?[\"SQUISHED\",\"EXPANDED\",\"FILL\"]:[\"SQUISHED\",\"EXPANDED\"];for(let a of i){const c=Dl(t[a],a===this.displayMode);e.push({object:Bt(c),click:function(){this.displayMode=a,this.config.displayMode=a,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)}})}return e}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys,height:this.sampleHeight,yOffset:0}}async getFeatures(e,t,i){const n=await this.featureSource.getFeatures({chr:e,start:t,end:i});if(this.updateSampleKeys(n),this.initialSort){const e=this.initialSort;if(void 0===e.option||\"VALUE\"===e.option.toUpperCase())this.sortByValue(e,n);else if(\"ATTRIBUTE\"===e.option.toUpperCase()&&e.attribute){const t=\"DESC\"===e.direction?1:-1;this.sortByAttribute(e.attribute,t)}this.initialSort=void 0}return n}draw({context:e,pixelTop:t,pixelWidth:i,pixelHeight:n,features:r,bpPerPixel:s,bpStart:o}){if(xo.fillRect(e,0,t,i,n,{fillStyle:\"rgb(255, 255, 255)\"}),r&&r.length>0){if(this.checkForLog(r),\"shoebox\"===this.type&&!this.sbColorScale){const e=this.featureSource.hicFile.percentile95||2e3;this.sbColorScale=new gf({threshold:e,r:0,g:0,b:255})}const a={};let c;switch(this.sampleKeys.forEach((function(e,t){a[e]=t})),this.displayMode){case\"FILL\":this.sampleHeight=n/this.sampleKeys.length,c=0;break;case\"SQUISHED\":this.sampleHeight=this.squishedRowHeight,c=0;break;default:this.sampleHeight=this.expandedRowHeight,c=1}const l=this.sampleHeight;for(let e of r)e.pixelRect=void 0;const h=t+n,d=o+i*s+1,u=s;this.sampleYStart=void 0;for(let i of r){if(i.end<o||i.start>d)continue;const n=i.sampleKey||i.sample;i.row=a[n];const r=i.row*l+c;void 0===this.sampleYStart&&(this.sampleYStart=r);if(r+l<t||r>h)continue;const s=Math.max(i.start,o);let f=Math.round((s-o)/u);const p=Math.min(i.end,d),g=Math.round((p-o)/u);let m,w,b=Math.max(1,g-f);if(this.color?m=\"function\"==typeof this.color?this.color(i):this.color:this.colorTable&&(m=this.colorTable.getColor(i.value.toLowerCase())),\"mut\"===this.type)w=l-2*c,b<3&&(b=3,f-=1);else if(\"shoebox\"===this.type){m=this.sbColorScale.getColor(i.value);let e=l;if(l<.25){const t=.1+2*Math.abs(t.value);e=Math.min(1,t*l)}w=e-2*c}else{let e=i.value;this.isLog||(e=ys.log2(e/2)),m=e<-.1?this.negColorScale.getColor(e):e>.1?this.posColorScale.getColor(e):\"white\";let t=l;if(l<.25){const i=.1+2*Math.abs(e);t=Math.min(1,i*l)}w=t-2*c}i.pixelRect={x:f,y:r,w:b,h:w},e.fillStyle=m,e.fillRect(f,r,b,w)}}}checkForLog(e){if(void 0===this.isLog){this.isLog=!1;for(let t of e)if(t.value<0)return void(this.isLog=!0)}}computePixelHeight(e){if(!e)return 0;const t=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight;return this.updateSampleKeys(e),this.sampleKeys.length*t}async sortByValue(e,t){const i=e.chr;let n,r;if(e.position?(n=e.position-1,r=n+1):(n=e.start,r=e.end),t||(t=await this.featureSource.getFeatures({chr:i,start:n,end:r})),!t)return;this.updateSampleKeys(t);const s={},o=\"ASC\"===e.direction?1:-1,a=()=>{const e=r-n+1;for(let i of t){if(i.end<n)continue;if(i.start>r)break;const t=Math.max(n,i.start),o=(Math.min(r,i.end)-t)/e,a=i.sampleKey||i.sample,c=s[a]||0;s[a]=c+o*i.value}this.sampleKeys.sort((function(e,t){let i=s[e],n=s[t];return i||(i=o*Number.MAX_VALUE),n||(n=o*Number.MAX_VALUE),i===n?0:i>n?o:-1*o}))},c=()=>{for(let e of t){if(e.end<n)continue;if(e.start>r)break;const t=e.sampleKey||e.sample;(!s.hasOwnProperty(t)||e.value.localeCompare(s[t])>0)&&(s[t]=e.value)}this.sampleKeys.sort((function(e,t){let i=s[e]||\"\",n=s[t]||\"\";return o*i.localeCompare(n)}))};\"mut\"===this.type?c():a(),this.trackView.repaintViews()}sortByAttribute(e,t){this.sampleKeys=this.browser.sampleInfo.getSortedSampleKeysByAttribute(this.sampleKeys,e,t),this.trackView.repaintViews()}clickedFeatures(e){const t=super.clickedFeatures(e),i=e.y;return t.filter((function(e){const t=e.pixelRect;return t&&i>=t.y&&i<=t.y+t.h}))}hoverText(e){const t=this.clickedFeatures(e);if(t&&t.length>0)return`${t[0].sample}: ${t[0].value}`}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){i.length>0&&(i.push(\"<hr/>\"),i.push(\"<hr/>\"));const t=e._f||e,n=\"function\"==typeof t.popupData?t.popupData(this.type,this.browser.genome.id):this.extractPopupData(t);Array.prototype.push.apply(i,n)}return i}contextMenuItemList(e){const t=e.genomicLocation,i=t=>{const i=e.viewport.cachedFeatures;this.sortByValue(t,i)},n=e.referenceFrame.toBP(2.5);return[\"DESC\",\"ASC\"].map((r=>{const s=\"DESC\"===r?\"descending\":\"ascending\";return{label:\"seg\"===this.type||\"shoebox\"===this.type?`Sort by value (${s})`:`Sort by type (${s})`,click:()=>{const s={option:\"VALUE\",direction:r,chr:e.referenceFrame.chr,start:Math.floor(t-n),end:Math.floor(t+n)};i(s),this.config.sort=s}}}))}get supportsWholeGenome(){return(!1===this.config.indexed||!this.config.indexURL)&&!1!==this.config.supportsWholeGenome}updateSampleKeys(e){if(this.explicitSamples)return;const t=new Set(this.sampleKeys);for(let i of e){const e=i.sampleKey||i.sample;t.has(e)||(this.sampleKeys.push(e),t.add(e))}}}const Of={low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0},Uf={low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255},qf={indel:\"rgb(0,200,0)\",\"targeted region\":\"rgb(236,155,43)\",truncating:\"rgb(\\t150,0,0)\",\"non-coding transcript\":\"rgb(0,0,150)\",synonymous:\"rgb(109,165,95)\",silent:\"rgb(109,135,80)\",missense_mutation:\"rgb(72,130,187)\",missense:\"rgb(72,130,187)\",\"splice site\":\"rgb(143,83,155)\",splice_region:\"rgb(143,83,155)\",nonsense:\"rgb(216, 57,81)\",nonsense_mutation:\"rgb(216, 57,81)\",frame_shift_del:\"rgb(226,135,65)\",frame_shift_ins:\"rgb(226,135,65)\",in_frame_del:\"rgb(247,235,94)\",in_frame_ins:\"rgb(247,235,94)\",\"*other*\":\"rgb(159,91,50)\"};class Qf{constructor(e){this.paired=!0,this.firstAlignment=e,this.chr=e.chr,this.readName=e.readName,e.start<e.mate.position?(this.start=e.start,this.scStart=e.scStart,this.connectingStart=e.start+e.lengthOnRef,this.connectingEnd=e.mate.position):(this.start=e.mate.position,this.scStart=this.start,this.connectingStart=e.mate.position,this.connectingEnd=e.start),this.end=Math.max(e.mate.position,e.start+e.lengthOnRef),this.lengthOnRef=this.end-this.start;let t=Math.max(this.end,e.scStart+e.scLengthOnRef);this.scLengthOnRef=t-this.scStart}setSecondAlignment(e){this.secondAlignment=e;const t=this.firstAlignment;e.start>t.start?this.connectingEnd=e.start:this.connectingStart=e.start+e.lengthOnRef,this.start=Math.min(t.start,e.start),this.end=Math.max(t.start+t.lengthOnRef,e.start+e.lengthOnRef),this.lengthOnRef=this.end-this.start,this.scStart=Math.min(t.scStart,e.scStart);const i=Math.max(t.scStart+t.scLengthOnRef,e.scStart+e.scLengthOnRef);this.scLengthOnRef=i-this.scStart}containsLocation(e,t){const i=t?this.scStart:this.start,n=t?this.scLengthOnRef:this.lengthOnRef;return e>=i&&e<=i+n}alignmentContaining(e,t){return this.firstAlignment.containsLocation(e,t)?this.firstAlignment:this.secondAlignment&&this.secondAlignment.containsLocation(e,t)?this.secondAlignment:void 0}popupData(e){let t=this.firstAlignment.popupData(e);return this.secondAlignment&&(t.push(\"-------------------------------\"),t=t.concat(this.secondAlignment.popupData(e))),t}isPaired(){return!0}isMateMapped(){return!0}isProperPair(){return this.firstAlignment.isProperPair()}get fragmentLength(){return Math.abs(this.firstAlignment.fragmentLength)}get firstOfPairStrand(){return this.firstAlignment.firstOfPairStrand}get pairOrientation(){return this.firstAlignment.pairOrientation}hasTag(e){return this.firstAlignment.hasTag(e)||this.secondAlignment&&this.secondAlignment.hasTag(e)}getGroupValue({option:e,tag:t}){switch(e){case\"strand\":return this.isNegativeStrand()?\"-\":\"+\";case\"FIRST_IN_PAIR_STRAND\":return this.isPaired()?this.isFirstOfPair()?this.isNegativeStrand()?\"-\":\"+\":this.isSecondOfPair()?this.isNegativeStrand()?\"+\":\"-\":void 0:void 0;case\"START\":return this.start;case\"INSERT_SIZE\":return this.fragmentLength;case\"MATE_CHR\":return this.mate?this.mate.chr:void 0;case\"MQ\":return this.mq;case\"ALIGNED_READ_LENGTH\":return this.lengthOnRef;case\"TAG\":return this.tags()[t];case\"PHASE\":return this.tags().HP;case\"READ_ORDER\":return this.isPaired()&&this.isFirstOfPair()?\"FIRST\":this.isPaired()&&this.isSecondOfPair()?\"SECOND\":\"\";default:return}}}class Vf{static instances=new Map;static getKey(e,t,i){const n=\"\"+e+t+i;return Vf.instances.has(n)||Vf.instances.set(n,new Vf(e,t,i)),Vf.instances.get(n)}constructor(e,t,i){this.base=e,this.strand=t,this.modification=i,this.canonicalBase=\"+\"===this.strand?this.base:oc(this.base)}getCanonicalBase(){}toString(){return\"\"+this.base+this.strand+this.modification}static compare(e,t){const i=e.modification,n=t.modification;return i===n?e.strand.charAt(0)-t.strand.charAt(0):jf.has(i)&jf.has(n)?jf.get(i)-jf.get(n):jf.has(i)?1:jf.has(n)?-1:i>n?1:-1}}const jf=new Map([\"NONE_C\",\"NONE_T\",\"NONE_G\",\"NONE_A\",\"m\",\"h\",\"f\",\"c\",\"C\",\"g\",\"e\",\"b\",\"T\",\"U\",\"a\",\"A\",\"o\",\"G\",\"n\",\"N\"].map(((e,t)=>[e,t])));class Wf{constructor(e,t,i,n){this.base=e,this.modification=i,this.strand=t,this.likelihoods=n,this.canonicalBase=\"+\"==this.strand?this.base:oc(this.base),this.key=Vf.getKey(e,t,i)}containsPosition(e){return this.likelihoods.has(e)}is5mC(){return this.modification.equals(\"m\")&&(\"C\"===this.base&&\"+\"===this.strand||\"G\"===this.base&&\"-\"===this.strand)}fullName(){return Gf.get(this.modification)||this.modification}}const Gf=new Map;Gf.set(\"m\",\"5mC\"),Gf.set(\"h\",\"5hmC\"),Gf.set(\"f\",\"5fC\"),Gf.set(\"c\",\"5caC\"),Gf.set(\"g\",\"5hmU\"),Gf.set(\"e\",\"5fU\"),Gf.set(\"b\",\"5caU\"),Gf.set(\"a\",\"6mA\"),Gf.set(\"o\",\"8xoG\"),Gf.set(\"n\",\"Xao\"),Gf.set(\"C\",\"Unknown C\"),Gf.set(\"T\",\"Unknown T\"),Gf.set(\"A\",\"Unknown A\"),Gf.set(\"G\",\"Unknown G\"),Gf.set(\"N\",\"Unknown\");const $f=new Map([[\"m\",\"5mC\"],[\"h\",\"5hmC\"],[\"f\",\"5fC\"],[\"c\",\"5caC\"],[\"g\",\"5hmU\"],[\"e\",\"5fU\"],[\"b\",\"5caU\"],[\"a\",\"6mA\"],[\"o\",\"8xoG\"],[\"n\",\"Xao\"],[\"C\",\"Unknown C\"],[\"T\",\"Unknown T\"],[\"A\",\"Unknown A\"],[\"G\",\"Unknown G\"],[\"N\",\"Unknown\"]]);function Kf(e){return $f.has(e)?$f.get(e):\"Uknown\"}function Yf(e){if(!e)return!1;const t=e.length;if(0==t)return!1;for(let i=0;i<t;i++){const t=e.charAt(i);if(t<\"0\"||t>\"9\")return!1}return!0}function Xf(e){return e<0?e+256:e}class Zf{allModifications=new Set;simplexModifications=new Set;maxLikelihoods=new Map;nomodLikelihoods=new Map;lastThreshold;incrementCounts(e){if(!e.blocks)return;const t=e.getBaseModificationSets();if(t)for(let i of e.blocks)if(\"S\"!==i.type)for(let e=0;e<i.len;e++){let n,r=e+i.seqOffset,s=0,o=-1,a=255;for(let e of t){const t=Vf.getKey(e.base,e.strand,e.modification);this.allModifications.add(t);const i=e.likelihoods;if(e.containsPosition(r)){const c=Xf(i.get(r));a-=c,c>o&&(s=e.canonicalBase,o=c,n=t)}}if(0!=s){const t=i.start+e,r=Vf.getKey(s,\"+\",\"NONE_\"+s);this.allModifications.add(r);const c=(e,t,i,n)=>{let r=n.get(i);r||(r=new Map,n.set(i,r));let s=r.get(e);s||(s=[],r.set(e,s)),s.push(t)};c(t,o,n,this.maxLikelihoods),a>o?c(t,a,r,this.nomodLikelihoods):c(t,o,n,this.nomodLikelihoods)}}}getCount(e,t,i,n){this.lastThreshold=i;const r=255*i,s=n?this.nomodLikelihoods.get(t):this.maxLikelihoods.get(t);if(!s)return 0;const o=s.get(e);if(o){let e=0;for(let t of o){Xf(t)>=r&&e++}return e}return 0}getLikelihoodSum(e,t,i,n){this.lastThreshold=i;const r=255*i,s=(n?this.nomodLikelihoods.get(t):this.maxLikelihoods.get(t)).get(e);if(s){let e=0;for(let t of s){const i=Xf(t);i>=r&&(e+=i)}return e}return 0}popupData(e,t){const i=[];i.push(\"<b>Modifications with likelihood > \"+100*this.lastThreshold+\"%</b>\");for(let n of this.maxLikelihoods.keys()){if(this.maxLikelihoods.get(n).has(e)){let r=\"basemod2\"===t;const s=this.getCount(e,n,this.lastThreshold,r);if(s>0){const t=this.getLikelihoodSum(e,n,this.lastThreshold,r)/s*.3921568,o=Kf(n.modification);i.push(o+\" (\"+n.base+n.strand+\"): \"+s+\"  @ average likelihood \"+Math.round(t)+\"%\")}}}return i}computeSimplex(){const e=new Set(Array.from(this.allModifications).filter((e=>\"-\"===e.strand)).map((e=>e.modification)));for(let t of this.allModifications)\"+\"!==t.strand||e.has(t.modification)||(this.simplexModifications.add(t.modification),this.simplexModifications.add(\"NONE_\"+t.getCanonicalBase()))}}class Jf{constructor(){this.alignments=[],this.score=void 0}findAlignment(e,t=!1){const i=(e,i)=>i>=e.start&&i<e.start+(t?e.fragmentLength:e.lengthOnRef);let n;for(let r=0;r<this.alignments.length;r++){const s=this.alignments[r];if(e>=s.start&&e<s.start+(t?s.fragmentLength:s.lengthOnRef)){s.paired?s.firstAlignment&&i(s.firstAlignment,e)?n=s.firstAlignment:s.secondAlignment&&i(s.secondAlignment,e)&&(n=s.secondAlignment):n=s;break}}return n}getSortValue({position:e,option:t,tag:i,sortAsPairs:n},r){t||(t=\"BASE\");const s=this.findAlignment(e,n);if(void 0===s)return Number.MAX_VALUE;switch(t){case\"NUCLEOTIDE\":case\"BASE\":return function(e,t,i){let n;const r=Math.floor(i)-t.start;r<t.sequence.length&&(n=t.sequence.charAt(r));if(!n)return 0;const s=e.readBaseAt(i),o=e.readBaseQualityAt(i),a=t.coverageMap,c=Math.floor(i-a.bpStart),l=a.coverage[c];let h=0;if(e.insertions)for(let t of e.insertions)t.start===i&&(h=-l.ins);if(s)if(n=n.toUpperCase(),\"N\"===s&&0===h)h=2;else if(n!==s&&\"=\"!==s||0!==h){if(\"X\"===s||n!==s){h-=l[\"pos\"+s]+l[\"neg\"+s]+o/1e3}}else h=4-o/1e3;else{const e=l.del;e>0?h-=e:0===h&&(h=1)}return h}(s,r,e);case\"strand\":return s.strand?1:-1;case\"START\":return s.start;case\"TAG\":return s.tags()[i];case\"READ_NAME\":return s.readName;case\"INSERT_SIZE\":return-Math.abs(s.fragmentLength);case\"GAP_SIZE\":return-s.gapSizeAt(e);case\"MATE_CHR\":return s.mate?s.mate.chr:Number.MAX_VALUE;case\"MQ\":return void 0===s.mq?Number.MAX_VALUE:-s.mq;case\"ALIGNED_READ_LENGTH\":return-s.lengthOnRef;default:return Number.MAX_VALUE}}}var ep={fr:{F1R2:\"LR\",F2R1:\"LR\",F1F2:\"LL\",F2F1:\"LL\",R1R2:\"RR\",R2R1:\"RR\",R1F2:\"RL\",R2F1:\"RL\"},rf:{R1F2:\"LR\",R2F1:\"LR\",R1R2:\"LL\",R2R1:\"LL\",F1F2:\"RR\",F2F1:\"RR\",F1R2:\"RL\",F2R1:\"RL\"},ff:{F2F1:\"LR\",R1R2:\"LR\",F2R1:\"LL\",R1F2:\"LL\",R2F1:\"RR\",F1R2:\"RR\",R2R1:\"RL\",F1F2:\"RL\"}};class tp{#A=[];baseModificationKeys=new Set;constructor(e,t,i,{samplingWindowSize:n,samplingDepth:r,alleleFreqThreshold:s,colorBy:o}){this.alleleFreqThreshold=void 0===s?.2:s,this.samplingWindowSize=n||100,this.samplingDepth=r||1e3,this.chr=e,this.start=Math.floor(t),this.end=Math.ceil(i),this.length=i-t,this.coverageMap=new np(e,t,i,this.alleleFreqThreshold),this.downsampledIntervals=[],o&&o.startsWith(\"basemod\")&&(this.baseModCounts=new Zf),this.alignments=[],this.pairsCache=new Map,this.downsampledReads=new Set,this.currentBucket=new ip(this.start,this.start+this.samplingWindowSize,this),this.hasPairs=!1}pack({viewAsPairs:e,showSoftClips:t,expectedPairOrientation:i,groupBy:n,displayMode:r}){let s=this.allAlignments();s=e?function(e){const t=new Map,i=e.map((e=>{if(ap(e)){let i=t.get(e.readName);return i?(i.setSecondAlignment(e),t.delete(e.readName),i):(i=new Qf(e),t.set(e.readName,i),i)}return e}));return i}(s):function(e){return e.flatMap((e=>e instanceof Qf?[e.firstAlignment,e.secondAlignment].filter(Boolean):[e]))}(s),this.packAlignmentRows(s,t,i,n,r),this.alignments&&delete this.alignments}packAlignmentRows(e,t,i,n,r){this.#A=[];const s=(e,i)=>{e.sort((function(e,i){return t?e.scStart-i.scStart:e.start-i.start}));const n=new op(i);let r,s=0,o=0;const a=new Set,c=()=>{r=new Jf,n.push(r),s=0,o=0,a.clear()};for(c();e.length>0;)if(o>=0&&o<e.length){const i=e[o];a.add(i),r.alignments.push(i),s=t?i.scStart+i.scLengthOnRef+2:i.start+i.lengthOnRef+2,o=cp(e,(e=>(t?e.scStart:e.start)>s),o)}else e=e.filter((e=>!a.has(e))),c();return n},o=(e,t)=>{e.sort((function(e,t){return e.start-t.start}));const i=new op(t),{start:n,end:r}=this.viewport.genomicRange();for(let t of e)if(t.end<n||t.start>r)this.#A.push(t);else{const e=new Jf;e.alignments.push(t),i.push(e)}return i};if(!e||0===e.length)return new Map;{const t=new Map;if(n)for(let r of e){const e=lp(r,n,i)||\"\";t.has(e)||t.set(e,[]),t.get(e).push(r)}else t.set(\"\",e);const a=new Map,c=Array.from(t.keys()).sort(function(e,t){switch(e){case\"pairOrientation\":return function(e){const t=[\"LL\",\"RR\",\"RL\",\"LR\",\"\"];return(e,i)=>t.indexOf(e)-t.indexOf(i)}();case\"strand\":case\"firstOfPairStrand\":return up;default:return e&&e.startsWith(\"base:\")?dp:fp}}(n));for(let e of c){const i=t.get(e),n=\"FULL\"===r?o(i,e):s(i,e);a.set(e,n)}this.packedGroups=a}}push(e){this.hasPairs=this.hasPairs||e.isPaired(),this.coverageMap.incCounts(e);const t=e.getBaseModificationSets();if(t)for(let e of t)this.baseModificationKeys.add(e.key);this.baseModCounts&&this.baseModCounts.incrementCounts(e),this.downsampledReads.has(e.readName)?this.currentBucket.downsampledCount++:(e.start>=this.currentBucket.end&&(this.finishBucket(),this.currentBucket=new ip(e.start,e.start+this.samplingWindowSize,this)),this.currentBucket.addAlignment(e))}finish(){void 0!==this.currentBucket&&this.finishBucket(),this.hasAlignments=this.alignments.length>0,this.alignments.sort((function(e,t){return e.start-t.start})),this.baseModCounts&&this.baseModCounts.computeSimplex(),delete this.currentBucket,delete this.pairsCache,delete this.downsampledReads}contains(e,t,i){return this.chr===e&&this.start<=t&&this.end>=i}hasDownsampledIntervals(){return this.downsampledIntervals&&this.downsampledIntervals.length>0}finishBucket(){this.alignments=this.alignments.concat(this.currentBucket.alignments),this.currentBucket.downsampledCount>0&&this.downsampledIntervals.push(new sp(this.currentBucket.start,this.currentBucket.end,this.currentBucket.downsampledCount))}allAlignments(){if(this.alignments)return this.alignments;if(this.packedGroups){const e=Array.from(this.packedGroups.values()).flatMap((e=>e.rows.flatMap((e=>e.alignments))));if(this.#A&&this.#A.length>0)for(let t of this.#A)e.push(t);return e}return[]}getMax(e,t){return this.coverageMap.getMax(e,t)}sortRows(e){if(this.packedGroups)for(let t of this.packedGroups.values())t.sortRows(e,this)}}class ip{constructor(e,t,{samplingDepth:i,downsampledReads:n,pairsCache:r}){this.start=e,this.end=t,this.alignments=[],this.downsampledCount=0,this.samplingDepth=i,this.downsampledReads=n,this.pairsCache=r,this.hasPairs=!1}addAlignment(e){this.hasPairs=this.hasPairs||e.isPaired();const t=this.hasPairs?Math.ceil(this.samplingDepth/2):this.samplingDepth;if(ap(e)){const t=this.pairsCache.get(e.readName);if(t)return t.setSecondAlignment(e),void this.pairsCache.delete(e.readName)}if(this.alignments.length<t)if(ap(e)){const t=new Qf(e);this.pairsCache.set(e.readName,t),this.alignments.push(t)}else this.alignments.push(e);else{const i=Math.floor(Math.random()*(t+this.downsampledCount-1));if(i<t){const t=this.alignments[i];if(this.pairsCache.has(t.readName)&&this.pairsCache.delete(t.readName),ap(e)){const t=new Qf(e);this.pairsCache.set(e.readName,t),this.alignments[i]=t}else this.alignments[i]=e;this.downsampledReads.add(t.readName)}else this.downsampledReads.add(e.readName);this.downsampledCount++}}}class np{constructor(e,t,i,n){this.chr=e,this.bpStart=t,this.length=i-t,this.coverage=new Array(this.length),this.maximum=0,this.threshold=n,this.qualityWeight=!0}getMax(e,t){let i=0;const n=this.coverage.length;for(let r=0;r<n;r++){const n=this.bpStart+r;if(n>t)break;const s=this.coverage[r];n>=e&&s&&(i=Math.max(i,s.total))}return i}incCounts(e){var t=this;if(void 0===e.blocks?i(e):e.blocks.forEach((function(e){i(e)})),e.gaps)for(let i of e.gaps)if(\"D\"===i.type){const e=i.start-t.bpStart;for(let n=e;n<e+i.len;n++)n<0||(this.coverage[n]||(this.coverage[n]=new rp(t.threshold)),this.coverage[n].del++)}if(e.insertions)for(let i of e.insertions){const e=i.start-this.bpStart;e<0||(this.coverage[e]||(this.coverage[e]=new rp(t.threshold)),this.coverage[e].ins++)}function i(i){if(\"S\"===i.type)return;const n=e.seq,r=e.qual,s=i.seqOffset;for(let o=i.start-t.bpStart,a=0;a<i.len;o++,a++){t.coverage[o]||(t.coverage[o]=new rp(t.threshold));const i=null==n?\"N\":n.charAt(s+a),c=e.strand?\"pos\"+i:\"neg\"+i,l=r&&s+a<r.length?r[s+a]:30;t.coverage[o][c]+=1,t.coverage[o][\"qual\"+i]+=l,t.coverage[o].total+=1,t.coverage[o].qual+=l,t.maximum=Math.max(t.coverage[o].total,t.maximum)}}}getPosCount(e,t){const i=e-this.bpStart;if(i<0||i>=this.coverage.length)return 0;const n=this.coverage[i];switch(t){case\"A\":case\"a\":return n.posA;case\"C\":case\"c\":return n.posC;case\"T\":case\"t\":return n.posT;case\"G\":case\"g\":return n.posG;case\"N\":case\"n\":return n.posN;default:return 0}}getNegCount(e,t){const i=e-this.bpStart;if(i<0||i>=this.coverage.length)return 0;const n=this.coverage[i];switch(t){case\"A\":case\"a\":return n.negA;case\"C\":case\"c\":return n.negC;case\"T\":case\"t\":return n.negT;case\"G\":case\"g\":return n.negG;case\"N\":case\"n\":return n.negN;default:return 0}}getCount(e,t){return this.getPosCount(e,t)+this.getNegCount(e,t)}getTotalCount(e){const t=e-this.bpStart;return t>=0&&t<this.coverage.length?this.coverage[t].total:0}}class rp{constructor(e){this.qualityWeight=!0,this.posA=0,this.negA=0,this.posT=0,this.negT=0,this.posC=0,this.negC=0,this.posG=0,this.negG=0,this.posN=0,this.negN=0,this.pos=0,this.neg=0,this.qualA=0,this.qualT=0,this.qualC=0,this.qualG=0,this.qualN=0,this.qual=0,this.total=0,this.del=0,this.ins=0,this.threshold=e}hoverText(){const e=this.posA+this.posT+this.posC+this.posG+this.posN,t=this.negA+this.negT+this.negC+this.negG+this.negN;return`${this.total} (${e}+, ${t}-)`}isMismatch(e){const t=this.threshold*(this.qualityWeight&&this.qual?this.qual:this.total);let i=0;for(let t of[\"A\",\"T\",\"C\",\"G\"])t!==e&&(i+=this.qualityWeight&&this.qual?this[\"qual\"+t]:this[\"pos\"+t]+this[\"neg\"+t]);return i>=t}}class sp{constructor(e,t,i){this.start=e,this.end=t,this.counts=i}popupData(e){return[{name:\"start\",value:Math.floor(this.start+1)},{name:\"end\",value:this.end},{name:\"# downsampled:\",value:this.counts}]}}class op{pixelTop=0;pixelBottom=0;rows=[];constructor(e){this.name=this.name}push(e){this.rows.push(e)}get length(){return this.rows.length}sortRows(e,t){const i=[],n=[];for(let t of this.rows){void 0!==t.findAlignment(e.position,e.sortAsPairs)?i.push(t):n.push(t)}i.sort(((i,n)=>{const r=e.direction,s=i.getSortValue(e,t),o=n.getSortValue(e,t);if(void 0===o&&void 0!==o)return 1;if(void 0!==s&&void 0===o)return-1;const a=s>o?1:s<o?-1:0;return!0===r?a:-a}));for(let e of n)i.push(e);this.rows=i}}function ap(e){return e.isPaired()&&e.mate&&e.isMateMapped()&&e.chr===e.mate.chr&&(e.isFirstOfPair()||e.isSecondOfPair())&&!(e.isSecondary()||e.isSupplementary())}function cp(e,t,i){let n=i-1,r=e.length;for(;1+n<r;){const i=n+(r-n>>1);t(e[i])?r=i:n=i}return r}function lp(e,t,i){let n,r,s;if(t.startsWith(\"tag:\"))n=t.substring(4),t=\"tag\";else if(t.startsWith(\"base:\")){const e=t.split(\":\");3===e.length&&(t=\"base\",r=e[1],s=Number.parseInt(e[2].replaceAll(\",\",\"\"))-1)}switch(t){case\"strand\":return e.strand?\"+\":\"-\";case\"firstOfPairStrand\":const t=e.firstOfPairStrand;return void 0===t?\"\":t?\"+\":\"-\";case\"mateChr\":return e.mate&&e.isMateMapped()?e.mate.chr:\"\";case\"pairOrientation\":return ep[i][e.pairOrientation]||\"\";case\"chimeric\":return e.tags().SA?\"chimeric\":\"\";case\"supplementary\":return e.isSupplementary?\"supplementary\":\"\";case\"readOrder\":return e.isPaired()&&e.isFirstOfPair()?\"first\":e.isPaired()&&e.isSecondOfPair()?\"second\":\"\";case\"phase\":return e.tags().HP||\"\";case\"tag\":return e.tags()[n]||\"\";case\"base\":if(e.chr===r&&e.start<=s&&e.end>s){const t=e.readBaseAt(s);return t||\"GAP\"}return\"\";default:return}}const hp=new Map([[\"A\",1],[\"T\",2],[\"C\",3],[\"G\",4],[\"N\",5],[\"GAP\",5],[\"\",7]]);function dp(e,t){return hp.has(e)&&hp.has(t)?hp.get(e)-hp.get(t):e.localeCompare(t,void 0,{sensitivity:\"base\"})}function up(e,t){return e===t?0:e&&t?-e.localeCompare(t):e?1:-1}function fp(e,t){if(e||t){if(e){if(t){if(e===t)return 0;if(Va(e)&&(Va(t),1))return Number.parseFloat(e)-Number.parseFloat(t);{let i=e.toString(),n=t.toString();return i.localeCompare(n,void 0,{sensitivity:\"base\"})}}return-1}return 1}return 0}class pp{constructor(e){const t=e.split(\",\");this.chr=t[0],this.start=parseInt(t[1]),this.strand=t[2].charAt(0),this.mapQ=parseInt(t[4]),this.numMismatches=parseInt(t[5]),this.lenOnRef=function(e){let t=0,i=\"\";for(let n=0;n<e.length;n++){const r=e.charCodeAt(n);if(r>47&&r<58)i+=e.charAt(n);else{switch(r){case 78:case 68:case 77:case 61:case 88:t+=parseInt(i.toString())}i=\"\"}}return t}(t[3])}printString(){return this.chr+\":\"+Rt(this.start)+\"-\"+Rt(this.start+this.lenOnRef)+\" (\"+this.strand+\") = \"+Rt(this.lenOnRef)+\"bp @MAPQ: \"+this.mapQ+\" NM: \"+this.numMismatches}}function gp(e){return e.split(\";\").filter((e=>e.length>0)).map((e=>new pp(e)))}const mp={c:1,C:1,s:2,S:2,i:4,I:4,f:4};class wp{constructor(){this.hidden=!1}isMapped(){return!(4&this.flags)}isPaired(){return!!(1&this.flags)}isProperPair(){return!!(2&this.flags)}isFirstOfPair(){return!!(64&this.flags)}isSecondOfPair(){return!!(128&this.flags)}isSecondary(){return!!(256&this.flags)}isSupplementary(){return!!(2048&this.flags)}isFailsVendorQualityCheck(){return!!(512&this.flags)}isDuplicate(){return!!(1024&this.flags)}isMateMapped(){return!(8&this.flags)}isNegativeStrand(){return!!(16&this.flags)}isMateNegativeStrand(){return!!(32&this.flags)}hasTag(e){const t=this.tagDict||function(e){let t=0;const i=e.length,n={};for(;t<i;){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const s=String.fromCharCode(e[t++]);let o;if(\"A\"===s)o=String.fromCharCode(e[t]),t++;else if(\"i\"===s||\"I\"===s)o=vp(e,t),t+=4;else if(\"c\"===s)o=Cp(e,t),t++;else if(\"C\"===s)o=_p(e,t),t++;else if(\"s\"===s||\"S\"===s)o=yp(e,t),t+=2;else if(\"f\"===s)o=Ap(e,t),t+=4;else if(\"Z\"===s)for(o=\"\";;){var r=e[t++];if(0===r)break;o+=String.fromCharCode(r)}else{if(\"B\"!==s){o=\"Error unknown type: \"+s,n[i]=o;break}{const r=String.fromCharCode(e[t++]);let s=mp[r];if(void 0===s){n[i]=`Error: unknown element type '${r}'`;break}const a=vp(e,t);t+=4;const c=t+a*s;o=[];const l=new DataView(e.buffer);for(;t<c;){switch(r){case\"c\":o.push(l.getInt8(t));break;case\"C\":o.push(l.getUint8(t));break;case\"s\":o.push(l.getInt16(t));break;case\"S\":o.push(l.getUint16(t));break;case\"i\":o.push(l.getInt32(t));break;case\"I\":o.push(l.getUint32(t));break;case\"f\":o.push(l.getFloat32(t))}t+=s}}}n[i]=o}return n}(this.tagBA);return t.hasOwnProperty(e)}tags(){return this.tagDict}getTag(e){return this.tags()[e]}get firstOfPairStrand(){if(this.isPaired()){if(this.isFirstOfPair())return this.strand;if(this.isMateMapped())return this.mate.strand}}containsLocation(e,t){const i=t?this.scStart:this.start,n=t?this.scLengthOnRef:this.lengthOnRef;return e>=i&&e<=i+n}popupData(e){const t=[];if(e=Math.floor(e),this.insertions){const n=this.seq;for(let r of this.insertions){var i=r.start;if(e===i||e===i-1)return t.push({name:\"Insertion\",value:n.substr(r.seqOffset,r.len)}),t.push({name:\"Location\",value:i}),t}}t.push({name:\"Read Name\",value:this.readName}),t.push(\"<hr/>\"),t.push({name:\"Alignment Start\",value:Rt(1+this.start),borderTop:!0}),t.push({name:\"Read Strand\",value:!0===this.strand?\"(+)\":\"(-)\",borderTop:!0});let n=this.cigar;if(n&&n.length>50){const e=25;n=`${n.substring(0,e-2)} ... ${n.substring(n.length-e+2)}`}t.push({name:\"Cigar\",value:n}),t.push({name:\"Mapping Quality\",value:this.mq}),t.push({name:\"Secondary\",value:a(this.isSecondary())}),t.push({name:\"Supplementary\",value:a(this.isSupplementary())}),t.push({name:\"Duplicate\",value:a(this.isDuplicate())}),t.push({name:\"Failed QC\",value:a(this.isFailsVendorQualityCheck())}),this.isPaired()&&(t.push(\"<hr/>\"),t.push({name:\"First in Pair\",value:!this.isSecondOfPair(),borderTop:!0}),t.push({name:\"Mate is Mapped\",value:a(this.isMateMapped())}),this.pairOrientation&&t.push({name:\"Pair Orientation\",value:this.pairOrientation}),this.isMateMapped()&&(t.push({name:\"Mate Chromosome\",value:this.mate.chr}),t.push({name:\"Mate Start\",value:this.mate.position+1}),t.push({name:\"Mate Strand\",value:!0===this.mate.strand?\"(+)\":\"(-)\"}),t.push({name:\"Insert Size\",value:this.fragmentLength})));const r=this.tags();if(r.hasOwnProperty(\"SA\")){t.push(\"<hr/>\"),t.push({name:\"Supplementary Alignments\",value:\"\"});const e=gp(r.SA);if(e){t.push(\"<ul>\");for(let i of e)t.push(`<li>${i.printString()}</li>`);t.push(\"</ul>\")}}const s=new Set([\"SA\",\"MD\"]);t.push(\"<hr/>\");for(let e in r)s.has(e)||t.push({name:e,value:r[e]});t.push({name:\"Hidden Tags\",value:\"SA, MD\"}),t.push(\"<hr/>\"),t.push({name:\"Genomic Location: \",value:Rt(1+e)}),t.push({name:\"Read Base:\",value:this.readBaseAt(e)}),t.push({name:\"Base Quality:\",value:this.readBaseQualityAt(e)});const o=this.getBaseModificationSets();if(o){const i=this.positionToReadIndex(e);if(void 0!==i){let e=!1;for(let n of o)if(n.containsPosition(i)){e||(t.push(\"<hr/>\"),t.push(\"<b>Base modifications:</b>\"),e=!0);const r=Math.round(100/255*Xf(n.likelihoods.get(i)));t.push(`${n.fullName()} @ likelihood =  ${r}%`)}}}return t;function a(e){return e?\"Yes\":\"No\"}}readBaseAt(e){const t=Fp(this.blocks,e);if(t){if(\"*\"===this.seq)return\"*\";{const i=t.seqIndexAt(e);return this.seq[i]}}}readBaseQualityAt(e){const t=Fp(this.blocks,e);if(t){if(\"*\"===this.qual)return 30;{const i=t.seqIndexAt(e);return i>=0&&this.qual&&i<this.qual.length?this.qual[i]:30}}}gapSizeAt(e){if(this.gaps)for(let t of this.gaps)if(e>=t.start&&e<t.start+t.len)return t.len;return 0}softClippedBlocks(){let e,t,i;for(let n of this.blocks)\"S\"===n.type?i?t=n:e=n:\"H\"!==n.type&&(i=!0);return{left:e,right:t}}getBaseModificationSets(){if(!this.baseModificationSets&&(this.tagDict.MM||this.tagDict.Mm)){const e=this.tagDict.MM||this.tagDict.Mm,t=this.tagDict.ML||this.tagDict.Ml;!Mt(e)||t&&!Array.isArray(t)||(0===e.length?this.baseModificationSets=bp:this.baseModificationSets=function(e,t,i,n){n&&(i=cc(i));const r=[],s=e.split(\";\");let o=0;for(let e of s){const s=e.split(\",\"),a=s[0].charAt(0),c=s[0].charAt(1),l=s[0].endsWith(\".\");if(1==s.length);else{const e=s[0].endsWith(\".\")||s[0].endsWith(\"?\")?s[0].substring(2,s[0].length-1):s[0].substring(2);let h=[];if(e.length>1)if(Yf(e))h.push(e);else for(let t=0;t<e.length;t++)h.push(e.substring(t,t+1));else h.push(e);const d=new Map;for(let e of h)d.set(e,new Map);let u=1,f=Number.parseInt(s[u++]),p=0,g=0;for(;p<i.length;){if(\"N\"===a||i[p]===a){const e=n?i.length-1-p:p;if(g===f){for(let i of h){const n=t?t[o++]:255;d.get(i).set(e,n)}if(u<s.length)f=Number.parseInt(s[u++]),g=0;else{if(!l)break;f=-1}}else{if(l)for(let t of h)d.get(t).set(e,0);g++}}p++}for(let e of h)r.push(new Wf(a,c,e,d.get(e)))}}return r}(e,t,this.seq,this.isNegativeStrand()))}return this.baseModificationSets}getGroupValue(e,t,i){const n=this;switch(e){case\"strand\":return n.strand?\"+\":\"-\";case\"firstOfPairStrand\":const e=n.firstOfPairStrand;return void 0===e?\"\":e?\"+\":\"-\";case\"mateChr\":return n.mate&&n.isMateMapped()?n.mate.chr:\"\";case\"pairOrientation\":return ep[i][n.pairOrientation]||\"\";case\"chimeric\":return n.tags().SA?\"chimeric\":\"\";case\"supplementary\":return n.isSupplementary?\"supplementary\":\"\";case\"readOrder\":return n.isPaired()&&n.isFirstOfPair()?\"first\":n.isPaired()&&n.isSecondOfPair()?\"second\":\"\";case\"phase\":return n.tags().HP||\"\";case\"tag\":return n.tags()[t]||\"\";default:return}}positionToReadIndex(e){const t=Fp(this.blocks,e);return t?e-t.start+t.seqOffset:void 0}}const bp=new Set;function Fp(e,t){for(let i=0;i<e.length;i++){const n=e[i];if(t>=n.start&&t<n.start+n.len)return n}}function vp(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function yp(e,t){return e[t+1]<<8|e[t]}function Ap(e,t){return new DataView(e.buffer).getFloat32(t)}function Cp(e,t){return new DataView(e.buffer).getInt8(t)}function _p(e,t){return new DataView(e.buffer).getUint8(t)}class xp{constructor(e){e&&Object.assign(this,e)}seqIndexAt(e){return Math.floor(e)-this.start+this.seqOffset}}class kp{constructor(e){e||(e={}),this.vendorFailed=e.vendorFailed=!1!==e.vendorFailed,this.duplicate=e.duplicate=!1!==e.duplicate,this.secondary=e.secondary||!1,this.supplementary=e.supplementary||!1,this.mq=e.mq||0,e.readgroups&&(this.readgroups=new Set(e.readgroups))}pass(e){if(!e.isMapped())return!1;if(this.vendorFailed&&e.isFailsVendorQualityCheck())return!1;if(this.duplicate&&e.isDuplicate())return!1;if(this.secondary&&e.isSecondary())return!1;if(this.supplementary&&e.isSupplementary())return!1;if(e.mq<this.mq)return!1;if(this.readgroups){const t=e.tags().RG;return this.readgroups.has(t)}return!0}}const Ip=Dp(new Uint8Array([66,65,77,1]),0),Sp=[\"=\",\"A\",\"C\",\"M\",\"G\",\"R\",\"S\",\"V\",\"T\",\"W\",\"Y\",\"H\",\"K\",\"D\",\"B\",\"N\"],Ep=[\"M\",\"I\",\"D\",\"N\",\"S\",\"H\",\"P\",\"=\",\"X\",\"?\",\"?\",\"?\",\"?\",\"?\",\"?\",\"?\"],Np={c:1,C:1,s:2,S:2,i:4,I:4,f:4},Bp=1e4,Mp={readHeader:async function(e,t,i){const n=gs(await Qs.loadArrayBuffer(e,t));return Mp.decodeBamHeader(n,i)},decodeBamHeader:function(e){const t=Dp(e,0);if(t!==Ip)throw new Error(\"BAM header errror: bad magic number.  This could be caused by either a corrupt or missing file.\");const i=Dp(e,4);let n=\"\";for(var r=0;r<i;++r)n+=String.fromCharCode(e[r+8]);const s=Dp(e,i+8);let o=i+12;const a={},c=[];for(r=0;r<s;++r){const t=Dp(e,o);let i=\"\";for(var l=0;l<t-1;++l)i+=String.fromCharCode(e[o+4+l]);a[i]=r,c[r]=i,o=o+8+t}return{magicNumber:t,size:o,chrNames:c,chrToIndex:a}},bam_tag2cigar:function(e,t,i,n,r,s){function o(e){return\"C\"===e||\"c\"===e||\"A\"===e?1:\"S\"===e||\"s\"===e?2:\"I\"===e||\"i\"===e||\"f\"===e?4:0}if(1!==s.length||r.start<0)return!1;for(var a=i+(n+1>>1)+n;a+4<t;){if(\"CG\"===String.fromCharCode(e[a])+String.fromCharCode(e[a+1]))break;var c=String.fromCharCode(e[a+2]);if(\"B\"===c)a+=8+o(c=String.fromCharCode(e[a+3]))*Dp(e,a+4);else if(\"Z\"===c||\"H\"===c)for(a+=3;0!==e[a++];);else a+=3+o(c)}if(a>=t)return!1;if(\"B\"!==String.fromCharCode(e[a+2])||\"I\"!==String.fromCharCode(e[a+3]))return!1;var l=Dp(e,a+4),h=a+8;if(h+4*l>t)return!1;var d=\"\",u=0;s.length=0,a=h;for(var f=0;f<l;++f,a+=4){var p=Dp(e,a),g=p>>4,m=Ep[15&p];\"M\"!==m&&\"EQ\"!==m&&\"X\"!==m&&\"D\"!==m&&\"N\"!==m&&\"=\"!==m||(u+=g),d=d+g+m,s.push({len:g,ltr:m})}return r.cigar=d,r.lengthOnRef=u,!0},decodeBamRecords:function(e,t,i,n,r,s,o,a){for(;t<e.length;){const u=t+Dp(e,t)+4,f=new wp,p=Dp(e,t+4),g=Dp(e,t+8);if(u>e.length)return;if(p<0){t=u;continue}if(void 0!==r&&(p>r||g>o))return!0;if(void 0!==r&&p<r){t=u;continue}const m=Dp(e,t+12),w=(65280&m)>>8,b=255&m,F=Dp(e,t+16),v=(4294901760&F)>>16,y=65535&F,A=Dp(e,t+20),C=Dp(e,t+24),_=Dp(e,t+28),x=Dp(e,t+32);let k=[];for(let i=0;i<b-1;++i)k.push(String.fromCharCode(e[t+36+i]));k=k.join(\"\");let I=0,S=\"\",E=t+36+b;const N=[];let B;for(let t=0;t<y;++t){var c=Dp(e,E),l=c>>4,h=Ep[15&c];\"M\"!==h&&\"EQ\"!==h&&\"X\"!==h&&\"D\"!==h&&\"N\"!==h&&\"=\"!==h||(I+=l),S=S+l+h,E+=4,B={len:l,ltr:h},N.push(B)}if(f.chr=n[p],f.start=g,f.flags=v,f.strand=!(16&v),f.readName=k,f.cigar=S,f.lengthOnRef=I,f.fragmentLength=x,f.mq=w,Mp.bam_tag2cigar(e,u,E,A,f,N),f.end=f.start+f.lengthOnRef,f.end<s){t=u;continue}let M=[];const R=A+1>>1;for(let t=0;t<R;++t){var d=e[E+t];M.push(Sp[(240&d)>>4]),M.push(Sp[15&d])}M=M.slice(0,A).join(\"\"),E+=R;const D=[];for(let t=0;t<A;++t)D.push(e[E+t]);E+=A,C>=0&&(f.mate={chr:n[C],position:_,strand:!(32&v)}),f.seq=M,f.qual=D;const T=new Uint8Array(e.buffer.slice(E,u));f.tagDict=zp(T),this.setPairOrientation(f),(void 0===a||a.pass(f))&&(Rp(f,N),i.push(f)),t=u}},decodeSamRecords:function(e,t,i,n,r,s){var o,a,c,l,h,d,u,f,p,g;for(l=(o=Dt(e)).length,!1,a=0;a<l;a++)if(h=o[a].split(\"\\t\"),(p=new wp).chr=h[2],p.start=Number.parseInt(h[3])-1,p.flags=Number.parseInt(h[1]),p.readName=h[0],p.strand=!(16&p.flags),p.mq=Number.parseInt(h[4]),p.cigar=h[5],p.fragmentLength=Number.parseInt(h[8]),p.seq=h[9],\"*\"!==p.chr&&p.isMapped()&&p.chr===i){if(p.start>r)break;if(f=0,(g=Tp(p.cigar)).forEach((function(e){var t=e.len,i=e.ltr;\"M\"!==i&&\"EQ\"!==i&&\"X\"!==i&&\"D\"!==i&&\"N\"!==i&&\"=\"!==i||(f+=t)})),p.lengthOnRef=f,!(p.start+f<n)){for(d=h[10],p.qual=[],c=0;c<d.length;c++)p.qual[c]=d.charCodeAt(c)-33;p.tagDict=h.length<11?{}:Lp(h.slice(11)),p.isMateMapped()&&(u=h[6],p.mate={chr:\"=\"===u?p.chr:u,position:Number.parseInt(h[7]),strand:!(32&p.flags)}),this.setPairOrientation(p),(void 0===s||s.pass(p))&&(Rp(p,g),t.push(p))}}},setReaderDefaults:function(e,t){e.filter=\"function\"==typeof t.filter?{pass:t.filter}:new kp(t.filter),t.readgroup&&(e.filter.readgroups=new Set([t.readgroup])),e.alleleFreqThreshold=void 0===t.alleleFreqThreshold?.2:t.alleleFreqThreshold,e.samplingWindowSize=void 0===t.samplingWindowSize?100:t.samplingWindowSize,e.samplingDepth=void 0===t.samplingDepth?500:t.samplingDepth,e.samplingDepth>Bp&&(console.log(\"Warning: attempt to set sampling depth > maximum value of \"+Bp),e.samplingDepth=Bp)},setPairOrientation:function(e){if(e.isMapped()&&e.mate&&e.isMateMapped()&&e.mate.chr===e.chr){var t=e.strand?\"F\":\"R\",i=e.mate,n=i.strand?\"F\":\"R\",r=\" \",s=\" \";e.isFirstOfPair()?(r=\"1\",s=\"2\"):e.isSecondOfPair()&&(r=\"2\",s=\"1\");var o=[],a=e.fragmentLength,c=e.end-e.start;if(0===a)a=(e.start<i.position?i.position+c:i.position-c)-e.start;a>0?(o[0]=t,o[1]=r,o[2]=n,o[3]=s):(o[2]=t,o[3]=r,o[0]=n,o[1]=s),e.pairOrientation=o.join(\"\")}}};function Rp(e,t){const i=[];let n,r,s=0,o=e.start;e.scStart=e.start,e.scLengthOnRef=e.lengthOnRef;for(let a of t){let t;switch(a.ltr){case\"H\":case\"P\":break;case\"S\":t=o,e.scLengthOnRef+=a.len,0===i.length&&(e.scStart-=a.len,t-=a.len),i.push(new xp({start:t,seqOffset:s,len:a.len,type:\"S\"})),s+=a.len;break;case\"N\":case\"D\":void 0===r&&(r=[]),r.push({start:o,len:a.len,type:a.ltr}),o+=a.len;break;case\"I\":void 0===n&&(n=[]),n.push(new xp({start:o,len:a.len,seqOffset:s,type:\"I\"})),s+=a.len;break;case\"M\":case\"EQ\":case\"=\":case\"X\":i.push(new xp({start:o,seqOffset:s,len:a.len,type:\"M\"})),s+=a.len,o+=a.len;break;default:console.log(\"Error processing cigar element: \"+a.len+a.ltr)}}e.blocks=i,e.insertions=n,e.gaps=r}function Dp(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function Tp(e){var t,i,n,r,s,o,a,c,l;for(t=[],i=[],s=null,r=e.length,n=0;n<r;n++)o=e.charAt(n),l=void 0,(l=o.charCodeAt(0))>=48&&l<=57?i.push(o):(a=o,c=Number.parseInt(i.join(\"\")),i=[],null!==s&&s.ltr===a?s.len+=c:(s={len:c,ltr:a},t.push(s)));return t}function Lp(e){var t={};return e.forEach((function(e){var i=e.split(\":\");t[i[0]]=i[2]})),t}function zp(e){let t=0;const i=e.length,n={},r=new DataView(e.buffer);for(;t<i;){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const o=String.fromCharCode(e[t++]);let a;if(\"A\"===o)a=String.fromCharCode(e[t]),t++;else if(\"i\"===o||\"I\"===o)a=r.getInt32(t,!0),t+=4;else if(\"c\"===o)a=r.getInt8(t,!0),t++;else if(\"C\"===o)a=r.getUint8(t,!0),t++;else if(\"s\"===o||\"S\"===o)a=r.getInt16(t,!0),t+=2;else if(\"f\"===o)a=r.getFloat32(t,!0),t+=4;else if(\"Z\"===o)for(a=\"\";;){var s=e[t++];if(0===s)break;a+=String.fromCharCode(s)}else{if(\"B\"!==o){a=\"Error unknown type: \"+o,n[i]=a;break}{const s=String.fromCharCode(e[t++]);let o=Np[s];if(void 0===o){n[i]=`Error: unknown element type '${s}'`;break}const c=r.getInt32(t,!0);t+=4;const l=t+c*o;for(a=[];t<l;){switch(s){case\"c\":a.push(r.getInt8(t,!0));break;case\"C\":a.push(r.getUint8(t,!0));break;case\"s\":a.push(r.getInt16(t,!0));break;case\"S\":a.push(r.getUint16(t,!0));break;case\"i\":a.push(r.getInt32(t,!0));break;case\"I\":a.push(r.getUint32(t,!0));break;case\"f\":a.push(r.getFloat32(t,!0))}t+=o}}}n[i]=a}return n}class Hp{chrAliasTable=new Map;constructor(e,t){this.config=e,this.genome=t,this.bamPath=e.url,this.isDataUri=Ga(e.url),Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(!this.alignmentCache){let e;if(this.isDataUri){const t=function(e){const t=e.split(\",\"),i=t[0].split(\":\")[1];let n=t[1];n=i.indexOf(\"base64\")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s<n.length;s++)r[s]=n.charCodeAt(s);return r}(this.bamPath);e=gs(t.buffer)}else{e=gs(await Qs.loadArrayBuffer(this.bamPath,Ua(this.config)))}this.alignmentCache=this.#C(e)}const n=await this.#_(e),r=this.alignmentCache.queryFeatures(n,t,i),s=new tp(e,t,i,this.config);for(let e of r)s.push(e);return s.finish(),s}#C(e){const t=[];return this.header=Mp.decodeBamHeader(e),Mp.decodeBamRecords(e,this.header.size,t,this.header.chrNames,void 0,0,Number.MAX_SAFE_INTEGER,this.filter),new Zs(t,this.genome)}async#_(e){const t=new Set(this.header.chrNames);if(t.has(e))return e;if(this.chrAliasTable.has(e))return this.chrAliasTable.get(e);if(this.genome){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>t.has(e)));e.length>0&&(n=e[0])}return this.chrAliasTable.set(e,n),n}return e}}class Pp{chrAliasTable=new Map;constructor(e,t){this.config=e,this.genome=t,this.bamPath=e.url,this.baiPath=e.indexURL,Mp.setReaderDefaults(this,e),this._blockLoader=new yh(e)}async readAlignments(e,t,i){const n=await this.#x(e),r=new tp(e,t,i,this.config);if(void 0===n)return r;{const e=(await this.getIndex()).chunksForRange(n,t,i);if(!e||0===e.length)return r;for(let s of e){const e=await this._blockLoader.getData(s.minv,s.maxv);if(Mp.decodeBamRecords(e,s.minv.offset,r,this.header.chrNames,n,t,i,this.filter))break}return r.finish(),r}}async#x(e){if(await this.getHeader(),this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.header.chrToIndex[e];if(void 0===t){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>void 0!==this.header.chrToIndex[e]));e.length>0&&(n=e[0],t=this.header.chrToIndex[e[0]])}this.chrAliasTable.set(e,n)}return t}async getHeader(){if(!this.header){const e=this.genome,t=await this.getIndex();let i;if(t.firstBlockPosition){const e=Ua(this.config,{range:{start:t.firstBlockPosition,size:26}}),n=ms(await Qs.loadArrayBuffer(this.bamPath,e));i=t.firstBlockPosition+n}else i=64e3;const n=Ua(this.config,{range:{start:0,size:i}});this.header=await Mp.readHeader(this.bamPath,n,e)}return this.header}async getIndex(){return this.index||(this.index=await gh(this.baiPath,this.config)),this.index}async getChrIndex(){if(this.chrToIndex)return this.chrToIndex;{const e=await this.getHeader();return this.chrToIndex=e.chrToIndex,this.indexToChr=e.chrNames,this.chrNames=new Set(e.chrNames),this.chrToIndex}}}class Op{constructor(e,t){this.config=e,this.genome=t;const i={};e.sources.sequences.forEach((function(n){const r=t?t.getChromosomeName(n):n;i[r]=function(e,t,i){const n={url:e.sources.url.replace(\"$CHR\",i)};e.sources.indexURL&&(n.indexURL=e.sources.indexURL.replace(\"$CHR\",i));const r=Object.assign(e,n);return new Pp(r,t)}(e,t,n)})),this.bamReaders=i,Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(this.bamReaders.hasOwnProperty(e)){let n=this.bamReaders[e];return await n.readAlignments(e,t,i)}return new tp(e,t,i,this.config)}}const Up=function(e,t){this.config=e,this.genome=t,Mp.setReaderDefaults(this,e)};function qp(){const e=this,t=this.genome;if(this.header)return Promise.resolve(this.header);{const i=this.config.url+\"?file=\"+this.config.alignmentFile+\"&options=-b,-H\",n=Ua(this.config);return Mp.readHeader(i,n,t).then((function(t){return e.header=t,t}))}}Up.prototype.readAlignments=function(e,t,i){var n=this;return qp.call(n).then((function(r){var s,o;return s=r.chrAliasTable.hasOwnProperty(e)?r.chrAliasTable[e]:e,o=n.config.url+\"?reference=\"+n.config.referenceFile+\"&file=\"+n.config.alignmentFile+\"&region=\"+s+\":\"+t+\"-\"+i,Qs.loadString(o,Ua(n.config)).then((function(o){var a;return r.chrToIndex[s],a=new tp(e,t,i,n.config),Mp.decodeSamRecords(o,a,s,t,i,n.filter),a}))}))};class Qp extends Rh{constructor(e,t){super(e,t),Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(!this.header){const e=gs((await this.readHeaderData()).buffer);this.header=Mp.decodeBamHeader(e,this.genome),this.chrAliasTable=new Map;for(let e of this.header.chrNames)this.chrAliasTable.set(e,this.genome.getChromosomeName(e))}let n=this.chrAliasTable.has(e)?this.chrAliasTable.get(e):e;const r=gs((await this.readData(n,t,i)).buffer);this.header=Mp.decodeBamHeader(r,this.genome);const s=this.header.chrToIndex[e],o=new tp(e,t,i,this.config);return Mp.decodeBamRecords(r,this.header.size,o,this.header.chrNames,s,t,i,this.filter),o.finish(),o}}\n",
-       "/*! For license information please see cram-bundle.js.LICENSE.txt */for(var Vp=(()=>{var e={4923:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(8712),s=i(5931),o=i(9747);function a(e,t){const[i,n,r,s,o,a]=t,c=i;e[c]||(e[c]=[]),e[c].push({start:n,span:r,containerStart:s,sliceStart:o,sliceBytes:a})}t.default=class{constructor(e){this.filehandle=(0,s.open)(e.url,e.path,e.filehandle)}parseIndex(){return n(this,void 0,void 0,(function*(){const e={},t=31===(i=yield this.filehandle.readFile())[0]&&139===i[1]?(0,r.unzip)(i):i;var i;if(t.length>4&&21578050===t.readUInt32LE(0))throw new o.CramMalformedError(\"invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support\");let n=[],s=\"\";for(const i of t)if(i>=48&&i<=57||!s&&45===i)s+=String.fromCharCode(i);else if(9===i)n.push(Number.parseInt(s,10)),s=\"\";else if(10===i)n.push(Number.parseInt(s,10)),s=\"\",a(e,n),n=[];else if(13!==i&&32!==i)throw new o.CramMalformedError(\"invalid .crai index file\");return s&&n.push(Number.parseInt(s,10)),6===n.length&&a(e,n),Object.entries(e).forEach((([t,i])=>{const n=i;e[t]=n.sort(((e,t)=>e.start-t.start||e.span-t.span))})),e}))}getIndex(){return this.parseIndexP||(this.parseIndexP=this.parseIndex().catch((e=>{throw this.parseIndexP=void 0,e}))),this.parseIndexP}hasDataForReferenceSequence(e){return n(this,void 0,void 0,(function*(){return!!(yield this.getIndex())[e]}))}getEntriesForRange(e,t,i){return n(this,void 0,void 0,(function*(){const n=(yield this.getIndex())[e];if(!n)return[];const r=e=>{const n=e.start,r=e.start+e.span;return n>i?-1:r<=t?1:0},s=[];for(const e of n)0===r(e)&&s.push(e);return s}))}}},9508:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=class{constructor(e,t){this.parameters=e,this.dataType=t}}},368:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`)}decode(e,t,i,n){return(0,o.getBits)(t.content,n.coreBlock,this.parameters.length)-this.parameters.offset}}t.default=a},8635:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=n(i(9508)),s=i(400);class o extends r.default{constructor(e,t,i){super(e,t),this.instantiateCodec=i}decode(e,t,i,n){const r=this._getLengthCodec().decode(e,t,i,n),s=this._getDataCodec(),o=new Uint8Array(r);for(let a=0;a<r;a+=1)o[a]=s.decode(e,t,i,n);return o}_getLengthCodec(){const e=this.parameters.lengthsEncoding;return this.instantiateCodec(e,\"int\")}_getDataCodec(){const e=this.parameters.valuesEncoding;return this.instantiateCodec(e,\"byte\")}}t.default=o,\"_getLengthCodec _getDataCodec\".split(\" \").forEach((e=>{(0,s.tinyMemoize)(o,e)}))},4839:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{decode(e,t,i,n){const{blockContentId:s}=this.parameters,o=i[s];if(!o)throw new r.CramMalformedError(`no block found with content ID ${s}`);const a=n.externalBlocks.getCursor(s);return this._decodeByteArray(o,a)}_decodeByteArray(e,t){const i=e.content,{stopByte:n}=this.parameters,r=t.bytePosition;let s=t.bytePosition;for(;i[s]!==n&&s<i.length;){if(s===i.length)throw new o.CramBufferOverrunError(\"byteArrayStop reading beyond length of data buffer?\");s+=1}return t.bytePosition=s+1,i.subarray(r,s)}}t.default=a},8153:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(400),a=i(612);class c extends s.default{constructor(e,t){if(super(e,t),\"int\"===this.dataType)this._decodeData=this._decodeInt;else{if(\"byte\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by EXTERNAL codec`);this._decodeData=this._decodeByte}}decode(e,t,i,n){const{blockContentId:s}=this.parameters,o=i[s];if(!o)throw new r.CramMalformedError(`no block found with content ID ${s}}`);const a=n.externalBlocks.getCursor(s);return this._decodeData(o,a)}_decodeInt(e,t){const[i,n]=(0,o.parseItf8)(e.content,t.bytePosition);return t.bytePosition=t.bytePosition+n,i}_decodeByte(e,t){if(t.bytePosition>=e.content.length)throw new a.CramBufferOverrunError(\"attempted to read beyond end of block. this file seems truncated.\");return e.content[t.bytePosition++]}}t.default=c},8185:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`)}decode(e,t,i,n){let r=1;for(;0===(0,o.getBits)(t.content,n.coreBlock,1);)r+=1;return((0,o.getBits)(t.content,n.coreBlock,r-1)|1<<r-1)-this.parameters.offset}}t.default=a},612:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.CramBufferOverrunError=void 0,t.getBits=function(e,t,n){let r=0;if(t.bytePosition+(7-t.bitPosition+n)/8>e.length)throw new i(\"read error during 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t=0;t<this.parameters.numCodes;t++)e[t]={symbol:this.parameters.symbols[t],bitLength:this.parameters.bitLengths[t]};e=e.sort(((e,t)=>e.bitLength-t.bitLength||e.symbol-t.symbol)),this.codeBook={},e.forEach((e=>{this.codeBook[e.bitLength]||(this.codeBook[e.bitLength]=[]),this.codeBook[e.bitLength].push(e.symbol)}))}buildCodes(){this.codes={};let e=0,t=-1;Object.entries(this.codeBook).forEach((([i,n])=>{const s=Number.parseInt(i,10);n.forEach((i=>{const n={bitLength:s,value:i,bitCode:0};t+=1;const o=s-e;if(t<<=o,n.bitCode=t,e+=o,function(e){let t=e-(e>>1)&1431655765;return t=(858993459&t)+(t>>2&858993459),16843009*(t+(t>>4)&252645135)>>24}(t)>s)throw new r.CramMalformedError(\"Symbol out of range\");this.codes[i]=n}))}))}buildCaches(){this.sortedCodes=Object.values(this.codes).sort(((e,t)=>e.bitLength-t.bitLength||e.bitCode-t.bitCode)),this.sortedValuesByBitCode=this.sortedCodes.map((e=>e.value)),this.sortedBitCodes=this.sortedCodes.map((e=>e.bitCode)),this.sortedBitLengthsByBitCode=this.sortedCodes.map((e=>e.bitLength));const e=Math.max(...this.sortedBitCodes);this.bitCodeToValue=new Array(e+1).fill(-1);for(let e=0;e<this.sortedBitCodes.length;e+=1)this.bitCodeToValue[this.sortedCodes[e].bitCode]=e}decode(e,t,i,n){return this._decode(e,t,n.coreBlock)}_decodeZeroLengthCode(){return this.sortedCodes[0].value}_decode(e,t,i){const n=t.content;let s=0,a=0;for(let e=0;e<this.sortedCodes.length;e+=1){const t=this.sortedCodes[e].bitLength;a<<=t-s,a|=(0,o.getBits)(n,i,t-s),s=t;{const i=this.bitCodeToValue[a];if(i>-1&&this.sortedBitLengthsByBitCode[i]===t)return this.sortedValuesByBitCode[i];for(let i=e;this.sortedCodes[i+1].bitLength===t&&i<this.sortedCodes.length;i+=1)e+=1}}throw new r.CramMalformedError(\"Huffman symbol not found.\")}}t.default=a},6524:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.instantiateCodec=function e(t,i){const n=(s=\"ignore\"===i?0:t.codecId,u[s]);var s;if(!n)throw new r.CramUnimplementedError(`no codec implemented for codec ID ${t.codecId}`);return new n(t.parameters,i,e)};const r=i(9747),s=n(i(4341)),o=n(i(8153)),a=n(i(4839)),c=n(i(8635)),l=n(i(368)),h=n(i(8185)),d=n(i(99)),u={1:o.default,3:s.default,4:c.default,5:a.default,6:l.default,7:d.default,9:h.default}},99:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new 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0===a?(r=this.parameters.K,s=(0,o.getBits)(t.content,n.coreBlock,r)):(r=a+this.parameters.K-1,s=1<<r|(0,o.getBits)(t.content,n.coreBlock,r)),s-this.parameters.offset}}t.default=a},7295:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default={CRAM_FLAG_PRESERVE_QUAL_SCORES:1,CRAM_FLAG_DETACHED:2,CRAM_FLAG_MATE_DOWNSTREAM:4,CRAM_FLAG_NO_SEQ:8,CRAM_FLAG_MASK:15,CRAM_M_REVERSE:1,CRAM_M_UNMAP:2,BAM_FPAIRED:1,BAM_FPROPER_PAIR:2,BAM_FUNMAP:4,BAM_FMUNMAP:8,BAM_FREVERSE:16,BAM_FMREVERSE:32,BAM_FREAD1:64,BAM_FREAD2:128,BAM_FSECONDARY:256,BAM_FQCFAIL:512,BAM_FDUP:1024,BAM_FSUPPLEMENTARY:2048,BAM_CMATCH:0,BAM_CINS:1,BAM_CDEL:2,BAM_CREF_SKIP:3,BAM_CSOFT_CLIP:4,BAM_CHARD_CLIP:5,BAM_CPAD:6,BAM_CEQUAL:7,BAM_CDIFF:8,BAM_CBACK:9,BAM_CIGAR_STR:\"MIDNSHP:XB\",BAM_CIGAR_SHIFT:4,BAM_CIGAR_MASK:15,BAM_CIGAR_TYPE:246183}},7219:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0});const 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t[0][e[0]>>6&3]=\"C\",t[0][e[0]>>4&3]=\"G\",t[0][e[0]>>2&3]=\"T\",t[0][3&e[0]]=\"N\",t[1][e[1]>>6&3]=\"A\",t[1][e[1]>>4&3]=\"G\",t[1][e[1]>>2&3]=\"T\",t[1][3&e[1]]=\"N\",t[2][e[2]>>6&3]=\"A\",t[2][e[2]>>4&3]=\"C\",t[2][e[2]>>2&3]=\"T\",t[2][3&e[2]]=\"N\",t[3][e[3]>>6&3]=\"A\",t[3][e[3]>>4&3]=\"C\",t[3][e[3]>>2&3]=\"G\",t[3][3&e[3]]=\"N\",t[4][e[4]>>6&3]=\"A\",t[4][e[4]>>4&3]=\"C\",t[4][e[4]>>2&3]=\"G\",t[4][3&e[4]]=\"T\",t}(e.preservation.SM),this.dataSeriesEncoding=e.dataSeriesEncoding,this.tagEncoding=e.tagEncoding}getCodecForTag(e){const t=this.tagCodecCache[e];if(t)return t;{const t=this.tagEncoding[e];if(!t)throw new Error(\"Error, no tag encoding\");const i=(0,n.instantiateCodec)(t,\"byteArray\");return this.tagCodecCache[e]=i,i}}getTagNames(e){return this.tagIdsDictionary[e]}getCodecForDataSeries(e){let t=this.dataSeriesCodecCache[e];if(void 0===t){const i=this.dataSeriesEncoding[e];if(i){const o=s[e];if(!o)throw new r.CramMalformedError(`data series name ${e} not defined in 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0:e.numRecords))return null;const{majorVersion:t}=yield this.file.getDefinition(),i=(0,h.getSectionParsers)(t),n=yield this.getFirstBlock();if(void 0===n)return;if(\"COMPRESSION_HEADER\"!==n.contentType)throw new o.CramMalformedError(`invalid content type ${n.contentType} in compression header block`);const r=(0,a.parseItem)(n.content,i.cramCompressionHeader.parser,0,n.contentPosition);return Object.assign(Object.assign({},n),{parsedContent:r})}))}getFirstBlock(){return n(this,void 0,void 0,(function*(){const e=yield this.getHeader();if(e)return this.file.readBlock(e._endPosition)}))}getCompressionScheme(){return n(this,void 0,void 0,(function*(){const e=yield this.getCompressionHeaderBlock();if(e)return new l.default(e.parsedContent)}))}getSlice(e,t){return new c.default(this,e,t)}_readContainerHeader(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield 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\").forEach((e=>{(0,a.tinyMemoize)(d,e)}))},6794:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(8287),o=r(i(928)),a=r(i(7392)),c=r(i(6960)),l=r(i(235)),h=i(1307),d=i(9747),u=i(8712),f=r(i(9989)),p=i(3165),g=r(i(78)),m=i(5931),w=i(400),b=i(5417);class F{constructor(e){var t;if(this.file=(0,m.open)(e.url,e.path,e.filehandle),this.validateChecksums=!0,this.fetchReferenceSequenceCallback=e.seqFetch,this.options={checkSequenceMD5:e.checkSequenceMD5,cacheSize:null!==(t=e.cacheSize)&&void 0!==t?t:2e4},this.featureCache=new a.default({maxSize:this.options.cacheSize}),function(){const e=new Uint32Array([287454020]),t=new Uint8Array(e.buffer);return 68===t[0]?0:17===t[0]?1:2}()>0)throw new Error(\"Detected big-endian machine, may be unable to run\")}read(e,t,i,n){return this.file.read(e,t,i,n)}stat(){return this.file.stat()}getDefinition(){return n(this,void 0,void 0,(function*(){const{maxLength:e,parser:t}=(0,p.cramFileDefinition)(),i=s.Buffer.allocUnsafe(e);yield this.file.read(i,0,e,0);const n=t(i).value;if(2!==n.majorVersion&&3!==n.majorVersion)throw new d.CramUnimplementedError(`CRAM version ${n.majorVersion} not supported`);return n}))}getSamHeader(){return n(this,void 0,void 0,(function*(){const e=yield this.getContainerById(0);if(!e)throw new d.CramMalformedError(\"file contains no containers\");const t=yield e.getFirstBlock();if(void 0===t)return(0,b.parseHeaderText)(\"\");const i=t.content,n=i.readInt32LE(0),r=i.toString(\"utf8\",4,4+n);return this.header=r,(0,b.parseHeaderText)(r)}))}getHeaderText(){return n(this,void 0,void 0,(function*(){return yield this.getSamHeader(),this.header}))}getContainerById(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t);let n=i.cramFileDefinition.maxLength;const{size:r}=yield this.file.stat(),{cramContainerHeader1:s}=i;let o;for(let t=0;t<=e;t++){if(n+s.maxLength+8>=r)return;o=this.getContainerAtPosition(n);const i=yield o.getHeader();if(!i)throw new d.CramMalformedError(`container ${e} not found in file`);if(0===t){n=i._endPosition;for(let e=0;e<i.numBlocks;e++){const e=yield this.readBlock(n);if(void 0===e)return;n=e._endPosition}}else n+=i._size+i.length}return o}))}checkCrc32(e,t,i,r){return n(this,void 0,void 0,(function*(){const n=s.Buffer.allocUnsafe(t);yield this.file.read(n,0,t,e);const a=o.default.unsigned(n);if(a!==i)throw new d.CramMalformedError(`crc mismatch in ${r}: recorded CRC32 = ${i}, but calculated CRC32 = ${a}`)}))}containerCount(){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.getDefinition(),t=(0,p.getSectionParsers)(e),{size:i}=yield this.file.stat(),{cramContainerHeader1:n}=t;let r=0,s=t.cramFileDefinition.maxLength;for(;s+n.maxLength+8<i;){const e=yield this.getContainerAtPosition(s).getHeader();if(!e)break;if(0===r){s=e._endPosition;for(let t=0;t<e.numBlocks;t++){const e=yield this.readBlock(s);if(void 0===e)return;s=e._endPosition}}else s+=e._size+e.length;r+=1}return r}))}getContainerAtPosition(e){return new g.default(this,e)}readBlockHeader(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t),{cramBlockHeader:n}=i,{size:r}=yield this.file.stat();if(e+n.maxLength>=r)return;const o=s.Buffer.allocUnsafe(n.maxLength);return yield this.file.read(o,0,n.maxLength,e),(0,w.parseItem)(o,n.parser,0,e)}))}_parseSection(e,t){return n(this,arguments,void 0,(function*(e,t,i=e.maxLength,n){let r;if(n)r=n;else{const{size:e}=yield this.file.stat();if(t+i>=e)return;r=s.Buffer.allocUnsafe(i),yield this.file.read(r,0,i,t)}const o=(0,w.parseItem)(r,e.parser,0,t);if(o._size!==i)throw new d.CramMalformedError(`section read error: requested size ${i} does not equal parsed size ${o._size}`);return o}))}_uncompress(e,t,i){return n(this,void 0,void 0,(function*(){if(\"gzip\"===e)(0,u.unzip)(t).copy(i);else if(\"bzip2\"===e){const e=l.default.array(t);let n,r=l.default.header(e),o=0;do{n=l.default.decompress(e,r),-1!==n&&(s.Buffer.from(n).copy(i,o),o+=n.length,r-=n.length)}while(-1!==n)}else if(\"lzma\"===e){const e=new Response(new h.XzReadableStream((n=t,new ReadableStream({start(e){e.enqueue(n),e.close()}}))));s.Buffer.from(yield e.arrayBuffer()).copy(i)}else if(\"rans\"===e)(0,f.default)(t,i);else if(\"rans4x16\"===e)c.default.r4x16_uncompress(t,i);else if(\"arith\"===e)c.default.arith_uncompress(t,i);else if(\"fqzcomp\"===e)c.default.fqzcomp_uncompress(t,i);else{if(\"tok3\"!==e)throw new d.CramUnimplementedError(`${e} decompression not yet implemented`);c.default.tok3_uncompress(t,i)}var n}))}readBlock(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t),n=yield this.readBlockHeader(e);if(void 0===n)return;const r=n._endPosition,o=s.Buffer.allocUnsafe(n.uncompressedSize),a=Object.assign(Object.assign({},n),{_endPosition:r,contentPosition:r,content:o});if(\"raw\"!==n.compressionMethod){const e=s.Buffer.allocUnsafe(n.compressedSize);yield this.read(e,0,n.compressedSize,r),yield this._uncompress(n.compressionMethod,e,o)}else yield this.read(o,0,n.uncompressedSize,r);if(t>=3){const t=yield this._parseSection(i.cramBlockCrc32,r+n.compressedSize);if(void 0===t)return;a.crc32=t.crc32,this.validateChecksums&&(yield this.checkCrc32(e,n._size+n.compressedSize,t.crc32,\"block data\")),a._endPosition=t._endPosition,a._size=a.compressedSize+i.cramBlockCrc32.maxLength}else a._endPosition=r+a.compressedSize,a._size=a.compressedSize;return a}))}}t.default=F,\"getDefinition getSectionParsers getSamHeader\".split(\" \").forEach((e=>{(0,w.tinyMemoize)(F,e)}))},7390:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=t.CramRecord=void 0;var r=i(8401);Object.defineProperty(t,\"CramRecord\",{enumerable:!0,get:function(){return n(r).default}});var s=i(6794);Object.defineProperty(t,\"default\",{enumerable:!0,get:function(){return n(s).default}})},8401:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.MateFlagsDecoder=t.CramFlagsDecoder=t.BamFlagsDecoder=t.MateFlags=t.CramFlags=t.BamFlags=void 0;const r=n(i(7295)),s={a:0,A:0,c:1,C:1,g:2,G:2,t:3,T:3,n:4,N:4};function o(e){const t={};for(const[i,n]of e)t[`is${n}`]=e=>!!(e&i),t[`set${n}`]=e=>e|i;return t}t.BamFlags=[[1,\"Paired\"],[2,\"ProperlyPaired\"],[4,\"SegmentUnmapped\"],[8,\"MateUnmapped\"],[16,\"ReverseComplemented\"],[32,\"MateReverseComplemented\"],[64,\"Read1\"],[128,\"Read2\"],[256,\"Secondary\"],[512,\"FailedQc\"],[1024,\"Duplicate\"],[2048,\"Supplementary\"]],t.CramFlags=[[1,\"PreservingQualityScores\"],[2,\"Detached\"],[4,\"WithMateDownstream\"],[8,\"DecodeSequenceAsStar\"]],t.MateFlags=[[1,\"OnNegativeStrand\"],[2,\"Unmapped\"]],t.BamFlagsDecoder=o(t.BamFlags),t.CramFlagsDecoder=o(t.CramFlags),t.MateFlagsDecoder=o(t.MateFlags),t.default=class{constructor({flags:e,cramFlags:t,readLength:i,mappingQuality:n,lengthOnRef:r,qualityScores:s,mateRecordNumber:o,readBases:a,readFeatures:c,mateToUse:l,readGroupId:h,readName:d,sequenceId:u,uniqueId:f,templateSize:p,alignmentStart:g,tags:m}){this.flags=e,this.cramFlags=t,this.readLength=i,this.mappingQuality=n,this.lengthOnRef=r,this.qualityScores=s,a&&(this.readBases=a),this.readGroupId=h,this.readName=d,this.sequenceId=u,this.uniqueId=f,this.templateSize=p,this.alignmentStart=g,this.tags=m,c&&(this.readFeatures=c),l&&(this.mate={flags:l.mateFlags,readName:l.mateReadName,sequenceId:l.mateSequenceId,alignmentStart:l.mateAlignmentStart}),o&&(this.mateRecordNumber=o)}isPaired(){return!!(this.flags&r.default.BAM_FPAIRED)}isProperlyPaired(){return!!(this.flags&r.default.BAM_FPROPER_PAIR)}isSegmentUnmapped(){return!!(this.flags&r.default.BAM_FUNMAP)}isMateUnmapped(){return!!(this.flags&r.default.BAM_FMUNMAP)}isReverseComplemented(){return!!(this.flags&r.default.BAM_FREVERSE)}isMateReverseComplemented(){return!!(this.flags&r.default.BAM_FMREVERSE)}isRead1(){return!!(this.flags&r.default.BAM_FREAD1)}isRead2(){return!!(this.flags&r.default.BAM_FREAD2)}isSecondary(){return!!(this.flags&r.default.BAM_FSECONDARY)}isFailedQc(){return!!(this.flags&r.default.BAM_FQCFAIL)}isDuplicate(){return!!(this.flags&r.default.BAM_FDUP)}isSupplementary(){return!!(this.flags&r.default.BAM_FSUPPLEMENTARY)}isDetached(){return!!(this.cramFlags&r.default.CRAM_FLAG_DETACHED)}hasMateDownStream(){return!!(this.cramFlags&r.default.CRAM_FLAG_MATE_DOWNSTREAM)}isPreservingQualityScores(){return!!(this.cramFlags&r.default.CRAM_FLAG_PRESERVE_QUAL_SCORES)}isUnknownBases(){return!!(this.cramFlags&r.default.CRAM_FLAG_NO_SEQ)}getReadBases(){if(!this.readBases&&this._refRegion){const e=function(e,t){if(!e.lengthOnRef&&!e.readLength)return null;if(e.isUnknownBases())return null;const i=e.alignmentStart-t.start;if(!e.readFeatures)return t.seq.slice(i,i+(e.lengthOnRef||0)).toUpperCase();let n=\"\",r=i,s=0;for(;n.length<e.readLength;)if(s<e.readFeatures.length){const i=e.readFeatures[s];if(\"Q\"===i.code||\"q\"===i.code)s+=1;else if(i.pos===n.length+1)if(s+=1,\"b\"===i.code){const e=i.data;n+=e,r+=e.length}else\"B\"===i.code?(n+=i.data[0],r+=1):\"X\"===i.code?(n+=i.sub,r+=1):\"I\"===i.code?n+=i.data:\"D\"===i.code?r+=i.data:\"i\"===i.code?n+=i.data:\"N\"===i.code?r+=i.data:\"S\"===i.code?n+=i.data:\"P\"===i.code||i.code;else if(s<e.readFeatures.length){const e=t.seq.slice(r,r+i.pos-n.length-1);n+=e,r+=e.length}}else{const i=t.seq.slice(r,r+e.readLength-n.length);n+=i,r+=i.length}return n.toUpperCase()}(this,this._refRegion);e&&(this.readBases=e)}return this.readBases}getPairOrientation(){if(!this.isSegmentUnmapped()&&this.isPaired()&&!this.isMateUnmapped()&&this.mate&&this.sequenceId===this.mate.sequenceId){const e=this.isReverseComplemented()?\"R\":\"F\",t=this.isMateReverseComplemented()?\"R\":\"F\";let i=\" \",n=\" \";this.isRead1()?(i=\"1\",n=\"2\"):this.isRead2()&&(i=\"2\",n=\"1\");const r=[];let s=this.templateLength||this.templateSize;if(void 0===s)throw new Error(\"One of templateSize and templateLength must be set\");return this.alignmentStart>this.mate.alignmentStart&&s>0&&(s=-s),s>0?(r[0]=e,r[1]=i,r[2]=t,r[3]=n):(r[2]=e,r[3]=i,r[0]=t,r[1]=n),r.join(\"\")}return null}addReferenceSequence(e,t){this.readFeatures&&this.readFeatures.forEach((i=>{\"X\"===i.code&&function(e,t,i,n){const r=n.refPos-t.start,o=t.seq.charAt(r);o&&(n.ref=o);let a=s[o];void 0===a&&(a=4);const c=i.substitutionMatrix[a][n.data];c&&(n.sub=c)}(0,e,t,i)})),!this.readBases&&e.start<=this.alignmentStart&&e.end>=this.alignmentStart+(this.lengthOnRef||this.readLength)-1&&(this._refRegion=e)}toJSON(){const e={};return Object.keys(this).forEach((t=>{t.startsWith(\"_\")||(e[t]=this[t])})),e.readBases=this.getReadBases(),e}}},3165:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.cramFileDefinition=r,t.cramBlockHeader=s,t.cramBlockCrc32=o,t.cramTagDictionary=c,t.cramPreservationMap=l,t.isMappedSliceHeader=function(e){return\"number\"==typeof e.refSeqId},t.getSectionParsers=function(e){return{cramFileDefinition:r(),cramBlockHeader:s(),cramBlockCrc32:o(),cramDataSeriesEncodingMap:p(),cramTagEncodingMap:g(),cramCompressionHeader:{parser:(e,t)=>{const{value:i,offset:n}=l().parser(e,t);t=n;const{value:r,offset:s}=p().parser(e,t);t=s;const{value:o,offset:a}=g().parser(e,t);return t=a,{value:{dataSeriesEncoding:h(r),preservation:h(i),tagEncoding:h(o)},offset:t}}},cramEncoding:{parser:(e,t)=>f(e,t)},cramUnmappedSliceHeader:d(e),cramMappedSliceHeader:u(e),cramContainerHeader1:m(e),cramContainerHeader2:w(e)}};const n=i(400);function r(){return{parser:(e,t=0)=>{const i=e,n=new DataView(i.buffer,i.byteOffset,i.length);let r=0;const s=e.subarray(r,r+4).toString();r+=4;const o=n.getUint8(r);r+=1;const a=n.getUint8(r);r+=1;const c=i.subarray(r,r+20).toString().replaceAll(\"\\0\",\"\");return r+=20,{value:{magic:s,majorVersion:o,minorVersion:a,fileId:c},offset:r}},maxLength:26}}function s(){return{parser:(e,t=0)=>{const i=e,r=new DataView(i.buffer,i.byteOffset,i.length);let s=0;const o=r.getUint8(s),a=[\"raw\",\"gzip\",\"bzip2\",\"lzma\",\"rans\",\"rans4x16\",\"arith\",\"fqzcomp\",\"tok3\"][o];if(!a)throw new Error(`compression method number ${o} not implemented`);s+=1;const c=r.getUint8(s),l=[\"FILE_HEADER\",\"COMPRESSION_HEADER\",\"MAPPED_SLICE_HEADER\",\"UNMAPPED_SLICE_HEADER\",\"EXTERNAL_DATA\",\"CORE_DATA\"][c];if(!l)throw new Error(`invalid block content type id ${c}`);s+=1;const[h,d]=(0,n.parseItf8)(e,s);s+=d;const[u,f]=(0,n.parseItf8)(e,s);s+=f;const[p,g]=(0,n.parseItf8)(e,s);return s+=g,{offset:s,value:{uncompressedSize:p,compressedSize:u,contentId:h,contentType:l,compressionMethod:a}}},maxLength:17}}function o(){return{parser:(e,t)=>{const i=e,n=new DataView(i.buffer,i.byteOffset,i.length).getUint32(t,!0);return{offset:t+=4,value:{crc32:n}}},maxLength:4}}function a(e,t,i){const n=e.toString(\"utf8\",t,i),r=[];for(let e=0;e<n.length;e+=3)r.push(n.slice(e,e+3));return r}function c(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const s=e.subarray(t,t+i);t+=i;const o=[];let c=0,l=0;for(;l<s.length;l++)s[l]||(o.push(a(s,c,l)),c=l+1);return l>c&&o.push(a(s,c,l)),{value:{size:i,ents:o},offset:t}}}}function l(){return{parser:(e,t)=>{const i=e,r=new DataView(i.buffer,i.byteOffset,i.length),[s,o]=(0,n.parseItf8)(e,t);t+=o;const[a,l]=(0,n.parseItf8)(e,t);t+=l;const h=[];for(let i=0;i<a;i++){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);if(t+=2,\"MI\"===i||\"UI\"===i||\"PI\"===i||\"RN\"===i||\"AP\"===i||\"RR\"===i)h.push({key:i,value:!!r.getUint8(t)}),t+=1;else if(\"SM\"===i)h.push({key:i,value:[r.getUint8(t),r.getUint8(t+1),r.getUint8(t+2),r.getUint8(t+3),r.getUint8(t+4)]}),t+=5;else{if(\"TD\"!==i)throw new Error(`unknown key ${i}`);{const{offset:n,value:r}=c().parser(e,t);h.push({key:i,value:r.ents}),t=n}}}return{value:{mapSize:s,mapCount:a,ents:h},offset:t}}}}function h(e){const t={};for(const{key:i,value:n}of e.ents)t[i]&&console.warn(`duplicate key ${i} in map`),t[i]=n;return t}function d(e){return{parser:(t,i)=>{const[r,s]=(0,n.parseItf8)(t,i);i+=s;let o=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);i+=r,o=e}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);i+=r,o=e}else console.warn(\"recordCounter=0\");const[a,c]=(0,n.parseItf8)(t,i);i+=c;const[l,h]=(0,n.parseItf8)(t,i);i+=h;const d=[];for(let e=0;e<l;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,d.push(e)}let u;return e>=2&&(u=[...t.subarray(i,i+16)],i+=16),{value:{recordCounter:o,md5:u,contentIds:d,numContentIds:l,numBlocks:a,numRecords:r},offset:i}},maxLength:e=>40+5*e}}function u(e){return{parser:(t,i)=>{const[r,s]=(0,n.parseItf8)(t,i);i+=s;const[o,a]=(0,n.parseItf8)(t,i);i+=a;const[c,l]=(0,n.parseItf8)(t,i);i+=l;const[h,d]=(0,n.parseItf8)(t,i);i+=d;let u=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);i+=r,u=e}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);i+=r,u=e}else console.warn(\"majorVersion is <2, recordCounter set to 0\");const[f,p]=(0,n.parseItf8)(t,i);i+=p;const[g,m]=(0,n.parseItf8)(t,i);i+=m;const w=[];for(let e=0;e<g;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,w.push(e)}const[b,F]=(0,n.parseItf8)(t,i);let v;return i+=F,e>=2&&(v=[...t.subarray(i,i+16)],i+=16),{value:{md5:v,numBlocks:f,numRecords:h,numContentIds:g,refSeqSpan:c,refSeqId:r,refSeqStart:o,recordCounter:u,refBaseBlockId:b,contentIds:w},offset:i}},maxLength:e=>60+5*e}}function f(e,t){const i=e,r=new DataView(i.buffer,i.byteOffset,i.length),[s,o]=(0,n.parseItf8)(e,t);t+=o;const[a,c]=(0,n.parseItf8)(e,t);t+=c;const l={};if(0===s);else if(1===s){const[i,r]=(0,n.parseItf8)(e,t);l.blockContentId=i,t+=r}else if(2===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.M=s,t+=o}else if(3===s){const i=(0,n.parseItf8)(e,t),r=i[0];t+=i[1];const s=[];for(let i=0;i<r;i++){const i=(0,n.parseItf8)(e,t);s.push(i[0]),t+=i[1]}l.symbols=s;const o=(0,n.parseItf8)(e,t),a=i[0];l.numLengths=a,l.numCodes=r,l.numLengths=a,t+=o[1];const c=[];for(let i=0;i<a;i++){const i=(0,n.parseItf8)(e,t);t+=i[1],c.push(i[0])}l.bitLengths=c}else if(4===s){const{value:i,offset:n}=f(e,t);l.lengthsEncoding=i,t=n;const{value:r,offset:s}=f(e,t);l.valuesEncoding=r,t=s}else if(5===s){l.stopByte=r.getUint8(t),t+=1;const[i,s]=(0,n.parseItf8)(e,t);l.blockContentId=i,t+=s}else if(6===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.length=s,t+=o}else if(7===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.K=s,t+=o}else if(8===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.log2m=s,t+=o}else{if(9!==s)throw new Error(`unknown codecId ${s}`);{const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r}}return{value:{codecId:s,parametersBytes:a,parameters:l},offset:t}}function p(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const[s,o]=(0,n.parseItf8)(e,t);t+=o;const a=[];for(let i=0;i<s;i++){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const{value:n,offset:r}=f(e,t);t=r,a.push({key:i,value:n})}return{value:{mapSize:i,ents:a,mapCount:s},offset:t}}}}function g(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const[s,o]=(0,n.parseItf8)(e,t);t+=o;const a=[];for(let i=0;i<s;i++){const[i,r]=(0,n.parseItf8)(e,t);t+=r;const s=String.fromCharCode(i>>16&255)+String.fromCharCode(i>>8&255)+String.fromCharCode(255&i),{value:o,offset:c}=f(e,t);t=c,a.push({key:s,value:o})}return{value:{mapSize:i,ents:a,mapCount:s},offset:t}}}}function m(e){return{maxLength:52,parser:(t,i)=>{const r=t,s=new DataView(r.buffer,r.byteOffset,r.length).getInt32(i,!0);i+=4;const[o,a]=(0,n.parseItf8)(t,i);i+=a;const[c,l]=(0,n.parseItf8)(t,i);i+=l;const[h,d]=(0,n.parseItf8)(t,i);i+=d;const[u,f]=(0,n.parseItf8)(t,i);i+=f;let p,g=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);g=e,i+=r}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);g=e,i+=r}else console.warn(\"setting recordCounter=0\");if(e>1){const[e,r]=(0,n.parseLtf8)(t,i);p=e,i+=r}const[m,w]=(0,n.parseItf8)(t,i);i+=w;const[b,F]=(0,n.parseItf8)(t,i);return{value:{length:s,refSeqId:o,refSeqStart:c,alignmentSpan:h,numBlocks:m,numLandmarks:b,numBases:p,recordCounter:g,numRecords:u},offset:i+=F}}}}function w(e){return{parser:(t,i)=>{const r=t,s=new DataView(r.buffer,r.byteOffset,r.length),[o,a]=(0,n.parseItf8)(t,i);i+=a;const c=[];for(let e=0;e<o;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,c.push(e)}let l;return e>=3&&(l=s.getUint32(i,!0),i+=4),{value:Object.assign(Object.assign({},void 0===l?{}:{crc32:l}),{numLandmarks:o,landmarks:c}),offset:i}},maxLength:e=>5+5*e+4}}},6484:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,c,l,h,d,u,f){let p=t(\"BF\");const g=t(\"CF\");if(!(0,s.isMappedSliceHeader)(c.parsedContent))throw new Error(\"slice header not mapped\");const m=u>1&&-2===c.parsedContent.refSeqId?t(\"RI\"):c.parsedContent.refSeqId,w=t(\"RL\");let b=t(\"AP\");i.APdelta&&(b+=d.lastAlignmentStart),d.lastAlignmentStart=b;const F=t(\"RG\");let v,y,A,C;if(i.readNamesIncluded&&(v=o(t(\"RN\"))),r.CramFlagsDecoder.isDetached(g)){const e=t(\"MF\");let n;i.readNamesIncluded||(n=o(t(\"RN\")),v=n);const s=t(\"NS\"),a=t(\"NP\");(e||s>-1)&&(y={mateFlags:e,mateSequenceId:s,mateAlignmentStart:a,mateReadName:n}),A=t(\"TS\"),r.MateFlagsDecoder.isUnmapped(e)&&(p=r.BamFlagsDecoder.setMateUnmapped(p)),r.MateFlagsDecoder.isOnNegativeStrand(e)&&(p=r.BamFlagsDecoder.setMateReverseComplemented(p))}else r.CramFlagsDecoder.isWithMateDownstream(g)&&(C=t(\"NF\")+f+1);const _=t(\"TL\");if(_<0)throw new n.CramMalformedError(\"invalid TL index\");const x={},k=i.getTagNames(_),I=k.length;for(let t=0;t<I;t+=1){const n=k[t],r=n.slice(0,2),s=n.slice(2,3),o=i.getCodecForTag(n).decode(e,l,h,d);x[r]=\"number\"==typeof o?o:a(s,o)}let S,E,N,B,M;if(r.BamFlagsDecoder.isSegmentUnmapped(p))if(r.CramFlagsDecoder.isDecodeSequenceAsStar(g))M=null,B=null;else{const e=new Array(w);for(let i=0;i<e.length;i+=1)e[i]=t(\"BA\");if(M=String.fromCharCode(...e),r.CramFlagsDecoder.isPreservingQualityScores(g)){B=new Array(w);for(let i=0;i<e.length;i+=1)B[i]=t(\"QS\")}}else{const e=t(\"FN\");if(e&&(S=function(e,t,i,r,s){let o=0,a=e-1;const c=new Array(t);function l([e,t]){const n=i(t);if(\"character\"===e)return String.fromCharCode(n);if(\"string\"===e){let e=\"\";for(let t=0;t<n.byteLength;t++)e+=String.fromCharCode(n[t]);return e}return\"numArray\"===e?n.toArray():n}for(let e=0;e<t;e+=1){const t=String.fromCharCode(i(\"FC\")),r=i(\"FP\"),h={B:[\"character\",\"BA\"],S:[\"string\",s>1?\"SC\":\"IN\"],X:[\"number\",\"BS\"],D:[\"number\",\"DL\"],I:[\"string\",\"IN\"],i:[\"character\",\"BA\"],b:[\"string\",\"BB\"],q:[\"numArray\",\"QQ\"],Q:[\"number\",\"QS\"],H:[\"number\",\"HC\"],P:[\"number\",\"PD\"],N:[\"number\",\"RS\"]}[t];if(!h)throw new n.CramMalformedError(`invalid read feature code \"${t}\"`);let d=l(h);const u={B:[\"number\",\"QS\"]}[t];u&&(d=[d,l(u)]),o+=r;const f=o;a+=r;const p=a;\"D\"===t||\"N\"===t?a+=d:\"I\"===t||\"S\"===t?a-=d.length:\"i\"===t&&(a-=1),c[e]={code:t,pos:f,refPos:p,data:d}}return c}(b,e,t,0,u)),E=w,S)for(const{code:e,data:t}of S)\"D\"===e||\"N\"===e?E+=t:\"I\"===e||\"S\"===e?E-=t.length:\"i\"===e&&(E-=1);if(Number.isNaN(E)&&(console.warn(`${v||`${m}:${b}`} record has invalid read features`),E=w),N=t(\"MQ\"),r.CramFlagsDecoder.isPreservingQualityScores(g)){B=new Array(w);for(let e=0;e<B.length;e++)B[e]=t(\"QS\")}}return{readLength:w,sequenceId:m,cramFlags:g,flags:p,alignmentStart:b,readGroupId:F,readName:v,mateToUse:y,templateSize:A,mateRecordNumber:C,readFeatures:S,lengthOnRef:E,mappingQuality:N,qualityScores:B,readBases:M,tags:x}};const n=i(9747),r=i(8401),s=i(3165);function o(e){let t=\"\";for(let i=0;i<e.length&&0!==e[i];i++)t+=String.fromCharCode(e[i]);return t}function a(e,t){if(\"Z\"===e)return o(t);if(\"A\"===e)return String.fromCharCode(t[0]);if(\"I\"===e)return new Uint32Array(t.buffer)[0];if(\"i\"===e)return new Int32Array(t.buffer)[0];if(\"s\"===e)return new Int16Array(t.buffer)[0];if(\"S\"===e)return new Uint16Array(t.buffer)[0];if(\"c\"===e)return new Int8Array(t.buffer)[0];if(\"C\"===e)return t[0];if(\"f\"===e)return new Float32Array(t.buffer)[0];if(\"H\"===e)return Number.parseInt(o(t).replace(/^0x/,\"\"),16);if(\"B\"===e)return function(e){const t=String.fromCharCode(e[0]),i=new DataView(e.buffer).getUint32(1,!0),n=new Array(i);if(e=e.slice(5),\"c\"===t){const t=new Int8Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"C\"===t){const t=new Uint8Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"s\"===t){const t=new Int16Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"S\"===t){const t=new Uint16Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"i\"===t){const t=new Int32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"I\"===t){const t=new Uint32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else{if(\"f\"!==t)throw new Error(`unknown type: ${t}`);{const t=new Float32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}}return n}(t);throw new n.CramMalformedError(`Unrecognized tag type ${e}`)}},6771:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(9747),o=i(400),a=r(i(7295)),c=r(i(6484)),l=r(i(8401)),h=i(3165),d=i(612);function u(e,t,i,n){const r=!!(n.mate||void 0!==n.mateRecordNumber&&n.mateRecordNumber!==t);i.readName||(i.readName=String(i.uniqueId),n.readName=i.readName),i.mate={sequenceId:n.sequenceId,alignmentStart:n.alignmentStart,uniqueId:n.uniqueId},n.readName&&(i.mate.readName=n.readName),n.mate||void 0!==n.mateRecordNumber||(n.mate={sequenceId:i.sequenceId,alignmentStart:i.alignmentStart,uniqueId:i.uniqueId},i.readName&&(n.mate.readName=i.readName)),i.flags|=a.default.BAM_FPAIRED,n.flags&a.default.BAM_FUNMAP&&(i.flags|=a.default.BAM_FMUNMAP),i.flags&a.default.BAM_FUNMAP&&(n.flags|=a.default.BAM_FMUNMAP),n.flags&a.default.BAM_FREVERSE&&(i.flags|=a.default.BAM_FMREVERSE),i.flags&a.default.BAM_FREVERSE&&(n.flags|=a.default.BAM_FMREVERSE),void 0===i.templateLength&&(r?function(e,t,i){const n=function t(i){const n=[i];if(void 0!==i.mateRecordNumber&&i.mateRecordNumber>=0){const r=e[i.mateRecordNumber];if(!r)throw new s.CramMalformedError(\"intra-slice mate record not found, this file seems malformed\");n.push(...t(r))}return n}(i),r=n.map((e=>e.alignmentStart)),o=n.map((e=>e.alignmentStart+e.readLength-1)),a=Math.max(...o)-Math.min(...r)+1;a>=0&&n.forEach((e=>{if(void 0!==e.templateLength)throw new s.CramMalformedError(\"mate pair group has some members that have template lengths already, this file seems malformed\");e.templateLength=a}))}(e,0,i):function(e,t){const i=Math.min(e.alignmentStart,t.alignmentStart),n=Math.max(e.alignmentStart+e.readLength-1,t.alignmentStart+t.readLength-1)-i+1;e.templateLength=n,t.templateLength=n}(i,n)),i.mateRecordNumber=void 0}class f{constructor(e,t,i){this.container=e,this.containerPosition=t,this.sliceSize=i,this.file=e.file}getHeader(){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.file.getDefinition(),t=(0,h.getSectionParsers)(e),i=yield this.container.getHeader();if(!i)throw new Error(\"no container header detected\");const n=yield this.file.readBlock(i._endPosition+this.containerPosition);if(void 0===n)throw new Error(\"block header undefined\");if(\"MAPPED_SLICE_HEADER\"===n.contentType){const e=(0,o.parseItem)(n.content,t.cramMappedSliceHeader.parser,0,i._endPosition);return Object.assign(Object.assign({},n),{parsedContent:e})}if(\"UNMAPPED_SLICE_HEADER\"===n.contentType){const e=(0,o.parseItem)(n.content,t.cramUnmappedSliceHeader.parser,0,i._endPosition);return Object.assign(Object.assign({},n),{parsedContent:e})}throw new s.CramMalformedError(`error reading slice header block, invalid content type ${n.contentType}`)}))}getBlocks(){return n(this,void 0,void 0,(function*(){const e=yield this.getHeader();let t=e._endPosition;const i=new Array(e.parsedContent.numBlocks);for(let e=0;e<i.length;e++){const n=yield this.file.readBlock(t);if(void 0===n)throw new Error(\"block undefined\");i[e]=n,t=i[e]._endPosition}return i}))}getCoreDataBlock(){return n(this,void 0,void 0,(function*(){return(yield this.getBlocks())[0]}))}_getBlocksContentIdIndex(){return n(this,void 0,void 0,(function*(){const e=yield this.getBlocks(),t={};return e.forEach((e=>{\"EXTERNAL_DATA\"===e.contentType&&(t[e.contentId]=e)})),t}))}getBlockByContentId(e){return n(this,void 0,void 0,(function*(){return(yield this._getBlocksContentIdIndex())[e]}))}getReferenceRegion(){return n(this,void 0,void 0,(function*(){const e=(yield this.getHeader()).parsedContent;if(!(0,h.isMappedSliceHeader)(e))throw new Error(\"slice header not mapped\");if(e.refSeqId<0)return;const t=yield this.container.getCompressionScheme();if(void 0===t)throw new Error(\"compression scheme undefined\");if(e.refBaseBlockId>=0){const t=yield this.getBlockByContentId(e.refBaseBlockId);if(!t)throw new s.CramMalformedError(\"embedded reference specified, but reference block does not exist\");return{seq:t.data.toString(\"utf8\"),start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan}}if(t.referenceRequired||this.file.fetchReferenceSequenceCallback){if(!this.file.fetchReferenceSequenceCallback)throw new Error(\"reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence\");const t=yield this.file.fetchReferenceSequenceCallback(e.refSeqId,e.refSeqStart,e.refSeqStart+e.refSeqSpan-1);if(t.length!==e.refSeqSpan)throw new s.CramArgumentError(\"seqFetch callback returned a reference sequence of the wrong length\");return{seq:t,start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan}}}))}getAllRecords(){return this.getRecords((()=>!0))}_fetchRecords(){return n(this,void 0,void 0,(function*(){var e,t;const{majorVersion:i}=yield this.file.getDefinition(),n=yield this.container.getCompressionScheme();if(void 0===n)throw new Error(\"compression scheme undefined\");const r=yield this.getHeader(),a=yield this._getBlocksContentIdIndex();if(i>1&&this.file.options.checkSequenceMD5&&(0,h.isMappedSliceHeader)(r.parsedContent)&&r.parsedContent.refSeqId>=0&&\"0000000000000000\"!==(null===(e=r.parsedContent.md5)||void 0===e?void 0:e.join(\"\"))){const e=yield this.getReferenceRegion();if(e){const{seq:i,start:n,end:a}=e,c=(0,o.sequenceMD5)(i),l=null===(t=r.parsedContent.md5)||void 0===t?void 0:t.map((e=>(e<16?\"0\":\"\")+e.toString(16))).join(\"\");if(c!==l)throw new s.CramMalformedError(`MD5 checksum reference mismatch for ref ${r.parsedContent.refSeqId} pos ${n}..${a}. recorded MD5: ${l}, calculated MD5: ${c}`)}}const f=yield this.getCoreDataBlock(),p={lastAlignmentStart:(0,h.isMappedSliceHeader)(r.parsedContent)?r.parsedContent.refSeqStart:0,coreBlock:{bitPosition:7,bytePosition:0},externalBlocks:{map:new Map,getCursor(e){let t=this.map.get(e);return void 0===t&&(t={bitPosition:7,bytePosition:0},this.map.set(e,t)),t}}},g=e=>{const t=n.getCodecForDataSeries(e);if(!t)throw new s.CramMalformedError(`no codec defined for ${e} data series`);return t.decode(this,f,a,p)},m=new Array(r.parsedContent.numRecords);for(let t=0;t<m.length;t+=1)try{const e=(0,c.default)(this,g,n,r,f,a,p,i,t);m[t]=new l.default(Object.assign(Object.assign({},e),{uniqueId:r.contentPosition+r.parsedContent.recordCounter+t+1}))}catch(e){if(e instanceof d.CramBufferOverrunError){console.warn(\"read attempted beyond end of buffer, file seems truncated.\");break}throw e}for(let e=0;e<m.length;e+=1){const{mateRecordNumber:t}=m[e];void 0!==t&&t>=0&&u(m,e,m[e],m[t])}return m}))}getRecords(e){return n(this,void 0,void 0,(function*(){const t=this.container.filePosition+this.containerPosition;let i=this.file.featureCache.get(t.toString());i||(i=this._fetchRecords(),this.file.featureCache.set(t.toString(),i));const r=(yield i).filter(e);if(r.length&&this.file.fetchReferenceSequenceCallback){const e=yield this.getHeader();if((0,h.isMappedSliceHeader)(e.parsedContent)&&(e.parsedContent.refSeqId>=0||-2===e.parsedContent.refSeqId)){const t=e.parsedContent.refSeqId>=0?e.parsedContent.refSeqId:void 0,i=yield this.container.getCompressionScheme();if(void 0===i)throw new Error(\"compression scheme undefined\");const s={};for(const e of r){const i=void 0!==t?t:e.sequenceId;let n=s[i];n||(n={id:i,start:e.alignmentStart,end:Number.NEGATIVE_INFINITY,seq:null},s[i]=n);const r=e.alignmentStart+(e.lengthOnRef||e.readLength)-1;r>n.end&&(n.end=r),e.alignmentStart<n.start&&(n.start=e.alignmentStart)}yield Promise.all(Object.values(s).map((e=>n(this,void 0,void 0,(function*(){-1!==e.id&&e.start<=e.end&&this.file.fetchReferenceSequenceCallback&&(e.seq=yield this.file.fetchReferenceSequenceCallback(e.id,e.start,e.end))})))));for(const e of r){const n=s[void 0!==t?t:e.sequenceId];if(null==n?void 0:n.seq){const t=n.seq;e.addReferenceSequence(Object.assign(Object.assign({},n),{seq:t}),i)}}}}return r}))}}t.default=f,\"getHeader getBlocks _getBlocksContentIdIndex\".split(\" \").forEach((e=>{(0,o.tinyMemoize)(f,e)}))},400:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.itf8Size=function(e){return-128&e?-16384&e?-2097152&e?-268435456&e?5:4:3:2:1},t.parseItf8=function(e,t){let i=t;const n=e[i];let r;if(n<128?(r=n,i+=1):n<192?(r=16383&(n<<8|e[i+1]),i+=2):n<224?(r=2097151&(n<<16|e[i+1]<<8|e[i+2]),i+=3):n<240?(r=268435455&(n<<24|e[i+1]<<16|e[i+2]<<8|e[i+3]),i+=4):(r=(15&n)<<28|e[i+1]<<20|e[i+2]<<12|e[i+3]<<4|15&e[i+4],i+=5),i>e.length)throw new o.CramBufferOverrunError(\"Attempted to read beyond end of buffer; this file seems truncated.\");return[r,i-t]},t.parseLtf8=function(e,t){let i=t;const n=e[i];let r;if(n<128)r=n,i+=1;else if(n<192)r=16383&(e[i]<<8|e[i+1]),i+=2;else if(n<224)r=2097151&(e[i]<<16|e[i+1]<<8|e[i+2]),r=(63&n)<<16|e.readUInt16LE(i+1),i+=3;else if(n<240)r=268435455&(e[i]<<24|e[i+1]<<16|e[i+2]<<8|e[i+3]),i+=4;else if(n<248)r=(15&e[i])*Math.pow(2,32)+(e[i+1]<<24)|e[i+2]<<16|e[i+3]<<8|e[i+4],i+=5;else if(n<252)r=((7&e[i])<<8|e[i+1])*Math.pow(2,32)+(e[i+2]<<24)|e[i+3]<<16|e[i+4]<<8|e[i+5],i+=6;else if(n<254)r=((3&e[i])<<16|e[i+1]<<8|e[i+2])*Math.pow(2,32)+(e[i+3]<<24)|e[i+4]<<16|e[i+5]<<8|e[i+6],i+=7;else if(n<255){if(r=s.default.fromBytesBE(e.slice(i+1,i+8)),r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new Error(\"integer overflow\");r=r.toNumber(),i+=8}else{if(r=s.default.fromBytesBE(e.slice(i+1,i+9)),r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new Error(\"integer overflow\");r=r.toNumber(),i+=9}return[r,i-t]},t.parseItem=function(e,t,i=0,n=0){const{offset:r,value:s}=t(e,i);return Object.assign(Object.assign({},s),{_endPosition:r+n,_size:r-i})},t.tinyMemoize=function(e,t){const i=e.prototype[t],n=`_memo_${t}`;e.prototype[t]=function(){if(!(n in this)){const e=i.call(this);this[n]=e,Promise.resolve(e).catch((()=>{delete this[n]}))}return this[n]}},t.sequenceMD5=function(e){return(0,r.default)(e.toUpperCase().replaceAll(/[^\\u0021-\\u007e]/g,\"\"))};const r=n(i(3503)),s=n(i(8570)),o=i(612)},9747:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.CramArgumentError=t.CramSizeLimitError=t.CramMalformedError=t.CramUnimplementedError=t.CramError=void 0;class i extends Error{}t.CramError=i;class n extends Error{}t.CramUnimplementedError=n,t.CramMalformedError=class extends i{},t.CramSizeLimitError=class extends i{},t.CramArgumentError=class extends i{}},7806:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.IndexedCramFile=t.CraiIndex=t.CramRecord=t.CramFile=void 0;var r=i(7390);Object.defineProperty(t,\"CramFile\",{enumerable:!0,get:function(){return n(r).default}}),Object.defineProperty(t,\"CramRecord\",{enumerable:!0,get:function(){return r.CramRecord}});var s=i(4923);Object.defineProperty(t,\"CraiIndex\",{enumerable:!0,get:function(){return n(s).default}});var o=i(6014);Object.defineProperty(t,\"IndexedCramFile\",{enumerable:!0,get:function(){return n(o).default}})},6014:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(9747),o=r(i(7390));t.default=class{constructor(e){var t;if(this.cram=null!==(t=e.cram)&&void 0!==t?t:new o.default({url:e.cramUrl,path:e.cramPath,filehandle:e.cramFilehandle,seqFetch:e.seqFetch,checkSequenceMD5:e.checkSequenceMD5,cacheSize:e.cacheSize}),!(this.cram instanceof o.default))throw new Error(\"invalid arguments: no cramfile\");this.index=e.index}getRecordsForRange(e,t,i){return n(this,arguments,void 0,(function*(e,t,i,n={}){if(n.viewAsPairs=n.viewAsPairs||!1,n.pairAcrossChr=n.pairAcrossChr||!1,n.maxInsertSize=n.maxInsertSize||2e5,\"string\"==typeof e)throw new s.CramUnimplementedError(\"string sequence names not yet supported\");const r=e,o=yield this.index.getEntriesForRange(r,t,i),a=n=>n.sequenceId===e&&n.alignmentStart<=i&&void 0!==n.lengthOnRef&&n.alignmentStart+n.lengthOnRef-1>=t,c=yield Promise.all(o.map((e=>this.getRecordsInSlice(e,a))));let l=Array.prototype.concat(...c);if(n.viewAsPairs){const e={},t={};for(const i of l){const n=i.readName;if(void 0===n)throw new Error(\"readName undefined\");const r=i.uniqueId;e[n]||(e[n]=0),e[n]+=1,t[r]=1}const i={};Object.entries(e).forEach((([e,t])=>{1===t&&(i[e]=!0)}));const s=[];for(const e of l){const t=e.readName;if(void 0===t)throw new Error(\"readName undefined\");if(i[t]&&e.mate&&(e.mate.sequenceId===r||n.pairAcrossChr)&&Math.abs(e.alignmentStart-e.mate.alignmentStart)<n.maxInsertSize){const t=this.index.getEntriesForRange(e.mate.sequenceId,e.mate.alignmentStart,e.mate.alignmentStart+1);s.push(t)}}const o=yield Promise.all(s);let a=[];for(const e of o)a.push(...e);a=a.sort(((e,t)=>e.toString().localeCompare(t.toString()))).filter(((e,t,i)=>!t||e.toString()!==i[t-1].toString()));const c=[];for(const e of a){let n=this.cram.featureCache.get(e.toString());n||(n=this.getRecordsInSlice(e,(()=>!0)),this.cram.featureCache.set(e.toString(),n));const r=n.then((e=>{const n=[];for(const r of e){if(void 0===r.readName)throw new Error(\"readName undefined\");i[r.readName]&&!t[r.uniqueId]&&n.push(r)}return n}));c.push(r)}const h=yield Promise.all(c);if(h.length){const e=h.reduce(((e,t)=>e.concat(t)));l=l.concat(e)}}return l}))}getRecordsInSlice({containerStart:e,sliceStart:t,sliceBytes:i},n){return this.cram.getContainerAtPosition(e).getSlice(t,i).getRecords(n)}hasDataForReferenceSequence(e){return this.index.hasDataForReferenceSequence(e)}}},5931:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.RemoteFile=t.LocalFile=void 0,t.open=function(e,t,i){if(i)return i;if(e)return new n.RemoteFile(e);if(t)return new n.LocalFile(t);throw new Error(\"no url, path, or filehandle provided, cannot open\")};const n=i(1113);var r=i(1113);Object.defineProperty(t,\"LocalFile\",{enumerable:!0,get:function(){return r.LocalFile}}),Object.defineProperty(t,\"RemoteFile\",{enumerable:!0,get:function(){return r.RemoteFile}})},6476:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.RANS_BYTE_L=t.TOTFREQ=t.TF_SHIFT=void 0,t.TF_SHIFT=12,t.TOTFREQ=4096,t.RANS_BYTE_L=1<<23},997:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,n){let a=e.getInt(),c=e.getInt(),l=e.getInt(),h=e.getInt();const d=n.remaining(),u=-4&d;for(let r=0;r<u;r+=4){const d=t.R[o.default.get(a,s.TF_SHIFT)],u=t.R[o.default.get(c,s.TF_SHIFT)],f=t.R[o.default.get(l,s.TF_SHIFT)],p=t.R[o.default.get(h,s.TF_SHIFT)];n.putAt(r,d),n.putAt(r+1,u),n.putAt(r+2,f),n.putAt(r+3,p),a=o.default.advanceSymbolStep(a,i[255&d],s.TF_SHIFT),c=o.default.advanceSymbolStep(c,i[255&u],s.TF_SHIFT),l=o.default.advanceSymbolStep(l,i[255&f],s.TF_SHIFT),h=o.default.advanceSymbolStep(h,i[255&p],s.TF_SHIFT),a=o.default.renormalize(a,e),c=o.default.renormalize(c,e),l=o.default.renormalize(l,e),h=o.default.renormalize(h,e)}let f;switch(n.setPosition(u),3&d){case 0:break;case 1:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f);break;case 2:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(c,s.TF_SHIFT)],o.default.advanceSymbol(c,e,i[255&f],s.TF_SHIFT),n.put(f);break;case 3:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(c,s.TF_SHIFT)],o.default.advanceSymbol(c,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(l,s.TF_SHIFT)],o.default.advanceSymbol(l,e,i[255&f],s.TF_SHIFT),n.put(f);break;default:throw new r.CramMalformedError(\"invalid output size encountered during rANS decoding\")}n.setPosition(0)};const r=i(9747),s=i(6476),o=n(i(488))},7960:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,n){const o=t.remaining();let a=e.getInt(),c=e.getInt(),l=e.getInt(),h=e.getInt();const d=o>>2;let u=0,f=d,p=2*d,g=3*d,m=0,w=0,b=0,F=0;for(;u<d;u+=1,f+=1,p+=1,g+=1){const o=255&i[m].R[s.default.get(a,r.TF_SHIFT)],d=255&i[w].R[s.default.get(c,r.TF_SHIFT)],v=255&i[b].R[s.default.get(l,r.TF_SHIFT)],y=255&i[F].R[s.default.get(h,r.TF_SHIFT)];t.putAt(u,o),t.putAt(f,d),t.putAt(p,v),t.putAt(g,y),a=s.default.advanceSymbolStep(a,n[m][o],r.TF_SHIFT),c=s.default.advanceSymbolStep(c,n[w][d],r.TF_SHIFT),l=s.default.advanceSymbolStep(l,n[b][v],r.TF_SHIFT),h=s.default.advanceSymbolStep(h,n[F][y],r.TF_SHIFT),a=s.default.renormalize(a,e),c=s.default.renormalize(c,e),l=s.default.renormalize(l,e),h=s.default.renormalize(h,e),m=o,w=d,b=v,F=y}for(;g<o;g+=1){const o=255&i[F].R[s.default.get(h,r.TF_SHIFT)];t.putAt(g,o),h=s.default.advanceSymbol(h,e,n[F][o],r.TF_SHIFT),F=o}};const r=i(6476),s=n(i(488))},488:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0});const n=i(9747),r=i(6476);class s{constructor(){this.F=void 0,this.C=void 0}}function o(e,t,i,n){return i*(e>>n)+(e&(1<<n)-1)-t}t.default={FC:s,AriDecoder:class{constructor(){this.fc=new Array(256);for(let e=0;e<this.fc.length;e+=1)this.fc[e]=new s;this.R=null}},DecodingSymbol:class{constructor(){this.start=void 0,this.freq=void 0}},symbolInit:function(e,t,i){if(!(t<=65536))throw new n.CramMalformedError(\"assertion failed: start <= 1<<16\");if(!(i<=65536-t))throw new n.CramMalformedError(\"assertion failed: freq <= 1<<16\");e.start=t,e.freq=i},advanceStep:o,advanceSymbolStep:function(e,t,i){return o(e,t.start,t.freq,i)},get:function(e,t){return e&(1<<t)-1},advanceSymbol:function(e,t,i,n){return function(e,t,i,n,s){if((e=n*(e>>s)+(e&(1<<s)-1)-i)<r.RANS_BYTE_L)do{e=e<<8|255&t.get()}while(e<r.RANS_BYTE_L);return e}(e,t,i.start,i.freq,n)},renormalize:function(e,t){if(e<r.RANS_BYTE_L)do{e=e<<8|255&t.get()}while(e<r.RANS_BYTE_L);return e}}},1971:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.readStatsO0=function(e,t,i){let n=0,r=0,c=255&e.get();do{null==t.fc[c]&&(t.fc[c]=new o.default.FC),t.fc[c].F=255&e.get(),t.fc[c].F>=128&&(t.fc[c].F&=-129,t.fc[c].F=(127&t.fc[c].F)<<8|255&e.get()),t.fc[c].C=r,o.default.symbolInit(i[c],t.fc[c].C,t.fc[c].F),t.R||(t.R=new Array(s.TOTFREQ)),t.R.fill(c,r,r+t.fc[c].F),r+=t.fc[c].F,0===n&&c+1===(255&e.getByteAt(e.position()))?(c=255&e.get(),n=255&e.get()):0!==n?(n-=1,c+=1):c=255&e.get()}while(0!==c);a(r<s.TOTFREQ)},t.readStatsO1=function(e,t,i){let n=0,r=255&e.get();do{let c=0,l=0,h=255&e.get();null==t[r]&&(t[r]=new o.default.AriDecoder);do{null==t[r].fc[h]&&(t[r].fc[h]=new o.default.FC),t[r].fc[h].F=255&e.get(),t[r].fc[h].F>=128&&(t[r].fc[h].F&=-129,t[r].fc[h].F=(127&t[r].fc[h].F)<<8|255&e.get()),t[r].fc[h].C=l,0===t[r].fc[h].F&&(t[r].fc[h].F=s.TOTFREQ),null==i[r][h]&&(i[r][h]=new o.default.RansDecSymbol),o.default.symbolInit(i[r][h],t[r].fc[h].C,t[r].fc[h].F),null==t[r].R&&(t[r].R=new Array(s.TOTFREQ)),t[r].R.fill(h,l,l+t[r].fc[h].F),l+=t[r].fc[h].F,a(l<=s.TOTFREQ),0===c&&h+1===(255&e.getByteAt(e.position()))?(h=255&e.get(),c=255&e.get()):0!==c?(c-=1,h+=1):h=255&e.get()}while(0!==h);0===n&&r+1===(255&e.getByteAt(e.position()))?(r=255&e.get(),n=255&e.get()):0!==n?(n-=1,r+=1):r=255&e.get()}while(0!==r)};const r=i(9747),s=i(6476),o=n(i(488));function a(e){if(!e)throw new r.CramMalformedError(\"assertion failed\")}},9989:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i=0){if(0===e.length)return t.fill(0),t;const n=new d(e,i),u=n.get();if(0!==u&&1!==u)throw new s.CramMalformedError(`Invalid rANS order ${u}`);if(n.getInt()!==n.remaining()-h)throw new s.CramMalformedError(\"Incorrect input length.\");const f=n.getInt(),p=new d(t||r.Buffer.allocUnsafe(f));if(p.length<f)throw new s.CramMalformedError(`Output buffer too small to fit ${f} bytes.`);switch(u){case 0:return function(e,t){const i=new o.default.AriDecoder,n=new Array(256);for(let e=0;e<n.length;e+=1)n[e]=new o.default.DecodingSymbol;return(0,a.readStatsO0)(e,i,n),(0,c.default)(e,i,n,t),t}(n,p);case 1:return function(e,t){const i=new Array(256);for(let e=0;e<i.length;e+=1)i[e]=new o.default.AriDecoder;const n=new Array(256);for(let e=0;e<n.length;e+=1){n[e]=new Array(256);for(let t=0;t<n[e].length;t+=1)n[e][t]=new o.default.DecodingSymbol}return(0,a.readStatsO1)(e,i,n),(0,l.default)(e,t,i,n),t}(n,p);default:throw new s.CramMalformedError(`Invalid rANS order: ${u}`)}};const r=i(8287),s=i(9747),o=n(i(488)),a=i(1971),c=n(i(997)),l=n(i(7960)),h=4;class d{constructor(e,t=0){this._buffer=e,this._position=t,this.length=e.length}get(){const e=this._buffer[this._position];return this._position+=1,e}getByte(){return this.get()}getByteAt(e){return this._buffer[e]}position(){return this._position}put(e){return this._buffer[this._position]=e,this._position+=1,e}putAt(e,t){return this._buffer[e]=t,t}setPosition(e){return this._position=e,e}getInt(){const e=this._buffer.readInt32LE(this._position);return this._position+=4,e}remaining(){return this._buffer.length-this._position}}},5417:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.parseHeaderText=function(e){const t=e.split(/\\r?\\n/),i=[];for(const e of t){const[t,...n]=e.split(/\\t/);t&&i.push({tag:t.slice(1),data:n.map((e=>{const t=e.indexOf(\":\");return-1!==t?{tag:e.slice(0,t),value:e.slice(t+1)}:{tag:e,value:\"\"}}))})}return i}},8712:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.unzip=function(e){return r.Buffer.from((0,n.inflate)(e))};const n=i(1668),r=i(8287)},635:(e,t,i)=>{var n=i(8287).Buffer;const r=i(4646),s=i(8706),o=i(9614),a=i(235),c=128;e.exports=class{decode(e){return this.stream=new s(e),this.decodeStream(this.stream)}decodeStream(e,t=0){var i=this.stream.ReadByte();16&i||(t=this.stream.ReadUint7());var n,r=t,s=1&i;if(8&i)return this.decodeStripe(this.stream,t);if(i&c&&([n,r]=this.decodePackMeta(this.stream)),32&i)var o=this.decodeCat(this.stream,r);else o=4&i?this.decodeExt(this.stream,r):64&i?s?this.decodeRLE1(this.stream,r):this.decodeRLE0(this.stream,r):s?this.decode1(this.stream,r):this.decode0(this.stream,r);return i&c&&(o=this.decodePack(o,n,t)),o}encode(e,t){if(this.stream=new s(\"\",0,1.1*e.length+100),this.stream.WriteByte(t),16&t||this.stream.WriteUint7(e.length),8&t)return n.concat([this.stream.buf.slice(0,this.stream.pos),this.encodeStripe(this.stream,e,t>>8)]);var i,r=1&t,o=e.length;return t&c&&([i,e,o]=this.encodePack(e)),t&c&&this.stream.WriteStream(i),64&t?r?this.encodeRLE1(e,o,this.stream):this.encodeRLE0(e,o,this.stream):r?this.encode1(e,o,this.stream):this.encode0(e,o,this.stream)}decode0(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);var a=new o(s),c=new r(e);c.RangeStartDecode(e);for(var l=0;l<t;l++)i[l]=a.ModelDecode(e,c);return i}encode0(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new o(n);i.WriteByte(n);var c=new r(i);for(s=0;s<t;s++)a.ModelEncode(i,c,e[s]);return c.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decode1(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new Array(s),c=0;c<s;c++)a[c]=new o(s);var l=new r(e);l.RangeStartDecode(e);var h=0;for(c=0;c<t;c++)i[c]=a[h].ModelDecode(e,l),h=i[c];return i}encode1(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new Array(n);for(s=0;s<n;s++)a[s]=new o(n);i.WriteByte(n);var c=new r(i),l=0;for(s=0;s<t;s++)a[l].ModelEncode(i,c,e[s]),l=e[s];return c.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeExt(e,t){var i=new n.allocUnsafe(t),r=a.array(e.buf.slice(e.pos)),s=a.header(r),o=0;do{var c=a.decompress(r,s);-1!=c&&(n.from(c).copy(i,o),o+=c.length,s-=c.length)}while(-1!=c);return i}encodeExt(e,t){}decodeRLE0(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new o(s),c=new Array(258),l=0;l<=257;l++)c[l]=new o(4);var h=new r(e);for(h.RangeStartDecode(e),l=0;l<t;){i[l]=a.ModelDecode(e,h);for(var d=c[i[l]].ModelDecode(e,h),u=d,f=256;3==d;)d=c[f].ModelDecode(e,h),f=257,u+=d;for(var p=1;p<=u;p++)i[l+p]=i[l];l+=u+1}return i}encodeRLE0(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new o(n),c=new Array(258);for(s=0;s<=257;s++)c[s]=new o(4);i.WriteByte(n);var l=new r(i);for(s=0;s<t;){a.ModelEncode(i,l,e[s]);for(var h=1;s+h<t&&e[s+h]==e[s];)h++;h--;var d=e[s];e[s],s+=h+1;var u=h>=3?3:h;for(c[d].ModelEncode(i,l,u),h-=u,d=256;3==u;)u=h>=3?3:h,c[d].ModelEncode(i,l,u),d=257,h-=u}return l.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeRLE1(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new Array(s),c=0;c<s;c++)a[c]=new o(s);var l=new Array(258);for(c=0;c<=257;c++)l[c]=new o(4);var h=new r(e);h.RangeStartDecode(e);var d=0;for(c=0;c<t;){i[c]=a[d].ModelDecode(e,h),d=i[c];for(var u=l[i[c]].ModelDecode(e,h),f=u,p=256;3==u;)u=l[p].ModelDecode(e,h),p=257,f+=u;for(var g=1;g<=f;g++)i[c+g]=i[c];c+=f+1}return i}encodeRLE1(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new Array(n);for(s=0;s<n;s++)a[s]=new o(n);var c=new Array(258);for(s=0;s<=257;s++)c[s]=new o(4);i.WriteByte(n);for(var l=new r(i),h=(s=0,0);s<t;){a[h].ModelEncode(i,l,e[s]);for(var d=1;s+d<t&&e[s+d]==e[s];)d++;d--;var u=e[s];h=e[s],s+=d+1;var f=d>=3?3:d;for(c[u].ModelEncode(i,l,f),d-=f,u=256;3==f;)f=d>=3?3:d,c[u].ModelEncode(i,l,f),u=257,d-=f}return l.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodePackMeta(e){this.nsym=e.ReadByte();for(var t=new Array(this.nsym),i=0;i<this.nsym;i++)t[i]=e.ReadByte();return[t,e.ReadUint7()]}decodePack(e,t,i){var r=new n.allocUnsafe(i);if(this.nsym<=1)for(var s=0;s<i;s++)r[s]=t[0];else if(this.nsym<=2){s=0;for(var o=0;s<i;s++){if(s%8==0)var a=e[o++];r[s]=t[1&a],a>>=1}}else if(this.nsym<=4)for(s=0,o=0;s<i;s++)s%4==0&&(a=e[o++]),r[s]=t[3&a],a>>=2;else{if(!(this.nsym<=16))return e;for(s=0,o=0;s<i;s++)s%2==0&&(a=e[o++]),r[s]=t[15&a],a>>=4}return r}packMeta(e){for(var t=new s(\"\",0,1024),i=new Array(256),n=0;n<e.length;n++)i[e[n]]=1;var r=0;for(n=0;n<256;n++)i[n]&&(i[n]=++r);for(t.WriteByte(r),n=0;n<256;n++)i[n]&&(t.WriteByte(n),i[n]--);return[t,i,r]}encodePack(e){var t,i,r;[t,i,r]=this.packMeta(e);var s=e.length,o=0;if(r<=1)return t.WriteUint7(0),[t,new n.allocUnsafe(0),0];if(r<=2){for(var a=new n.allocUnsafe(Math.floor((s+7)/8)),c=(o=0,0);o<(-8&s);o+=8,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<1)+(i[e[o+2]]<<2)+(i[e[o+3]]<<3)+(i[e[o+4]]<<4)+(i[e[o+5]]<<5)+(i[e[o+6]]<<6)+(i[e[o+7]]<<7);if(o<s){a[c]=0;for(var l=0;o<s;)a[c]|=i[e[o++]]<<l,l++;c++}return t.WriteUint7(c),[t,a,a.length]}if(r<=4){for(a=new n.allocUnsafe(Math.floor((s+3)/4)),o=0,c=0;o<(-4&s);o+=4,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<2)+(i[e[o+2]]<<4)+(i[e[o+3]]<<6);if(o<s){for(a[c]=0,l=0;o<s;)a[c]|=i[e[o++]]<<l,l+=2;c++}return t.WriteUint7(c),[t,a,a.length]}if(r<=16){for(a=new n.allocUnsafe(Math.floor((s+1)/2)),o=0,c=0;o<(-2&s);o+=2,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<4);return o<s&&(a[c++]=i[e[o++]]),t.WriteUint7(c),[t,a,a.length]}return t.WriteUint7(e.length),[t,e,e.length]}encodeStripe(e,t,i){0==i&&(i=4);for(var n=new Array(i),r=new Array(i),o=0;o<i;o++)r[o]=Math.floor(t.length/i)+(t.length%i>o),n[o]=new Array(r[o]);for(var a=0,c=0;c<t.length;c+=i,a++)for(var l=0;l<i;l++)a<n[l].length&&(n[l][a]=t[c+l]);var h=new Array(i),d=0;for(o=0;o<i;o++){var u=this.encode(n[o],0),f=this.encode(n[o],1);h[o]=f.length<u.length?f:u,d+=h[o].length}var p=new s(\"\",0,d+5*i+1);for(p.WriteByte(i),o=0;o<i;o++)p.WriteUint7(h[o].length);for(o=0;o<i;o++)p.WriteData(h[o],h[o].length);return p.buf.slice(0,p.buf.pos)}decodeStripe(e,t){for(var i=e.ReadByte(),r=new Array(i),s=new Array(i),o=0;o<i;o++)r[o]=e.ReadUint7();var a=new Array(i);for(o=0;o<i;o++)s[o]=Math.floor(t/i)+(t%i>o),a[o]=this.decodeStream(e,s[o]);var c=new n.allocUnsafe(t);for(o=0;o<i;o++)for(var l=0;l<s[o];l++)c[l*i+o]=a[o][l];return c}decodeCat(e,t){for(var i=new n.allocUnsafe(t),r=0;r<t;r++)i[r]=e.ReadByte();return i}}},4646:e=>{e.exports=class{constructor(e){this.low=0,this.range=4294967295,this.code=0,this.FFnum=0,this.carry=0,this.cache=0}RangeStartDecode(e){for(var t=0;t<5;t++)this.code=(this.code<<8)+e.ReadByte();this.code&=4294967295,this.code>>>=0}RangeGetFrequency(e){return this.range=Math.floor(this.range/e),Math.floor(this.code/this.range)}RangeDecode(e,t,i,n){for(this.code-=t*this.range,this.range*=i;this.range<1<<24;)this.range*=256,this.code=256*this.code+e.ReadByte()}RangeShiftLow(e){if(this.low<4278190080|this.carry){for(e.WriteByte(this.cache+this.carry);this.FFnum;)e.WriteByte(this.carry-1),this.FFnum--;this.cache=this.low>>>24,this.carry=0}else this.FFnum++;this.low<<=8,this.low>>>=0}RangeEncode(e,t,i,n){var r=this.low;for(this.range=Math.floor(this.range/n),this.low+=t*this.range,this.low>>>=0,this.range*=i,this.low<r&&(0!=this.carry&&console.log(\"ERROR: Multiple carry\"),this.carry=1);this.range<1<<24;)this.range*=256,this.RangeShiftLow(e)}RangeFinishEncode(e){for(var t=0;t<5;t++)this.RangeShiftLow(e)}}},9614:e=>{e.exports=class{constructor(e=256){this.total_freq=e,this.max_sym=e-1,this.S=new Array,this.F=new Array;for(var t=0;t<=this.max_sym;t++)this.S[t]=t,this.F[t]=1}ModelDecode(e,t){for(var i=t.RangeGetFrequency(this.total_freq),n=0,r=0;n+this.F[r]<=i;)n+=this.F[r++];t.RangeDecode(e,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise();var s=this.S[r];if(r>0&&this.F[r]>this.F[r-1]){var o=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=o,o=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=o}return s}ModelRenormalise(){this.total_freq=0;for(var e=0;e<=this.max_sym;e++)this.F[e]-=Math.floor(this.F[e]/2),this.total_freq+=this.F[e]}ModelEncode(e,t,i){for(var n=0,r=0;this.S[r]!=i;r++)n+=this.F[r];if(t.RangeEncode(e,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise(),i=this.S[r],r>0&&this.F[r]>this.F[r-1]){var s=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=s,s=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=s}}}},6038:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706),s=i(9614),o=i(4646);function a(e,t,i){for(var n=0,r=0,s=-1,o=new Array(1024);r<i;){var a=e.ReadByte();if(o[n++]=a,r+=a,a==s){var c=e.ReadByte();for(r+=a*c;c--;)o[n++]=a}s=a}var l=0;for(n=0,r=0;r<i;){var h=0;do{var d=o[n++];h+=d}while(255==d);for(;h--;)t[r++]=l;l++}}function c(e,t,i){var n=e.context;return t.qctx=(t.qctx<<e.qshift)+e.qtab[i],n+=(t.qctx&(1<<e.qbits)-1)<<e.qloc,e.do_pos&&(n+=e.ptab[Math.min(t.p,1023)]<<e.ploc),e.do_delta&&(n+=e.dtab[Math.min(t.delta,255)]<<e.dloc,t.delta+=t.prevq!=i?1:0,t.prevq=i),e.do_sel&&(n+=t.s<<e.sloc),t.p--,65535&n}function l(e){var t={};t.context=e.ReadUint16(),t.pflags=e.ReadByte(),t.do_dedup=2&t.pflags,t.fixed_len=4&t.pflags,t.do_sel=8&t.pflags,t.do_qmap=16&t.pflags,t.do_pos=32&t.pflags,t.do_delta=64&t.pflags,t.do_qtab=128&t.pflags,t.max_sym=e.ReadByte();var i=e.ReadByte();if(t.qbits=i>>4,t.qshift=15&i,i=e.ReadByte(),t.qloc=i>>4,t.sloc=15&i,i=e.ReadByte(),t.ploc=i>>4,t.dloc=15&i,t.qmap=new Array(256),16&t.pflags)for(var n=0;n<t.max_sym;n++)t.qmap[n]=e.ReadByte();else for(n=0;n<256;n++)t.qmap[n]=n;if(t.qtab=new Array(1024),t.qbits>0&&128&t.pflags)a(e,t.qtab,256);else for(n=0;n<256;n++)t.qtab[n]=n;return t.ptab=new Array(1024),32&t.pflags&&a(e,t.ptab,1024),t.dtab=new Array(256),64&t.pflags&&a(e,t.dtab,256),t}function h(e,t,i,n,r,s){i.max_sel>0?r.s=n.sel.ModelDecode(e,t):r.s=0,r.x=i.stab[r.s];var o=i.params[r.x];if(o.fixed_len>=0){var a=n.len[0].ModelDecode(e,t);a|=n.len[1].ModelDecode(e,t)<<8,a|=n.len[2].ModelDecode(e,t)<<16,a|=n.len[3].ModelDecode(e,t)<<24,o.fixed_len>0&&(o.fixed_len=-a)}else a=-o.fixed_len;r.len=a,i.do_rev&&(s[r.rec]=n.rev.ModelDecode(e,t)),r.is_dup=0,2&o.pflags&&n.dup.ModelDecode(e,t)&&(r.is_dup=1),r.p=a,r.delta=0,r.qctx=0,r.prevq=0,r.rec++}function d(e,t,i){for(var n=0,r=0,s=new Array(2*i),o=0;n<i;){for(var a=n;n<i&&t[n]==r;)n++;var c=n-a;do{var l=Math.min(255,c);s[o++]=l,c-=l}while(255==l);r++}var h=-1,d=new Array(2*i),u=0;for(n=0;n<o;){var f=s[n++];if(d[u++]=f,f==h){for(a=n;n<o&&s[n]==h&&n-a<255;)n++;d[u++]=n-a}else h=f}e.WriteData(d,u)}e.exports={decode:function(e,t){return function(e,t){var i=e.ReadUint7(),r=function(e){var t={max_sym:0};if(5==e.ReadByte()){var i=e.ReadByte(),n=1&i?e.ReadByte():1,r=i.nparam>1?i.nparam-1:0,s=new Array(256);if(2&i)r=e.ReadByte(),a(e,s,256);else{for(var o=0;o<n;o++)s[o]=o;for(;o<256;o++)s[o]=n-1}t.do_rev=4&i,t.stab=s,t.max_sel=r,t.params=new Array(t.nparam);for(var c=0;c<n;c++)t.params[c]=l(e),t.max_sym<t.params[c].max_sym&&(t.max_sym=t.params[c].max_sym);return t}console.error(\"Invalid FQZComp version number\")}(e);if(r){var d=r.params,u=new Array(t.length),f=function(e){var t={};t.qual=new Array(65536);for(var i=0;i<65536;i++)t.qual[i]=new s(e.max_sym+1);for(t.len=new Array(4),i=0;i<4;i++)t.len[i]=new s(256);return t.rev=new s(2),t.dup=new s(2),e.max_sel>0&&(t.sel=new s(e.max_sel+1)),t}(r),p=new o(e);p.RangeStartDecode(e);for(var g=new n.allocUnsafe(i),m={qctx:0,prevq:0,delta:0,p:0,s:0,x:0,len:0,is_dup:0,rec:0},w=0;w<i;){if(0==m.p){if(h(e,p,r,f,m,u),m.is_dup>0&&f.dup.ModelDecode(e,p)){for(var b=0;b<len;b++)g[w+b]=g[w+b-m.len];w+=m.len,m.p=0;continue}t.push(m.len);var F=(d=r.params[m.x]).context}var v=f.qual[F].ModelDecode(e,p);g[w++]=d.qmap[v],F=c(d,m,v)}return r.do_rev&&function(e,t,i,n){for(var r=0,s=0;s<t;){if(i[r])for(var o=0,a=n[r]-1;o<a;){var c=e[s+o];e[s+o]=e[s+a],e[s+a]=c,o++,a--}s+=n[r++]}}(g,i,u,t),g}}(new r(e),t)},encode:function(e,t,i){for(var n=new Array(2),a=new Array(2),c=new Array(2),l=new Array(2),h=new Array(256),u=0;u<2;u++)n[u]=new Array(256),a[u]=new Array(256),c[u]=new Array(1024),l[u]=new Array(256);(p=new r(\"\",0,1.1*e.length+100)).WriteUint7(e.length);var f=function(e,t,i,n){for(var r=i[0],s=0;s<i.length&&i[s]==r;s++);var o=s==i.length?1:0,a=0,c=0;for(s=0;s<256;s++)n[0][s]=0;var l=0,h=0;for(s=0;s<e.length;s++)0==h&&(h=t[l<t.length-1?l++:l]),n[0][e[s]]++,h--;for(s=0;s<256;s++)n[0][s]&&(c<s&&(c=s),a++);var d=5,u=0;return a<=16&&(u=1,d=a<=2?1:a<=4?2:a<=8?3:4),[{qbits:8+(d>4),qshift:d,qloc:7,pbits:7,pshift:t[0]>128?1:0,ploc:0,dbits:d>4?0:1,dshift:3,dloc:15,sbits:0,sloc:15,do_stab:0,context:0,max_sym:c,nsym:a,do_qmap:u,do_dedup:0,fixed_len:1==t.length?1:0,do_sel:0,do_rev:0,do_pos:1,do_delta:d<=4?1:0,do_qtab:0,qbits:8+(d>4)-(0==o),sbits:1,sloc:15-(d<=4),do_stab:1,do_sel:1}]}(e,t,i,n),p=function(e,t,i,n,r,s,o){for(var a=[0,1,1,1,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7],c=0;c<t.length;c++)o[c]=c;for(;c<256;c++)o[c]=t.length-1;e.WriteByte(5);var l=(t.length>1?1:0)|(t[0].do_stab?2:0);if(e.WriteByte(l),1&l&&e.WriteByte(t.length),2&l){var h=1<<t[0].sbits;h>0&&h--,e.WriteByte(h),d(e,o,256)}for(var u=0;u<t.length;u++){if(e.WriteUint16(t[u].context),e.WriteByte((t[u].do_qtab?128:0)|(t[u].do_delta?64:0)|(t[u].do_pos?32:0)|(t[u].do_qmap?16:0)|(t[u].do_sel?8:0)|(t[u].fixed_len?4:0)|(t[u].do_dedup?2:0)),t[u].do_qmap?e.WriteByte(t[u].nsym):e.WriteByte(t[u].max_sym),e.WriteByte(t[u].qbits<<4|t[u].qshift),e.WriteByte(t[u].qloc<<4|t[u].sloc),e.WriteByte(t[u].ploc<<4|t[u].dloc),t[u].do_qmap){t[u].max_sym=t[u].nsym;var f=0;for(c=0;c<256;c++)i[u][c]&&(e.WriteByte(c),i[u][c]=f++);for(;f<t[u].nsym;f++)e.WriteByte(0)}else for(c=0;c<256;c++)i[u][c]=c;if(t[u].qbits>0){for(c=0;c<256;c++)n[u][c]=c;t[u].do_qtab&&d(e,n[u],256)}if(t[u].pbits>0){for(c=0;c<1024;c++)r[u][c]=Math.min((1<<t[u].pbits)-1,c>>t[u].pshift);d(e,r[u],1024)}if(t[u].dbits>0){for(c=0;c<256;c++)a[c]>(1<<t[u].dbits)-1&&(a[c]=(1<<t[u].dbits)-1);for(c=0;c<256;c++)s[u][c]=a[Math.min(a.length-1,c>>t[u].dshift)];d(e,s[u],256)}}return e}(p,f,n,a,c,l,h);return function(e,t,i,n,r,a,c,l,h,d){var u=1<<r[0].sbits;u>0&&u--;for(var f=t.length,p=0,g=0;g<r.length;g++)p<r[g].max_sym&&(p=r[g].max_sym);for(var m=new Array(65536),w=0;w<65536;w++)m[w]=new s(p+1);var b=new Array(4);for(w=0;w<4;w++)b[w]=new s(256);new s(2),new s(2);for(var F=new s(u+1),v=new o(t),y=(g=0,w=0,0);w<f;){if(0==g){var A=n[y];r[0].sbits>0&&F.ModelEncode(e,v,A);var C=d[A],_=i[Math.min(i.length-1,y++)];r[C].fixed_len?r[C].fixed_len>0&&(b[0].ModelEncode(e,v,255&_),b[1].ModelEncode(e,v,_>>8&255),b[2].ModelEncode(e,v,_>>16&255),b[3].ModelEncode(e,v,_>>24&255),r[C].fixed_len=-1):(b[0].ModelEncode(e,v,255&_),b[1].ModelEncode(e,v,_>>8&255),b[2].ModelEncode(e,v,_>>16&255),b[3].ModelEncode(e,v,_>>24&255)),r[C].do_dedup&&process.exit(1),g=_;var x=0,k=r[C].context,I=0,S=0}var E=t[w++],N=a[C][E];m[k].ModelEncode(e,v,N),I=(I<<r[C].qshift)+c[C][N],k=r[C].context,k+=(I&(1<<r[C].qbits)-1)<<r[C].qloc,r[C].pbits>0&&(k+=l[C][Math.min(g,1023)]<<r[C].ploc),r[C].dbits>0&&(k+=h[C][Math.min(x,255)]<<r[C].dloc,x+=S!=N?1:0,S=N),r[C].do_sel&&(k+=A<<r[C].sloc),k&=65535,g--}return v.RangeFinishEncode(e),e.buf.slice(0,e.pos)}(p,e,t,i,f,n,a,c,l,h)}}},6960:(e,t,i)=>{var n=i(8287).Buffer,r=i(5460),s=i(8223),o=i(635),a=i(6038),c=i(5997);e.exports={r4x8_uncompress:function(e,t){r.decode(e).copy(t,0,0)},r4x16_uncompress:function(e,t){s.decode(e).copy(t,0,0)},arith_uncompress:function(e,t){o.decode(e).copy(t,0,0)},fqzcomp_uncompress:function(e,t){var i=new Array;a.decode(e,i).copy(t,0,0)},tok3_uncompress:function(e,t){var i=c.decode(e,0,\"\\0\");n.from(i,\"binary\").copy(t,0,0)}}},8706:(e,t,i)=>{var n=i(8287).Buffer;e.exports=class{constructor(e,t=0,i=0){0!=i?(this.buf=n.allocUnsafe(i),this.length=i):(this.buf=e,this.length=e.length),this.pos=t}EOF(){return this.pos>=this.length}ReadData(e){var t=this.buf.slice(this.pos,this.pos+e);return this.pos+=e,t}ReadByte(){const e=this.buf[this.pos];return this.pos++,e}ReadChar(){const e=this.buf[this.pos];return this.pos++,String.fromCharCode(e)}ReadUint16(){return this.ReadByte()|this.ReadByte()<<8}ReadUint32(){const e=this.buf.readInt32LE(this.pos);return this.pos+=4,e}ReadString(){var e=\"\";do{var t=this.buf[this.pos++];t&&(e+=String.fromCharCode(t))}while(t);return e}ReadUint7(){var e=0;do{var t=this.ReadByte();e=e<<7|127&t}while(128&t);return e}ReadITF8(){var e=this.buf[this.pos];return this.pos++,e>=240?(e=(15&e)<<28,e+=(this.buf[this.pos+0]<<20)+(this.buf[this.pos+1]<<12)+(this.buf[this.pos+2]<<4)+(this.buf[this.pos+3]>>4),this.pos+=4):e>=224?(e=(15&e)<<24,e+=(this.buf[this.pos+0]<<16)+(this.buf[this.pos+1]<<8)+(0|this.buf[this.pos+2]),this.pos+=3):e>=192?(e=(31&e)<<16,e+=(this.buf[this.pos+0]<<8)+(0|this.buf[this.pos+1]),this.pos+=2):e>=128&&(e=(63&e)<<8,e+=this.buf[this.pos],this.pos++),e}WriteByte(e){this.buf[this.pos++]=e}WriteChar(e){this.buf[this.pos++]=e.charCodeAt(0)}WriteString(e){for(var t=0;t<e.length;t++)this.buf[this.pos++]=e.charCodeAt(t);this.buf[this.pos++]=0}WriteData(e,t){for(var i=0;i<t;i++)this.buf[this.pos++]=e[i]}WriteStream(e){this.WriteData(e.buf,e.pos)}WriteUint16(e){this.WriteByte(255&e),this.WriteByte(e>>8&255)}WriteUint32(e){this.buf.writeInt32LE(e,this.pos),this.pos+=4}WriteUint7(e){var t=0,i=e;do{t+=7,i>>=7}while(i>0);do{t-=7,this.WriteByte((e>>t&127)+((t>0)<<7))}while(t>0)}WriteITF8(e){e<0&&(e=1+e),e<=127?this.buf[this.pos++]=e:e<=16383?(this.buf[this.pos++]=128|Math.floor(e/256),this.buf[this.pos++]=255&e):e<131071?(this.buf[this.pos++]=192|Math.floor(e/65536),this.buf[this.pos++]=255&Math.floor(e/256),this.buf[this.pos++]=255&e):e<268435455?(this.buf[this.pos++]=224|Math.floor(e/16777216),this.buf[this.pos++]=255&Math.floor(e/65536),this.buf[this.pos++]=255&Math.floor(e/256),this.buf[this.pos++]=255&e):(this.buf[this.pos++]=240|Math.floor(e/268435456),this.buf[this.pos++]=255&Math.floor(e/1048576),this.buf[this.pos++]=255&Math.floor(e/4096),this.buf[this.pos++]=255&Math.floor(e/4),this.buf[this.pos++]=15&e)}WriteByteNeg(e){this.buf[--this.pos]=e}}},5460:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706);function s(e){return 4095&e}function o(e,t){for(var i=0;t>=e[i+1];)i++;return i}function a(e){for(var t=new 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o=0,a=0,c=0;for(i=0,n=0;n<256;n++)0!=e[n]&&(o<e[n]&&(o=e[n],a=n),e[n]=Math.floor(e[n]*s),0==e[n]&&(e[n]=1),i+=e[n]);i<r?e[a]+=r-i:i-r<e[a]/2&&e[a]>2?e[a]-=i-r:i!=r&&(s=r/i,c=1)}while(c)}function b(e,t){for(var i=0,n=0;n<256;n++)i+=e[n];if(0!=i&&i!=1<<t){for(var r=0;i<1<<t;)i*=2,r++;for(n=0;n<256;n++)e[n]<<=r}}function F(e,t){for(var i=0,n=0;n<256;n++)if(t[n])if(i>0)i--;else if(e.WriteByte(n),n>0&&t[n-1]>0){for(i=n+1;i<256&&t[i];i++);i-=n+1,e.WriteByte(i)}e.WriteByte(0)}function v(e){const t=e.length;var i=new r(\"\",0,780),s=new Array(256);!function(e,t){for(var i=0;i<256;i++)t[i]=0;for(i=0;i<e.length;i++)t[e[i]]++}(e,s);var o=Math.ceil(Math.log2(t));o>12&&(o=12),w(s,o),function(e,t){F(e,t);for(var i=0;i<256;i++)t[i]&&e.WriteUint7(t[i])}(i,s),w(s,12);var a=new Array(256);a[0]=0;for(var c=1;c<256;c++)a[c]=a[c-1]+s[c-1];var l=new Array(4);for(c=0;c<4;c++)l[c]=32768;var u=new r(\"\",1.05*t+100|0,1.05*t+100|0);for(c=t-1;c>=0;c--)l[c%4]=d(l[c%4],u,a[e[c]],s[e[c]],12);for(c=3;c>=0;c--)h(l[c],u);return n.concat([i.buf.slice(0,i.pos),u.buf.slice(u.pos,u.length)],i.pos+u.length-u.pos)}e.exports={decode:function(e){return f(new r(e),0)},encode:p}},5997:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706),s=i(8223);var o=new(i(635));function a(e,t){for(var i=e+\"\";i.length<t;)i=\"0\"+i;return i}function c(e,t,i,n){var r=e[0][0].ReadByte(),s=n-e[0][r].ReadUint32();if(5==r)return t[n]=t[s],i[n]=i[s],t[n];var o=1;t[n]=\"\",i[n]=new Array(256);do{switch(r=e[o][0].ReadByte()){case 2:i[n][o]=e[o][2].ReadChar();break;case 1:i[n][o]=e[o][1].ReadString();break;case 7:i[n][o]=e[o][7].ReadUint32();break;case 3:var c=e[o][3].ReadUint32(),l=e[o][4].ReadByte();i[n][o]=a(c,l);break;case 8:i[n][o]=(0|i[s][o])+e[o][8].ReadByte();break;case 9:c=(0|i[s][o])+e[o][9].ReadByte(),l=i[s][o].length,i[n][o]=a(c,l);break;case 10:i[n][o]=i[s][o];break;default:i[n][o]=\"\"}t[n]+=i[n][o++]}while(12!=r);return t[n]}function l(e,t,i,n,r,s){for(var o=0;o<n.length;o++)if(!(i>0&&5==t[o][0].type)&&t[o][i])switch(e[0].WriteByte(t[o][i].type),t[o][i].type){case 6:e[6].WriteUint32(t[o][i].val);break;case 5:e[5].WriteUint32(t[o][i].val);break;case 1:e[1].WriteString(t[o][i].val);break;case 2:e[2].WriteChar(t[o][i].val);break;case 7:e[7].WriteUint32(t[o][i].val);break;case 3:e[3].WriteUint32(t[o][i].val),e[4].WriteByte(t[o][i].val.length);break;case 8:case 9:e[t[o][i].type].WriteByte(t[o][i].val)}}function h(e,t,i,n){for(var r=0;r<=12;r++)if(!(e[r].pos<=0)){n.WriteByte(r+(0==r?128:0)),e[r]=e[r].buf.slice(0,e[r].pos);var s=d(e[r],i);n.WriteUint7(s.length),n.WriteData(s,s.length)}}function d(e,t){var i,n=1<<30,r=[0,1,64,65,128,129,201];for(var a in r){var c=r[a];if(!(1&c&&e.length<100||8&c&&e.length%4!=0)){try{var l=t?o.encode(e,c):s.encode(e,c)}catch(e){l=0}l&&n>l.length&&(n=l.length,i=l)}}return i}function u(e,t,i,n,r){var s=0,o=r-1;e[r]=new Array(256),t[n]?e[r][0]={type:5,val:r-t[n]}:e[r][0]={type:6,val:0==r?0:1},t[n]=r;for(var a=n.match(/([a-zA-Z0-9]{1,9})|([^a-zA-Z0-9]+)/g),c=0;c<a.length;c++){var l=c+1,h=1,d=a[c];if(a[c].match(/^0+[0-9]*$/g)?h=3:a[c].match(/^[0-9]+$/g)?h=7:1==a[c].length&&(h=2),o>=0&&e[o][l])if(e[o][l].str==a[c])h=10,d=\"\";else if(7==e[o][l].type||8==e[o][l].type){var u=d-e[o][l].str;i[l]++,u>=0&&u<256&&i[l]>r/2&&(h=8,d=u)}else 3!=e[o][l].type&&9!=e[o][l].type||e[o][l].str.length!=d.length||(u=d-e[o][l].str,i[l]++,u>=0&&u<256&&i[l]>r/2&&(h=9,d=u));e[r][l]={str:a[c],val:d,type:h},s<e[r][l].val.length+3&&(s=e[r][l].val.length+3)}return e[r][++l]={type:12},[l+1,s]}e.exports={encode:function(e,t){var i=e.toString();\"\\n\"==i[i.length-1]&&(i=i.substring(0,i.length-1));var n=i.split(\"\\n\"),s=new r(\"\",0,2*i.length+1e4);s.WriteUint32(i.length),s.WriteUint32(n.length),s.WriteByte(t);for(var o=new Array(n.length),a={},c=new Array(256).fill(0),d=0,f=0,p=0;p<n.length;p++){var[g,m]=u(o,a,c,n[p],p);d<g&&(d=g),f<m&&(f=m)}for(var w=0;w<d;w++){for(var b=new Array(13),F=0;F<=12;F++)b[F]=new r(\"\",0,n.length*f);l(b,o,w,n),h(b,0,t,s)}return s.buf.slice(0,s.pos)},decode:function(e,t,i){(e=new r(e)).ReadUint32();var a=e.ReadUint32(),l=e.ReadByte(),h=function(e,t,i,a){for(var c=-1,l=new Array(256);!e.EOF();){var h=e.ReadByte(),d=128&h,u=64&h,f=63&h;if(d&&(l[++c]=new Array(13)),0!=f&&d){var p=new Array(a-1).fill(10);l[c][0]=new r(n.from([f].concat(p)))}if(u){var g=e.ReadByte(),m=e.ReadByte();l[c][f]=new r(l[g][m].buf)}else{var w=e.ReadUint7(),b=e.ReadData(w);l[c][f]=i?o.decode(b):s.decode(b),l[c][f]=new r(l[c][f])}}return l}(e,0,l,a),d=new Array(a),u=new Array(a),f=\"\";void 0===i&&(i=\"\\n\");for(var p=0;p<a;p++)f+=c(h,d,u,p)+i;return f}}},7526:(e,t)=>{t.byteLength=function(e){var t=a(e),i=t[0],n=t[1];return 3*(i+n)/4-n},t.toByteArray=function(e){var t,i,s=a(e),o=s[0],c=s[1],l=new r(function(e,t,i){return 3*(t+i)/4-i}(0,o,c)),h=0,d=c>0?o-4:o;for(i=0;i<d;i+=4)t=n[e.charCodeAt(i)]<<18|n[e.charCodeAt(i+1)]<<12|n[e.charCodeAt(i+2)]<<6|n[e.charCodeAt(i+3)],l[h++]=t>>16&255,l[h++]=t>>8&255,l[h++]=255&t;return 2===c&&(t=n[e.charCodeAt(i)]<<2|n[e.charCodeAt(i+1)]>>4,l[h++]=255&t),1===c&&(t=n[e.charCodeAt(i)]<<10|n[e.charCodeAt(i+1)]<<4|n[e.charCodeAt(i+2)]>>2,l[h++]=t>>8&255,l[h++]=255&t),l},t.fromByteArray=function(e){for(var t,n=e.length,r=n%3,s=[],o=16383,a=0,l=n-r;a<l;a+=o)s.push(c(e,a,a+o>l?l:a+o));return 1===r?(t=e[n-1],s.push(i[t>>2]+i[t<<4&63]+\"==\")):2===r&&(t=(e[n-2]<<8)+e[n-1],s.push(i[t>>10]+i[t>>4&63]+i[t<<2&63]+\"=\")),s.join(\"\")};for(var i=[],n=[],r=\"undefined\"!=typeof Uint8Array?Uint8Array:Array,s=\"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/\",o=0;o<64;++o)i[o]=s[o],n[s.charCodeAt(o)]=o;function a(e){var t=e.length;if(t%4>0)throw new Error(\"Invalid string. 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Received type number');return d(e)}return l(e,t,i)}function l(e,t,i){if(\"string\"==typeof e)return function(e,t){if(\"string\"==typeof t&&\"\"!==t||(t=\"utf8\"),!c.isEncoding(t))throw new TypeError(\"Unknown encoding: \"+t);const i=0|g(e,t);let n=a(i);const r=n.write(e,t);return r!==i&&(n=n.slice(0,r)),n}(e,t);if(ArrayBuffer.isView(e))return function(e){if(K(e,Uint8Array)){const t=new Uint8Array(e);return f(t.buffer,t.byteOffset,t.byteLength)}return u(e)}(e);if(null==e)throw new TypeError(\"The first argument must be one of type string, Buffer, ArrayBuffer, Array, or Array-like Object. Received type \"+typeof e);if(K(e,ArrayBuffer)||e&&K(e.buffer,ArrayBuffer))return f(e,t,i);if(\"undefined\"!=typeof SharedArrayBuffer&&(K(e,SharedArrayBuffer)||e&&K(e.buffer,SharedArrayBuffer)))return f(e,t,i);if(\"number\"==typeof e)throw new TypeError('The \"value\" argument must not be of type number. Received type number');const n=e.valueOf&&e.valueOf();if(null!=n&&n!==e)return c.from(n,t,i);const r=function(e){if(c.isBuffer(e)){const t=0|p(e.length),i=a(t);return 0===i.length||e.copy(i,0,0,t),i}return void 0!==e.length?\"number\"!=typeof e.length||Y(e.length)?a(0):u(e):\"Buffer\"===e.type&&Array.isArray(e.data)?u(e.data):void 0}(e);if(r)return r;if(\"undefined\"!=typeof Symbol&&null!=Symbol.toPrimitive&&\"function\"==typeof e[Symbol.toPrimitive])return c.from(e[Symbol.toPrimitive](\"string\"),t,i);throw new TypeError(\"The first argument must be one of type string, Buffer, ArrayBuffer, Array, or Array-like Object. 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reading blob\"))},t.onabort=()=>{n(new Error(\"blob reading was aborted\"))},t.onload=()=>{t.result&&\"string\"!=typeof t.result?i(t.result):n(new Error(\"unknown error reading blob\"))},t.readAsArrayBuffer(e)}))}class l{constructor(e){this.blob=e,this.size=e.size}async read(e,t=0,i,n=0){if(!i)return{bytesRead:0,buffer:e};const r=n,o=r+i,a=await c(this.blob.slice(r,o)),l=s.Buffer.from(a);return{bytesRead:l.copy(e,t),buffer:l}}async readFile(e){const t=\"string\"==typeof e?e:null==e?void 0:e.encoding;if(\"utf8\"===t)return function(e){const t=new FileReader;return new Promise(((i,n)=>{t.onerror=()=>{t.abort(),n(new Error(\"problem reading blob\"))},t.onabort=()=>{n(new Error(\"blob reading was aborted\"))},t.onload=()=>{t.result&&\"string\"==typeof t.result?i(t.result):n(new Error(\"unknown error reading blob\"))},t.readAsText(e)}))}(this.blob);if(t)throw new Error(`unsupported encoding: ${t}`);const i=await c(this.blob);return s.Buffer.from(i)}async stat(){return{size:this.size}}async close(){}}function h(e,t={}){return new a(e,t)}function d(e,t,i,n={}){if(void 0!==i)return i;if(void 0!==e)return h(e,n);if(void 0!==t)return new(r())(t,n);throw new Error(\"no url, path, or filehandle provided, cannot open\")}},251:(e,t)=>{t.read=function(e,t,i,n,r){var s,o,a=8*r-n-1,c=(1<<a)-1,l=c>>1,h=-7,d=i?r-1:0,u=i?-1:1,f=e[t+d];for(d+=u,s=f&(1<<-h)-1,f>>=-h,h+=a;h>0;s=256*s+e[t+d],d+=u,h-=8);for(o=s&(1<<-h)-1,s>>=-h,h+=n;h>0;o=256*o+e[t+d],d+=u,h-=8);if(0===s)s=1-l;else{if(s===c)return o?NaN:1/0*(f?-1:1);o+=Math.pow(2,n),s-=l}return(f?-1:1)*o*Math.pow(2,s-n)},t.write=function(e,t,i,n,r,s){var o,a,c,l=8*s-r-1,h=(1<<l)-1,d=h>>1,u=23===r?Math.pow(2,-24)-Math.pow(2,-77):0,f=n?0:s-1,p=n?1:-1,g=t<0||0===t&&1/t<0?1:0;for(t=Math.abs(t),isNaN(t)||t===1/0?(a=isNaN(t)?1:0,o=h):(o=Math.floor(Math.log(t)/Math.LN2),t*(c=Math.pow(2,-o))<1&&(o--,c*=2),(t+=o+d>=1?u/c:u*Math.pow(2,1-d))*c>=2&&(o++,c/=2),o+d>=h?(a=0,o=h):o+d>=1?(a=(t*c-1)*Math.pow(2,r),o+=d):(a=t*Math.pow(2,d-1)*Math.pow(2,r),o=0));r>=8;e[i+f]=255&a,f+=p,a/=256,r-=8);for(o=o<<r|a,l+=r;l>0;e[i+f]=255&o,f+=p,o/=256,l-=8);e[i+f-p]|=128*g}},8570:e=>{e.exports=i;var t=null;try{t=new WebAssembly.Instance(new WebAssembly.Module(new Uint8Array([0,97,115,109,1,0,0,0,1,13,2,96,0,1,127,96,4,127,127,127,127,1,127,3,7,6,0,1,1,1,1,1,6,6,1,127,1,65,0,11,7,50,6,3,109,117,108,0,1,5,100,105,118,95,115,0,2,5,100,105,118,95,117,0,3,5,114,101,109,95,115,0,4,5,114,101,109,95,117,0,5,8,103,101,116,95,104,105,103,104,0,0,10,191,1,6,4,0,35,0,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,126,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,127,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,128,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,129,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,130,34,4,66,32,135,167,36,0,32,4,167,11])),{}).exports}catch(e){}function i(e,t,i){this.low=0|e,this.high=0|t,this.unsigned=!!i}function n(e){return!0===(e&&e.__isLong__)}i.prototype.__isLong__,Object.defineProperty(i.prototype,\"__isLong__\",{value:!0}),i.isLong=n;var r={},s={};function o(e,t){var i,n,o;return t?(o=0<=(e>>>=0)&&e<256)&&(n=s[e])?n:(i=c(e,(0|e)<0?-1:0,!0),o&&(s[e]=i),i):(o=-128<=(e|=0)&&e<128)&&(n=r[e])?n:(i=c(e,e<0?-1:0,!1),o&&(r[e]=i),i)}function a(e,t){if(isNaN(e))return t?w:m;if(t){if(e<0)return w;if(e>=f)return A}else{if(e<=-p)return C;if(e+1>=p)return y}return e<0?a(-e,t).neg():c(e%u|0,e/u|0,t)}function c(e,t,n){return new i(e,t,n)}i.fromInt=o,i.fromNumber=a,i.fromBits=c;var l=Math.pow;function h(e,t,i){if(0===e.length)throw Error(\"empty string\");if(\"NaN\"===e||\"Infinity\"===e||\"+Infinity\"===e||\"-Infinity\"===e)return m;if(\"number\"==typeof t?(i=t,t=!1):t=!!t,(i=i||10)<2||36<i)throw RangeError(\"radix\");var n;if((n=e.indexOf(\"-\"))>0)throw Error(\"interior hyphen\");if(0===n)return h(e.substring(1),t,i).neg();for(var r=a(l(i,8)),s=m,o=0;o<e.length;o+=8){var c=Math.min(8,e.length-o),d=parseInt(e.substring(o,o+c),i);if(c<8){var u=a(l(i,c));s=s.mul(u).add(a(d))}else s=(s=s.mul(r)).add(a(d))}return s.unsigned=t,s}function d(e,t){return\"number\"==typeof e?a(e,t):\"string\"==typeof e?h(e,t):c(e.low,e.high,\"boolean\"==typeof t?t:e.unsigned)}i.fromString=h,i.fromValue=d;var u=4294967296,f=u*u,p=f/2,g=o(1<<24),m=o(0);i.ZERO=m;var w=o(0,!0);i.UZERO=w;var b=o(1);i.ONE=b;var F=o(1,!0);i.UONE=F;var v=o(-1);i.NEG_ONE=v;var y=c(-1,2147483647,!1);i.MAX_VALUE=y;var A=c(-1,-1,!0);i.MAX_UNSIGNED_VALUE=A;var C=c(0,-2147483648,!1);i.MIN_VALUE=C;var _=i.prototype;_.toInt=function(){return this.unsigned?this.low>>>0:this.low},_.toNumber=function(){return this.unsigned?(this.high>>>0)*u+(this.low>>>0):this.high*u+(this.low>>>0)},_.toString=function(e){if((e=e||10)<2||36<e)throw RangeError(\"radix\");if(this.isZero())return\"0\";if(this.isNegative()){if(this.eq(C)){var t=a(e),i=this.div(t),n=i.mul(t).sub(this);return i.toString(e)+n.toInt().toString(e)}return\"-\"+this.neg().toString(e)}for(var r=a(l(e,6),this.unsigned),s=this,o=\"\";;){var c=s.div(r),h=(s.sub(c.mul(r)).toInt()>>>0).toString(e);if((s=c).isZero())return h+o;for(;h.length<6;)h=\"0\"+h;o=\"\"+h+o}},_.getHighBits=function(){return this.high},_.getHighBitsUnsigned=function(){return this.high>>>0},_.getLowBits=function(){return this.low},_.getLowBitsUnsigned=function(){return this.low>>>0},_.getNumBitsAbs=function(){if(this.isNegative())return this.eq(C)?64:this.neg().getNumBitsAbs();for(var e=0!=this.high?this.high:this.low,t=31;t>0&&!(e&1<<t);t--);return 0!=this.high?t+33:t+1},_.isZero=function(){return 0===this.high&&0===this.low},_.eqz=_.isZero,_.isNegative=function(){return!this.unsigned&&this.high<0},_.isPositive=function(){return this.unsigned||this.high>=0},_.isOdd=function(){return!(1&~this.low)},_.isEven=function(){return!(1&this.low)},_.equals=function(e){return n(e)||(e=d(e)),(this.unsigned===e.unsigned||this.high>>>31!=1||e.high>>>31!=1)&&this.high===e.high&&this.low===e.low},_.eq=_.equals,_.notEquals=function(e){return!this.eq(e)},_.neq=_.notEquals,_.ne=_.notEquals,_.lessThan=function(e){return this.comp(e)<0},_.lt=_.lessThan,_.lessThanOrEqual=function(e){return this.comp(e)<=0},_.lte=_.lessThanOrEqual,_.le=_.lessThanOrEqual,_.greaterThan=function(e){return this.comp(e)>0},_.gt=_.greaterThan,_.greaterThanOrEqual=function(e){return this.comp(e)>=0},_.gte=_.greaterThanOrEqual,_.ge=_.greaterThanOrEqual,_.compare=function(e){if(n(e)||(e=d(e)),this.eq(e))return 0;var t=this.isNegative(),i=e.isNegative();return t&&!i?-1:!t&&i?1:this.unsigned?e.high>>>0>this.high>>>0||e.high===this.high&&e.low>>>0>this.low>>>0?-1:1:this.sub(e).isNegative()?-1:1},_.comp=_.compare,_.negate=function(){return!this.unsigned&&this.eq(C)?C:this.not().add(b)},_.neg=_.negate,_.add=function(e){n(e)||(e=d(e));var t=this.high>>>16,i=65535&this.high,r=this.low>>>16,s=65535&this.low,o=e.high>>>16,a=65535&e.high,l=e.low>>>16,h=0,u=0,f=0,p=0;return f+=(p+=s+(65535&e.low))>>>16,u+=(f+=r+l)>>>16,h+=(u+=i+a)>>>16,h+=t+o,c((f&=65535)<<16|(p&=65535),(h&=65535)<<16|(u&=65535),this.unsigned)},_.subtract=function(e){return n(e)||(e=d(e)),this.add(e.neg())},_.sub=_.subtract,_.multiply=function(e){if(this.isZero())return m;if(n(e)||(e=d(e)),t)return c(t.mul(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned);if(e.isZero())return m;if(this.eq(C))return e.isOdd()?C:m;if(e.eq(C))return this.isOdd()?C:m;if(this.isNegative())return e.isNegative()?this.neg().mul(e.neg()):this.neg().mul(e).neg();if(e.isNegative())return this.mul(e.neg()).neg();if(this.lt(g)&&e.lt(g))return a(this.toNumber()*e.toNumber(),this.unsigned);var i=this.high>>>16,r=65535&this.high,s=this.low>>>16,o=65535&this.low,l=e.high>>>16,h=65535&e.high,u=e.low>>>16,f=65535&e.low,p=0,w=0,b=0,F=0;return b+=(F+=o*f)>>>16,w+=(b+=s*f)>>>16,b&=65535,w+=(b+=o*u)>>>16,p+=(w+=r*f)>>>16,w&=65535,p+=(w+=s*u)>>>16,w&=65535,p+=(w+=o*h)>>>16,p+=i*f+r*u+s*h+o*l,c((b&=65535)<<16|(F&=65535),(p&=65535)<<16|(w&=65535),this.unsigned)},_.mul=_.multiply,_.divide=function(e){if(n(e)||(e=d(e)),e.isZero())throw Error(\"division by zero\");var i,r,s;if(t)return this.unsigned||-2147483648!==this.high||-1!==e.low||-1!==e.high?c((this.unsigned?t.div_u:t.div_s)(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned):this;if(this.isZero())return this.unsigned?w:m;if(this.unsigned){if(e.unsigned||(e=e.toUnsigned()),e.gt(this))return w;if(e.gt(this.shru(1)))return F;s=w}else{if(this.eq(C))return e.eq(b)||e.eq(v)?C:e.eq(C)?b:(i=this.shr(1).div(e).shl(1)).eq(m)?e.isNegative()?b:v:(r=this.sub(e.mul(i)),s=i.add(r.div(e)));if(e.eq(C))return this.unsigned?w:m;if(this.isNegative())return e.isNegative()?this.neg().div(e.neg()):this.neg().div(e).neg();if(e.isNegative())return this.div(e.neg()).neg();s=m}for(r=this;r.gte(e);){i=Math.max(1,Math.floor(r.toNumber()/e.toNumber()));for(var o=Math.ceil(Math.log(i)/Math.LN2),h=o<=48?1:l(2,o-48),u=a(i),f=u.mul(e);f.isNegative()||f.gt(r);)f=(u=a(i-=h,this.unsigned)).mul(e);u.isZero()&&(u=b),s=s.add(u),r=r.sub(f)}return s},_.div=_.divide,_.modulo=function(e){return n(e)||(e=d(e)),t?c((this.unsigned?t.rem_u:t.rem_s)(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned):this.sub(this.div(e).mul(e))},_.mod=_.modulo,_.rem=_.modulo,_.not=function(){return c(~this.low,~this.high,this.unsigned)},_.and=function(e){return n(e)||(e=d(e)),c(this.low&e.low,this.high&e.high,this.unsigned)},_.or=function(e){return n(e)||(e=d(e)),c(this.low|e.low,this.high|e.high,this.unsigned)},_.xor=function(e){return n(e)||(e=d(e)),c(this.low^e.low,this.high^e.high,this.unsigned)},_.shiftLeft=function(e){return 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e=this.high,t=this.low;return[e>>>24,e>>>16&255,e>>>8&255,255&e,t>>>24,t>>>16&255,t>>>8&255,255&t]},i.fromBytes=function(e,t,n){return n?i.fromBytesLE(e,t):i.fromBytesBE(e,t)},i.fromBytesLE=function(e,t){return new i(e[0]|e[1]<<8|e[2]<<16|e[3]<<24,e[4]|e[5]<<8|e[6]<<16|e[7]<<24,t)},i.fromBytesBE=function(e,t){return new i(e[4]<<24|e[5]<<16|e[6]<<8|e[7],e[0]<<24|e[1]<<16|e[2]<<8|e[3],t)}},3503:(e,t,i)=>{var n,r,s,o,a;n=i(3939),r=i(2151).utf8,s=i(652),o=i(2151).bin,(a=function(e,t){e.constructor==String?e=t&&\"binary\"===t.encoding?o.stringToBytes(e):r.stringToBytes(e):s(e)?e=Array.prototype.slice.call(e,0):Array.isArray(e)||e.constructor===Uint8Array||(e=e.toString());for(var i=n.bytesToWords(e),c=8*e.length,l=1732584193,h=-271733879,d=-1732584194,u=271733878,f=0;f<i.length;f++)i[f]=16711935&(i[f]<<8|i[f]>>>24)|4278255360&(i[f]<<24|i[f]>>>8);i[c>>>5]|=128<<c%32,i[14+(c+64>>>9<<4)]=c;var p=a._ff,g=a._gg,m=a._hh,w=a._ii;for(f=0;f<i.length;f+=16){var 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e.state=c,c.strm=e,c.wrap=a,c.gzhead=null,c.w_bits=n,c.w_size=1<<c.w_bits,c.w_mask=c.w_size-1,c.hash_bits=s+7,c.hash_size=1<<c.hash_bits,c.hash_mask=c.hash_size-1,c.hash_shift=~~((c.hash_bits+F-1)/F),c.window=new r.Buf8(2*c.w_size),c.head=new r.Buf16(c.hash_size),c.prev=new r.Buf16(c.w_size),c.lit_bufsize=1<<s+6,c.pending_buf_size=4*c.lit_bufsize,c.pending_buf=new r.Buf8(c.pending_buf_size),c.d_buf=1*c.lit_bufsize,c.l_buf=3*c.lit_bufsize,c.level=t,c.strategy=o,c.method=i,U(e)}n=[new H(0,0,0,0,(function(e,t){var i=65535;for(i>e.pending_buf_size-5&&(i=e.pending_buf_size-5);;){if(e.lookahead<=1){if(T(e),0===e.lookahead&&t===l)return 1;if(0===e.lookahead)break}e.strstart+=e.lookahead,e.lookahead=0;var n=e.block_start+i;if((0===e.strstart||e.strstart>=n)&&(e.lookahead=e.strstart-n,e.strstart=n,N(e,!1),0===e.strm.avail_out))return 1;if(e.strstart-e.block_start>=e.w_size-y&&(N(e,!1),0===e.strm.avail_out))return 1}return 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1;if(0===e.lookahead)break}if(e.match_length=0,e.lookahead>=F&&e.strstart>0&&(n=a[r=e.strstart-1])===a[++r]&&n===a[++r]&&n===a[++r]){o=e.strstart+v;do{}while(n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&r<o);e.match_length=v-(o-r),e.match_length>e.lookahead&&(e.match_length=e.lookahead)}if(e.match_length>=F?(i=s._tr_tally(e,1,e.match_length-F),e.lookahead-=e.match_length,e.strstart+=e.match_length,e.match_length=0):(i=s._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++),i&&(N(e,!1),0===e.strm.avail_out))return 1}return e.insert=0,4===t?(N(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(N(e,!1),0===e.strm.avail_out)?1:2}(r,t):n[r.level].func(r,t);if(3!==p&&4!==p||(r.status=x),1===p||3===p)return 0===e.avail_out&&(r.last_flush=-1),h;if(2===p&&(1===t?s._tr_align(r):5!==t&&(s._tr_stored_block(r,0,0,!1),3===t&&(S(r.head),0===r.lookahead&&(r.strstart=0,r.block_start=0,r.insert=0))),E(e),0===e.avail_out))return r.last_flush=-1,h}return 4!==t?h:r.wrap<=0?1:(2===r.wrap?(B(r,255&e.adler),B(r,e.adler>>8&255),B(r,e.adler>>16&255),B(r,e.adler>>24&255),B(r,255&e.total_in),B(r,e.total_in>>8&255),B(r,e.total_in>>16&255),B(r,e.total_in>>24&255)):(M(r,e.adler>>>16),M(r,65535&e.adler)),E(e),r.wrap>0&&(r.wrap=-r.wrap),0!==r.pending?h:1)},t.deflateEnd=function(e){var t;return e&&e.state?(t=e.state.status)!==A&&69!==t&&73!==t&&91!==t&&t!==C&&t!==_&&t!==x?k(e,d):(e.state=null,t===_?k(e,-3):h):d},t.deflateSetDictionary=function(e,t){var i,n,s,a,c,l,u,f,p=t.length;if(!e||!e.state)return d;if(2===(a=(i=e.state).wrap)||1===a&&i.status!==A||i.lookahead)return d;for(1===a&&(e.adler=o(e.adler,t,p,0)),i.wrap=0,p>=i.w_size&&(0===a&&(S(i.head),i.strstart=0,i.block_start=0,i.insert=0),f=new r.Buf8(i.w_size),r.arraySet(f,t,p-i.w_size,i.w_size,0),t=f,p=i.w_size),c=e.avail_in,l=e.next_in,u=e.input,e.avail_in=p,e.next_in=0,e.input=t,T(i);i.lookahead>=F;){n=i.strstart,s=i.lookahead-(F-1);do{i.ins_h=(i.ins_h<<i.hash_shift^i.window[n+F-1])&i.hash_mask,i.prev[n&i.w_mask]=i.head[i.ins_h],i.head[i.ins_h]=n,n++}while(--s);i.strstart=n,i.lookahead=F-1,T(i)}return i.strstart+=i.lookahead,i.block_start=i.strstart,i.insert=i.lookahead,i.lookahead=0,i.match_length=i.prev_length=F-1,i.match_available=0,e.next_in=l,e.input=u,e.avail_in=c,i.wrap=a,h},t.deflateInfo=\"pako deflate (from Nodeca project)\"},7414:e=>{e.exports=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name=\"\",this.comment=\"\",this.hcrc=0,this.done=!1}},7293:e=>{e.exports=function(e,t){var i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_,x,k;i=e.state,n=e.next_in,x=e.input,r=n+(e.avail_in-5),s=e.next_out,k=e.output,o=s-(t-e.avail_out),a=s+(e.avail_out-257),c=i.dmax,l=i.wsize,h=i.whave,d=i.wnext,u=i.window,f=i.hold,p=i.bits,g=i.lencode,m=i.distcode,w=(1<<i.lenbits)-1,b=(1<<i.distbits)-1;e:do{p<15&&(f+=x[n++]<<p,p+=8,f+=x[n++]<<p,p+=8),F=g[f&w];t:for(;;){if(f>>>=v=F>>>24,p-=v,0==(v=F>>>16&255))k[s++]=65535&F;else{if(!(16&v)){if(64&v){if(32&v){i.mode=12;break e}e.msg=\"invalid literal/length code\",i.mode=30;break e}F=g[(65535&F)+(f&(1<<v)-1)];continue t}for(y=65535&F,(v&=15)&&(p<v&&(f+=x[n++]<<p,p+=8),y+=f&(1<<v)-1,f>>>=v,p-=v),p<15&&(f+=x[n++]<<p,p+=8,f+=x[n++]<<p,p+=8),F=m[f&b];;){if(f>>>=v=F>>>24,p-=v,16&(v=F>>>16&255)){if(A=65535&F,p<(v&=15)&&(f+=x[n++]<<p,(p+=8)<v&&(f+=x[n++]<<p,p+=8)),(A+=f&(1<<v)-1)>c){e.msg=\"invalid distance too far back\",i.mode=30;break e}if(f>>>=v,p-=v,A>(v=s-o)){if((v=A-v)>h&&i.sane){e.msg=\"invalid distance too far back\",i.mode=30;break e}if(C=0,_=u,0===d){if(C+=l-v,v<y){y-=v;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}}else if(d<v){if(C+=l+d-v,(v-=d)<y){y-=v;do{k[s++]=u[C++]}while(--v);if(C=0,d<y){y-=v=d;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}}}else if(C+=d-v,v<y){y-=v;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}for(;y>2;)k[s++]=_[C++],k[s++]=_[C++],k[s++]=_[C++],y-=3;y&&(k[s++]=_[C++],y>1&&(k[s++]=_[C++]))}else{C=s-A;do{k[s++]=k[C++],k[s++]=k[C++],k[s++]=k[C++],y-=3}while(y>2);y&&(k[s++]=k[C++],y>1&&(k[s++]=k[C++]))}break}if(64&v){e.msg=\"invalid distance code\",i.mode=30;break e}F=m[(65535&F)+(f&(1<<v)-1)]}}break}}while(n<r&&s<a);n-=y=p>>3,f&=(1<<(p-=y<<3))-1,e.next_in=n,e.next_out=s,e.avail_in=n<r?r-n+5:5-(n-r),e.avail_out=s<a?a-s+257:257-(s-a),i.hold=f,i.bits=p}},1447:(e,t,i)=>{var n=i(9805),r=i(3269),s=i(4823),o=i(7293),a=i(1998),c=0,l=-2,h=1,d=12,u=30,f=852,p=592;function g(e){return(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24)}function m(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new n.Buf16(320),this.work=new n.Buf16(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}function w(e){var t;return e&&e.state?(t=e.state,e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=h,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new n.Buf32(f),t.distcode=t.distdyn=new n.Buf32(p),t.sane=1,t.back=-1,c):l}function b(e){var t;return e&&e.state?((t=e.state).wsize=0,t.whave=0,t.wnext=0,w(e)):l}function F(e,t){var i,n;return e&&e.state?(n=e.state,t<0?(i=0,t=-t):(i=1+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?l:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,b(e))):l}function v(e,t){var i,n;return e?(n=new m,e.state=n,n.window=null,(i=F(e,t))!==c&&(e.state=null),i):l}var y,A,C=!0;function _(e){if(C){var t;for(y=new n.Buf32(512),A=new n.Buf32(32),t=0;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(a(1,e.lens,0,288,y,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;a(2,e.lens,0,32,A,0,e.work,{bits:5}),C=!1}e.lencode=y,e.lenbits=9,e.distcode=A,e.distbits=5}function x(e,t,i,r){var s,o=e.state;return null===o.window&&(o.wsize=1<<o.wbits,o.wnext=0,o.whave=0,o.window=new n.Buf8(o.wsize)),r>=o.wsize?(n.arraySet(o.window,t,i-o.wsize,o.wsize,0),o.wnext=0,o.whave=o.wsize):((s=o.wsize-o.wnext)>r&&(s=r),n.arraySet(o.window,t,i-r,s,o.wnext),(r-=s)?(n.arraySet(o.window,t,i-r,r,0),o.wnext=r,o.whave=o.wsize):(o.wnext+=s,o.wnext===o.wsize&&(o.wnext=0),o.whave<o.wsize&&(o.whave+=s))),0}t.inflateReset=b,t.inflateReset2=F,t.inflateResetKeep=w,t.inflateInit=function(e){return v(e,15)},t.inflateInit2=v,t.inflate=function(e,t){var i,f,p,m,w,b,F,v,y,A,C,k,I,S,E,N,B,M,R,D,T,L,z,H,P=0,O=new n.Buf8(4),U=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];if(!e||!e.state||!e.output||!e.input&&0!==e.avail_in)return l;(i=e.state).mode===d&&(i.mode=13),w=e.next_out,p=e.output,F=e.avail_out,m=e.next_in,f=e.input,b=e.avail_in,v=i.hold,y=i.bits,A=b,C=F,L=c;e:for(;;)switch(i.mode){case h:if(0===i.wrap){i.mode=13;break}for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(2&i.wrap&&35615===v){i.check=0,O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0),v=0,y=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&v)<<8)+(v>>8))%31){e.msg=\"incorrect header check\",i.mode=u;break}if(8!=(15&v)){e.msg=\"unknown compression method\",i.mode=u;break}if(y-=4,T=8+(15&(v>>>=4)),0===i.wbits)i.wbits=T;else if(T>i.wbits){e.msg=\"invalid window size\",i.mode=u;break}i.dmax=1<<T,e.adler=i.check=1,i.mode=512&v?10:d,v=0,y=0;break;case 2:for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(i.flags=v,8!=(255&i.flags)){e.msg=\"unknown compression method\",i.mode=u;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=u;break}i.head&&(i.head.text=v>>8&1),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0,i.mode=3;case 3:for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.head&&(i.head.time=v),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,O[2]=v>>>16&255,O[3]=v>>>24&255,i.check=s(i.check,O,4,0)),v=0,y=0,i.mode=4;case 4:for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.head&&(i.head.xflags=255&v,i.head.os=v>>8),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0,i.mode=5;case 5:if(1024&i.flags){for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.length=v,i.head&&(i.head.extra_len=v),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&((k=i.length)>b&&(k=b),k&&(i.head&&(T=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Array(i.head.extra_len)),n.arraySet(i.head.extra,f,m,k,T)),512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,i.length-=k),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===b)break e;k=0;do{T=f[m+k++],i.head&&T&&i.length<65536&&(i.head.name+=String.fromCharCode(T))}while(T&&k<b);if(512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,T)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===b)break e;k=0;do{T=f[m+k++],i.head&&T&&i.length<65536&&(i.head.comment+=String.fromCharCode(T))}while(T&&k<b);if(512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,T)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=u;break}v=0,y=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=d;break;case 10:for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}e.adler=i.check=g(v),v=0,y=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=w,e.avail_out=F,e.next_in=m,e.avail_in=b,i.hold=v,i.bits=y,2;e.adler=i.check=1,i.mode=d;case d:if(5===t||6===t)break e;case 13:if(i.last){v>>>=7&y,y-=7&y,i.mode=27;break}for(;y<3;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}switch(i.last=1&v,y-=1,3&(v>>>=1)){case 0:i.mode=14;break;case 1:if(_(i),i.mode=20,6===t){v>>>=2,y-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg=\"invalid block type\",i.mode=u}v>>>=2,y-=2;break;case 14:for(v>>>=7&y,y-=7&y;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if((65535&v)!=(v>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=u;break}if(i.length=65535&v,v=0,y=0,i.mode=15,6===t)break e;case 15:i.mode=16;case 16:if(k=i.length){if(k>b&&(k=b),k>F&&(k=F),0===k)break e;n.arraySet(p,f,m,k,w),b-=k,m+=k,F-=k,w+=k,i.length-=k;break}i.mode=d;break;case 17:for(;y<14;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(i.nlen=257+(31&v),v>>>=5,y-=5,i.ndist=1+(31&v),v>>>=5,y-=5,i.ncode=4+(15&v),v>>>=4,y-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=u;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;y<3;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.lens[U[i.have++]]=7&v,v>>>=3,y-=3}for(;i.have<19;)i.lens[U[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,z={bits:i.lenbits},L=a(0,i.lens,0,19,i.lencode,0,i.work,z),i.lenbits=z.bits,L){e.msg=\"invalid code lengths set\",i.mode=u;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;N=(P=i.lencode[v&(1<<i.lenbits)-1])>>>16&255,B=65535&P,!((E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(B<16)v>>>=E,y-=E,i.lens[i.have++]=B;else{if(16===B){for(H=E+2;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v>>>=E,y-=E,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=u;break}T=i.lens[i.have-1],k=3+(3&v),v>>>=2,y-=2}else if(17===B){for(H=E+3;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}y-=E,T=0,k=3+(7&(v>>>=E)),v>>>=3,y-=3}else{for(H=E+7;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}y-=E,T=0,k=11+(127&(v>>>=E)),v>>>=7,y-=7}if(i.have+k>i.nlen+i.ndist){e.msg=\"invalid bit length 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e;b--,v+=f[m++]<<y,y+=8}if(N&&!(240&N)){for(M=E,R=N,D=B;N=(P=i.lencode[D+((v&(1<<M+R)-1)>>M)])>>>16&255,B=65535&P,!(M+(E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}v>>>=M,y-=M,i.back+=M}if(v>>>=E,y-=E,i.back+=E,i.length=B,0===N){i.mode=26;break}if(32&N){i.back=-1,i.mode=d;break}if(64&N){e.msg=\"invalid literal/length code\",i.mode=u;break}i.extra=15&N,i.mode=22;case 22:if(i.extra){for(H=i.extra;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.length+=v&(1<<i.extra)-1,v>>>=i.extra,y-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;N=(P=i.distcode[v&(1<<i.distbits)-1])>>>16&255,B=65535&P,!((E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(!(240&N)){for(M=E,R=N,D=B;N=(P=i.distcode[D+((v&(1<<M+R)-1)>>M)])>>>16&255,B=65535&P,!(M+(E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}v>>>=M,y-=M,i.back+=M}if(v>>>=E,y-=E,i.back+=E,64&N){e.msg=\"invalid distance code\",i.mode=u;break}i.offset=B,i.extra=15&N,i.mode=24;case 24:if(i.extra){for(H=i.extra;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.offset+=v&(1<<i.extra)-1,v>>>=i.extra,y-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=u;break}i.mode=25;case 25:if(0===F)break e;if(k=C-F,i.offset>k){if((k=i.offset-k)>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=u;break}k>i.wnext?(k-=i.wnext,I=i.wsize-k):I=i.wnext-k,k>i.length&&(k=i.length),S=i.window}else S=p,I=w-i.offset,k=i.length;k>F&&(k=F),F-=k,i.length-=k;do{p[w++]=S[I++]}while(--k);0===i.length&&(i.mode=21);break;case 26:if(0===F)break e;p[w++]=i.length,F--,i.mode=21;break;case 27:if(i.wrap){for(;y<32;){if(0===b)break e;b--,v|=f[m++]<<y,y+=8}if(C-=F,e.total_out+=C,i.total+=C,C&&(e.adler=i.check=i.flags?s(i.check,p,C,w-C):r(i.check,p,C,w-C)),C=F,(i.flags?v:g(v))!==i.check){e.msg=\"incorrect data check\",i.mode=u;break}v=0,y=0}i.mode=28;case 28:if(i.wrap&&i.flags){for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=u;break}v=0,y=0}i.mode=29;case 29:L=1;break e;case u:L=-3;break e;case 31:return-4;default:return l}return e.next_out=w,e.avail_out=F,e.next_in=m,e.avail_in=b,i.hold=v,i.bits=y,(i.wsize||C!==e.avail_out&&i.mode<u&&(i.mode<27||4!==t))&&x(e,e.output,e.next_out,C-e.avail_out)?(i.mode=31,-4):(A-=e.avail_in,C-=e.avail_out,e.total_in+=A,e.total_out+=C,i.total+=C,i.wrap&&C&&(e.adler=i.check=i.flags?s(i.check,p,C,e.next_out-C):r(i.check,p,C,e.next_out-C)),e.data_type=i.bits+(i.last?64:0)+(i.mode===d?128:0)+(20===i.mode||15===i.mode?256:0),(0===A&&0===C||4===t)&&L===c&&(L=-5),L)},t.inflateEnd=function(e){if(!e||!e.state)return l;var t=e.state;return t.window&&(t.window=null),e.state=null,c},t.inflateGetHeader=function(e,t){var i;return e&&e.state&&2&(i=e.state).wrap?(i.head=t,t.done=!1,c):l},t.inflateSetDictionary=function(e,t){var i,n=t.length;return e&&e.state?0!==(i=e.state).wrap&&11!==i.mode?l:11===i.mode&&r(1,t,n,0)!==i.check?-3:x(e,t,n,n)?(i.mode=31,-4):(i.havedict=1,c):l},t.inflateInfo=\"pako inflate (from Nodeca project)\"},1998:(e,t,i)=>{var n=i(9805),r=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],s=[16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78],o=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0],a=[16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64];e.exports=function(e,t,i,c,l,h,d,u){var f,p,g,m,w,b,F,v,y,A=u.bits,C=0,_=0,x=0,k=0,I=0,S=0,E=0,N=0,B=0,M=0,R=null,D=0,T=new n.Buf16(16),L=new n.Buf16(16),z=null,H=0;for(C=0;C<=15;C++)T[C]=0;for(_=0;_<c;_++)T[t[i+_]]++;for(I=A,k=15;k>=1&&0===T[k];k--);if(I>k&&(I=k),0===k)return l[h++]=20971520,l[h++]=20971520,u.bits=1,0;for(x=1;x<k&&0===T[x];x++);for(I<x&&(I=x),N=1,C=1;C<=15;C++)if(N<<=1,(N-=T[C])<0)return-1;if(N>0&&(0===e||1!==k))return-1;for(L[1]=0,C=1;C<15;C++)L[C+1]=L[C]+T[C];for(_=0;_<c;_++)0!==t[i+_]&&(d[L[t[i+_]]++]=_);if(0===e?(R=z=d,b=19):1===e?(R=r,D-=257,z=s,H-=257,b=256):(R=o,z=a,b=-1),M=0,_=0,C=x,w=h,S=I,E=0,g=-1,m=(B=1<<I)-1,1===e&&B>852||2===e&&B>592)return 1;for(;;){F=C-E,d[_]<b?(v=0,y=d[_]):d[_]>b?(v=z[H+d[_]],y=R[D+d[_]]):(v=96,y=0),f=1<<C-E,x=p=1<<S;do{l[w+(M>>E)+(p-=f)]=F<<24|v<<16|y}while(0!==p);for(f=1<<C-1;M&f;)f>>=1;if(0!==f?(M&=f-1,M+=f):M=0,_++,0==--T[C]){if(C===k)break;C=t[i+d[_]]}if(C>I&&(M&m)!==g){for(0===E&&(E=I),w+=x,N=1<<(S=C-E);S+E<k&&!((N-=T[S+E])<=0);)S++,N<<=1;if(B+=1<<S,1===e&&B>852||2===e&&B>592)return 1;l[g=M&m]=I<<24|S<<16|w-h}}return 0!==M&&(l[w+M]=C-E<<24|64<<16),u.bits=I,0}},4674:e=>{e.exports={2:\"need dictionary\",1:\"stream end\",0:\"\",\"-1\":\"file error\",\"-2\":\"stream error\",\"-3\":\"data error\",\"-4\":\"insufficient memory\",\"-5\":\"buffer error\",\"-6\":\"incompatible version\"}},3665:(e,t,i)=>{var n=i(9805);function r(e){for(var t=e.length;--t>=0;)e[t]=0}var s=15,o=16,a=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0],c=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13],l=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7],h=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],d=new Array(576);r(d);var u=new Array(60);r(u);var f=new Array(512);r(f);var p=new Array(256);r(p);var g=new Array(29);r(g);var m,w,b,F=new Array(30);function v(e,t,i,n,r){this.static_tree=e,this.extra_bits=t,this.extra_base=i,this.elems=n,this.max_length=r,this.has_stree=e&&e.length}function y(e,t){this.dyn_tree=e,this.max_code=0,this.stat_desc=t}function A(e){return e<256?f[e]:f[256+(e>>>7)]}function C(e,t){e.pending_buf[e.pending++]=255&t,e.pending_buf[e.pending++]=t>>>8&255}function 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M(e,t,i){var n,r,s,o,l=0;if(0!==e.last_lit)do{n=e.pending_buf[e.d_buf+2*l]<<8|e.pending_buf[e.d_buf+2*l+1],r=e.pending_buf[e.l_buf+l],l++,0===n?x(e,r,t):(x(e,(s=p[r])+256+1,t),0!==(o=a[s])&&_(e,r-=g[s],o),x(e,s=A(--n),i),0!==(o=c[s])&&_(e,n-=F[s],o))}while(l<e.last_lit);x(e,256,t)}function R(e,t){var i,n,r,o=t.dyn_tree,a=t.stat_desc.static_tree,c=t.stat_desc.has_stree,l=t.stat_desc.elems,h=-1;for(e.heap_len=0,e.heap_max=573,i=0;i<l;i++)0!==o[2*i]?(e.heap[++e.heap_len]=h=i,e.depth[i]=0):o[2*i+1]=0;for(;e.heap_len<2;)o[2*(r=e.heap[++e.heap_len]=h<2?++h:0)]=1,e.depth[r]=0,e.opt_len--,c&&(e.static_len-=a[2*r+1]);for(t.max_code=h,i=e.heap_len>>1;i>=1;i--)B(e,o,i);r=l;do{i=e.heap[1],e.heap[1]=e.heap[e.heap_len--],B(e,o,1),n=e.heap[1],e.heap[--e.heap_max]=i,e.heap[--e.heap_max]=n,o[2*r]=o[2*i]+o[2*n],e.depth[r]=(e.depth[i]>=e.depth[n]?e.depth[i]:e.depth[n])+1,o[2*i+1]=o[2*n+1]=r,e.heap[1]=r++,B(e,o,1)}while(e.heap_len>=2);e.heap[--e.heap_max]=e.heap[1],function(e,t){var i,n,r,o,a,c,l=t.dyn_tree,h=t.max_code,d=t.stat_desc.static_tree,u=t.stat_desc.has_stree,f=t.stat_desc.extra_bits,p=t.stat_desc.extra_base,g=t.stat_desc.max_length,m=0;for(o=0;o<=s;o++)e.bl_count[o]=0;for(l[2*e.heap[e.heap_max]+1]=0,i=e.heap_max+1;i<573;i++)(o=l[2*l[2*(n=e.heap[i])+1]+1]+1)>g&&(o=g,m++),l[2*n+1]=o,n>h||(e.bl_count[o]++,a=0,n>=p&&(a=f[n-p]),c=l[2*n],e.opt_len+=c*(o+a),u&&(e.static_len+=c*(d[2*n+1]+a)));if(0!==m){do{for(o=g-1;0===e.bl_count[o];)o--;e.bl_count[o]--,e.bl_count[o+1]+=2,e.bl_count[g]--,m-=2}while(m>0);for(o=g;0!==o;o--)for(n=e.bl_count[o];0!==n;)(r=e.heap[--i])>h||(l[2*r+1]!==o&&(e.opt_len+=(o-l[2*r+1])*l[2*r],l[2*r+1]=o),n--)}}(e,t),I(o,h,e.bl_count)}function D(e,t,i){var n,r,s=-1,o=t[1],a=0,c=7,l=4;for(0===o&&(c=138,l=3),t[2*(i+1)+1]=65535,n=0;n<=i;n++)r=o,o=t[2*(n+1)+1],++a<c&&r===o||(a<l?e.bl_tree[2*r]+=a:0!==r?(r!==s&&e.bl_tree[2*r]++,e.bl_tree[32]++):a<=10?e.bl_tree[34]++:e.bl_tree[36]++,a=0,s=r,0===o?(c=138,l=3):r===o?(c=6,l=3):(c=7,l=4))}function 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v(d,a,257,286,s),w=new v(u,c,0,30,s),b=new v(new Array(0),l,0,19,7)}(),L=!0),e.l_desc=new y(e.dyn_ltree,m),e.d_desc=new y(e.dyn_dtree,w),e.bl_desc=new y(e.bl_tree,b),e.bi_buf=0,e.bi_valid=0,S(e)},t._tr_stored_block=z,t._tr_flush_block=function(e,t,i,n){var r,s,o=0;e.level>0?(2===e.strm.data_type&&(e.strm.data_type=function(e){var t,i=4093624447;for(t=0;t<=31;t++,i>>>=1)if(1&i&&0!==e.dyn_ltree[2*t])return 0;if(0!==e.dyn_ltree[18]||0!==e.dyn_ltree[20]||0!==e.dyn_ltree[26])return 1;for(t=32;t<256;t++)if(0!==e.dyn_ltree[2*t])return 1;return 0}(e)),R(e,e.l_desc),R(e,e.d_desc),o=function(e){var t;for(D(e,e.dyn_ltree,e.l_desc.max_code),D(e,e.dyn_dtree,e.d_desc.max_code),R(e,e.bl_desc),t=18;t>=3&&0===e.bl_tree[2*h[t]+1];t--);return e.opt_len+=3*(t+1)+5+5+4,t}(e),r=e.opt_len+3+7>>>3,(s=e.static_len+3+7>>>3)<=r&&(r=s)):r=s=i+5,i+4<=r&&-1!==t?z(e,t,i,n):4===e.strategy||s===r?(_(e,2+(n?1:0),3),M(e,d,u)):(_(e,4+(n?1:0),3),function(e,t,i,n){var r;for(_(e,t-257,5),_(e,i-1,5),_(e,n-4,4),r=0;r<n;r++)_(e,e.bl_tree[2*h[r]+1],3);T(e,e.dyn_ltree,t-1),T(e,e.dyn_dtree,i-1)}(e,e.l_desc.max_code+1,e.d_desc.max_code+1,o+1),M(e,e.dyn_ltree,e.dyn_dtree)),S(e),n&&E(e)},t._tr_tally=function(e,t,i){return e.pending_buf[e.d_buf+2*e.last_lit]=t>>>8&255,e.pending_buf[e.d_buf+2*e.last_lit+1]=255&t,e.pending_buf[e.l_buf+e.last_lit]=255&i,e.last_lit++,0===t?e.dyn_ltree[2*i]++:(e.matches++,t--,e.dyn_ltree[2*(p[i]+256+1)]++,e.dyn_dtree[2*A(t)]++),e.last_lit===e.lit_bufsize-1},t._tr_align=function(e){_(e,2,3),x(e,256,d),function(e){16===e.bi_valid?(C(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=255&e.bi_buf,e.bi_buf>>=8,e.bi_valid-=8)}(e)}},4442:e=>{e.exports=function(){this.input=null,this.next_in=0,this.avail_in=0,this.total_in=0,this.output=null,this.next_out=0,this.avail_out=0,this.total_out=0,this.msg=\"\",this.state=null,this.data_type=2,this.adler=0}},7392:e=>{class t{constructor(e={}){if(!(e.maxSize&&e.maxSize>0))throw new TypeError(\"`maxSize` must be a number greater than 0\");this.maxSize=e.maxSize,this.cache=new Map,this.oldCache=new Map,this._size=0}_set(e,t){this.cache.set(e,t),this._size++,this._size>=this.maxSize&&(this._size=0,this.oldCache=this.cache,this.cache=new Map)}get(e){if(this.cache.has(e))return this.cache.get(e);if(this.oldCache.has(e)){const t=this.oldCache.get(e);return this.oldCache.delete(e),this._set(e,t),t}}set(e,t){return this.cache.has(e)?this.cache.set(e,t):this._set(e,t),this}has(e){return this.cache.has(e)||this.oldCache.has(e)}peek(e){return this.cache.has(e)?this.cache.get(e):this.oldCache.has(e)?this.oldCache.get(e):void 0}delete(e){const t=this.cache.delete(e);return t&&this._size--,this.oldCache.delete(e)||t}clear(){this.cache.clear(),this.oldCache.clear(),this._size=0}*keys(){for(const[e]of this)yield e}*values(){for(const[,e]of this)yield e}*[Symbol.iterator](){for(const e of this.cache)yield e;for(const e of this.oldCache){const[t]=e;this.cache.has(t)||(yield e)}}get size(){let e=0;for(const t of this.oldCache.keys())this.cache.has(t)||e++;return this._size+e}}e.exports=t},1307:function(e,t,i){var n;n=e=>(()=>{var 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MRg0BIAggDEEBaiICNgIAIAQgDGohCyACIQwgCy0AAA0ODAALCyAGQgA3AwAgAEEANgKoASAAQQM2AgAgBkEIakIANwMACyAAIAEoAgQ2AhAgACABKAIQNgIUIAAoArAJIAEQmYCAgAAhDCAAIAApA0ggASgCBCAAKAIQa618Ig43A0ggACAAKQNQIAEoAhAgACgCFCICayILrXwiDzcDUCAOIAApAzBWDQ0gDyAAKQM4Vg0NAkACQAJAAkAgACgCIEF/ag4EAAMDAQMLIAEoAgwgAmogCyAAKAIYEI2AgIAArSEODAELIAEoAgwgAmogCyAAKQMYEI+AgIAAIQ4LIAAgDjcDGAsgDEEBRw0OAkAgACkDMCIOQn9RDQAgDiAGKQMAUg0OCwJAIAApAzgiDkJ/UQ0AQQchDCAOIAApA1BSDQ8LIAAgACkDSCAANQJAfCAAKQNgfCIPNwNgQgQhDgJAAkACQCAAKAIgQX9qDgQBAgIAAgtCCCEOCyAFIA4gD3w3AwALIAAgACkDaCAAKQNQfDcDaCAAIAVBGCAAKAJwEI2AgIAANgJwIABBBDYCACAAIAApA1hCAXw3A1gLAkAgBikDACIOQgODUA0AIA5CAXwhDiABKAIEIQwgASgCCCELA0AgCyAMRg0NIAEgDEEBaiICNgIEIAEoAgAgDGotAAANDiAGIA43AwAgDkIDgyEPIA5CAXwhDiACIQwgD0IAUg0ACwsgAEEFNgIAC0EBIQIgACgCIEF/ag4EBgcHBQcLIAAgARCSgICAACIMQQFHDQsgAEEHNgIAC0EAIAAoAhBrIQggAEGAAWopAwAhDiABKAIEIQwCQANAIA4gCCAMaq18QgODUA0BAkAgDCABKAIIRw0AIAAgARCTgICAAAwLCyABIAxBAWoiAjYCBCABKAIAIAxqIQsgAiEMIAstAAANCwwACwsgACABEJOAgIAAQQchDCAFIABBkAFqQRgQhICAgAANCiAAQQg2AgALIAAgAUEgEJSAgIAAIgxBAUcNCSAAQQk2AgBBDCELIABBDDYCrAEMAQsgACgCrAEhCwsgAEGoAWogACgCqAEiDGpBCGogASgCACABKAIEIgJqIAEoAgggAmsiAiALIAxrIgwgAiAMSRsiAhCHgICAABogASABKAIEIAJqNgIEQQAhDCAAQQAgACgCqAEgAmoiAiACIAAoAqwBIgtGGzYCqAEgAiALRw0HIAAQlYCAgAAhDAwHC0EBIQIgACABQcAAEJSAgIAAIgxBAUcNBgwBC0EBIQIgACABQSAQlICAgAAiDEEBRw0FCyAAIAI2AgAMAAsLQQYhDAwCC0EAIQwMAQtBByEMCwJAAkAgACgCJA0AAkACQCAMDgIAAwELQQdBCCABKAIEIAEoAghGGyEMCyABIAk2AhAgASADNgIEIAwPCwJAIAwNACADIAEoAgRHDQAgCSABKAIQRw0AIAAtACghASAAQQE6ACggAUEDdA8LIABBADoAKAsgDAuaAQEDfwJAIAAoAgQiBA0AIABCADcDCAsgAigCACEFA0ACQCAFIANJDQBBAA8LIAEgBWotAAAhBiACIAVBAWoiBTYCACAAIAZB/wBxrSAErYYgACkDCIQ3AwgCQAJAIAZBgAFxDQACQCAGDQBBByEGIAQNAgsgAEEANgIEQQEPC0EHIQYgACAEQQdqIgQ2AgQgBEE/Rw0BCwsgBguhAgIDfwF+IABBkAFqIQIgAUEEaiEDA0ACQCAAIAEoAgAgAyABKAIIEJGAgIAAIgRBAUYNACAAQYABaiIDIAMpAwAgASgCBCAAKAIQIgNrIgKtfDcDACAAIAMgASgCAGogAiAAKAIYEI2AgIAArTcDGCAEDwsCQAJAAkACQAJAIAAoAngOAwACAQMLIAAgACkDCCIFNwOIAQJAIAUgACkDWFENAEEHDwsgAEEBNgJ4DAMLIAAgACkDmAEgACkDCHw3A5gBIAAgAkEYIAAoAqABEI2AgIAANgKgASAAQQE2AnggACAAKQOIAUJ/fCIFNwOIAQwCCyAAQQI2AnggACAAKQOQASAAKQMIfDcDkAELIAApA4gBIQULIAVCAFINAAtBAQtAAQJ/IABBgAFqIgIgAikDACABKAIEIAAoAhAiAmsiA618NwMAIAAgAiABKAIAaiADIAAoAhgQjYCAgACtNwMYC3wBBH8gASgCBCEDIAEoAgghBANAAkAgBCADRw0AQQAPCyABIANBAWoiBTYCBAJAIAEoAgAgA2otAAAgACkDGCAAKAIEIgOtiKdB/wFxRg0AQQcPCyAAIANBCGoiBjYCBCAFIQMgBiACSQ0ACyAAQQA2AgQgAEIANwMYQQELbwEBf0EHIQECQCAAQboBai8AAEHZtAFHDQAgAEG0AWpBBkEAEI2AgIAAIABBsAFqKAAARw0AIABBgAFqKQMAQgKIIAA1ALQBUg0AIABBuAFqLQAADQBBAUEHIAAoAiAgAEG5AWotAABGGyEBCyABC7QCAQR/AkACQCAAKAIkRQ0AIAAoAgAhAwwBC0EAIQMgAEEAOgAoIABCADcDACAAQgA3AxggAEHIAGpBAEHkABCGgICAABogAEGsAWpBDDYCAEEBIQILIABByABqIQQCQAJAA0ACQCADQQpHDQAgASgCBCIDIAEoAggiBUYNAiABKAIAIQYCQANAIAYgA2otAAANASABIANBAWoiAzYCBCAAIAAoAgRBAWpBA3E2AgQgBSADRg0EDAALCwJAIAAoAgRFDQBBBw8LIAAoAiRFDQAgAEEAOgAoIABCADcDACAAQgA3AxggBEEAQeQAEIaAgIAAGiAAQQw2AqwBCyAAIAEQkICAgAAiA0EBRw0CQQohAyAAQQo2AgAMAAsLAkAgAg0AQQAPC0EHQQEgACgCBBshAwsgAwt1AQF/AkBBuAkQgICAgAAiAkUNACACIAA2AiQgAiAAIAEQm4CAgAAiADYCsAkCQCAARQ0AIAJBADoAKCACQgA3AwAgAkIANwMYIAJByABqQQBB5AAQhoCAgAAaIAJBrAFqQQw2AgAgAg8LIAIQgoCAgAALQQALHgACQCAARQ0AIAAoArAJEJ2AgIAAIAAQgoCAgAALC4ARAQx/IABB6N0BaiECIABB1ABqIQMgAEEcaiIEQQhqIQUCQAJAA0AgACgCQCEGAkACQAJAAkACQAJAAkACQAJAAkACQAJAAkACQAJAAkAgASgCBCIHIAEoAggiCEkNACAGQQdGDQEMEgsgBg4JAQIDBAUGBwAJDwsgACgCTCEGDAcLQQEhCSABIAdBAWo2AgQgASgCACAHai0AACIHRQ0IAkACQCAHQd8BSw0AIAdBAUcNAQsgAEGAAjsBUAJAIAAoAjwNACAAIAEoAgwgASgCECIGajYCGCAAIAEoAhQgBms2AiwLIARCADcCACAFQgA3AgAMCwsgAC0AUEUNCgwOCyABIAdBAWo2AgQgASgCACAHai0AACEHIABBAjYCQCAAIAdBCHQgACgCSGo2AkgMDAsgASAHQQFqNgIEIAEoAgAgB2otAAAhByAAQQM2AkAgACAHIAAoAkhqQQFqNgJIDAsLIAEgB0EBajYCBCABKAIAIAdqLQAAIQcgAEEENgJAIAAgB0EIdDYCTAwKCyABIAdBAWo2AgQgASgCACAHai0AACEHIAAgACgCRDYCQCAAIAcgACgCTGpBAWo2AkwMCQsgASAHQQFqNgIEQQchCSABKAIAIAdqLQAAIgdB4AFLDQNBACEGAkACQCAHQS1PDQBBACEIDAELIAdBU2oiByAHQf8BcUEtbiIIQS1sayEHIAhBAWohCAsgAEF/IAh0QX9zNgJ0AkAgB0H/AXFBCUkNACAHQXdqIgcgB0H/AXFBCW4iBkEJbGshByAGQQFqIQYLIAAgBjYCcCAAIAdB/wFxIgc2AmwgBiAHakEESw0DIANCADcCACADQQhqQgA3AgAgA0EQakEANgIAIABBfyAGdEF/czYCcEH4ACEHA0AgACAHakGACDsBACAHQQJqIgdB5N0BRw0ACyAAQQY2AkAgAEEFNgIIIABC/////w83AgALIAAoAkwiCUEFSQ0IAkAgACgCCCIHRQ0AIAdBf2ohBiABKAIEIQcgASgCCCEKA0AgCiAHRg0LIAEgB0EBaiIINgIEIAEoAgAgB2otAAAhByAAIAY2AgggACAHIAAoAgRBCHRyNgIEIAghByAGQX9qIgZBf0cNAAsLIABBBzYCQCAAIAlBe2oiBjYCTAsgACAAKAIgIgcgASgCFCABKAIQayIIIAAoAkgiCiAIIApJGyIIaiAAKAIsIgogCiAHayAISxs2AiggASgCCCIJIAEoAgQiCGshBwJAAkACQCAAKALk3QEiCg0AIAYNAUEAIQYLIABB5N0BaiILIApqQQRqIAEoAgAgCGogByAGIAprIgZBKiAKayIIIAggBksbIgYgBiAHSxsiBxCHgICAABoCQAJAIAcgACgC5N0BIghqIgYgACgCTEcNACALIAhqIAdqQQRqQQBBPyAGaxCGgICAABogACgC5N0BIAdqIQYMAQsCQCAGQRRLDQAgACAGNgLk3QEgASABKAIEIAdqNgIEDAMLIAZBa2ohBgsgAEEANgIQIAAgAjYCDCAAIAY2AhRBByEJIAAQmoCAgABFDQMgACgCECIIIAAoAuTdASIKIAdqSw0DIAAgACgCTCAIayIGNgJMAkAgCiAITQ0AIAAgCiAIayIHNgLk3QEgAiALIAhqQQRqIAcQhYCAgAAaDAILIABBADYC5N0BIAEgASgCBCAIIApraiIINgIEIAEoAggiCSAIayEHCwJAIAdBFUkNACAAIAg2AhAgACABKAIANgIMIAAgCUFraiAIIAZqIAcgBkEVakkbNgIUQQchCSAAEJqAgIAARQ0DIAAoAkwiByAAKAIQIgggASgCBGsiBkkNAyABIAg2AgQgACAHIAZrIgY2AkwgASgCCCAIayIHQRRLDQELIAIgASgCACAIaiAGIAcgByAGSxsiBxCHgICAABogACAHNgLk3QEgASABKAIEIAdqNgIECyAAKAIgIgYgACgCHCIIayEHAkAgACgCPEUNAAJAIAYgACgCLEcNACAAQQA2AiALIAEoAgwgASgCEGogACgCGCAIaiAHEIeAgIAAGiAAKAIgIQYLIAAgBjYCHCABIAEoAhAgB2oiBjYCECAAIAAoAkggB2siBzYCSAJAIAcNAEEHIQkgACgCTA0CIAAoAmgNAiAAKAIEDQIgAEEANgJADAULQQAhCSAGIAEoAhRGDQEgASgCBCABKAIIRw0GIAAoAuTdASAAKAJMTw0GDAELIAAoAkwiCkUNAUEAIQkgCCAHTQ0AA0AgASgCFCIGIAEoAhAiC00NASAAIAogCiAAKAIsIAAoAiAiDGsiDSAIIAdrIgggBiALayIGIAggBkkbIgYgBiANSxsiBiAGIApLGyIGazYCTCAMIAAoAhhqIAEoAgAgB2ogBhCFgICAABogACAAKAIgIAZqIgc2AiACQCAAKAIkIAdPDQAgACAHNgIkCwJAIAAoAjxFDQACQCAHIAAoAixHDQAgAEEANgIgCyABKAIMIAEoAhBqIAEoAgAgASgCBGogBhCFgICAABogACgCICEHCyAAIAc2AhwgASABKAIQIAZqNgIQIAEgASgCBCAGaiIHNgIEIAAoAkwiCkUNAiABKAIIIgggB0sNAAsLIAkPCyAAQQA2AkAMAwsgB0EYdEEYdUF/Sg0BIABBATYCQCAAIAdBEHRBgID8AHE2AkgCQCAHQcABSQ0AIABBBTYCRCAAQQA6AFEMAwsgAC0AUQ0DIABBBjYCRCAHQaABSQ0CIANCADcCACADQRBqQQA2AgAgA0EIakIANwIAQfgAIQcDQCAAIAdqQYAIOwEAIAdBAmoiB0Hk3QFHDQALCyAAQQU2AgggAEL/////DzcCAAwBCyAHQQJLDQEgAEKDgICAgAE3AkAMAAsLQQcPC0EAC/8XARJ/IABBGGohAQJAIABBIGooAgAiAiAAQShqKAIAIgNPDQAgAEHoAGoiBCgCAEUNACABIAQgACgCVBCegICAABogACgCKCEDIAAoAiAhAgsCQCACIANPDQAgAEHcDWohBSAAQegAaiEGIABB4BVqIQcgAEHUAGohCANAIAAoAhAiCSAAKAIUSw0BIAAgACgCZCIKQQV0aiAAKAJ0IAJxIgtBAXRqIgxB+ABqIQ0CQAJAIAAoAgAiBEGAgIAISQ0AIAAoAgQhDgwBCyAAIARBCHQiBDYCACAAIAlBAWoiAzYCECAAIAAoAgRBCHQgACgCDCAJai0AAHIiDjYCBCADIQkLAkACQCAOIARBC3YgDS8BACIPbCIDTw0AIAAgAzYCACANIA9BgBAgD2tBBXZqOwEAIAJBf2ohBAJAIAINACAAKAIsIARqIQQLAkACQCAAKAIkIg8NAEEAIQQMAQsgACgCGCAEai0AACEECyAAKAJwIAJxIAAoAmwiDXQgBEEIIA1rdmohDAJAAkAgCkEGSw0AQQEhBANAIAAgDEGADGxqIARBAXQiBGpB5B1qIQ0CQAJAIANB////B00NACADIQoMAQsgACADQQh0Igo2AgAgACAJQQFqIgM2AhAgACAOQQh0IAAoAgwgCWotAAByIg42AgQgAyEJCwJAAkAgDiAKQQt2IA0vAQAiD2wiA0kNACAAIA4gA2siDjYCBCAAIAogA2siAzYCACANIA8gD0EFdms7AQAgBEEBciEEDAELIAAgAzYCACANIA9BgBAgD2tBBXZqOwEACyAEQYACSQ0ADAILCyACIAAoAlQiDUF/c2ohBAJAIAIgDUsNACAAKAIsIARqIQQLAkACQCAPDQBBACEQDAELIAAoAhggBGotAAAhEAtBASEEQYACIQ0DQCAAIAxBgAxsaiAQQQF0IhAgDXEiESANaiAEakEBdGpB5B1qIQ8CQAJAIANB////B00NACADIQsMAQsgACADQQh0Igs2AgAgACAJQQFqIgM2AhAgACAOQQh0IAAoAgwgCWotAAByIg42AgQgAyEJCwJAAkAgDiALQQt2IA8vAQAiCmwiA08iEg0AIAAgAzYCACAKQYAQIAprQQV2aiEKDAELIAAgDiADayIONgIEIAAgCyADayIDNgIAIAogCkEFdmshCkEAIQ0LIA8gCjsBACANIBFzIQ0gBEEBdCASciIEQYACSQ0ACwsgACACQQFqNgIgIAAoAhggAmogBDoAAAJAIAAoAiQgACgCICICTw0AIAAgAjYCJAtBACEDAkAgACgCZCIEQQRJDQACQCAEQQlLDQAgBEF9aiEDDAELIARBemohAwsgACADNgJkDAELIAAgDiADayIONgIEIAAgBCADayIDNgIAIA0gDyAPQQV2azsBACAAIApBAXRqIg9B+ANqIQQCQAJAIANB////B00NACAJIQoMAQsgACADQQh0IgM2AgAgACAJQQFqIgo2AhAgACAOQQh0IAAoAgwgCWotAAByIg42AgQLAkACQCAOIANBC3YgBC8BACINbCIJSQ0AIAAgDiAJayIONgIEIAAgAyAJayIDNgIAIAQgDSANQQV2azsBACAPQZAEaiENAkACQCADQf///wdNDQAgCiEQDAELIAAgA0EIdCIDNgIAIAAgCkEBaiIQNgIQIAAgDkEIdCAAKAIMIApqLQAAciIONgIECwJAAkAgDiADQQt2IA0vAQAiCWwiBE8NACANIAlBgBAgCWtBBXZqOwEAIAxB2ARqIQMCQCAEQf///wdLDQAgACAEQQh0IgQ2AgAgACAQQQFqNgIQIAAgDkEIdCAAKAIMIBBqLQAAciIONgIECwJAIA4gBEELdiADLwEAIg1sIglJDQAgACAOIAlrNgIEIAAgBCAJazYCACADIA0gDUEFdms7AQAMAgsgAyANQYAQIA1rQQV2ajsBACAAIAk2AgAgAEEBNgJoIABBCUELIAAoAmRBB0kbNgJkDAMLIAAgDiAEayIONgIEIA0gCSAJQQV2azsBACAPQagEaiENAkACQCADIARrIgNB////B00NACAQIQoMAQsgACADQQh0IgM2AgAgACAQQQFqIgo2AhAgACAOQQh0IAAoAgwgEGotAAByIg42AgQLAkACQCAOIANBC3YgDS8BACIEbCIJTw0AIAAgCTYCACANIARBgBAgBGtBBXZqOwEAIAAoAlghAwwBCyAAIA4gCWsiDjYCBCANIAQgBEEFdms7AQAgD0HABGohBAJAIAMgCWsiA0H///8HSw0AIAAgA0EIdCIDNgIAIAAgCkEBajYCECAAIA5BCHQgACgCDCAKai0AAHIiDjYCBAsCQAJAIA4gA0ELdiAELwEAIg1sIglPDQAgACAJNgIAIAQgDUGAECANa0EFdmo7AQAgACgCXCEDDAELIAAgDiAJazYCBCAAIAMgCWs2AgAgACgCYCEDIAAgACgCXDYCYCAEIA0gDUEFdms7AQALIAAgACgCWDYCXAsgACAAKAJUNgJYIAAgAzYCVAsgAEEIQQsgACgCZEEHSRs2AmQgACAHIAsQn4CAgAAMAQsgBCANQYAQIA1rQQV2ajsBACAAIAk2AgAgACAAKAJcNgJgIAAgACkCVDcCWCAAQQdBCiAAKAJkQQdJGzYCZCAAIAUgCxCfgICAACAAKAJoIgNBfmpBAyADQQZJGyEKIAAoAgAhA0EBIQ4DQCAAIApBB3RqIA5BAXQiDmpB2AdqIQ0CQAJAIANBgICACEkNACAAKAIEIQQMAQsgACADQQh0IgM2AgAgACAAKAIQIgRBAWo2AhAgACAAKAIEQQh0IAQgACgCDGotAAByIgQ2AgQLAkACQCAEIANBC3YgDS8BACIJbCIPSQ0AIAAgBCAPayIENgIEIAAgAyAPayIDNgIAIA0gCSAJQQV2azsBACAOQQFyIQ4MAQsgACAPNgIAIA0gCUGAECAJa0EFdmo7AQAgDyEDCyAOQcAASQ0ACwJAIA5BQGoiCUEDSw0AIAAgCTYCVAwBCyAAIA5BAXFBAnIiDTYCVCAJQQF2IQ8CQCAJQQ1LDQAgACANIA9Bf2oiDHQiCzYCVEEBIQ0gCCALQQF0akGEC2ohEEE/IA5rIRFBACEPA0AgECARIA1qQQF0aiEOAkACQCADQf///wdNDQAgAyEKDAELIAAgA0EIdCIKNgIAIAAgACgCECIDQQFqNgIQIAAgBEEIdCADIAAoAgxqLQAAciIENgIECwJAAkAgBCAKQQt2IA4vAQAiCWwiA0kNACAAIAQgA2siBDYCBCAAIAogA2siAzYCACAOIAkgCUEFdms7AQAgAEEBIA90IAtqIgs2AlQgDUEBdEEBciENDAELIAAgAzYCACAOIAlBgBAgCWtBBXZqOwEAIA1BAXQhDQsgDCAPQQFqIg9HDQAMAgsLIA9Be2ohDgNAAkAgA0H///8HSw0AIAAgA0EIdCIDNgIAIAAgACgCECIJQQFqNgIQIARBCHQgCSAAKAIMai0AAHIhBAsgACADQQF2IgM2AgAgACAEIANrIgRBH3UiCSANQQF0akEBaiINNgJUIAAgCSADcSAEaiIENgIEIA5Bf2oiDg0ACyAAIA1BBHQiCzYCVEEAIQ9BASEOA0AgACAOQQF0Ig5qQbwNaiENAkACQCADQf///wdNDQAgAyEKDAELIAAgA0EIdCIKNgIAIAAgACgCECIDQQFqNgIQIAAgBEEIdCADIAAoAgxqLQAAciIENgIECwJAAkAgBCAKQQt2IA0vAQAiCWwiA0kNACAAIAQgA2siBDYCBCAAIAogA2siAzYCACANIAkgCUEFdms7AQAgAEEBIA90IAtqIgs2AlQgDkEBciEODAELIAAgAzYCACANIAlBgBAgCWtBBXZqOwEACyAPQQFqIg9BBEcNAAsLAkAgASAGIAAoAlQQnoCAgAANAEEADwsgACgCICECCyACIAAoAihJDQALC0EBIQMCQCAAKAIAIgRB////B0sNACAAIARBCHQ2AgBBASEDIAAgACgCECIEQQFqNgIQIAAgACgCBEEIdCAEIAAoAgxqLQAAcjYCBAsgAwtwAQF/AkBBqN4BEICAgIAAIgJFDQAgAkE0aiABNgIAIAJBPGogADYCAAJAAkACQCAAQX9qDgIAAQILIAIgARCAgICAACIANgIYIAANASACEIKAgIAADAILIAJBADYCGCACQThqQQA2AgALIAIPC0EAC9IBAQJ/QQYhAgJAIAFBJ0sNACAAQTBqIAFBAXFBAnIgAUEBdkELanQiATYCAAJAAkAgAEE8aigCACIDRQ0AQQQhAiABIABBNGooAgBLDQIgAEEsaiABNgIAIANBAkcNACAAQThqIgMoAgAgAU8NACAAIAE2AjggACgCGBCCgICAACAAIAAoAjAQgICAgAAiATYCGCABDQBBAyECDAELQQAhAiAAQQA2AkAgAEHQAGpBAToAACAAQegAakEANgIAIABB5N0BaiEDCyADQQA2AgALIAILIwACQCAAQTxqKAIARQ0AIAAoAhgQgoCAgAALIAAQgoCAgAAL9QEBBH9BACEDAkAgACgCDCACTQ0AIAAoAhggAk0NACABIAEoAgAiBCAAKAIQIAAoAggiBWsiBiAEIAYgBEkbIgRrNgIAIAUgAkF/c2ohAQJAIAUgAksNACAAKAIUIAFqIQELIAAoAgAiAiABai0AACEGQQEhAyAAIAVBAWo2AgggAiAFaiAGOgAAAkAgBEF/aiICRQ0AA0AgACgCACIFQQAgAUEBaiIBIAEgACgCFEYbIgFqLQAAIQQgACAAKAIIIgZBAWo2AgggBSAGaiAEOgAAIAJBf2oiAg0ACwsgACgCDCAAKAIIIgFPDQAgACABNgIMCyADC8gEAQd/AkACQCAAKAIAIgNBgICACEkNACAAKAIEIQQMAQsgACADQQh0IgM2AgAgACAAKAIQIgVBAWo2AhAgACAAKAIEQQh0IAUgACgCDGotAAByIgQ2AgQLAkACQCAEIANBC3YgAS8BACIGbCIFTw0AIAEgBkGAECAGa0EFdmo7AQAgASACQQR0akEEaiEHQQghCEECIQkMAQsgACAEIAVrIgQ2AgQgASAGIAZBBXZrOwEAAkAgAyAFayIDQf///wdLDQAgACADQQh0IgM2AgAgACAAKAIQIgVBAWo2AhAgACAEQQh0IAUgACgCDGotAAByIgQ2AgQLAkAgBCADQQt2IAEvAQIiBmwiBU8NACABIAZBgBAgBmtBBXZqOwECIAEgAkEEdGpBhAJqIQdBCCEIQQohCQwBCyAAIAQgBWsiBDYCBCABIAYgBkEFdms7AQIgAUGEBGohByADIAVrIQVBgAIhCEESIQkLIABB6ABqIAk2AgBBASEBA0AgByABQQF0IgFqIQMCQAJAIAVB////B00NACAFIQIMAQsgACAFQQh0IgI2AgAgACAAKAIQIgVBAWo2AhAgACAEQQh0IAUgACgCDGotAAByIgQ2AgQLAkACQCAEIAJBC3YgAy8BACIGbCIFSQ0AIAAgBCAFayIENgIEIAAgAiAFayIFNgIAIAMgBiAGQQV2azsBACABQQFyIQEMAQsgACAFNgIAIAMgBkGAECAGa0EFdmo7AQALIAEgCEkNAAsgAEHoAGogASAIayAJajYCAAsLNQEAQYAICy4IAAAAEAAAABgAAAAgAAAAKAAAADAAAABAAAAAUAAAAIAAAAAAAQAA/Td6WFoA\"},t=>{t.exports=e}],i={};function 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-       "/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */var Jp={read:function(e,t,i,n,r){var s,o,a=8*r-n-1,c=(1<<a)-1,l=c>>1,h=-7,d=i?r-1:0,u=i?-1:1,f=e[t+d];for(d+=u,s=f&(1<<-h)-1,f>>=-h,h+=a;h>0;s=256*s+e[t+d],d+=u,h-=8);for(o=s&(1<<-h)-1,s>>=-h,h+=n;h>0;o=256*o+e[t+d],d+=u,h-=8);if(0===s)s=1-l;else{if(s===c)return o?NaN:1/0*(f?-1:1);o+=Math.pow(2,n),s-=l}return(f?-1:1)*o*Math.pow(2,s-n)},write:function(e,t,i,n,r,s){var o,a,c,l=8*s-r-1,h=(1<<l)-1,d=h>>1,u=23===r?Math.pow(2,-24)-Math.pow(2,-77):0,f=n?0:s-1,p=n?1:-1,g=t<0||0===t&&1/t<0?1:0;for(t=Math.abs(t),isNaN(t)||t===1/0?(a=isNaN(t)?1:0,o=h):(o=Math.floor(Math.log(t)/Math.LN2),t*(c=Math.pow(2,-o))<1&&(o--,c*=2),(t+=o+d>=1?u/c:u*Math.pow(2,1-d))*c>=2&&(o++,c/=2),o+d>=h?(a=0,o=h):o+d>=1?(a=(t*c-1)*Math.pow(2,r),o+=d):(a=t*Math.pow(2,d-1)*Math.pow(2,r),o=0));r>=8;e[i+f]=255&a,f+=p,a/=256,r-=8);for(o=o<<r|a,l+=r;l>0;e[i+f]=255&o,f+=p,o/=256,l-=8);e[i+f-p]|=128*g}};\n",
-       "/*!\n",
-       "     * The buffer module from node.js, for the browser.\n",
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-       "     * @author   Feross Aboukhadijeh <https://feross.org>\n",
-       "     * @license  MIT\n",
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e>>>=0,t||Ig(e,4,this.length),Jp.read(this,e,!1,23,4)},ng.prototype.readDoubleLE=function(e,t){return e>>>=0,t||Ig(e,8,this.length),Jp.read(this,e,!0,52,8)},ng.prototype.readDoubleBE=function(e,t){return e>>>=0,t||Ig(e,8,this.length),Jp.read(this,e,!1,52,8)},ng.prototype.writeUintLE=ng.prototype.writeUIntLE=function(e,t,i,n){if(e=+e,t>>>=0,i>>>=0,!n){Sg(this,e,t,i,Math.pow(2,8*i)-1,0)}let r=1,s=0;for(this[t]=255&e;++s<i&&(r*=256);)this[t+s]=e/r&255;return t+i},ng.prototype.writeUintBE=ng.prototype.writeUIntBE=function(e,t,i,n){if(e=+e,t>>>=0,i>>>=0,!n){Sg(this,e,t,i,Math.pow(2,8*i)-1,0)}let r=i-1,s=1;for(this[t+r]=255&e;--r>=0&&(s*=256);)this[t+r]=e/s&255;return t+i},ng.prototype.writeUint8=ng.prototype.writeUInt8=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,1,255,0),this[t]=255&e,t+1},ng.prototype.writeUint16LE=ng.prototype.writeUInt16LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,65535,0),this[t]=255&e,this[t+1]=e>>>8,t+2},ng.prototype.writeUint16BE=ng.prototype.writeUInt16BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,65535,0),this[t]=e>>>8,this[t+1]=255&e,t+2},ng.prototype.writeUint32LE=ng.prototype.writeUInt32LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,4294967295,0),this[t+3]=e>>>24,this[t+2]=e>>>16,this[t+1]=e>>>8,this[t]=255&e,t+4},ng.prototype.writeUint32BE=ng.prototype.writeUInt32BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,4294967295,0),this[t]=e>>>24,this[t+1]=e>>>16,this[t+2]=e>>>8,this[t+3]=255&e,t+4},ng.prototype.writeBigUInt64LE=Gg((function(e,t=0){return Eg(this,e,t,BigInt(0),BigInt(\"0xffffffffffffffff\"))})),ng.prototype.writeBigUInt64BE=Gg((function(e,t=0){return Ng(this,e,t,BigInt(0),BigInt(\"0xffffffffffffffff\"))})),ng.prototype.writeIntLE=function(e,t,i,n){if(e=+e,t>>>=0,!n){const n=Math.pow(2,8*i-1);Sg(this,e,t,i,n-1,-n)}let r=0,s=1,o=0;for(this[t]=255&e;++r<i&&(s*=256);)e<0&&0===o&&0!==this[t+r-1]&&(o=1),this[t+r]=(e/s|0)-o&255;return t+i},ng.prototype.writeIntBE=function(e,t,i,n){if(e=+e,t>>>=0,!n){const n=Math.pow(2,8*i-1);Sg(this,e,t,i,n-1,-n)}let r=i-1,s=1,o=0;for(this[t+r]=255&e;--r>=0&&(s*=256);)e<0&&0===o&&0!==this[t+r+1]&&(o=1),this[t+r]=(e/s|0)-o&255;return t+i},ng.prototype.writeInt8=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,1,127,-128),e<0&&(e=255+e+1),this[t]=255&e,t+1},ng.prototype.writeInt16LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,32767,-32768),this[t]=255&e,this[t+1]=e>>>8,t+2},ng.prototype.writeInt16BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,32767,-32768),this[t]=e>>>8,this[t+1]=255&e,t+2},ng.prototype.writeInt32LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,2147483647,-2147483648),this[t]=255&e,this[t+1]=e>>>8,this[t+2]=e>>>16,this[t+3]=e>>>24,t+4},ng.prototype.writeInt32BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,2147483647,-2147483648),e<0&&(e=4294967295+e+1),this[t]=e>>>24,this[t+1]=e>>>16,this[t+2]=e>>>8,this[t+3]=255&e,t+4},ng.prototype.writeBigInt64LE=Gg((function(e,t=0){return Eg(this,e,t,-BigInt(\"0x8000000000000000\"),BigInt(\"0x7fffffffffffffff\"))})),ng.prototype.writeBigInt64BE=Gg((function(e,t=0){return Ng(this,e,t,-BigInt(\"0x8000000000000000\"),BigInt(\"0x7fffffffffffffff\"))})),ng.prototype.writeFloatLE=function(e,t,i){return Mg(this,e,t,!0,i)},ng.prototype.writeFloatBE=function(e,t,i){return Mg(this,e,t,!1,i)},ng.prototype.writeDoubleLE=function(e,t,i){return Rg(this,e,t,!0,i)},ng.prototype.writeDoubleBE=function(e,t,i){return Rg(this,e,t,!1,i)},ng.prototype.copy=function(e,t,i,n){if(!ng.isBuffer(e))throw new TypeError(\"argument should be a Buffer\");if(i||(i=0),n||0===n||(n=this.length),t>=e.length&&(t=e.length),t||(t=0),n>0&&n<i&&(n=i),n===i)return 0;if(0===e.length||0===this.length)return 0;if(t<0)throw new RangeError(\"targetStart out of bounds\");if(i<0||i>=this.length)throw new RangeError(\"Index out of range\");if(n<0)throw new RangeError(\"sourceEnd out of bounds\");n>this.length&&(n=this.length),e.length-t<n-i&&(n=e.length-t+i);const r=n-i;return this===e&&\"function\"==typeof Uint8Array.prototype.copyWithin?this.copyWithin(t,i,n):Uint8Array.prototype.set.call(e,this.subarray(i,n),t),r},ng.prototype.fill=function(e,t,i,n){if(\"string\"==typeof e){if(\"string\"==typeof t?(n=t,t=0,i=this.length):\"string\"==typeof i&&(n=i,i=this.length),void 0!==n&&\"string\"!=typeof n)throw new TypeError(\"encoding must be a string\");if(\"string\"==typeof n&&!ng.isEncoding(n))throw new TypeError(\"Unknown encoding: \"+n);if(1===e.length){const t=e.charCodeAt(0);(\"utf8\"===n&&t<128||\"latin1\"===n)&&(e=t)}}else\"number\"==typeof e?e&=255:\"boolean\"==typeof e&&(e=Number(e));if(t<0||this.length<t||this.length<i)throw new RangeError(\"Out of range index\");if(i<=t)return this;let r;if(t>>>=0,i=void 0===i?this.length:i>>>0,e||(e=0),\"number\"==typeof e)for(r=t;r<i;++r)this[r]=e;else{const s=ng.isBuffer(e)?e:ng.from(e,n),o=s.length;if(0===o)throw new TypeError('The value \"'+e+'\" is invalid for argument \"value\"');for(r=0;r<i-t;++r)this[r+t]=s[r%o]}return this};const Dg={};function Tg(e,t,i){Dg[e]=class extends i{constructor(){super(),Object.defineProperty(this,\"message\",{value:t.apply(this,arguments),writable:!0,configurable:!0}),this.name=`${this.name} [${e}]`,this.stack,delete this.name}get code(){return e}set code(e){Object.defineProperty(this,\"code\",{configurable:!0,enumerable:!0,value:e,writable:!0})}toString(){return`${this.name} [${e}]: ${this.message}`}}}function Lg(e){let t=\"\",i=e.length;const n=\"-\"===e[0]?1:0;for(;i>=n+4;i-=3)t=`_${e.slice(i-3,i)}${t}`;return`${e.slice(0,i)}${t}`}function zg(e,t,i,n,r,s){if(e>i||e<t){const n=\"bigint\"==typeof t?\"n\":\"\";let r;throw r=s>3?0===t||t===BigInt(0)?`>= 0${n} and < 2${n} ** ${8*(s+1)}${n}`:`>= -(2${n} ** 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Received ${r}`,n}),RangeError);const Og=/[^+/0-9A-Za-z-_]/g;function Ug(e,t){let i;t=t||1/0;const n=e.length;let r=null;const s=[];for(let o=0;o<n;++o){if(i=e.charCodeAt(o),i>55295&&i<57344){if(!r){if(i>56319){(t-=3)>-1&&s.push(239,191,189);continue}if(o+1===n){(t-=3)>-1&&s.push(239,191,189);continue}r=i;continue}if(i<56320){(t-=3)>-1&&s.push(239,191,189),r=i;continue}i=65536+(r-55296<<10|i-56320)}else r&&(t-=3)>-1&&s.push(239,191,189);if(r=null,i<128){if((t-=1)<0)break;s.push(i)}else if(i<2048){if((t-=2)<0)break;s.push(i>>6|192,63&i|128)}else if(i<65536){if((t-=3)<0)break;s.push(i>>12|224,i>>6&63|128,63&i|128)}else{if(!(i<1114112))throw new Error(\"Invalid code point\");if((t-=4)<0)break;s.push(i>>18|240,i>>12&63|128,i>>6&63|128,63&i|128)}}return s}function qg(e){return Zp.toByteArray(function(e){if((e=(e=e.split(\"=\")[0]).trim().replace(Og,\"\")).length<2)return\"\";for(;e.length%4!=0;)e+=\"=\";return e}(e))}function Qg(e,t,i,n){let r;for(r=0;r<n&&!(r+i>=t.length||r>=e.length);++r)t[r+i]=e[r];return r}function Vg(e,t){return e instanceof t||null!=e&&null!=e.constructor&&null!=e.constructor.name&&e.constructor.name===t.name}function jg(e){return e!=e}const Wg=function(){const e=\"0123456789abcdef\",t=new Array(256);for(let i=0;i<16;++i){const n=16*i;for(let r=0;r<16;++r)t[n+r]=e[i]+e[r]}return t}();function Gg(e){return\"undefined\"==typeof BigInt?$g:e}function $g(){throw new Error(\"BigInt not supported\")}class Kg{constructor(e,t){this.position=0,this.url=e,this.config=t,Ht(e)||!1===t.cacheFetches?this.useCache=!1:(this.useCache=!0,this.cache=new Yg({fetch:(e,t)=>this._fetch(e,t),fetchSize:t.fetchSize||1e4}))}async _fetch(e,t){const i={start:e,size:t};this._stat={size:void 0};const n=await Qs.loadArrayBuffer(this.url,Ua(this.config,{range:i}));return ng.from(n)}async read(e,t=0,i=1/0,n=0){if(this.useCache)await this.cache.get(e,t,n,i);else{(await this._fetch(n,i)).copy(e,t)}return{bytesRead:i,buffer:e}}async readFile(){const e=await Qs.loadArrayBuffer(this.url,Ua(this.config));return ng.from(e)}async stat(){if(!this._stat){const e=ng.allocUnsafe(10);if(await this.read(e,0,10,0),!this._stat)throw new Error(`unable to determine size of file at ${this.url}`)}return this._stat}}class Yg{constructor({fetch:e,fetchSize:t=3e4}){this.fetch=e,this.position=0,this.buffer=ng.allocUnsafe(0),this.fetchSize=t}async get(e,t,i,n){if(e.length<t+n)throw new Error(\"output buffer not big enough for request\");if(i>=this.position&&i+n<=this.position+this.buffer.length);else{const e=Math.max(n,this.fetchSize);this.buffer=await this.fetch(i,e),this.position=i}const r=t,s=i-this.position,o=s+n;this.buffer.copy(e,r,s,o)}}class Xg{chrAliasTable=new Map;constructor(e,t,i){this.config=e,this.browser=i,this.genome=t,this.cramFile=new Vp.CramFile({filehandle:e.fileHandle?e.fileHandle:new Kg(e.url,e),seqFetch:e.seqFetch||async function(e,t,i){const n=this.genome,r=await this.getHeader(),s=n.getChromosomeName(r.indexToChr[e]);return this.genome.getSequence(s,t-1,i)}.bind(this),checkSequenceMD5:void 0===e.checkSequenceMD5||e.checkSequenceMD5});const n=e.indexFileHandle?e.indexFileHandle:new Kg(e.indexURL,e);this.indexedCramFile=new Vp.IndexedCramFile({cram:this.cramFile,index:new Vp.CraiIndex({filehandle:n}),fetchSizeLimit:e.fetchSizeLimit||1e9}),Mp.setReaderDefaults(this,e)}async getHeader(){if(!this.header){const e=await this.cramFile.getSamHeader(),t={},i=[],n=[];for(let r of e)if(\"SQ\"===r.tag){for(let e of r.data)if(\"SN\"===e.tag){const n=e.value;t[n]=i.length,i.push(n);break}}else\"RG\"===r.tag&&n.push(r.data);this.header={indexToChr:i,chrToIndex:t,chrNames:Object.keys(t),readGroups:n}}return this.header}async#x(e){if(await this.getHeader(),this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.header.chrToIndex[e];if(void 0===t){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>void 0!==this.header.chrToIndex[e]));e.length>0&&(n=e[0],t=this.header.chrToIndex[e[0]])}this.chrAliasTable.set(e,n)}return t}async readAlignments(e,t,i){const n=await this.getHeader(),r=await this.#x(e),s=new tp(e,t,i,this.config);if(void 0===r)return s;try{const e=await this.indexedCramFile.getRecordsForRange(r,t,i);for(let a of e){const e=a.sequenceId,c=a.alignmentStart,l=c+a.lengthOnRef;if(e<0)continue;if(e>r||c>i)return;if(e<r)continue;if(l<t)continue;const h=o(a,n.chrNames);this.filter.pass(h)&&s.push(h)}return s.finish(),s}catch(e){let t=e.message;throw t&&t.indexOf(\"MD5\")>=0&&(t=\"Sequence mismatch. Is this the correct genome for the loaded CRAM?\"),this.browser.alert.present(new Error(t)),e}function o(e,t){const i=new wp;if(i.chr=t[e.sequenceId],i.start=e.alignmentStart-1,i.lengthOnRef=e.lengthOnRef,i.flags=e.flags,i.strand=!(16&e.flags),i.fragmentLength=e.templateLength||e.templateSize,i.mq=e.mappingQuality,i.end=e.alignmentStart+e.lengthOnRef,i.readGroupId=e.readGroupId,e.mate&&void 0!==e.mate.sequenceId){const n=void 0!==e.mate.flags?!(1&e.mate.flags):!(32&e.flags);i.mate={chr:t[e.mate.sequenceId],position:e.mate.alignmentStart,strand:n}}return i.seq=e.getReadBases(),i.qual=e.qualityScores,i.tagDict=e.tags,i.readName=e.readName,function(e,t){const i=[];let n,r,s=0,o=\"\";if(t.scStart=t.start,t.scLengthOnRef=t.lengthOnRef,e.readFeatures)for(let a of e.readFeatures){const e=a.code,c=a.data,l=a.pos-1,h=a.refPos-1;switch(e){case\"S\":case\"I\":case\"i\":case\"N\":case\"D\":if(l>s){const e=l-s;i.push(new xp({start:h-e,seqOffset:s,len:e,type:\"M\"})),s+=e,o+=e+\"M\"}if(\"S\"===e){let n=h;t.scLengthOnRef+=c.length,0===l&&(t.scStart-=c.length,n-=c.length);const r=c.length;i.push(new xp({start:n,seqOffset:s,len:r,type:\"S\"})),s+=r,o+=r+e}else if(\"I\"===e||\"i\"===e){void 0===n&&(n=[]);const t=\"i\"===e?1:c.length;n.push(new xp({start:h,len:t,seqOffset:s,type:\"I\"})),s+=t,o+=t+e}else\"D\"!==e&&\"N\"!==e||(r||(r=[]),r.push({start:h,len:c,type:e}),o+=c+e);break;case\"H\":case\"P\":o+=c+e}}const a=e.readLength-s;a>0&&(i.push(new xp({start:e.alignmentStart+e.lengthOnRef-a-1,seqOffset:s,len:a,type:\"M\"})),o+=a+\"M\");t.blocks=i,t.insertions=n,t.gaps=r,t.cigar=o}(e,i),i.mate&&i.start>i.mate.position&&i.fragmentLength>0&&(i.fragmentLength=-i.fragmentLength),Mp.setPairOrientation(i),i}}}const Zg=2291137574,Jg=2273964779,em=[84,68,70,52],tm=new Uint8Array([66,65,77,1]),im=[67,82,65,77],nm=[31,139],rm=4,sm=new Set([\"narrowpeak\",\"broadpeak\",\"regionpeak\",\"peaks\",\"bedgraph\",\"wig\",\"gff3\",\"gff\",\"gtf\",\"fusionjuncspan\",\"refflat\",\"seg\",\"aed\",\"bed\",\"bedMethyl\",\"vcf\",\"bb\",\"bigbed\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\",\"bw\",\"bigwig\",\"bam\",\"tdf\",\"refgene\",\"genepred\",\"genepredext\",\"bedpe\",\"bp\",\"snp\",\"rmsk\",\"cram\",\"gwas\",\"maf\",\"mut\",\"hiccups\",\"fasta\",\"fa\",\"fna\",\"pytor\",\"hic\",\"qtl\"]);function om(e,t){const i=Math.min(e.length,t.length);if(0==i)return!1;for(let n=0;n<i;n++)if(e[n]!==t[n])return!1;return!0}async function am(e){let t;const i=e.filename||await ja(e.url);return i&&(t=await function(e){if(!e)return;if((e=e.toLowerCase()).endsWith(\"refgene.txt.gz\")||e.endsWith(\"refgene.txt.bgz\")||e.endsWith(\"refgene.txt\")||e.endsWith(\"refgene.sorted.txt.gz\")||e.endsWith(\"refgene.sorted.txt.bgz\"))return\"refgene\";e.endsWith(\".gz\")&&(e=e.substring(0,e.length-3));e.endsWith(\".bgz\")&&(e=e.substring(0,e.length-4));(e.endsWith(\".txt\")||e.endsWith(\".tab\")||e.endsWith(\".tsv\"))&&(e=e.substring(0,e.length-4));const t=e.lastIndexOf(\".\"),i=t<0?e:e.substring(t+1);switch(i){case\"bw\":return\"bigwig\";case\"bb\":return\"bigbed\";case\"fasta\":case\"fa\":case\"fna\":return\"fasta\";default:return sm.has(i)?i:void 0}}(i)),t||(t=await async function(e){const t=e.url;let i=Ua(e,{range:{start:0,size:1e3}}),n=await Qs.loadArrayBuffer(t,i),r=new Uint8Array(n);if(om(r,nm)){if(0!==(r[3]&rm)&&66===r[12]&&67===r[13]){i=Ua(e,{range:{start:0,size:ms(n)}}),n=await Qs.loadArrayBuffer(t,i),r=gs(n)}else i=Ua(e,{}),n=await Qs.loadArrayBuffer(t,i),r=ps(n),e._filecontents=r}if(om(r,tm))return\"bam\";if(om(r,im))return\"cram\";const s=!0;let o=new yc(new DataView(n),s).getUInt();if(o===Zg)return\"bigwig\";if(o===Jg)return\"bigbed\";if(om(r,em))return\"tdf\";const a=new TextDecoder(\"utf-8\").decode(r),c=a.split(/\\r?\\n/)[0];if(c.startsWith(\"##fileformat=VCF\"))return\"vcf\";if(c.startsWith(\"##gff-version 3\"))return\"gff3\";if(c.startsWith(\"##gff-version\"))return\"gff\";if(c.startsWith(\"##fileformat=\"))return c.substring(13).toLowerCase();if(xh.isQTL(c))return\"qtl\";if(Jl.isGWAS(c))return\"gwas\";if(Dc(c.split(\"\\t\")))return\"hiccups\";return null}(e)),t}class cm{constructor(e,t){const i=t.genome;if(this.config=e,this.genome=i,Ga(e.url)&&(this.config.indexed=!1),\"ga4gh\"===e.sourceType)throw Error(\"Unsupported source type 'ga4gh'\");if(\"pysam\"===e.sourceType)this.bamReader=new Up(e,i);else if(\"htsget\"===e.sourceType)this.bamReader=new Qp(e,i);else if(\"shardedBam\"===e.sourceType)this.bamReader=new Op(e,i);else if(\"cram\"===e.format)this.bamReader=new Xg(e,i,t);else{if(!this.config.indexURL&&!1!==e.indexed)if(Mt(this.config.url)){const e=function(e,t){if(Mt(e)){if(e.includes(\"?\")){const i=e.indexOf(\"?\");return e.substring(0,i)+\".\"+t+e.substring(i)}return e+\".\"+t}}(this.config.url,\"bai\");e?(console.warn(`Warning: no indexURL specified for ${this.config.url}.  Guessing ${e}`),this.config.indexURL=e):(console.warning(`Warning: no indexURL specified for ${this.config.url}.`),this.config.indexed=!1)}else console.warning(`Warning: no indexURL specified for ${this.config.name}.`),this.config.indexed=!1;!1!==this.config.indexed?this.bamReader=new Pp(e,i):this.bamReader=new Hp(e,i)}}async getAlignments(e,t,i){const n=this.genome,r=await this.bamReader.readAlignments(e,t,i);if(r.hasAlignments){const t=await n.getSequence(e,r.start,r.end);if(t)return r.coverageMap.refSeq=t,r.sequence=t,r;console.error(\"No sequence for: \"+e+\":\"+r.start+\"-\"+r.end)}return r}}class lm{constructor({chr:e,start:t,end:i}){this.chr=e,this.start=t,this.end=i}contains(e){return e.chr===this.chr&&e.start>=this.start&&e.end<=this.end}overlaps(e){return e.chr===this.chr&&!(e.end<this.start||e.start>this.end)}extend(e){e.chr===this.chr&&(this.start=Math.min(e.start,this.start),this.end=Math.max(e.end,this.end))}getLocusString(){if(\"all\"===this.chr)return\"all\";{const e=Rt(Math.floor(this.start)+1),t=Rt(Math.round(this.end));return`${this.chr}:${e}-${t}`}}static fromLocusString(e){if(\"all\"===e)return new lm({chr:\"all\"});const t=e.split(\":\"),i=t[0],n=t[1].split(\"-\"),r=Number.parseInt(n[0].replace(/,/g,\"\"))-1,s=Number.parseInt(n[1].replace(/,/g,\"\"));return new lm({chr:i,start:r,end:s})}}\n",
-       "/*!\n",
-       "     * vanilla-picker v2.12.1\n",
-       "     * https://vanilla-picker.js.org\n",
-       "     *\n",
-       "     * Copyright 2017-2021 Andreas Borgen (https://github.com/Sphinxxxx), Adam Brooks (https://github.com/dissimulate)\n",
-       "     * Released under the ISC license.\n",
-       "     */var hm=function(e,t){if(!(e instanceof t))throw new TypeError(\"Cannot call a class as a function\")},dm=function(){function e(e,t){for(var i=0;i<t.length;i++){var n=t[i];n.enumerable=n.enumerable||!1,n.configurable=!0,\"value\"in n&&(n.writable=!0),Object.defineProperty(e,n.key,n)}}return function(t,i,n){return i&&e(t.prototype,i),n&&e(t,n),t}}(),um=function(e,t){if(Array.isArray(e))return e;if(Symbol.iterator in Object(e))return function(e,t){var i=[],n=!0,r=!1,s=void 0;try{for(var o,a=e[Symbol.iterator]();!(n=(o=a.next()).done)&&(i.push(o.value),!t||i.length!==t);n=!0);}catch(e){r=!0,s=e}finally{try{!n&&a.return&&a.return()}finally{if(r)throw s}}return i}(e,t);throw new TypeError(\"Invalid attempt to destructure non-iterable instance\")};String.prototype.startsWith=String.prototype.startsWith||function(e){return 0===this.indexOf(e)},String.prototype.padStart=String.prototype.padStart||function(e,t){for(var i=this;i.length<e;)i=t+i;return i};var fm={cb:\"0f8ff\",tqw:\"aebd7\",q:\"-ffff\",qmrn:\"7fffd4\",zr:\"0ffff\",bg:\"5f5dc\",bsq:\"e4c4\",bck:\"---\",nch:\"ebcd\",b:\"--ff\",bvt:\"8a2be2\",brwn:\"a52a2a\",brw:\"deb887\",ctb:\"5f9ea0\",hrt:\"7fff-\",chcT:\"d2691e\",cr:\"7f50\",rnw:\"6495ed\",crns:\"8dc\",crms:\"dc143c\",cn:\"-ffff\",Db:\"--8b\",Dcn:\"-8b8b\",Dgnr:\"b8860b\",Dgr:\"a9a9a9\",Dgrn:\"-64-\",Dkhk:\"bdb76b\",Dmgn:\"8b-8b\",Dvgr:\"556b2f\",Drng:\"8c-\",Drch:\"9932cc\",Dr:\"8b--\",Dsmn:\"e9967a\",Dsgr:\"8fbc8f\",DsTb:\"483d8b\",DsTg:\"2f4f4f\",Dtrq:\"-ced1\",Dvt:\"94-d3\",ppnk:\"1493\",pskb:\"-bfff\",mgr:\"696969\",grb:\"1e90ff\",rbrc:\"b22222\",rwht:\"af0\",stg:\"228b22\",chs:\"-ff\",gnsb:\"dcdcdc\",st:\"8f8ff\",g:\"d7-\",gnr:\"daa520\",gr:\"808080\",grn:\"-8-0\",grnw:\"adff2f\",hnw:\"0fff0\",htpn:\"69b4\",nnr:\"cd5c5c\",ng:\"4b-82\",vr:\"0\",khk:\"0e68c\",vnr:\"e6e6fa\",nrb:\"0f5\",wngr:\"7cfc-\",mnch:\"acd\",Lb:\"add8e6\",Lcr:\"08080\",Lcn:\"e0ffff\",Lgnr:\"afad2\",Lgr:\"d3d3d3\",Lgrn:\"90ee90\",Lpnk:\"b6c1\",Lsmn:\"a07a\",Lsgr:\"20b2aa\",Lskb:\"87cefa\",LsTg:\"778899\",Lstb:\"b0c4de\",Lw:\"e0\",m:\"-ff-\",mgrn:\"32cd32\",nn:\"af0e6\",mgnt:\"-ff\",mrn:\"8--0\",mqm:\"66cdaa\",mmb:\"--cd\",mmrc:\"ba55d3\",mmpr:\"9370db\",msg:\"3cb371\",mmsT:\"7b68ee\",\"\":\"-fa9a\",mtr:\"48d1cc\",mmvt:\"c71585\",mnLb:\"191970\",ntc:\"5fffa\",mstr:\"e4e1\",mccs:\"e4b5\",vjw:\"dead\",nv:\"--80\",c:\"df5e6\",v:\"808-0\",vrb:\"6b8e23\",rng:\"a5-\",rngr:\"45-\",rch:\"da70d6\",pgnr:\"eee8aa\",pgrn:\"98fb98\",ptrq:\"afeeee\",pvtr:\"db7093\",ppwh:\"efd5\",pchp:\"dab9\",pr:\"cd853f\",pnk:\"c0cb\",pm:\"dda0dd\",pwrb:\"b0e0e6\",prp:\"8-080\",cc:\"663399\",r:\"--\",sbr:\"bc8f8f\",rb:\"4169e1\",sbrw:\"8b4513\",smn:\"a8072\",nbr:\"4a460\",sgrn:\"2e8b57\",ssh:\"5ee\",snn:\"a0522d\",svr:\"c0c0c0\",skb:\"87ceeb\",sTb:\"6a5acd\",sTgr:\"708090\",snw:\"afa\",n:\"-ff7f\",stb:\"4682b4\",tn:\"d2b48c\",t:\"-8080\",thst:\"d8bfd8\",tmT:\"6347\",trqs:\"40e0d0\",vt:\"ee82ee\",whT:\"5deb3\",wht:\"\",hts:\"5f5f5\",w:\"-\",wgrn:\"9acd32\"};function pm(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:1;return(t>0?e.toFixed(t).replace(/0+$/,\"\").replace(/\\.$/,\"\"):e.toString())||\"0\"}var gm=function(){function e(t,i,n,r){hm(this,e);var s=this;if(void 0===t);else if(Array.isArray(t))this.rgba=t;else if(void 0===n){var o=t&&\"\"+t;o&&function(t){if(t.startsWith(\"hsl\")){var i=t.match(/([\\-\\d\\.e]+)/g).map(Number),n=um(i,4),r=n[0],o=n[1],a=n[2],c=n[3];void 0===c&&(c=1),r/=360,o/=100,a/=100,s.hsla=[r,o,a,c]}else if(t.startsWith(\"rgb\")){var l=t.match(/([\\-\\d\\.e]+)/g).map(Number),h=um(l,4),d=h[0],u=h[1],f=h[2],p=h[3];void 0===p&&(p=1),s.rgba=[d,u,f,p]}else t.startsWith(\"#\")?s.rgba=e.hexToRgb(t):s.rgba=e.nameToRgb(t)||e.hexToRgb(t)}(o.toLowerCase())}else this.rgba=[t,i,n,void 0===r?1:r]}return dm(e,[{key:\"printRGB\",value:function(e){var t=(e?this.rgba:this.rgba.slice(0,3)).map((function(e,t){return pm(e,3===t?3:0)}));return e?\"rgba(\"+t+\")\":\"rgb(\"+t+\")\"}},{key:\"printHSL\",value:function(e){var t=[360,100,100,1],i=[\"\",\"%\",\"%\",\"\"],n=(e?this.hsla:this.hsla.slice(0,3)).map((function(e,n){return pm(e*t[n],3===n?3:1)+i[n]}));return e?\"hsla(\"+n+\")\":\"hsl(\"+n+\")\"}},{key:\"printHex\",value:function(e){var t=this.hex;return e?t:t.substring(0,7)}},{key:\"rgba\",get:function(){if(this._rgba)return this._rgba;if(!this._hsla)throw new Error(\"No color is set\");return this._rgba=e.hslToRgb(this._hsla)},set:function(e){3===e.length&&(e[3]=1),this._rgba=e,this._hsla=null}},{key:\"rgbString\",get:function(){return this.printRGB()}},{key:\"rgbaString\",get:function(){return this.printRGB(!0)}},{key:\"hsla\",get:function(){if(this._hsla)return this._hsla;if(!this._rgba)throw new Error(\"No color is set\");return this._hsla=e.rgbToHsl(this._rgba)},set:function(e){3===e.length&&(e[3]=1),this._hsla=e,this._rgba=null}},{key:\"hslString\",get:function(){return this.printHSL()}},{key:\"hslaString\",get:function(){return this.printHSL(!0)}},{key:\"hex\",get:function(){var e=this.rgba.map((function(e,t){return t<3?e.toString(16):Math.round(255*e).toString(16)}));return\"#\"+e.map((function(e){return e.padStart(2,\"0\")})).join(\"\")},set:function(t){this.rgba=e.hexToRgb(t)}}],[{key:\"hexToRgb\",value:function(e){var t=(e.startsWith(\"#\")?e.slice(1):e).replace(/^(\\w{3})$/,\"$1F\").replace(/^(\\w)(\\w)(\\w)(\\w)$/,\"$1$1$2$2$3$3$4$4\").replace(/^(\\w{6})$/,\"$1FF\");if(!t.match(/^([0-9a-fA-F]{8})$/))throw new Error(\"Unknown hex color; \"+e);var i=t.match(/^(\\w\\w)(\\w\\w)(\\w\\w)(\\w\\w)$/).slice(1).map((function(e){return parseInt(e,16)}));return i[3]=i[3]/255,i}},{key:\"nameToRgb\",value:function(t){var i=t.toLowerCase().replace(\"at\",\"T\").replace(/[aeiouyldf]/g,\"\").replace(\"ght\",\"L\").replace(\"rk\",\"D\").slice(-5,4),n=fm[i];return void 0===n?n:e.hexToRgb(n.replace(/\\-/g,\"00\").padStart(6,\"f\"))}},{key:\"rgbToHsl\",value:function(e){var t=um(e,4),i=t[0],n=t[1],r=t[2],s=t[3];i/=255,n/=255,r/=255;var o=Math.max(i,n,r),a=Math.min(i,n,r),c=void 0,l=void 0,h=(o+a)/2;if(o===a)c=l=0;else{var d=o-a;switch(l=h>.5?d/(2-o-a):d/(o+a),o){case i:c=(n-r)/d+(n<r?6:0);break;case n:c=(r-i)/d+2;break;case r:c=(i-n)/d+4}c/=6}return[c,l,h,s]}},{key:\"hslToRgb\",value:function(e){var t=um(e,4),i=t[0],n=t[1],r=t[2],s=t[3],o=void 0,a=void 0,c=void 0;if(0===n)o=a=c=r;else{var l=function(e,t,i){return i<0&&(i+=1),i>1&&(i-=1),i<1/6?e+6*(t-e)*i:i<.5?t:i<2/3?e+(t-e)*(2/3-i)*6:e},h=r<.5?r*(1+n):r+n-r*n,d=2*r-h;o=l(d,h,i+1/3),a=l(d,h,i),c=l(d,h,i-1/3)}var u=[255*o,255*a,255*c].map(Math.round);return u[3]=s,u}}]),e}(),mm=function(){function e(){hm(this,e),this._events=[]}return dm(e,[{key:\"add\",value:function(e,t,i){e.addEventListener(t,i,!1),this._events.push({target:e,type:t,handler:i})}},{key:\"remove\",value:function(t,i,n){this._events=this._events.filter((function(r){var s=!0;return t&&t!==r.target&&(s=!1),i&&i!==r.type&&(s=!1),n&&n!==r.handler&&(s=!1),s&&e._doRemove(r.target,r.type,r.handler),!s}))}},{key:\"destroy\",value:function(){this._events.forEach((function(t){return e._doRemove(t.target,t.type,t.handler)})),this._events=[]}}],[{key:\"_doRemove\",value:function(e,t,i){e.removeEventListener(t,i,!1)}}]),e}();function wm(e,t,i){var n=!1;function r(e,t,i){return Math.max(t,Math.min(e,i))}function s(e,s,o){if(o&&(n=!0),n){e.preventDefault();var a=t.getBoundingClientRect(),c=a.width,l=a.height,h=s.clientX,d=s.clientY,u=r(h-a.left,0,c),f=r(d-a.top,0,l);i(u/c,f/l)}}function o(e,t){1===(void 0===e.buttons?e.which:e.buttons)?s(e,e,t):n=!1}function a(e,t){1===e.touches.length?s(e,e.touches[0],t):n=!1}e.add(t,\"mousedown\",(function(e){o(e,!0)})),e.add(t,\"touchstart\",(function(e){a(e,!0)})),e.add(window,\"mousemove\",o),e.add(t,\"touchmove\",a),e.add(window,\"mouseup\",(function(e){n=!1})),e.add(t,\"touchend\",(function(e){n=!1})),e.add(t,\"touchcancel\",(function(e){n=!1}))}var bm=\"keydown\",Fm=\"mousedown\",vm=\"focusin\";function ym(e,t){return(t||document).querySelector(e)}function Am(e){e.preventDefault(),e.stopPropagation()}function Cm(e,t,i,n,r){e.add(t,bm,(function(e){i.indexOf(e.key)>=0&&(r&&Am(e),n(e))}))}var _m=function(){function e(t){hm(this,e),this.settings={popup:\"right\",layout:\"default\",alpha:!0,editor:!0,editorFormat:\"hex\",cancelButton:!1,defaultColor:\"#0cf\"},this._events=new mm,this.onChange=null,this.onDone=null,this.onOpen=null,this.onClose=null,this.setOptions(t)}return dm(e,[{key:\"setOptions\",value:function(e){var t=this;if(e){var i=this.settings;if(e instanceof HTMLElement)i.parent=e;else{i.parent&&e.parent&&i.parent!==e.parent&&(this._events.remove(i.parent),this._popupInited=!1),function(e,t,i){for(var n in e)i&&i.indexOf(n)>=0||(t[n]=e[n])}(e,i),e.onChange&&(this.onChange=e.onChange),e.onDone&&(this.onDone=e.onDone),e.onOpen&&(this.onOpen=e.onOpen),e.onClose&&(this.onClose=e.onClose);var n=e.color||e.colour;n&&this._setColor(n)}var r=i.parent;if(r&&i.popup&&!this._popupInited){var s=function(e){return t.openHandler(e)};this._events.add(r,\"click\",s),Cm(this._events,r,[\" \",\"Spacebar\",\"Enter\"],s),this._popupInited=!0}else e.parent&&!i.popup&&this.show()}}},{key:\"openHandler\",value:function(e){if(this.show()){e&&e.preventDefault(),this.settings.parent.style.pointerEvents=\"none\";var t=e&&e.type===bm?this._domEdit:this.domElement;setTimeout((function(){return t.focus()}),100),this.onOpen&&this.onOpen(this.colour)}}},{key:\"closeHandler\",value:function(e){var t=e&&e.type,i=!1;if(e)if(t===Fm||t===vm){var n=(this.__containedEvent||0)+100;e.timeStamp>n&&(i=!0)}else Am(e),i=!0;else i=!0;i&&this.hide()&&(this.settings.parent.style.pointerEvents=\"\",t!==Fm&&this.settings.parent.focus(),this.onClose&&this.onClose(this.colour))}},{key:\"movePopup\",value:function(e,t){this.closeHandler(),this.setOptions(e),t&&this.openHandler()}},{key:\"setColor\",value:function(e,t){this._setColor(e,{silent:t})}},{key:\"_setColor\",value:function(e,t){if(\"string\"==typeof e&&(e=e.trim()),e){t=t||{};var i=void 0;try{i=new gm(e)}catch(e){if(t.failSilently)return;throw e}if(!this.settings.alpha){var n=i.hsla;n[3]=1,i.hsla=n}this.colour=this.color=i,this._setHSLA(null,null,null,null,t)}}},{key:\"setColour\",value:function(e,t){this.setColor(e,t)}},{key:\"show\",value:function(){if(!this.settings.parent)return!1;if(this.domElement){var e=this._toggleDOM(!0);return this._setPosition(),e}var t=function(e){var t=document.createElement(\"div\");return t.innerHTML=e,t.firstElementChild}(this.settings.template||'<div class=\"picker_wrapper\" tabindex=\"-1\"><div class=\"picker_arrow\"></div><div class=\"picker_hue picker_slider\"><div class=\"picker_selector\"></div></div><div class=\"picker_sl\"><div class=\"picker_selector\"></div></div><div class=\"picker_alpha picker_slider\"><div class=\"picker_selector\"></div></div><div class=\"picker_editor\"><input aria-label=\"Type a color name or hex value\"/></div><div class=\"picker_sample\"></div><div class=\"picker_done\"><button>Ok</button></div><div class=\"picker_cancel\"><button>Cancel</button></div></div>');return this.domElement=t,this._domH=ym(\".picker_hue\",t),this._domSL=ym(\".picker_sl\",t),this._domA=ym(\".picker_alpha\",t),this._domEdit=ym(\".picker_editor input\",t),this._domSample=ym(\".picker_sample\",t),this._domOkay=ym(\".picker_done button\",t),this._domCancel=ym(\".picker_cancel button\",t),t.classList.add(\"layout_\"+this.settings.layout),this.settings.alpha||t.classList.add(\"no_alpha\"),this.settings.editor||t.classList.add(\"no_editor\"),this.settings.cancelButton||t.classList.add(\"no_cancel\"),this._ifPopup((function(){return t.classList.add(\"popup\")})),this._setPosition(),this.colour?this._updateUI():this._setColor(this.settings.defaultColor),this._bindEvents(),!0}},{key:\"hide\",value:function(){return this._toggleDOM(!1)}},{key:\"destroy\",value:function(){this._events.destroy(),this.domElement&&this.settings.parent.removeChild(this.domElement)}},{key:\"_bindEvents\",value:function(){var e=this,t=this,i=this.domElement,n=this._events;function r(e,t,i){n.add(e,t,i)}r(i,\"click\",(function(e){return e.preventDefault()})),wm(n,this._domH,(function(e,i){return t._setHSLA(e)})),wm(n,this._domSL,(function(e,i){return t._setHSLA(null,e,1-i)})),this.settings.alpha&&wm(n,this._domA,(function(e,i){return t._setHSLA(null,null,null,1-i)}));var s=this._domEdit;r(s,\"input\",(function(e){t._setColor(this.value,{fromEditor:!0,failSilently:!0})})),r(s,\"focus\",(function(e){var t=this;t.selectionStart===t.selectionEnd&&t.select()})),this._ifPopup((function(){var t=function(t){return e.closeHandler(t)};r(window,Fm,t),r(window,vm,t),Cm(n,i,[\"Esc\",\"Escape\"],t);var s=function(t){e.__containedEvent=t.timeStamp};r(i,Fm,s),r(i,vm,s),r(e._domCancel,\"click\",t)}));var o=function(t){e._ifPopup((function(){return e.closeHandler(t)})),e.onDone&&e.onDone(e.colour)};r(this._domOkay,\"click\",o),Cm(n,i,[\"Enter\"],o)}},{key:\"_setPosition\",value:function(){var e=this.settings.parent,t=this.domElement;e!==t.parentNode&&e.appendChild(t),this._ifPopup((function(i){\"static\"===getComputedStyle(e).position&&(e.style.position=\"relative\");var n=!0===i?\"popup_right\":\"popup_\"+i;[\"popup_top\",\"popup_bottom\",\"popup_left\",\"popup_right\"].forEach((function(e){e===n?t.classList.add(e):t.classList.remove(e)})),t.classList.add(n)}))}},{key:\"_setHSLA\",value:function(e,t,i,n,r){r=r||{};var s=this.colour,o=s.hsla;[e,t,i,n].forEach((function(e,t){(e||0===e)&&(o[t]=e)})),s.hsla=o,this._updateUI(r),this.onChange&&!r.silent&&this.onChange(s)}},{key:\"_updateUI\",value:function(e){if(this.domElement){e=e||{};var t=this.colour,i=t.hsla,n=\"hsl(\"+360*i[0]+\", 100%, 50%)\",r=t.hslString,s=t.hslaString,o=this._domH,a=this._domSL,c=this._domA,l=ym(\".picker_selector\",o),h=ym(\".picker_selector\",a),d=ym(\".picker_selector\",c);b(0,l,i[0]),this._domSL.style.backgroundColor=this._domH.style.color=n,b(0,h,i[1]),F(0,h,1-i[2]),a.style.color=r,F(0,d,1-i[3]);var u=r,f=u.replace(\"hsl\",\"hsla\").replace(\")\",\", 0)\"),p=\"linear-gradient(\"+[u,f]+\")\";if(this._domA.style.background=p+\", linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0 / 2em 2em,\\n                   linear-gradient(45deg, lightgrey 25%,       white 25%,       white 75%, lightgrey 75%) 1em 1em / 2em 2em\",!e.fromEditor){var g=this.settings.editorFormat,m=this.settings.alpha,w=void 0;switch(g){case\"rgb\":w=t.printRGB(m);break;case\"hsl\":w=t.printHSL(m);break;default:w=t.printHex(m)}this._domEdit.value=w}this._domSample.style.color=s}function b(e,t,i){t.style.left=100*i+\"%\"}function F(e,t,i){t.style.top=100*i+\"%\"}}},{key:\"_ifPopup\",value:function(e,t){this.settings.parent&&this.settings.popup?e&&e(this.settings.popup):t&&t()}},{key:\"_toggleDOM\",value:function(e){var t=this.domElement;if(!t)return!1;var i=e?\"\":\"none\",n=t.style.display!==i;return n&&(t.style.display=i),n}}]),e}(),xm=document.createElement(\"style\");function km(e){if(Im[e])return Im[e];if(Im[\"chr\"+e]){const t=Im[\"chr\"+e];return Im[e]=t,t}{const r=(t=Math.round(255*Math.random()).toString(10),i=Math.round(255*Math.random()).toString(10),n=Math.round(255*Math.random()).toString(10),\"rgb(\"+t+\",\"+i+\",\"+n+\")\");return Im[e]=r,r}var t,i,n}xm.textContent='.picker_wrapper.no_alpha .picker_alpha{display:none}.picker_wrapper.no_editor .picker_editor{position:absolute;z-index:-1;opacity:0}.picker_wrapper.no_cancel .picker_cancel{display:none}.layout_default.picker_wrapper{display:flex;flex-flow:row wrap;justify-content:space-between;align-items:stretch;font-size:10px;width:25em;padding:.5em}.layout_default.picker_wrapper input,.layout_default.picker_wrapper button{font-size:1rem}.layout_default.picker_wrapper>*{margin:.5em}.layout_default.picker_wrapper::before{content:\"\";display:block;width:100%;height:0;order:1}.layout_default .picker_slider,.layout_default .picker_selector{padding:1em}.layout_default .picker_hue{width:100%}.layout_default .picker_sl{flex:1 1 auto}.layout_default .picker_sl::before{content:\"\";display:block;padding-bottom:100%}.layout_default .picker_editor{order:1;width:6.5rem}.layout_default .picker_editor input{width:100%;height:100%}.layout_default .picker_sample{order:1;flex:1 1 auto}.layout_default .picker_done,.layout_default .picker_cancel{order:1}.picker_wrapper{box-sizing:border-box;background:#f2f2f2;box-shadow:0 0 0 1px silver;cursor:default;font-family:sans-serif;color:#444;pointer-events:auto}.picker_wrapper:focus{outline:none}.picker_wrapper button,.picker_wrapper input{box-sizing:border-box;border:none;box-shadow:0 0 0 1px silver;outline:none}.picker_wrapper button:focus,.picker_wrapper button:active,.picker_wrapper input:focus,.picker_wrapper input:active{box-shadow:0 0 2px 1px #1e90ff}.picker_wrapper button{padding:.4em .6em;cursor:pointer;background-color:#f5f5f5;background-image:linear-gradient(0deg, gainsboro, transparent)}.picker_wrapper button:active{background-image:linear-gradient(0deg, transparent, gainsboro)}.picker_wrapper button:hover{background-color:#fff}.picker_selector{position:absolute;z-index:1;display:block;-webkit-transform:translate(-50%, -50%);transform:translate(-50%, -50%);border:2px solid #fff;border-radius:100%;box-shadow:0 0 3px 1px #67b9ff;background:currentColor;cursor:pointer}.picker_slider .picker_selector{border-radius:2px}.picker_hue{position:relative;background-image:linear-gradient(90deg, red, yellow, lime, cyan, blue, magenta, red);box-shadow:0 0 0 1px silver}.picker_sl{position:relative;box-shadow:0 0 0 1px silver;background-image:linear-gradient(180deg, white, rgba(255, 255, 255, 0) 50%),linear-gradient(0deg, black, rgba(0, 0, 0, 0) 50%),linear-gradient(90deg, #808080, rgba(128, 128, 128, 0))}.picker_alpha,.picker_sample{position:relative;background:linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0/2em 2em,linear-gradient(45deg, lightgrey 25%, white 25%, white 75%, lightgrey 75%) 1em 1em/2em 2em;box-shadow:0 0 0 1px silver}.picker_alpha .picker_selector,.picker_sample .picker_selector{background:none}.picker_editor input{font-family:monospace;padding:.2em .4em}.picker_sample::before{content:\"\";position:absolute;display:block;width:100%;height:100%;background:currentColor}.picker_arrow{position:absolute;z-index:-1}.picker_wrapper.popup{position:absolute;z-index:2;margin:1.5em}.picker_wrapper.popup,.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{background:#f2f2f2;box-shadow:0 0 10px 1px rgba(0,0,0,.4)}.picker_wrapper.popup .picker_arrow{width:3em;height:3em;margin:0}.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{content:\"\";display:block;position:absolute;top:0;left:0;z-index:-99}.picker_wrapper.popup .picker_arrow::before{width:100%;height:100%;-webkit-transform:skew(45deg);transform:skew(45deg);-webkit-transform-origin:0 100%;transform-origin:0 100%}.picker_wrapper.popup .picker_arrow::after{width:150%;height:150%;box-shadow:none}.popup.popup_top{bottom:100%;left:0}.popup.popup_top .picker_arrow{bottom:0;left:0;-webkit-transform:rotate(-90deg);transform:rotate(-90deg)}.popup.popup_bottom{top:100%;left:0}.popup.popup_bottom .picker_arrow{top:0;left:0;-webkit-transform:rotate(90deg) scale(1, -1);transform:rotate(90deg) scale(1, -1)}.popup.popup_left{top:0;right:100%}.popup.popup_left .picker_arrow{top:0;right:0;-webkit-transform:scale(-1, 1);transform:scale(-1, 1)}.popup.popup_right{top:0;left:100%}.popup.popup_right .picker_arrow{top:0;left:0}',document.documentElement.firstElementChild.appendChild(xm),_m.StyleElement=xm;const Im={chrX:\"rgb(204, 153, 0)\",chrY:\"rgb(153, 204, 0\",chrUn:\"rgb(50, 50, 50)\",chr1:\"rgb(80, 80, 255)\",chrI:\"rgb(139, 155, 187)\",chr2:\"rgb(206, 61, 50)\",chrII:\"rgb(206, 61, 50)\",chr2a:\"rgb(216, 71, 60)\",chr2b:\"rgb(226, 81, 70)\",chr3:\"rgb(116, 155, 88)\",chrIII:\"rgb(116, 155, 88)\",chr4:\"rgb(240, 230, 133)\",chrIV:\"rgb(240, 230, 133)\",chr5:\"rgb(70, 105, 131)\",chr6:\"rgb(186, 99, 56)\",chr7:\"rgb(93, 177, 221)\",chr8:\"rgb(128, 34, 104)\",chr9:\"rgb(107, 215, 107)\",chr10:\"rgb(213, 149, 167)\",chr11:\"rgb(146, 72, 34)\",chr12:\"rgb(131, 123, 141)\",chr13:\"rgb(199, 81, 39)\",chr14:\"rgb(213, 143, 92)\",chr15:\"rgb(122, 101, 165)\",chr16:\"rgb(228, 175, 105)\",chr17:\"rgb(59, 27, 83)\",chr18:\"rgb(205, 222, 183)\",chr19:\"rgb(97, 42, 121)\",chr20:\"rgb(174, 31, 99)\",chr21:\"rgb(231, 199, 111)\",chr22:\"rgb(90, 101, 94)\",chr23:\"rgb(204, 153, 0)\",chr24:\"rgb(153, 204, 0)\",chr25:\"rgb(51, 204, 0)\",chr26:\"rgb(0, 204, 51)\",chr27:\"rgb(0, 204, 153)\",chr28:\"rgb(0, 153, 204)\",chr29:\"rgb(10, 71, 255)\",chr30:\"rgb(71, 117, 255)\",chr31:\"rgb(255, 194, 10)\",chr32:\"rgb(255, 209, 71)\",chr33:\"rgb(153, 0, 51)\",chr34:\"rgb(153, 26, 0)\",chr35:\"rgb(153, 102, 0)\",chr36:\"rgb(128, 153, 0)\",chr37:\"rgb(51, 153, 0)\",chr38:\"rgb(0, 153, 26)\",chr39:\"rgb(0, 153, 102)\",chr40:\"rgb(0, 128, 153)\",chr41:\"rgb(0, 51, 153)\",chr42:\"rgb(26, 0, 153)\",chr43:\"rgb(102, 0, 153)\",chr44:\"rgb(153, 0, 128)\",chr45:\"rgb(214, 0, 71)\",chr46:\"rgb(255, 20, 99)\",chr47:\"rgb(0, 214, 143)\",chr48:\"rgb(20, 255, 177)\"};class Sm{constructor(e){this.tracks=[],this.chordSets=[]}addChordSet(e){this.chordSets=this.chordSets.filter((t=>t.name!==e.name)),this.chordSets.push(e);let t=this.tracks.find((t=>e.trackName===t.name));t&&(t.chordSets=t.chordSets.filter((t=>t.name!==e.name)),t.chordSets.push(e)),t||(t=new Em(e),this.tracks.push(t))}clearChords(){this.tracks=[],this.chordSets=[]}getTrack(e){return this.tracks.find((t=>e===t.name))}getChordSet(e){return this.chordSets.find((t=>e===t.name))}}class Em{constructor(e){this.name=e.trackName,this.color=e.trackColor,this.visible=!0,this.chordSets=[e],this.id=(\"0000\"+(Math.random()*Math.pow(36,4)|0).toString(36)).slice(-4)}get chords(){if(1===this.chordSets.length)return this.chordSets[0].chords;const e=[];for(let t of this.chordSets)for(let i of t.chords)e.push(i);return e}}const Nm=Math.exp(5);class Bm{static isInstalled(){return void 0!==window.JBrowseReactCircularGenomeView&&void 0!==window.React&&void 0!==window.ReactDOM}constructor(e,t){if(t=t||{},this.config=t,Bm.isInstalled()){this.parent=e,this.groupByTrack=!0===t.groupByTrack,this.chordManager=new Sm(t);const i=document.createElement(\"div\");i.className=\"igv-circview-container\",e.appendChild(i),this.createControls(i),this.resetControlPanel();const n=document.createElement(\"div\");n.className=\"igv-circview-circular-genome-view\",i.appendChild(n),this.container=n,t.assembly&&this.setAssembly(t.assembly),this.width=t.width||500,this.height=t.height||500,this.setSize(this.width,this.height)}else console.error(\"JBrowse circular view is not installed\")}createControls(e){const t=document.createElement(\"div\");t.className=\"igv-circview-toolbar\",e.appendChild(t),this.toolbar=t;const i=document.createElement(\"div\");i.className=\"igv-circview-track-panel\",e.appendChild(i),this.controlPanel=i,this.controlPanel.style.display=\"none\";const n=document.createElement(\"div\");n.className=\"igv-circview-toolbar-button-container\",this.toolbar.appendChild(n),this.showControlsButton=document.createElement(\"div\"),this.showControlsButton.className=\"igv-circview-button\",n.appendChild(this.showControlsButton),this.showControlsButton.innerText=\"none\"===this.controlPanel.style.display?\"Show Controls\":\"Hide Controls\",this.showControlsButton.addEventListener(\"click\",(e=>{this.controlPanel.querySelectorAll(\"div\").length>0&&(\"none\"===this.controlPanel.style.display?(this.controlPanel.style.display=\"flex\",e.target.innerText=\"Hide Controls\"):(this.controlPanel.style.display=\"none\",e.target.innerText=\"Show Controls\"))}));let r=document.createElement(\"div\");r.className=\"igv-circview-button\",n.appendChild(r),r.innerText=\"Clear All\",r.addEventListener(\"click\",(()=>{this.clearChords()})),!1!==this.config.showCloseButton&&(r=document.createElement(\"div\"),r.className=\"igv-circview-button\",n.appendChild(r),r.innerText=\"Close\",r.addEventListener(\"click\",(()=>{this.visible=!1})))}resetControlPanel(){this.controlPanel.innerHTML=\"\",this.controlPanel.appendChild(this.createGroupByCB());const e=this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets;for(let t of e)this.addToControlPanel(t)}createGroupByCB(){const e=document.createElement(\"input\");e.type=\"checkbox\",e.id=\"groupByCB\",e.style.width=\"1.4em\",e.style.height=\"1.4em\",e.checked=this.groupByTrack,e.onclick=e=>{this.groupByTrack=e.target.checked,this.resetControlPanel(),this.render()};const t=document.createElement(\"label\");t.for=\"groupByCB\",t.innerText=\"Group by track\",t.style.color=\"black\",t.style.paddingLeft=\"10px\";const i=document.createElement(\"div\");return i.style.width=\"100%\",i.style.paddingTop=\"5px\",i.style.paddingBottom=\"5px\",i.style.background=\"rgb(216, 230, 234)\",i.appendChild(e),i.appendChild(t),i}addToControlPanel(e){const t=document.createElement(\"div\");this.controlPanel.appendChild(t);const i=document.createElement(\"div\");i.className=\"igv-circview-button\",t.appendChild(i),i.innerText=!0===e.visible?\"Hide\":\"Show\",i.addEventListener(\"click\",(t=>{!0===e.visible?(this.hideChordSet(e.name),t.target.innerText=\"Show\"):(this.showChordSet(e.name),t.target.innerText=\"Hide\")}));const n=document.createElement(\"input\"),r=e=>200*Math.log(e*Nm),s=document.createElement(\"div\");s.className=\"igv-circview-button\",s.innerHTML=\"&nbsp;&nbsp;&nbsp;&nbsp;\",t.appendChild(s),s.style.backgroundColor=Mm(e.color,1);const o={parent:s,popup:\"right\",editorFormat:\"rgb\",color:e.color,onChange:({rgbaString:t})=>{s.style.backgroundColor=Mm(t,1),this.setColor(e.name,t),n.value=r(Rm(e.color))}},a=new _m(o);n.setAttribute(\"title\",\"Adjust transparency of arcs\"),n.type=\"range\",n.style.width=\"100px\",n.style.marginRight=\"10px\",n.setAttribute(\"class\",\"range\"),n.setAttribute(\"min\",\"0\"),n.setAttribute(\"max\",\"1000\"),n.value=r(Rm(e.color)),n.oninput=()=>{const t=(i=n.value,Math.exp(i/200)/Nm);var i;this.setColor(e.name,Mm(e.color,t)),a.setColor(e.color)},t.appendChild(n);const c=document.createElement(\"div\");c.style.color=\"black\",t.appendChild(c),c.innerText=c.title=e.name}setAssembly(e){const t=this.genomeId||Lm();if(this.genomeId===t)return;this.chordManager.clearChords(),this.genomeId=t,this.chrNames=new Set(e.chromosomes.map((e=>Dm(e.name))));const i=[],n=[];for(let t of e.chromosomes){const e=Dm(t.name);n.push(t.color||km(e)),i.push({refName:e,uniqueId:e,start:0,end:t.bpLength})}this.assembly={name:e.name,sequence:{trackId:t,type:\"ReferenceSequenceTrack\",adapter:{type:\"FromConfigSequenceAdapter\",features:i}},refNameColors:n},this.render()}addChords(e,t={}){const i=t.name||t.track||\"*\",n=i.split(\" \")[0].replaceAll(\"%20\",\" \"),r={name:i.replaceAll(\"%20\",\" \"),trackName:n,chords:e,color:t.color||\"black\",trackColor:t.trackColor||t.color||\"black\",visible:!0,id:t.id||Lm()};this.chordManager.addChordSet(r),this.resetControlPanel(),this.render()}setSize(e,t){if(t=t||e,this.width=e,this.height=t,this.viewState){const i=this.viewState.session.view;i.setWidth(e),i.setHeight(t),i.setBpPerPx(i.minBpPerPx)}}getSize(){return Math.min(this.width,this.height)}clearChords(){this.chordManager.clearChords(),this.resetControlPanel(),this.render()}clearSelection(){this.viewState.pluginManager.rootModel.session.clearSelection()}show(){this.parent.style.display=\"block\"}hide(){this.parent.style.display=\"none\"}get visible(){return\"none\"!==this.parent.style.display}set visible(e){this.parent.style.display=e?\"block\":\"none\"}hideChordSet(e){let t=this.getChordSet(e);t?(t.visible=!1,this.render()):console.warn(`No track with name: ${name}`)}showChordSet(e){let t=this.getChordSet(e);t?(t.visible=!0,this.render()):console.warn(`No track with name: ${e}`)}deleteTrack(e){let t=this.tracks.findIndex((t=>e===t.name));t>=0&&this.tracks.splice(t,1),this.render()}getChordSet(e){return this.groupByTrack?this.chordManager.getTrack(e):this.chordManager.getChordSet(e)}setColor(e,t){const i=this.getChordSet(e);if(i){i.color=t;const e=i.id;for(let i of this.viewState.config.tracks)if(e===i.trackId){i.displays[0].renderer.strokeColor.set(t);break}}}render(){const{createViewState:e,JBrowseCircularGenomeView:t}=JBrowseReactCircularGenomeView;ReactDOM.unmountComponentAtNode(this.container);const i=(this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets).filter((e=>e.visible)),n=[],r=[];for(let e of i)n.push({trackId:e.id,name:e.name,assemblyNames:[\"forIGV\"],type:\"VariantTrack\",adapter:{type:\"FromConfigAdapter\",features:e.chords}}),r.push(e.color);this.viewState=e({assembly:this.assembly,tracks:n});for(let e=0;e<i.length;e++)this.viewState.config.tracks[e].displays[0].renderer.strokeColor.set(r[e]);this.element=React.createElement(t,{viewState:this.viewState}),this.setSize(this.width,this.height),ReactDOM.render(this.element,this.container);const s=this.config.onChordClick||Tm;for(let e=0;e<i.length;e++)this.viewState.session.view.showTrack(this.viewState.config.tracks[e].trackId),s&&(this.viewState.pluginManager.jexl.addFunction(\"onChordClick\",s),this.viewState.config.tracks[e].displays[0].onChordClick.set(\"jexl:onChordClick(feature, track, pluginManager)\"))}}function Mm(e,t){const[i,n,r,s]=e.split(\",\");return`${i},${n},${r},${t})`}function Rm(e){return e.startsWith(\"rgba(\")?Number(e.split(\",\")[3].replace(\")\",\"\")):1}function Dm(e){return e.startsWith(\"chr\")?e.substring(3):e}function Tm(e,t,i){console.log(e)}function Lm(){return(\"0000\"+(Math.random()*Math.pow(36,4)|0).toString(36)).slice(-4)}if(\"undefined\"!=typeof document){function BA(e){for(let t of document.styleSheets)if(t=t.href?t.href.replace(/^.*[\\\\\\/]/,\"\"):\"\",t===e)return!0;return!1}BA(\"circular-view.css\")||function(){const e=document.createElement(\"style\");e.setAttribute(\"type\",\"text/css\"),e.innerHTML='.igv-circview-container {\\n  width: fit-content;\\n  height: fit-content;\\n  box-sizing: content-box;\\n  color: dimgray;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  background-color: white;\\n  border-color: dimgray;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-circview-toolbar {\\n  position: relative;\\n  width: 100%;\\n  height: 32px;\\n  background-color: lightgrey;\\n  border-bottom-style: solid;\\n  border-bottom-color: dimgray;\\n  border-bottom-width: thin;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n\\n.igv-circview-toolbar-button-container {\\n  height: 100%;\\n  width: fit-content;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-circview-toolbar-button-container > div {\\n  margin: 4px;\\n}\\n\\n.igv-circview-track-panel {\\n  z-index: 1024;\\n  position: absolute;\\n  top: 33px;\\n  left: 0;\\n  width: 100%;\\n  height: fit-content;\\n  border-bottom-style: solid;\\n  border-bottom-color: dimgray;\\n  border-bottom-width: thin;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n.igv-circview-track-panel > div {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-circview-track-panel > div > div {\\n  margin: 4px;\\n}\\n\\n.igv-circview-swatch-button {\\n  cursor: pointer;\\n  padding: 5px;\\n  width: 8px;\\n  height: 8px;\\n  border: 1px solid #8d8b8b;\\n  border-radius: 16px;\\n}\\n\\n.igv-circview-button {\\n  cursor: pointer;\\n  padding: 5px;\\n  color: #444;\\n  vertical-align: middle;\\n  text-align: center;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  border: 1px solid #8d8b8b;\\n  border-radius: 4px;\\n  background: #efefef;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.2);\\n}\\n\\n.igv-circview-button:hover {\\n  background: #efefef;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\\n}\\n\\n.igv-circview-button:active {\\n  color: #007bff;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\\n}\\n\\n/*# sourceMappingURL=circular-view.css.map */\\n',document.head.insertBefore(e,document.head.childNodes[document.head.childNodes.length-1])}()}const zm=e=>e.startsWith(\"chr\")?e.substring(3):e;function Hm(e){const t=[],i=[];if(e.wgChromosomeNames)for(let n of e.wgChromosomeNames){const r=e.getChromosome(n);i.push(Nu(r.name)),t.push({name:r.name,bpLength:r.bpLength})}return t}function Pm(e,t,i,n){const r=t.color||\"rgb(0,0,255)\",s=_s.addAlpha(\"all\"===i.chr?r:Nu(i.chr),n),o=_s.addAlpha(r,n),a=t.name.replaceAll(\" \",\"%20\"),c=\"all\"===i.chr?a:`${a}  ${i.chr}:${i.start}-${i.end}`;t.browser.circularView.addChords(e,{track:c,color:s,trackColor:o}),t.browser.circularViewVisible||(t.browser.circularViewVisible=!0)}class Om{constructor(e,{minTLENPercentile:t,maxTLENPercentile:i}){this.totalCount=0,this.frCount=0,this.rfCount=0,this.ffCount=0,this.sumF=0,this.sumF2=0,this.lp=void 0===t?.1:t,this.up=void 0===i?99.5:i,this.isizes=[],this.compute(e)}compute(e){for(let n of e)if(n.isProperPair()){var t=Math.abs(n.fragmentLength);this.sumF+=t,this.sumF2+=t*t,this.isizes.push(t);var i=n.pairOrientation;if(\"string\"==typeof i&&4===i.length)switch(\"\"+i.charAt(0)+i.charAt(2)){case\"FF\":case\"RR\":this.ffCount++;break;case\"FR\":this.frCount++;break;case\"RF\":this.rfCount++}this.totalCount++}this.ffCount/this.totalCount>.9?this.orienation=\"ff\":this.frCount/this.totalCount>.9?this.orienation=\"fr\":this.rfCount/this.totalCount>.9&&(this.orienation=\"rf\"),this.minTLEN=0===this.lp?0:Um(this.isizes,this.lp),this.maxTLEN=Um(this.isizes,this.up)}}function Um(e,t){if(0!==e.length){var i=Math.floor(e.length*(t/100));return e.sort((function(e,t){return e-t})),e[i]}}const qm=\"rgb(255,0,255)\",Qm=\"rgb(0,0,255)\",Vm=\"rgb(132, 178, 158)\",jm=new Map;jm.set(\"m\",\"rgb(255,0,0)\"),jm.set(\"h\",qm),jm.set(\"o\",\"rgb(111, 78, 129)\"),jm.set(\"f\",\"rgb(246, 200, 95)\"),jm.set(\"c\",\"rgb(157, 216, 102)\"),jm.set(\"g\",\"rgb(255, 160, 86)\"),jm.set(\"e\",\"rgb(141, 221, 208)\"),jm.set(\"b\",\"rgb(202, 71, 47)\"),jm.set(\"h\",qm),jm.set(\"a\",\"rgb(51,0,111)\"),jm.set(\"NONE_A\",Qm),jm.set(\"NONE_C\",Qm),jm.set(\"NONE_T\",Qm),jm.set(\"NONE_G\",Qm),jm.set(\"NONE_N\",Qm);const Wm=new Map;function Gm(e,t,i){let n=function(e,t){return jm.has(e)?jm.get(e):Vm}(e),r=Xf(t);if(r>255)return n;const s=e+r+i;if(r<0&&(r=0),!Wm.has(s)){const e=\"basemod2\"===i?Math.max(20,Math.min(255,r*r/50-4*r+200+20)):Math.max(20,Math.min(255,.006127*r*r)),[t,o,a]=_s.rgbComponents(n);Wm.set(s,`rgba(${t},${o},${a},${e/255})`)}return Wm.get(s)}class $m{constructor(e){this.alignmentTrack=e}updateContext(e){this.context=e}drawModifications(e,t,i,n,r,s){const{ctx:o,pixelEnd:a,bpStart:c,bpPerPixel:l}=n,h=e.getBaseModificationSets();if(h){let n;const d=r.split(\":\");2==d.length&&(r=d[0],n=d[1]);for(let d of e.blocks){if(\"S\"===d.type)continue;const e=t,u=i;let f=Math.max(1,1/l);for(let t=d.seqOffset;t<d.seqOffset+d.len;t++){let i=(d.start+(t-d.seqOffset)-c)/l;if(i>a)break;if(i+f<0)continue;let p,g=-1,m=255,w=0;for(let e of h)if((!n||e.modification===n)&&e.containsPosition(t)){const i=Xf(e.likelihoods.get(t));m-=i,(!p||i>g)&&(p=e.modification,w=e.canonicalBase,g=i)}if(p){const t=255*s;let n;m>g&&\"basemod2\"===r&&m>=t?n=Gm(\"NONE_\"+w,m,r):g>=t&&(n=Gm(p,g,r)),o.fillStyle=n,f<3&&(f=3,i--),o.fillRect(i,e,f,Math.max(1,u-2))}}}}}}const Km=new Set([\"firstOfPairStrand\"]);class Ym extends Hl{static defaults={viewAsPairs:!1,showSoftClips:!1,showAllBases:!1,showInsertions:!0,showMismatches:!0,colorBy:void 0,groupBy:void 0,displayMode:\"EXPANDED\",alignmentRowHeight:14,squishedRowHeight:3,negStrandColor:\"rgba(150, 150, 230, 0.75)\",posStrandColor:\"rgba(230, 150, 150, 0.75)\",baseModPosStrandColor:\"rgb(195, 195, 195)\",baseModNegStrandColor:\"rgb(195, 210, 195)\",insertionColor:\"rgb(138, 94, 161)\",insertionTextColor:\"white\",showInsertionText:!1,deletionColor:\"black\",deletionTextColor:\"black\",showDeletionText:!1,skippedColor:\"rgb(150, 170, 170)\",pairConnectorColor:void 0,smallTLENColor:\"rgb(0, 0, 150)\",largeTLENColor:\"rgb(200, 0, 0)\",expectedPairOrientation:\"fr\",rlColor:\"rgb(0, 150, 0)\",rrColor:\"rgb(20, 50, 200)\",llColor:\"rgb(0, 150, 150)\",bamColorTag:\"YC\",hideSmallIndels:!1,indelSizeThreshold:1,highlightColor:void 0,minTLEN:void 0,maxTLEN:void 0,tagColorPallete:\"Set1\"};_colorTables=new Map;_baseModifications=new Set;constructor(e,t){super(e,t),(e.colorTable||e.tagColorTable)&&(this.colorTable=new ao(e.tagColorTable)),e.largeFragmentLengthColor&&(this.largeTLENColor=e.largeFragmentLengthColor),e.pairOrienation&&(this.expectedPairOrientation=e.pairOrientation),e.smallFragmentLengthColor&&(this.smallTLENColor=e.smallFragmentLengthColor),e.largeFragmentLengthColor&&(this.largeTLENColor=e.largeFragmentLengthColor),e.minFragmentLength&&(this.minTLEN=e.minFragmentLength),e.maxFragmentLength&&(this.maxTLEN=e.maxFragmentLength),e.displayMode&&(this.displayMode=e.displayMode.toUpperCase()),e.colorBy&&e.colorByTag&&(this.colorBy=e.colorBy+\":\"+e.colorByTag),this.featureSource=this.parent.featureSource,this.top=0===e.coverageTrackHeight?0:e.coverageTrackHeight+5,this.pairColors={RL:this.rlColor,RR:this.rrColor,LL:this.llColor},e.highlightedReads&&this.setHighlightedReads(e.highlightedReads),this.hasPairs=!1,this.hasSupplemental=!1,this._groupByTags=[],this._groupByPositions=[],e.groupBy&&(this.groupBy=e.groupBy,e.groupBy.startsWith(\"base:\")&&this._groupByPositions.push(e.groupBy.substring(5)),e.groupBy.startsWith(\"tag:\")&&this._groupByTags.push(e.groupBy.substring(4))),this._locusChange=Zm.bind(this),this.browser.on(\"locuschange\",this._locusChange)}init(e){this.parent=e.parent,delete e.parent,super.init(e)}dispose(){this.browser.off(\"locuschage\",this._locusChange)}get baseModRenderer(){return this._baseModRenderer||(this._baseModRenderer=new $m(this)),this._baseModRenderer}get baseModificationThreshold(){return this.parent.baseModificationThreshold}setTop(e,t){this.top=0===e.height||!1===t?0:5+e.height}setHighlightedReads(e,t){if(!Array.isArray(e)||!e.every((e=>\"string\"==typeof e)))throw new Error(\"AlignmentTrack.setHighlightedReads() only accept array of strings\");t&&(this.highlightColor=t),this.highlightedReads=new Set(e)}computePixelHeight(e){if(e.packedGroups){let t=e.hasDownsampledIntervals()?15:0;const i=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;for(let n of e.packedGroups.values())t+=i*n.length+10;return t+5}return 0}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=r+s*n+1,a=this.showSoftClips,c=this.showAllBases,l=this.browser.nucleotideColors;i.save();for(let e of t.baseModificationKeys)this._baseModifications.add(e.modification);let h=t.sequence;h&&(h=h.toUpperCase());let d=0;this.colorBy||(this.colorBy=this.hasPairs?\"unexpectedPair\":\"none\");let u=e.pixelTop;this.top&&i.translate(0,this.top);const f=u+e.pixelHeight;t.hasDownsampledIntervals()?(d=15,t.downsampledIntervals.forEach((function(e){var t=(e.start-r)/n,s=(e.end-r)/n;s-t>5&&(t+=1,s-=1),xo.fillRect(i,t,2,s-t,8,{fillStyle:\"black\"})}))):d=0,this.alignmentsYOffset=d;const p=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight,g=t.packedGroups;if(g){let t=d;for(let n of g.keys()){const a=g.get(n),c=a.rows,l=c.length;a.pixelTop=t;for(let e=0;e<l;e++){const i=c[e],n=p<=4?p:p-2;if(t>f)break;if(t+n<u)t+=p;else{for(let e of i.alignments)if(this.browser.circularView&&(this.hasSupplemental=this.hasSupplemental||e.hasTag(\"SA\")),!(e.start+e.lengthOnRef<r)){if(e.start>o)break;!0!==e.hidden&&(e instanceof Qf?(m.call(this,e,t,n),w.call(this,e.firstAlignment,t,n),e.secondAlignment&&w.call(this,e.secondAlignment,t,n)):w.call(this,e,t,n))}t+=p}}if(a.pixelBottom=t,this.groupBy&&n){i.save(),i.font=\"400 12px sans-serif\";const r=i.measureText(n),o=r.width+10,c=-e.pixelShift+e.viewportWidth-o-10,l=r.actualBoundingBoxAscent+r.actualBoundingBoxDescent+10,h=Math.min(a.pixelTop+l-1,a.pixelBottom);i.textAlign=\"center\",i.fillStyle=\"white\",i.strokeStyle=\"lightGray\",xo.roundRect(i,c,h-r.actualBoundingBoxAscent-5,o,l,2,1,1),i.fillStyle=\"black\",i.fillText(n,c+o/2,h),xo.dashedLine(i,0,t,s,t),i.restore(),t+=10}}}function m(e,t,s){var a=this.getConnectorColor(e.firstAlignment),c=(e.connectingStart-r)/n,l=(e.connectingEnd-r)/n,h=t+s/2;e.connectingEnd<r||e.connectingStart>o||(e.mq<=0&&(a=_s.addAlpha(a,.15)),xo.setProperties(i,{fillStyle:a,strokeStyle:a}),xo.strokeLine(i,c,h,l,h))}function w(e,d,u){if(e.start+e.lengthOnRef<r||e.start>o)return;const f=a?e.blocks:e.blocks.filter((e=>\"S\"!==e.type));let g=this.getAlignmentColor(e);const m=g;e.mq<=0&&(g=_s.addAlpha(g,.15)),xo.setProperties(i,{fillStyle:g,strokeStyle:m});const w=[];for(let e=0;e<f.length;e++){const t=f[e];if(!(e!==f.length-1&&f[e+1].start<r)&&(w.push(...b.call(this,t,e)),t.start+t.len>o))break}if(e.gaps){const t=d+u/2;for(let s of e.gaps){const e=(s.start-r)/n,o=(s.start+s.len-r)/n,a=o-e,c=s.len.toString(),l=6*c.length,h=e+a/2,u=\"D\"===s.type?this.deletionColor:this.skippedColor;if(xo.strokeLine(i,e,t,o,t,{strokeStyle:u,lineWidth:2}),this.showDeletionText&&s.len>1&&a>=l+8){const e=h-l/2;xo.fillRect(i,e-1,d-1,l+2,12,{fillStyle:\"white\"}),xo.fillText(i,c,e,d+10,{font:\"normal 10px monospace\",fillStyle:this.deletionTextColor})}}}if(e.insertions&&this.showInsertions){let t=-1;for(let s of e.insertions){if(this.hideSmallIndels&&s.len<=this.indelSizeThreshold)continue;if(s.start<r)continue;if(s.start>o)break;const e=s.start-r,a=s.len.toString(),c=2+6*a.length,l=this.showInsertionText&&1!==s.len?Math.round(s.len/n):2,h=Math.max(Math.min(c,l),2),f=e/n-h/2;if(f-t>2){const e={fillStyle:this.insertionColor};xo.fillRect(i,f-2,d,h+4,2,e),xo.fillRect(i,f,d+2,h,u-4,e),xo.fillRect(i,f-2,d+u-2,h+4,2,e),this.showInsertionText&&s.len>1&&l>c&&xo.fillText(i,a,f+1,d+10,{font:\"normal 10px monospace\",fillStyle:this.insertionTextColor}),t=f}}}for(let{bbox:e,baseColor:t,readChar:r}of w){if(n<=.1&&e.height>=8){const n=Math.min(10,e.height);i.font=n+\"px sans-serif\";const s=e.x+e.width/2;xo.strokeText(i,r,s-i.measureText(r).width/2,n-1+e.y,{strokeStyle:t})}else xo.fillRect(i,e.x,e.y,e.width,e.height,{fillStyle:t})}if(this.colorBy&&this.colorBy.startsWith(\"basemod\")){const t={ctx:i,bpPerPixel:n,bpStart:r,bpEnd:o,pixelEnd:s};this.baseModRenderer.drawModifications(e,d,u,t,this.colorBy,this.baseModificationThreshold)}function b(o,a){const w=[],b=o.start-t.start,F=(o.start-r)/n,v=(o.start+o.len-r)/n,y=Math.max(1,v-F),A=100/n,C=Math.min(p/2,A/6),_=\"S\"===o.type,x=e.mq<=0||this.selectedReadName===e.readName||_||this.highlightedReads&&this.highlightedReads.has(e.readName);let k=m;this.selectedReadName===e.readName?k=\"red\":_?k=\"rgb(50,50,50)\":this.highlightedReads&&this.highlightedReads.has(e.readName)&&(k=this.highlightColor||\"#00ff00\");const I=!0===e.strand&&a===f.length-1,S=!1===e.strand&&0===a;if(I|S){let e,t;I?(e=[F,v,v+C,v,F,F],t=[d,d,d+u/2,d+u,d+u,d]):S&&(e=[v,F,F-C,F,v,v],t=[d,d,d+u/2,d+u,d+u,d]),xo.fillPolygon(i,e,t,{fillStyle:g}),x&&xo.strokePolygon(i,e,t,{strokeStyle:k})}else xo.fillRect(i,F,d,y,u,{fillStyle:g}),x&&(i.save(),i.strokeStyle=k,i.strokeRect(F,d,y,u),i.restore());if(_||c||this.showMismatches&&h&&e.seq&&\"*\"!==e.seq){const t=e.seq?e.seq.toUpperCase():void 0,i=e.qual,a=o.seqOffset,f=Math.max(1,1/n);for(let e=0,p=o.len;e<p;e++){const p=(o.start+e-r)/n;if(p+f<0)continue;if(p>s)break;let g=t?t.charAt(a+e):\"\";const m=b+e>=0?h.charAt(b+e):\"\";if(\"=\"===g&&(g=m),\"X\"===g||m!==g||_||c){let t=l[g]||\"rgb(0,0,0)\";if(!_&&void 0!==i&&i.length>a+e){t=Xm(i[a+e],t)}w.push({bbox:{x:p,y:d,width:f,height:u},baseColor:t,readChar:g})}}}return w}}i.restore()}popupData(e){const t=this.getClickedObject(e);return t?t.popupData(e.genomicLocation):void 0}menuItemList(){let e=[];e.push(\"<hr/>\");const t=Bt('<div class=\"igv-track-menu-category\">');t.text(\"Color by:\"),e.push({name:void 0,object:t,click:void 0,init:void 0});const i=[];i.push({key:\"none\",label:\"none\"}),i.push({key:\"strand\",label:\"read strand\"}),this.hasPairs&&(i.push({key:\"firstOfPairStrand\",label:\"first-of-pair strand\"}),i.push({key:\"pairOrientation\",label:\"pair orientation\"}),i.push({key:\"tlen\",label:\"insert size (TLEN)\"}),i.push({key:\"unexpectedPair\",label:\"pair orientation & insert size (TLEN)\"})),i.push({key:\"tag\",label:\"tag\"});for(let t of i){const i=void 0===this.colorBy&&\"none\"===t.key||this.colorBy===t.key;e.push(this.colorByCB(t,i))}const n=this._baseModifications.size;if(n>0){e.push('<hr style=\"border-top:1px dotted;border-bottom: none;\">');let t=1===n?\"base modification\":\"base modification (all)\";if(e.push(this.basemodColorByCB({key:\"basemod\",label:t})),n>1)for(let t of this._baseModifications)e.push(this.basemodColorByCB({key:\"basemod:\"+t,label:`base modification (${Kf(t)})`}));if(e.push('<hr style=\"border-top:1px dotted;border-bottom: none;\">'),t=1===n?\"base modification 2-color\":\"base modification 2-color (all)\",e.push(this.basemodColorByCB({key:\"basemod2\",label:t})),n>1)for(let t of this._baseModifications)e.push(this.basemodColorByCB({key:\"basemod2:\"+t,label:`base modification 2-color (${Kf(t)})`}))}e.push(\"<hr/>\");const r=Bt('<div class=\"igv-track-menu-category\">');r.text(\"Group by:\"),e.push({name:void 0,object:r,click:void 0,init:void 0});const s=[];s.push({key:\"none\",label:\"none\"}),s.push({key:\"strand\",label:\"read strand\"}),this.hasPairs&&(s.push({key:\"firstOfPairStrand\",label:\"first-of-pair strand\"}),s.push({key:\"pairOrientation\",label:\"pair orientation\"}),s.push({key:\"mateChr\",label:\"chromosome of mate\"})),s.push({key:\"chimeric\",label:\"chimeric\"}),s.push({key:\"supplementary\",label:\"supplementary flag\"}),s.push({key:\"readOrder\",label:\"read order\"});for(let e of this._groupByTags)s.push({key:`tag:${e}`,label:`tag:${e}`});for(let e of this._groupByPositions)s.push({key:`base:${e}`,label:`base:${e}`});s.push({key:\"tag\",label:\"tag...\"});for(let t of s){const i=void 0===this.groupBy&&\"none\"===t.key||this.groupBy===t.key;e.push(this.groupByCB(t,i))}e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"Show all bases\",this.showAllBases)),click:function(){this.alignmentTrack.showAllBases=!this.alignmentTrack.showAllBases,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show mismatches\",this.showMismatches)),click:function(){this.alignmentTrack.showMismatches=!this.alignmentTrack.showMismatches,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show insertions\",this.showInsertions)),click:function(){this.alignmentTrack.showInsertions=!this.alignmentTrack.showInsertions,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show soft clips\",this.showSoftClips)),click:function(){this.alignmentTrack.showSoftClips=!this.alignmentTrack.showSoftClips;const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this);this.trackView.repaintViews()}}),this.hasPairs&&(e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"View as pairs\",this.viewAsPairs)),click:function(){const e=!this.alignmentTrack.viewAsPairs;if(e&&this.groupBy&&!Km.has(this.groupBy))return void this.browser.alert.present(`'View as Pairs' is incompatible with 'Group By ${this.groupBy}'`);this.alignmentTrack.viewAsPairs=e;const t=this.getCachedAlignmentContainers();for(let e of t)e.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(e.push(\"<hr/>\"),this.hasPairs&&e.push({label:\"Add discordant pairs to circular view\",click:function(){for(let e of this.trackView.viewports)this.addPairedChordsForViewport(e)}}),this.hasSupplemental&&e.push({label:\"Add split reads to circular view\",click:function(){for(let e of this.trackView.viewports)this.addSplitChordsForViewport(e)}})),e.push(\"<hr/>\");const o=Bt('<div class=\"igv-track-menu-category\">');o.text(\"Display mode:\"),e.push({name:void 0,object:o,click:void 0,init:void 0});for(let t of[\"EXPANDED\",\"SQUISHED\",\"FULL\"])e.push({object:Bt(Dl(t.toLowerCase(),this.displayMode===t)),click:function(){this.alignmentTrack.setDisplayMode(t)}});return e}setDisplayMode(e){const t=\"FULL\"===this.displayMode||\"FULL\"===e;if(this.displayMode=e,t){const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this)}this.trackView.checkContentHeight(),this.trackView.repaintViews()}colorByCB(e,t){const i=Bt(Dl(e.label,t));if(\"tag\"!==e.key){function n(){this.alignmentTrack.colorBy=e.key,this.trackView.repaintViews()}return{name:void 0,object:i,click:n,init:void 0}}{function r(e){const t=this.alignmentTrack.colorBy.startsWith(\"tag:\")?this.alignmentTrack.colorBy.substring(4):\"\";this.browser.inputDialog.present({label:\"Tag Name\",value:t,callback:e=>{const t=this.alignmentTrack;e?(t.colorBy=\"tag:\"+e,t.colorTable||(t.colorTable=new oo(\"Set1\"))):t.colorBy=void 0,this.trackView.repaintViews()}},e)}return{name:void 0,object:i,dialog:r,init:void 0}}}basemodColorByCB(e){const t=this.colorBy===e.key;return{name:void 0,object:Bt(Dl(e.label,t)),click:function(){this.alignmentTrack.colorBy=e.key,this.trackView.repaintViews()},init:void 0}}groupByCB(e,t){return{name:void 0,object:Bt(Dl(e.label,t)),dialog:function(t){const i=()=>this.alignmentTrack.repackAlignments();if(\"tag\"===e.key){let e=\"\";this.alignmentTrack.groupBy&&this.alignmentTrack.groupBy.startsWith(\"tag:\")&&(e=this.alignmentTrack.groupBy.substring(4)),this.browser.inputDialog.present({label:\"Tag Name\",value:e,callback:e=>{e&&(this.alignmentTrack.groupBy=\"tag:\"+e,this.alignmentTrack._groupByTags.push(e),i())}},t)}else\"none\"===e.key?this.alignmentTrack.groupBy=void 0:this.alignmentTrack.groupBy=e.key,i()},init:void 0}}repackAlignments(){const e=this.getCachedAlignmentContainers();for(let t of e)\"function\"==typeof t.pack&&t.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}contextMenuItemList(e){const t=e.viewport,i=[],n=i=>{const n=this.sortObject,r=!n||n.position!==Math.floor(e.genomicLocation)||!n.direction,s={chr:t.referenceFrame.chr,position:Math.floor(e.genomicLocation),option:i,direction:r,sortAsPairs:t.trackView.track.viewAsPairs};this.sortObject=s,t.cachedFeatures.sortRows(s),t.repaint()};i.push(\"<b>Sort by...</b>\"),i.push({label:\"&nbsp; base\",click:()=>n(\"BASE\")}),i.push({label:\"&nbsp; read strand\",click:()=>n(\"strand\")}),i.push({label:\"&nbsp; start location\",click:()=>n(\"START\")}),i.push({label:\"&nbsp; insert size\",click:()=>n(\"INSERT_SIZE\")}),i.push({label:\"&nbsp; gap size\",click:()=>n(\"GAP_SIZE\")}),i.push({label:\"&nbsp; chromosome of mate\",click:()=>n(\"MATE_CHR\")}),i.push({label:\"&nbsp; mapping quality\",click:()=>n(\"MQ\")}),i.push({label:\"&nbsp; read name\",click:()=>n(\"READ_NAME\")}),i.push({label:\"&nbsp; aligned read length\",click:()=>n(\"ALIGNED_READ_LENGTH\")}),i.push({label:\"&nbsp; tag\",click:()=>{const i=this.sortObject,n=!i||i.position!==Math.floor(e.genomicLocation)||!i.direction,r={label:\"Tag Name\",value:this.sortByTag?this.sortByTag:\"\",callback:i=>{if(i){const r={chr:t.referenceFrame.chr,position:Math.floor(e.genomicLocation),option:\"TAG\",tag:i,direction:n};this.sortByTag=i,this.sortObject=r,t.cachedFeatures.sortRows(r),t.repaint()}}};this.browser.inputDialog.present(r,e.event)}}),i.push(\"<hr/>\");const r=`${t.referenceFrame.chr}:${Rt(Math.floor(e.genomicLocation)+1)}`;i.push({label:`Group by base @${r}`,click:()=>{this._groupByPositions.push(r),this.groupBy=`base:${r}`;const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),i.push(\"<hr/>\");const s=this.getClickedObject(e);if(s){const t=this.showSoftClips,n=\"function\"==typeof s.alignmentContaining?s.alignmentContaining(e.genomicLocation,t):s;if(n){n.isPaired()&&n.isMateMapped()&&i.push({label:\"View mate in split screen\",click:()=>{if(n.mate){const t=e.viewport.referenceFrame,i=this.browser.genome.getChromosome(n.mate.chr);if(i){this.selectedReadName=n.readName;const r=t.bpPerPixel*e.viewport.getWidth(),s=n.mate.position-r/2,o=n.mate.position+r/2;this.browser.addMultiLocusPanel(i.name,s,o,t)}else this.browser.alert.present(`Reference does not contain chromosome: ${n.mate.chr}`)}},init:void 0}),i.push({label:\"View read sequence\",click:()=>{const e=n.seq;e&&\"*\"!==e?this.browser.alert.present(e):this.browser.alert.present(\"Read sequence: *\")}}),Xa()&&i.push({label:\"Copy read sequence\",click:async()=>{const e=n.seq;try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}});const t=n.seq;if(t&&\"*\"!==t){t.length<Qd&&i.push({label:\"BLAT read sequence\",click:()=>{const e=n.isNegativeStrand()?cc(t):t,i=`${n.readName} - blat`,r=`${this.name} - ${i}`;jd({sequence:e,browser:this.browser,name:i,title:r})}});const e=n.softClippedBlocks();e.left&&e.left.len>20&&e.left.len<Qd&&i.push({label:\"BLAT left soft-clipped sequence\",click:()=>{const i=t.substr(e.left.seqOffset,e.left.len),r=n.isNegativeStrand()?cc(i):i,s=`${n.readName} - blat left clip`,o=`${this.name} - ${s}`;jd({sequence:r,browser:this.browser,name:s,title:o})}}),e.right&&e.right.len>20&&e.right.len<Qd&&i.push({label:\"BLAT right soft-clipped sequence\",click:()=>{const i=t.substr(e.right.seqOffset,e.right.len),r=n.isNegativeStrand()?cc(i):i,s=`${n.readName} - blat right clip`,o=`${this.name} - ${s}`;jd({sequence:r,browser:this.browser,name:s,title:o})}})}i.push(\"<hr/>\")}}return this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(this.hasPairs&&i.push({label:\"Add discordant pairs to circular view\",click:()=>{this.addPairedChordsForViewport(t)}}),this.hasSupplemental&&i.push({label:\"Add split reads to circular view\",click:()=>{this.addSplitChordsForViewport(t)}}),i.push(\"<hr/>\")),i}getClickedObject(e){let t=e.viewport.cachedFeatures;if(!t)return;const i=e.y-this.top,n=e.genomicLocation;if(t.packedGroups){let e=Number.MAX_VALUE;for(let r of t.packedGroups.values())if(e=Math.min(e,r.pixelTop),i>r.pixelTop&&i<=r.pixelBottom){const e=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;let t=Math.floor((i-r.pixelTop)/e);if(t>=0&&t<r.length){const e=r.rows[t].alignments.filter((e=>e.containsLocation(n,this.showSoftClips)));if(e.length>0)return e[0]}}}if(i<minGroupY&&t.downsampledIntervals)for(const e of t.downsampledIntervals)if(e.start<=n&&e.end>=n)return e}getConnectorColor(e){if(this.pairConnectorColor)return this.pairConnectorColor;let t=this.colorBy;switch(t&&t.startsWith(\"tag:\")&&(t.substring(4),t=\"tag\"),t){case\"strand\":case\"firstOfPairStrand\":case\"pairOrientation\":case\"tag\":return this.color?\"function\"==typeof this.color?this.color(e):this.color:\"rgb(200, 200, 200)\";default:return this.getAlignmentColor(e)}}getAlignmentColor(e){let t;t=this.color?\"function\"==typeof this.color?this.color(e):this.color:\"rgb(185, 185, 185)\";let i,n=this.colorBy;switch(n&&n.startsWith(\"tag:\")&&(i=n.substring(4),n=\"tag\"),n){case\"basemod\":case\"basemod2\":t=e.strand?this.baseModPosStrandColor:this.baseModNegStrandColor;break;case\"strand\":t=e.strand?this.posStrandColor:this.negStrandColor;break;case\"firstOfPairStrand\":const r=e.firstOfPairStrand;void 0!==r&&(t=r?this.posStrandColor:this.negStrandColor);break;case\"unexpectedPair\":case\"pairOrientation\":if(e.pairOrientation){const i=ep[this.expectedPairOrientation];if(i){const n=this.pairColors[i[e.pairOrientation]];if(n){t=n;break}}}if(\"pairOrientation\"===n)break;case\"tlen\":case\"fragmentLength\":e.mate&&e.isMateMapped()&&(e.mate.chr!==e.chr?t=Nu(e.mate.chr):this.minTemplateLength&&Math.abs(e.fragmentLength)<this.minTemplateLength?t=this.smallTLENColor:this.maxTemplateLength&&Math.abs(e.fragmentLength)>this.maxTemplateLength&&(t=this.largeTLENColor));break;case\"tag\":const s=e.tags()[i];void 0!==s&&(this.bamColorTag===i&&(t=_s.createColorStringSafe(s)),this.colorTable||(this.colorTable=new oo(this.tagColorPallete)),t=this.colorTable.getColor(s))}return t}get nucleotideColors(){return this.browser.nucleotideColors}get minTemplateLength(){return void 0!==this.minTLEN?this.minTLEN:this.parent._pairedEndStats?this.parent._pairedEndStats.minTLEN:0}get maxTemplateLength(){return void 0!==this.maxTLEN?this.maxTLEN:this.parent._pairedEndStats?this.parent._pairedEndStats.maxTLEN:1e3}getState(){const e=super.getState();return this.highlightedReads&&(e.highlightedReads=Array.from(this.highlightedReads)),e}get name(){return this.parent.name}set name(e){this.parent.name=e}get color(){return this.parent.color}set color(e){this.parent.color=e}get trackView(){return this.parent.trackView}get getCachedAlignmentContainers(){return this.parent.getCachedAlignmentContainers}get sortObject(){return this.parent.sortObject}set sortObject(e){this.parent.sortObject=e}addPairedChordsForViewport(e){return this.parent.addPairedChordsForViewport(e)}addSplitChordsForViewport(e){return this.parent.addSplitChordsForViewport(e)}}function Xm(e,t){let i;return i=e<5?.1:Math.max(.1,Math.min(1,.1+.9*(e-5)/15)),i=Math.round(10*i)/10,i<1&&(t=_s.addAlpha(t,i)),t}function Zm(){\"FULL\"!==this.displayMode||this.browser.isTrackPanning()||this.repackAlignments()}function Jm(e,t,i,n,r,s,o,a,c){const l=o.baseModCounts,h=o.coverageMap;if(l){let o;const d=a.split(\":\");2==d.length&&(a=d[0],o=d[1]);const u=Array.from(l.allModifications);u.sort(Vf.compare);const f=h.getTotalCount(s);if(!u.filter((e=>o?o===e.modification:!e.modification.startsWith(\"NONE_\"))).find((e=>l.getCount(s,e,0,!1)>0)))return;for(let d of u){if(d.modification.startsWith(\"NONE_\")&&\"basemod2\"!==a)continue;if(o&&o!==d.modification&&!d.modification.startsWith(\"NONE_\"))continue;const u=d.base,p=oc(u),g=h.getCount(s,u)+h.getCount(s,p),m=l.simplexModifications.has(d.modification)?h.getPosCount(s,u)+h.getNegCount(s,p):g;if(0==m)continue;const w=\"basemod2\"===a,b=l.getCount(s,d,c,w);if(0==b)continue;const F=g/f*(b/m),v=Math.round(F*r),y=l.getLikelihoodSum(s,d,c,w)/b,A=i-v,C=Gm(d.modification,y,a);e.fillStyle=C,e.fillRect(t,A,n,v),i=A}}}class ew{constructor(e,t){this.featureType=\"numeric\",this.parent=t,this.featureSource=t.featureSource,this.paintAxis=cd,this.top=0,this.autoscale=e.autoscale||void 0===e.max,e.coverageColor&&(this.color=e.coverageColor),this.autoscale||(this.dataRange={min:e.min||0,max:e.max})}get height(){return this.parent.coverageTrackHeight}draw(e){const t=e.pixelTop;e.pixelHeight;const i=this.parent.browser.nucleotideColors;if(t>this.height)return;const n=e.context,r=e.features,s=r.coverageMap;let o;s.refSeq&&(o=s.refSeq.toUpperCase());const a=e.bpPerPixel,c=e.bpStart,l=c+e.pixelWidth*a+1;let h;h=this.color?this.color:this.parent.color&&\"function\"!=typeof this.parent.color?_s.darkenLighten(this.parent.color,-35):\"rgb(150, 150, 150)\",xo.setProperties(n,{fillStyle:h,strokeStyle:h});const d=Math.max(1,1/a);for(let e=0,t=s.coverage.length;e<t;e++){const t=s.bpStart+e;if(t<c)continue;if(t>l)break;const i=s.coverage[e];if(!i)continue;const r=i.total/this.dataRange.max*this.height,o=this.height-r,h=(t-c)/a;xo.fillRect(n,h,o,d,r)}if(o)for(let e=0,t=s.coverage.length;e<t;e++){const t=s.bpStart+e;if(t<c)continue;if(t>l)break;const h=s.coverage[e];if(!h)continue;const u=h.total/this.dataRange.max*this.height;let f=this.height-u;const p=Math.floor((t-c)/a),g=o[e];if(this.parent.colorBy&&this.parent.colorBy.startsWith(\"basemod\"))Jm(n,p,this.height,d,u,t,r,this.parent.colorBy,this.parent.baseModificationThreshold);else if(h.isMismatch(g)){xo.setProperties(n,{fillStyle:i[g]}),xo.fillRect(n,p,f,d,u);let e=0;for(let t of[\"A\",\"C\",\"T\",\"G\"]){const r=(h[\"pos\"+t]+h[\"neg\"+t])/this.dataRange.max*this.height;f=this.height-r-e,e+=r,xo.setProperties(n,{fillStyle:i[t]}),xo.fillRect(n,p,f,d,r)}}}}getClickedObject(e){let t=e.viewport.cachedFeatures;if(!t||0===t.length)return;const i=Math.floor(e.genomicLocation),n=t.coverageMap,r=Math.floor(i-n.bpStart),s=n.coverage[r];return s?{coverage:s,baseModCounts:t.baseModCounts,hoverText:()=>n.coverage[r].hoverText()}:void 0}popupData(e){const t=[],{coverage:i,baseModCounts:n}=this.getClickedObject(e);if(i){const r=Math.floor(e.genomicLocation),s=e.viewport.referenceFrame;t.push(s.chr+\":\"+Rt(1+r)),t.push({name:\"Total Count\",value:i.total});let o=i.posA+i.negA;o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posA+\"+, \"+i.negA+\"- )\"),t.push({name:\"A\",value:o}),o=i.posC+i.negC,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posC+\"+, \"+i.negC+\"- )\"),t.push({name:\"C\",value:o}),o=i.posG+i.negG,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posG+\"+, \"+i.negG+\"- )\"),t.push({name:\"G\",value:o}),o=i.posT+i.negT,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posT+\"+, \"+i.negT+\"- )\"),t.push({name:\"T\",value:o}),o=i.posN+i.negN,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posN+\"+, \"+i.negN+\"- )\"),t.push({name:\"N\",value:o}),t.push(\"<HR/>\"),t.push({name:\"DEL\",value:i.del.toString()}),t.push({name:\"INS\",value:i.ins.toString()}),n&&(t.push(\"<hr/>\"),t.push(...n.popupData(r,this.parent.colorBy)))}return t}}class tw extends Hl{static defaults={alleleFreqThreshold:.2,visibilityWindow:3e4,showCoverage:!0,showAlignments:!0,height:300,coverageTrackHeight:50,baseModificationThreshold:0};constructor(e,t){super(e,t)}init(e){this.type=\"alignment\",this.featureSource=new cm(e,this.browser);const t=Object.assign({parent:this},e);this.coverageTrack=new ew(t,this);const i=Object.assign({parent:this},e);this.alignmentTrack=new Ym(i,this.browser),super.init(e),this.showAlignments||(this._height=this.coverageTrackHeight),e.sort&&(Array.isArray(e.sort)?this.assignSort(e.sort[0]):this.assignSort(e.sort))}dispose(){this.alignmentTrack.dispose()}setHighlightedReads(e,t){this.alignmentTrack.setHighlightedReads(e,t),this.updateViews()}get expectedPairOrientation(){return this.alignmentTrack.expectedPairOrientation}get viewAsPairs(){return this.alignmentTrack.viewAsPairs}get colorBy(){return this.alignmentTrack.colorBy}set height(e){this._height=e,this.showAlignments&&(this.alignmentTrack.height=this.showCoverage?e-this.coverageTrackHeight:e)}get height(){return this._height}sort(e){e=this.assignSort(e);for(let t of this.trackView.viewports)if(t.containsPosition(e.chr,e.position)){const i=t.cachedFeatures;i&&(i.sortRows(e),t.repaint())}}assignSort(e){if(e.locus){const t=function(e){const t=e.split(\":\"),i=t[1].split(\"-\"),n={chr:t[0],start:Number.parseInt(i[0].replace(/,/g,\"\"))-1};return i.length>1?n.end=Number.parseInt(i[1].replace(/,/g,\"\")):n.end=n.start+1,n}(e.locus);e.chr=t.chr,e.position=t.start}else e.position--;return e.direction=\"ASC\"===e.direction||!0===e.direction,e.chr=this.browser.genome.getChromosomeName(e.chr),this.sortObject=e,this.sortObject}async getFeatures(e,t,i,n,r){const s=await this.featureSource.getAlignments(e,t,i);if(s.viewport=r,s.hasPairs&&!this._pairedEndStats&&!this.config.maxFragmentLength){const e=new Om(s.allAlignments(),this.config);e.totalCount>99&&(this._pairedEndStats=e)}s.pack(this.alignmentTrack);const o=this.sortObject;return o&&o.chr===e&&o.position>=t&&o.position<=i&&s.sortRows(o),this.alignmentTrack.hasPairs=this.alignmentTrack.hasPairs||s.hasPairs,s}computePixelHeight(e){return(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.computePixelHeight(e):0)}draw(e){xo.fillRect(e.context,0,e.pixelTop,e.pixelWidth,e.pixelHeight,{fillStyle:\"rgb(255, 255, 255)\"}),!0===this.showCoverage&&this.coverageTrackHeight>0?(this.trackView.axisCanvas.style.display=\"block\",this.coverageTrack.draw(e)):this.trackView.axisCanvas.style.display=\"none\",!0===this.showAlignments&&(this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.alignmentTrack.draw(e))}paintAxis(e,t,i){this.coverageTrack.paintAxis(e,t,this.coverageTrackHeight)}contextMenuItemList(e){return this.alignmentTrack.contextMenuItemList(e)}popupData(e){return!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight?this.coverageTrack.popupData(e):this.alignmentTrack.popupData(e)}clickedFeatures(e){let t;return t=!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight?this.coverageTrack.getClickedObject(e):this.alignmentTrack.getClickedObject(e),t?[t]:void 0}hoverText(e){if(!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight){const t=this.coverageTrack.getClickedObject(e);if(t)return t.hoverText()}}menuItemList(){let e=[];e=e.concat(this.numericDataMenuItems()),e=e.concat(this.alignmentTrack.menuItemList());const t=()=>{if(!this.autoHeight){const e=(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.height:0);this.trackView.setTrackHeight(e)}};return e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"Show Coverage\",this.showCoverage)),click:function(){this.showCoverage=!this.showCoverage,t(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show Alignments\",this.showAlignments)),click:function(){this.showAlignments=!this.showAlignments,t(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),e}getState(){const e=super.getState();return this.sortObject&&(e.sort={chr:this.sortObject.chr,position:this.sortObject.position+1,option:this.sortObject.option,direction:this.sortObject.direction?\"ASC\":\"DESC\"}),Object.assign(e,this.alignmentTrack.getState()),e}getCachedAlignmentContainers(){return this.trackView.viewports.map((e=>e.cachedFeatures))}get dataRange(){return this.coverageTrack.dataRange}set dataRange(e){this.coverageTrack.dataRange=e}get logScale(){return this.coverageTrack.logScale}set logScale(e){this.coverageTrack.logScale=e}get autoscale(){return this.coverageTrack.autoscale}set autoscale(e){this.coverageTrack.autoscale=e}addPairedChordsForViewport(e){const t=this.maxTemplateLength,i=[],n=e.referenceFrame;for(let r of e.cachedFeatures.allAlignments())r.end>=n.start&&r.start<=n.end&&(r.paired?r.end-r.start>t&&i.push(r):r.mate&&r.mate.chr&&(r.mate.chr!==r.chr||Math.max(r.fragmentLength)>t)&&i.push(r));Pm((e=>{const t=[];for(let i of e)if(i.paired)i.firstAlignment&&i.secondAlignment&&t.push({uniqueId:i.readName,refName:zm(i.firstAlignment.chr),start:i.firstAlignment.start,end:i.firstAlignment.end,mate:{refName:zm(i.secondAlignment.chr),start:i.secondAlignment.start,end:i.secondAlignment.end}});else{const e=i.mate;e&&e.chr&&e.position&&t.push({uniqueId:i.readName,refName:zm(i.chr),start:i.start,end:i.end,mate:{refName:zm(e.chr),start:e.position-1,end:e.position}})}return t})(i),this,n,.02)}addSplitChordsForViewport(e){const t=[],i=e.referenceFrame;for(let n of e.cachedFeatures.allAlignments()){const e=n.hasTag(\"SA\");n.end>=i.start&&n.start<=i.end&&e&&t.push(n)}Pm((e=>{const t=e=>{const t=gp(e.tags().SA);let n=0;for(let r of t)r.start!==e.start&&i.push({uniqueId:`${e.readName}_${n++}`,refName:zm(e.chr),start:e.start,end:e.end,mate:{refName:zm(r.chr),start:r.start,end:r.start+r.lenOnRef}})},i=[];for(let i of e)i.paired?(t(i.firstAlignment),i.secondAlignment&&t(i.secondAlignment)):t(i);return i})(t),this,i,.02)}}class iw extends Hl{static defaults={height:250,theta:Math.PI/4,arcOrientation:\"UP\",showBlocks:!0,blockHeight:3,thickness:1,color:\"rgb(180,25,137)\",alpha:.02,logScale:!0};constructor(e,t){super(e,t)}init(e){super.init(e),!1===e.arcOrientation?this.arcOrientation=\"DOWN\":!0===e.arcOrientation?this.arcOrientation=\"UP\":e.arcOrientation?this.arcOrientation=e.arcOrientation.toUpperCase():this.arcOrientation=\"UP\",this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta),this.arcType=function(e){if(!e.arcType)return\"nested\";switch(e.arcType){case\"chiapet\":return\"inView\";case\"chiapetoutbound\":return\"partialInView\";default:return e.arcType}}(e),this.painter={flipAxis:\"DOWN\"===this.arcOrientation,dataRange:this.dataRange,paintAxis:cd},e.valueColumn?(this.valueColumn=e.valueColumn,this.hasValue=!0):e.useScore&&(this.hasValue=!0,this.valueColumn=\"score\"),e.max?(this.dataRange={min:e.min||0,max:e.max},this.autoscale=!1):this.autoscale=!0,e.featureSource?(this.featureSource=e.featureSource,delete e._featureSource):(this.featureSource=Ad(e,this.browser.genome),this.featureSource.getWGFeatures=aw)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow(),this.featureSource.visibilityWindow=this.visibilityWindow),this}get supportsWholeGenome(){return!0}async getFeatures(e,t,i){const n=this.visibilityWindow,r=await this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n});return void 0===this.hasValue&&r&&r.length>0&&(this.hasValue=void 0!==r[0].score),r}draw(e){\"proportional\"===this.arcType||\"inView\"===this.arcType||\"partialInView\"===this.arcType?this.drawProportional(e):this.drawNested(e)}drawNested(e){const t=e.context,i=e.pixelWidth,n=e.pixelHeight,r=e.viewportWidth,s=e.bpPerPixel,o=e.bpStart,a=s;xo.fillRect(t,0,e.pixelTop,i,n,{fillStyle:\"rgb(255, 255, 255)\"});const c=e.features;if(c){(function(){let e=0;for(let t of c){let n=(t.start-o)/a,r=(t.end-o)/a;n>=0&&r<=i&&(e=Math.max(e,r-n))}let t=Math.min(r,e)/2;if(e>0){let e=(n-10)/t;this.theta=function(e){let t,i=[.01570925532366355,.15838444032453644,.3249196962329063,.5095254494944288,.7265425280053609,.9999999999999999],n=[.031415926535897934,.3141592653589793,.6283185307179586,.9424777960769379,1.2566370614359172,1.5707963267948966];for(t=0;t<i.length&&!(i[t]>e);t++);let r=0===t?0:i[t-1],s=t<i.length?i[t]:1,o=(e-r)/(s-r),a=0===t?0:n[t-1],c=t<n.length?n[t]:Math.PI/2;return Math.min(Math.PI/2,a+o*(c-a))}(e),this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta)}}).call(this);const s=\"UP\"===this.arcOrientation,h=s?e.pixelHeight:0;t.font=\"8px sans-serif\",t.textAlign=\"center\";for(let e of c){let n;if(e.drawState=void 0,\"function\"==typeof this.color?n=this.color(e):(n=this.color||e.color||\"rgb(180,25,137)\",n&&this.config.useScore&&(n=ow(n,(l=e.score,Math.min(1,.11+l/779*.89).toString())))),t.lineWidth=e.thickness||this.thickness||1,e.chr1===e.chr2||\"all\"===e.chr){const{m1:c,m2:l}=nw(e,this.browser.genome);let d=Math.round((c-o)/a),u=Math.round((l-o)/a);if(u<0||d>i)continue;let f=u-d;f<3&&(f=3,d--);const p=f/2,g=p/this.sinTheta,m=this.cosTheta*g,w=d+p;let b,F,v;if(s?(b=this.height+m,F=Math.PI+Math.PI/2-this.theta,v=Math.PI+Math.PI/2+this.theta):(b=-m,F=Math.PI/2-this.theta,v=Math.PI/2+this.theta),this.showBlocks&&\"all\"!==e.chr){const i=(e.start1-o)/a,n=(e.end1-o)/a,r=(e.start2-o)/a,c=(e.end2-o)/a,l=s?-this.blockHeight:this.blockHeight;t.fillRect(i,h,n-i,l),t.fillRect(r,h,c-r,l)}n&&!this.config.useScore&&f>r&&(n=ow(n,this.alpha)),t.strokeStyle=n,t.fillStyle=n,t.beginPath(),t.arc(w,b,g,F,v,!1),t.stroke(),e.drawState={xc:w,yc:b,r:g}}else{let r=Math.round((e.start-o)/a),c=Math.round((e.end-o)/a);if(c<0||r>i)continue;let l=c-r;l<3&&(l=3,r--);const h=e.chr===e.chr1?e.chr2:e.chr1;t.strokeStyle=n,t.fillStyle=ow(Nu(h),.5),s?(t.fillRect(r,this.height/2,l,this.height/2),t.fillText(h,r+l/2,this.height/2-5),e.drawState={x:r,y:this.height/2,w:l,h:this.height/2}):(t.fillRect(r,0,l,this.height/2),t.fillText(h,r+l/2,this.height/2+13),e.drawState={x:r,y:0,w:l,h:this.height/2})}}}var l}getScaleFactor(e,t,i,n){return n?i/(Math.log10(t+1)-(e<=0?0:Math.log10(e+1))):i/(t-e)}drawProportional(e){const t=e.context,i=e.pixelWidth,n=e.pixelHeight,r=e.bpPerPixel,s=e.bpStart,o=r,a=e.referenceFrame.start,c=e.referenceFrame.end,l=\"UP\"===this.arcOrientation;xo.fillRect(t,0,e.pixelTop,i,n,{fillStyle:\"rgb(255, 255, 255)\"});const h=e.features;if(h&&h.length>0){const n=0,r=this.getScaleFactor(n,this.dataRange.max,e.pixelHeight-1,this.logScale),d=l?e.pixelHeight:0;for(let e of h){e.drawState=void 0;const n=this.valueColumn?e[this.valueColumn]:e.score;if(void 0===n||Number.isNaN(n))continue;const h=Math.round((this.logScale?Math.log10(n+1):n)*r);if(e.chr1===e.chr2||\"all\"===e.chr){const{m1:i,m2:r}=nw(e,this.browser.genome);let u=Math.round((i-s)/o),f=Math.round((r-s)/o)-u;if(f<3&&(f=3,u--),n<this.dataRange.min||n>this.dataRange.max)continue;if(\"proportional\"!==this.arcType){const e=\"partialInView\"===this.arcType,t=i>=a&&r<=c;let n=!1,s=!1;if(!t&&e&&(n=a<=i&&i<=c,n||(s=a<=r&&r<=c)),!(t||n||s))continue}const p=f/2,g=u+f/2;e.drawState={xc:g,yc:d,radiusX:p,radiusY:h};const m=l,w=e.color||this.color;if(t.strokeStyle=w,t.lineWidth=e.thickness||this.thickness||1,!0===t.isSVG?t.strokeEllipse(g,d,p,h,0,0,Math.PI,m):(t.beginPath(),t.ellipse(g,d,p,h,0,0,Math.PI,m),t.stroke()),this.alpha&&(t.fillStyle=ow(w,this.alpha),!0===t.isSVG?t.fillEllipse(g,d,p,h,0,0,Math.PI,m):t.fill()),this.showBlocks&&\"all\"!==e.chr){t.fillStyle=w;const i=(e.start1-s)/o,n=(e.end1-s)/o,r=(e.start2-s)/o,a=(e.end2-s)/o,c=l?-this.blockHeight:this.blockHeight;t.fillRect(i,d,n-i,c),t.fillRect(r,d,a-r,c)}}else{let r=Math.round((e.start-s)/o),a=Math.round((e.end-s)/o);if(a<0||r>i||n<this.dataRange.min||n>this.dataRange.max)continue;const c=Math.min(h,this.height-13);let d=a-r;d<3&&(d=3,r--);const u=e.chr===e.chr1?e.chr2:e.chr1;if(t.font=\"8px sans-serif\",t.textAlign=\"center\",t.fillStyle=ow(Nu(u),.5),l){const i=this.height-c;t.fillRect(r,i,d,c),t.fillText(u,r+d/2,i-5),e.drawState={x:r,y:i,w:d,h:c}}else t.fillRect(r,0,d,c),t.fillText(u,r+d/2,c+13),e.drawState={x:r,y:0,w:d,h:c}}}}}clearAxis(e,t,i){xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"})}paintAxis(e,t,i){const n={min:0,max:this.dataRange.max};\"proportional\"===this.arcType||\"inView\"===this.arcType||\"partialInView\"===this.arcType?(this.painter.flipAxis=\"DOWN\"===this.arcOrientation,this.painter.dataRange=n,this.painter.paintAxis(e,t,i)):this.clearAxis(e,t,i)}menuItemList(){let e=[];if(this.hasValue){e.push(\"<hr/>\");const t={nested:\"Nested\",proportional:\"Proportional - All\",inView:\"Proportional - Both Ends in View\",partialInView:\"Proportional - One End in View\"};e.push(\"<b>Arc Type</b>\");for(let i of[\"nested\",\"proportional\",\"inView\",\"partialInView\"])e.push({object:Bt(Dl(t[i],i===this.arcType)),click:function(){this.arcType=i,this.trackView.repaintViews()}})}return e.push(\"<hr/>\"),e.push({name:\"Toggle arc direction\",click:function(){this.arcOrientation=\"UP\"===this.arcOrientation?\"DOWN\":\"UP\",this.trackView.repaintViews()}}),e.push({name:this.showBlocks?\"Hide Blocks\":\"Show Blocks\",click:function(){this.showBlocks=!this.showBlocks,this.trackView.repaintViews()}}),\"proportional\"!==this.arcType&&\"inView\"!==this.arcType&&\"partialInView\"!==this.arcType||(e=e.concat(this.numericDataMenuItems())),this.browser.circularView&&(e.push(\"<hr/>\"),e.push({label:\"Add interactions to circular view\",click:function(){for(let e of this.trackView.viewports)this.addChordsForViewport(e.referenceFrame)}})),e}contextMenuItemList(e){if(this.browser.circularView){const t=e.viewport,i=[];return i.push({label:\"Add interactions to circular view\",click:()=>{const e=t.referenceFrame;this.addChordsForViewport(e)}}),i.push(\"<hr/>\"),i}}addChordsForViewport(e){let t;if(\"all\"===e.chr)t=Object.values(this.featureSource.getAllFeatures()).flat();else{t=this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end).filter((e=>e.drawState))}if(0===t.length)return;Pm(t.map((e=>{const t=e._f||e;return{uniqueId:`${t.chr1}:${t.start1}-${t.end1}_${t.chr2}:${t.start2}-${t.end2}`,refName:zm(t.chr1),start:t.start1,end:t.end1,mate:{refName:zm(t.chr2),start:t.start2,end:t.end2}}})),this,e,.5)}doAutoscale(e){let t=0;if(e)for(let i of e){const e=this.valueColumn?i[this.valueColumn]:i.score;Number.isNaN(e)||(t=Math.max(t,e))}return{min:0,max:t}}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){const t=e._||e;if(i.push({name:\"Region 1\",value:rw(t.chr1,t.start1,t.end1,t.strand1)}),i.push({name:\"Region 2\",value:rw(t.chr2,t.start2,t.end2,t.strand2)}),t.name&&i.push({name:\"Name\",value:t.name}),void 0!==t.value&&i.push({name:\"Value\",value:t.value}),void 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i})(s,r)},utf8border:(e,t)=>{(t=t||e.length)>e.length&&(t=e.length);let i=t-1;for(;i>=0&&128==(192&e[i]);)i--;return i<0||0===i?t:i+Kw[e[i]]>t?i:t}};var Xw=function(){this.input=null,this.next_in=0,this.avail_in=0,this.total_in=0,this.output=null,this.next_out=0,this.avail_out=0,this.total_out=0,this.msg=\"\",this.state=null,this.data_type=2,this.adler=0},Zw=function(e,t){let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_,x;const k=e.state;i=e.next_in,_=e.input,n=i+(e.avail_in-5),r=e.next_out,x=e.output,s=r-(t-e.avail_out),o=r+(e.avail_out-257),a=k.dmax,c=k.wsize,l=k.whave,h=k.wnext,d=k.window,u=k.hold,f=k.bits,p=k.lencode,g=k.distcode,m=(1<<k.lenbits)-1,w=(1<<k.distbits)-1;e:do{f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=p[u&m];t:for(;;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,0===F)x[r++]=65535&b;else{if(!(16&F)){if(64&F){if(32&F){k.mode=12;break e}e.msg=\"invalid literal/length code\",k.mode=30;break e}b=p[(65535&b)+(u&(1<<F)-1)];continue t}for(v=65535&b,F&=15,F&&(f<F&&(u+=_[i++]<<f,f+=8),v+=u&(1<<F)-1,u>>>=F,f-=F),f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=g[u&w];;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,16&F){if(y=65535&b,F&=15,f<F&&(u+=_[i++]<<f,f+=8,f<F&&(u+=_[i++]<<f,f+=8)),y+=u&(1<<F)-1,y>a){e.msg=\"invalid distance too far back\",k.mode=30;break e}if(u>>>=F,f-=F,F=r-s,y>F){if(F=y-F,F>l&&k.sane){e.msg=\"invalid distance too far back\",k.mode=30;break e}if(A=0,C=d,0===h){if(A+=c-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}else if(h<F){if(A+=c+h-F,F-=h,F<v){v-=F;do{x[r++]=d[A++]}while(--F);if(A=0,h<v){F=h,v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}}else if(A+=h-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}for(;v>2;)x[r++]=C[A++],x[r++]=C[A++],x[r++]=C[A++],v-=3;v&&(x[r++]=C[A++],v>1&&(x[r++]=C[A++]))}else{A=r-y;do{x[r++]=x[A++],x[r++]=x[A++],x[r++]=x[A++],v-=3}while(v>2);v&&(x[r++]=x[A++],v>1&&(x[r++]=x[A++]))}break}if(64&F){e.msg=\"invalid distance code\",k.mode=30;break 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0!==_&&(r[f+_]=g-y<<24|64<<16),a.bits=F,0},{Z_FINISH:sb,Z_BLOCK:ob,Z_TREES:ab,Z_OK:cb,Z_STREAM_END:lb,Z_NEED_DICT:hb,Z_STREAM_ERROR:db,Z_DATA_ERROR:ub,Z_MEM_ERROR:fb,Z_BUF_ERROR:pb,Z_DEFLATED:gb}=jw,mb=12,wb=30,bb=e=>(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24);function Fb(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new Uint16Array(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}var vb,yb,Ab=e=>{if(!e||!e.state)return db;const t=e.state;return e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=1,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new Int32Array(852),t.distcode=t.distdyn=new Int32Array(592),t.sane=1,t.back=-1,cb},Cb=e=>{if(!e||!e.state)return db;const t=e.state;return t.wsize=0,t.whave=0,t.wnext=0,Ab(e)},_b=(e,t)=>{let i;if(!e||!e.state)return db;const n=e.state;return t<0?(i=0,t=-t):(i=1+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?db:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,Cb(e))},xb=(e,t)=>{if(!e)return db;const i=new Fb;e.state=i,i.window=null;const n=_b(e,t);return n!==cb&&(e.state=null),n},kb=!0,Ib=e=>{if(kb){vb=new Int32Array(512),yb=new Int32Array(32);let t=0;for(;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(rb(1,e.lens,0,288,vb,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;rb(2,e.lens,0,32,yb,0,e.work,{bits:5}),kb=!1}e.lencode=vb,e.lenbits=9,e.distcode=yb,e.distbits=5},Sb=(e,t,i,n)=>{let r;const s=e.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new Uint8Array(s.wsize)),n>=s.wsize?(s.window.set(t.subarray(i-s.wsize,i),0),s.wnext=0,s.whave=s.wsize):(r=s.wsize-s.wnext,r>n&&(r=n),s.window.set(t.subarray(i-n,i-n+r),s.wnext),(n-=r)?(s.window.set(t.subarray(i-n,i),0),s.wnext=n,s.whave=s.wsize):(s.wnext+=r,s.wnext===s.wsize&&(s.wnext=0),s.whave<s.wsize&&(s.whave+=r))),0},Eb=(e,t)=>{let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_=0;const x=new Uint8Array(4);let k,I;const S=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(!e||!e.state||!e.output||!e.input&&0!==e.avail_in)return db;i=e.state,i.mode===mb&&(i.mode=13),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,d=a,u=c,C=cb;e:for(;;)switch(i.mode){case 1:if(0===i.wrap){i.mode=13;break}for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(2&i.wrap&&35615===l){i.check=0,x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0),l=0,h=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&l)<<8)+(l>>8))%31){e.msg=\"incorrect header check\",i.mode=wb;break}if((15&l)!==gb){e.msg=\"unknown compression method\",i.mode=wb;break}if(l>>>=4,h-=4,A=8+(15&l),0===i.wbits)i.wbits=A;else if(A>i.wbits){e.msg=\"invalid window size\",i.mode=wb;break}i.dmax=1<<i.wbits,e.adler=i.check=1,i.mode=512&l?10:mb,l=0,h=0;break;case 2:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.flags=l,(255&i.flags)!==gb){e.msg=\"unknown compression method\",i.mode=wb;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=wb;break}i.head&&(i.head.text=l>>8&1),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0,i.mode=3;case 3:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.time=l),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,x[2]=l>>>16&255,x[3]=l>>>24&255,i.check=Qw(i.check,x,4,0)),l=0,h=0,i.mode=4;case 4:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.xflags=255&l,i.head.os=l>>8),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0,i.mode=5;case 5:if(1024&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length=l,i.head&&(i.head.extra_len=l),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&(f=i.length,f>a&&(f=a),f&&(i.head&&(A=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Uint8Array(i.head.extra_len)),i.head.extra.set(n.subarray(s,s+f),A)),512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,i.length-=f),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.name+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.comment+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=wb;break}l=0,h=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=mb;break;case 10:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}e.adler=i.check=bb(l),l=0,h=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,hb;e.adler=i.check=1,i.mode=mb;case mb:if(t===ob||t===ab)break e;case 13:if(i.last){l>>>=7&h,h-=7&h,i.mode=27;break}for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}switch(i.last=1&l,l>>>=1,h-=1,3&l){case 0:i.mode=14;break;case 1:if(Ib(i),i.mode=20,t===ab){l>>>=2,h-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg=\"invalid block type\",i.mode=wb}l>>>=2,h-=2;break;case 14:for(l>>>=7&h,h-=7&h;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if((65535&l)!=(l>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=wb;break}if(i.length=65535&l,l=0,h=0,i.mode=15,t===ab)break e;case 15:i.mode=16;case 16:if(f=i.length,f){if(f>a&&(f=a),f>c&&(f=c),0===f)break e;r.set(n.subarray(s,s+f),o),a-=f,s+=f,c-=f,o+=f,i.length-=f;break}i.mode=mb;break;case 17:for(;h<14;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.nlen=257+(31&l),l>>>=5,h-=5,i.ndist=1+(31&l),l>>>=5,h-=5,i.ncode=4+(15&l),l>>>=4,h-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=wb;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.lens[S[i.have++]]=7&l,l>>>=3,h-=3}for(;i.have<19;)i.lens[S[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,k={bits:i.lenbits},C=rb(0,i.lens,0,19,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid code lengths set\",i.mode=wb;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(b<16)l>>>=m,h-=m,i.lens[i.have++]=b;else{if(16===b){for(I=m+2;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l>>>=m,h-=m,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=wb;break}A=i.lens[i.have-1],f=3+(3&l),l>>>=2,h-=2}else if(17===b){for(I=m+3;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=3+(7&l),l>>>=3,h-=3}else{for(I=m+7;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=11+(127&l),l>>>=7,h-=7}if(i.have+f>i.nlen+i.ndist){e.msg=\"invalid bit length repeat\",i.mode=wb;break}for(;f--;)i.lens[i.have++]=A}}if(i.mode===wb)break;if(0===i.lens[256]){e.msg=\"invalid code -- missing end-of-block\",i.mode=wb;break}if(i.lenbits=9,k={bits:i.lenbits},C=rb(1,i.lens,0,i.nlen,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid literal/lengths set\",i.mode=wb;break}if(i.distbits=6,i.distcode=i.distdyn,k={bits:i.distbits},C=rb(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,k),i.distbits=k.bits,C){e.msg=\"invalid distances set\",i.mode=wb;break}if(i.mode=20,t===ab)break e;case 20:i.mode=21;case 21:if(a>=6&&c>=258){e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,Zw(e,u),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,i.mode===mb&&(i.back=-1);break}for(i.back=0;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(w&&!(240&w)){for(F=m,v=w,y=b;_=i.lencode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,i.length=b,0===w){i.mode=26;break}if(32&w){i.back=-1,i.mode=mb;break}if(64&w){e.msg=\"invalid literal/length code\",i.mode=wb;break}i.extra=15&w,i.mode=22;case 22:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;_=i.distcode[l&(1<<i.distbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(!(240&w)){for(F=m,v=w,y=b;_=i.distcode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,64&w){e.msg=\"invalid distance code\",i.mode=wb;break}i.offset=b,i.extra=15&w,i.mode=24;case 24:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.offset+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=wb;break}i.mode=25;case 25:if(0===c)break e;if(f=u-c,i.offset>f){if(f=i.offset-f,f>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=wb;break}f>i.wnext?(f-=i.wnext,p=i.wsize-f):p=i.wnext-f,f>i.length&&(f=i.length),g=i.window}else g=r,p=o-i.offset,f=i.length;f>c&&(f=c),c-=f,i.length-=f;do{r[o++]=g[p++]}while(--f);0===i.length&&(i.mode=21);break;case 26:if(0===c)break e;r[o++]=i.length,c--,i.mode=21;break;case 27:if(i.wrap){for(;h<32;){if(0===a)break e;a--,l|=n[s++]<<h,h+=8}if(u-=c,e.total_out+=u,i.total+=u,u&&(e.adler=i.check=i.flags?Qw(i.check,r,u,o-u):Uw(i.check,r,u,o-u)),u=c,(i.flags?l:bb(l))!==i.check){e.msg=\"incorrect data check\",i.mode=wb;break}l=0,h=0}i.mode=28;case 28:if(i.wrap&&i.flags){for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=wb;break}l=0,h=0}i.mode=29;case 29:C=lb;break e;case wb:C=ub;break e;case 31:return fb;default:return db}return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,(i.wsize||u!==e.avail_out&&i.mode<wb&&(i.mode<27||t!==sb))&&Sb(e,e.output,e.next_out,u-e.avail_out),d-=e.avail_in,u-=e.avail_out,e.total_in+=d,e.total_out+=u,i.total+=u,i.wrap&&u&&(e.adler=i.check=i.flags?Qw(i.check,r,u,e.next_out-u):Uw(i.check,r,u,e.next_out-u)),e.data_type=i.bits+(i.last?64:0)+(i.mode===mb?128:0)+(20===i.mode||15===i.mode?256:0),(0===d&&0===u||t===sb)&&C===cb&&(C=pb),C},Nb={inflateReset:Cb,inflateReset2:_b,inflateResetKeep:Ab,inflateInit:e=>xb(e,15),inflateInit2:xb,inflate:Eb,inflateEnd:e=>{if(!e||!e.state)return db;let t=e.state;return t.window&&(t.window=null),e.state=null,cb},inflateGetHeader:(e,t)=>{if(!e||!e.state)return db;const i=e.state;return 2&i.wrap?(i.head=t,t.done=!1,cb):db},inflateSetDictionary:(e,t)=>{const i=t.length;let n,r,s;return e&&e.state?(n=e.state,0!==n.wrap&&11!==n.mode?db:11===n.mode&&(r=1,r=Uw(r,t,i,0),r!==n.check)?ub:(s=Sb(e,t,i,i),s?(n.mode=31,fb):(n.havedict=1,cb))):db},inflateInfo:\"pako inflate (from Nodeca project)\"};var Bb=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name=\"\",this.comment=\"\",this.hcrc=0,this.done=!1},Mb=Object.prototype.toString,{Z_NO_FLUSH:Rb,Z_FINISH:Db,Z_OK:Tb,Z_STREAM_END:Lb,Z_NEED_DICT:zb,Z_STREAM_ERROR:Hb,Z_DATA_ERROR:Pb,Z_MEM_ERROR:Ob}=jw;function Ub(e){this.options=Gw.assign({chunkSize:65536,windowBits:15,to:\"\"},e||{});const t=this.options;t.raw&&t.windowBits>=0&&t.windowBits<16&&(t.windowBits=-t.windowBits,0===t.windowBits&&(t.windowBits=-15)),!(t.windowBits>=0&&t.windowBits<16)||e&&e.windowBits||(t.windowBits+=32),t.windowBits>15&&t.windowBits<48&&(15&t.windowBits||(t.windowBits|=15)),this.err=0,this.msg=\"\",this.ended=!1,this.chunks=[],this.strm=new Xw,this.strm.avail_out=0;let i=Nb.inflateInit2(this.strm,t.windowBits);if(i!==Tb)throw new Error(Vw[i]);if(this.header=new Bb,Nb.inflateGetHeader(this.strm,this.header),t.dictionary&&(\"string\"==typeof t.dictionary?t.dictionary=Yw.string2buf(t.dictionary):\"[object ArrayBuffer]\"===Mb.call(t.dictionary)&&(t.dictionary=new Uint8Array(t.dictionary)),t.raw&&(i=Nb.inflateSetDictionary(this.strm,t.dictionary),i!==Tb)))throw new Error(Vw[i])}function qb(e,t){const i=new Ub(t);if(i.push(e),i.err)throw i.msg||Vw[i.err];return i.result}Ub.prototype.push=function(e,t){const i=this.strm,n=this.options.chunkSize,r=this.options.dictionary;let s,o,a;if(this.ended)return!1;for(o=t===~~t?t:!0===t?Db:Rb,\"[object ArrayBuffer]\"===Mb.call(e)?i.input=new Uint8Array(e):i.input=e,i.next_in=0,i.avail_in=i.input.length;;){for(0===i.avail_out&&(i.output=new Uint8Array(n),i.next_out=0,i.avail_out=n),s=Nb.inflate(i,o),s===zb&&r&&(s=Nb.inflateSetDictionary(i,r),s===Tb?s=Nb.inflate(i,o):s===Pb&&(s=zb));i.avail_in>0&&s===Lb&&i.state.wrap>0&&0!==e[i.next_in];)Nb.inflateReset(i),s=Nb.inflate(i,o);switch(s){case Hb:case Pb:case zb:case Ob:return this.onEnd(s),this.ended=!0,!1}if(a=i.avail_out,i.next_out&&(0===i.avail_out||s===Lb))if(\"string\"===this.options.to){let e=Yw.utf8border(i.output,i.next_out),t=i.next_out-e,r=Yw.buf2string(i.output,e);i.next_out=t,i.avail_out=n-t,t&&i.output.set(i.output.subarray(e,e+t),0),this.onData(r)}else this.onData(i.output.length===i.next_out?i.output:i.output.subarray(0,i.next_out));if(s!==Tb||0!==a){if(s===Lb)return s=Nb.inflateEnd(this.strm),this.onEnd(s),this.ended=!0,!0;if(0===i.avail_in)break}}return!0},Ub.prototype.onData=function(e){this.chunks.push(e)},Ub.prototype.onEnd=function(e){e===Tb&&(\"string\"===this.options.to?this.result=this.chunks.join(\"\"):this.result=Gw.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg};var Qb=function(e,t){return(t=t||{}).raw=!0,qb(e,t)},Vb={Inflate:Ub,inflate:qb,inflateRaw:Qb,ungzip:qb,constants:jw},{Inflate:jb,inflate:Wb,inflateRaw:Gb,ungzip:$b}=Vb,Kb=Wb,Yb=$b;var Xb=new Map([[1,function(e,t){let i=new Uint8Array(e);return Kb(i).buffer}],[2,function(e,t){let i=e.byteLength,n=new Uint8Array(i),r=Math.floor(i/t),s=new DataView(e);for(var o=0;o<t;o++)for(var a=0;a<r;a++)n[o+a*t]=s.getUint8(o*r+a);return n.buffer}],[3,function(e,t){return function(e){for(var t=e.byteLength%2!=0,i=e.byteLength-4,n=new DataView(e),r=0,s=0,o=0;o<i-1;o+=2){s=(s+(r=(r+n.getUint16(o,!0))%65535))%65535}if(t){s=(s+(r=(r+n.getUint8(i-1))%65535))%65535}var[a,c]=Aw.unpack_from(\">HH\",e,i);if(c%=65535,r!=(a%=65535)||s!=c)throw'ValueError(\"fletcher32 checksum invalid\")'}(e),e.slice(0,-4)}]]),Zb=class{constructor(e,t){this.fh=e,this.offset=t,this.depth=null}async init(){this.all_nodes=new Map,await this._read_root_node(),await this._read_children()}async _read_children(){let e=this.depth;for(;e>0;){for(var t of this.all_nodes.get(e))for(var i of t.get(\"addresses\"))this._add_node(await this._read_node(i,e-1));e--}}async _read_root_node(){let e=await this._read_node(this.offset,null);this._add_node(e),this.depth=e.get(\"node_level\")}_add_node(e){let t=e.get(\"node_level\");this.all_nodes.has(t)?this.all_nodes.get(t).push(e):this.all_nodes.set(t,[e])}async _read_node(e,t){let i=await this._read_node_header(e,t);return i.set(\"keys\",[]),i.set(\"addresses\",[]),i}async _read_node_header(e){throw\"NotImplementedError: must define _read_node_header in implementation class\"}},Jb=class extends Zb{constructor(){super(...arguments),pw(this,\"B_LINK_NODE\",new Map([[\"signature\",\"4s\"],[\"node_type\",\"B\"],[\"node_level\",\"B\"],[\"entries_used\",\"H\"],[\"left_sibling\",\"Q\"],[\"right_sibling\",\"Q\"]]))}async _read_node_header(e,t){let i=await gw(this.B_LINK_NODE,this.fh,e);if(null!=t&&i.get(\"node_level\")!=t)throw\"node level does not match\";return i}},eF=class extends Jb{constructor(e,t){super(e,t),pw(this,\"NODE_TYPE\",0),this.ready=this.init()}async _read_node(e,t){let i=await this._read_node_header(e,t);e+=bw(this.B_LINK_NODE);let n=[],r=[],s=i.get(\"entries_used\");for(var o=0;o<s;o++){let t=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8;let i=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8,n.push(t),r.push(i)}return n.push((await Aw.unpack_from_async(\"<Q\",this.fh,e))[0]),i.set(\"keys\",n),i.set(\"addresses\",r),i}symbol_table_addresses(){var e=[],t=this.all_nodes.get(0);for(var i of t)e=e.concat(i.get(\"addresses\"));return e}},tF=class extends Jb{constructor(e,t,i){super(e,t),pw(this,\"NODE_TYPE\",1),this.dims=i,this.ready=this.init()}async _read_node(e,t){let i=await this._read_node_header(e,t);e+=bw(this.B_LINK_NODE);var n=[],r=[];let s=i.get(\"entries_used\");for(var o=0;o<s;o++){let[t,i]=await Aw.unpack_from_async(\"<II\",this.fh,e);e+=8;let s=\"<\"+this.dims.toFixed()+\"Q\",o=Aw.calcsize(s),a=await Aw.unpack_from_async(s,this.fh,e);e+=o;let c=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8,n.push(new Map([[\"chunk_size\",t],[\"filter_mask\",i],[\"chunk_offset\",a]])),r.push(c)}return i.set(\"keys\",n),i.set(\"addresses\",r),i}async construct_data_from_chunks(e,t,i,n){var r,s,o;if(i instanceof Array){let e=i[0];if(\"REFERENCE\"==e){if(8!=i[1])throw\"NotImplementedError('Unsupported Reference type')\";i=\"<u8\",r=\"getUint64\",s=!1,o=8}else{if(\"VLEN_STRING\"!=e&&\"VLEN_SEQUENCE\"!=e)throw\"NotImplementedError('datatype not implemented')\";r=\"getVLENStruct\",s=!1,o=16}}else[r,s,o]=yw(i);var a=t.reduce((function(e,t){return e*t}),1),c=e.reduce((function(e,t){return e*t}),1);let l=t.length;var h=1;e.slice().map((function(e){let t=h;return h*=e,t}));h=1;var d=t.slice().reverse().map((function(e){let t=h;return h*=e,t})).reverse(),u=new Array(a);let f=c*o;for(var p of this.all_nodes.get(0)){let i=p.get(\"keys\"),a=p.get(\"addresses\"),h=i.length;for(var g=0;g<h;g++){let h=i[g],p=a[g];var m;if(null==n)m=await this.fh.slice(p,p+f);else{m=await this.fh.slice(p,p+h.get(\"chunk_size\"));let e=h.get(\"filter_mask\");m=this._filter_chunk(m,e,n,o)}for(var w=h.get(\"chunk_offset\").slice(),b=w.slice(),F=b.map((function(){return 0})),v=new Cw(m),y=0;y<c;y++){for(var A=l-1;A>=0&&F[A]>=e[A];A--)F[A]=0,b[A]=w[A],A>0&&(F[A-1]+=1,b[A-1]+=1);if(b.slice(0,-1).every((function(e,i){return e<t[i]}))){let e=y*o,t=v[r](e,!s,o),i=b.slice(0,-1).reduce((function(e,t,i){return t*d[i]+e}),0);u[i]=t}F[l-1]+=1,b[l-1]+=1}}}return u}_filter_chunk(e,t,i,n){let r=i.length,s=e.slice();for(var o=r-1;o>=0;o--){if(t&1<<o)continue;let e=i[o],r=e.get(\"filter_id\"),a=e.get(\"client_data\");if(!Xb.has(r))throw'NotImplementedError(\"Filter with id:'+r.toFixed()+' not supported\")';s=Xb.get(r)(s,n,a)}return s}},iF=class extends Zb{constructor(e,t){super(e,t),pw(this,\"B_TREE_HEADER\",new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"node_type\",\"B\"],[\"node_size\",\"I\"],[\"record_size\",\"H\"],[\"depth\",\"H\"],[\"split_percent\",\"B\"],[\"merge_percent\",\"B\"],[\"root_address\",\"Q\"],[\"root_nrecords\",\"H\"],[\"total_nrecords\",\"Q\"]])),pw(this,\"B_LINK_NODE\",new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"node_type\",\"B\"]])),this.ready=this.init()}async _read_root_node(){let e=await this._read_tree_header(this.offset);this.address_formats=this._calculate_address_formats(e),this.header=e,this.depth=e.get(\"depth\");let t=[e.get(\"root_address\"),e.get(\"root_nrecords\"),e.get(\"total_nrecords\")],i=await this._read_node(t,this.depth);this._add_node(i)}async _read_tree_header(e){return await gw(this.B_TREE_HEADER,this.fh,this.offset)}_calculate_address_formats(e){let t=e.get(\"node_size\"),i=e.get(\"record_size\"),n=0,r=0,s=new Map,o=e.get(\"depth\");for(var a=0;a<=o;a++){let e,c,l,h=\"\",d=\"\",u=\"\";if(0==a?(e=0,c=0,l=0):1==a?(e=8,h=\"<Q\",c=this._required_bytes(n),d=this._int_format(c),l=0):(e=8,h=\"<Q\",c=this._required_bytes(n),d=this._int_format(c),l=this._required_bytes(r),u=this._int_format(l)),s.set(a,[e,c,l,h,d,u]),a<o){let s=e+c+l;n=this._nrecords_max(t,i,s),r>0?r*=n:r=n}}return s}_nrecords_max(e,t,i){return Math.floor((e-10-i)/(t+i))}_required_bytes(e){return Math.ceil(_w(e)/8)}_int_format(e){return[\"<B\",\"<H\",\"<I\",\"<Q\"][e-1]}async _read_node(e,t){let[i,n,r]=e,s=this._read_node_header(i,t);i+=bw(this.B_LINK_NODE);let o=this.header.get(\"record_size\"),a=[];for(let e=0;e<n;e++){let e=await this._parse_record(this.fh,i,o);i+=o,a.push(e)}let c=[],l=this.address_formats.get(t);if(0!=t){let[e,t,r,s,o,a]=l;for(let l=0;l<=n;l++){let n=(await Aw.unpack_from_async(s,this.fh,i))[0];i+=e;let l=(await Aw.unpack_from_async(o,this.fh,i))[0];i+=t;let h=l;r>0&&(h=(await Aw.unpack_from_async(a,this.fh,i))[0],i+=r),c.push([n,l,h])}}return s.set(\"keys\",a),s.set(\"addresses\",c),s}async _read_node_header(e,t){let i=await gw(this.B_LINK_NODE,this.fh,e);return i.set(\"node_level\",t),i}*iter_records(){for(let e of this.all_nodes.values())for(let t of e)for(let e of t.get(\"keys\"))yield e}_parse_record(e){throw\"NotImplementedError\"}},nF=class extends iF{constructor(){super(...arguments),pw(this,\"NODE_TYPE\",5)}async _parse_record(e,t,i){let n=(await Aw.unpack_from_async(\"<I\",e,t))[0];t+=4;const r=await e.slice(t,t+7);return new Map([[\"namehash\",n],[\"heapid\",r]])}},rF=class extends iF{constructor(){super(...arguments),pw(this,\"NODE_TYPE\",6)}async _parse_record(e,t,i){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];t+=8;const r=await e.slice(t,t+7);return new Map([[\"creationorder\",n],[\"heapid\",r]])}},sF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await Aw.unpack_from_async(\"<B\",e,t+8);var n;if(0==i)n=await gw(uF,e,t),this._end_of_sblock=t+fF;else{if(2!=i&&3!=i)throw\"unsupported superblock version: \"+i.toFixed();n=await gw(pF,e,t),this._end_of_sblock=t+gF}if(n.get(\"format_signature\")!=hF)throw\"Incorrect file signature: \"+n.get(\"format_signature\");if(8!=n.get(\"offset_size\")||8!=n.get(\"length_size\"))throw\"File uses non-64-bit addressing\";this.version=n.get(\"superblock_version\"),this._contents=n,this._root_symbol_table=null,this._fh=e}async get_offset_to_dataobjects(){if(0==this.version){var e=new aF(this._fh,this._end_of_sblock,!0);return await e.ready,this._root_symbol_table=e,e.group_offset}if(2==this.version||3==this.version)return this._contents.get(\"root_group_address\");throw\"Not implemented version = \"+this.version.toFixed()}},oF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await gw(vF,e,t);ww(\"HEAP\"==i.get(\"signature\")),ww(0==i.get(\"version\"));let n=i.get(\"address_of_data_segment\"),r=await e.slice(n,n+i.get(\"data_segment_size\"));i.set(\"heap_data\",r),this._contents=i,this.data=r}get_object_name(e){let t=new Uint8Array(this.data).indexOf(0,e)-e;return Aw.unpack_from(\"<\"+t.toFixed()+\"s\",this.data,e)[0]}},aF=class{constructor(e,t,i=!1){this.ready=this.init(e,t,i)}async init(e,t,i){var n;if(i)n=new Map([[\"symbols\",1]]);else{if(\"SNOD\"!=(n=await gw(bF,e,t)).get(\"signature\"))throw\"incorrect node type\";t+=FF}for(var r=[],s=n.get(\"symbols\"),o=0;o<s;o++)r.push(await gw(mF,e,t)),t+=wF;return i&&(this.group_offset=r[0].get(\"object_header_address\")),this.entries=r,this._contents=n,this}assign_name(e){this.entries.forEach((function(t){let i=t.get(\"link_name_offset\"),n=e.get_object_name(i);t.set(\"link_name\",n)}))}get_links(e){var t={};return this.entries.forEach((function(i){let n=i.get(\"cache_type\"),r=i.get(\"link_name\");if(0==n||1==n)t[r]=i.get(\"object_header_address\");else if(2==n){let n=i.get(\"scratch\"),o=new ArrayBuffer(4),a=new Uint8Array(o);for(var s=0;s<4;s++)a[s]=n.charCodeAt(s);let c=Aw.unpack_from(\"<I\",o,0)[0];t[r]=e.get_object_name(c)}})),t}},cF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await gw(yF,e,t);t+=AF;let n=i.get(\"collection_size\")-AF,r=await e.slice(t,t+n);this.heap_data=r,this._header=i,this._objects=null}get objects(){if(null==this._objects){this._objects=new Map;for(var e=0;e<=this.heap_data.byteLength-_F;){let t=mw(CF,this.heap_data,e);if(0==t.get(\"object_index\"))break;e+=_F;let i=this.heap_data.slice(e,e+t.get(\"object_size\"));this._objects.set(t.get(\"object_index\"),i),e+=Fw(t.get(\"object_size\"))}}return this._objects}},lF=class{constructor(e,t){this.fh=e,this.ready=this.init(t)}async init(e){let t=await gw(xF,this.fh,e);if(e+=bw(xF),ww(\"FRHP\"==t.get(\"signature\")),ww(0==t.get(\"version\")),t.get(\"filter_info_size\")>0)throw\"Filter info size not supported on FractalHeap\";if(t.get(\"btree_address_huge_objects\")!=dF)throw\"Huge objects not implemented in FractalHeap\";t.set(\"btree_address_huge_objects\",null),t.get(\"root_block_address\")==dF&&t.set(\"root_block_address\",null);let i=t.get(\"log2_maximum_heap_size\"),n=this._min_size_nbits(i),r=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"heap_header_adddress\",\"Q\"],[\"block_offset\",`${n}B`]]);this.indirect_block_header=new Map(r),this.indirect_block_header_size=bw(r),2&~t.get(\"flags\")||r.set(\"checksum\",\"I\"),this.direct_block_header=r,this.direct_block_header_size=bw(r);let s=t.get(\"maximum_direct_block_size\");this._managed_object_offset_size=this._min_size_nbits(i);let o=Math.min(s,t.get(\"max_managed_object_size\"));this._managed_object_length_size=this._min_size_integer(o);let a=t.get(\"starting_block_size\"),c=t.get(\"table_width\");if(!(a>0))throw\"Starting block size == 0 not implemented\";let l=Number(Math.floor(Math.log2(s)));ww(1n<<BigInt(l)==s);let h=Number(Math.floor(Math.log2(a)));ww(1n<<BigInt(h)==a),this._max_direct_nrows=l-h+2;let d=Math.floor(Math.log2(c));ww(1<<d==c),this._indirect_nrows_sub=d+h-1,this.header=t,this.nobjects=t.get(\"managed_object_count\")+t.get(\"huge_object_count\")+t.get(\"tiny_object_count\");let u=[],f=t.get(\"root_block_address\"),p=0;if(null!=f&&(p=t.get(\"indirect_current_rows_count\")),p>0)for await(let e of this._iter_indirect_block(this.fh,f,p))u.push(e);else{let e=await this._read_direct_block(this.fh,f,a);u.push(e)}let g=u.reduce(((e,t)=>e+t.byteLength),0),m=new Uint8Array(g),w=0;u.forEach((e=>{m.set(new Uint8Array(e),w),w+=e.byteLength})),this.managed=m.buffer}async _read_direct_block(e,t,i){let n=await e.slice(t,t+i);return ww(\"FHDB\"==mw(this.direct_block_header,n).get(\"signature\")),n}get_data(e){let t=Aw.unpack_from(\"<B\",e,0)[0],i=t>>4&3,n=1;if(0==i){ww(0==t>>6);let i=this._managed_object_offset_size,r=xw(i,e,n);n+=i,i=this._managed_object_length_size;let s=xw(i,e,n);return this.managed.slice(r,r+s)}throw 1==i?\"tiny objectID not supported in FractalHeap\":2==i?\"huge objectID not supported in FractalHeap\":\"unknown objectID type in FractalHeap\"}_min_size_integer(e){return this._min_size_nbits(_w(e))}_min_size_nbits(e){return Math.ceil(e/8)}async*_iter_indirect_block(e,t,i){let n=await gw(this.indirect_block_header,e,t);t+=this.indirect_block_header_size,ww(\"FHIB\"==n.get(\"signature\"));let r=n.get(\"block_offset\").reduce(((e,t,i)=>e+(t<<8*i)),0);n.set(\"block_offset\",r);let[s,o]=this._indirect_info(i),a=[];for(let i=0;i<s;i++){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];if(t+=8,n==dF)break;let r=this._calc_block_size(i);a.push([n,r])}let c=[];for(let i=s;i<s+o;i++){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];if(t+=8,n==dF)break;let r=this._calc_block_size(i),s=this._iblock_nrows_from_block_size(r);c.push([n,s])}for(let[t,i]of a){let n=await this._read_direct_block(e,t,i);yield n}for(let[t,i]of c)for await(let n of this._iter_indirect_block(e,t,i))yield n}_calc_block_size(e){let t=Math.floor(e/this.header.get(\"table_width\"));return 2**Math.max(t-1,0)*this.header.get(\"starting_block_size\")}_iblock_nrows_from_block_size(e){let t=Math.floor(Math.log2(e));return ww(2**t==e),t-this._indirect_nrows_sub}_indirect_info(e){let t,i,n=this.header.get(\"table_width\"),r=e*n,s=this._max_direct_nrows*n;return e<=s?(t=r,i=0):(t=s,i=r-s),[t,i]}_int_format(e){return[\"B\",\"H\",\"I\",\"Q\"][e-1]}},hF=Aw.unpack_from(\"8s\",new Uint8Array([137,72,68,70,13,10,26,10]).buffer)[0],dF=Aw.unpack_from(\"<Q\",new Uint8Array([255,255,255,255,255,255,255,255]).buffer)[0],uF=new Map([[\"format_signature\",\"8s\"],[\"superblock_version\",\"B\"],[\"free_storage_version\",\"B\"],[\"root_group_version\",\"B\"],[\"reserved_0\",\"B\"],[\"shared_header_version\",\"B\"],[\"offset_size\",\"B\"],[\"length_size\",\"B\"],[\"reserved_1\",\"B\"],[\"group_leaf_node_k\",\"H\"],[\"group_internal_node_k\",\"H\"],[\"file_consistency_flags\",\"L\"],[\"base_address_lower\",\"Q\"],[\"free_space_address\",\"Q\"],[\"end_of_file_address\",\"Q\"],[\"driver_information_address\",\"Q\"]]),fF=bw(uF),pF=new Map([[\"format_signature\",\"8s\"],[\"superblock_version\",\"B\"],[\"offset_size\",\"B\"],[\"length_size\",\"B\"],[\"file_consistency_flags\",\"B\"],[\"base_address\",\"Q\"],[\"superblock_extension_address\",\"Q\"],[\"end_of_file_address\",\"Q\"],[\"root_group_address\",\"Q\"],[\"superblock_checksum\",\"I\"]]),gF=bw(pF),mF=new Map([[\"link_name_offset\",\"Q\"],[\"object_header_address\",\"Q\"],[\"cache_type\",\"I\"],[\"reserved\",\"I\"],[\"scratch\",\"16s\"]]),wF=bw(mF),bF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved_0\",\"B\"],[\"symbols\",\"H\"]]),FF=bw(bF),vF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved\",\"3s\"],[\"data_segment_size\",\"Q\"],[\"offset_to_free_list\",\"Q\"],[\"address_of_data_segment\",\"Q\"]]),yF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved\",\"3s\"],[\"collection_size\",\"Q\"]]),AF=bw(yF),CF=new Map([[\"object_index\",\"H\"],[\"reference_count\",\"H\"],[\"reserved\",\"I\"],[\"object_size\",\"Q\"]]),_F=bw(CF),xF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"object_index_size\",\"H\"],[\"filter_info_size\",\"H\"],[\"flags\",\"B\"],[\"max_managed_object_size\",\"I\"],[\"next_huge_object_index\",\"Q\"],[\"btree_address_huge_objects\",\"Q\"],[\"managed_freespace_size\",\"Q\"],[\"freespace_manager_address\",\"Q\"],[\"managed_space_size\",\"Q\"],[\"managed_alloc_size\",\"Q\"],[\"next_directblock_iterator_address\",\"Q\"],[\"managed_object_count\",\"Q\"],[\"huge_objects_total_size\",\"Q\"],[\"huge_object_count\",\"Q\"],[\"tiny_objects_total_size\",\"Q\"],[\"tiny_object_count\",\"Q\"],[\"table_width\",\"H\"],[\"starting_block_size\",\"Q\"],[\"maximum_direct_block_size\",\"Q\"],[\"log2_maximum_heap_size\",\"H\"],[\"indirect_starting_rows_count\",\"H\"],[\"root_block_address\",\"Q\"],[\"indirect_current_rows_count\",\"H\"]]),kF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];if(1==i)var[n,r,s]=await this._parse_v1_objects(e,t);else{if(i!=\"O\".charCodeAt(0))throw\"InvalidHDF5File('unknown Data Object Header')\";var[n,r,s]=await this._parse_v2_objects(e,t)}this.fh=e,this.msgs=n,this.msg_data=r,this.offset=t,this._global_heaps={},this._header=s,this._filter_pipeline=null,this._chunk_params_set=!1,this._chunks=null,this._chunk_dims=null,this._chunk_address=null}get dtype(){let e=this.find_msg_type(ev)[0].get(\"offset_to_message\");return new kw(this.fh,e).dtype}get chunks(){return this._get_chunk_params().then((()=>this._chunks))}get shape(){let e=this.find_msg_type(ZF)[0].get(\"offset_to_message\");return async function(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];var n;if(1==i)ww(1==(n=await gw(TF,e,t)).get(\"version\")),t+=LF;else{if(2!=i)throw\"InvalidHDF5File('unknown dataspace message version')\";ww(2==(n=await gw(zF,e,t)).get(\"version\")),t+=HF}let r=n.get(\"dimensionality\");return(await Aw.unpack_from_async(\"<\"+(2*r).toFixed()+\"I\",e,t)).filter((function(e,t){return t%2==0}))}(this.fh,e)}async get_filter_pipeline(){if(null!=this._filter_pipeline)return this._filter_pipeline;let e=this.find_msg_type(rv);if(!e.length)return this._filter_pipeline=null,this._filter_pipeline;var t=e[0].get(\"offset_to_message\");let[i,n]=await Aw.unpack_from_async(\"<BB\",this.fh,t);t+=Aw.calcsize(\"<BB\");var r=[];if(1==i){await Aw.unpack_from_async(\"<HI\",this.fh,t),t+=Aw.calcsize(\"<HI\");for(var s=0;s<n;s++){let e=await gw(YF,this.fh,t);t+=XF;let i=Fw(e.get(\"name_length\"),8),n=\"<\"+i.toFixed()+\"s\",s=(await Aw.unpack_from_async(n,this.fh,t))[0];e.set(\"filter_name\",s),t+=i,n=\"<\"+e.get(\"client_data_values\").toFixed()+\"I\";let o=await Aw.unpack_from_async(n,this.fh,t);e.set(\"client_data\",o),t+=4*e.get(\"client_data_values\"),e.get(\"client_data_values\")%2&&(t+=4),r.push(e)}}else{if(2!=i)throw`version ${i} is not supported`;for(let e=0;e<n;e++){let e=new Map,i=this.fh,n=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2,e.set(\"filter_id\",n);let s=0;n>255&&(s=(await Aw.unpack_from_async(\"<H\",i,t))[0],t+=2);let o=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2;let a=(1&o)>0;e.set(\"optional\",a);let c,l=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2,s>0&&(c=(await Aw.unpack_from_async(`${s}s`,i,t))[0],t+=s),e.set(\"name\",c);let h=await Aw.unpack_from_async(`<${l}i`,i,t);t+=4*l,e.set(\"client_data_values\",h),r.push(e)}}return this._filter_pipeline=r,this._filter_pipeline}find_msg_type(e){return this.msgs.filter((function(t){return t.get(\"type\")==e}))}async get_attributes(){let e={},t=this.find_msg_type(sv);for(let i of t){let t=i.get(\"offset_to_message\"),[n,r]=await this.unpack_attribute(t);e[n]=r}return e}async get_fillvalue(){var e,t=this.find_msg_type(tv)[0].get(\"offset_to_message\");let i=(await Aw.unpack_from_async(\"<B\",this.fh,t))[0];var n,r,s;if(1==i||2==i)n=await gw(WF,this.fh,t),t+=GF,e=n.get(\"fillvalue_defined\");else{if(3!=i)throw'InvalidHDF5File(\"Unknown fillvalue msg version: \"'+String(i);n=await gw($F,this.fh,t),t+=KF,e=32&n.get(\"flags\")}if(e?(r=(await Aw.unpack_from_async(\"<I\",this.fh,t))[0],t+=4):r=0,r){let[e,i,n]=yw(await this.dtype);s=new Cw(await this.fh.slice(t,t+n))[e](t,!i,n)}else s=0;return s}async unpack_attribute(e){let t=(await Aw.unpack_from_async(\"<B\",this.fh,e))[0];var i,n;if(1==t)ww(1==(i=await gw(EF,this.fh,e)).get(\"version\")),e+=NF,n=8;else{if(3!=t)throw\"unsupported attribute message version: \"+t;ww(3==(i=await gw(BF,this.fh,e)).get(\"version\")),e+=MF,n=1}let r=i.get(\"name_size\"),s=(await Aw.unpack_from_async(\"<\"+r.toFixed()+\"s\",this.fh,e))[0];var o;s=s.replace(/\\x00$/,\"\"),e+=Fw(r,n);try{o=await new kw(this.fh,e).dtype}catch(e){return console.warn(\"Attribute \"+s+\" type not implemented, set to null.\"),[s,null]}e+=Fw(i.get(\"datatype_size\"),n);let a=await this.determine_data_shape(this.fh,e),c=a.reduce((function(e,t){return e*t}),1);if(e+=Fw(i.get(\"dataspace_size\"),n),5===o.datatype_class)l=await this.fh.slice(e,e+o.size);else{var l=await this._attr_value(o,this.fh,c,e);0==a.length&&(l=l[0])}return[s,l]}async determine_data_shape(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];var n;if(1==i)ww(1==(n=await gw(TF,e,t)).get(\"version\")),t+=LF;else{if(2!=i)throw\"unknown dataspace message version\";ww(2==(n=await gw(zF,e,t)).get(\"version\")),t+=HF}let r=n.get(\"dimensionality\");return await Aw.unpack_from_async(\"<\"+r.toFixed()+\"Q\",e,t)}async _attr_value(e,t,i,n){var r=new Array(i);if(e instanceof Array){let l=e[0];for(var s=0;s<i;s++)if(\"VLEN_STRING\"==l){let i=e[2];var[o,a]=await this._vlen_size_and_data(t,n);const c=new TextDecoder(0==i?\"ascii\":\"utf-8\");r[s]=c.decode(a),n+=16}else if(\"REFERENCE\"==l){var c=await Aw.unpack_from_async(\"<Q\",t,n);r[s]=c,n+=8}else{if(\"VLEN_SEQUENCE\"!=l)throw\"NotImplementedError\";{let i=e[1];var[o,a]=this._vlen_size_and_data(t,n);r[s]=this._attr_value(i,a,o,0),n+=16}}}else{let[o,a,c]=yw(e);const l=await t.slice(n,n+i*c);let h=new Cw(l,0),d=0;for(s=0;s<i;s++)r[s]=h[o](d,!a,c),d+=c}return r}async _vlen_size_and_data(e,t){let i=(await Aw.unpack_from_async(\"<I\",e,t))[0],n=await gw(SF,e,t+4),r=n.get(\"collection_address\");var s;return ww(n.get(\"collection_address\")<Number.MAX_SAFE_INTEGER),r in this._global_heaps||(s=new cF(this.fh,r),await s.ready,this._global_heaps[r]=s),[i,(s=this._global_heaps[r]).objects.get(n.get(\"object_index\"))]}async _parse_v1_objects(e,t){let i=await gw(RF,e,t);ww(1==i.get(\"version\"));let n=i.get(\"total_header_messages\");for(var r=i.get(\"object_header_size\"),s=t+bw(RF),o=await e.slice(s,s+r),a=[[s,r]],c=0,l=0,h=new Array(n),d=0;d<n;d++){l>=r&&([s,r]=a[++c],l=0);let t=await gw(PF,e,s+l),i=s+l+OF;if(t.set(\"offset_to_message\",i),t.get(\"type\")==ov){var[u,f]=await Aw.unpack_from_async(\"<QQ\",e,i);a.push([u,f])}l+=OF+t.get(\"size\"),h[d]=t}return[h,o,i]}async _parse_v2_objects(e,t){var[i,n,r]=await this._parse_v2_header(e,t);t=r;for(var s=[],o=i.get(\"size_of_chunk_0\"),a=e.slice(t,t+=o),c=[[r,o]],l=0,h=0;;){if(h>=o-qF){let e=c[++l];if(null==e)break;[r,o]=e,h=0}let t=await gw(UF,e,r+h),i=r+h+qF+n;if(t.set(\"offset_to_message\",i),t.get(\"type\")==ov){var[d,u]=await Aw.unpack_from_async(\"<QQ\",e,i);c.push([d+4,u-4])}h+=qF+t.get(\"size\")+n,s.push(t)}return[s,a,i]}async _parse_v2_header(e,t){let i=await gw(DF,e,t);var n;if(t+=bw(DF),ww(2==i.get(\"version\")),n=4&i.get(\"flags\")?2:0,ww(!(16&i.get(\"flags\"))),32&i.get(\"flags\")){let n=await Aw.unpack_from_async(\"<4I\",e,t);t+=16,i.set(\"access_time\",n[0]),i.set(\"modification_time\",n[1]),i.set(\"change_time\",n[2]),i.set(\"birth_time\",n[3])}let r=[\"<B\",\"<H\",\"<I\",\"<Q\"][3&i.get(\"flags\")];return i.set(\"size_of_chunk_0\",(await Aw.unpack_from_async(r,e,t))[0]),[i,n,t+=Aw.calcsize(r)]}async find_link(e){if(this._links){for(link of this._links)if(e===link[0])return link}else{const t=[];for await(const i of this.iter_links()){if(e===i[0])return i;t.push(i)}this._links=t}}async get_links(){const e=[];for await(const t of this.iter_links())e.push(t);return Object.fromEntries(e)}async*iter_links(){for(let e of this.msgs)e.get(\"type\")==av?yield*this._iter_links_from_symbol_tables(e):e.get(\"type\")==iv?yield this._get_link_from_link_msg(e):e.get(\"type\")==JF&&(yield*this._iter_link_from_link_info_msg(e))}async*_iter_links_from_symbol_tables(e){ww(16==e.get(\"size\"));let t=await gw(QF,this.fh,e.get(\"offset_to_message\"));yield*this._iter_links_btree_v1(t.get(\"btree_address\"),t.get(\"heap_address\"))}async*_iter_links_btree_v1(e,t){let i=new eF(this.fh,e);await i.ready;let n=new oF(this.fh,t);await n.ready;for(let e of 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t=e.get(\"offset_to_message\"),i=await this._decode_link_info_msg(this.fh,t),n=i.get(\"heap_address\"),r=i.get(\"name_btree_address\"),s=i.get(\"order_btree_address\");null!=r&&(yield*this._iter_links_btree_v2(r,s,n))}async*_iter_links_btree_v2(e,t,i){let n,r=new lF(this.fh,i);await r.ready;const s=null!=t;s?(n=new rF(this.fh,t),await n.ready):(n=new nF(this.fh,e),await n.ready);let o=new Map;for(let e of n.iter_records()){let t=r.get_data(e.get(\"heapid\")),[i,n]=await this._decode_link_msg(t,0);const a=s?i:n[0];o.set(a,n)}let a=Array.from(o.keys()).sort();for(let e of a)yield o.get(e)}async _decode_link_info_msg(e,t){let[i,n]=await Aw.unpack_from_async(\"<BB\",e,t);ww(0==i),t+=2,(1&n)>0&&(t+=8);let r=(2&n)>0?jF:VF,s=await gw(r,e,t),o=new Map;for(let[e,t]of s.entries())o.set(e,t==IF?null:t);return o}get is_dataset(){return this.find_msg_type(ZF).length>0}async get_data(){let e=this.find_msg_type(nv)[0].get(\"offset_to_message\");var[t,i,n,r]=await 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wv(this.pytor_keys),n=i.get_rd_bins(),r=i.get_snp_bins();this.available_bins=[...new Set(n,r)],this.available_bins.includes(e)||(e=this.available_bins.at(-1));const s=await t.get(\"rd_chromosomes\");await s.dtype;let o=await s.value,a=await this.rd_stat(e);var c=[],l=[],h=[],d=[],u=[],f=[];for(let t of o){let i=new gv(t,e);var p=i.signals.raw_RD;let n=await this.get_chr_signal(t,e,p,a);c=c.concat(n);var g=i.signals.gc_RD;let r=await this.get_chr_signal(t,e,g,a);l=l.concat(r);let s=i.signals.gc_partition,o=await this.get_chr_signal(t,e,s,a);h=h.concat(o);let m=await this.rd_call_combined(t,e,a,i);d=d.concat(m);let w=i.signals.baf_i1,b=await this.get_baf_signals_v2(t,e,w);u=u.concat(b[0]),f=f.concat(b[1])}this.callers=[],0!=d.length&&this.callers.push(\"ReadDepth\"),0!=d.length&&this.callers.push(\"2D\");var m={},w={RD_Raw:c,RD_Raw_gc_coor:l,ReadDepth:h,\"2D\":d,BAF1:u,BAF2:f};return m[e]=w,m}decode_segments(e){let t=[],i=[];for(let n of e)4294967295==n?(t.push(i),i=[]):i.push(n);return t}async rd_call_combined(e,t,i,n){let r,s=[],o=n.signals.Mosaic_segments;if(this.pytor_keys.includes(o)){const e=await this.h5_obj.get(o);let t=await e.value;r=this.decode_segments(t)}let a=n.signals.Mosaic_calls;if(this.pytor_keys.includes(a)){const n=await this.h5_obj.get(a);let o=await n.to_array();r.forEach(((n,r)=>{n.forEach(((n,a)=>{s.push({chr:e,start:n*t,end:(n+1)*t,value:o[0][r]/i[4]*2})}))}))}return s}async rd_stat(e){let t,i=`rd_stat_${e}_auto`;if(this.pytor_keys.includes(i)){const e=await this.h5_obj.get(i);t=await e.value}return t}async get_chr_signal(e,t,i,n){let r=[];if(this.pytor_keys.includes(i)){const s=await this.h5_obj.get(i);(await s.value).forEach(((i,s)=>{r.push({chr:e,start:s*t,end:(s+1)*t,value:i/n[4]*2})}))}return r}async get_baf_signals(e,t,i,n=-1){let r=[],s=[];if(this.pytor_keys.includes(i)){let o=await this.h5_obj.get(i);(await o.to_array()).forEach(((i,o)=>{let a=Math.max(...i);const c=i.indexOf(a);let l=Math.max(c/200,1-c/200);r.push({chr:e,start:o*t,end:(o+1)*t,value:n*l}),.5!=l&&s.push({chr:e,start:o*t,end:(o+1)*t,value:n*(1-l)})}))}return[r,s]}async get_baf_signals_v2(e,t,i,n=-1){let r=[],s=[];if(this.pytor_keys.includes(i)){let o=await this.h5_obj.get(i);(await o.to_array()).forEach(((i,o)=>{isNaN(i)||(r.push({chr:e,start:o*t,end:(o+1)*t,value:n*(.5-i)}),.5!=i&&s.push({chr:e,start:o*t,end:(o+1)*t,value:n*(.5+i)}))}))}return[r,s]}}class wv{constructor(e){this.signals=e}get_rd_bins(){let e=[];this.signals.forEach((t=>{let i=t.match(/^his_rd_p_(.*)_(\\d+)$/);i&&e.push({chr:i[1],bin_size:i[2]})}));return[...new Set(e.map((e=>Number(e.bin_size))))]}get_snp_bins(){let e=[];this.signals.forEach((t=>{let i=t.match(/^snp_likelihood_(.*)_(\\d+)_mask$/);i&&e.push({chr:i[1],bin_size:i[2]})}));return[...new Set(e.map((e=>Number(e.bin_size))))]}}function bv(e){let t=function(e){if(e.length<4)return e;let t,i,n,r,s,o;return t=e.slice().sort(((e,t)=>e-t)),t.length/4%1==0?(i=.5*(t[t.length/4]+t[t.length/4+1]),n=.5*(t[t.length*(3/4)]+t[t.length*(3/4)+1])):(i=t[Math.floor(t.length/4+1)],n=t[Math.ceil(t.length*(3/4)+1)]),r=n-i,s=n+1.5*r,o=i-1.5*r,t.filter((e=>e>=o&&e<=s))}(e);const i=t.length,n=t.reduce(((e,t)=>e+t))/i,r=Math.sqrt(t.map((e=>Math.pow(e-n,2))).reduce(((e,t)=>e+t))/i);return[n,r]}var Fv={range_function:function(e,t,i){return Array(Math.ceil((t-e)/i)).fill(e).map(((e,t)=>e+t*i))},getDistParams:bv,linspace:function(e,t,i){if(void 0===i&&(i=Math.max(Math.round(t-e)+1,1)),i<2)return 1===i?[e]:[];var n=Array(i);for(let r=--i;r>=0;r--)n[r]=(r*t+(i-r)*e)/i;return n},GetFit:class{constructor(e){this.allBins=e}getValues(){return Object.values(this.allBins).reduce(((e,t)=>e.concat(t.filter((e=>e.binScore>0)).map((e=>e.binScore)))),[])}getMean(e){return e.reduce((function(e,t){return e+t}))/e.length}fit_data(){return bv(this.getValues())}histogram(e,t){const i=t[1]-t[0],n=[];e.forEach(((e,r)=>{t.forEach(((t,r)=>{if(n[t]||(n[t]={count:0}),t<=e&&e<t+i)return n[t].count++,!1}))}));const r=[];return n.forEach(((e,t)=>{r.push(e.count)})),r}}};function vv(e,t){return isNaN(e)||isNaN(t)||t<=0?NaN:0===e?.5:.5+.5*(yv(.5*t,.5,1)-yv(.5*t,.5,t/(t+e*e)))*Math.sign(e)}function yv(e,t,i){if(0==i)return 0;if(1==i)return 1;{let n=xv(e+t)-xv(e)-xv(t)+e*Math.log(i)+t*Math.log(1-i);return i<(e+1)/(e+t+2)?Math.exp(n)*Av(e,t,i)/e:1-Math.exp(n)*Av(t,e,1-i)/t}}function Av(e,t,i,n=1e3){let r=1,s=1,o=1,a=e+t,c=e+1,l=e-1,h=1-a*i/c;for(let d=0;d<=n;d++){let n=parseFloat(d+1),u=n+n,f=n*(t-n)*i/((l+u)*(e+u)),p=r+f*s,g=h+f*o;f=-(e+n)*(a+n)*i/((c+u)*(e+u));let m=g+f*h,w=r;if(s=p/m,o=g/m,r=(p+f*r)/m,h=1,Math.abs(r-w)<3e-7*Math.abs(r))return r}}function Cv(e){if(0==e||1==e)return 1;return e*Cv(e-1)}function _v(e){let t;var i=[75122.633153,80916.6278952,36308.2951477,8687.24529705,1168.92649479,83.8676043424,2.50662827511],n=0,r=1;if(0==e)t=1e99;else if(e%1==0)t=Cv(e-1);else{for(let t=0;t<i.length;t++)n+=i[t]*Math.pow(e,t),r*=e+t;t=n*Math.pow(e+5.5,e+.5)*Math.exp(-(e+5.5))/r}return t}function xv(e){return Math.log(_v(e))}var kv={TdistributionCDF:vv,gamma:_v,t_test_1_sample:function(e,t,i,n){0==i&&(i=1);var r=(e-t)/i*Math.sqrt(n);return 1-vv(Math.abs(r),n-1)},t_test_2_samples:function(e,t,i,n,r,s){0==t&&(t=1),0==r&&(r=1);var o=(e-n)/Math.sqrt(t**2/i+r**2/s),a=(t**2/i+r**2/s)**2*(i-1)*(s-1)/(t**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-vv(Math.abs(o),parseInt(a+.5))}};function Iv(e){return e.reduce((function(e,t){return e>t?e:t}))}function Sv(e,t,i,n){return t*Math.exp(-1*(e-i)**2/(2*n**2))/Math.sqrt(2*Math.PI)/n}function Ev(e,t,i,n){return Math.exp(-1*(e-i)**2/(t**2+n**2))}function Nv(e,t){let i;try{i=e.reduce(((e,i,n)=>e+Math.min(i,t[n])))}catch{return console.log(\"Failed to find likelihood overlap: \",e,t),0}return i}function Bv(e,t,i,n){return 0==t&&0==n?{nl:.5*(e+i),ne:0}:{nl:(e*n*n+i*t*t)/(t*t+n*n),ne:Math.sqrt(t*t*n*n/(t*t+n*n))}}function Mv(e,t){let i=parseInt(t*(e.length-1)),n=t*(e.length-1)-i;return i<e.length-1?e[i]*(1-n)+e[i+1]*n:e[i]}function Rv(e){const t=e.length,i=Math.max(...e);let n=e.indexOf(i);n>Math.floor(t/2)&&(n=t-1-n);const r=(t/2-n)/(t+1),s=Math.floor((t/2+n)/2),o=t-1-s;let a=e.slice(s,o+1).reduce(((e,t)=>e+t),0)/e.reduce(((e,t)=>e+t),0);return n===Math.floor(t/2)&&(a=1),{mean:r,p:a}}var Dv=class{constructor(e,t){this.wigFeatures=e,this.binSize=t}get_fit(){var e=new Fv.GetFit(this.wigFeatures),[t,i]=e.fit_data();return{globalMean:t,globalStd:i}}async call_2d(e=null,t=null,i=\"both\",n=.1,r=0,s=10,o=0){let a=this.get_fit();this.globalMean=a.globalMean,this.globalStd=a.globalStd;let c=null==e?.05*this.binSize/3e9:e,l=null==t?parseInt(this.binSize/1e4):t,h=[],d=[],u=[],f=[],p=[],g=[];for(const[e,t]of Object.entries(this.wigFeatures)){let e=[],i=[],s=[];t.forEach(((t,n)=>{t.hets_count>4&&t.dp_count>l&&(e.push([n]),i.push(t.binScore),s.push(t.likelihood_score),delete t.likelihood_score)}));let o=[];for(let e=1;e<i.length;e++)o.push(Math.abs(i[e]-i[e-1]));let a=[0];for(let e=1;e<o.length;e++)a.push(Math.min(o[e-1],o[e]));a.push(0);let g=i.map(((e,t)=>Math.sqrt(Math.sqrt(e)**2+this.globalStd**2+Math.pow(a[t]/2,2)))),m=[];for(let t=0;t<e.length-1;t++){let n=0;try{n=Nv(s[t],s[t+1])}catch{console.log(\"Overlap failed: \",t,s[t],e[t+1],s[t+1])}let r=Ev(i[t],g[t],i[t+1],g[t+1]);m.push(r*n)}for(;m.length>0;){m=m.filter((e=>\"number\"==typeof e));let t=Iv(m);if(isNaN(t)&&console.log(\"NaN value\",m),t<c)break;let n,r,o=m.indexOf(t),a=Bv(i[o],g[o],i[o+1],g[o+1]);try{n=s[o].map(((e,t)=>e*s[o+1][t])),r=n.reduce(((e,t)=>e+t))}catch{console.log(s),console.log(\"max_overlap:\",t,o,m.length),console.log(\"likelihood: \",o,s[o],s[o+1]),console.log(\"nlh: \",r)}if(i[o]=a.nl,g[o]=a.ne,s[o]=n.map((function(e){return e/r})),e[o].push(...e[o+1]),i.splice(o+1,1),g.splice(o+1,1),e.splice(o+1,1),s.splice(o+1,1),m.splice(o,1),o<m.length){let e=Ev(i[o],g[o],i[o+1],g[o+1])*Nv(s[o],s[o+1]);m[o]=e}if(o>0){let e=Ev(i[o-1],g[o-1],i[o],g[o])*Nv(s[o-1],s[o]);m[o-1]=e}}let w=-1;for(;;){m=[];for(let t=0;t<i.length;t++)for(let r=t;r<i.length;r++)e[r][0]-e[t].at(-1)<n*(e[t].length+e[r].length)&&m.push(Ev(i[t],g[t],i[r],g[r])*Nv(s[t],s[r]));if(0==m.length)break;let t=Iv(m);if(t<c)break;let r=0,o=1;for(;r<e.length-1;){let a=Ev(i[r],g[r],i[o],g[o])*Nv(s[r],s[o]);if(e[o][0]-e[r].at(-1)<n*(e[r].length+e[o].length)&&a==t){let t=Bv(i[r],g[r],i[r+1],g[r+1]);i[r]=t.nl,g[r]=t.ne;let n=s[r].map(((e,t)=>e*s[r+1][t])),a=n.reduce(((e,t)=>e+t));s[r]=n.map((function(e){return e/a})),e[r].push(...e[r+1]),e[r]=e[r].sort(((e,t)=>e-t)),i.splice(o,1),g.splice(o,1),e.splice(o,1),s.splice(o,1),o>=e.length&&(r+=1,o=r+1)}else o+=1,o>=e.length&&(r+=1,o=r+1)}if(w==e.length)break;w=e.length}e.forEach(((e,n)=>{let o=Rv(s[n]);e.length>1&&(e.forEach(((e,s)=>{d.push(t[e]),o.mean<=r&&h.push(t[e]),t[e].segment_score=i[n]})),u.push(i[n]),f.push(g[n]),p.push(s[n]))}))}let m=parseInt(1e3*(1-o));0==m&&(m=1);let w=Fv.linspace(o,1,m),b={},F={};for(let e=10;e>-1;e--)for(let t=0;t<e/2+1;t++){let n,r,s=e-t,o=w.map(((t,i)=>1-t+t*e/2)),a=e/2;e>0?(n=.5-t/(t+s),r=w.map(((e,i)=>.5-(1-e+e*t)/(2-2*e+(t+s)*e)))):(n=0,r=w.map(((e,t)=>0*e)));for(let i=0;i<u.length;i++){let c=Sv(a*this.globalMean,1,u[i],f[i])*Mv(p[i],.5+n);i in F?F[i].push([e,t,s,c,1]):F[i]=[e,t,s,c,1];let l=0,h=0,d=0;o.forEach(((e,t)=>{if(!isNaN(r[t])){let n=Sv(e*this.globalMean,1,u[i],f[i])*Mv(p[i],.5+r[t]);l+=n,n>h&&(h=n,d=w[t])}})),i in b?b[i].push([e,t,s,l/w.length,d]):b[i]=[e,t,s,l/w.length,d]}for(let e=0;e<u.length;e++)if(\"germline\"==i)b[e].sort(((e,t)=>e[3]-t[3]));else if(b[e].sort(((e,t)=>e[3]-t[3])),\"both\"==i&&(F[e].sort(((e,t)=>e[3]-t[3])),F[e][0][3]>b[e][0][3])){let t=b[e].filter((t=>t[0]!=F[e][0][0]&&t[1]<=F[e][0][1]));b[e]=[F[e][0]].push(...t)}for(let e=0;e<u.length;e++)b[e][0][0],b[e][0][0],u[e],this.globalMean,kv.t_test_1_sample(this.globalMean,u[e],f[e],g[e])}return{binScore:this.formatDataStructure(this.wigFeatures,\"binScore\",this.globalMean),segment_score:this.formatDataStructure(this.wigFeatures,\"segment_score\",this.globalMean)}}formatDataStructure(e,t,i=1){const n=[];for(const[r,s]of Object.entries(e))s.forEach((e=>{var r={...e};1!=i&&(r.value=e[t]/i*2),n.push(r)}));return n}formatDataStructure_BAF(e,t=-1){const i=[],n=[];for(const[r,s]of Object.entries(this.wigFeatures))s.forEach((r=>{var s={...r},o={...r};let a=r[e];.5!=a&&(o.value=t*(1-a),n.push(o)),s.value=t*a,i.push(s)}));return[i,n]}};const Tv=2871e6;function Lv(e){for(var t=1,i=1,n=1*e,r=1;r<50;r++)t*=r,n+=(i*=-1)*Math.pow(e,2*r+1)/(t*(2*r+1));return 2*n/Math.sqrt(3.14159265358979)}function zv(e,t,i,n,r){var s=new Ov(i.slice(n,r));return 0==s.std&&(s.std=t>0?t*s.mean/e:1),Uv(e,s.mean,s.std,r-n)/(r-n)}function Hv(e,t,i,n,r){var s=new Ov(i.slice(n,r));if(s.mean<e){var o=(s.max-s.mean)/(t*Math.sqrt(2));return Math.pow(.5*(1+Lv(o)),r-n)}o=(s.min-s.mean)/(t*Math.sqrt(2));return Math.pow(.5*(1-Lv(o)),r-n)}function Pv(e,t,i,n,r,s,o=1e3){for(var a=zv(e,t,i,n,r),c=0,l=!1;a>s&!l&c<o;){l=!0,c+=1;var[h,d,u,f]=[1e10,1e10,1e10,1e10];if(n>0&&(h=zv(e,t,i,n-1,r)),r-n>2)var d=zv(e,t,i,n+1,r),u=zv(e,t,i,n,r-1);if(r<i.length)var f=zv(e,t,i,n,r+1);Math.min[f]<a&&(l=!1,h==Math.min[f]&&(n-=1,a=h),elif(d==Math.min[f]),n+=1,a=d,elif(u==Math.min[f]),r-=1,a=u,elif(f==Math.min[f]),r+=1,a=f)}return a<=s?r:0}class Ov{constructor(e){this.data=e,this.mean=e.reduce(((e,t)=>e+t))/e.length,this.std=Math.sqrt(e.reduce(((e,t)=>(t-this.mean)**2))/e.length)}}function Uv(e,t,i,n){0==i&&(i=1);var r=(e-t)/i*Math.sqrt(n);return 1-kv.TdistributionCDF(Math.abs(r),n-1)}function qv(e,t,i,n,r,s){0==t&&(t=1),0==r&&(r=1);var o=(e-n)/Math.sqrt(t**2/i+r**2/s),a=(t**2/i+r**2/s)**2*(i-1)*(s-1)/(t**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-kv.TdistributionCDF(Math.abs(o),parseInt(a+.5))}var Qv=class{constructor(e,t,i){this.rd=e,this.mean=t,this.std=i,this.bin_bands=[2,3,4,5,6,7,8,10,12,14,16,20,24,28,32,40,48,56,64,80,96,112,128]}get_rd_signal_bandwidth(e){var t=[];return e.forEach(((e,i)=>{var n=0;n=e>this.mean/4?this.mean/(this.std**2*e):4/this.std**2,t.push(n)})),t}meanShiftCaller(e,t=3){var i={};return Object.entries(this.rd).forEach((([e,n])=>{var r=new Array(n.length).fill(!1),s=new Array(n.length);for(let e=0;e<n.length;e++)r[e]||(s[e]=n[e]);this.bin_bands.forEach(((e,i)=>{var o=r.map(((e,t)=>!e)),a=[];Object.entries(n).forEach((([e,t])=>{a.push(t.binScore)}));var c=[0],l=0;for(let e=0;e<r.length;e++)r[e]?l>0&&(c.push(c[c.length-1]+l-1),l=0):l+=1;c.shift();for(let i=0;i<t;i++){var h=this.get_rd_signal_bandwidth(a),d=new Array(a.length).fill(0);for(let t=0;t<a.length;t++)for(let i=t-3*e;i<=t+3*e+1;i++)if(!(i<0||i>=a.length||Math.abs(t-i)>=a.length)){var u=(i-t)*Math.exp(-.5*(i-t)**2/e**2)*Math.exp(-.5*(a[t]-a[i])**2*h[t]);d[t]+=u}for(var f=new Array,p=0;p<d.length-1;p++)d[p]<0&d[p+1]>=0&&f.push(p);f.push(d.length-1),f=f.concat(c).sort(((e,t)=>e-t)),f=Array.from(new Set(f));var g=0;for(p=0;p<f.length;p++){var m=a.slice(g,f[p]+1),w=m.reduce(((e,t)=>e+t))/m.length;a.fill(w,g,f[p]+1),g=f[p]+1}}p=0;for(var b=0;p<s.length;p++)o[p]&&(s[p]=a[b],b++);for(f=new Array,p=0;p<s.length-1;p++){Math.abs(s[p+1]-s[p])>.01&&f.push(p+1)}f.unshift(0),f.push(s.length),r=new Array(this.rd.length).fill(!1);for(p=1;p<f.length;p++){var F=[f[p-1],f[p]],v=[f[p-1],f[p-1]];if(!(p>1))continue;v[0]=f[p-2];var y=[f[p],f[p]];if(!(p<f.length-1))continue;y[1]=f[p+1];var A=F[1]-F[0],C=v[1]-v[0],_=y[1]-y[0];if(A<=1)continue;var x=new Ov(s.slice(F[0],F[1]));if(_<=15||C<=15||A<=15){var k=1.8*Math.sqrt(s[v[0]]/this.mean)*this.std;if(Math.abs(s[v[0]]-s[F[0]])<k)continue;if(k=1.8*Math.sqrt(s[y[0]]/this.mean)*this.std,Math.abs(s[y[0]]-s[F[0]])<k)continue}else{var I=s.slice(v[0],v[1]),S=new Ov(I),E=s.slice(y[0],y[1]),N=new Ov(E);if(qv(x.mean,x.std,x.data.length,S.mean,S.std,S.data.length)>.01/Tv*bin_size*(A+C))continue;if(qv(x.mean,x.std,x.data.length,N.mean,N.std,N.data.length)>.01/Tv*bin_size*(A+_))continue}if(Uv(this.mean,x.mean,x.std,x.data.length)>.05)continue;let e=a.slice(F[0],F[1]);var B=new Ov(e);r.fill(!0,F[0],F[1]),s.fill(B.mean,F[0],F[1])}})),i[e]=s})),i}call_mean_shift(e=3){for(var t=new Array(this.rd.length).fill(!1),i=new Array(this.rd.length),n=0;n<this.rd.length;n++)t[n]||(i[n]=this.rd[n]);return this.bin_bands.forEach(((n,r)=>{var s=t.map(((e,t)=>!e)),o=[];s.forEach(((e,t)=>{e&&o.push(this.rd[t])}));for(var a=[0],c=0,l=0;l<t.length;l++)t[l]?c>0&&(a.push(a[a.length-1]+c-1),c=0):c+=1;a.shift();for(var h=0;h<e;h++){var d=this.get_rd_signal_bandwidth(o),u=new Array(o.length).fill(0);for(l=0;l<o.length;l++)for(var f=l-3*n;f<=l+3*n+1;f++)if(!(f<0||f>=o.length||Math.abs(l-f)>=o.length)){var p=(f-l)*Math.exp(-.5*(f-l)**2/n**2)*Math.exp(-.5*(o[l]-o[f])**2*d[l]);u[l]+=p}var g=new Array;for(l=0;l<u.length-1;l++)u[l]<0&u[l+1]>=0&&g.push(l);g.push(u.length-1),g=g.concat(a).sort(((e,t)=>e-t)),g=Array.from(new Set(g));var m=0;for(l=0;l<g.length;l++){var w=o.slice(m,g[l]+1),b=w.reduce(((e,t)=>e+t))/w.length;o.fill(b,m,g[l]+1),m=g[l]+1}}for(l=0,f=0;l<i.length;l++)s[l]&&(i[l]=o[f],f++);for(g=new Array,l=0;l<i.length-1;l++){Math.abs(i[l+1]-i[l])>.01&&g.push(l+1)}g.unshift(0),g.push(i.length),t=new Array(this.rd.length).fill(!1);for(l=1;l<g.length;l++){var F=[g[l-1],g[l]],v=[g[l-1],g[l-1]];if(l>1){v[0]=g[l-2];var y=[g[l],g[l]];if(l<g.length-1){y[1]=g[l+1];var A=F[1]-F[0],C=v[1]-v[0],_=y[1]-y[0];if(!(A<=1)){var x=new Ov(i.slice(F[0],F[1]));if(_<=15||C<=15||A<=15){var k=1.8*Math.sqrt(i[v[0]]/this.mean)*this.std;if(Math.abs(i[v[0]]-i[F[0]])<k)continue;if(k=1.8*Math.sqrt(i[y[0]]/this.mean)*this.std,Math.abs(i[y[0]]-i[F[0]])<k)continue}else{var I=i.slice(v[0],v[1]),S=new Ov(I),E=i.slice(y[0],y[1]),N=new Ov(E);if(qv(x.mean,x.std,x.data.length,S.mean,S.std,S.data.length)>3.483106931382794e-9*(A+C))continue;if(qv(x.mean,x.std,x.data.length,N.mean,N.std,N.data.length)>3.483106931382794e-9*(A+_))continue}if(!(Uv(this.mean,x.mean,x.std,x.data.length)>.05)){var B=new Ov(this.rd.slice(F[0],F[1]));t.fill(!0,F[0],F[1]),i.fill(B.mean,F[0],F[1])}}}}}})),i}cnv_calling(e=1e5){var t=.25*this.mean,i=this.mean-t,n=this.mean+t,r=2971e6,s=this.meanShiftCaller(e),o={},a=[];return Object.entries(s).forEach((([c,l])=>{for(var h=!1;!h;){h=!0;var d=new Array(1).fill(0);for(let e=0;e<l.length-1;e++){Math.abs(l[e+1]-l[e])>.01&&d.push(e+1)}d.push(l.length);for(let e=0;e<d.length-2;e++){var u=Math.abs(l[d[e]]-l[d[e+1]]);if(u<t){var f=u+1,p=u+1;if(e>0&&(f=Math.abs(l[d[e]]-l[d[e-1]])),e<d.length-3&&(p=Math.abs(s[d[e+1]]-l[d[e+2]])),u<f&&u<p){h=!1;var g=new Ov(l.slice(d[e],d[e+2]));l.fill(g.mean,d[e],d[e+2]),d.splice(e+1,e+1)}}}}var m=[];Object.entries(this.rd[c]).forEach((([e,t])=>{m.push(t.binScore)}));for(var w,b=new Array(l.length).fill(\"\"),F=0,v=.05*e/r;F<l.length;){for(var y=F,A=F;F<l.length&l[F]<i;)F+=1;if((_=F)>A+1){var C=Pv(this.mean,this.std,m,A,_,v);if(C){var _=C;b.fill(\"D\",A,_)}}for(A=F;F<l.length&l[F]>n;)F+=1;(_=F)>A+1&&(C=Pv(this.mean,this.std,m,A,_,v))&&(_=C,b.fill(\"A\",A,_)),F==y&&(F+=1)}for(F=0;F<l.length;){for(;F<l.length&\"\"!=b[F];)F+=1;for(A=F;F<l.length&l[F]<i;)F+=1;(_=F)>A+1&&(Hv(this.mean,this.std,m,A,_)<1682935038707506e-26&&b.fill([\"d\"]*(_-A),A,_),F-=1),F+=1}(F=0)<l.length&&(w=b[F]),A=0;for(var x=[...m];F<l.length;){for(;b[F]==w&&!((F+=1)>=b.length););if(F>A){var k=new Ov(x.slice(A,F));x.fill(k.mean,A,F)}F<l.length&&(w=b[F]),A=F}for(o[c]=x,F=0;F<l.length;){if(\"\"==(w=b[F])){F+=1;continue}for(A=F;F<l.length&w==b[F];)F+=1;let t,i=new Ov(x.slice(A,F)).mean/this.mean;t=\"D\"==w?\"deletion\":\"duplication\";let n={chr:c,start:e*A+1,end:e*F,size:e*(F-A+1),value:2*i,event_type:t};a.push(n)}})),[o,a]}};class Vv{constructor(e,t){this.allVariants=e,this.rowBinSize=1e4,this.binSize=t,this.binFactor=parseInt(t/this.rowBinSize)}async read_rd_baf(e=\"ReadDepth\"){var t={};for(let e=this.allVariants.length-1;e>=0;e--){var i;let n=this.allVariants[e];this.allVariants.splice(e,1);let r=n.chr;i=Math.max(Math.floor(n.start/this.rowBinSize),0),t[r]||(t[r]=[]),t[r][i]||(t[r][i]={chr:r,start:i*this.rowBinSize,end:(i+1)*this.rowBinSize,dp_sum_score:0,dp_count:0,hets_count:0,hets:[]});const s=Object.values(n.calls);if(1!==s.length)throw Error(`Unexpected number of genotypes: ${s.length}.  CNVPytor expects 1 and only 1 genotype`);const o=s[0],a=o.info.DP;a&&(t[r][i].dp_sum_score+=Number.parseInt(a),t[r][i].dp_count++);let c=o.info.AD.split(\",\"),l=o.genotype;if(0==l[0]&&1==l[1]||1==l[0]&&0==l[1]){t[r][i].hets_count++;let e=parseInt(c[0]),n=parseInt(c[1]);t[r][i].hets.push({ref:e,alt:n})}}this.chromosomes=Object.keys(t);var n,r=this.adjust_bin_size(t);if(\"ReadDepth\"==e){n=new Wv(r,this.binSize).ReadDepth_caller();var s=this.formatDataStructure_BAF(r,\"max_likelihood\")}else if(\"2D\"==e){let e=new Dv(r,this.binSize),t=await e.call_2d();n=[t.binScore,[],t.segment_score];s=e.formatDataStructure_BAF(\"max_likelihood\",-1)}return[n,s]}formatDataStructure(e,t,i=1){const n=[];for(const[s,o]of Object.entries(e))for(let e of o){var r={...e};1!=i&&(r.value=e[t]/i*2),n.push(r)}return n}format_BAF_likelihood(e){const t=[];for(const[n,r]of Object.entries(e))for(let e of r){var i={...e};.5!=e.value&&(i.value=1-e.value,t.push(i))}return t}get_max_min_score(e){if(e.likelihood_score.length>0){const t=Math.max(...e.likelihood_score),i=e.likelihood_score.indexOf(t);e.value=Math.max(i/100,1-i/100),e.min_score=Math.min(i/100,1-i/100)}else e.score=0;return e}async getAllbins(){const e=await this.computeDepthFeatures();return new Fv.GetFit(e).fit_data(),e}formatDataStructure_BAF(e,t,i=-1){const n=[],r=[];for(const[a,c]of Object.entries(e))for(let e of c){var s={...e},o={...e};let a=e[t];.5!=a&&(o.value=i*(1-a),r.push(o)),s.value=i*a,n.push(s)}return[n,r]}adjust_bin_size(e){var t={};for(let r of this.chromosomes){t[r]||(t[r]=[]);for(let s=0;s<e[r].length/this.binFactor;s++){const o=s;t[r][s]||(t[r][s]={chr:r,start:o*this.binSize,end:(o+1)*this.binSize,dp_count:0,hets_count:0,binScore:0,likelihood_score:[],dp_sum_score:0});for(var i=s*this.binFactor;i<this.binFactor*s+this.binFactor;i++)if(e[r][i]&&(t[r][s].dp_sum_score+=e[r][i].dp_sum_score,t[r][s].dp_count+=e[r][i].dp_count,t[r][s].hets_count+=e[r][i].hets_count,0!=e[r][i].hets.length))for(let o of e[r][i].hets)if(0==t[r][s].likelihood_score.length)t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,t)=>jv(o.ref,o.alt,e)));else{var n=0;t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,i)=>{var a=t[r][s].likelihood_score[i]*jv(o.ref,o.alt,e);return n+=a,a})),t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,i)=>t[r][s].likelihood_score[i]/n))}t[r][s].binScore=100*parseInt(t[r][s].dp_sum_score/t[r][s].dp_count);const a=this.get_max_min_score(t[r][s]);t[r][s].max_likelihood=a.value}}return t}}function jv(e,t,i,n=!0){return Math.pow(i,e)*Math.pow(1-i,t)+Math.pow(i,t)*Math.pow(1-i,e)}class Wv{constructor(e,t){this.wigFeatures=e,this.binSize=t}ReadDepth_caller(){var e=new Fv.GetFit(this.wigFeatures),[t,i]=e.fit_data(),n=new Qv(this.wigFeatures,t,i),r=n.meanShiftCaller(this.binSize),s=n.cnv_calling();return Object.entries(this.wigFeatures).forEach((([e,t])=>{t.forEach(((t,i)=>{t.partition_level=parseInt(r[e][i]),t.partition_call=parseInt(s[0][e][i])}))})),[this.formatDataStructure(\"binScore\",t),this.formatDataStructure(\"partition_level\",t),this.formatDataStructure(\"partition_call\",t),s[1]]}formatDataStructure(e,t=1){const i=[];for(const[r,s]of Object.entries(this.wigFeatures))for(let r of s){var n={...r};1!=t&&(n.value=r[e]/t*2),i.push(n)}return i}}class Gv extends Hl{static DEFAULT_TRACK_HEIGHT=250;constructor(e,t){super(e,t)}init(e){this.featureType=\"numeric\",this.type=\"cnvpytor\",e.max||(this.defaultScale=!0,this.autoscale=!1),e.height||(e.height=Gv.DEFAULT_TRACK_HEIGHT),this.type=\"cnvpytor\",this.graphType=e.graphType||\"points\",this.bin_size=e.bin_size||1e5,this.signal_name=e.signal_name||\"rd_snp\",this.cnv_caller=e.cnv_caller||\"2D\",this.colors=e.colors||[\"gray\",\"black\",\"green\",\"blue\"],super.init(e)}get supportsWholeGenome(){return!0}get_signals(){let e=[];return\"rd_snp\"==this.signal_name?e=[\"RD_Raw\",\"RD_Raw_gc_coor\",this.cnv_caller,\"BAF1\",\"BAF2\"]:\"rd\"==this.signal_name?e=[\"RD_Raw\",\"RD_Raw_gc_coor\",this.cnv_caller]:\"snp\"==this.signal_name?e=[\"BAF1\",\"BAF2\"]:\"cnh\"==this.signal_name&&(e=[this.cnv_caller]),e}get_signal_colors(){return[{singal_name:\"RD_Raw\",color:this.colors[0]},{singal_name:\"RD_Raw_gc_coor\",color:this.colors[1]},{singal_name:\"ReadDepth\",color:this.colors[2]},{singal_name:\"2D\",color:this.colors[2]},{singal_name:\"BAF1\",color:this.colors[3]},{singal_name:\"BAF2\",color:this.colors[3]}]}async postInit(){if(\"vcf\"==this.config.format){let e;this.featureSource?e=Object.values(this.featureSource.getAllFeatures()).flat():(this.featureSource=this.featureSource||Ad(this.config,this.browser.genome),this.header=await this.getHeader(),e=this.featureSource.reader.features);const t=new Vv(e,this.bin_size);let i,n,r;this.wigFeatures_obj={},this.wigFeatures_obj[this.bin_size]={},\"2D\"==this.cnv_caller?(r=await t.read_rd_baf(\"2D\"),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size][\"2D\"]=i[2],this.available_callers=[\"2D\"]):(r=await t.read_rd_baf(),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size].ReadDepth=i[2],this.available_callers=[\"ReadDepth\"]),this.wigFeatures_obj[this.bin_size].RD_Raw=i[0],this.wigFeatures_obj[this.bin_size].RD_Raw_gc_coor=i[1],this.wigFeatures_obj[this.bin_size].BAF1=n[0],this.wigFeatures_obj[this.bin_size].BAF2=n[1],this.available_bins=[this.bin_size],this.set_available_callers()}else this.cnvpytor_obj=new mv(this.config.url,this.bin_size),this.wigFeatures_obj=await this.cnvpytor_obj.get_rd_signal(this.bin_size),this.available_bins=this.cnvpytor_obj.available_bins,this.available_callers=this.cnvpytor_obj.callers,this.set_available_callers();this.tracks=[];const e=[];this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(let t in this.wigFeatures_obj)for(const[i,n]of Object.entries(this.wigFeatures_obj[t]))if(this.signals.includes(i)){let t={type:\"wig\"};t.features=n,t.name=i,t.color=this.signal_colors.filter((e=>e.singal_name===i)).map((e=>e.color));const r=await this.browser.createTrack(t);r?(r.isMergedTrack=!0,r.autoscale=!1,this.tracks.push(r)):console.warn(\"Could not create track \"+t),\"function\"==typeof r.postInit&&e.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let e of this.tracks)e.autoscale=!1,e.dataRange=this.dataRange;return Promise.all(e)}set_available_callers(){this.available_callers.includes(this.cnv_caller)||(this.available_callers.length>0?this.cnv_caller=this.available_callers[0]:this.cnv_caller=null)}async getHeader(){if(!this.header){if(\"function\"==typeof this.featureSource.getHeader){const e=await this.featureSource.getHeader();e&&(this.callSets=e.callSets||[]),this.header=e}this.sampleKeys=this.callSets?this.callSets.map((e=>e.sample)):[],this.sampleNames=this.sampleKeys}return this.header}get height(){return this._height}set height(e){if(this._height=e,this.tracks)for(let t of this.tracks)t.height=e,t.config.height=e}menuItemList(){let e=[];void 0!==this.flipAxis&&e.push({label:\"Flip y-axis\",click:function(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),e=e.concat(this.numericDataMenuItems()),e.push(\"<hr/>\"),e.push(\"Bin Sizes\");for(let t of this.available_bins){const i=Dl(t,t===this.bin_size);e.push({object:Bt(i),click:async function(){this.bin_size=t,this.trackView.startSpinner(),await this.recreate_tracks(t),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}e.push(\"<hr/>\"),e.push(\"Signal Type\");let t={rd_snp:\"RD and BAF Likelihood\",rd:\"RD Signal\",snp:\"BAF Likelihood\"};for(let i in t){const n=Dl(t[i],i===this.signal_name);e.push({object:Bt(n),click:async function(){this.signal_name=i,await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}e.push(\"<hr/>\"),e.push(\"CNV caller\");for(let t of this.available_callers){const i=Dl(t,t===this.cnv_caller);e.push({object:Bt(i),click:async function(){this.cnv_caller=t,this.trackView.startSpinner(),await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}if(this.variantState){e.push(\"<hr/>\");for(let t of this.available_callers)e.push({label:\"Convert to variant track\",click:()=>{this.convertToVariant()}})}return e}async recreate_tracks(e){this.tracks=[];const t=[];e in this.wigFeatures_obj||(this.wigFeatures_obj={...this.wigFeatures_obj,...await this.cnvpytor_obj.get_rd_signal(e)}),this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(const[i,n]of Object.entries(this.wigFeatures_obj[e]))if(this.signals.includes(i)){let e={type:\"wig\"};e.features=n,e.name=i,e.color=this.signal_colors.filter((e=>e.singal_name===i)).map((e=>e.color));const r=await this.browser.createTrack(e);r?(r.isMergedTrack=!0,r.autoscale=!1,this.tracks.push(r)):console.warn(\"Could not create track \"+e),\"function\"==typeof r.postInit&&t.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let e of this.tracks)e.autoscale=!1,e.dataRange=this.dataRange;return Promise.all(t)}async getFeatures(e,t,i,n){if(this.tracks){const r=this.tracks.map((r=>r.getFeatures(e,t,i,n)));return Promise.all(r)}}getScaleFactor(e,t,i,n){return n?i/(Math.log10(t+1)-(e<=0?0:Math.log10(e+1))):i/(t-e)}computeYPixelValue(e,t){return(this.flipAxis?e-this.dataRange.min:this.dataRange.max-e)*t}computeYPixelValueInLogScale(e,t){let i=this.dataRange.max,n=this.dataRange.min;return i<=0?0:(n<=-1&&(n=0),n=n<=0?0:Math.log10(n+1),i=Math.log10(i+1),e=Math.log10(e+1),(this.flipAxis?e-n:i-e)*t)}draw(e){const t=e.features;if(!t)return;if(this.defaultScale&&(\"rd_snp\"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||-1,max:this.config.max||this.dataRange.max||5}:\"rd\"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||0,max:this.config.max||this.dataRange.max||5}:\"snp\"==this.signal_name&&(this.dataRange={min:this.config.min||this.dataRange.min||-1,max:this.config.max||this.dataRange.max||0})),this.autoscale&&(this.dataRange=function(e,t){let i=0,n=-Number.MAX_VALUE;for(let e of t)for(let t of e)void 0===t.value||Number.isNaN(t.value)||(i=Math.min(i,t.value),n=Math.max(n,t.value));return{min:i,max:n}}(e.referenceFrame.chr,t)),this.tracks)for(let i=0,n=this.tracks.length;i<n;i++){const n=Object.assign({},e);n.features=t[i],this.tracks[i].dataRange=this.dataRange,this.tracks[i].flipAxis=this.flipAxis,this.tracks[i].logScale=this.logScale,this.graphType&&(this.tracks[i].graphType=this.graphType),this.tracks[i].draw(n)}const i=this.getScaleFactor(this.dataRange.min,this.dataRange.max,e.pixelHeight,this.logScale),n=e=>this.logScale?this.computeYPixelValueInLogScale(e,i):this.computeYPixelValue(e,i);if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=n(t.y),r={strokeStyle:t.color,strokeWidth:1};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,r):xo.strokeLine(e.context,0,i,e.pixelWidth,i,r)}let r=n(2);xo.dashedLine(e.context,0,r,e.pixelWidth,r,5,{strokeStyle:\"lightgray\",strokeWidth:.5})}paintAxis(e,t,i){var n,r,s,o,a,c,l,h={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};if(void 0===this.dataRange||void 0===this.dataRange.max||void 0===this.dataRange.min)return;let d=void 0!==this.flipAxis&&this.flipAxis;function u(e){return e<0?Math.abs(e):0===e?\"0\":Math.abs(e)>=10||e%1==0?e.toFixed():Math.abs(e)>=1?e.toFixed(1):e.toFixed(2)}xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"}),n=(l=.95*t)-8,a={x:r=l,y:s=o=.01*i},xo.strokeLine(e,n,s,r,o,h),xo.fillText(e,u(d?this.dataRange.min:this.dataRange.max),n+4,s+12,h),c={x:r,y:s=o=.99*i},xo.strokeLine(e,n,s,r,o,h),xo.fillText(e,u(d?this.dataRange.max:this.dataRange.min),n+4,s-4,h),xo.strokeLine(e,a.x,a.y,c.x,c.y,h);const f=this.getScaleFactor(this.dataRange.min,this.dataRange.max,i,this.logScale),p=e=>this.logScale?this.computeYPixelValueInLogScale(e,f):this.computeYPixelValue(e,f),g=Math.ceil((this.dataRange.max-this.dataRange.min)/10);for(let t=Math.ceil(this.dataRange.min+1);t<Math.round(this.dataRange.max-.4);t+=g){const i=p(t);xo.strokeLine(e,45,i,50,i,h),xo.fillText(e,u(d?this.dataRange.max-t:t),44,i+4,h)}}popupData(e,t){const i=t||e.viewport.cachedFeatures;if(i&&i.length===this.tracks.length){const t=[];for(let n=0;n<this.tracks.length;n++){n>0&&t.push(\"<hr/>\"),t.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${this.tracks[n].name}</div>`);const r=this.tracks[n].popupData(e,i[n]);t.push(...r)}return t}}async convertToVariant(){this.variantState&&(Object.setPrototypeOf(this,Yv.prototype),this.init(this.variantState),await this.postInit(),this.trackView.clearCachedFeatures(),this.variantState.trackHeight&&this.trackView.setTrackHeight(this.variantState.trackHeight),this.trackView.checkContentHeight(),this.trackView.updateViews(),delete this.variantState)}}const $v=Mt,Kv=10;class Yv extends Hl{static defaults={displayMode:\"EXPANDED\",sortDirection:\"ASC\",showGenotypes:!0,expandedVariantHeight:10,squishedVariantHeight:2,squishedCallHeight:1,expandedCallHeight:10,expandedVGap:2,squishedVGap:1,expandedGroupGap:10,squishedGroupGap:5,featureHeight:14,noGenotypeColor:\"rgb(200,180,180)\",noCallColor:\"rgb(225, 225, 225)\",nonRefColor:\"rgb(200, 200, 215)\",mixedColor:\"rgb(200, 220, 200)\",homrefColor:\"rgb(200, 200, 200)\",homvarColor:\"rgb(17,248,254)\",hetvarColor:\"rgb(34,12,253)\",refColor:\"rgb(0,0,220)\",altColor:\"rgb(255,0,0)\",visibilityWindow:void 0,labelDisplayMode:void 0,type:\"variant\"};_sortDirections=new Map;constructor(e,t){super(e,t)}init(e){if(super.init(e),e.variantHeight&&(this.expandedVariantHeight=e.variantHeight),this.featureSource=Ad(e,this.browser.genome),this.colorTables=new Map,e.colorTable){const t=e.colorBy||\"*\";this.colorTables.set(t,new ao(e.colorTable))}if(this.strokecolor=e.strokecolor,this._context_hook=e.context_hook,e.color&&(this.colorBy=void 0),this.nVariantRows=1,e.samples)for(let t of e.samples)this.sampleKeys=e.samples;e.sort&&(this.initialSort=e.sort),this._colorByItems=new Map([[\"none\",\"None\"]])}async postInit(){if(this.header=await this.getHeader(),this.header.INFO){const e=new Set(Object.keys(this.header.INFO));this.config.colorBy?this.colorBy=this.config.colorBy:!this.config.color&&e.has(\"AF\")&&(this.colorBy=\"AF\"),e.has(\"AF\")&&this._colorByItems.set(\"AF\",\"Allele frequency\"),e.has(\"VT\")&&this._colorByItems.set(\"VT\",\"Variant Type\"),e.has(\"SVTYPE\")&&this._colorByItems.set(\"SVTYPE\",\"SV Type\")}if(this.config.colorBy&&!this._colorByItems.has(this.config.colorBy)&&this._colorByItems.set(this.config.colorBy,this.config.colorBy),!this.disposed){if(this.header&&!this.sampleKeys&&(this.sampleKeys=this.header.sampleNameMap?Array.from(this.header.sampleNameMap.keys()):[]),void 0===this.visibilityWindow&&!1!==this.config.indexed){const e=Ht(this.config.url)?this.config.url.name:this.config.url;$v(e)&&e.toLowerCase().includes(\"gnomad\")?this.visibilityWindow=1e3:\"function\"==typeof this.featureSource.defaultVisibilityWindow?this.visibilityWindow=await this.featureSource.defaultVisibilityWindow():this.visibilityWindow=1e6}return this}}get supportsWholeGenome(){return!this.config.indexURL||!0===this.config.supportsWholeGenome}get color(){return this._color||\"rgb(0,0,150)\"}set color(e){this._color=e,e&&(this.colorBy=void 0)}async getHeader(){return this.header||\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getSampleCount(){return this.sampleKeys?this.sampleKeys.length:0}async getFeatures(e,t,i,n){void 0===this.header&&(this.header=await this.getHeader());const r=await this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow});if(this.initialSort){const e=this.initialSort;if(void 0===e.option||\"GENOTYPE\"===e.option.toUpperCase())this.sortSamplesByGenotype(e,r);else if(\"ATTRIBUTE\"===e.option.toUpperCase()&&e.attribute){const t=\"ASC\"===e.direction?1:-1;this.sortByAttribute(e.attribute,t)}this.initialSort=void 0}return r}hasSamples(){return this.getSampleCount()>0}getSamples(){const e=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,i=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=t*((\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight)+e),r=Kv+t*(i+e);return{names:this.sampleKeys,yOffset:r,height:n}}computePixelHeight(e){if(!e||0===e.length)return Kv;const t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,i=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,n=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,r=\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s=!1===this.showGenotypes?0:this.getSampleCount()*t;return Kv+t*(n+i)+i+(s+1)*(r+i)}variantRowCount(e){this.nVariantRows=e}draw({context:e,pixelWidth:t,pixelHeight:i,bpPerPixel:n,bpStart:r,pixelTop:s,features:o}){xo.fillRect(e,0,s,t,i,{fillStyle:\"rgb(255, 255, 255)\"});const a=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,c=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,l=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=Kv+c*(l+a);let h=this.sampleColumns;const d=this.hasSamples();if(h&&d&&!1!==this.showGenotypes&&xo.strokeLine(e,0,this.variantBandHeight,t,this.variantBandHeight,{strokeStyle:\"rgb(224,224,224) \"}),o){const i=\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,a=r+t*n+1;for(let t of o){if(t.end<r)continue;if(t.start>a)break;const o=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,c=Kv+(\"COLLAPSED\"===this.displayMode?0:t.row*(o+s)),l=o;let h=(t.start-r)/n,u=(t.end-r)/n,f=Math.max(1,u-h);f<3?(f=3,h-=1):f>5&&(h+=1,f-=2);const p=t._f||t;let g;try{g=p.alleleFreq()}catch(e){console.log(e)}if(\"AF\"===this.colorBy&&g){const t=Math.min(1,g)*l,i=l-t;e.fillStyle=p.isFiltered()?this.refColorFiltered:this.refColor,e.fillRect(h,c,f,i),e.fillStyle=p.isFiltered()?this.altColorFiltered:this.altColor,e.fillRect(h,c+i,f,t)}else e.fillStyle=this.getColorForFeature(p),e.fillRect(h,c,f,l);let m=this.getVariantStrokecolor(p);if(m&&(e.strokeStyle=m,e.strokeRect(h,c,f,l)),this.callContextHook(p,e,h,c,f,l),d&&!1!==this.showGenotypes){const t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+s,this.sampleHeight=t*(i+s);let n=0;for(let t of this.sampleKeys){const r=this.header.sampleNameMap.get(t),o=p.calls[r];if(o){const t=\"COLLAPSED\"===this.displayMode?0:p.row,r=this.sampleYOffset+n*this.sampleHeight+t*(i+s);let a=!0,c=!0,l=!1;if(o.genotype)for(let e of o.genotype){if(\".\"===e){l=!0;break}0!==e&&(c=!1),0===e&&(a=!1)}o.genotype?e.fillStyle=l?this.noCallColor:c?this.homrefColor:a?this.homvarColor:this.hetvarColor:e.fillStyle=this.noGenotypeColor,e.fillRect(h,r,f,i)}n++}}}}else console.log(\"No feature list\")}get refColorFiltered(){return this._refColorFiltered||(this._refColorFiltered=_s.addAlpha(this.refColor,.2)),this._refColorFiltered}get altColorFiltered(){return this._altColorFiltered||(this._altColorFiltered=_s.addAlpha(this.altColor,.2)),this._altColorFiltered}getColorForFeature(e){const t=e._f||e;let i;if(this.colorBy&&\"none\"!==this.colorBy){const e=t.getAttributeValue(this.colorBy);i=void 0!==e?this.getVariantColorTable(this.colorBy).getColor(e):\"gray\"}else i=this.color?\"function\"==typeof this.color?this.color(e):this.color:\"NONVARIANT\"===t.type?this.nonRefColor:\"MIXED\"===t.type?this.mixedColor:this.color;return t.isFiltered()&&(i=_s.addAlpha(i,.2)),i}getVariantStrokecolor(e){const t=e._f||e;let i;return i=this.strokecolor?\"function\"==typeof this.strokecolor?this.strokecolor(t):this.strokecolor:void 0,i}callContextHook(e,t,i,n,r,s){if(this._context_hook&&\"function\"==typeof this._context_hook){const o=e._f||e;t.save(),this._context_hook(o,t,i,n,r,s),t.restore()}}clickedFeatures(e){let t=super.clickedFeatures(e);const i=\"EXPANDED\"===this.displayMode?this.expandedVGap:this.squishedVGap,n=i+(\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),r=e.y;if(r<=this.variantBandHeight){const e=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=Math.floor((r-Kv)/(e+i));\"COLLAPSED\"!==this.displayMode&&(t=t.filter((e=>e.row===n)))}else if(this.sampleKeys){const e=r-this.variantBandHeight,i=Math.floor(e/this.sampleHeight);if(i>=0&&i<this.sampleKeys.length){const r=Math.floor((e-i*this.sampleHeight)/n),s=\"COLLAPSED\"===this.displayMode?t:t.filter((e=>e.row===r)),o=this.sampleKeys[i],a=this.header.sampleNameMap.get(o);t=s.map((e=>{const t=e.calls[a];return t.genotypeString=function(e,t){if(e.genotype){let i=\"\";if(\".\"===t.alternateBases)i=\"No Call\";else{const n=t.alternateBases.split(\",\");for(let r of e.genotype)if(i.length>0&&(i+=\" | \"),\".\"===r)i+=\".\";else if(0===r)i+=t.referenceBases;else{i+=n[r-1].replace(\"<\",\"&lt;\")}}return i}}(t,e),t}))}}return t}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=this.browser.genome.id;let r=[];for(let e of t){const t=e._f||e;if(r.length>0&&r.push({html:'<hr style=\"border-top-width:2px ;border-color: #c9c3ba\" />'}),\"function\"==typeof t.popupData){const e=t.popupData(i,n);Array.prototype.push.apply(r,e)}}return r}menuItemList(){const e=[];if(this.header.INFO&&this.header.INFO){const t=this._colorByItems;e.push(\"<hr/>\");const i=Bt('<div class=\"igv-track-menu-category igv-track-menu-border-top\">');i.text(\"Color by:\"),e.push({name:void 0,object:i,click:void 0,init:void 0});for(let n of t.keys()){const r=this.colorBy===n;e.push(this.colorByCB({key:n,label:t.get(n)},r))}e.push(this.colorByCB({key:\"info\",label:\"Info field...\"}))}if(!0===Hf(this.browser.sampleInfo,this.sampleKeys)){e.push(\"<hr/>\"),e.push(\"Sort by attribute:\");for(const s of this.browser.sampleInfo.attributeNames)if(this.sampleKeys.some((e=>{const t=this.browser.sampleInfo.getAttributes(e);return t&&t[s]}))){const o=Bt(\"<div>\");function a(){const e=this._sortDirections.get(s)||1;this.sortByAttribute(s,e),this.config.sort={option:\"ATTRIBUTE\",attribute:s,direction:e>0?\"ASC\":\"DESC\"},this._sortDirections.set(s,-1*e)}o.html(`&nbsp;&nbsp;${s.split(Uu.emptySpaceReplacement).join(\" \")}`),e.push({object:o,click:a})}}e.push(\"<hr/>\"),this.getSampleCount()>0&&(e.push({object:Bt('<div class=\"igv-track-menu-border-top\">')}),e.push({object:Bt(Dl(\"Show Genotypes\",this.showGenotypes)),click:function(){this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.browser.sampleNameControl.performClickWithState(this.browser,this.showGenotypes),this.browser.sampleInfoControl.performClickWithState(this.browser,this.showGenotypes)}})),e.push({object:Bt('<div class=\"igv-track-menu-border-top\">')});for(let c of[\"COLLAPSED\",\"SQUISHED\",\"EXPANDED\"]){e.push({object:Bt(Dl({COLLAPSED:\"Collapse\",SQUISHED:\"Squish\",EXPANDED:\"Expand\"}[c],c===this.displayMode)),click:function(){this.displayMode=c,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return this.browser.circularView&&(e.push(\"<hr>\"),e.push({label:\"Add SVs to circular view\",click:function(){for(let e of this.trackView.viewports)this.sendChordsForViewport(e)}})),this.canCovertToPytor()&&(e.push(\"<hr>\"),e.push({label:\"Convert to CNVpytor track\",click:function(){this.convertToPytor()}})),e}contextMenuItemList(e){const t=[];if(this.hasSamples()&&this.showGenotypes){const i=e.viewport.referenceFrame,n=e.genomicLocation,r=i.toBP(2.5),s=this._sortDirections.get(\"genotype\")||1;this._sortDirections.set(\"genotype\",-1*s),t.push({label:\"Sort by genotype\",click:t=>{const i={direction:s,option:\"genotype\",chr:e.viewport.referenceFrame.chr,start:Math.floor(n-r),end:Math.ceil(n+r)},o=e.viewport.cachedFeatures;this.sortSamplesByGenotype(i,o),this.config.sort=i}}),t.push(\"<hr/>\")}if(this.browser.circularView){const i=e.viewport;t.push({label:\"Add SVs to Circular View\",click:()=>{this.sendChordsForViewport(i)}}),t.push(\"<hr/>\")}return t}async sortSamplesByGenotype({chr:e,position:t,start:i,end:n,direction:r},s){if(void 0===i&&(i=t-1),void 0===n&&(n=t),s||(s=await this.featureSource.getFeatures({chr:e,start:i,end:n})),!s)return;const o=new Map,a=\"ASC\"===r?1:-1;for(let e of s)if(!(e.end<i)){if(e.start>n)break;for(let t of e.calls){const e=t.sample,i=t.zygosityScore();o.set(e,o.has(e)?o.get(e)+i:i)}}this.sampleKeys.sort((function(e,t){let i=o.get(e)||0,n=o.get(t)||0;return a*(i-n)})),this.trackView.repaintViews()}sortByAttribute(e,t){this.config.sort={option:\"ATTRIBUTE\",attribute:e,direction:1===t?\"ASC\":\"DESC\"},this.sampleKeys=this.browser.sampleInfo.getSortedSampleKeysByAttribute(this.sampleKeys,e,t),this.trackView.repaintViews()}sendChordsForViewport(e){const t=e.referenceFrame;let i;if(\"all\"===t.chr){const e=this.featureSource.getAllFeatures(),t=Object.keys(e).map((t=>e[t]));i=[].concat(...t)}else i=this.featureSource.featureCache.queryFeatures(t.chr,t.start,t.end);Pm(i.filter((e=>{const t=e._f||e;return t.info&&t.info.CHR2&&t.info.END&&(t.info.CHR2!==t.chr||Math.abs(Number.parseInt(t.info.END)-t.pos)>1e6)})).map((e=>{const t=e._f||e,i=Number.parseInt(t.info.END),n=i-100,r=i+100;return{uniqueId:`${t.chr}:${t.start}-${t.end}_${t.info.CHR2}:${t.info.END}`,refName:zm(t.chr),start:t.start,end:t.end,mate:{refName:zm(t.info.CHR2),start:n,end:r}}})),this,t,.5)}colorByCB(e,t){const i=Bt(Dl(e.label,t));if(\"info\"!==e.key){function n(){const t=\"none\"===e.key?void 0:e.key;this.colorBy=t,this.config.colorBy=t,this.trackView.repaintViews()}return{name:void 0,object:i,click:n,init:void 0}}{function r(e){this.browser.inputDialog.present({label:\"Info field\",value:\"\",callback:e=>{e?(this.colorBy=e,this._colorByItems.set(e,e)):this.colorBy=void 0,this.trackView.repaintViews()}},e)}return{name:void 0,object:i,dialog:r,init:void 0}}}getState(){const e=super.getState();return this.color&&\"function\"!=typeof this.color&&(e.color=this.color),e}getVariantColorTable(e){if(this.colorTables.has(e))return this.colorTables.get(e);if(this.colorTables.has(\"*\"))return this.colorTables.get(\"*\");{let t;if(\"SVTYPE\"===e)t=Xv;else t=new oo(\"Set1\");return this.colorTables.set(e,t),t}}paintAxis(){}canCovertToPytor(){return!this.config.indexURL&&(!!this.header&&(1===Object.keys(this.sampleKeys).length&&this.header.FORMAT&&this.header.FORMAT.AD&&this.header.FORMAT.DP))}async convertToPytor(){this.variantState={...this.config,...this.getState()},this.variantState.trackHeight=this.height,this.trackView.startSpinner(),setTimeout((async()=>{try{const e=Object.assign({},this.config);Object.setPrototypeOf(this,Gv.prototype),this.init(e),await this.postInit(),this.trackView.clearCachedFeatures(),this.trackView.setTrackHeight(this.config.height||Gv.DEFAULT_TRACK_HEIGHT),this.trackView.checkContentHeight(),this.trackView.updateViews()}finally{this.trackView.stopSpinner()}}),100)}}const Xv=new ao({DEL:\"#ff2101\",INS:\"#001888\",DUP:\"#028401\",INV:\"#008688\",CNV:\"#8931ff\",BND:\"#891100\",\"*\":\"#002eff\"}),Zv={timeout:5e3,type:\"plain\",url:\"https://igv.org/genomes/locus.php?genome=$GENOME$&name=$FEATURE$\",coords:0};async function Jv(e,t){const i=e.searchConfig||Zv;let n;t=t.toUpperCase();const r=e.tracks.filter((e=>e.searchable));for(let e of r){const i=await e.search(t);if(i)return i}if(e.config&&!1!==e.config.search)try{return n=await async function(e,t,i){let n=i.url.replace(\"$FEATURE$\",t.toUpperCase());n.indexOf(\"$GENOME$\")>-1&&(n=n.replace(\"$GENOME$\",e.genome.id?e.genome.id:\"hg19\"));const r=i.timeout?{timeout:i.timeout}:void 0,s=await Qs.loadString(n,r);return function(e,t,i){let n;n=\"plain\"===i.type?function(e,t){const i=[],n=Dt(t);for(let t of n){const n=t.split(\"\\t\");if(n.length>=3){const t=n[1].split(\":\"),r=t[1].split(\"-\");i.push({chromosome:e.genome.getChromosomeName(t[0].trim()),start:parseInt(r[0].replace(/,/g,\"\")),end:parseInt(r[1].replace(/,/g,\"\")),name:n[0].toUpperCase()})}}return i}(e,t):JSON.parse(t);i.resultsField&&(n=n[i.resultsField]);if(n&&0!==n.length){const e=i.chromosomeField||\"chromosome\",t=i.startField||\"start\",r=i.endField||\"end\",s=i.coords||1;let o;o=Array.isArray(n)?n[0]:n,o.hasOwnProperty(e)&&o.hasOwnProperty(t)||console.error(\"Search service results must include chromosome and start fields: \"+o);const a=o[e];let c=o[t]-s,l=o[r];void 0===l&&(l=c+1);const h={chr:a,start:c,end:l};if(!o.type||o.type,i.geneField&&i.snpField){const e=o[i.geneField]||o[i.snpField];e&&(h.name=e.toUpperCase())}return h}return}(e,s,i)}(e,t,i),n}catch(e){console.log(\"Search service not available \"+e)}}function ey(e,t=!1){const i=e.split(\"\\t\");if(i.length>2)try{const e=i[0],t=parseInt(i[1].replace(/,/g,\"\"),10)-1,n=parseInt(i[2].replace(/,/g,\"\"),10);if(!isNaN(t)&&!isNaN(n))return{chr:e,start:t,end:n}}catch(e){}const n=e.split(\":\"),r={chr:n[0]};if(n.length>1){let e,i=n[1].split(\"-\");if(i.length>2){if(!n[1].startsWith(\"-\"))return;{const e=n[1].indexOf(\"-\",1);if(e>0){i=[n[1].substring(0,e),n[1].substring(e+1)]}}}if(e=i[0].replace(/,/g,\"\"),isNaN(e))return;if(r.start=parseInt(e,10)-1,r.end=r.start+1,1===i.length&&(r.start-=20,r.end+=20),2===i.length){if(e=i[1].replace(/,/g,\"\"),isNaN(e))return;if(r.end=parseInt(e,10),r.start<0&&!t){const e=-extent.start;r.start+=e,r.end+=e}}}return r}class ty extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"qtl\",this.name=e.name;const t=e.minLogP||e.min,i=e.maxLogP||e.max;this.dataRange={min:void 0!==t?t:3.5,max:i||25},this.autoscale=!i||e.autoscale,this.autoscalePercentile=void 0===e.autoscalePercentile?98:e.autoscalePercentile,this.background=e.background,this.divider=e.divider||\"rgb(225,225,225)\",this.dotSize=e.dotSize||2,this.height=e.height||100,this.disableButtons=e.disableButtons,this.featureSource=Ad(e,this.browser.genome)}paintAxis(e,t,i){const n=(this.dataRange.max-this.dataRange.min)/i,r={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"});const s=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let o=4;o<=this.dataRange.max;o+=s){const s=.85*t,a=s-5,c=s,l=i-(o-this.dataRange.min)/n;xo.strokeLine(e,a,l,c,l,r),l>8&&xo.fillText(e,o,a-1,l+2,r)}r.textAlign=\"center\",xo.fillText(e,\"-log10(pvalue)\",t/4,i/2,r,{rotate:{angle:-90}})}async getFeatures(e,t,i){const n=this.visibilityWindow;return await this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const{context:t,referenceFrame:i,pixelWidth:n,pixelHeight:r}=e;this.background&&xo.fillRect(t,0,0,n,r,{fillStyle:this.background}),xo.strokeLine(t,0,r-1,n,r-1,{strokeStyle:this.divider}),i.feature&&i.feature.match(/RS[0-9]+/);const s=i=>{const s=i?2*this.dotSize:this.dotSize,o=e.bpStart,a=(this.dataRange.max-this.dataRange.min)/r;for(let d of e.features){const u=(d.start-o+.5)/e.bpPerPixel;if(u<0)continue;if(u>n)break;const f=d.phenotype;let p;if(this.browser.qtlSelections.qtl?(l=this.browser.qtlSelections.qtl,h=d,p=l.chr===h.chr&&l.start===h.start&&l.pValue===h.pValue):p=this.browser.qtlSelections.snps.size>0?this.browser.qtlSelections.hasSnp(d.snp)&&this.browser.qtlSelections.hasPhenotype(f):this.browser.qtlSelections.hasPhenotype(f),!i||p){var c=-Math.log(d.pValue)/Math.LN10;if(c>=this.dataRange.min){let e;c>this.dataRange.max?(c=this.dataRange.max,e=!0):e=!1;const n=Math.max(0+s,r-Math.round((c-this.dataRange.min)/a));let o;d.px=u,d.py=n,d.radius=s,i&&p?(o=this.browser.qtlSelections.colorForGene(f),xo.setProperties(t,{fillStyle:o,strokeStyle:\"black\"})):(o=e?\"rgb(150, 150, 150)\":\"rgb(180, 180, 180)\",xo.setProperties(t,{fillStyle:o,strokeStyle:o})),xo.fillCircle(t,u,n,s),xo.strokeCircle(t,u,n,s)}}}var l,h};s(!1),s(!0)}popupData(e,t){if(void 0===t&&(t=e.viewport.cachedFeatures),!t||0===t.length)return[];const i=this.name,n=[];for(let r of this._clickedFeatures(e,t))n.length>0&&n.push(\"<hr/>\"),\"function\"==typeof r.popupData?n.push(...r.popupData(e)):n.push({name:\"snp id\",value:r.snp},{name:\"gene id\",value:r.gencodeId},{name:\"gene name\",value:r.geneSymbol},{name:\"p value\",value:r.pValue},{name:\"tissue\",value:i});return n}_clickedFeatures(e,t){const i=(e,t)=>Math.sqrt((e.px-t.canvasX)*(e.px-t.canvasX)+(e.py-t.canvasY)*(e.py-t.canvasY)),n=t.filter((t=>i(t,e)<6));if(n.length>1){n.sort(((t,n)=>i(t,e)-i(n,e)));const t=i(n[0],e);return n.filter((n=>i(n,e)<=t))}return n}contextMenuItemList(e){const t=[],i=e.viewport.cachedFeatures;if(i){const n=this._clickedFeatures(e,i);n.length>0&&(t.push({label:\"Highlight associated features\",click:async()=>{this.browser.qtlSelections.clear();for(let e of n)this.browser.qtlSelections.qtl=e,this.browser.qtlSelections.addPhenotype(e.phenotype);this.browser.repaintViews()}}),t.push(\"<hr>\"))}return t}menuItemList(){const e=[];return e.push(...this.numericDataMenuItems()),e.push(\"<hr/>\"),e.push({label:\"Search for...\",dialog:function(e){this.browser.inputDialog.present({label:\"Search for snp or phenotype\",value:\"\",callback:async e=>{if(e){e=e.trim().toUpperCase();const t=t=>((t.phenotype&&t.phenotype.toUpperCase())===e||t.snp&&t.snp.toUpperCase()===e)&&-Math.log(t.pValue)/Math.LN10>this.dataRange.min;let i,n,r,s=await this.featureSource.findFeatures(t);if(0==s.length){await this.browser.search(e)&&(s=await this.featureSource.findFeatures(t))}if(s.length>0){this.browser.qtlSelections.clear();const t=new Set;i=s[0].chr,n=s[0].start,r=s[0].end;for(let o of s)o.snp&&o.snp.toUpperCase()===e&&this.browser.qtlSelections.addSnp(o.snp),this.browser.qtlSelections.addPhenotype(o.phenotype),t.add(o.phenotype),o.chr===i&&(n=Math.min(n,o.start),r=Math.max(r,o.end));const o=this.browser.genome.getChromosomeName(i);for(let e of t){const t=await Jv(this.browser,e);t&&o===this.browser.genome.getChromosomeName(t.chr)&&(n=Math.min(n,t.start),r=Math.max(r,t.end))}const a=Math.floor(.1*(r-n));n=Math.max(0,n-a),r+=a,await this.browser.search(`${i}:${n}-${r}`)}}}},e)}}),e}doAutoscale(e){let t=this.config.max||25;if(e.length>0){const i=e.map((e=>-Math.log(e.pValue)/Math.LN10));i.sort(((e,t)=>e-t));t=i[Math.floor(i.length*(this.autoscalePercentile/100))]}return this.dataRange.max=Math.max(t,10),this.dataRange}}const iy={X:\"rgb(204, 153, 0)\",Y:\"rgb(153, 204, 0)\",Un:\"darkGray)\",1:\"rgb(80, 80, 255)\",2:\"rgb(206, 61, 50)\",\"2a\":\"rgb(210, 65, 55)\",\"2b\":\"rgb(215, 70, 60)\",3:\"rgb(116, 155, 88)\",4:\"rgb(240, 230, 133)\",5:\"rgb(70, 105, 131)\",6:\"rgb(186, 99, 56)\",7:\"rgb(93, 177, 221)\",8:\"rgb(128, 34, 104)\",9:\"rgb(107, 215, 107)\",10:\"rgb(213, 149, 167)\",11:\"rgb(146, 72, 34)\",12:\"rgb(131, 123, 141)\",13:\"rgb(199, 81, 39)\",14:\"rgb(213, 143, 92)\",15:\"rgb(122, 101, 165)\",16:\"rgb(228, 175, 105)\",17:\"rgb(59, 27, 83)\",18:\"rgb(205, 222, 183)\",19:\"rgb(97, 42, 121)\",20:\"rgb(174, 31, 99)\",21:\"rgb(231, 199, 111)\",22:\"rgb(90, 101, 94)\",23:\"rgb(204, 153, 0)\",24:\"rgb(153, 204, 0)\",25:\"rgb(51, 204, 0)\",26:\"rgb(0, 204, 51)\",27:\"rgb(0, 204, 153)\",28:\"rgb(0, 153, 204)\",29:\"rgb(10, 71, 255)\",30:\"rgb(71, 117, 255)\",31:\"rgb(255, 194, 10)\",32:\"rgb(255, 209, 71)\",33:\"rgb(153, 0, 51)\",34:\"rgb(153, 26, 0)\",35:\"rgb(153, 102, 0)\",36:\"rgb(128, 153, 0)\",37:\"rgb(51, 153, 0)\",38:\"rgb(0, 153, 26)\",39:\"rgb(0, 153, 102)\",40:\"rgb(0, 128, 153)\",41:\"rgb(0, 51, 153)\",42:\"rgb(26, 0, 153)\",43:\"rgb(102, 0, 153)\",44:\"rgb(153, 0, 128)\",45:\"rgb(214, 0, 71)\",46:\"rgb(255, 20, 99)\",47:\"rgb(0, 214, 143)\",48:\"rgb(20, 255, 177)\"};for(let DA of Object.keys(iy)){iy[\"chr\"+DA]=iy[DA]}for(let TA=1;TA<=48;TA++){if(10===TA)continue;const LA=ny(TA);iy[LA]=iy[TA.toString()]}function ny(e){if(!+e)return!1;for(var t=String(+e).split(\"\"),i=[\"\",\"C\",\"CC\",\"CCC\",\"CD\",\"D\",\"DC\",\"DCC\",\"DCCC\",\"CM\",\"\",\"X\",\"XX\",\"XXX\",\"XL\",\"L\",\"LX\",\"LXX\",\"LXXX\",\"XC\",\"\",\"I\",\"II\",\"III\",\"IV\",\"V\",\"VI\",\"VII\",\"VIII\",\"IX\"],n=\"\",r=3;r--;)n=(i[+t.pop()+10*r]||\"\")+n;return Array(+t.join(\"\")+1).join(\"M\")+n}class ry extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.useChrColors=void 0===e.useChrColors||e.useChrColors,this.trait=e.trait,this.posteriorProbability=e.posteriorProbability,this.valueProperty=\"bed\"===e.format?\"score\":\"value\",this.height=e.height||100,this.autoscale=e.autoscale,this.autoscalePercentile=void 0===e.autoscalePercentile?98:e.autoscalePercentile,this.background=e.background,this.divider=e.divider||\"rgb(225,225,225)\",this.dotSize=e.dotSize||3,this.popoverWindow=void 0===e.popoverWindow?1e8:e.popoverWindow,this.useChrColors?this.colorScale=new ao(e.colorTable||iy):e.color?this.colorScale=new ff(e.color):this.colorScale=new df(e.colorScale||{thresholds:[5e-8,5e-4,.5],colors:[\"rgb(255,50,50)\",\"rgb(251,100,100)\",\"rgb(251,170,170)\",\"rgb(227,238,249)\"]}),this.featureSource=Ad(e,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),this.autoscale||(this.posteriorProbability?this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?1:this.config.max}:this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?25:this.config.max}),this}get supportsWholeGenome(){return!0}async getFeatures(e,t,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const t=e.features,i=e.context,n=e.pixelWidth,r=e.pixelHeight;if(this.background&&xo.fillRect(i,0,0,n,r,{fillStyle:this.background}),xo.strokeLine(i,0,r-1,n,r-1,{strokeStyle:this.divider}),t){const s=e.bpPerPixel,o=e.bpStart,a=o+n*s+1;for(let e of t){const t=e.start;if(t<o)continue;if(t>a)break;let n;if(this.posteriorProbability)n=e[this.valueProperty];else{const t=e[this.valueProperty];if(!t)continue;n=-Math.log10(t)}const c=this.useChrColors?e._f?e._f.chr:e.chr:n,l=this.colorScale.getColor(c),h=(this.dataRange.max-this.dataRange.min)/r,d=Math.round((t-o)/s),u=Math.max(this.dotSize,r-Math.round((n-this.dataRange.min)/h));l&&xo.setProperties(i,{fillStyle:l,strokeStyle:\"black\"}),xo.fillCircle(i,d,u,this.dotSize),e.px=d,e.py=u}}}paintAxis(e,t,i){xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"});var n={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};const r=(this.dataRange.max-this.dataRange.min)/i;if(this.posteriorProbability){const t=.1;for(let s=this.dataRange.min;s<this.dataRange.max;s+=t){const t=i-Math.round((s-this.dataRange.min)/r);xo.strokeLine(e,45,t-2,50,t-2,n),xo.fillText(e,s.toFixed(1),44,t+2,n)}}else{const t=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let s=this.dataRange.min;s<this.dataRange.max;s+=t){const t=i-Math.round((s-this.dataRange.min)/r);xo.strokeLine(e,45,t,50,t,n),xo.fillText(e,Math.floor(s),44,t+4,n)}}n.textAlign=\"center\",this.posteriorProbability?xo.fillText(e,\"PPA\",t/2,i/2,n,{rotate:{angle:-90}}):xo.fillText(e,\"-log10(pvalue)\",t/2,i/2,n,{rotate:{angle:-90}})}popupData(e,t){void 0===t&&(t=e.viewport.cachedFeatures);let i=[];const n=e.viewport.trackView.track;if(t){let r=0;for(let s of t){const t=Math.abs(e.canvasX-s.px),o=Math.abs(e.canvasY-s.py);if(t<this.dotSize&&o<this.dotSize){if(r>0&&i.push(\"<HR/>\"),5==r){i.push(\"...\");break}if(s=s._f||s,\"function\"==typeof s.popupData)i=i.concat(s.popupData());else{const e=s[this.valueProperty],t=s.chr,r=Rt(s.start+1);i.push({name:\"chromosome\",value:t}),i.push({name:\"position\",value:r}),i.push({name:\"name\",value:s.name}),n.posteriorProbability?i.push({name:\"posterior probability\",value:e}):i.push({name:\"pValue\",value:e})}r++}}}return i}menuItemList(){return this.numericDataMenuItems()}doAutoscale(e){if(e.length>0){const t=this.valueProperty,i=this.posteriorProbability,n=e.map((function(e){const n=e[t];return{value:i?n:-Math.log(n)/Math.LN10}}));this.dataRange=qa(n)}else this.posteriorProbability?this.dataRange={min:this.config.min||0,max:this.config.max||1}:this.dataRange={min:this.config.max||25,max:this.config.min||0};return this.dataRange}}class sy extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.autoscale=e.autoscale||void 0===e.max,this.dataRange={min:e.min||0,max:e.max},this.windowFunction=e.windowFunction||\"mean\",this.paintAxis=cd,this.graphType=e.graphType||\"bar\",e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):this.featureSource=Ad(this.config,this.browser.genome),this.visibilityWindow=-1,this.featureSource.visibilityWindow=this.visibilityWindow}async postInit(){if(\"function\"==typeof this.featureSource.getHeader){if(this.header=await this.featureSource.getHeader(),this.disposed)return;if(this.sampleKeys=this.header.columnNames.slice(3),this.setTrackProperties(this.header),this.header.hasOwnProperty(\"clickToHighlight\")){let e=this.header.clickToHighlight;this.config.clickToHighlight=e,this.config.samplesClickedToHighlight={}}if(this.header.hasOwnProperty(\"highlight\")){this.config.highlightSamples={};let e=this.header.highlight;Array.isArray(e)||(e=[e]);for(let t of e){const e=t.split(\";\");2===e.length&&(this.config.highlightSamples[e[0]]=e[1])}}}}menuItemList(){return this.numericDataMenuItems()}async getFeatures(e,t,i){const n=await this.featureSource.getFeatures({chr:e,start:0,end:Number.MAX_SAFE_INTEGER,visibilityWindow:this.visibilityWindow});let r,s;for(let e=1;e<n.length-1;e++)if(void 0===r&&n[e].end>t&&(r=e-1),void 0===s&&n[e].start>i){s=e+1;break}return void 0===r&&(r=0),void 0===s&&(s=n.length),n.slice(r,s)}draw(e){const{features:t,context:i,bpPerPixel:n,bpStart:r,pixelWidth:s,pixelHeight:o}=e,a=e=>(this.dataRange.max-e)/(this.dataRange.max-this.dataRange.min)*o,c=function(e){let t=Math.floor((e-r)/n);return isNaN(t)&&console.warn(\"isNaN(x). feature start \"+Rt(e)+\" bp start \"+Rt(r)),t};if(t&&t.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const e=this.config.highlightSamples,n=this.config.onlyHandleClicksForHighlightedSamples,r=this.config.clickToHighlight;let s=-1,o={},l=[],h=[];this.clickDetectorCache={};for(let d of t){const t=c(d.start),u=c(d.end),f=s>=0?c(s):t;if(!isNaN(t)&&!isNaN(u)){this.clickDetectorCache[t]=[],this.clickDetectorCache[u]=[];for(let s=0;s<d.values.length;s++){const c=this.sampleKeys[s],p=d.values[s],g=a(p);if(t-f>=1){const s=o[c],h=a(s),d=e&&e[c];d?l.push([f,h,t,g,d]):r&&c in this.config.samplesClickedToHighlight?l.push([f,h,t,g,this.config.samplesClickedToHighlight[c]]):xo.strokeLine(i,f,h,t,g,{strokeStyle:\"#D9D9D9\"}),n&&!(c in e)||this.clickDetectorCache[t].push([f,h,t,g,c,d||\"gray\"])}if(u-t>=1){const s=e&&e[c];s?h.push([t,g,u,g,s]):r&&c in this.config.samplesClickedToHighlight?h.push([t,g,u,g,this.config.samplesClickedToHighlight[c]]):xo.strokeLine(i,t,g,u,g,{strokeStyle:\"gray\"}),n&&!(c in e)||this.clickDetectorCache[u].push([t,g,u,g,c,s||\"gray\"])}o[c]=p}s=d.end}}for(let e of l)xo.strokeLine(i,e[0],e[1],e[2],e[3],{strokeStyle:e[4],lineWidth:1.3});for(let e of h)xo.strokeLine(i,e[0],e[1],e[2],e[3],{strokeStyle:e[4],lineWidth:2})}(e=>{if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=a(t.y),n={strokeStyle:t.color,strokeWidth:2};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,n):xo.strokeLine(e.context,0,i,e.pixelWidth,i,n)}})(e)}doAutoscale(e){let t,i;return e.length>0?(t=Number.MAX_VALUE,i=-Number.MAX_VALUE,e.forEach((function(e){t=Math.min(t,...e.values),i=Math.max(i,...e.values)})),t-=.01,i+=.01):(t=0,i=100),{min:t,max:i}}clickedFeatures(e){const t=e.canvasX,i=e.canvasY;let n=null;for(n of Object.keys(this.clickDetectorCache))if(n=parseInt(n),n>=t)break;if(n){let e=Number.MAX_VALUE,o=[];const a=this.clickDetectorCache[n];for(let n of a){const r=n[0],s=n[2];if(t<r||t>s)return[];const a=n[1],c=n[3];if(i<Math.min(a,c)-10||i>Math.max(a,c)+10)continue;const l=oy(t,i,r,a,s,c);l<e&&(o=[{name:n[4],color:n[5]}],e=l)}if(e<5){if(this.config.clickToHighlight){if(o[0].name in this.config.samplesClickedToHighlight)delete this.config.samplesClickedToHighlight[o[0].name];else if(\"any\"===this.config.clickToHighlight){var r=[\"red\",\"darkblue\",\"green\",\"teal\",\"olivedrab\",\"orange\",\"maroon\",\"purple\",\"blue\",\"gold\"],s=r[Math.floor(Math.random()*(r.length+1))];this.config.samplesClickedToHighlight[o[0].name]=s}else this.config.samplesClickedToHighlight[o[0].name]=this.config.clickToHighlight;this.trackView.repaintViews()}return o}}return[]}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];return t.forEach((function(e){for(let t of Object.keys(e))Oa(e[t])&&i.push({name:t,value:e[t]})})),i}get supportsWholeGenome(){return!1}}function oy(e,t,i,n,r,s){const o=r-i,a=s-n,c=Math.abs(o*(n-t)-(i-e)*a),l=Math.sqrt(o*o+a*a);return l>0?c/l:0}class ay extends Hl{static defaults={height:300,theta:Math.PI/2,arcOrientation:\"UP\"};constructor(e,t){super(e,t),!1===e.arcOrientation?this.arcOrientation=\"DOWN\":!0===e.arcOrientation?this.arcOrientation=\"UP\":e.arcOrientation?this.arcOrientation=e.arcOrientation.toUpperCase():this.arcOrientation=\"UP\",\"bp\"===e.format?this.featureSource=new ly(e,t.genome):this.featureSource=new ud(e,t.genome)}async getFeatures(e,t,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const t=e.context,i=Math.PI/2,n=e.pixelWidth,r=e.pixelHeight;e.viewportWidth;const s=e.bpPerPixel,o=e.bpStart,a=s,c=\"UP\"===this.arcOrientation;xo.fillRect(t,0,e.pixelTop,n,r,{fillStyle:\"rgb(255, 255, 255)\"});const l=e.features;if(l){cy(l,1);for(let e of l)if(e.startLeft){let n=Math.round((e.startLeft-o)/a),r=Math.round((e.startRight-o)/a),s=Math.round((e.endLeft-o)/a),l=Math.round((e.endRight-o)/a);t.fillStyle=e.color,t.strokeStyle=e.color,t.beginPath();let h=(n+l)/2,d=(l-n)/2,u=this.height,f=Math.PI+(Math.PI/2-i),p=2*Math.PI-(Math.PI/2-i);c?(t.arc(h,u,d,f,p),t.lineTo(s,u)):(u=0,t.arc(h,u,d,p,f),t.lineTo(l,u));const g=(r+s)/2,m=(s-r)/2,w=u;c?(t.arc(g,w,m,p,f,!0),t.lineTo(n,w)):(t.arc(g,w,m,f,p,!0),t.lineTo(s,w)),t.stroke(),t.fill(),e.drawState={x1:h,y1:u,r1:d,x2:g,y2:w,r2:m,sa:f,ea:p}}else{let n=Math.round((e.start-o)/a),r=Math.round((e.end-o)/a);t.strokeStyle=e.color,t.beginPath();let s=(n+r)/2,l=(r-n)/2,h=this.height,d=Math.PI+(Math.PI/2-i),u=2*Math.PI-(Math.PI/2-i);c?t.arc(s,h,l,d,u):(h=0,t.arc(s,h,l,u,d)),t.stroke(),e.drawState={x1:s,y1:h,r1:l,sa:d,ea:u}}}}clickedFeatures(e){const t=super.clickedFeatures(e),i=[];cy(t,-1);for(let n of t){const t=n.drawState,r=e.canvasX-t.x1,s=e.canvasY-t.y1,o=Math.sqrt(r*r+s*s),a=t.r1+3;let c,l;if(void 0===t.x2)c=o,l=t.r1-3;else{const i=e.canvasX-t.x2,n=e.canvasY-t.y2;c=Math.sqrt(i*i+n*n),l=t.r2-3}if(o<a&&c>l){i.push(n);break}}return i}popupData(e,t){if(void 0===t&&(t=this.clickedFeatures(e)),t&&t.length>0)return this.extractPopupData(t[0],this.getGenomeId())}menuItemList(){return[{name:\"Toggle arc direction\",click:function(){this.arcOrientation=\"UP\"===this.arcOrientation?\"DOWN\":\"UP\",this.trackView.repaintViews()}}]}}function cy(e,t){e.sort((function(e,i){const n=void 0===e.score?-Number.MAX_VALUE:e.score,r=void 0===i.score?-Number.MAX_VALUE:i.score;return(void 0===t?1:t)*(n-r)}))}class ly{constructor(e,t){this.config=e,this.genome=t}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome;if(this.featureCache)return this.featureCache.queryFeatures(e,t,i);{const n=Ua(this.config),r=await Qs.loadByteArray(this.config.url,n);return this.featureCache=new Zs(function(e){if(!e)return null;const t=mh(e);let i,n=!0;const r=[],s=[],o=[];for(;void 0!==(i=t.nextLine());){const e=i.split(\"\\t\");if(n&&i.startsWith(\"color:\")){const t=\"rgb(\"+e[1]+\",\"+e[2]+\",\"+e[3]+\")\";r.push(t),e.length>4&&s.push(e[4])}else{n=!1;const t=e[0],i=Number.parseInt(e[1])-1,c=Number.parseInt(e[2])-1,l=Number.parseInt(e[3]),h=Number.parseInt(e[4]);var a=Number.parseInt(e[5]);const d=r[a];let u;u=i<=h?{chr:t,startLeft:Math.min(i,c),startRight:Math.max(i,c),endLeft:Math.min(l,h),endRight:Math.max(l,h),color:d,score:a}:{chr:t,startLeft:Math.min(l,h),startRight:Math.max(l,h),endLeft:Math.min(i,c),endRight:Math.max(i,c),color:d,score:a},u.start=u.startLeft,u.end=u.endRight,s.length>a&&(u.description=s[a]),o.push(u)}}return o}(r),s),this.featureCache.queryFeatures(e,t,i)}}}class hy{constructor(e){this.browser=e,this.type=\"ideogram\",this.height=16,this.order=Number.MIN_SAFE_INTEGER,this.disableButtons=!0,this.ignoreTrackMenu=!0}computePixelHeight(e){return this.height}draw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,features:r}){const s=t.chr,o=t.genome.getChromosome(s);if(void 0===o||i<=0||n<=0||\"all\"===s.toLowerCase())return;!function({ctx:e,chr:t,referenceFrame:i,genome:n,width:r,height:s,stainColors:o,features:a}){const c=1,l=.5*c,h=0;if(void 0===n)return;xo.fillRect(e,0,0,r,s,{fillStyle:_s.greyScale(255)});const d=a;if(d){const t=h+s/2,i=[],n=[];if(0===d.length)return;const a=r/d[d.length-1].end;e.beginPath(),xo.roundRect(e,l,l+h,r-2*l,s-2*l,(s-2*l)/2,0,1),e.clip();for(let r=0;r<d.length;r++){const l=d[r],u=a*l.start,f=a*l.end;\"c\"===l.type?(\"p\"===l.name.charAt(0)?(i[0]=u,n[0]=s+h,i[1]=u,n[1]=h,i[2]=f,n[2]=t):(i[0]=f,n[0]=s+h,i[1]=f,n[1]=h,i[2]=u,n[2]=t),e.fillStyle=\"rgb(150, 0, 0)\",e.strokeStyle=\"rgb(150, 0, 0)\",xo.polygon(e,i,n,1,0)):(e.fillStyle=dy(o,l),xo.fillRect(e,u,c+h,f-u,s-2*c))}}e.strokeStyle=_s.greyScale(41),xo.roundRect(e,l,l+h,r-2*l,s-2*l,(s-2*l)/2,0,1)}({ctx:e,features:r,chr:s,referenceFrame:t,genome:t.genome,width:i,height:n,stainColors:[]});const a=Math.round(t.bpPerPixel*i),c=t.start;let l=o.bpLength;const h=t.genome.getCytobands(s);if(h&&h.length>0&&h[h.length-1].end&&(l=Math.max(l,h[h.length-1].end),o.bpLength=l),a<l){const t=a/l,r=c/l;let s=Math.floor(r*i),o=Math.floor(t*i);s=Math.max(0,s),s=Math.min(i-o,s),e.save(),e.strokeStyle=\"red\",e.lineWidth=o<2?1:2;const h=s+e.lineWidth/2;o=o<2?1:o-e.lineWidth;const d=e.lineWidth/2,u=n-e.lineWidth;e.strokeRect(h,d,o,u),e.restore()}}dispose(){this.trackView=void 0}}function dy(e,t){if(\"c\"===t.type)return\"rgb(150, 10, 10)\";var i=t.stain,n=230;\"p\"===t.type&&(n=Math.floor(230-i/100*230));var r=e[n];return r||(r=\"rgb(\"+n+\",\"+n+\",\"+n+\")\",e[n]=r),r}let uy=new oo(\"Dark2\");[\"GT/AG\",\"CT/AC\",\"GC/AG\",\"CT/GC\",\"AT/AC\",\"GT/AT\",\"non-canonical\"].forEach((e=>{uy.getColor(e)}));class fy extends Hl{static defaults={margin:10,colorByNumReadsThreshold:5,height:100};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=e.type||\"junctions\",e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):this.featureSource=e.featureSource?e.featureSource:Ad(e,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get supportsWholeGenome(){return!1}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}computePixelHeight(e){return this.height}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=e.pixelHeight,a=r+s*n+1;if(this.isMergedTrack||xo.fillRect(i,0,e.pixelTop,s,o,{fillStyle:\"rgb(255, 255, 255)\"}),t){const s={};s.referenceFrame=e.viewport.referenceFrame,s.referenceFrameStart=s.referenceFrame.start,s.referenceFrameEnd=s.referenceFrameStart+s.referenceFrame.toBP(e.viewport.getWidth()),s.featureZoomOutTracker={};for(let e of t)if(!(e.end<r)){if(e.start>a)break;this.renderJunction(e,r,n,o,i,s)}}else console.log(\"No feature list\")}renderJunction(e,t,i,n,r,s){e.isVisible=!1;const o=Math.round((e.start-t)/i),a=Math.round((e.end-t)/i),c=(o+a)/2;if(a-o<=3){if(c in s.featureZoomOutTracker)return;s.featureZoomOutTracker[c]=!0}if(this.config.hideAnnotatedJunctions&&\"true\"===e.attributes.annotated_junction)return;if(this.config.hideUnannotatedJunctions&&\"false\"===e.attributes.annotated_junction)return;if(this.config.hideMotifs&&this.config.hideMotifs.includes(e.attributes.motif))return;if(this.config.hideStrand===e.strand)return;if(this.config.minJunctionEndsVisible){let t=0;if(e.start>=s.referenceFrameStart&&e.start<=s.referenceFrameEnd&&(t+=1),e.end>=s.referenceFrameStart&&e.end<=s.referenceFrameEnd&&(t+=1),t<this.config.minJunctionEndsVisible)return}let l,h,d,u;if(e.attributes.uniquely_mapped){if(l=parseInt(e.attributes.uniquely_mapped),l<this.config.minUniquelyMappedReads)return;if(h=parseInt(e.attributes.multi_mapped),d=l+h,d<this.config.minTotalReads)return;if(d>0&&h/d>this.config.maxFractionMultiMappedReads)return;if(e.attributes.maximum_spliced_alignment_overhang&&parseInt(e.attributes.maximum_spliced_alignment_overhang)<this.config.minSplicedAlignmentOverhang)return}if(e.attributes.num_samples_with_this_junction){if(u=parseInt(e.attributes.num_samples_with_this_junction),this.config.minSamplesWithThisJunction&&u<this.config.minSamplesWithThisJunction)return;if(this.config.maxSamplesWithThisJunction&&u>this.config.maxSamplesWithThisJunction)return;if(e.attributes.num_samples_total&&(e.attributes.percent_samples_with_this_junction=100*u/Number(e.attributes.num_samples_total),this.config.minPercentSamplesWithThisJunction&&(e.attributes.percent_samples_with_this_junction<this.config.minPercentSamplesWithThisJunction||e.attributes.percent_samples_with_this_junction>this.config.maxPercentSamplesWithThisJunction)))return}const f=this.margin,p=n,g=f+.5*p;let m=f;const w=f+p-10,b=(o+c)/2,F=(c+a)/2;let v,y,A=1;e.attributes.line_width?A=Number(e.attributes.line_width):(void 0===this.config.thicknessBasedOn||\"numUniqueReads\"===this.config.thicknessBasedOn?A=l:\"numReads\"===this.config.thicknessBasedOn?A=d:\"numSamplesWithThisJunction\"===this.config.thicknessBasedOn&&void 0!==u&&(A=u),A=1+Math.log(A+1)/Math.log(12)),void 0===this.config.bounceHeightBasedOn||\"random\"===this.config.bounceHeightBasedOn?v=(e.start+e.end)%7:\"distance\"===this.config.bounceHeightBasedOn?v=6*(e.end-e.start)/(s.referenceFrameEnd-s.referenceFrameStart):\"thickness\"===this.config.bounceHeightBasedOn&&(v=2*A),m+=p*Math.max(7-v,0)/10,y=e.attributes.color?e.attributes.color:void 0===this.config.colorBy||\"numUniqueReads\"===this.config.colorBy?l>this.config.colorByNumReadsThreshold?\"blue\":\"#AAAAAA\":\"numReads\"===this.config.colorBy?d>this.config.colorByNumReadsThreshold?\"blue\":\"#AAAAAA\":\"isAnnotatedJunction\"===this.config.colorBy?\"true\"===e.attributes.annotated_junction?\"#b0b0ec\":\"orange\":\"strand\"===this.config.colorBy?\"+\"===e.strand?\"#b0b0ec\":\"#ecb0b0\":\"motif\"===this.config.colorBy?uy.getColor(e.attributes.motif):\"#AAAAAA\";let C=\"\";e.attributes.label?C=e.attributes.label.replace(/_/g,\" \"):void 0===this.config.labelWith||\"uniqueReadCount\"===this.config.labelWith?C=l:\"totalReadCount\"===this.config.labelWith?C=d:\"numSamplesWithThisJunction\"===this.config.labelWith?void 0!==u&&(C=u):\"percentSamplesWithThisJunction\"===this.config.labelWith?void 0!==e.attributes.percent_samples_with_this_junction&&(C=e.attributes.percent_samples_with_this_junction.toFixed(0)+\"%\"):\"motif\"===this.config.labelWith&&void 0!==e.attributes.motif&&(C+=e.attributes.motif),\"uniqueReadCount\"===this.config.labelWithInParen?C+=\" (\"+l+\")\":\"totalReadCount\"===this.config.labelWithInParen?C+=\" (\"+d+\")\":\"multiMappedReadCount\"===this.config.labelWithInParen?h>0&&(C+=\" (+\"+h+\")\"):\"numSamplesWithThisJunction\"===this.config.labelWithInParen?void 0!==u&&(C+=\" (\"+u+\")\"):\"percentSamplesWithThisJunction\"===this.config.labelWithInParen?void 0!==e.attributes.percent_samples_with_this_junction&&(C+=\" (\"+e.attributes.percent_samples_with_this_junction.toFixed(0)+\"%)\"):\"motif\"===this.config.labelWithInParen&&void 0!==e.attributes.motif&&(C+=` ${e.attributes.motif}`),e.isVisible=!0,r.beginPath(),r.moveTo(o,w),r.bezierCurveTo(b,m,F,m,a,w),r.lineWidth=A,r.strokeStyle=y,r.stroke();const _=(e,t,i,n)=>{e.beginPath(),e.moveTo(t,i),e.lineTo(t-n/2,i-n),e.lineTo(t+n/2,i-n),e.lineTo(t,i),e.closePath(),e.fill()};if(e.attributes.left_shape||e.attributes.right_shape){r.fillStyle=y;const t=r.lineWidth>2?10:7;e.attributes.left_shape&&_(r,o,w,t),e.attributes.right_shape&&_(r,a,w,t)}r.fillText(C,c-r.measureText(C).width/2,(7*m+g)/8)}clickedFeatures(e){return super.clickedFeatures(e).filter((function(e){return e.isVisible&&e.attributes}))}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=[];for(let e of t){const t=\"function\"==typeof e.popupData?e.popupData(i):this.extractPopupData(e._f||e,this.getGenomeId());t&&(n.length>0&&n.push(\"<hr/><hr/>\"),Array.prototype.push.apply(n,t))}return n}dispose(){this.trackView=void 0}}const py={min:0,max:3e3,color:\"rgb(0,0,255)\"};class gy{constructor(e){e=e||py,this.max=e.max,this.min=e.min||0,this.cache=[],this.nbins=1e3,this.binsize=(this.max-this.min)/this.nbins,this.updateColor(e.color||\"rgb(0,0,255)\")}updateColor(e){const t=e.substring(4).replace(\")\",\"\").split(\",\");3===t.length&&(this.r=Number.parseInt(t[0].trim()),this.g=Number.parseInt(t[1].trim()),this.b=Number.parseInt(t[2].trim())),this.cache=[]}setMinMax(e,t){this.min=e,this.max=t,this.cache=[],this.binsize=(this.max-this.min)/this.nbins}getColor(e){if(e<this.min)return\"white\";const t=Math.floor((Math.min(this.max,e)-this.min)/this.binsize);if(void 0===this.cache[t]){const i=(ys.clamp(e,0,this.max)-0)/(this.max-0);this.cache[t]=`rgba(${this.r},${this.g},${this.b}, ${i})`}return this.cache[t]}toJson(){return{min:this.min,max:this.max,color:`rgb(${this.r},${this.g},${this.b})`}}static parse(e){const t=e.split(\",\"),i={min:Number.parseFloat(t[0]),max:Number.parseFloat(t[1]),color:`${t[2]},${t[3]},${t[4]}`};return new gy(i)}}class my extends Hl{static defaults={height:300,rowHeight:3,max:3e3,visibilityWindow:1e4};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"shoebox\",this.height=e.height||300,this.rowHeight=e.rowHeight||3,this.max=e.max||3e3,this.sampleKeys=[];for(let e=1;e<=100;e++)this.sampleKeys.push(e);const t=Object.assign({},this.config);t.format=\"shoebox\",this.featureSource=Ad(t,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))if(this.header&&this.setTrackProperties(this.header),this.config.colorScale&&this.config.colorScale.max&&this.config.colorScale.color)this.colorScale=new gy(this.config.colorScale);else{const e=this.dataRange.min,t=this.dataRange.max;this.colorScale=new gy({min:e,max:t,color:this.color})}}get color(){return this._color||\"rgb(0,0,255)\"}set color(e){this._color=e,this.colorScale&&this.colorScale.updateColor(e)}menuItemList(){const e=[];e.push(\"<hr/>\");let t=Bt(\"<div>\");return t.text(\"Set data range\"),e.push({object:t,dialog:function(){this.trackView.track.selected?this.browser.dataRangeDialog.configure(this.trackView.browser.getSelectedTrackViews()):this.browser.dataRangeDialog.configure(this.trackView),this.browser.dataRangeDialog.present(Bt(this.browser.columnContainer))}}),e}setDataRange({min:e,max:t}){this.dataRange.min=e,this.dataRange.max=t,this.colorScale.min=e,this.colorScale.max=t,this.trackView.repaintViews()}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys,height:this.rowHeight,yOffset:0}}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}draw({context:e,pixelTop:t,pixelWidth:i,pixelHeight:n,features:r,bpPerPixel:s,bpStart:o}){if(xo.fillRect(e,0,t,i,n,{fillStyle:\"rgb(255, 255, 255)\"}),r&&r.length>0){const a=this.rowHeight,c=t+n,l=o+i*s+1,h=a;for(let i of r){if(i.end<o||i.start>l)continue;const n=Math.round((i.start-o)/s),r=Math.round((i.end-o)/s),d=Math.max(1,r-n);let u=0;for(let r=i.values.length-1;r>=0;r--){const s=i.values[r],o=u*a;if(o+a<t||o>c)continue;const l=this.colorScale.getColor(s);e.fillStyle=l,e.fillRect(n,o,d,h),u++}}}}computePixelHeight(e){return e&&0!==e.length?e[0].values.length*this.rowHeight:0}clickedFeatures(e){const t=super.clickedFeatures(e),i=e.y;return t.filter((function(e){const t=e.pixelRect;return t&&i>=t.y&&i<=t.y+t.h}))}hoverText(e){const t=this.clickedFeatures(e);if(t&&t.length>0)return`${t[0].sample}: ${t[0].value}`}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){i.length>0&&(i.push(\"<hr/>\"),i.push(\"<hr/>\"));const t=e._f||e,n=\"function\"==typeof t.popupData?t.popupData(this.type,this.browser.genome.id):this.extractPopupData(t);Array.prototype.push.apply(i,n)}return i}get supportsWholeGenome(){return!1}getState(){const e=super.getState();return e.colorScale=this.colorScale.toJson(),e}}const wy=new Map([[\"ideogram\",(e,t)=>new hy(e,t)],[\"sequence\",(e,t)=>new Zd(e,t)],[\"feature\",(e,t)=>new Hd(e,t)],[\"seg\",(e,t)=>new Pf(e,t)],[\"mut\",(e,t)=>new Pf(e,t)],[\"maf\",(e,t)=>new Pf(e,t)],[\"shoebox\",(e,t)=>new my(e,t)],[\"wig\",(e,t)=>new ld(e,t)],[\"merged\",(e,t)=>new tf(e,t)],[\"alignment\",(e,t)=>new tw(e,t)],[\"interaction\",(e,t)=>new iw(e,t)],[\"interact\",(e,t)=>new iw(e,t)],[\"variant\",(e,t)=>new Yv(e,t)],[\"qtl\",(e,t)=>new ty(e,t)],[\"eqtl\",(e,t)=>new ty(e,t)],[\"gwas\",(e,t)=>new ry(e,t)],[\"arc\",(e,t)=>new ay(e,t)],[\"gcnv\",(e,t)=>new sy(e,t)],[\"junction\",(e,t)=>new fy(e,t)],[\"blat\",(e,t)=>new Vd(e,t)],[\"cnvpytor\",(e,t)=>new Gv(e,t)]]);class by{constructor(e,t){const i=(new DOMParser).parseFromString(e,\"text/xml\");this.processRootNode(i,t);const n=i.getElementsByTagName(\"Resource\"),r=i.getElementsByTagName(\"Track\"),s=r&&r.length>0,o=[];this.tracks=o;const a=new Map;Array.from(n).forEach((function(e,t){var i={url:e.getAttribute(\"path\"),indexURL:e.getAttribute(\"index\"),order:t};a.set(i.url,i),s||o.push(i)})),s&&Array.from(r).forEach((function(e){const t=e.getElementsByTagName(\"Track\");if(t&&t.length>0){const i={type:\"merged\",tracks:[]};Fy(e,i),o.push(i),Array.from(t).forEach((function(e){e.processed=!0;const t=e.getAttribute(\"id\"),n=a.get(t);n&&(i.tracks.push(n),Fy(e,n),n.autoscale=!1,i.height=n.height)}))}else if(!e.processed){const t=e.getAttribute(\"id\"),i=a.get(t);i&&(o.push(i),Fy(e,i))}}))}processRootNode(e,t){const i=e.getElementsByTagName(\"Session\");!i||i.length;const n=i.item(0),r=n.getAttribute(\"genome\"),s=n.getAttribute(\"locus\"),o=n.getAttribute(\"ucscID\");t&&t.hasOwnProperty(r)?this.genome=r:(this.reference={fastaURL:r},o&&(this.reference.id=o)),s&&(this.locus=s)}}function Fy(e,t){t.name=e.getAttribute(\"name\");const i=e.getAttribute(\"color\");i&&(t.color=\"rgb(\"+i+\")\");const n=e.getAttribute(\"altColor\");i&&(t.altColor=\"rgb(\"+n+\")\");const r=e.getAttribute(\"height\");r&&(t.height=parseInt(r));const s=e.getAttribute(\"autoScale\");s&&(t.autoscale=\"true\"===s);const o=e.getAttribute(\"autoscaleGroup\");o&&(t.autoscaleGroup=o);const a=e.getAttribute(\"windowFunction\");a&&(t.windowFunction=a);const c=e.getAttribute(\"visibilityWindow\")||e.getAttribute(\"featureVisibilityWindow\");c&&(t.visibilityWindow=c);const l=e.getAttribute(\"indexed\");l&&(t.indexed=\"true\"===l);const h=e.getAttribute(\"normalize\");h&&(t.normalize=\"true\"===h);const d=e.getElementsByTagName(\"DataRange\");if(d.length>0){const e=d.item(0);t.min=Number(e.getAttribute(\"minimum\")),t.max=Number(e.getAttribute(\"maximum\")),t.logScale=\"LOG\"===e.getAttribute(\"type\")}}class vy{constructor(e,t,i,n,r){this.genome=e,this.chr=t,this.start=i,this.end=n,this.bpPerPixel=r,this.id=s()}get center(){return(this.start+this.end)/2}get locusSearchString(){return`${this.chr}:${this.start+1}-${this.end}`}extend(e){const t=Math.min(e.start,this.start),i=Math.max(e.end,this.end),n=(i-t)/(this.end-this.start);this.start=t,this.end=i,this.bpPerPixel*=n}calculateEnd(e){return this.start+this.bpPerPixel*e}calculateCenter(e){return this.start+this.bpPerPixel*e/2}calculateBPP(e,t){return(e-this.start)/t}set(e){this.chr=e.chr,this.start=e.start,this.bpPerPixel=e.bpPerPixel}toPixels(e){return e/this.bpPerPixel}toBP(e){return this.bpPerPixel*e}shift(e){this.start+=e,this.end+=e}shiftPixels(e,t,i){const n=this.start,r=e*this.bpPerPixel;return this.start+=r,i&&this.clampStart(t),this.end=this.start+t*this.bpPerPixel,n!==this.start}clampStart(e){const t=this.genome.getChromosome(this.chr).bpStart||0;if(this.start=Math.max(t,this.start),e){const{bpLength:t}=this.genome.getChromosome(this.chr),i=t-e*this.bpPerPixel;this.start>i&&(this.start=i)}}async zoomWithScaleFactor(e,t,i,n){const r=void 0===n?this.start+this.toBP(i/2):n,s=this.start,o=this.bpPerPixel,a=this.getChromosome().bpLength,c=t<1?e.minimumBases()/i:a/i;this.bpPerPixel=t<1?Math.max(this.bpPerPixel*t,c):Math.min(this.bpPerPixel*t,c);const l=this.bpPerPixel*i;this.start=r-.5*l,this.clampStart(i),this.end=this.start+l;(s!==this.start||o!==this.bpPerPixel)&&await e.updateViews(!0)}getChromosome(){return this.genome.getChromosome(this.chr)}getMultiLocusLabelBPLengthOnly(e){const t=\"&nbsp\",i=Math.floor(this.start)+1,n=Math.round(this.start+this.bpPerPixel*e);return`${t}${this.chr}${t}${Wa(n-i)}${t}`}getMultiLocusLabelLocusOnly(e){const t=\"&nbsp\",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(e);return`${t}${i}:${n}-${r}${t}`}getMultiLocusLabel(e){const t=\"&nbsp\",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(e),s=Math.floor(this.start)+1;return`${t}${i}:${n}-${r}${t}${t}(${Wa(Math.round(this.start+this.bpPerPixel*e)-s)})${t}`}getPresentationLocusComponents(e){if(\"all\"===this.chr)return{chr:this.chr};{const t=Rt(Math.floor(this.start)+1),i=Rt(Math.round(this.start+this.bpPerPixel*e));return{chr:this.chr,start:t,end:i}}}getLocusString(){if(\"all\"===this.chr)return\"all\";return`${this.genome.getChromosomeDisplayName(this.chr)}:${Rt(Math.floor(this.start)+1)}-${Rt(Math.round(this.end))}`}description(e){console.log(` ${e||\"\"} referenceFrame - ${this.chr} bpp ${this.bpPerPixel.toFixed(3)} start ${Rt(Math.round(this.start))} end ${Rt(Math.round(this.end))} `)}overlaps(e){return this.chr===e.chr&&this.end>=e.start&&e.end>=this.start}}function yy(){return\"3.0.9\"}const Ay=\"Maximum sequence count exceeded\";class Cy{constructor(t,i){this.container=e({class:\"igv-chromosome-select-widget-container\"}),i.appendChild(this.container),this.select=document.createElement(\"select\"),this.select.setAttribute(\"name\",\"chromosome-select-widget\"),this.container.appendChild(this.select),this.select.addEventListener(\"change\",(()=>{this.select.blur(),\"\"!==this.select.value&&Ay!==this.select.value&&t.search(this.select.value)})),this.showAllChromosomes=!1!==t.config.showAllChromosomes,this.genome=t.genome}show(){this.container.style.display=\"flex\"}hide(){this.container.style.display=\"none\"}setValue(e){this.select.value=this.genome.getChromosomeDisplayName(e)}update(e){this.genome=e;const t=e.wgChromosomeNames.map((t=>e.getChromosomeDisplayName(t)))||[];if(this.showAllChromosomes&&e.chromosomeNames.length>1){const i=new Set(t);let n=0;for(let r of e.chromosomeNames){if(1e3==++n){t.push(Ay);break}i.has(r)||(r=e.getChromosomeDisplayName(r),t.push(r))}}this.select.innerHTML=\"\",e.showWholeGenomeView()&&t.unshift(\"all\");for(let i of t){const t=document.createElement(\"option\");t.setAttribute(\"value\",i),t.innerText=e.getChromosomeDisplayName(i),this.select.appendChild(t)}}}class _y{constructor(t,i){this.container=e({class:\"igv-windowsize-panel-container\"}),t.appendChild(this.container),i.on(\"locuschange\",(e=>{this.updatePanel(e)})),this.browser=i}show(){this.container.style.display=\"block\"}hide(){this.container.style.display=\"none\"}updatePanel(e){const t=this.browser.calculateViewportWidth(this.browser.referenceFrameList.length);this.container.innerText=1===e.length?Wa(Math.round(t*e[0].bpPerPixel)):\"\"}}class xy extends Ju{constructor(e,t,i,n){super(e,t,\"Select Tracks\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>multi select</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"multi-select\">\\n            <rect id=\"backdrop-copy-3\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-copy-3\" transform=\"translate(81, 427)\" fill=\"#737373\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy-2\" transform=\"translate(82, 277)\">\\n                <rect id=\"Rectangle\" fill-opacity=\"0.33\" fill=\"#CFCECE\" x=\"133\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke-opacity=\"0.32659528\" stroke=\"#CFCECE\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy\" transform=\"translate(81, 119)\" fill=\"#737373\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-17\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>multi select hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"multi-select-hover\">\\n            <rect id=\"backdrop-copy-4\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-copy-3\" transform=\"translate(81, 427)\" fill=\"#FFFFFF\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke=\"#FFFFFF\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy-2\" transform=\"translate(82, 277)\">\\n                <rect id=\"Rectangle\" fill-opacity=\"0.33\" fill=\"#CFCECE\" x=\"133\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke-opacity=\"0.33\" stroke=\"#CFCECE\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy\" transform=\"translate(81, 119)\" fill=\"#FFFFFF\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-17\" stroke=\"#FFFFFF\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n        </g>\\n    </g>\\n</svg>',!1),this.navbar=i,this.enableMultiTrackSelection=!1,this.button.addEventListener(\"mouseenter\",(e=>{!1===n&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(e=>{!1===n&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{this.setMultiTrackSelection(!this.enableMultiTrackSelection)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler)}setMultiTrackSelection(e){this.enableMultiTrackSelection=e,this.setState(this.enableMultiTrackSelection),!1===this.enableMultiTrackSelection&&this.navbar.overlayTrackButton.setVisibility(!1);for(const t of this.browser.trackViews)t.enableTrackSelection(e)}}class ky{constructor(t,i){this.browser=i,this.columnContainer=t,this.horizontalGuide=e({class:\"igv-cursor-guide-horizontal\"}),t.appendChild(this.horizontalGuide),this.verticalGuide=e({class:\"igv-cursor-guide-vertical\"}),t.appendChild(this.verticalGuide),this.addMouseHandler(i),this.setVisibility(i.config.showCursorGuide)}addMouseHandler(e){this.boundMouseMoveHandler=function(t){t.target.tagName;const{x:i,y:n}=a(t,this.columnContainer);if(this.horizontalGuide.style.top=`${n}px`,\"CANVAS\"===t.target.tagName){const n=function(e,t){for(;e.parentElement;){if(e.parentElement.classList.contains(t))return e.parentElement;e=e.parentElement}return}(t.target,\"igv-viewport\");if(n&&e.getRulerTrackView()){this.verticalGuide.style.left=`${i}px`;const r=e.root.querySelectorAll(\".igv-column\");let s;const o=n.parentElement;for(let e=0;e<r.length;e++)void 0===s&&o===r[e]&&(s=e);if(void 0!==s){const i=e.getRulerTrackView().viewports[s].mouseMove(t);if(i){const{start:e,bp:t,end:n}=i,r=(t-e)/(n-e);this.customMouseHandler&&this.customMouseHandler({start:e,bp:t,end:n,interpolant:r})}}}}}.bind(this),this.columnContainer.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandler(){this.columnContainer.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}setVisibility(e){!0===e?this.show():this.hide()}show(){this.verticalGuide.style.display=\"block\",this.horizontalGuide.style.display=\"block\"}hide(){if(this.verticalGuide.style.display=\"none\",this.horizontalGuide.style.display=\"none\",this.browser.getRulerTrackView())for(let e of this.browser.getRulerTrackView().viewports)e.$tooltip.hide()}}class Iy extends Ju{constructor(e,t){super(e,t,\"Crosshairs\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>cursor</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"cursor\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-3\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group\" transform=\"translate(5, 9)\" stroke-width=\"24\">\\n                <line x1=\"0.5\" y1=\"212.5\" x2=\"614.5\" y2=\"212.5\" id=\"Line\"></line>\\n                <line x1=\"-115.5\" y1=\"303.5\" x2=\"490.5\" y2=\"303.5\" id=\"Line-Copy\" transform=\"translate(187.5, 303.5) scale(-1, 1) rotate(90) translate(-187.5, -303.5)\"></line>\\n            </g>\\n            <circle id=\"Oval\" stroke-width=\"24\" cx=\"191.5\" cy=\"221.5\" r=\"88.5\"></circle>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>cursor hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"cursor-hover\">\\n            <rect id=\"Rectangle-Copy-5\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group-Copy-2\" transform=\"translate(5, 9)\" stroke=\"#FFFFFF\" stroke-width=\"24\">\\n                <line x1=\"0.5\" y1=\"212.5\" x2=\"614.5\" y2=\"212.5\" id=\"Line\"></line>\\n                <line x1=\"-115.5\" y1=\"303.5\" x2=\"490.5\" y2=\"303.5\" id=\"Line-Copy\" transform=\"translate(187.5, 303.5) scale(-1, 1) rotate(90) translate(-187.5, -303.5)\"></line>\\n            </g>\\n            <circle id=\"Oval\" stroke=\"#FFFFFF\" stroke-width=\"24\" cx=\"191.5\" cy=\"221.5\" r=\"88.5\"></circle>\\n        </g>\\n    </g>\\n</svg>',t.doShowCursorGuide),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowCursorGuide&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowCursorGuide&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowCursorGuide=!t.doShowCursorGuide,t.setCursorGuideVisibility(t.doShowCursorGuide),this.setState(t.doShowCursorGuide)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showCursorTrackingGuideButton)}}class Sy extends Ju{constructor(e,t){super(e,t,\"Center Line\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>centerline</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"centerline\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-2\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"6.5\" y1=\"312.5\" x2=\"618.5\" y2=\"312.5\" id=\"Line-Copy\" stroke-width=\"31\" transform=\"translate(312.5, 312.5) scale(-1, 1) rotate(90) translate(-312.5, -312.5)\"></line>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>centerline hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"centerline-hover\">\\n            <rect id=\"Rectangle-Copy-9\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"6.5\" y1=\"312.5\" x2=\"618.5\" y2=\"312.5\" id=\"Line-Copy\" stroke=\"#FFFFFF\" stroke-width=\"31\" transform=\"translate(312.5, 312.5) scale(-1, 1) rotate(90) translate(-312.5, -312.5)\"></line>\\n        </g>\\n    </g>\\n</svg>',t.config.showCenterGuide),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowCenterLine&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowCenterLine&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowCenterLine=!t.doShowCenterLine,t.setCenterLineVisibility(t.doShowCenterLine),this.setState(t.doShowCenterLine)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showCenterGuideButton)}}class Ey extends Ju{constructor(e,t){super(e,t,\"Track Labels\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>track labels</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"track-labels\" fill=\"#FFFFFF\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-27\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"group\" transform=\"translate(52.2778, 149.7248)\" stroke-width=\"24\">\\n                <path d=\"M448.444444,87.1189616 L448.444444,322.431462 L166.619398,322.431462 L19.2344421,204.775212 L166.619398,87.1189616 L448.444444,87.1189616 Z M244.028212,163.997434 C232.925565,163.997434 222.874656,168.493347 215.598982,175.760254 C208.318067,183.032394 203.815972,193.079106 203.815972,204.175675 C203.815972,215.272243 208.318067,225.318955 215.598982,232.591095 C222.874656,239.858002 232.925565,244.353915 244.028212,244.353915 C255.130858,244.353915 265.181767,239.858002 272.457442,232.591095 C279.738356,225.318955 284.240451,215.272243 284.240451,204.175675 C284.240451,193.079106 279.738356,183.032394 272.457442,175.760254 C265.181767,168.493347 255.130858,163.997434 244.028212,163.997434 Z\" id=\"backdrop\"></path>\\n                <path d=\"M495.232604,12 L495.232604,264.550423 L193.616935,264.550423 L35.4455183,138.275212 L193.616935,12 L495.232604,12 Z M168.133512,95.1660194 C156.441871,95.1660194 145.858581,99.8943121 138.197214,107.534302 C130.523695,115.18641 125.780417,125.758499 125.780417,137.434423 C125.780417,149.110347 130.523695,159.682435 138.197214,167.334543 C145.858581,174.974533 156.441871,179.702826 168.133512,179.702826 C179.825153,179.702826 190.408443,174.974533 198.06981,167.334543 C205.743329,159.682435 210.486607,149.110347 210.486607,137.434423 C210.486607,125.758499 205.743329,115.18641 198.06981,107.534302 C190.408443,99.8943121 179.825153,95.1660194 168.133512,95.1660194 Z\" id=\"hero\"></path>\\n            </g>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>track labels hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"track-labels-hover\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-29\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"group\" transform=\"translate(52.2778, 149.7248)\" fill=\"#FFFFFF\" stroke-width=\"24\">\\n                <path d=\"M448.444444,85.1189616 L448.444444,320.431462 L166.619398,320.431462 L19.2344421,202.775212 L166.619398,85.1189616 L448.444444,85.1189616 Z M244.028212,161.997434 C232.925565,161.997434 222.874656,166.493347 215.598982,173.760254 C208.318067,181.032394 203.815972,191.079106 203.815972,202.175675 C203.815972,213.272243 208.318067,223.318955 215.598982,230.591095 C222.874656,237.858002 232.925565,242.353915 244.028212,242.353915 C255.130858,242.353915 265.181767,237.858002 272.457442,230.591095 C279.738356,223.318955 284.240451,213.272243 284.240451,202.175675 C284.240451,191.079106 279.738356,181.032394 272.457442,173.760254 C265.181767,166.493347 255.130858,161.997434 244.028212,161.997434 Z\" id=\"backdrop\"></path>\\n                <path d=\"M495.232604,12 L495.232604,264.550423 L193.616935,264.550423 L35.4455183,138.275212 L193.616935,12 L495.232604,12 Z M168.133512,95.1660194 C156.441871,95.1660194 145.858581,99.8943121 138.197214,107.534302 C130.523695,115.18641 125.780417,125.758499 125.780417,137.434423 C125.780417,149.110347 130.523695,159.682435 138.197214,167.334543 C145.858581,174.974533 156.441871,179.702826 168.133512,179.702826 C179.825153,179.702826 190.408443,174.974533 198.06981,167.334543 C205.743329,159.682435 210.486607,149.110347 210.486607,137.434423 C210.486607,125.758499 205.743329,115.18641 198.06981,107.534302 C190.408443,99.8943121 179.825153,95.1660194 168.133512,95.1660194 Z\" id=\"hero\"></path>\\n            </g>\\n        </g>\\n    </g>\\n</svg>',t.config.showTrackLabels),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowTrackLabels&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowTrackLabels&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowTrackLabels=!t.doShowTrackLabels,t.setTrackLabelVisibility(t.doShowTrackLabels),this.setState(t.doShowTrackLabels)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showTrackLabelButton)}}class Ny extends Ju{constructor(e,t){super(e,t,[\"ROI\",\"Regions of Interest Table\"],ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>roi</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"roi\">\\n            <rect id=\"Rectangle-Copy-23\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <text id=\"ROI\" font-family=\"HelveticaNeue-Bold, Helvetica Neue\" font-size=\"258\" font-weight=\"bold\" fill=\"#737373\">\\n                <tspan x=\"81.445\" y=\"389\">ROI</tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>roi hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"roi-hover\">\\n            <rect id=\"Rectangle-Copy-24\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <text id=\"ROI\" font-family=\"HelveticaNeue-Bold, Helvetica Neue\" font-size=\"258\" font-weight=\"bold\" fill=\"#FFFFFF\">\\n                <tspan x=\"81.445\" y=\"389\">ROI</tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>',!1),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowROITable&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowROITable&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>this.buttonHandler(!t.doShowROITable))),this.setVisibility(!1)}buttonHandler(e){this.setState(e),this.browser.setROITableVisibility(e)}}class By extends Ju{constructor(e,t){super(e,t,\"Sample Info\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample info</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-info\">\\n            <rect id=\"Rectangle-Copy-6\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group-2\" transform=\"translate(8, 149)\">\\n                <rect id=\"Rectangle\" fill=\"#8DD3C7\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#FBB4AE\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#7FC97F\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#E41A1C\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#3F70AE\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"Group-2-Copy\" transform=\"translate(8, 251)\">\\n                <rect id=\"Rectangle\" fill=\"#E41A1C\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BC80BD\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#FFFFB3\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"Group-2-Copy-2\" transform=\"translate(314, 404) scale(-1, 1) translate(-314, -404)translate(8, 353)\">\\n                <rect id=\"Rectangle\" fill=\"#1B9E77\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BAD1E9\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#4DAF4A\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#CBF03E\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <rect id=\"Rectangle-Copy-10\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample info hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-info-hover\">\\n            <rect id=\"Rectangle-Copy-14\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-2\" transform=\"translate(314, 404) scale(-1, 1) translate(-314, -404)translate(8, 353)\">\\n                <rect id=\"Rectangle\" fill=\"#1B9E77\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BAD1E9\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#4DAF4A\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#CBF03E\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"row-1\" transform=\"translate(8, 251)\">\\n                <rect id=\"Rectangle\" fill=\"#E41A1C\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BC80BD\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#FFFFB3\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"row-0\" transform=\"translate(8, 149)\">\\n                <rect id=\"Rectangle\" fill=\"#8DD3C7\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#FBB4AE\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#7FC97F\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#E41A1C\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#3F70AE\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <rect id=\"Rectangle-Copy-15\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <rect id=\"scrim\" fill=\"#000000\" style=\"mix-blend-mode: hue;\" x=\"8\" y=\"149\" width=\"612\" height=\"306\"></rect>\\n        </g>\\n    </g>\\n</svg>',!1),this.showSampleInfo=!1,this.button.addEventListener(\"mouseenter\",(()=>{!1===this.showSampleInfo&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===this.showSampleInfo&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>{this.performClickWithState(t,void 0)}))}performClickWithState(e,t){this.showSampleInfo=void 0===t?!this.showSampleInfo:t;e.columnContainer.querySelector(\".igv-sample-info-column\").style.display=!1===this.showSampleInfo?\"none\":\"flex\",this.setState(this.showSampleInfo),e.layoutChange()}setButtonVisibility(e){this.showSampleInfo=e,this.setState(this.showSampleInfo),!0===this.showSampleInfo?this.show():this.hide()}}class My extends Ju{constructor(e,t){super(e,t,\"Sample Names\",'<svg width=\"90px\" height=\"20px\" viewBox=\"0 0 90 20\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"igv-navbar-button-group\">\\n            <rect id=\"Rectangle\" x=\"0.5\" y=\"0.5\" width=\"89\" height=\"18\" rx=\"6\"></rect>\\n            <text id=\"igv-text-button-label\" x=\"50%\" y=\"50%\" dy=\".1em\" font-family=\"Helvetica\" font-size=\"12\" font-weight=\"normal\" letter-spacing=\"-0.372\">\\n                <tspan id=\"igv-navbar-button-label\"></tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample names</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-names\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-13\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"80\" y1=\"465\" x2=\"541\" y2=\"464.5\" id=\"Line-3-Copy-3\" stroke-width=\"32\"></line>\\n            <line x1=\"80\" y1=\"312.5\" x2=\"542\" y2=\"313\" id=\"Line-3\" stroke-width=\"32\"></line>\\n            <line x1=\"80\" y1=\"158\" x2=\"541\" y2=\"158\" id=\"Line-3-Copy\" stroke-width=\"32\"></line>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample names hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-names-hover\">\\n            <rect id=\"Rectangle-Copy-18\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"80\" y1=\"465\" x2=\"541\" y2=\"464.5\" id=\"Line-3-Copy-3\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n            <line x1=\"80\" y1=\"312.5\" x2=\"542\" y2=\"313\" id=\"Line-3\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n            <line x1=\"80\" y1=\"158\" x2=\"541\" y2=\"158\" id=\"Line-3-Copy\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n        </g>\\n    </g>\\n</svg>',t.config.showSampleNames),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.showSampleNames&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.showSampleNames&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>{this.performClickWithState(t,void 0)})),!0===t.config.showSampleNameButton?this.show():this.hide()}performClickWithState(e,t){e.showSampleNames=void 0===t?!e.showSampleNames:t;e.columnContainer.querySelector(\".igv-sample-name-column\").style.display=!1===e.showSampleNames?\"none\":\"flex\",this.setState(e.showSampleNames),e.layoutChange()}}class Ry{constructor(t,i){this.parent=t,this.popover=e({class:\"igv-ui-dropdown\"}),t.appendChild(this.popover),this.popoverContent=e(),this.popover.appendChild(this.popoverContent),this.popover.style.display=\"none\",this.shim=i}configure(e){if(0===e.length)return;const t=nc(e,this.popover);for(const{object:e}of t)this.popoverContent.appendChild(e)}present(e){this.popover.style.display=\"block\";let{x:t,y:i}=a(e,this.parent);this.popover.style.left=`${t+this.shim.left}px`,this.popover.style.top=`${i+this.shim.top}px`}_present(e){this.popover.style.display=\"block\";let{x:t,y:i,width:n}=a(e,this.parent);t+=this.shim.left,i+=this.shim.top,this.popover.style.top=`${i}px`;const{width:r}=this.popover.getBoundingClientRect(),s=t+r,o=s-n;this.popover.style.left=`${s>n?t-o:t}px`}dismiss(){this.popover.style.display=\"none\"}}class Dy extends Ju{constructor(e,t){super(e,t,\"Save Image\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>save image</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"save-image\">\\n            <rect id=\"border\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"frame\" transform=\"translate(66, 66)\" fill=\"#737373\" fill-rule=\"nonzero\">\\n                <path d=\"M54.75,493 C39.69375,493 26.8046875,487.639062 16.0828125,476.917187 C5.3609375,466.195312 0,453.30625 0,438.25 L0,274 L54.75,274 L54.75,438.25 L219,438.25 L219,493 L54.75,493 Z\" id=\"Path\"></path>\\n                <path d=\"M274,493 L274,438.25 L438.25,438.25 L438.25,274 L493,274 L493,438.25 C493,453.30625 487.639062,466.195312 476.917187,476.917187 C466.195312,487.639062 453.30625,493 438.25,493 L274,493 Z\" id=\"Path\"></path>\\n                <path d=\"M0,219 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Hy(t,i,u.get(0)),!1===t.showNavigation&&this.$navigation.hide()}navbarDidResize(){const e=this.$navigation.width(),t=this.currentNavbarButtonClass();\"igv-navbar-text-button\"===t&&(this.textButtonContainerWidth=this.navbarRightContainer.getBoundingClientRect().width);const i=this.browser,n=i.isMultiLocusWholeGenomeView()||i.referenceFrameList&&mu.isWholeGenomeView(i.referenceFrameList[0].chr);n?this.windowSizePanel.hide():this.windowSizePanel.show();const{x:r,width:s}=this.navbarLeftContainer.getBoundingClientRect(),o=r+s,{x:a}=this.navbarRightContainer.getBoundingClientRect();let c;if(\"igv-navbar-text-button\"===t&&a-o<8)c=\"igv-navbar-icon-button\";else if(this.textButtonContainerWidth&&\"igv-navbar-icon-button\"===t){e-o-this.textButtonContainerWidth>8&&(c=\"igv-navbar-text-button\")}let l;c&&t!==c&&(this.currentClass=c,this.browser.fireEvent(\"navbar-resize\",[c])),l=n?\"igv-zoom-widget-hidden\":e>860?\"igv-zoom-widget\":\"igv-zoom-widget-900\",Bt(this.zoomWidget.zoomContainer).removeClass(),Bt(this.zoomWidget.zoomContainer).addClass(l)}setCenterLineButtonVisibility(e){e?this.centerLineButton.setVisibility(!e):this.centerLineButton.setVisibility(this.config.showCenterGuideButton)}setCursorGuideVisibility(e){e?this.cursorGuide.show():this.cursorGuide.hide()}updateGenome(e){let t=e.id&&e.id.length<20?e.id:`${e.id.substring(0,8)}...${e.id.substring(e.id.length-8)}`;this.$current_genome.text(t),this.$current_genome.attr(\"title\",e.description);!1!==this.config.showChromosomeWidget&&!1!==e.showChromosomeWidget&&e.chromosomeNames&&e.chromosomeNames.length>1?(this.chromosomeSelectWidget.update(e),this.chromosomeSelectWidget.show()):this.chromosomeSelectWidget.hide()}updateLocus(e,t){this.$searchInput&&this.$searchInput.val(e),this.chromosomeSelectWidget&&(this.chromosomeSelectWidget.select.value=t)}currentNavbarButtonClass(){return this.currentClass}setEnableTrackSelection(e){this.multiTrackSelectButton.setMultiTrackSelection(e)}getEnableTrackSelection(){return this.multiTrackSelectButton.enableMultiTrackSelection}hide(){this.$navigation.hide()}show(){this.$navigation.show()}}const Oy=(e,t)=>{const i=0===e?t.nextElementSibling:t.previousElementSibling;t.remove(),i.remove()},Uy=t=>{const i=e({class:\"igv-column-shim\"});Ya(i,t);const 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Vy=function(t,i){this.button=e({class:\"igv-navbar-button\"}),t.appendChild(this.button),this.button.textContent=\"circular view\",this.button.addEventListener(\"click\",(()=>{i.circularViewVisible=!i.circularViewVisible})),this.browser=i,this.setVisibility(i.config.showCircularViewButton),this.setState(i.circularViewVisible)};Vy.prototype.setVisibility=function(e){!0===e?this.show():this.hide()},Vy.prototype.setState=function(e){!0===e?this.button.classList.add(\"igv-navbar-button-clicked\"):this.button.classList.remove(\"igv-navbar-button-clicked\")},Vy.prototype.show=function(){this.button.style.display=\"block\",this.setState(this.browser.circularViewVisible)},Vy.prototype.hide=function(){this.button.style.display=\"none\"};class jy{constructor(t,i){this.browser=t,this.container=e({class:\"igv-roi-menu\"}),i.appendChild(this.container);const n=e();this.container.appendChild(n),u(n,(()=>this.container.style.display=\"none\")),this.body=e(),this.container.appendChild(this.body),this.container.style.display=\"none\"}async present(e,t,i,n,r,s){const o=this.menuItems(e,t,i,n,r,s);this.browser.menuPopup.presentTrackContextMenu(i,o)}menuItems(e,t,i,n,r,s){const o=e.name?[`<b>${e.name}</b><br/>`]:[];return\"name\"in t&&o.push(`<b>ROI Set: ${t.name}</b>`),o.length>0&&o.push(\"<hr/>\"),t.isUserDefined&&o.push({label:\"Set description ...\",click:()=>{const t={label:\"Description\",value:e.name||\"\",callback:()=>{const t=this.browser.inputDialog.value||\"\";e.name=t.trim(),this.browser.roiManager.repaintTable()}};this.browser.inputDialog.present(t,i)}}),Xa()&&e.end-e.start<1e6&&o.push({label:\"Copy reference sequence\",click:async()=>{this.container.style.display=\"none\";let t=await this.browser.genome.getSequence(e.chr,e.start,e.end);t||(t=\"Unknown sequence\");try{await navigator.clipboard.writeText(t)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),e.end-e.start<=25e3&&o.push({label:\"BLAT reference sequence\",click:async()=>{this.container.style.display=\"none\";const{chr:t,start:i,end:n}=e;let r=await this.browser.genome.getSequence(t,i,n);if(r){const e=`blat: ${t}:${i+1}-${n}`,s=`blat: ${t}:${i+1}-${n}`;jd({sequence:r,browser:this.browser,name:e,title:s})}}}),t.isUserDefined&&o.push(\"<hr/>\",{label:\"Delete\",click:async()=>{t.removeFeature(e);const i=await t.getAllFeatures();0===Object.keys(i).length&&n.deleteUserDefinedROISet(),n.deleteRegionWithKey(s.dataset.region,r),n.repaintTable()}}),o}dispose(){this.container.innerHTML=\"\"}}class Wy extends Pd{constructor(e){const t={browser:e,parent:e.columnContainer,headerTitle:\"Regions of 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n=e({class:\"igv-roi-table-button\"});this._footerDOM.appendChild(n),n.id=\"igv-roi-hide-show-button\",n.textContent=\"Hide all ROIs\",this.toggleROIButton=n,this.boundToggleDisplayButtonHandler=function(e){e.preventDefault(),e.stopPropagation(),this.browser.roiManager.toggleROIs()}.bind(this),this.toggleROIButton.addEventListener(\"click\",this.boundToggleDisplayButtonHandler)}setROIVisibility(e){const t=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let i=0;i<t.length;i++){const n=t[i];!1===e?$y(n,0):n.style.backgroundColor=n.dataset.color}this.toggleROIButton.textContent=!1===e?\"Show all ROIs\":\"Hide all ROIs\"}setTableRowSelectionState(e){super.setTableRowSelectionState(e);const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\");if(t.length>0&&t.length<2){const{locus:e}=Jy(t[0].dataset.region),{chr:i,start:n,end:r}=ey(e,this.browser.isSoftclipped());Gy(this.copySequenceButton,r-n<1e6)}else Gy(this.copySequenceButton,!1)}dispose(){document.removeEventListener(\"click\",this.boundGotoButtonHandler),document.removeEventListener(\"click\",this.boundCopySequenceButtonHandler),document.removeEventListener(\"click\",this.boundToggleDisplayButtonHandler),this.browser.roiTableControl.buttonHandler(!1),super.dispose()}static getColumnFormatConfiguration(e){return!0===e?[{label:\"Chr\",width:\"20%\"},{label:\"Start\",width:\"15%\"},{label:\"End\",width:\"15%\"},{label:\"Description\",width:\"30%\"},{label:\"ROI Set\",width:\"20%\"}]:[{label:\"Chr\",width:\"25%\"},{label:\"Start\",width:\"20%\"},{label:\"End\",width:\"20%\"},{label:\"Description\",width:\"35%\"}]}static gotoButtonHandler(e){e.stopPropagation();const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\"),i=[];for(let e of t){const{locus:t}=Jy(e.dataset.region);i.push(t)}for(let e of this.tableDOM.querySelectorAll(\".igv-roi-table-row\"))e.classList.remove(\"igv-roi-table-row-selected\");this.setTableRowSelectionState(!1),i.length>0&&this.browser.search(i.join(\" \"))}}function Gy(e,t){e.style.pointerEvents=t?\"auto\":\"none\",e.style.color=ro(t?\"licorice\":\"silver\"),e.style.borderColor=ro(t?\"licorice\":\"silver\")}function $y(e,t){const i=window.getComputedStyle(e).backgroundColor.match(/[\\d.]+/g);3===i.length&&i.push(1),i[3]=t,e.style.backgroundColor=`rgba(${i.join(\", \")})`}class Ky{constructor(e){this.browser=e,this.roiMenu=new jy(e,e.columnContainer),this.roiTable=new Wy(e,e.columnContainer),this.top=0,this.roiSets=[],this.boundLocusChangeHandler=Yy.bind(this),e.on(\"locuschange\",this.boundLocusChangeHandler);this.observer=new MutationObserver((()=>{const t=e.findTracks((e=>new Set([\"ideogram\",\"ruler\"]).has(e.type))),[i,n]=t.map((e=>e.trackView.viewports[0].$viewport.get(0))).map((e=>function(e){const t=window.getComputedStyle(e),i=parseInt(t.marginTop),n=parseInt(t.marginBottom),{top:r,bottom:s,height:o}=e.getBoundingClientRect();return{top:Math.floor(r)-i,bottom:Math.floor(s)+n,height:Math.floor(o)+i+n}}(e))),r=i?i.height:0,s=n?n.height:0,o=e.columnContainer.querySelectorAll(\".igv-roi-region\");if(o)for(const e of o)e.style.marginTop=`${r+s+-.5}px`})),this.observer.observe(e.columnContainer,{attributes:!0,childList:!0,subtree:!0})}async reset(){this.roiSets.length>0&&this.browser.roiTableControl.setVisibility(!0);const e=this.roiSets.map((e=>this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e})));e.length>0&&await Promise.all(e);const t=await this.getTableRecords();if(this.roiTable.renderTable(t),this.roiSets.length>0){const e=this.roiSets[0].isVisible;this.roiTable.setROIVisibility(e)}}async loadROI(e,t){const i=Array.isArray(e)?e:[e];for(let e of i)!e.name&&e.url&&(e.name=await ja(e.url)),e.url&&!e.format&&(e.format=await am(e)),this.roiSets.push(new ku(e,t));await this.reset()}clearROIs(){this.roiTable.clearTable();const e=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let t of e)t.remove();for(let e of this.roiSets)e.dispose();this.roiSets=[]}async getTableRecords(){const e=[];for(let t of this.roiSets){const i=t.name||\"\",n=await t.getAllFeatures();for(let t of Object.keys(n))for(let r of n[t])e.push({setName:i,feature:r})}return e}presentTable(){this.roiTable.present()}async repaintTable(){const e=await this.getTableRecords();this.roiTable.renderTable(e)}dismissTable(){this.roiTable.dismiss()}roiTableIsVisible(){return this.roiTable.isVisible()}async updateUserDefinedROISet(e){let t=await this.getUserDefinedROISet();void 0===t&&(t=this.initializeUserDefinedROISet()),t.addFeature(e),this.setROITableButtonVisibility(!0),await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t});const i=await this.getTableRecords();this.roiTable.renderTable(i)}setROITableButtonVisibility(e){this.browser.roiTableControl.setVisibility(e)}toggleROIs(){const e=!this.roiSets[0].isVisible;this.roiTable.setROIVisibility(e);for(const t of this.roiSets)t.isVisible=e}async renderAllROISets(){for(let e of this.roiSets)await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e})}async renderROISet({browser:e,pixelTop:t,roiSet:i}){const n=e.columnContainer.querySelectorAll(\".igv-column\");for(let r=0;r<n.length;r++){let{chr:s,start:o,end:a,bpPerPixel:c}=e.referenceFrameList[r];const l=n[r].querySelectorAll(\".igv-roi-region\");for(let e of l){const t=e.dataset.region,{chr:i,start:n,end:r}=Jy(t);(i!==s||r<o||n>a)&&e.remove()}const h=await i.getFeatures(s,o,a);if(h)for(let l of h){const h=Xy(s,l.start,l.end),{x:d,width:u}=Iu(Math.max(o,l.start),Math.min(a,l.end),o,c),f=n[r].querySelector(Zy(h));if(f)f.style.left=`${d}px`,f.style.width=`${u}px`;else{const s=this.createRegionElement(e.columnContainer,t,d,u,i,h,l);n[r].appendChild(s)}}}}createRegionElement(t,i,n,r,s,o,c){const l=e({class:\"igv-roi-region\"});l.style.top=`${i}px`,l.style.left=`${n}px`,l.style.width=`${r}px`,l.style.backgroundColor=s.color,l.dataset.color=s.color,l.dataset.region=o;const h=e();return l.appendChild(h),h.style.backgroundColor=s.headerColor,h.addEventListener(\"click\",(e=>{e.preventDefault(),e.stopPropagation(),a(e,t),this.roiMenu.present(c,s,e,this,t,l)})),l}renderSVGContext(e,t,{deltaX:i,deltaY:n}){for(const r of e.querySelectorAll(\".igv-roi-region\")){const{x:e,y:s,width:o,height:a}=r.getBoundingClientRect();t.fillStyle=r.style.backgroundColor,t.fillRect(e-i,s+n,o,a);const c=r.querySelector(\"div\"),{x:l,y:h,width:d,height:u}=c.getBoundingClientRect();t.fillStyle=c.style.backgroundColor,t.fillRect(l-i,h+n,d,u)}}getUserDefinedROISet(){return this.roiSets.find((e=>!0===e.isUserDefined))}deleteUserDefinedROISet(){this.roiSets=this.roiSets.filter((e=>!0!==e.isUserDefined))}initializeUserDefinedROISet(){const e=new ku({name:\"user defined\",isUserDefined:!0,features:[]},this.browser.genome);return this.roiSets.push(e),e}async deleteRegionWithKey(e,t){t.querySelectorAll(Zy(e)).forEach((e=>e.remove()));0===(await this.getTableRecords()).length&&(this.browser.roiTableControl.buttonHandler(!1),this.setROITableButtonVisibility(!1))}toJSON(){return this.roiSets.map((e=>e.toJSON()))}dispose(){this.browser.off(\"locuschange\",this.boundLocusChangeHandler);const e=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let t of e)t.remove();this.roiMenu&&this.roiMenu.dispose(),this.roiTable&&this.roiTable.dispose();for(let e of this.roiSets)e.dispose();for(let e of Object.keys(this))this[e]=void 0}}function Yy(){this.renderAllROISets()}function Xy(e,t,i){return`${e}-${t}-${i}`}function Zy(e){return`[data-region=\"${e}\"]`}function Jy(e){let t=e.split(\"-\"),i=parseInt(t.pop()),n=parseInt(t.pop()),r=t.join(\"-\");return{chr:r,start:n,end:i,locus:`${r}:${n}-${i}`,bedRecord:`${r}\\t${n}\\t${i}`}}class eA{constructor(e,t){this.name=e.name,this.featureSource=e.featureSource||Ad(e,t),this.color=e.color||_u}async getFeatures(e,t,i){return this.featureSource.getFeatures({chr:e,start:t,end:i})}draw(e){const{context:t,bpPerPixel:i,bpStart:n,pixelTop:r,pixelHeight:s,pixelWidth:o,features:a}=e;if(!a)return;const c=n+o*i+1;for(let{start:e,end:o}of a){if(o<n)continue;if(e>c)break;const{x:a,width:l}=Iu(e,o,n,i);xo.fillRect(t,a,r,l,s,{fillStyle:this.color})}}}class tA{aliasRecordCache=new Map;constructor(e,t,i){(t=t||{}).url=e,this.reader=new Zh(t,i)}async preload(e){await this.reader.preload();for(let t of e)await this.search(t)}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}async search(e){if(!this.aliasRecordCache.has(e)){const t=await this.reader.search(e);if(t)for(let e of Object.keys(t))\"start\"!==e&&\"end\"!==e&&this.aliasRecordCache.set(t[e],t)}return this.aliasRecordCache.get(e)}async getChromosomeNames(){return await this.reader.loadHeader(),Array.from(this.reader.chrNames)}}class iA{aliasRecordCache=new Map;constructor(e,t,i){this.aliasURL=e,this.config=t,this.genome=i}async preload(){return this.loadAliases()}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}async loadAliases(){const e=await Qs.loadString(this.aliasURL,Ua(this.config)),t=Dt(e),i=t[0];i.startsWith(\"#\")&&(this.headings=i.substring(1).split(\"\\t\").map((e=>e.trim())),this.altNameSets=this.headings.slice(1));const n=this.genome.chromosomeNames?new Set(this.genome.chromosomeNames):new Set;for(let e of t)if(!e.startsWith(\"#\")&&e.length>0){const t=e.split(\"\\t\");let i=t.find((e=>n.has(e)));i||(i=t[0]);const r={chr:i};for(let e=0;e<t.length;e++){r[this.headings?this.headings[e]:e]=t[e],this.aliasRecordCache.set(t[e],r)}this.aliasRecordCache.set(i.toLowerCase(),r),this.aliasRecordCache.set(i.toUpperCase(),r)}}async search(e){return 0===this.aliasRecordCache.size&&await this.loadAliases(),this.aliasRecordCache.get(e)}}class nA{constructor(e,t,i,n){this.start=e,this.end=t,this.name=i,this.stain=0,\"acen\"===n?this.type=\"c\":(this.type=n.charAt(1),\"p\"===this.type&&(this.stain=parseInt(n.substring(4))))}}class rA{cytobandMap=new Map;constructor(e,t,i){(t=t||{}).url=e,this.source=new od(t,i)}async getCytobands(e){if(this.cytobandMap.has(e))return this.cytobandMap.get(e);{let t=await this.#k(e);return t||(t=[]),this.cytobandMap.set(e,t),t}}async#k(e){return(await this.source.getFeatures({chr:e})).map((e=>new nA(e.start,e.end,e.name,e.gieStain)))}}class sA{cytobands=new Map;constructor(e,t){this.url=e,this.config=t}async getCytobands(e){return 0===this.cytobands.size&&await this.#I(),this.cytobands.get(e)}async#I(){let e,t;if(Ga(this.url)){const t=vs(this.url);e=\"\";const i=t.length;for(let n=0;n<i;n++)e+=String.fromCharCode(t[n])}else e=await Qs.loadString(this.url,Ua(this.config));let i=[];const n=Dt(e);for(let e of n){const n=e.split(\"\\t\"),r=n[0];if(t||(t=r),r!==t&&(this.cytobands.set(t,i),i=[],t=r),5===n.length){const e=parseInt(n[1]),t=parseInt(n[2]),r=n[3],s=n[4];i.push(new nA(e,t,r,s))}}}async getChromosomeNames(){return 0===this.cytobands.size&&await this.#I(),Array.from(this.cytobands.keys())}async getChromosomes(){0===this.cytobands.size&&await this.#I();const e=[];let t=0;for(let[i,n]of this.cytobands.entries())e.push(new lc(i,t++,n[n.length-1].end));return e}}class oA{aliasRecordCache=new Map;constructor(e,t){this.genomeID=e,this.update(e,t)}async preload(){}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}update(e,t){if(t){const i=[];for(let n of t){if(this.aliasRecordCache.has(n))continue;let t=!1;const r={chr:n};if(i.push(r),n.startsWith(\"gi|\")){const e=oA.getNCBIName(n);r[\"ncbi-gi-versioned\"]=e;const t=e.lastIndexOf(\".\");if(t>0){const e=e.substring(0,t);r[\"ncbi-gi\"]=e}}else{if(e.startsWith(\"hg\")||e.startsWith(\"GRCh\")||\"1kg_ref\"===e||\"b37\"===e)switch(n){case\"23\":r.ucsc=\"chrX\",t=!0;break;case\"24\":r.ucsc=\"chrY\",t=!0;break;case\"chrX\":r.ncbi=\"23\",t=!0;break;case\"chrY\":r.ncbi=\"24\",t=!0}else if(e.startsWith(\"mm\")||e.startsWith(\"GRCm\")||e.startsWith(\"rheMac\"))switch(n){case\"21\":r.ucsc=\"chrX\",t=!0;break;case\"22\":r.ucsc=\"chrY\",t=!0;break;case\"chrX\":r.ncbi=\"21\",t=!0;break;case\"chrY\":r.ncbi=\"22\",t=!0}if(t)continue;\"chrM\"===n?r.ncbi=\"MT\":\"MT\"===n?r.ucsc=\"chrM\":n.toLowerCase().startsWith(\"chr\")?r.ncbi=n.substring(3):Number.isInteger(Number(n))&&(r.ucsc=\"chr\"+n)}}for(let e of i){for(let t of Object.values(e))this.aliasRecordCache.set(t,e);this.aliasRecordCache.set(e.chr.toLowerCase(),e),this.aliasRecordCache.set(e.chr.toUpperCase(),e)}}}search(e){return this.aliasRecordCache.get(e)}static getNCBIName(e){const t=e.split(\"\\\\|\");return t[t.length-1]}}class aA{#S;static async createGenome(e,t){const i=new aA(e,t);return await i.init(),i}constructor(e,t){this.config=e,this.browser=t,this.id=e.id||function(e){return void 0!==e.id?e.id:e.fastaURL&&Mt(e.fastaURL)&&!e.fastaURL.startsWith(\"data:\")?e.fastaURL:e.fastaURL&&e.fastaURL.name?e.fastaURL.name:\"\"}(e),this.name=e.name,this.nameSet=e.nameSet}async init(){const e=this.config;if(this.sequence=await Nc(e,this.browser),e.chromSizesURL?this.chromosomes=await async function(e){const t=new Map;let i;if(Ga(e)){let t=vs(e);i=\"\";for(let e of t)i+=String.fromCharCode(e)}else i=await Qs.load(e,{});const n=Fc(i);let r=0;for(let e of n){const i=e.split(\"\\t\");if(i.length>1){const e=Number.parseInt(i[1]);t.set(i[0],new lc(i[0],r++,e))}}return t}(e.chromSizesURL):this.chromosomes=this.sequence.chromosomes||new Map,this.chromosomes.size>0&&(this.chromosomeNames=Array.from(this.chromosomes.keys())),e.chromAliasBbURL?(this.chromAlias=new tA(e.chromAliasBbURL,Object.assign({},e),this),this.chromosomeNames||(this.chromosomeNames=await this.chromAlias.getChromosomeNames())):e.aliasURL?this.chromAlias=new iA(e.aliasURL,Object.assign({},e),this):this.chromosomeNames&&(this.chromAlias=new oA(this.id,this.chromosomeNames)),e.cytobandBbURL)this.cytobandSource=new rA(e.cytobandBbURL,Object.assign({},e),this),this.chromosomeNames||(this.chromosomeNames=await this.cytobandSource.getChromosomeNames());else if(e.cytobandURL&&(this.cytobandSource=new sA(e.cytobandURL,Object.assign({},e)),this.chromosomeNames||(this.chromosomeNames=await this.cytobandSource.getChromosomeNames()),0===this.chromosomes.size)){const e=await this.cytobandSource.getChromosomes();for(let t of e)this.chromosomes.set(e.name,e)}if(!1!==e.wholeGenomeView&&this.chromosomes.size>0&&(e.chromosomeOrder?Array.isArray(e.chromosomeOrder)?this.#S=e.chromosomeOrder:this.#S=e.chromosomeOrder.split(\",\").map((e=>e.trim())):this.#S=function(e){const t=[];let i,n=1;for(let r of e.values()){if(i){if(r.bpLength<i/100)continue;i=((n-1)*i+r.bpLength)/n,t.push(r.name)}else i=r.bpLength,t.push(r.name);n++}return t}(this.chromosomes),await this.chromAlias.preload(this.#S)),this.wholeGenomeView=!1!==e.wholeGenomeView&&this.#S&&this.chromosomes.size>1,this.wholeGenomeView){const e=this.#S.reduce(((e,t)=>e+this.chromosomes.get(t).bpLength),0);this.chromosomes.set(\"all\",new lc(\"all\",0,e))}}get description(){return this.config.description||`${this.id}\\n${this.name}`}get infoURL(){return this.config.infoURL}showWholeGenomeView(){return this.wholeGenomeView}toJSON(){return Object.assign({},this.config,{tracks:void 0})}get initialLocus(){return this.config.locus?this.config.locus:this.getHomeChromosomeName()}getHomeChromosomeName(){return this.showWholeGenomeView()&&this.chromosomes.has(\"all\")?\"all\":this.chromosomeNames[0]}getChromosomeName(e){return this.chromAlias?this.chromAlias.getChromosomeName(e,this.chromosomes.keys()):e}getChromosomeDisplayName(e){return this.nameSet&&this.chromAlias&&this.chromAlias.getChromosomeAlias(e,this.nameSet)||e}getChromosome(e){return this.chromAlias&&(e=this.chromAlias.getChromosomeName(e)),this.chromosomes.get(e)}async loadChromosome(e){if(this.chromAlias){const t=await this.chromAlias.search(e);t&&(e=t.chr)}if(!this.chromosomes.has(e)){let t;const i=await this.sequence.getSequenceRecord(e);i&&(t=new lc(e,0,i.bpLength)),this.chromosomes.set(e,t)}return this.chromosomes.get(e)}async getAliasRecord(e){if(this.chromAlias)return this.chromAlias.search(e)}async getCytobands(e){if(this.cytobandSource){const t=this.getChromosomeName(e);return await this.cytobandSource.getCytobands(t)}}getChromosomes(){return this.chromosomes}get wgChromosomeNames(){return this.#S?this.#S.slice():void 0}get showChromosomeWidget(){return this.config.showChromosomeWidget}getGenomeCoordinate(e,t){var i=this.getCumulativeOffset(e);if(void 0!==i)return i+t}getChromosomeCoordinate(e){let t;void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=computeCumulativeOffsets.call(this));let i=0;for(let n of this.#S){const r=this.cumulativeOffsets[n];if(r>e){return{chr:t,position:e-i}}t=n,i=r}return{chr:this.#S[this.#S.length-1],position:0}}getCumulativeOffset(e){void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=function(){let e={},t=0;for(let i of this.#S){e[i]=Math.floor(t);t+=this.getChromosome(i).bpLength}return e}.call(this));const t=this.getChromosomeName(e);return this.cumulativeOffsets[t]}getGenomeLength(){if(!this.bpLength){let e=0;for(let t of this.#S){e+=this.chromosomes.get(t).bpLength}this.bpLength=e}return this.bpLength}async getSequence(e,t,i){return e=this.getChromosomeName(e),this.sequence.getSequence(e,t,i)}getSequenceInterval(e,t,i){return\"function\"==typeof this.sequence.getSequenceInterval?this.sequence.getSequenceInterval(e,t,i):void 0}}class cA{constructor(){this.clear()}clear(){this.phenotypeColors=new Map,this.snps=new Set,this.qtl=null}isEmpty(){return 0===this.phenotypeColors.size&&0===this.snps.size&&null===this.qtl}addSnp(e){e=e.toUpperCase(),this.snps.add(e)}addPhenotype(e){e=e.toUpperCase();const t=this.phenotypeColors.size;if(!this.phenotypeColors.has(e.toUpperCase())){const i=t<lA.length?lA[t]:_s.randomRGB(0,255);this.phenotypeColors.set(e.toUpperCase(),i)}}hasSnp(e){return e&&this.snps.has(e.toUpperCase())}hasPhenotype(e){return e&&this.phenotypeColors.has(e.toUpperCase())}hasQTL(e){return this.qtls.has(e)}colorForGene(e){return e?this.phenotypeColors.get(e.toUpperCase()):\"black\"}toJSON(){const e={};return this.phenotypeColors.size>0&&(e.phenotypes=Array.from(this.phenotypeColors.keys())),this.snps.size>0&&(e.snps=Array.from(this.snps)),this.qtl&&(e.qtl=this.qtl),e}static fromJSON(e){const t=new cA;if(e.phenotypes)for(let i of e.phenotypes)t.addPhenotype(i);if(e.snps)for(let i of e.snps)t.addSnp(i);return e.qtl&&(t.qtl=e.qtl),t}}const lA=[];lA.push(\"rgb(228,26,28)\"),lA.push(\"rgb(55,126,184)\"),lA.push(\"rgb(77,175,74)\"),lA.push(\"rgb(166,86,40)\"),lA.push(\"rgb(152,78,163)\"),lA.push(\"rgb(255,127,0)\"),lA.push(\"rgb(247,129,191)\"),lA.push(\"rgb(255,255,51)\"),lA.push(\"rgb(102,194,165)\"),lA.push(\"rgb(252,141,98)\"),lA.push(\"rgb(141, 160, 203)\"),lA.push(\"rgb(231, 138, 195)\"),lA.push(\"rgb(166, 216, 84)\"),lA.push(\"rgb(255, 217, 47)\"),lA.push(\"rgb(229, 196, 148)\"),lA.push(\"rgb( 141, 211, 199)\"),lA.push(\"rgb(255, 255, 179)\"),lA.push(\"rgb(190, 186, 218)\"),lA.push(\"rgb(251, 128, 114)\"),lA.push(\"rgb(128, 177, 211)\"),lA.push(\"rgb(253, 180, 98)\"),lA.push(\"rgb(179, 222, 105)\"),lA.push(\"rgb(252, 205, 229)\"),lA.push(\"rgb(188, 128, 189)\"),lA.push(\"rgb(204, 235, 197)\"),lA.push(\"rgb(255, 237, 111)\");class hA{constructor(t){this.parent=t,this.container=e({class:\"igv-ui-generic-dialog-container\"}),t.appendChild(this.container);const n=e({class:\"igv-ui-generic-dialog-header\"});this.container.appendChild(n),this.label=e({class:\"igv-ui-generic-dialog-one-liner\"}),this.container.appendChild(this.label),this.label.text=\"Unlabeled\",this.input_container=e({class:\"igv-ui-generic-dialog-input\"}),this.container.appendChild(this.input_container);let r='<input type=\"range\" id=\"igv-slider-dialog-input\" name=\"igv-slider-dialog-input\" />';this._input=document.createRange().createContextualFragment(r).firstChild,this.input_container.appendChild(this._input),r='<output id=\"igv-slider-dialog-output\" name=\"igv-slider-dialog-output\" for=\"igv-slider-dialog-input\"></output>',this._output=document.createRange().createContextualFragment(r).firstChild,this.input_container.appendChild(this._output);const s=e({class:\"igv-ui-generic-dialog-ok-cancel\"});this.container.appendChild(s),this.ok=e(),s.appendChild(this.ok),this.ok.textContent=\"OK\",this.cancel=e(),s.appendChild(this.cancel),this.cancel.textContent=\"Cancel\",i(this.container),this._input.addEventListener(\"input\",(()=>{const e=parseFloat(this._input.value)/this._scaleFactor;this.callback(e),this._output.value=`${e.toFixed(2)}`}),!1),this.ok.addEventListener(\"click\",(()=>{if(\"function\"==typeof this.callback){const e=parseFloat(this._input.value)/this._scaleFactor;this.callback(e),this.callback=void 0}this._input.value=void 0,i(this.container)}));const o=()=>{this._input.value=void 0,i(this.container)};this.cancel.addEventListener(\"click\",o),u(n,o),p(this.container,n)}get value(){return Ea.sanitize(this._input.value)}present(e,t){this.label.textContent=e.label,this._scaleFactor=e.scaleFactor;const[i,r,s]=[e.min,e.max,e.value].map((e=>Math.floor(this._scaleFactor*e).toString()));this._input.min=i,this._input.max=r,this._input.value=s;const o=parseFloat(s)/this._scaleFactor;this._output.value=`${o.toFixed(2)}`,this.callback=e.callback||e.click,n(this.container),this.clampLocation(t.clientX,t.clientY)}clampLocation(e,t){const{width:i,height:n}=this.container.getBoundingClientRect(),r=window.innerHeight,s=window.innerWidth,o=Math.min(r-n,t),a=Math.min(s-i,e);this.container.style.left=`${a}px`,this.container.style.top=`${o}px`}}class dA{qtlSelections=new cA;constructor(t,i){this.config=t,this.guid=s(),this.namespace=\".browser_\"+this.guid,this.parent=i;let n=i.shadowRoot;if(!n){n=i.attachShadow({mode:\"open\"});const e=new CSSStyleSheet;e.replaceSync('.igv-ui-dropdown {\\n  cursor: default;\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  z-index: 2048;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: 1px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div {\\n  overflow-y: auto;\\n  overflow-x: hidden;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div > div {\\n  padding: 4px;\\n  width: 100%;\\n  overflow-x: hidden;\\n  text-overflow: ellipsis;\\n  white-space: nowrap;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: 1px;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div > div:last-child {\\n  border-bottom-color: transparent;\\n  border-bottom-width: 0;\\n}\\n.igv-ui-dropdown > div > div:hover {\\n  cursor: pointer;\\n  background-color: rgba(0, 0, 0, 0.04);\\n}\\n\\n.igv-ui-popover {\\n  cursor: default;\\n  position: absolute;\\n  z-index: 2048;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: 1px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  background-color: white;\\n}\\n.igv-ui-popover > div:first-child {\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-width: 0;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-popover > div:first-child > div:first-child {\\n  margin-left: 4px;\\n}\\n.igv-ui-popover > div:first-child > div:last-child {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-popover > div:first-child > div:last-child:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-popover > div:last-child {\\n  user-select: text;\\n  overflow-y: auto;\\n  overflow-x: hidden;\\n  max-height: 400px;\\n  max-width: 800px;\\n  background-color: white;\\n  border-bottom-width: 0;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n}\\n.igv-ui-popover > div:last-child > div {\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  min-width: 220px;\\n  overflow-x: hidden;\\n  text-overflow: ellipsis;\\n  white-space: nowrap;\\n}\\n.igv-ui-popover > div:last-child > div > span {\\n  font-weight: bolder;\\n}\\n.igv-ui-popover > div:last-child hr {\\n  width: 100%;\\n}\\n\\n.igv-ui-alert-dialog-container {\\n  box-sizing: content-box;\\n  position: absolute;\\n  z-index: 2048;\\n  top: 50%;\\n  left: 50%;\\n  width: 400px;\\n  height: 200px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  outline: none;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 15px;\\n  font-weight: 400;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-ui-alert-dialog-container > div:first-child {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-alert-dialog-container > div:first-child div:first-child {\\n  padding-left: 8px;\\n}\\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body {\\n  -webkit-user-select: text;\\n  -moz-user-select: text;\\n  -ms-user-select: text;\\n  user-select: text;\\n  color: #373737;\\n  width: 100%;\\n  height: calc(100% - 24px - 64px);\\n  overflow-y: scroll;\\n}\\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body .igv-ui-alert-dialog-body-copy {\\n  margin: 16px;\\n  width: auto;\\n  height: auto;\\n  overflow-wrap: break-word;\\n  word-break: break-word;\\n  background-color: white;\\n  border: unset;\\n}\\n.igv-ui-alert-dialog-container > div:last-child {\\n  width: 100%;\\n  margin-bottom: 10px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-ui-alert-dialog-container > div:last-child div {\\n  margin: unset;\\n  width: 40px;\\n  height: 30px;\\n  line-height: 30px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  border-color: #2B81AF;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-ui-alert-dialog-container > div:last-child div:hover {\\n  cursor: pointer;\\n  border-color: #25597f;\\n  background-color: #25597f;\\n}\\n\\n.igv-ui-color-swatch {\\n  position: relative;\\n  box-sizing: content-box;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: wrap;\\n  justify-content: center;\\n  align-items: center;\\n  width: 32px;\\n  height: 32px;\\n  border-style: solid;\\n  border-width: 2px;\\n  border-color: white;\\n  border-radius: 4px;\\n}\\n\\n.igv-ui-color-swatch:hover {\\n  border-color: dimgray;\\n}\\n\\n.igv-ui-colorpicker-menu-close-button {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 32px;\\n  margin-top: 4px;\\n  margin-bottom: 4px;\\n  padding-right: 8px;\\n}\\n.igv-ui-colorpicker-menu-close-button i.fa {\\n  display: block;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  color: #5f5f5f;\\n}\\n.igv-ui-colorpicker-menu-close-button i.fa:hover,\\n.igv-ui-colorpicker-menu-close-button i.fa:focus,\\n.igv-ui-colorpicker-menu-close-button i.fa:active {\\n  cursor: pointer;\\n  color: #0f0f0f;\\n}\\n\\n.igv-ui-generic-dialog-container {\\n  box-sizing: content-box;\\n  position: fixed;\\n  top: 0;\\n  left: 0;\\n  width: 300px;\\n  height: fit-content;\\n  padding-bottom: 16px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  z-index: 2048;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-one-liner {\\n  color: #373737;\\n  width: 95%;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-top: 8px;\\n  padding-left: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input {\\n  margin-top: 8px;\\n  width: 95%;\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  padding-left: 8px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input > div {\\n  width: fit-content;\\n  height: 100%;\\n  font-size: 16px;\\n  text-align: right;\\n  padding-right: 8px;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\\n  width: 50%;\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input {\\n  margin-top: 8px;\\n  width: calc(100% - 16px);\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input[type=range] {\\n  width: 70%;\\n  -webkit-appearance: none;\\n  background: linear-gradient(90deg, white, black);\\n  outline: none;\\n  margin: 0;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input output {\\n  display: block;\\n  height: 100%;\\n  width: 20%;\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel {\\n  width: 100%;\\n  height: 28px;\\n  padding-top: 16px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div {\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:first-child {\\n  margin-left: 32px;\\n  margin-right: 0;\\n  background-color: #5ea4e0;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:last-child {\\n  margin-left: 0;\\n  margin-right: 32px;\\n  background-color: #c4c4c4;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n\\n.igv-ui-generic-container {\\n  box-sizing: content-box;\\n  position: absolute;\\n  z-index: 2048;\\n  background-color: white;\\n  cursor: pointer;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: wrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-container > div:first-child {\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  height: 24px;\\n  width: 100%;\\n  background-color: #dddddd;\\n}\\n.igv-ui-generic-container > div:first-child > div {\\n  display: block;\\n  color: #5f5f5f;\\n  cursor: pointer;\\n  width: 14px;\\n  height: 14px;\\n  margin-right: 8px;\\n  margin-bottom: 4px;\\n}\\n\\n.igv-ui-dialog {\\n  z-index: 2048;\\n  position: fixed;\\n  width: fit-content;\\n  height: fit-content;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  background-color: white;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-dialog .igv-ui-dialog-one-liner {\\n  width: 95%;\\n  height: 24px;\\n  line-height: 24px;\\n  text-align: left;\\n  margin: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n  font-weight: bold;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel {\\n  width: 100%;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div {\\n  margin: 16px;\\n  margin-top: 32px;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child {\\n  background-color: #5ea4e0;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child {\\n  background-color: #c4c4c4;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok {\\n  width: 100%;\\n  height: 36px;\\n  margin-top: 32px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok div {\\n  width: 98px;\\n  height: 36px;\\n  line-height: 36px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  border-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok div:hover {\\n  cursor: pointer;\\n  background-color: #25597f;\\n}\\n\\n.igv-ui-panel, .igv-ui-panel-row, .igv-ui-panel-column {\\n  z-index: 2048;\\n  background-color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  display: flex;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-ui-panel-column {\\n  display: flex;\\n  flex-direction: column;\\n}\\n\\n.igv-ui-panel-row {\\n  display: flex;\\n  flex-direction: row;\\n}\\n\\n.igv-ui-textbox {\\n  background-color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  display: flex;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-ui-table {\\n  background-color: white;\\n}\\n\\n.igv-ui-table thead {\\n  position: sticky;\\n  top: 0;\\n}\\n\\n.igv-ui-table th {\\n  text-align: left;\\n}\\n\\n.igv-ui-table td {\\n  padding-right: 20px;\\n}\\n\\n.igv-ui-table tr:hover {\\n  background-color: lightblue;\\n}\\n\\n.igv-ui-center-fixed {\\n  left: 50%;\\n  top: 50%;\\n  transform: translate(-50%, -50%);\\n}\\n\\n.igv-navbar {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  box-sizing: border-box;\\n  width: 100%;\\n  color: #444;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  line-height: 32px;\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  margin-top: 2px;\\n  margin-bottom: 6px;\\n  height: 32px;\\n  border-style: solid;\\n  border-radius: 3px;\\n  border-width: thin;\\n  border-color: #bfbfbf;\\n  background-color: #f3f3f3;\\n}\\n.igv-navbar .igv-navbar-left-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  height: 32px;\\n  line-height: 32px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-logo {\\n  width: 34px;\\n  height: 32px;\\n  margin-right: 8px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\\n  height: 32px;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  user-select: none;\\n  line-height: 32px;\\n  vertical-align: middle;\\n  text-align: center;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  height: 100%;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n  height: 100%;\\n  width: 125px;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\\n  display: block;\\n  cursor: pointer;\\n  width: 100px;\\n  height: 75%;\\n  outline: none;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  margin-left: 8px;\\n  height: 22px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 240px;\\n  height: 22px;\\n  line-height: 22px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\\n  cursor: text;\\n  width: 85%;\\n  height: 22px;\\n  line-height: 22px;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  text-align: left;\\n  padding-left: 8px;\\n  margin-right: 8px;\\n  outline: none;\\n  border-style: solid;\\n  border-radius: 3px;\\n  border-width: thin;\\n  border-color: #bfbfbf;\\n  background-color: white;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\\n  cursor: pointer;\\n  height: 16px;\\n  width: 16px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\\n  margin-left: 4px;\\n  user-select: none;\\n}\\n.igv-navbar .igv-navbar-right-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\\n  position: relative;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-hidden {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  height: 100%;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\\n  color: #737373;\\n  font-size: 18px;\\n  margin-left: 8px;\\n  user-select: none;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\\n  cursor: pointer;\\n  margin-left: unset;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: unset;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: 4px;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\\n  display: block;\\n  height: fit-content;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\\n  display: block;\\n  width: 125px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\\n  display: block;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\\n  color: #737373;\\n  font-size: 18px;\\n  height: 32px;\\n  line-height: 32px;\\n  margin-left: 8px;\\n  user-select: none;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\\n  cursor: pointer;\\n  margin-left: unset;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: unset;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: 4px;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\\n  width: 0;\\n  height: 0;\\n  display: none;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\\n  width: 0;\\n  height: 0;\\n  display: none;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\\n  display: block;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\\n  display: none;\\n}\\n\\n.igv-navbar-button {\\n  display: block;\\n  box-sizing: unset;\\n  padding-left: 6px;\\n  padding-right: 6px;\\n  height: 18px;\\n  text-transform: capitalize;\\n  user-select: none;\\n  line-height: 18px;\\n  text-align: center;\\n  vertical-align: middle;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 11px;\\n  font-weight: 200;\\n  color: #737373;\\n  background-color: #f3f3f3;\\n  border-color: #737373;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 6px;\\n}\\n\\n.igv-navbar-button:hover {\\n  cursor: pointer;\\n}\\n\\n.igv-navbar-button-clicked {\\n  color: white;\\n  background-color: #737373;\\n}\\n\\n.igv-navbar-icon-button {\\n  cursor: pointer;\\n  position: relative;\\n  width: 24px;\\n  height: 24px;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-icon-button > div:first-child {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: -18px;\\n  width: 24px;\\n  height: 24px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-icon-button > div:last-child {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 18px;\\n  width: 24px;\\n  height: 24px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n\\n.igv-navbar-text-button {\\n  cursor: pointer;\\n  position: relative;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  border: none;\\n  display: flex;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-navbar-text-button > div:nth-child(2) {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 0;\\n  width: 38px;\\n  height: 18px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-text-button > div:nth-child(3) {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 42px;\\n  width: 38px;\\n  height: 18px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n\\n#igv-text-button-label {\\n  text-anchor: middle;\\n  dominant-baseline: middle;\\n}\\n\\n.igv-navbar-text-button-svg-inactive rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n.igv-navbar-text-button-svg-inactive text {\\n  fill: #737373;\\n}\\n.igv-navbar-text-button-svg-inactive tspan {\\n  dominant-baseline: middle;\\n}\\n\\n.igv-navbar-text-button-svg-hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n.igv-navbar-text-button-svg-hover text {\\n  fill: white;\\n}\\n.igv-navbar-text-button-svg-hover tspan {\\n  dominant-baseline: middle;\\n}\\n\\n#igv-save-svg-group rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n#igv-save-svg-group text {\\n  fill: #737373;\\n}\\n\\n#igv-save-svg-group:hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n#igv-save-svg-group:hover text {\\n  fill: white;\\n}\\n\\n#igv-save-png-group rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n#igv-save-png-group text {\\n  fill: #737373;\\n}\\n\\n#igv-save-png-group:hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n#igv-save-png-group:hover text {\\n  fill: white;\\n}\\n\\n.igv-zoom-in-notice-container {\\n  z-index: 256;\\n  position: absolute;\\n  top: 8px;\\n  left: 50%;\\n  transform: translate(-50%, 0%);\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n  background-color: white;\\n}\\n.igv-zoom-in-notice-container > div {\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  padding-top: 2px;\\n  padding-bottom: 2px;\\n  width: 100%;\\n  height: 100%;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  color: #3f3f3f;\\n}\\n\\n.igv-zoom-in-notice {\\n  position: absolute;\\n  top: 10px;\\n  left: 50%;\\n}\\n.igv-zoom-in-notice div {\\n  position: relative;\\n  left: -50%;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #3f3f3f;\\n  background-color: rgba(255, 255, 255, 0.51);\\n  z-index: 64;\\n}\\n\\n.igv-container-spinner {\\n  position: absolute;\\n  top: 90%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  z-index: 1024;\\n  width: 24px;\\n  height: 24px;\\n  pointer-events: none;\\n  color: #737373;\\n}\\n\\n.igv-multi-locus-close-button {\\n  position: absolute;\\n  top: 2px;\\n  right: 0;\\n  padding-left: 2px;\\n  padding-right: 2px;\\n  width: 12px;\\n  height: 12px;\\n  color: #666666;\\n  background-color: white;\\n  z-index: 1000;\\n}\\n.igv-multi-locus-close-button > svg {\\n  vertical-align: top;\\n}\\n\\n.igv-multi-locus-close-button:hover {\\n  cursor: pointer;\\n  color: #434343;\\n}\\n\\n.igv-multi-locus-ruler-label {\\n  z-index: 64;\\n  position: absolute;\\n  top: 2px;\\n  left: 0;\\n  width: 100%;\\n  height: 12px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-multi-locus-ruler-label > div {\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  color: rgb(16, 16, 16);\\n  background-color: white;\\n}\\n.igv-multi-locus-ruler-label > div {\\n  cursor: pointer;\\n}\\n\\n.igv-multi-locus-ruler-label-square-dot {\\n  z-index: 64;\\n  position: absolute;\\n  left: 50%;\\n  top: 5%;\\n  transform: translate(-50%, 0%);\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\\n  width: 14px;\\n  height: 14px;\\n}\\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\\n  margin-left: 16px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  color: rgb(16, 16, 16);\\n}\\n\\n.igv-ruler-sweeper {\\n  display: none;\\n  pointer-events: none;\\n  position: absolute;\\n  top: 26px;\\n  bottom: 0;\\n  left: 0;\\n  width: 0;\\n  z-index: 99999;\\n  background-color: rgba(68, 134, 247, 0.25);\\n}\\n\\n.igv-ruler-tooltip {\\n  pointer-events: none;\\n  z-index: 128;\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: 1px;\\n  height: 32px;\\n  background-color: transparent;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ruler-tooltip > div {\\n  pointer-events: none;\\n  width: 128px;\\n  height: auto;\\n  padding: 1px;\\n  color: #373737;\\n  font-size: 10px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  background-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #373737;\\n}\\n\\n.igv-track-label {\\n  position: absolute;\\n  left: 8px;\\n  top: 8px;\\n  width: auto;\\n  height: auto;\\n  max-width: 50%;\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  text-align: center;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  border-color: #444;\\n  border-radius: 2px;\\n  border-style: solid;\\n  border-width: thin;\\n  background-color: white;\\n  z-index: 128;\\n  cursor: pointer;\\n}\\n\\n.igv-track-label:hover,\\n.igv-track-label:focus,\\n.igv-track-label:active {\\n  background-color: #e8e8e8;\\n}\\n\\n.igv-track-label-popup-shim {\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  padding-top: 4px;\\n}\\n\\n.igv-center-line {\\n  display: none;\\n  pointer-events: none;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  left: 50%;\\n  transform: translateX(-50%);\\n  z-index: 8;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  border-left-style: dashed;\\n  border-left-width: thin;\\n  border-right-style: dashed;\\n  border-right-width: thin;\\n}\\n\\n.igv-center-line-wide {\\n  background-color: rgba(0, 0, 0, 0);\\n  border-left-color: rgba(127, 127, 127, 0.51);\\n  border-right-color: rgba(127, 127, 127, 0.51);\\n}\\n\\n.igv-center-line-thin {\\n  background-color: rgba(0, 0, 0, 0);\\n  border-left-color: rgba(127, 127, 127, 0.51);\\n  border-right-color: rgba(0, 0, 0, 0);\\n}\\n\\n.igv-cursor-guide-horizontal {\\n  display: none;\\n  pointer-events: none;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  position: absolute;\\n  left: 0;\\n  right: 0;\\n  top: 50%;\\n  height: 1px;\\n  z-index: 32;\\n  margin-left: 50px;\\n  margin-right: 54px;\\n  border-top-style: dotted;\\n  border-top-width: thin;\\n  border-top-color: rgba(127, 127, 127, 0.76);\\n}\\n\\n.igv-cursor-guide-vertical {\\n  pointer-events: none;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  left: 50%;\\n  width: 1px;\\n  z-index: 32;\\n  border-left-style: dotted;\\n  border-left-width: thin;\\n  border-left-color: rgba(127, 127, 127, 0.76);\\n  display: none;\\n}\\n\\n.igv-user-feedback {\\n  position: fixed;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 512px;\\n  height: 360px;\\n  z-index: 2048;\\n  background-color: white;\\n  border-color: #a2a2a2;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #444;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-user-feedback div:first-child {\\n  position: relative;\\n  height: 24px;\\n  width: 100%;\\n  background-color: white;\\n  border-bottom-color: #a2a2a2;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-user-feedback div:first-child div {\\n  position: absolute;\\n  top: 2px;\\n  width: 16px;\\n  height: 16px;\\n  background-color: transparent;\\n}\\n.igv-user-feedback div:first-child div:first-child {\\n  left: 8px;\\n}\\n.igv-user-feedback div:first-child div:last-child {\\n  cursor: pointer;\\n  right: 8px;\\n}\\n.igv-user-feedback div:last-child {\\n  width: 100%;\\n  height: calc(100% - 24px);\\n  border-width: 0;\\n}\\n.igv-user-feedback div:last-child div {\\n  width: auto;\\n  height: auto;\\n  margin: 8px;\\n}\\n\\n.igv-generic-dialog-container {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: 300px;\\n  height: 200px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  z-index: 2048;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\\n  color: #373737;\\n  width: 95%;\\n  height: 24px;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-top: 8px;\\n  padding-left: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\\n  margin-top: 8px;\\n  width: 95%;\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  padding-left: 8px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\\n  width: 30%;\\n  height: 100%;\\n  font-size: 16px;\\n  text-align: right;\\n  padding-right: 8px;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\\n  width: 50%;\\n  font-size: 16px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input {\\n  margin-top: 8px;\\n  width: calc(100% - 16px);\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input input {\\n  font-size: 16px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\\n  width: 100%;\\n  height: 28px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\\n  margin-top: 32px;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\\n  margin-left: 32px;\\n  margin-right: 0;\\n  background-color: #5ea4e0;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\\n  margin-left: 0;\\n  margin-right: 32px;\\n  background-color: #c4c4c4;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok {\\n  width: 100%;\\n  height: 36px;\\n  margin-top: 32px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\\n  width: 98px;\\n  height: 36px;\\n  line-height: 36px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  border-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\\n  cursor: pointer;\\n  background-color: #25597f;\\n}\\n\\n.igv-generic-container {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  z-index: 2048;\\n  background-color: white;\\n  cursor: pointer;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: wrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-container div:first-child {\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  height: 24px;\\n  width: 100%;\\n  background-color: #dddddd;\\n}\\n.igv-generic-container div:first-child i {\\n  display: block;\\n  color: #5f5f5f;\\n  cursor: pointer;\\n  width: 14px;\\n  height: 14px;\\n  margin-right: 8px;\\n  margin-bottom: 4px;\\n}\\n\\n.igv-menu-popup {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: max-content;\\n  max-width: 400px;\\n  z-index: 512;\\n  cursor: pointer;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  color: #4b4b4b;\\n  background: white;\\n  border-radius: 4px;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-end;\\n  text-align: left;\\n}\\n.igv-menu-popup > div:not(:first-child) {\\n  width: 100%;\\n}\\n.igv-menu-popup > div:not(:first-child) > div {\\n  background: white;\\n}\\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\\n  padding-left: 4px;\\n  padding-right: 4px;\\n}\\n.igv-menu-popup > div:not(:first-child) > div:last-child {\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-color: transparent;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-menu-popup > div:not(:first-child) > div:hover {\\n  background: #efefef;\\n}\\n\\n.igv-menu-popup-shim {\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  padding-bottom: 1px;\\n  padding-top: 1px;\\n}\\n\\n.igv-menu-popup-header {\\n  position: relative;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-menu-popup-header div {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-menu-popup-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n\\n.igv-menu-popup-check-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 100%;\\n  height: 20px;\\n  margin-right: 4px;\\n  background-color: transparent;\\n}\\n.igv-menu-popup-check-container div {\\n  padding-top: 2px;\\n  padding-left: 8px;\\n}\\n.igv-menu-popup-check-container div:first-child {\\n  position: relative;\\n  width: 12px;\\n  height: 12px;\\n}\\n.igv-menu-popup-check-container div:first-child svg {\\n  position: absolute;\\n  width: 12px;\\n  height: 12px;\\n}\\n\\n.igv-user-feedback {\\n  position: fixed;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 512px;\\n  height: 360px;\\n  z-index: 2048;\\n  background-color: white;\\n  border-color: #a2a2a2;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #444;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-user-feedback div:first-child {\\n  position: relative;\\n  height: 24px;\\n  width: 100%;\\n  background-color: white;\\n  border-bottom-color: #a2a2a2;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-user-feedback div:first-child div {\\n  position: absolute;\\n  top: 2px;\\n  width: 16px;\\n  height: 16px;\\n  background-color: transparent;\\n}\\n.igv-user-feedback div:first-child div:first-child {\\n  left: 8px;\\n}\\n.igv-user-feedback div:first-child div:last-child {\\n  cursor: pointer;\\n  right: 8px;\\n}\\n.igv-user-feedback div:last-child {\\n  width: 100%;\\n  height: calc(100% - 24px);\\n  border-width: 0;\\n}\\n.igv-user-feedback div:last-child div {\\n  width: auto;\\n  height: auto;\\n  margin: 8px;\\n}\\n\\n.igv-loading-spinner-container {\\n  z-index: 1024;\\n  position: absolute;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 32px;\\n  height: 32px;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-loading-spinner-container > div {\\n  box-sizing: border-box;\\n  width: 100%;\\n  height: 100%;\\n  border-radius: 50%;\\n  border: 4px solid rgba(128, 128, 128, 0.5);\\n  border-top-color: rgb(255, 255, 255);\\n  animation: spin 1s ease-in-out infinite;\\n  -webkit-animation: spin 1s ease-in-out infinite;\\n}\\n\\n@keyframes spin {\\n  to {\\n    -webkit-transform: rotate(360deg);\\n    transform: rotate(360deg);\\n  }\\n}\\n@-webkit-keyframes spin {\\n  to {\\n    -webkit-transform: rotate(360deg);\\n    transform: rotate(360deg);\\n  }\\n}\\n.igv-roi-menu {\\n  position: absolute;\\n  z-index: 512;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  color: #4b4b4b;\\n  background-color: white;\\n  width: 192px;\\n  border-radius: 4px;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n}\\n.igv-roi-menu > div:first-child {\\n  height: 24px;\\n  border-top-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-roi-menu > div:first-child > div {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-roi-menu > div:first-child > div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-roi-menu > div:last-child {\\n  background-color: white;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-color: transparent;\\n  border-bottom-style: solid;\\n  border-bottom-width: 0;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  text-align: start;\\n  vertical-align: middle;\\n}\\n.igv-roi-menu > div:last-child > div {\\n  height: 24px;\\n  padding-left: 4px;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  border-bottom-color: #7f7f7f;\\n}\\n.igv-roi-menu > div:last-child > div:not(:first-child):hover {\\n  cursor: pointer;\\n  background-color: rgba(127, 127, 127, 0.1);\\n}\\n.igv-roi-menu > div:last-child div:first-child {\\n  font-style: italic;\\n  text-align: center;\\n  padding-right: 4px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n}\\n.igv-roi-menu > div:last-child > div:last-child {\\n  border-bottom-width: 0;\\n  border-bottom-color: transparent;\\n}\\n\\n.igv-roi-placeholder {\\n  font-style: normal;\\n  color: rgba(75, 75, 75, 0.6);\\n}\\n\\n.igv-roi-table {\\n  position: absolute;\\n  z-index: 1024;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  resize: both;\\n  overflow: hidden;\\n  width: min-content;\\n  max-width: 1600px;\\n  border-color: #7f7f7f;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  font-weight: 400;\\n  background-color: white;\\n  cursor: default;\\n}\\n.igv-roi-table > div {\\n  height: 24px;\\n  font-size: 14px;\\n  text-align: start;\\n  vertical-align: middle;\\n  line-height: 24px;\\n}\\n.igv-roi-table > div:first-child {\\n  border-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-top-width: 0;\\n  border-bottom-color: #7f7f7f;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-roi-table > div:first-child > div:first-child {\\n  text-align: center;\\n  white-space: nowrap;\\n  text-overflow: ellipsis;\\n  overflow: hidden;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  width: calc(100% - 4px - 12px);\\n}\\n.igv-roi-table > div:first-child > div:last-child {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7f7f7f;\\n}\\n.igv-roi-table > div:first-child > div:last-child > svg {\\n  display: block;\\n}\\n.igv-roi-table > div:first-child > div:last-child:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-roi-table > .igv-roi-table-description {\\n  padding: 4px;\\n  margin-left: 4px;\\n  word-break: break-all;\\n  overflow-y: auto;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-goto-explainer {\\n  margin-top: 5px;\\n  margin-left: 4px;\\n  color: #7F7F7F;\\n  font-style: italic;\\n  height: 24px;\\n  border-top: solid lightgray;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles {\\n  height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n  padding-right: 16px;\\n  background-color: white;\\n  border-top-color: #7f7f7f;\\n  border-top-style: solid;\\n  border-top-width: thin;\\n  border-bottom-color: #7f7f7f;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles > div {\\n  font-size: 14px;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-left: 4px;\\n  height: 24px;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  border-right-color: #7f7f7f;\\n  border-right-style: solid;\\n  border-right-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles > div:last-child {\\n  border-right: unset;\\n}\\n.igv-roi-table > .igv-roi-table-row-container {\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  overflow: auto;\\n  height: 360px;\\n  flex: 1 1 auto;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\\n  height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\\n  font-size: 14px;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-left: 4px;\\n  height: 24px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  border-right-color: transparent;\\n  border-right-style: solid;\\n  border-right-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:last-child {\\n  border-right: unset;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\\n  background-color: rgba(0, 0, 0, 0.04);\\n}\\n.igv-roi-table > div:last-child {\\n  min-height: 32px;\\n  height: 32px;\\n  line-height: 32px;\\n  border-top-color: #7f7f7f;\\n  border-top-style: solid;\\n  border-top-width: thin;\\n  border-bottom-color: transparent;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-width: 0;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n\\n.igv-roi-table-row-selected {\\n  background-color: rgba(0, 0, 0, 0.125);\\n}\\n\\n.igv-roi-table-button {\\n  cursor: pointer;\\n  height: 20px;\\n  user-select: none;\\n  line-height: 20px;\\n  text-align: center;\\n  vertical-align: middle;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 13px;\\n  font-weight: 400;\\n  color: black;\\n  padding-left: 6px;\\n  padding-right: 6px;\\n  background-color: rgb(239, 239, 239);\\n  border-color: black;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 3px;\\n}\\n\\n.igv-roi-table-button:hover {\\n  font-weight: 400;\\n  background-color: rgba(0, 0, 0, 0.13);\\n}\\n\\n.igv-roi-region {\\n  z-index: 64;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  pointer-events: none;\\n  overflow: visible;\\n  margin-top: 66px;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n}\\n.igv-roi-region > div {\\n  position: relative;\\n  width: 100%;\\n  height: 8px;\\n  pointer-events: auto;\\n}\\n\\n.igv-roi-menu-row {\\n  height: 24px;\\n  padding-left: 8px;\\n  font-size: small;\\n  text-align: start;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  background-color: white;\\n}\\n\\n.igv-roi-menu-row-edit-description {\\n  width: -webkit-fill-available;\\n  font-size: small;\\n  text-align: start;\\n  vertical-align: middle;\\n  background-color: white;\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  padding-bottom: 4px;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n}\\n.igv-roi-menu-row-edit-description > label {\\n  margin-left: 2px;\\n  margin-bottom: 0;\\n  display: block;\\n  width: -webkit-fill-available;\\n}\\n.igv-roi-menu-row-edit-description > input {\\n  display: block;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  margin-bottom: 1px;\\n  width: -webkit-fill-available;\\n}\\n\\n.igv-container {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  padding-top: 4px;\\n  user-select: none;\\n  -webkit-user-select: none;\\n  -ms-user-select: none;\\n  min-height: 160px;\\n}\\n\\n.igv-viewport {\\n  position: relative;\\n  margin-top: 5px;\\n  line-height: 1;\\n  overflow-x: hidden;\\n  overflow-y: hidden;\\n}\\n\\n.igv-viewport-content {\\n  position: relative;\\n  width: 100%;\\n}\\n.igv-viewport-content > canvas {\\n  position: relative;\\n  display: block;\\n}\\n\\n.igv-column-container {\\n  position: relative;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  width: 100%;\\n}\\n\\n.igv-column-shim {\\n  width: 1px;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  background-color: #545453;\\n}\\n\\n.igv-axis-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 50px;\\n}\\n.igv-axis-column > div {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 100%;\\n}\\n.igv-axis-column > div > div {\\n  z-index: 512;\\n  position: absolute;\\n  top: 8px;\\n  left: 8px;\\n  width: fit-content;\\n  height: fit-content;\\n  background-color: transparent;\\n  display: grid;\\n  align-items: start;\\n  justify-items: center;\\n}\\n.igv-axis-column > div > div > input {\\n  display: block;\\n  margin: unset;\\n  cursor: pointer;\\n}\\n\\n.igv-column {\\n  position: relative;\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-sample-info-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-sample-name-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-scrollbar-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 14px;\\n}\\n.igv-scrollbar-column > div {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 14px;\\n}\\n.igv-scrollbar-column > div > div {\\n  cursor: pointer;\\n  position: absolute;\\n  top: 0;\\n  left: 2px;\\n  width: 8px;\\n  border-width: 1px;\\n  border-style: solid;\\n  border-color: #c4c4c4;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n}\\n.igv-scrollbar-column > div > div:hover {\\n  background-color: #c4c4c4;\\n}\\n\\n.igv-track-drag-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 12px;\\n  background-color: white;\\n}\\n.igv-track-drag-column > .igv-track-drag-handle {\\n  z-index: 512;\\n  position: relative;\\n  cursor: pointer;\\n  margin-top: 5px;\\n  width: 100%;\\n  border-style: solid;\\n  border-width: 0;\\n  border-top-right-radius: 6px;\\n  border-bottom-right-radius: 6px;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-color {\\n  background-color: #c4c4c4;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-hover-color {\\n  background-color: #787878;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-selected-color {\\n  background-color: #0963fa;\\n}\\n.igv-track-drag-column > .igv-track-drag-shim {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 100%;\\n  border-style: solid;\\n  border-width: 0;\\n}\\n\\n.igv-gear-menu-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 28px;\\n}\\n.igv-gear-menu-column > div {\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  margin-top: 5px;\\n  width: 100%;\\n  background: white;\\n}\\n.igv-gear-menu-column > div > div {\\n  position: relative;\\n  margin-top: 4px;\\n  width: 16px;\\n  height: 16px;\\n  color: #7F7F7F;\\n}\\n.igv-gear-menu-column > div > div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n\\n/*# sourceMappingURL=igv.css.map */\\n'),n.adoptedStyleSheets=[e]}if(this.root=e({class:\"igv-container\"}),n.appendChild(this.root),this.spinner=e({class:\"igv-loading-spinner-container\"}),this.root.appendChild(this.spinner),this.spinner.appendChild(e()),this.spinner.style.width=\"64px\",this.spinner.style.height=\"64px\",this.stopSpinner(),this.alert=new La(this.root),this.columnContainer=e({class:\"igv-column-container\"}),this.root.appendChild(this.columnContainer),this.menuPopup=new Xu(this.columnContainer),this.menuUtils=new bo(this),this.initialize(t),this.trackViews=[],this.constants={dragThreshold:3,scrollThreshold:5,defaultColor:\"rgb(0,0,150)\",doubleClickDelay:t.doubleClickDelay||500},this.eventHandlers={},t.listeners)for(let e of Object.keys(t.listeners))this.on(e,t.listeners[e]);this.on(\"trackremoved\",(()=>{0===this.findTracks((e=>\"function\"==typeof e.getSamples)).length&&(this.sampleInfoControl.setButtonVisibility(!1),this.sampleNameViewportWidth=void 0,this.showSampleNames=!1,this.sampleNameControl.setState(this.showSampleNames),this.sampleNameControl.hide(),this.layoutChange())})),this.on(\"didchangecolumnlayout\",(()=>{if(yu.length>0){const e=yu.length;for(let t=0;t<e;t++)yu[t].dispose();yu.length=0}})),this.addEventHandlers(),this.sampleInfo=new Uu(this),this.createStandardControls(t),this.roiManager=new Ky(this)}get doShowROITable(){return this.roiManager.roiTableIsVisible()}startSpinner(){this.spinner.style.display=\"flex\"}stopSpinner(){this.spinner.style.display=\"none\"}initialize(e){this.flanking=e.flanking,this.crossDomainProxy=e.crossDomainProxy,this.formats=e.formats,this.trackDefaults=e.trackDefaults,this.nucleotideColors=e.nucleotideColors||Bc;for(let e of Object.keys(this.nucleotideColors))this.nucleotideColors[e.toLowerCase()]=this.nucleotideColors[e];this.doShowTrackLabels=e.showTrackLabels,this.doShowCenterLine=e.showCenterGuide,this.doShowCursorGuide=e.showCursorGuide,this.showSampleNames=e.showSampleNames,this.sampleNameViewportWidth=void 0,e.sampleNameViewportWidth&&(this.sampleNameViewportWidth=e.sampleNameViewportWidth),e.search&&(this.searchConfig={type:\"json\",url:e.search.url,coords:void 0===e.search.coords?1:e.search.coords,chromosomeField:e.search.chromosomeField||\"chromosome\",startField:e.search.startField||\"start\",endField:e.search.endField||\"end\",geneField:e.search.geneField||\"gene\",snpField:e.search.snpField||\"snp\",resultsField:e.search.resultsField})}createStandardControls(e){this.setTrackLabelVisibility(e.showTrackLabels),this.navbar=new Py(e,this),this.navbar.$navigation.insertBefore(Bt(this.columnContainer)),!1===e.showControls&&this.navbar.hide(),this.cursorGuide=new ky(this.columnContainer,this),this.inputDialog=new Na(this.root),this.inputDialog.container.id=`igv-input-dialog-${s()}`,this.dataRangeDialog=new _o(this,Bt(this.root)),this.dataRangeDialog.$container.get(0).id=`igv-data-range-dialog-${s()}`,this.genericColorPicker=new Ra({parent:this.columnContainer,width:432}),this.genericColorPicker.container.id=`igv-track-color-picker-${s()}`,this.sliderDialog=new hA(this.root),this.sliderDialog.container.id=`igv-slider-dialog-${s()}`}getSampleNameViewportWidth(){return void 0===this.sampleNameViewportWidth||!1===this.showSampleNames?0:this.sampleNameViewportWidth}getSampleInfoViewportWidth(){return this.getSampleInfoColumnWidth()}isMultiLocusMode(){return this.referenceFrameList&&this.referenceFrameList.length>1}isMultiLocusWholeGenomeView(){if(void 0===this.referenceFrameList||1===this.referenceFrameList.length)return!1;for(let e of this.referenceFrameList)if(\"all\"===e.chr.toLowerCase())return!0;return!1}currentLoci(){const e=e=>`${e.chr}:${e.start+1}-${e.end}`;return void 0===this.referenceFrameList||0===this.referenceFrameList.length?\"\":1===this.referenceFrameList.length?e(this.referenceFrameList[0]):this.referenceFrameList.map((t=>e(t)))}toSVG(){const{x:e,y:t,width:i,height:n}=this.columnContainer.getBoundingClientRect(),r=new lu({width:i,height:n,backdropColor:\"white\",multiLocusGap:0,viewbox:{x:0,y:0,width:i,height:n}}),s={deltaX:0,deltaY:-t};for(let e of this.trackViews)e.renderSVGContext(r,s);return s.deltaX=e,this.roiManager.renderSVGContext(this.columnContainer,r,s),r.getSerializedSvg(!0)}saveSVGtoFile(e,t){let i=this.toSVG();if(t){const e=document.createElement(\"svg\");e.innerHTML=i,t.append(e),t.appendChild(e)}const n=e||\"igvjs.svg\",r=URL.createObjectURL(new Blob([i],{type:\"application/octet-stream\"}));Pt(n,r),URL.revokeObjectURL(r)}savePNGtoFile(e){const t=this.toSVG(),i=new Blob([t],{type:\"image/svg+xml\"}),n=URL.createObjectURL(i),r=document.createElement(\"img\");r.addEventListener(\"load\",(()=>{const t=this.columnContainer.getBoundingClientRect(),i=window.devicePixelRatio,s=t.width*i,o=t.height*i,a=document.createElement(\"canvas\");a.width=s,a.height=o;const c=a.getContext(\"2d\");c.scale(i,i),c.drawImage(r,0,0);const l=a.toDataURL(\"image/png\");Pt(e=e||\"igvjs.png\",l),URL.revokeObjectURL(n)})),r.src=n}async loadSession(e){let t;return this.sampleInfo.initialize(),this.roiSets=[],t=e.url||e.file?await dA.loadSessionFile(e):e,this.loadSessionObject(t)}static async loadSessionFile(e){const t=e.url||e.file;let i;if(e.url&&Mt(e.url)&&(e.url.startsWith(\"blob:\")||e.url.startsWith(\"data:\"))){const t=dA.uncompressSession(e.url);i=JSON.parse(t)}else{let n=e.filename;if(n||(n=e.url?await ja(e.url):e.file.name),n.endsWith(\".xml\")){const e=mu.KNOWN_GENOMES,n=await Qs.loadString(t);i=new by(n,e)}else if(n.endsWith(\"hub.txt\")){i={reference:(await du.loadHub(t,e)).getGenomeConfig()}}else{if(!n.endsWith(\".json\"))throw Error(\"Unrecognized session file format:\"+n);i=await Qs.loadJson(t)}}return bA(i)}async loadSessionObject(e){this.cleanHouseForSession(),this.config=e,e.browsers&&(e=await async function(e){const t=e.browsers[0],i={},n=new Mf({url:t.url});await n.readHeaderAndFooter(),i.sampleNameViewportWidth=20,i.genome=\"hg38\";const r=t.state.split(\",\"),s=n.bpResolutions[Number.parseInt(r[2])],o=Number.parseInt(r[0]),a=Math.floor(Number.parseFloat(r[3])*s),c=a+Math.floor(1700*s);return i.locus=`${n.chromosomes[o].name}:${a}-${c}`,i.tracks=(t.tracks||[]).filter((e=>!(\"refgene\"===e.format||\"cellType\"===e.name))),i.tracks.push({type:\"shoebox\",url:t.url,name:t.name,colorScale:t.colorScale,_hicFile:n}),i}(e)),this.navbar.sampleInfoControl.setButtonVisibility(!1),this.showSampleNames=e.showSampleNames||!1,this.navbar.sampleNameControl.setState(!0===this.showSampleNames),e.sampleNameViewportWidth&&(this.sampleNameViewportWidth=e.sampleNameViewportWidth),$a(this.columnContainer,\"igv-axis-column\"),$a(this.columnContainer,\"igv-sample-info-column\"),$a(this.columnContainer,\"igv-sample-name-column\"),$a(this.columnContainer,\"igv-scrollbar-column\"),$a(this.columnContainer,\"igv-track-drag-column\"),$a(this.columnContainer,\"igv-gear-menu-column\");const t=e.reference||e.genome;if(!t)return void console.warn(\"No genome or reference object specified\");const i=Mt(t)?await mu.expandReference(this.alert,t):t;if(await this.loadReference(i,i.locus||e.locus),this.centerLineList=this.createCenterLineList(this.columnContainer),!1!==e.showIdeogram){const e=new hy(this);e.id=\"ideogram\";const t=new hf(this,this.columnContainer,e);this.trackViews.push(t)}if(!1!==e.showRuler){const e=new hf(this,this.columnContainer,new Wu(this));this.trackViews.push(e)}e.qtlSelections&&(this.qtlSelections=cA.fromJSON(e.qtlSelections)),this.roiManager.clearROIs(),e.roi?this.roiManager.loadROI(e.roi):await this.roiManager.reset();const n=[];if(e.sampleinfo)for(const t of e.sampleinfo)t.file?n.push(t.file):this.loadSampleInfo(t);const r=i.tracks||[],s=e.tracks?r.concat(e.tracks):r;0===s.filter((e=>\"sequence\"===e.type&&!e.url&&!e.fastaURL)).length&&s.push({type:\"sequence\",order:Wd,removable:!1});const o=s.filter((e=>void 0!==e.file)).map((({file:e})=>e)),a=s.filter((e=>void 0!==e.indexFile)).map((({indexFile:e})=>e));a.length>0&&o.push(...a),n.length>0&&o.push(...n),o.length>0&&alert(`Local files cannot be loaded automatically.\\nThis session contains references to these local files:\\n${o.map((e=>`    ${e}`)).join(\"\\n\")}`);const c=s.filter((e=>void 0===e.file));let l=1;for(let e of c)void 0===e.order&&(e.order=l++);await this.loadTrackList(c);for(let e of this.trackViews.filter((e=>\"ruler\"===e.track.type||\"ideogram\"===e.track.type)))await e.updateViews();return this.trackViews.some((e=>e.track.selected))&&this.navbar.setEnableTrackSelection(!0),this.updateUIWithReferenceFrameList(),this.updateLocusSearchWidget(),s}cleanHouseForSession(){for(let e of this.trackViews)e.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(\".igv-axis-column, .igv-column-shim, .igv-column, .igv-sample-info-column, .igv-sample-name-column, .igv-scrollbar-column, .igv-track-drag-column, .igv-gear-menu-column\").forEach((e=>e.remove())),this.trackViews=[],this.circularView&&this.circularView.clearChords()}async loadReference(e,t){let i;this.removeAllTracks(),this.roiManager.clearROIs(),this.navbar.setEnableTrackSelection(!1),i=e.gbkURL?await wd(e.gbkURL):await aA.createGenome(e,this);const n=void 0===this.genome||this.genome.id!==i.id;this.genome=i,this.navbar.updateGenome(i);let r=t||i.initialLocus;Array.isArray(r)&&(r=r.join(\" \"));if(!await this.search(r,!0))throw new Error(`Cannot set initial locus ${r}`);if(n){let t;if(e.hubURL){t=(await du.loadHub(e.hubURL)).getGroupedTrackConfigurations()}this.fireEvent(\"genomechange\",[{genome:i,trackConfigurations:t}]),this.circularView&&this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Hm(this.genome)})}}async loadGenome(e){let t;e.genarkAccession&&(e.url=hu(e.genarkAccession)),e.url&&(Mt(e.url)&&e.url.endsWith(\"/hub.txt\")?(e.hubURL=e.url,delete e.url):\"gbk\"===function(e){let t;if(e instanceof File)t=e.name;else{if(\"string\"!=typeof e)throw new Error(\"Input must be a File object or a URL string\");t=e}const i=t.split(\".\").pop();return i.split(\"?\")[0]}(e.url)&&(e.gbkURL=e.url,delete e.url));if(e.hubURL||e.url&&Mt(e.url)&&e.url.endsWith(\"/hub.txt\")){t=(await du.loadHub(e.hubURL||e.url,e)).getGenomeConfig()}else t=Mt(e)||!(e.url||e.fastaURL||e.twoBitURL||e.gbkURL)?await mu.expandReference(this.alert,e):e;let i;await this.loadReference(t),i=t.gbkURL||\"gbk\"===t.format?[{name:\"Annotations\",format:\"gbk\",url:t.gbkURL}]:t.tracks||[];return 0===i.filter((e=>\"sequence\"===e.type)).length&&i.push({type:\"sequence\",order:Wd}),await this.loadTrackList(i),await this.updateViews(),this.genome}async loadTrackHub(e){const t=bA((await du.loadHub(e.url,e)).getGenomeConfig());return this.loadGenome(t)}updateUIWithReferenceFrameList(){const e=this.referenceFrameList;this.isMultiLocusWholeGenomeView()||mu.isWholeGenomeView(e[0].chr),this.navbar.navbarDidResize(),mA(this.trackViews,this.doShowTrackLabels),this.doShowCenterLine&&mu.isWholeGenomeView(e[0].chr)&&this.navbar.centerLineButton.boundMouseClickHandler(),this.doShowCursorGuide&&mu.isWholeGenomeView(e[0].chr)&&this.navbar.cursorGuideButton.boundMouseClickHandler(),this.setCenterLineAndCenterLineButtonVisibility(mu.isWholeGenomeView(e[0].chr))}setCenterLineAndCenterLineButtonVisibility(e){e?this.navbar.centerLineButton.setVisibility(!1):this.navbar.centerLineButton.setVisibility(this.config.showCenterGuideButton);for(let t of this.centerLineList)e?this.setCenterLineVisibility(!e):this.setCenterLineVisibility(this.doShowCenterLine)}setTrackLabelVisibility(e){mA(this.trackViews,e)}setROITableVisibility(e){!0===e?this.roiManager.presentTable():this.roiManager.dismissTable()}setCursorGuideVisibility(e){e?this.cursorGuide.show():this.cursorGuide.hide()}setCustomCursorGuideMouseHandler(e){this.cursorGuide.customMouseHandler=e}setCenterLineVisibility(e){for(let t of this.centerLineList)!0===e?(t.show(),t.repaint()):t.hide()}async loadTrackList(e){let t=0;for(let i of e)void 0===i.order&&(i.order=t++);const i=[];for(let t of e)i.push(this._loadTrack(t));const n=await Promise.all(i);return this.trackViews.filter((function(e){return e.track.autoscaleGroup})).length>0&&this.updateViews(),n}async loadTrack(e){e.sync=!1!==e.sync;const t=this._loadTrack(e);return t&&e.autoscaleGroup&&(await t,this.updateViews()),t}async _loadTrack(e){Mt(e)&&(e=JSON.parse(e));try{if(e.hidden){const t=Ad(e,this.genome);return void await t.getFeatures({chr:\"1\",start:0,end:Number.MAX_SAFE_INTEGER})}const t=await this.createTrack(e);if(\"sampleinfo\"===e.type)return void this.layoutChange();if(void 0===t)return;return this.addTrack(e,t)}catch(t){let i=t.message||t.error||t.toString();const n={401:\"Access unauthorized\",403:\"Access forbidden\",404:\"Not found\"};n.hasOwnProperty(i)&&(i=n[i]),i=`${i} : ${Ht(e.url)?e.url.name:e.url}`;const r=new Error(i);throw console.error(r),r}}async addTrack(e,t){void 0===t.order&&(t.order=this.trackViews.length);const i=new hf(this,this.columnContainer,t);if(this.trackViews.push(i),mA(this.trackViews,this.doShowTrackLabels),\"function\"==typeof t.postInit)try{i.startSpinner(),await t.postInit()}finally{i.stopSpinner()}return t.autoscaleGroup||(e.sync?await i.updateViews():i.updateViews()),\"function\"==typeof t.hasSamples&&t.hasSamples()&&(this.sampleInfo.hasAttributes()&&this.sampleInfoControl.setButtonVisibility(!0),!1!==this.config.showSampleNameButton&&this.sampleNameControl.show()),this.reorderTracks(),this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()]),t.trackView.enableTrackSelection(this.navbar.getEnableTrackSelection()),t}async loadROI(e){return this.roiManager.loadROI(e,this.genome)}clearROIs(){this.roiManager.clearROIs()}async getUserDefinedROIs(){if(this.roiManager){const e=this.roiManager.getUserDefinedROISet();if(void 0===e)return[];const t=await e.getAllFeatures(),i=[];for(let e of Object.values(t))i.push(...e);return i}return[]}getRulerTrackView(){const e=this.trackViews.filter((({track:e})=>\"ruler\"===e.id));return e.length>0?e[0]:void 0}async createTrack(e){let t=await async function(e){return\"function\"==typeof e?e():e}\n",
-       "/*! pako 2.1.0 https://github.com/nodeca/pako @license (MIT AND Zlib) */(e.url||e.fastaURL);if(Mt(t)&&(t=t.trim()),t)if(e.format)e.format=e.format.toLowerCase();else if(e.fastaURL)e.format=\"fasta\";else if(e.sourceType)\"htsget\"===e.sourceType&&await Rh.inferFormat(e);else{const t=await am(e);t&&(e.format=t)}e.type&&Ha(e);let i=e.type?e.type.toLowerCase():void 0;if(!i){if(!e.format)throw Error(`Unrecognized track:  ${JSON.stringify(e)}`);if(\"hic\"===e.format){const t=new Mf(e);if(await t.readHeaderAndFooter(),!t.chromosomeIndexMap.celltype)throw Error(\"'.hic' files not supported\");i=\"shoebox\",e._hicFile=t}else if(i=za(e.format),\"bedtype\"===i){const t=Ad(e,this.genome);e._featureSource=t;const n=await t.trackType();i=n||\"annotation\"}e.type=i}if(this.trackDefaults&&i){const t=this.trackDefaults[i];if(t)for(let i in t)t.hasOwnProperty(i)&&void 0===e[i]&&(e[i]=t[i])}const n=function(e,t,i){let n;switch(e){case\"annotation\":case\"genes\":case\"fusionjuncspan\":case\"snp\":n=\"feature\";break;case\"seg\":case\"maf\":case\"mut\":n=\"seg\";break;case\"junctions\":case\"splicejunctions\":n=\"junction\";break;default:n=e}return wy.has(n)?wy.get(n)(t,i):void 0}(i,e,this);if(void 0!==n)return e.roi&&e.roi.length>0&&(n.roiSets=e.roi.map((e=>new eA(e,this.genome)))),n;this.alert.present(new Error(`Error creating track.  Could not determine track type for file: ${e.url||e}`),void 0)}reorderTracks(){this.trackViews.sort((function(e,t){const i=e=>\"ideogram\"===e.track.id?1:\"ruler\"===e.track.id?2:3,n=i(e),r=i(t);if(n===r){return(e.track.order||0)-(t.track.order||0)}return n-r}));for(let{axis:e,viewports:t,sampleInfoViewport:i,sampleNameViewport:n,outerScroll:r,dragHandle:s,gearContainer:o}of this.trackViews){e.remove();for(let{$viewport:e}of t)e.detach();i.viewport.remove(),n.viewport.remove(),r.remove(),s.remove(),o.remove()}const e=this.columnContainer.querySelectorAll(\".igv-column\");for(let{axis:t,viewports:i,sampleInfoViewport:n,sampleNameViewport:r,outerScroll:s,dragHandle:o,gearContainer:a}of this.trackViews){this.columnContainer.querySelector(\".igv-axis-column\").appendChild(t);for(let t=0;t<e.length;t++){const{$viewport:n}=i[t];e[t].appendChild(n.get(0))}this.columnContainer.querySelector(\".igv-sample-info-column\").appendChild(n.viewport),this.columnContainer.querySelector(\".igv-sample-name-column\").appendChild(r.viewport),this.columnContainer.querySelector(\".igv-scrollbar-column\").appendChild(s),this.columnContainer.querySelector(\".igv-track-drag-column\").appendChild(o),this.columnContainer.querySelector(\".igv-gear-menu-column\").appendChild(a)}}getTrackOrder(){return this.trackViews.filter((e=>e.track&&e.track.name)).map((e=>e.track.name))}getSelectedTrackViews(){return this.trackViews.filter((e=>!0===e.track.selected))}removeTrackByName(e){const t=this.trackViews.slice();for(let i of t)e===i.track.name&&this.removeTrack(i.track)}removeTrack(e){for(let t of this.trackViews)if(e===t.track){this._removeTrack(t.track);break}}_removeTrack(e){e.disposed||(this.trackViews.splice(this.trackViews.indexOf(e.trackView),1),this.fireEvent(\"trackremoved\",[e]),this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()]),e.trackView&&e.trackView.dispose())}removeAllTracks(){const e=this.trackViews;this.trackViews=[];for(let t of e)\"ruler\"!==t.track.id&&\"ideogram\"!==t.track.id?(this.fireEvent(\"trackremoved\",[t.track]),t.dispose()):this.trackViews.push(t)}get ideogramTrackView(){return this.trackViews[0]}get rulerTrackView(){return this.trackViews[1]}findTracks(e,t){let i=\"function\"==typeof e?t=>e(t.track):i=>t===i.track[e];return this.trackViews.filter(i).map((e=>e.track))}get tracks(){return this.trackViews.map((e=>e.track)).filter((e=>void 0!==e))}setTrackHeight(e){this.trackHeight=e,this.trackViews.forEach((function(t){t.setTrackHeight(e)}))}async visibilityChange(){this.layoutChange()}async layoutChange(){if(this.referenceFrameList.find((e=>e.bpPerPixel<0))){const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel=(t.end-t.start)/e}this.referenceFrameList&&this.navbar.navbarDidResize(),uA.call(this),await this.updateViews()}async updateViews(){const e=this.trackViews;this.updateLocusSearchWidget();for(let e of this.referenceFrameList)e.bpPerPixel<=10&&await this.genome.getSequence(e.chr,e.start,e.start+1);for(let e of this.centerLineList)e.repaint();if(this.dragObject)for(let t of e)await t.updateViews();else{const t={},i=[];for(const n of e)if(n.track.autoscaleGroup){const e=n.track.autoscaleGroup;t[e]||(t[e]=[]),t[e].push(n)}else i.push(n);if(Object.entries(t).length>0)for(const[e,i]of Object.entries(t)){const e=await Promise.all(i.map((e=>e.getInViewFeatures()))),t=qa(e.flat());for(const e of i)e.track.dataRange=Object.assign({},t),e.track.autoscale=!1;await Promise.all(i.map((e=>e.updateViews())))}await Promise.all(i.map((e=>e.updateViews())))}}repaintViews(){for(let e of this.trackViews)e.repaintViews()}updateLocusSearchWidget(){if(!this.referenceFrameList)return;const e=this.referenceFrameList,t=this.calculateViewportWidth(this.referenceFrameList.length);for(let i of e)i.end=i.start+i.bpPerPixel*t;const i=1===e.length?this.referenceFrameList[0].chr:\"\",n=this.referenceFrameList.map((e=>e.getLocusString())).join(\" \");this.navbar.updateLocus(n,i),this.fireEvent(\"locuschange\",[this.referenceFrameList])}calculateViewportWidth(e){let{width:t}=this.columnContainer.getBoundingClientRect();return t-=50+this.getSampleInfoViewportWidth()+this.getSampleNameViewportWidth()+14+12+28,t-=5*(e-1),Math.floor(t/e)}minimumBases(){return this.config.minimumBases}zoomIn(){this.zoomWithScaleFactor(.5)}zoomOut(){this.zoomWithScaleFactor(2)}async zoomWithScaleFactor(e,t,i){if(!this.referenceFrameList)return;const n=this.calculateViewportWidth(this.referenceFrameList.length);let r=i?[i]:this.referenceFrameList;for(let i of r)i.zoomWithScaleFactor(this,e,n,t)}async addMultiLocusPanel(e,t,i,n){if(!this.referenceFrameList)return;const r=this.calculateViewportWidth(1+this.referenceFrameList.length),s=this.calculateViewportWidth(this.referenceFrameList.length)/this.calculateViewportWidth(1+this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel*=s;const o=(i-t)/r,a=new vy(this.genome,e,t,i,o),c=n?this.referenceFrameList.indexOf(n):this.referenceFrameList.length-1,l=1+c,{$viewport:h}=this.trackViews[0].viewports[c],d=Uy(h.get(0).parentElement);if(this.fireEvent(\"didchangecolumnlayout\"),l===this.referenceFrameList.length){this.referenceFrameList.push(a);for(let e of this.trackViews){const t=zu(e,d,a);e.viewports.push(t)}}else{this.referenceFrameList.splice(l,0,a);for(let e of this.trackViews){const t=zu(e,d,a);e.viewports.splice(l,0,t)}}this.centerLineList=this.createCenterLineList(this.columnContainer),uA.call(this),await this.updateViews(!0)}createCenterLineList(e){const t=e.querySelectorAll(\".igv-center-line\");for(let e=0;e<t.length;e++)t[e].remove();const i=[],n=e.querySelectorAll(\".igv-column\");for(let e=0;e<n.length;e++)i.push(new Qy(this,this.referenceFrameList[e],n[e]));return i}async removeMultiLocusPanel(e){const t=this.referenceFrameList.indexOf(e),{$viewport:i}=this.trackViews[0].viewports[t];Oy(t,i.parent().get(0)),this.fireEvent(\"didchangecolumnlayout\");for(let{viewports:e}of this.trackViews)e[t].dispose(),e.splice(t,1);if(this.referenceFrameList.splice(t,1),1===this.referenceFrameList.length&&this.getRulerTrackView())for(let e of this.getRulerTrackView().viewports)e.dismissLocusLabel();const n=this.calculateViewportWidth(1+this.referenceFrameList.length)/this.calculateViewportWidth(this.referenceFrameList.length);await this.rescaleForMultiLocus(n)}async gotoMultilocusPanel(e){const t=this.referenceFrameList.indexOf(e);this.columnContainer.querySelectorAll(\".igv-column\").forEach(((e,i)=>{i===t||e.remove()})),this.columnContainer.querySelectorAll(\".igv-column-shim\").forEach((e=>e.remove()));for(let e of this.trackViews){const i=e.viewports[t];e.viewports.filter(((e,i)=>i!==t)).forEach((e=>e.dispose())),e.viewports=[i]}const i=this.calculateViewportWidth(1);e.bpPerPixel=(e.end-e.start)/i,this.referenceFrameList=[e],this.trackViews.forEach((({viewports:e})=>e.forEach((e=>e.setWidth(i))))),this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}async rescaleForMultiLocus(e){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel*=e;for(let{viewports:e}of this.trackViews)for(let i of e)i.setWidth(t);this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews()}async goto(e,t,i){await this.search(e+\":\"+t+\"-\"+i)}async doSearch(e,t){const i=await this.search(e,t);return i||this.alert.present(new Error(`Unrecognized locus: <b> ${e} </b>`)),i}async search(e,t){const i=await async function(e,t){if(void 0===t||\"\"===t.trim())return;const i=t.split(\" \");let n=[];const r=async t=>{if(\"all\"===t.trim().toLowerCase()||\"*\"===t)return e.genome.wholeGenomeView?{chr:\"all\",start:0,end:e.genome.getChromosome(\"all\").bpLength}:void 0;let i,n;if(t.includes(\":\")&&(i=ey(t,e.isSoftclipped()),i&&(n=await e.genome.loadChromosome(i.chr))),!n){i=void 0;const r=await Jv(e,t);r&&(i={chr:r.chr,start:r.start,end:r.end,name:(r.name||t).toUpperCase()}),i||(n=await e.genome.loadChromosome(t),n&&(i={chr:n.name}))}return i&&(n=n||await e.genome.loadChromosome(i.chr),i.chr=n.name,void 0===i.start&&void 0===i.end&&(i.start=0,i.end=n.bpLength)),i};for(let e of i){const t=await r(e);t&&n.push(t)}if(0===n.length){const e=await r(t.replaceAll(\" \",\"+\"));e&&n.push(e)}return 0===n.length?void 0:n}(this,e);if(i&&i.length>0){this.referenceFrameList=function(e,t,i,n,r,s){return e.map((e=>{const o=Object.assign({},e);if(i&&o.name&&(o.start=Math.max(0,o.start-i),o.end+=i),!s){const e=t.getChromosome(o.chr);Qa(e.bpLength,o,n)}return new vy(t,o.chr,o.start,o.end,(o.end-o.start)/r)}))}(i,this.genome,this.flanking,this.minimumBases(),this.calculateViewportWidth(i.length),this.isSoftclipped());for(let e of this.trackViews)e.removeViewportsFromColumnContainer();this.columnContainer.querySelectorAll(\".igv-column-shim, .igv-column\").forEach((e=>e.remove())),qy(this.columnContainer.querySelector(\".igv-sample-info-column\"),this.referenceFrameList.length),this.fireEvent(\"didchangecolumnlayout\");for(let e of this.trackViews)e.createViewports(this,this.columnContainer,this.referenceFrameList);return this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),t||await this.updateViews(),!0}return!1}async loadSampleInfo(e){await this.sampleInfo.loadSampleInfoFile(e.url);for(const{sampleInfoViewport:e}of this.trackViews)e.setWidth(this.getSampleInfoColumnWidth());this.findTracks((e=>\"function\"==typeof e.getSamples)).length>0&&(this.sampleInfoControl.performClickWithState(this,!0),this.sampleInfoControl.setButtonVisibility(!0));for(const{sampleInfoViewport:e}of this.trackViews)e.repaint()}getSampleInfoColumnWidth(){if(this.sampleInfo.attributeCount){const e=this.findTracks((e=>\"function\"==typeof e.getSamples)).length>0,t=this.sampleInfo.hasAttributes(),i=this.sampleInfoControl.showSampleInfo;return e&&t&&i?this.sampleInfo.attributeCount*Vu+8:0}return 0}on(e,t){this.eventHandlers[e]||(this.eventHandlers[e]=[]),this.eventHandlers[e].push(t)}un(e,t){this.off(e,t)}off(e,t){if(e)if(t){const i=this.eventHandlers[e];if(i&&0!==i.length){const n=i.indexOf(t);-1!==n&&this.eventHandlers[e].splice(n,1)}else console.warn(\"No handlers to remove for event: \"+e)}else this.eventHandlers[e]=[];else this.eventHandlers={}}fireEvent(e,t,i){const n=this.eventHandlers[e];if(void 0===n||0===n.length)return;const r=i||window;return n.map((function(e){return e.apply(r,t)}))[0]}dispose(){this.removeEventHandlers();for(let e of this.trackViews)e.dispose();this.roiManager&&this.roiManager.dispose()}toJSON(){const e={version:\"3.0.9\"};if(void 0!==this.showSampleNames&&(e.showSampleNames=this.showSampleNames),this.sampleNameViewportWidth&&(e.sampleNameViewportWidth=this.sampleNameViewportWidth),e.reference=this.genome.toJSON(),e.reference.fastaURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.fastaURL.name}.`);if(e.reference.indexURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.indexURL.name}.`);const t=[];let i=this.trackViews[0];for(let{referenceFrame:e}of i.viewports){const i=e.getLocusString();t.push(i)}e.locus=1===t.length?t[0]:t,e.roi=this.roiManager.toJSON(),this.qtlSelections.isEmpty()||(e.qtlSelections=this.qtlSelections.toJSON());const n=[],r=[];for(const{track:e}of this.trackViews)try{let t;\"function\"==typeof e.getState?t=Hl.localFileInspection(e.getState()):e.config&&(t=Hl.localFileInspection(e.config)),t&&(t.browser&&delete t.browser,t.order=e.order,n.push(t))}catch(t){const i=`Track: ${e.name}: ${t}`;console.error(i),r.push(i)}if(r.length>0){let e=1,t=\"Errors encountered saving session: </br>\";for(let i of r)t+=` (${e++}) ${i.toString()} <br/>`;throw Error(t)}e.tracks=n;const s=[];for(const e of n)for(const t of Object.keys(e))\"file\"!==t&&\"indexFile\"!==t||s.push(e[t]);const o=[];if(this.sampleInfo.sampleInfoFiles.length>0){const t=this.sampleInfo.toJSON();t.length>0&&(e.sampleinfo=t);for(const e of this.sampleInfo.sampleInfoFiles){const t=Hl.localFileInspection({url:e});t.file&&o.push(t.file)}o.length>0&&s.push(...o)}return s.length>0&&alert(`This session includes reference(s) to local file(s):\\n${s.map((e=>`    ${e}`)).join(\"\\n\")}\\nLocal files cannot be loaded automatically when a saved session is restored.`),e}compressedSession(){return function(e){const t=new Uint8Array(e.length);for(var i=0;i<e.length;i++)t[i]=e.charCodeAt(i);const n=new cs(t),r=String.fromCharCode.apply(null,n);return btoa(r).replace(/\\+/g,\".\").replace(/\\//g,\"_\").replace(/=/g,\"-\")}(JSON.stringify(this.toJSON()))}sessionURL(){const e=window.location.href.slice(),t=e.indexOf(\"?\");return(t>0?e.substring(0,t):e)+\"?sessionURL=blob:\"+this.compressedSession()}mouseDownOnViewport(e,t){var i;i=r(e),this.vpMouseDown={viewport:t,lastMouseX:i.x,mouseDownX:i.x,lastMouseY:i.y,mouseDownY:i.y,referenceFrame:t.referenceFrame}}cancelTrackPan(){const e=this.dragObject;this.dragObject=void 0,this.isScrolling=!1,this.vpMouseDown=void 0,e&&e.viewport.referenceFrame.start!==e.start&&(this.updateViews(),this.fireEvent(\"trackdragend\",[e.viewport]))}isTrackPanning(){return this.dragObject}isSoftclipped(){return void 0!==this.trackViews.find((e=>!0===e.track.showSoftClips))}startTrackDrag(e){this.dragTrack=e}updateTrackDrag(e){if(e&&this.dragTrack){const t=this.dragTrack,i=this.trackViews.indexOf(e),n=this.trackViews.indexOf(t),r=this.trackViews;r[i]=t,r[n]=e;const s=this.trackViews[i].track.order;this.trackViews[n].track.order=s;const o=r.length;let a=s;if(i<n)for(let e=i+1;e<o;e++){const t=r[e].track;if(!(t.order<=a))break;t.order=Math.min(Number.MAX_SAFE_INTEGER,a+1),a=t.order}else for(let e=i-1;e>0;e--){const t=r[e].track;if(!(t.order>=a))break;t.order=Math.max(-Number.MAX_SAFE_INTEGER,a-1),a=t.order}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()])):this.dragTrack=void 0}addEventHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers(),this.addKeyboardHandler()}removeEventHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers(),this.removeKeyboardHandler()}addWindowResizeHandler(){this.boundWindowResizeHandler=uA.bind(this),window.addEventListener(\"resize\",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener(\"resize\",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=pA.bind(this),this.root.addEventListener(\"mouseup\",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener(\"mouseup\",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=pA.bind(this),this.root.addEventListener(\"mouseleave\",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener(\"mouseleave\",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=fA.bind(this),this.boundColumnContainerTouchMoveHandler=fA.bind(this),this.boundColumnContainerMouseLeaveHandler=pA.bind(this),this.boundColumnContainerMouseUpHandler=pA.bind(this),this.boundColumnContainerTouchEndHandler=pA.bind(this),this.columnContainer.addEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener(\"touchmove\",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener(\"mouseleave\",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener(\"touchend\",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener(\"touchmove\",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener(\"mouseleave\",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener(\"touchend\",this.boundColumnContainerTouchEndHandler)}addKeyboardHandler(){this.keyUpHandler=gA.bind(this),document.addEventListener(\"keyup\",this.keyUpHandler)}removeKeyboardHandler(){console.log(\"Remove handler\"),document.addEventListener(\"keyup\",this.keyUpHandler)}static uncompressSession(e){let t;if(e.indexOf(\"/gzip;base64\")>0){t=vs(e);let i=\"\";for(let e of t)i+=String.fromCharCode(e);return i}return function(e){e=e.replace(/\\./g,\"+\").replace(/_/g,\"/\").replace(/-/g,\"=\");const t=atob(e),i=[];for(let e=0;e<t.length;e++)i.push(t.charCodeAt(e));const n=hs(i);let r=\"\";for(let e of n)r+=String.fromCharCode(e);return r}(e.substring(5))}createCircularView(e,t){var i;return t=!0===t,this.circularView=(i=this,new Bm(e,{onChordClick:(e,t,n)=>{const r=e.data,s=r.mate;function o(e){e.chr=i.genome.getChromosomeName(e.refName);let t=!1;for(let n of i.referenceFrameList){const i=lm.fromLocusString(n.getLocusString());if(i.contains(e)){t=!0;break}if(i.overlaps(e)){n.extend(e),t=!0;break}}if(!t){const t=2e3,n=(e.start+e.end)/2;i.addMultiLocusPanel(e.chr,n-t,n+t)}}o(r),o(s)}})),this.circularViewControl=new Vy(this.navbar.toggle_button_container,this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Hm(this.genome)}),this.circularViewVisible=t,this.circularView}get circularViewVisible(){return void 0!==this.circularView&&this.circularView.visible}set circularViewVisible(e){this.circularView&&(this.circularView.visible=e,this.circularViewControl.setState(e))}get sampleInfoControl(){return this.navbar.sampleInfoControl}get overlayTrackButton(){return this.navbar.overlayTrackButton}get roiTableControl(){return this.navbar.roiTableControl}get sampleInfoControl(){return this.navbar.sampleInfoControl}get sampleNameControl(){return this.navbar.sampleNameControl}}async function uA(){if(!this.referenceFrameList)return;const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList){const i=this.referenceFrameList.indexOf(t),{chr:n,genome:r}=t,{bpLength:s}=r.getChromosome(t.chr),o=t.toBP(e);mu.isWholeGenomeView(n)||o>s?t.bpPerPixel=s/e:t.end=t.start+t.toBP(e);for(let{viewports:t}of this.trackViews)t[i].setWidth(e)}this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}function fA(e){e.preventDefault();const{x:t,y:i}=r(e);if(this.vpMouseDown){const{viewport:e,referenceFrame:n}=this.vpMouseDown,r=Math.abs(t-this.vpMouseDown.mouseDownX)>Math.abs(i-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling)if(r)this.vpMouseDown.mouseDownX&&Math.abs(t-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:e,start:n.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(i-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const t=e.$viewport.height(),i=e.trackView.maxViewportContentHeight();this.vpMouseDown.r=t/i}if(this.dragObject){const i=!this.isSoftclipped();let r=this.vpMouseDown.lastMouseX-t;n.shiftPixels(r,e.$viewport.width(),i)&&this.updateViews(),this.fireEvent(\"trackdrag\")}if(this.isScrolling){const t=this.vpMouseDown.r*(this.vpMouseDown.lastMouseY-i);e.trackView.moveScroller(t)}this.vpMouseDown.lastMouseX=t,this.vpMouseDown.lastMouseY=i}}function pA(e){this.cancelTrackPan(),this.endTrackDrag()}async function gA(e){if(this.referenceFrameList&&!(this.referenceFrameList.length>1)&&(\"KeyF\"===e.code||\"KeyB\"===e.code)){const t=this.getSelectedTrackViews();if(t.length>0){const i=t[0].track;if(\"function\"==typeof i.nextFeatureAfter){const t=this.referenceFrameList[0],n=t.viewport?t.viewport.getWidth():this.calculateViewportWidth(this.referenceFrameList.length),r=\"all\"===t.chr.toLowerCase(),s=i.visibilityWindow;if(r||s&&s>0&&t.bpPerPixel*n>s)return;const o=\"KeyF\"===e.code,a=t.chr,c=t.center,l=await i.nextFeatureAfter(a,c,o);if(l){const i=await this.genome.getChromosomeName(l.chr);if(a===i){const i=(l.start+l.end)/2;if(e.shiftKey){const e=this.config.minimumBases||40,r=Math.max(e,1.1*(l.end-l.start));t.start=Math.max(0,i-r/2),t.end=i+r/2,t.bpPerPixel=(t.end-t.start)/n}else t.shift(i-c);this.updateViews()}else{t.chr=i;const r=(l.start+l.end)/2;if(e.shiftKey){const e=this.config.minimumBases||40,i=Math.max(e,1.1*(l.end-l.start));t.start=Math.max(0,r-i/2),t.end=t.start+i,t.bpPerPixel=(t.end-t.start)/n}else t.start=r-n*t.bpPerPixel/2,t.end=t.start+n*t.bpPerPixel;this.updateViews()}}}}}}function mA(e,t){for(let{viewports:i}of e)for(let e of i)e.$trackLabel&&(0===i.indexOf(e)&&!0===t?e.$trackLabel.show():e.$trackLabel.hide())}let wA=[];function bA(e){return void 0===e.minimumBases&&(e.minimumBases=40),void 0===e.showIdeogram&&(e.showIdeogram=!0),void 0===e.showCircularView&&(e.showCircularView=!1),void 0===e.showCircularViewButton&&(e.showCircularViewButton=!1),void 0===e.showTrackLabelButton&&(e.showTrackLabelButton=!0),void 0===e.showTrackLabels&&(e.showTrackLabels=!0),void 0===e.showCursorTrackingGuideButton&&(e.showCursorTrackingGuideButton=!0),void 0===e.showCursorGuide&&(e.showCursorGuide=e.showCursorTrackingGuide||!1),void 0===e.showCenterGuideButton&&(e.showCenterGuideButton=!0),void 0===e.showCenterGuide&&(e.showCenterGuide=!1),void 0===e.showSampleNames&&(e.showSampleNames=!1),void 0===e.showSVGButton&&(e.showSVGButton=!0),void 0===e.showControls&&(e.showControls=!0),void 0===e.showNavigation&&(e.showNavigation=!0),void 0===e.showRuler&&(e.showRuler=!0),void 0===e.flanking&&(e.flanking=1e3),void 0===e.pairsSupported&&(e.pairsSupported=!0),e.tracks||(e.tracks=[]),e}const FA=Qs.setApiKey;const vA=Qs.oauth;var yA={TrackUtils:Pa,IGVGraphics:xo,MenuUtils:bo,DataRangeDialog:_o,createTrack:async function(e,t){return await dA.prototype.createTrack.call(t,e)},createBrowser:async function(e,t){void 0===t&&(t={}),mu.KNOWN_GENOMES||await mu.initializeGenomes(t),bA(t),t.queryParametersSupported&&function(e){var t,i,n,r,s,o,a,c,l;let h,d,u;if(a=window.location.href,s={},t=a.indexOf(\"?\"),i=a.lastIndexOf(\"#\"),t>=0)for(i<0&&(i=a.length),n=t+1;n<i;)(r=a.indexOf(\"&\",n))<0&&(r=i),2===(o=a.substring(n,r).split(\"=\",2)).length?(c=o[0],l=decodeURIComponent(o[1]),\"file\"===c?h=l.split(\",\"):\"index\"===c?d=l.split(\",\"):\"name\"===c?u=l.split(\",\"):\"genome\"===c?!l.startsWith(\"https://\")&&!l.startsWith(\"http://\")||l.endsWith(\".json\")?(e[c]=l,e.reference=void 0):e.reference={fastaURL:l,indexURL:l+\".fai\"}:(\"reference\"===c&&(e.genome=void 0),e[c]=l),n=r+1):n++;if(h){e.tracks||(e.tracks=[]);for(let t=0;t<h.length;t++){if(h[t].endsWith(\".xml\")||h[t].endsWith(\".json\")){e.sessionURL=h[t];break}const i={url:h[t]};d&&d.length>t&&(i.indexURL=d[t]),u&&u.length>t&&(i.name=u[t]),e.tracks.push(i)}}}(t),t.apiKey&&Qs.setApiKey(t.apiKey),t.oauthToken&&Qs.setOauthToken(t.oauthToken),t.clientId&&!Ts()&&await async function(e){if(!google.accounts.oauth2.initTokenClient)throw new Error(\"Google accounts token client not loaded (https://accounts.google.com/gsi/client)\");if(Ts())throw new Error(\"Google client is already initialized\");const t={client_id:e.client_id||e.clientId,scope:e.scope||\"https://www.googleapis.com/auth/userinfo.profile\",state:e.state||\"igv\",error:e=>{throw new Error(e.type)},hint:e.hint,hosted_domain:e.hosted_domain},i=google.accounts.oauth2.initTokenClient(t);google.igv={tokenClient:i,apiKey:e.apiKey}}({client_id:t.clientId,apiKey:t.apiKey,scope:\"https://www.googleapis.com/auth/userinfo.profile\"});const i=new dA(t,e);wA.push(i),i.startSpinner();const n=t.sessionURL||t.session||t.hubURL;return n?await i.loadSession({url:n}):await i.loadSessionObject(t),i.stopSpinner(),i.navbar.navbarDidResize(),i},removeBrowser:function(e){e.dispose(),e.root.remove(),wA=wA.filter((t=>t!==e))},removeAllBrowsers:function(){for(let e of wA)e.dispose(),e.root.remove();wA=[]},visibilityChange:async function(){for(let e of wA)await e.visibilityChange()},setGoogleOauthToken:function(e){return Qs.setOauthToken(e)},setOauthToken:function(e,t){return Qs.setOauthToken(e,t)},oauth:vA,version:yy,setApiKey:FA,TrackBase:Hl,registerTrackClass:function(e,t){wy.set(e,((e,i)=>new t(e,i)))},registerTrackCreatorFunction:function(e,t){wy.set(e,t)},registerFileFormats:function(e,t){Sl[e]={fields:t}},loadSessionFile:dA.loadSessionFile};return yA}();\n",
-       "//# sourceMappingURL=igv.iife.js.map\n"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "/**\n",
-       " * Global handler for igv.js messages.  Messages have the form\n",
-       " * {\n",
-       " *     command  -- the command to execute\n",
-       " *     id -- the id of the igv.js browser, if applicable\n",
-       " *     data -- any data needed for the command\n",
-       " * }\n",
-       " */\n",
-       "\n",
-       "// Use a self-evaluating function to keep variables in this file scope, with the execption of the global handler\n",
-       "\n",
-       "(function () {\n",
-       "\n",
-       "    const isColab = window.google !== undefined && window.google.colab\n",
-       "    const isNotebook = !isColab && window.Jupyter !== undefined\n",
-       "\n",
-       "    let svgComm\n",
-       "    if (isNotebook) {\n",
-       "        svgComm = Jupyter.notebook.kernel.comm_manager.new_comm('svg', {})\n",
-       "    }\n",
-       "\n",
-       "    async function toSVG(displayID, locus, svg) {\n",
-       "        //console.log(isNotebook + \" \" + locus)\n",
-       "        if (isNotebook) {\n",
-       "            svgComm.send({\n",
-       "                \"display_id\": displayID,\n",
-       "                \"locus\": locus,\n",
-       "                \"svg\": svg\n",
-       "            })\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    console.log(\"Installing IGVMessageHandler\")\n",
-       "\n",
-       "    function convertUrlsAndPaths(session) {\n",
-       "        if (session.reference) {\n",
-       "            for (let pre of [\"fasta\", \"index\", \"cytoband\", \"cytobandBb\", \"compressedIndex\", \"alias\", \"aliasBb\",\n",
-       "            \"twoBit\", \"twoBitBpt\", \"chromAliasBb\", \"chromSizes\", \"trix\"]) {\n",
-       "                convert(session.reference, pre)\n",
-       "            }\n",
-       "            if (session.reference.tracks) {\n",
-       "                for (let t of session.reference.tracks) {\n",
-       "                    convert(t)\n",
-       "                    convert(t, \"index\")\n",
-       "                    if (!t.indexURL) {\n",
-       "                        t.indexed = false\n",
-       "                    }\n",
-       "                }\n",
-       "            }\n",
-       "        }\n",
-       "\n",
-       "        if (session.tracks) {\n",
-       "            for (let t of session.tracks) {\n",
-       "                convert(t)\n",
-       "                convert(t, \"index\")\n",
-       "                if (!t.indexURL) {\n",
-       "                    t.indexed = false\n",
-       "                }\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Return true if the sessionJson object contains only absolute URLs to resources\n",
-       "     */\n",
-       "    function safeToWeblink(sessionJson) {\n",
-       "        const unsafe = (url) => typeof url.startsWith != 'function' || !url.startsWith(\"http\")\n",
-       "        if (sessionJson.reference) {\n",
-       "            if (unsafe(sessionJson.reference.fastaURL)) return false\n",
-       "        }\n",
-       "        if (sessionJson.tracks) {\n",
-       "            const urls = sessionJson.tracks.filter(t => t.url).map(t => t.url)\n",
-       "            if (urls.some(unsafe)) return false\n",
-       "        }\n",
-       "        return true\n",
-       "    }\n",
-       "\n",
-       "    class MessageHandler {\n",
-       "\n",
-       "        constructor() {\n",
-       "            this.browserCache = new Map()\n",
-       "            this.messageQueue = new Queue()\n",
-       "        }\n",
-       "\n",
-       "        on(msg) {\n",
-       "            this.messageQueue.enqueue(msg)\n",
-       "            this.processQueue()\n",
-       "        }\n",
-       "\n",
-       "        async processQueue() {\n",
-       "\n",
-       "            const convertTrackData = (data) => {\n",
-       "                convert(data)\n",
-       "                convert(data, \"index\")\n",
-       "                if (!data.indexURL) {\n",
-       "                    data.indexed = false\n",
-       "                }\n",
-       "            }\n",
-       "\n",
-       "            if (!this.processing) {\n",
-       "                this.processing = true\n",
-       "                while (!this.messageQueue.isEmpty()) {\n",
-       "                    const msg = this.messageQueue.dequeue()\n",
-       "                    const command = msg.command\n",
-       "                    const browserID = msg.id\n",
-       "                    const data = msg.data\n",
-       "                    const browser = this.browserCache.get(browserID)\n",
-       "                    try {\n",
-       "                        switch (command) {\n",
-       "                            case \"createBrowser\":\n",
-       "\n",
-       "                                // custom button bar\n",
-       "                                const button_container = document.getElementById(`${browserID}_buttons`) // <= created from python\n",
-       "                                const customButtonDiv = document.createElement('div')\n",
-       "                                customButtonDiv.style = `background: #f3f3f3;padding: 5px;border-color: #bfbfbf;border-style: solid;border-width: thin;border-radius: 3px;`\n",
-       "                                button_container.appendChild(customButtonDiv)\n",
-       "\n",
-       "                                data.sync = true\n",
-       "                                convertUrlsAndPaths(data)\n",
-       "\n",
-       "                                const container = document.getElementById(`${browserID}_igvcontainer`)  // <= created from python\n",
-       "                                const newBrowser = await igv.createBrowser(container, data)\n",
-       "                                this.browserCache.set(browserID, newBrowser)\n",
-       "\n",
-       "                                // Add igv-notebook button bar\n",
-       "                                const toJsonButton = document.createElement('button')\n",
-       "                                toJsonButton.innerText = \"Save Session\"\n",
-       "                                toJsonButton.style = \"margin-right:5px\"\n",
-       "                                toJsonButton.addEventListener('click', (evt) => {\n",
-       "                                    let fn\n",
-       "                                    if (isNotebook) {\n",
-       "                                        fn = prompt(\"Filename:\", \"session.json\")\n",
-       "                                    } else {\n",
-       "                                        fn = \"session.json\"\n",
-       "                                    }\n",
-       "                                    if (fn) {\n",
-       "                                        const json = newBrowser.toJSON()\n",
-       "                                        const jsonString = JSON.stringify(json, null, '\\t')\n",
-       "                                        download(fn, jsonString)\n",
-       "                                    }\n",
-       "                                })\n",
-       "                                customButtonDiv.appendChild(toJsonButton)\n",
-       "\n",
-       "                                const webLinkNode = document.createElement('a')\n",
-       "                                webLinkNode.target = \"igvWeb\"\n",
-       "                                webLinkNode.innerText = \"Link to IGV-Web\"\n",
-       "                                webLinkNode.style.display = \"none\"\n",
-       "\n",
-       "                                const shareButton = document.createElement('button')\n",
-       "                                shareButton.innerText = \"Show IGV-Web Link\"\n",
-       "                                shareButton.style = \"margin-right:5px\"\n",
-       "                                shareButton.addEventListener('click', async (evt) => {\n",
-       "\n",
-       "                                    if (safeToWeblink(newBrowser.toJSON())) {\n",
-       "                                        const sessionURL = `https://igv.org/app?sessionURL=blob:${newBrowser.compressedSession()}`\n",
-       "                                        const shortURL = await shortenURL(sessionURL)\n",
-       "                                        webLinkNode.innerText = \"Link to IGV-Web\"\n",
-       "                                        webLinkNode.setAttribute(\"href\", shortURL)\n",
-       "                                        webLinkNode.style.display = \"inline-block\"\n",
-       "                                        shareButton.innerText = \"Update IGV-Web Link\"\n",
-       "                                    } else {\n",
-       "                                        webLinkNode.innerText = \"Cannot link -- non URL resources used\"\n",
-       "                                        webLinkNode.style.display = \"inline-block\"\n",
-       "                                    }\n",
-       "                                })\n",
-       "                                customButtonDiv.appendChild(shareButton)\n",
-       "                                customButtonDiv.appendChild(webLinkNode)\n",
-       "\n",
-       "                                if (isNotebook) {\n",
-       "                                    const toSVGButton = document.createElement('button')\n",
-       "                                    toSVGButton.innerText = \"To SVG\"\n",
-       "                                    toSVGButton.style = \"float:right\"\n",
-       "                                    toSVGButton.addEventListener('click', (evt) => {\n",
-       "                                        const locus = newBrowser.referenceFrameList.map(rf => rf.getLocusString()).join(' ')\n",
-       "                                        const svg = newBrowser.toSVG()\n",
-       "                                        toSVG(browserID, locus, svg)\n",
-       "                                    })\n",
-       "                                    customButtonDiv.appendChild(toSVGButton)\n",
-       "                                }\n",
-       "\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadSession\":\n",
-       "                                convertUrlsAndPaths(data)\n",
-       "                                browser.loadSessionObject(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadTrack\":\n",
-       "                                convertTrackData(data)\n",
-       "                                await browser.loadTrack(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadROI\":\n",
-       "                                if (Array.isArray(data)) {\n",
-       "                                    data.map(convertTrackData)\n",
-       "                                } else {\n",
-       "                                    convertTrackData(data)\n",
-       "                                }\n",
-       "                                await browser.loadROI(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"clearROIs\":\n",
-       "                                await browser.clearROIs()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"search\":\n",
-       "                                browser.search(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"zoomIn\":\n",
-       "                                browser.zoomIn()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"zoomOut\":\n",
-       "                                browser.zoomOut()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"remove\":\n",
-       "                                this.browserCache.delete(browserID)\n",
-       "                                document.getElementById(browserID).parentNode.removeChild(container)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"toSVG\":\n",
-       "                                const displayId = data\n",
-       "                                const svg = browser.toSVG()\n",
-       "                                const locus = browser.referenceFrameList.map(rf => rf.getLocusString()).join(' ')\n",
-       "                                toSVG(displayId, locus, svg)\n",
-       "                                break\n",
-       "\n",
-       "                            default:\n",
-       "                                console.error(\"Unrecognized method: \" + msg.command)\n",
-       "                        }\n",
-       "                    } catch (e) {\n",
-       "                        console.error(e)\n",
-       "                    }\n",
-       "                }\n",
-       "                this.processing = false\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Potentially convert a path to a local File-like object.\n",
-       "     * @param path\n",
-       "     * @returns {*}\n",
-       "     */\n",
-       "    function createNotebookFile(path) {\n",
-       "        if (!path ||\n",
-       "            path.startsWith(\"https://\") || path.startsWith(\"http://\") || path.startsWith(\"gs://\") || path.startsWith(\"data:\")) {\n",
-       "            return path\n",
-       "        } else {\n",
-       "            // Try to create a notebook file.  If no notebook file implementation is available for the kernel in\n",
-       "            // use (e.g. Jupyter Lab) treat as a URL.\n",
-       "            const nbFile = igv.createNotebookLocalFile({path})\n",
-       "            if (nbFile != null) {\n",
-       "                return nbFile\n",
-       "            } else {\n",
-       "                // Try to treat as relative URL.  This may or may not work\n",
-       "                return convertURL(path)\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Convert relative URLs to absolute.  Primarily for Jupyter Lab, not generally needed for Jupyter Notebook\n",
-       "     * @param url\n",
-       "     * @returns {*}\n",
-       "     */\n",
-       "    function convertURL(url) {\n",
-       "\n",
-       "        const pageURL = window.location.href\n",
-       "\n",
-       "        if (!url ||\n",
-       "            url.startsWith(\"https://\") ||\n",
-       "            url.startsWith(\"http://\") ||\n",
-       "            url.startsWith(\"gs://\") ||\n",
-       "            url.startsWith(\"data:\")) {\n",
-       "            return url\n",
-       "        } else if (isColab) {\n",
-       "            // Interpret relative url as a path.\n",
-       "            igv.createNotebookLocalFile({path: url})\n",
-       "        } else if (isNotebook) {\n",
-       "            // Jupyter Notebook\n",
-       "            //\n",
-       "            // Examples\n",
-       "            // https://hub-binder.mybinder.ovh/user/igvteam-igv-notebook-tnlb45ie/notebooks/examples/BamFiles-Jupyter.ipynb\n",
-       "            //   => https://hub-binder.mybinder.ovh/user/igvteam-igv-notebook-tnlb45ie/files/examples/data/gstt1_sample.bam\",\n",
-       "\n",
-       "            const baseURL = document.querySelector('body').getAttribute('data-base-url')\n",
-       "            const notebookPath = document.querySelector('body').getAttribute('data-notebook-path')\n",
-       "            const notebookName = document.querySelector('body').getAttribute('data-notebook-name')\n",
-       "            const notebookDir = notebookPath.slice(0, -1 * notebookName.length)\n",
-       "\n",
-       "            //`${location.origin}${base_path}files/${nb_dir}${url}`\n",
-       "            if (url.startsWith(\"/\")) {\n",
-       "                url = `files${url}`\n",
-       "                return encodeURI(`${location.origin}${baseURL}${url}`)\n",
-       "            } else {\n",
-       "                // URL is relative to notebook\n",
-       "                return encodeURI(`${location.origin}${baseURL}files/${notebookDir}${url}`)\n",
-       "            }\n",
-       "        } else if (pageURL.includes(\"/lab\")) {\n",
-       "\n",
-       "            console.log(\"Jupyter lab\")\n",
-       "            // Jupyter Lab\n",
-       "\n",
-       "            // Examples\n",
-       "            // http://localhost:8888/lab/workspaces/auto-N/tree/examples/BamFiles.ipynb\n",
-       "            //     =>  http://localhost:8888/files/examples/data/gstt1_sample.bam\n",
-       "            //\n",
-       "            // https://hub.gke2.mybinder.org/user/igvteam-igv-notebook-5ivkyktt/lab/tree/examples/BamFiles.ipynb\n",
-       "            //    => https://hub.gke2.mybinder.org/user/igvteam-igv-notebook-5ivkyktt/files/examples/data/gstt1_sample.bam\n",
-       "\n",
-       "            const baseIndex = pageURL.indexOf(\"/lab\")\n",
-       "            const baseURL = pageURL.substring(0, baseIndex)\n",
-       "\n",
-       "            if (url.startsWith(\"/\")) {\n",
-       "                return encodeURI(`${baseURL}/files${url}`)\n",
-       "            } else if (pageURL.includes(\"/tree/\")) {\n",
-       "                // Interpret URL as relative to notebook location.  This is not reliable, '/tree/' is not always in the page URL\n",
-       "                const treeIndex = pageURL.indexOf(\"/tree/\") + 6\n",
-       "                const lastSlashIndex = pageURL.lastIndexOf(\"/\")\n",
-       "                const notebookDir = pageURL.substring(treeIndex, lastSlashIndex)\n",
-       "                return encodeURI(`${baseURL}/files/${notebookDir}/${url}`)\n",
-       "            } else {\n",
-       "                // We don't know how to determine the notebook path\n",
-       "                console.warn(\"Page url missing '/tree/'.  Can't determine notebook path.\")\n",
-       "                return encodeURI(`${baseURL}/files/${url}`)\n",
-       "            }\n",
-       "        } else {\n",
-       "            // We should never get here,\n",
-       "            return encodeURI(url)\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    function convert(config, prefix) {\n",
-       "        const urlProp = prefix ? prefix + \"URL\" : \"url\"\n",
-       "        const pathProp = prefix ? prefix + \"Path\" : \"path\"\n",
-       "        if (config[pathProp]) {\n",
-       "            config[urlProp] = createNotebookFile(config[pathProp])\n",
-       "        } else if (config[urlProp]) {\n",
-       "            config[urlProp] = convertURL(config[urlProp])\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    class Queue {\n",
-       "        constructor() {\n",
-       "            this.elements = []\n",
-       "        }\n",
-       "\n",
-       "        enqueue(e) {\n",
-       "            this.elements.push(e)\n",
-       "        }\n",
-       "\n",
-       "        dequeue() {\n",
-       "            return this.elements.shift()\n",
-       "        }\n",
-       "\n",
-       "        isEmpty() {\n",
-       "            return this.elements.length == 0\n",
-       "        }\n",
-       "\n",
-       "        peek() {\n",
-       "            return !this.isEmpty() ? this.elements[0] : undefined\n",
-       "        }\n",
-       "\n",
-       "        length() {\n",
-       "            return this.elements.length\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    window.igv.MessageHandler = new MessageHandler()\n",
-       "\n",
-       "    function download(filename, text) {\n",
-       "\n",
-       "        const data = URL.createObjectURL(new Blob([text], {type: \"application/octet-stream\"}))\n",
-       "        const element = document.createElement('a')\n",
-       "        element.setAttribute('href', data)\n",
-       "        element.setAttribute('download', filename)\n",
-       "        element.style.display = 'none'\n",
-       "        document.body.appendChild(element)\n",
-       "        element.click()\n",
-       "        document.body.removeChild(element)\n",
-       "    }\n",
-       "\n",
-       "    async function shortenURL(url) {\n",
-       "        const endpoint = \"https://2et6uxfezb.execute-api.us-east-1.amazonaws.com/dev/tinyurl/\"\n",
-       "        const enc = encodeURIComponent(url)\n",
-       "        const response = await fetch(`${endpoint}${enc}`)\n",
-       "        if (response.ok) {\n",
-       "            return response.text()\n",
-       "        } else {\n",
-       "            throw new Error(response.statusText)\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    console.log(\"igv.MessageHandler installed\")\n",
-       "\n",
-       "})()"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "/**\n",
-       " * Mock objects to emulate the browser \"File\" class for use with Jupyter and Colab notebooks.  These objects delegate\n",
-       " * actual file reading to python.\n",
-       " */\n",
-       "\n",
-       "// Use a self-evaluating function to keep variables in this file scope\n",
-       "\n",
-       "(function () {\n",
-       "\n",
-       "    const isColab =  window.google !== undefined && window.google.colab\n",
-       "    const isNotebook =  !isColab &&  window.Jupyter !== undefined\n",
-       "\n",
-       "    igv.createNotebookLocalFile = function (options) {\n",
-       "        if (isColab) {\n",
-       "            return new ColabLocalFile(options)\n",
-       "        } else if (isNotebook) {\n",
-       "            return new JupyterLocalFile(options)\n",
-       "        } else {\n",
-       "            return undefined;  //TODO -- throw error?\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    // Start up a Comm object if in a Jupyter Notebook environment (i.e. not Colab or JupyterLab).\n",
-       "    let comm\n",
-       "    const pendingRequests = new Map()\n",
-       "    if (isNotebook) {\n",
-       "        console.log('registering comm')\n",
-       "        comm = Jupyter.notebook.kernel.comm_manager.new_comm('file_request', {})\n",
-       "        // Register a handler\n",
-       "        comm.on_msg(function (msg) {\n",
-       "            const id = msg.content.data.id\n",
-       "            const data = msg.content.data.data\n",
-       "            pendingRequests.set(id, data)\n",
-       "        })\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Emulates a browser \"File\" for Jupyter notebooks.  File reading is delegated to python via Comms messaging.\n",
-       "     * Polling is used to synchronize the async message passing.\n",
-       "     *\n",
-       "     * NOTE: This will not work for JupyterLab\n",
-       "     */\n",
-       "    class JupyterLocalFile {\n",
-       "\n",
-       "        constructor({path, name, start, end}) {\n",
-       "            this.type = 'JupyterLocalFile'\n",
-       "            this.path = path\n",
-       "            this.name = name || path\n",
-       "            this.start = start\n",
-       "            this.end = end\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a new Blob object containing the data in the specified range of bytes of the blob on which it's called.\n",
-       "         * @param start An index into the Blob indicating the first byte to include in the new Blob\n",
-       "         * @param end  An index into the Blob indicating the first byte that will *not* be included in the new Blob\n",
-       "         * @param contentType\n",
-       "         * @returns {*}\n",
-       "         */\n",
-       "        slice(start, end) {\n",
-       "            return new JupyterLocalFile({path: this.path, name: this.name, start, end})\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with an ArrayBuffer containing the entire contents of the Blob as binary data.\n",
-       "         *\n",
-       "         * @returns {Promise<*>}\n",
-       "         */\n",
-       "        async arrayBuffer() {\n",
-       "\n",
-       "            const id = uniqueID()\n",
-       "            const path = this.path\n",
-       "            const promise = new Promise((resolve, reject) => {\n",
-       "                let count = 0\n",
-       "\n",
-       "                function poll() {\n",
-       "\n",
-       "                    if (count > 100) {\n",
-       "                        console.error(`error reading ${path}: timed out`)\n",
-       "                        reject(`error reading ${path}: timed out`)\n",
-       "                    }\n",
-       "\n",
-       "                    count++\n",
-       "                    if (pendingRequests.has(id)) {\n",
-       "                        const data = pendingRequests.get(id)\n",
-       "                        const dataString = atob(data)\n",
-       "                        const bytes = new Uint8Array(dataString.length)\n",
-       "                        for (var i = 0; i < dataString.length; i++) {\n",
-       "                            bytes[i] = dataString.charCodeAt(i)\n",
-       "                        }\n",
-       "                        pendingRequests.delete(id)\n",
-       "                        resolve(bytes.buffer)\n",
-       "                    } else {\n",
-       "                        setTimeout(poll, 100)\n",
-       "                    }\n",
-       "                }\n",
-       "\n",
-       "                poll()\n",
-       "            })\n",
-       "\n",
-       "            const msg = (this.start === undefined) ?\n",
-       "                {id: id, 'path': this.path, 'method': 'arrayBuffer'} :\n",
-       "                {id: id, 'path': this.path, 'method': 'arrayBuffer', 'start': this.start, 'end': this.end}\n",
-       "\n",
-       "            comm.send(msg)\n",
-       "\n",
-       "            return promise\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with a USVString containing the entire contents of the Blob interpreted as UTF-8 text.\n",
-       "         *\n",
-       "         * @returns {Promise<string>}\n",
-       "         */\n",
-       "        async text() {\n",
-       "            throw Error(\"text not implemented\")\n",
-       "        }\n",
-       "\n",
-       "        stream() {\n",
-       "            throw Error(\"stream not implemented\")\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Emulates a browser \"File\" for Colab environments.\n",
-       "     */\n",
-       "    class ColabLocalFile {\n",
-       "\n",
-       "        constructor({path, name, start, end}) {\n",
-       "            this.type = 'ColabLocalFile'\n",
-       "            this.path = path\n",
-       "            this.name = name || path\n",
-       "            this.start = start\n",
-       "            this.end = end\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a new Blob object containing the data in the specified range of bytes of the blob on which it's called.\n",
-       "         * @param start An index into the Blob indicating the first byte to include in the new Blob\n",
-       "         * @param end  An index into the Blob indicating the first byte that will *not* be included in the new Blob\n",
-       "         * @param contentType\n",
-       "         * @returns {*}\n",
-       "         */\n",
-       "        slice(start, end) {\n",
-       "            return new ColabLocalFile({path: this.path, name: this.name, start, end})\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with an ArrayBuffer containing the entire contents of the Blob as\n",
-       "         * binary data.\n",
-       "         */\n",
-       "        async arrayBuffer() {\n",
-       "\n",
-       "            const args = (this.start === undefined) ?\n",
-       "                [this.path] :\n",
-       "                [this.path, this.start.toString(), this.end.toString()]\n",
-       "\n",
-       "            const result = await google.colab.kernel.invokeFunction(\n",
-       "                'ReadFile', // The callback name.\n",
-       "                args, // The arguments.\n",
-       "                {}) // kwargs\n",
-       "            const data = result.data[\"text/plain\"]\n",
-       "            const dataString = atob(data.substring(2, data.length - 1))\n",
-       "            const bytes = new Uint8Array(dataString.length)\n",
-       "            for (var i = 0; i < dataString.length; i++) {\n",
-       "                bytes[i] = dataString.charCodeAt(i)\n",
-       "            }\n",
-       "            return bytes.buffer\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with a USVString containing the entire contents of the Blob interpreted as UTF-8 text.\n",
-       "         *\n",
-       "         * @returns {Promise<string>}\n",
-       "         */\n",
-       "        async text() {\n",
-       "            throw Error(\"text not implemented\")\n",
-       "        }\n",
-       "\n",
-       "        stream() {\n",
-       "            throw Error(\"stream not implemented\")\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    let counter = 0\n",
-       "\n",
-       "    function uniqueID() {\n",
-       "        return `${Math.random()}-${counter++}`\n",
-       "    }\n",
-       "\n",
-       "})()"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/html": [
-       "<div id=\"jb_831280_buttons\"></div><div id=\"jb_831280_igvcontainer\"></div>"
-      ],
-      "text/plain": [
-       "<IPython.core.display.HTML object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "window.igv.MessageHandler.on({\"id\": \"jb_831280\", \"command\": \"createBrowser\", \"data\": {\"reference\": {\"id\": \"AgamP4\", \"name\": \"Anopheles gambiae (PEST)\", \"fastaURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_CHROMOSOMES_AgamP4.fa.fai\", \"tracks\": [{\"name\": \"Genes\", \"type\": \"annotation\", \"format\": \"gff3\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/reference/genome/agamp4/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz\", \"indexed\": false}]}, \"locus\": \"2L:2,422,600-2,422,700\", \"tracks\": [{\"name\": \"Filters - gamb_colu_arab\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/gamb_colu_arab/2L_sitefilters.vcf.gz\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/gamb_colu_arab/2L_sitefilters.vcf.gz.tbi\", \"format\": \"vcf\", \"type\": \"variant\", \"visibilityWindow\": 20000, \"height\": 30, \"colorBy\": \"FILTER\", \"colorTable\": {\"PASS\": \"#00cc96\", \"*\": \"#ef553b\"}}, {\"name\": \"Filters - gamb_colu\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/gamb_colu/2L_sitefilters.vcf.gz\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/gamb_colu/2L_sitefilters.vcf.gz.tbi\", \"format\": \"vcf\", \"type\": \"variant\", \"visibilityWindow\": 20000, \"height\": 30, \"colorBy\": \"FILTER\", \"colorTable\": {\"PASS\": \"#00cc96\", \"*\": \"#ef553b\"}}, {\"name\": \"Filters - arab\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/arab/2L_sitefilters.vcf.gz\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_agam_release/v3/site_filters/dt_20200416/vcf/arab/2L_sitefilters.vcf.gz.tbi\", \"format\": \"vcf\", \"type\": \"variant\", \"visibilityWindow\": 20000, \"height\": 30, \"colorBy\": \"FILTER\", \"colorTable\": {\"PASS\": \"#00cc96\", \"*\": \"#ef553b\"}}, {\"name\": \"SNPs\", \"url\": \"https://1177-vo-ml-lehmann-vmf00004.cog.sanger.ac.uk/VBS00256-4651STDY7017184.vcf.gz\", \"indexURL\": \"https://1177-vo-ml-lehmann-vmf00004.cog.sanger.ac.uk/VBS00256-4651STDY7017184.vcf.gz.tbi\", \"format\": \"vcf\", \"type\": \"variant\", \"visibilityWindow\": 20000, \"height\": 50}, {\"name\": \"Alignments\", \"url\": \"https://1177-vo-ml-lehmann-vmf00004.cog.sanger.ac.uk/VBS00256-4651STDY7017184.fixmate.bam\", \"indexURL\": \"https://1177-vo-ml-lehmann-vmf00004.cog.sanger.ac.uk/VBS00256-4651STDY7017184.fixmate.bam.bai\", \"format\": \"bam\", \"type\": \"alignment\", \"visibilityWindow\": 20000, \"height\": 500}], \"id\": \"jb_831280\"}})"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "ag3.view_alignments(\n",
     "    sample=ag3.sample_metadata(sample_sets=\"3.1\").iloc[0][\"sample_id\"],\n",
@@ -2644,7 +77,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14fb9ad2",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2657,7 +90,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c3f68890",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2670,7 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fe787f1c",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2683,7 +116,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "064a2953",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2696,7 +129,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cd41cf04",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -2708,413 +141,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
-   "id": "fe887a0a",
+   "execution_count": null,
+   "id": "12",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/javascript": [
-       "'use strict';\n",
-       "(function(root) {\n",
-       "  function now() {\n",
-       "    return new Date();\n",
-       "  }\n",
-       "\n",
-       "  const force = true;\n",
-       "\n",
-       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
-       "    root._bokeh_onload_callbacks = [];\n",
-       "    root._bokeh_is_loading = undefined;\n",
-       "  }\n",
-       "\n",
-       "const JS_MIME_TYPE = 'application/javascript';\n",
-       "  const HTML_MIME_TYPE = 'text/html';\n",
-       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
-       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
-       "\n",
-       "  /**\n",
-       "   * Render data to the DOM node\n",
-       "   */\n",
-       "  function render(props, node) {\n",
-       "    const script = document.createElement(\"script\");\n",
-       "    node.appendChild(script);\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when an output is cleared or removed\n",
-       "   */\n",
-       "  function handleClearOutput(event, handle) {\n",
-       "    function drop(id) {\n",
-       "      const view = Bokeh.index.get_by_id(id)\n",
-       "      if (view != null) {\n",
-       "        view.model.document.clear()\n",
-       "        Bokeh.index.delete(view)\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    const cell = handle.cell;\n",
-       "\n",
-       "    const id = cell.output_area._bokeh_element_id;\n",
-       "    const server_id = cell.output_area._bokeh_server_id;\n",
-       "\n",
-       "    // Clean up Bokeh references\n",
-       "    if (id != null) {\n",
-       "      drop(id)\n",
-       "    }\n",
-       "\n",
-       "    if (server_id !== undefined) {\n",
-       "      // Clean up Bokeh references\n",
-       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
-       "      cell.notebook.kernel.execute(cmd_clean, {\n",
-       "        iopub: {\n",
-       "          output: function(msg) {\n",
-       "            const id = msg.content.text.trim()\n",
-       "            drop(id)\n",
-       "          }\n",
-       "        }\n",
-       "      });\n",
-       "      // Destroy server and session\n",
-       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
-       "      cell.notebook.kernel.execute(cmd_destroy);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when a new output is added\n",
-       "   */\n",
-       "  function handleAddOutput(event, handle) {\n",
-       "    const output_area = handle.output_area;\n",
-       "    const output = handle.output;\n",
-       "\n",
-       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
-       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
-       "      return\n",
-       "    }\n",
-       "\n",
-       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
-       "\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
-       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
-       "      // store reference to embed id on output_area\n",
-       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
-       "    }\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
-       "      const bk_div = document.createElement(\"div\");\n",
-       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
-       "      const script_attrs = bk_div.children[0].attributes;\n",
-       "      for (let i = 0; i < script_attrs.length; i++) {\n",
-       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
-       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
-       "      }\n",
-       "      // store reference to server id on output_area\n",
-       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function register_renderer(events, OutputArea) {\n",
-       "\n",
-       "    function append_mime(data, metadata, element) {\n",
-       "      // create a DOM node to render to\n",
-       "      const toinsert = this.create_output_subarea(\n",
-       "        metadata,\n",
-       "        CLASS_NAME,\n",
-       "        EXEC_MIME_TYPE\n",
-       "      );\n",
-       "      this.keyboard_manager.register_events(toinsert);\n",
-       "      // Render to node\n",
-       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
-       "      render(props, toinsert[toinsert.length - 1]);\n",
-       "      element.append(toinsert);\n",
-       "      return toinsert\n",
-       "    }\n",
-       "\n",
-       "    /* Handle when an output is cleared or removed */\n",
-       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
-       "    events.on('delete.Cell', handleClearOutput);\n",
-       "\n",
-       "    /* Handle when a new output is added */\n",
-       "    events.on('output_added.OutputArea', handleAddOutput);\n",
-       "\n",
-       "    /**\n",
-       "     * Register the mime type and append_mime function with output_area\n",
-       "     */\n",
-       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
-       "      /* Is output safe? */\n",
-       "      safe: true,\n",
-       "      /* Index of renderer in `output_area.display_order` */\n",
-       "      index: 0\n",
-       "    });\n",
-       "  }\n",
-       "\n",
-       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
-       "  if (root.Jupyter !== undefined) {\n",
-       "    const events = require('base/js/events');\n",
-       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
-       "\n",
-       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
-       "      register_renderer(events, OutputArea);\n",
-       "    }\n",
-       "  }\n",
-       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
-       "    root._bokeh_timeout = Date.now() + 5000;\n",
-       "    root._bokeh_failed_load = false;\n",
-       "  }\n",
-       "\n",
-       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
-       "     \"<div style='background-color: #fdd'>\\n\"+\n",
-       "     \"<p>\\n\"+\n",
-       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
-       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
-       "     \"</p>\\n\"+\n",
-       "     \"<ul>\\n\"+\n",
-       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
-       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
-       "     \"</ul>\\n\"+\n",
-       "     \"<code>\\n\"+\n",
-       "     \"from bokeh.resources import INLINE\\n\"+\n",
-       "     \"output_notebook(resources=INLINE)\\n\"+\n",
-       "     \"</code>\\n\"+\n",
-       "     \"</div>\"}};\n",
-       "\n",
-       "  function display_loaded(error = null) {\n",
-       "    const el = document.getElementById(null);\n",
-       "    if (el != null) {\n",
-       "      const html = (() => {\n",
-       "        if (typeof root.Bokeh === \"undefined\") {\n",
-       "          if (error == null) {\n",
-       "            return \"BokehJS is loading ...\";\n",
-       "          } else {\n",
-       "            return \"BokehJS failed to load.\";\n",
-       "          }\n",
-       "        } else {\n",
-       "          const prefix = `BokehJS ${root.Bokeh.version}`;\n",
-       "          if (error == null) {\n",
-       "            return `${prefix} successfully loaded.`;\n",
-       "          } else {\n",
-       "            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n",
-       "          }\n",
-       "        }\n",
-       "      })();\n",
-       "      el.innerHTML = html;\n",
-       "\n",
-       "      if (error != null) {\n",
-       "        const wrapper = document.createElement(\"div\");\n",
-       "        wrapper.style.overflow = \"auto\";\n",
-       "        wrapper.style.height = \"5em\";\n",
-       "        wrapper.style.resize = \"vertical\";\n",
-       "        const content = document.createElement(\"div\");\n",
-       "        content.style.fontFamily = \"monospace\";\n",
-       "        content.style.whiteSpace = \"pre-wrap\";\n",
-       "        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n",
-       "        content.textContent = error.stack ?? error.toString();\n",
-       "        wrapper.append(content);\n",
-       "        el.append(wrapper);\n",
-       "      }\n",
-       "    } else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(() => display_loaded(error), 100);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function run_callbacks() {\n",
-       "    try {\n",
-       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
-       "        if (callback != null)\n",
-       "          callback();\n",
-       "      });\n",
-       "    } finally {\n",
-       "      delete root._bokeh_onload_callbacks\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
-       "  }\n",
-       "\n",
-       "  function load_libs(css_urls, js_urls, callback) {\n",
-       "    if (css_urls == null) css_urls = [];\n",
-       "    if (js_urls == null) js_urls = [];\n",
-       "\n",
-       "    root._bokeh_onload_callbacks.push(callback);\n",
-       "    if (root._bokeh_is_loading > 0) {\n",
-       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
-       "      return null;\n",
-       "    }\n",
-       "    if (js_urls == null || js_urls.length === 0) {\n",
-       "      run_callbacks();\n",
-       "      return null;\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
-       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
-       "\n",
-       "    function on_load() {\n",
-       "      root._bokeh_is_loading--;\n",
-       "      if (root._bokeh_is_loading === 0) {\n",
-       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
-       "        run_callbacks()\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    function on_error(url) {\n",
-       "      console.error(\"failed to load \" + url);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < css_urls.length; i++) {\n",
-       "      const url = css_urls[i];\n",
-       "      const element = document.createElement(\"link\");\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.rel = \"stylesheet\";\n",
-       "      element.type = \"text/css\";\n",
-       "      element.href = url;\n",
-       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
-       "      document.body.appendChild(element);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < js_urls.length; i++) {\n",
-       "      const url = js_urls[i];\n",
-       "      const element = document.createElement('script');\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.async = false;\n",
-       "      element.src = url;\n",
-       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
-       "      document.head.appendChild(element);\n",
-       "    }\n",
-       "  };\n",
-       "\n",
-       "  function inject_raw_css(css) {\n",
-       "    const element = document.createElement(\"style\");\n",
-       "    element.appendChild(document.createTextNode(css));\n",
-       "    document.body.appendChild(element);\n",
-       "  }\n",
-       "\n",
-       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.1.min.js\"];\n",
-       "  const css_urls = [];\n",
-       "\n",
-       "  const inline_js = [    function(Bokeh) {\n",
-       "      Bokeh.set_log_level(\"info\");\n",
-       "    },\n",
-       "function(Bokeh) {\n",
-       "    }\n",
-       "  ];\n",
-       "\n",
-       "  function run_inline_js() {\n",
-       "    if (root.Bokeh !== undefined || force === true) {\n",
-       "      try {\n",
-       "            for (let i = 0; i < inline_js.length; i++) {\n",
-       "      inline_js[i].call(root, root.Bokeh);\n",
-       "    }\n",
-       "\n",
-       "      } catch (error) {throw error;\n",
-       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(run_inline_js, 100);\n",
-       "    } else if (!root._bokeh_failed_load) {\n",
-       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
-       "      root._bokeh_failed_load = true;\n",
-       "    } else if (force !== true) {\n",
-       "      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
-       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  if (root._bokeh_is_loading === 0) {\n",
-       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
-       "    run_inline_js();\n",
-       "  } else {\n",
-       "    load_libs(css_urls, js_urls, function() {\n",
-       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
-       "      run_inline_js();\n",
-       "    });\n",
-       "  }\n",
-       "}(window));"
-      ],
-      "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded(error = null) {\n    const el = document.getElementById(null);\n    if (el != null) {\n      const html = (() => {\n        if (typeof root.Bokeh === \"undefined\") {\n          if (error == null) {\n            return \"BokehJS is loading ...\";\n          } else {\n            return \"BokehJS failed to load.\";\n          }\n        } else {\n          const prefix = `BokehJS ${root.Bokeh.version}`;\n          if (error == null) {\n            return `${prefix} successfully loaded.`;\n          } else {\n            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n          }\n        }\n      })();\n      el.innerHTML = html;\n\n      if (error != null) {\n        const wrapper = document.createElement(\"div\");\n        wrapper.style.overflow = \"auto\";\n        wrapper.style.height = \"5em\";\n        wrapper.style.resize = \"vertical\";\n        const content = document.createElement(\"div\");\n        content.style.fontFamily = \"monospace\";\n        content.style.whiteSpace = \"pre-wrap\";\n        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n        content.textContent = error.stack ?? error.toString();\n        wrapper.append(content);\n        el.append(wrapper);\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(() => display_loaded(error), 100);\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.1.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n      try {\n            for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n\n      } catch (error) {throw error;\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/html": [
-       "\n",
-       "            <table class=\"malariagen-af1\">\n",
-       "                <thead>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\" colspan=\"2\">MalariaGEN Af1 API client</th>\n",
-       "                    </tr>\n",
-       "                    <tr><td colspan=\"2\" style=\"text-align: left\">\n",
-       "                        Please note that data are subject to terms of use,\n",
-       "                        for more information see <a href=\"https://www.malariagen.net/data\">\n",
-       "                        the MalariaGEN website</a> or contact support@malariagen.net.\n",
-       "                        See also the <a href=\"https://malariagen.github.io/malariagen-data-python/v0.0.0/Af1.html\">Af1 API docs</a>.\n",
-       "                    </td></tr>\n",
-       "                </thead>\n",
-       "                <tbody>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Storage URL\n",
-       "                        </th>\n",
-       "                        <td>gs://vo_afun_release_master_us_central1/</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Data releases available\n",
-       "                        </th>\n",
-       "                        <td>1.0, 1.1, 1.2, 1.3, 1.4</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Results cache\n",
-       "                        </th>\n",
-       "                        <td>None</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Cohorts analysis\n",
-       "                        </th>\n",
-       "                        <td>20240515</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Site filters analysis\n",
-       "                        </th>\n",
-       "                        <td>dt_20200416</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Software version\n",
-       "                        </th>\n",
-       "                        <td>malariagen_data 0.0.0</td>\n",
-       "                    </tr>\n",
-       "                    <tr>\n",
-       "                        <th style=\"text-align: left\">\n",
-       "                            Client location\n",
-       "                        </th>\n",
-       "                        <td>England, United Kingdom</td>\n",
-       "                    </tr>\n",
-       "                </tbody>\n",
-       "            </table>\n",
-       "        "
-      ],
-      "text/plain": [
-       "<MalariaGEN Af1 API client>\n",
-       "Storage URL             : gs://vo_afun_release_master_us_central1/\n",
-       "Data releases available : 1.0, 1.1, 1.2, 1.3, 1.4\n",
-       "Results cache           : None\n",
-       "Cohorts analysis        : 20240515\n",
-       "Site filters analysis   : dt_20200416\n",
-       "Software version        : malariagen_data 0.0.0\n",
-       "Client location         : England, United Kingdom\n",
-       "---\n",
-       "Please note that data are subject to terms of use,\n",
-       "for more information see https://www.malariagen.net/data\n",
-       "or contact support@malariagen.net. For API documentation see \n",
-       "https://malariagen.github.io/malariagen-data-python/v0.0.0/Af1.html"
-      ]
-     },
-     "execution_count": 5,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "af1 = malariagen_data.Af1(pre=True)\n",
     "af1"
@@ -3122,731 +152,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
-   "id": "9d6bbf22",
+   "execution_count": null,
+   "id": "13",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
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n,r,s=-1,o=t[1],a=0,c=7,l=4;for(0===o&&(c=138,l=3),n=0;n<=i;n++)if(r=o,o=t[2*(n+1)+1],!(++a<c&&r===o)){if(a<l)do{di(e,r,e.bl_tree)}while(0!=--a);else 0!==r?(r!==s&&(di(e,r,e.bl_tree),a--),di(e,16,e.bl_tree),hi(e,a-3,2)):a<=10?(di(e,17,e.bl_tree),hi(e,a-3,3)):(di(e,18,e.bl_tree),hi(e,a-11,7));a=0,s=r,0===o?(c=138,l=3):r===o?(c=6,l=3):(c=7,l=4)}};let Ai=!1;const Ci=(e,t,i,n)=>{hi(e,0+(n?1:0),3),gi(e),li(e,i),li(e,~i),i&&e.pending_buf.set(e.window.subarray(t,t+i),e.pending),e.pending+=i};var _i=e=>{Ai||((()=>{let e,t,i,n,r;const s=new Array(16);for(i=0,n=0;n<28;n++)for(ti[n]=i,e=0;e<1<<Gt[n];e++)ei[i++]=n;for(ei[i-1]=n,r=0,n=0;n<16;n++)for(ii[n]=r,e=0;e<1<<$t[n];e++)Jt[r++]=n;for(r>>=7;n<jt;n++)for(ii[n]=r<<7,e=0;e<1<<$t[n]-7;e++)Jt[256+r++]=n;for(t=0;t<=Wt;t++)s[t]=0;for(e=0;e<=143;)Xt[2*e+1]=8,e++,s[8]++;for(;e<=255;)Xt[2*e+1]=9,e++,s[9]++;for(;e<=279;)Xt[2*e+1]=7,e++,s[7]++;for(;e<=287;)Xt[2*e+1]=8,e++,s[8]++;for(fi(Xt,287,s),e=0;e<jt;e++)Zt[2*e+1]=5,Zt[2*e]=ui(e,5);ri=new ni(Xt,Gt,257,Vt,Wt),si=new ni(Zt,$t,0,jt,Wt),oi=new ni(new Array(0),Kt,0,19,7)})(),Ai=!0),e.l_desc=new ai(e.dyn_ltree,ri),e.d_desc=new ai(e.dyn_dtree,si),e.bl_desc=new ai(e.bl_tree,oi),e.bi_buf=0,e.bi_valid=0,pi(e)},xi=(e,t,i,n)=>{let r,s,o=0;e.level>0?(2===e.strm.data_type&&(e.strm.data_type=(e=>{let t,i=4093624447;for(t=0;t<=31;t++,i>>>=1)if(1&i&&0!==e.dyn_ltree[2*t])return 0;if(0!==e.dyn_ltree[18]||0!==e.dyn_ltree[20]||0!==e.dyn_ltree[26])return 1;for(t=32;t<Qt;t++)if(0!==e.dyn_ltree[2*t])return 1;return 0})(e)),Fi(e,e.l_desc),Fi(e,e.d_desc),o=(e=>{let t;for(vi(e,e.dyn_ltree,e.l_desc.max_code),vi(e,e.dyn_dtree,e.d_desc.max_code),Fi(e,e.bl_desc),t=18;t>=3&&0===e.bl_tree[2*Yt[t]+1];t--);return e.opt_len+=3*(t+1)+5+5+4,t})(e),r=e.opt_len+3+7>>>3,s=e.static_len+3+7>>>3,s<=r&&(r=s)):r=s=i+5,i+4<=r&&-1!==t?Ci(e,t,i,n):4===e.strategy||s===r?(hi(e,2+(n?1:0),3),bi(e,Xt,Zt)):(hi(e,4+(n?1:0),3),((e,t,i,n)=>{let r;for(hi(e,t-257,5),hi(e,i-1,5),hi(e,n-4,4),r=0;r<n;r++)hi(e,e.bl_tree[2*Yt[r]+1],3);yi(e,e.dyn_ltree,t-1),yi(e,e.dyn_dtree,i-1)})(e,e.l_desc.max_code+1,e.d_desc.max_code+1,o+1),bi(e,e.dyn_ltree,e.dyn_dtree)),pi(e),n&&gi(e)},ki={_tr_init:_i,_tr_stored_block:Ci,_tr_flush_block:xi,_tr_tally:(e,t,i)=>(e.pending_buf[e.sym_buf+e.sym_next++]=t,e.pending_buf[e.sym_buf+e.sym_next++]=t>>8,e.pending_buf[e.sym_buf+e.sym_next++]=i,0===t?e.dyn_ltree[2*i]++:(e.matches++,t--,e.dyn_ltree[2*(ei[i]+Qt+1)]++,e.dyn_dtree[2*ci(t)]++),e.sym_next===e.sym_end),_tr_align:e=>{hi(e,2,3),di(e,256,Xt),(e=>{16===e.bi_valid?(li(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=255&e.bi_buf,e.bi_buf>>=8,e.bi_valid-=8)})(e)}};var Ii=(e,t,i,n)=>{let r=65535&e,s=e>>>16&65535,o=0;for(;0!==i;){o=i>2e3?2e3:i,i-=o;do{r=r+t[n++]|0,s=s+r|0}while(--o);r%=65521,s%=65521}return r|s<<16};const Si=new Uint32Array((()=>{let e,t=[];for(var i=0;i<256;i++){e=i;for(var n=0;n<8;n++)e=1&e?3988292384^e>>>1:e>>>1;t[i]=e}return t})());var Ei=(e,t,i,n)=>{const r=Si,s=n+i;e^=-1;for(let i=n;i<s;i++)e=e>>>8^r[255&(e^t[i])];return~e},Ni={2:\"need dictionary\",1:\"stream end\",0:\"\",\"-1\":\"file error\",\"-2\":\"stream error\",\"-3\":\"data error\",\"-4\":\"insufficient memory\",\"-5\":\"buffer error\",\"-6\":\"incompatible version\"},Bi={Z_NO_FLUSH:0,Z_PARTIAL_FLUSH:1,Z_SYNC_FLUSH:2,Z_FULL_FLUSH:3,Z_FINISH:4,Z_BLOCK:5,Z_TREES:6,Z_OK:0,Z_STREAM_END:1,Z_NEED_DICT:2,Z_ERRNO:-1,Z_STREAM_ERROR:-2,Z_DATA_ERROR:-3,Z_MEM_ERROR:-4,Z_BUF_ERROR:-5,Z_NO_COMPRESSION:0,Z_BEST_SPEED:1,Z_BEST_COMPRESSION:9,Z_DEFAULT_COMPRESSION:-1,Z_FILTERED:1,Z_HUFFMAN_ONLY:2,Z_RLE:3,Z_FIXED:4,Z_DEFAULT_STRATEGY:0,Z_BINARY:0,Z_TEXT:1,Z_UNKNOWN:2,Z_DEFLATED:8};const{_tr_init:Mi,_tr_stored_block:Ri,_tr_flush_block:Di,_tr_tally:Ti,_tr_align:Li}=ki,{Z_NO_FLUSH:zi,Z_PARTIAL_FLUSH:Hi,Z_FULL_FLUSH:Pi,Z_FINISH:Oi,Z_BLOCK:Ui,Z_OK:qi,Z_STREAM_END:Qi,Z_STREAM_ERROR:Vi,Z_DATA_ERROR:ji,Z_BUF_ERROR:Wi,Z_DEFAULT_COMPRESSION:Gi,Z_FILTERED:$i,Z_HUFFMAN_ONLY:Ki,Z_RLE:Yi,Z_FIXED:Xi,Z_DEFAULT_STRATEGY:Zi,Z_UNKNOWN:Ji,Z_DEFLATED:en}=Bi,tn=258,nn=262,rn=42,sn=113,on=666,an=(e,t)=>(e.msg=Ni[t],t),cn=e=>2*e-(e>4?9:0),ln=e=>{let t=e.length;for(;--t>=0;)e[t]=0},hn=e=>{let t,i,n,r=e.w_size;t=e.hash_size,n=t;do{i=e.head[--n],e.head[n]=i>=r?i-r:0}while(--t);t=r,n=t;do{i=e.prev[--n],e.prev[n]=i>=r?i-r:0}while(--t)};let dn=(e,t,i)=>(t<<e.hash_shift^i)&e.hash_mask;const un=e=>{const t=e.state;let i=t.pending;i>e.avail_out&&(i=e.avail_out),0!==i&&(e.output.set(t.pending_buf.subarray(t.pending_out,t.pending_out+i),e.next_out),e.next_out+=i,t.pending_out+=i,e.total_out+=i,e.avail_out-=i,t.pending-=i,0===t.pending&&(t.pending_out=0))},fn=(e,t)=>{Di(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,un(e.strm)},pn=(e,t)=>{e.pending_buf[e.pending++]=t},gn=(e,t)=>{e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=255&t},mn=(e,t,i,n)=>{let r=e.avail_in;return r>n&&(r=n),0===r?0:(e.avail_in-=r,t.set(e.input.subarray(e.next_in,e.next_in+r),i),1===e.state.wrap?e.adler=Ii(e.adler,t,r,i):2===e.state.wrap&&(e.adler=Ei(e.adler,t,r,i)),e.next_in+=r,e.total_in+=r,r)},wn=(e,t)=>{let i,n,r=e.max_chain_length,s=e.strstart,o=e.prev_length,a=e.nice_match;const c=e.strstart>e.w_size-nn?e.strstart-(e.w_size-nn):0,l=e.window,h=e.w_mask,d=e.prev,u=e.strstart+tn;let f=l[s+o-1],p=l[s+o];e.prev_length>=e.good_match&&(r>>=2),a>e.lookahead&&(a=e.lookahead);do{if(i=t,l[i+o]===p&&l[i+o-1]===f&&l[i]===l[s]&&l[++i]===l[s+1]){s+=2,i++;do{}while(l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&l[++s]===l[++i]&&s<u);if(n=tn-(u-s),s=u-tn,n>o){if(e.match_start=t,o=n,n>=a)break;f=l[s+o-1],p=l[s+o]}}}while((t=d[t&h])>c&&0!=--r);return o<=e.lookahead?o:e.lookahead},bn=e=>{const t=e.w_size;let i,n,r;do{if(n=e.window_size-e.lookahead-e.strstart,e.strstart>=t+(t-nn)&&(e.window.set(e.window.subarray(t,t+t-n),0),e.match_start-=t,e.strstart-=t,e.block_start-=t,e.insert>e.strstart&&(e.insert=e.strstart),hn(e),n+=t),0===e.strm.avail_in)break;if(i=mn(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=i,e.lookahead+e.insert>=3)for(r=e.strstart-e.insert,e.ins_h=e.window[r],e.ins_h=dn(e,e.ins_h,e.window[r+1]);e.insert&&(e.ins_h=dn(e,e.ins_h,e.window[r+3-1]),e.prev[r&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=r,r++,e.insert--,!(e.lookahead+e.insert<3)););}while(e.lookahead<nn&&0!==e.strm.avail_in)},Fn=(e,t)=>{let i,n,r,s=e.pending_buf_size-5>e.w_size?e.w_size:e.pending_buf_size-5,o=0,a=e.strm.avail_in;do{if(i=65535,r=e.bi_valid+42>>3,e.strm.avail_out<r)break;if(r=e.strm.avail_out-r,n=e.strstart-e.block_start,i>n+e.strm.avail_in&&(i=n+e.strm.avail_in),i>r&&(i=r),i<s&&(0===i&&t!==Oi||t===zi||i!==n+e.strm.avail_in))break;o=t===Oi&&i===n+e.strm.avail_in?1:0,Ri(e,0,0,o),e.pending_buf[e.pending-4]=i,e.pending_buf[e.pending-3]=i>>8,e.pending_buf[e.pending-2]=~i,e.pending_buf[e.pending-1]=~i>>8,un(e.strm),n&&(n>i&&(n=i),e.strm.output.set(e.window.subarray(e.block_start,e.block_start+n),e.strm.next_out),e.strm.next_out+=n,e.strm.avail_out-=n,e.strm.total_out+=n,e.block_start+=n,i-=n),i&&(mn(e.strm,e.strm.output,e.strm.next_out,i),e.strm.next_out+=i,e.strm.avail_out-=i,e.strm.total_out+=i)}while(0===o);return a-=e.strm.avail_in,a&&(a>=e.w_size?(e.matches=2,e.window.set(e.strm.input.subarray(e.strm.next_in-e.w_size,e.strm.next_in),0),e.strstart=e.w_size,e.insert=e.strstart):(e.window_size-e.strstart<=a&&(e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,e.insert>e.strstart&&(e.insert=e.strstart)),e.window.set(e.strm.input.subarray(e.strm.next_in-a,e.strm.next_in),e.strstart),e.strstart+=a,e.insert+=a>e.w_size-e.insert?e.w_size-e.insert:a),e.block_start=e.strstart),e.high_water<e.strstart&&(e.high_water=e.strstart),o?4:t!==zi&&t!==Oi&&0===e.strm.avail_in&&e.strstart===e.block_start?2:(r=e.window_size-e.strstart,e.strm.avail_in>r&&e.block_start>=e.w_size&&(e.block_start-=e.w_size,e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,r+=e.w_size,e.insert>e.strstart&&(e.insert=e.strstart)),r>e.strm.avail_in&&(r=e.strm.avail_in),r&&(mn(e.strm,e.window,e.strstart,r),e.strstart+=r,e.insert+=r>e.w_size-e.insert?e.w_size-e.insert:r),e.high_water<e.strstart&&(e.high_water=e.strstart),r=e.bi_valid+42>>3,r=e.pending_buf_size-r>65535?65535:e.pending_buf_size-r,s=r>e.w_size?e.w_size:r,n=e.strstart-e.block_start,(n>=s||(n||t===Oi)&&t!==zi&&0===e.strm.avail_in&&n<=r)&&(i=n>r?r:n,o=t===Oi&&0===e.strm.avail_in&&i===n?1:0,Ri(e,e.block_start,i,o),e.block_start+=i,un(e.strm)),o?3:1)},vn=(e,t)=>{let i,n;for(;;){if(e.lookahead<nn){if(bn(e),e.lookahead<nn&&t===zi)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),0!==i&&e.strstart-i<=e.w_size-nn&&(e.match_length=wn(e,i)),e.match_length>=3)if(n=Ti(e,e.strstart-e.match_start,e.match_length-3),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=3){e.match_length--;do{e.strstart++,e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart}while(0!=--e.match_length);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=dn(e,e.ins_h,e.window[e.strstart+1]);else n=Ti(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(fn(e,!1),0===e.strm.avail_out))return 1}return e.insert=e.strstart<2?e.strstart:2,t===Oi?(fn(e,!0),0===e.strm.avail_out?3:4):e.sym_next&&(fn(e,!1),0===e.strm.avail_out)?1:2},yn=(e,t)=>{let i,n,r;for(;;){if(e.lookahead<nn){if(bn(e),e.lookahead<nn&&t===zi)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),e.prev_length=e.match_length,e.prev_match=e.match_start,e.match_length=2,0!==i&&e.prev_length<e.max_lazy_match&&e.strstart-i<=e.w_size-nn&&(e.match_length=wn(e,i),e.match_length<=5&&(e.strategy===$i||3===e.match_length&&e.strstart-e.match_start>4096)&&(e.match_length=2)),e.prev_length>=3&&e.match_length<=e.prev_length){r=e.strstart+e.lookahead-3,n=Ti(e,e.strstart-1-e.prev_match,e.prev_length-3),e.lookahead-=e.prev_length-1,e.prev_length-=2;do{++e.strstart<=r&&(e.ins_h=dn(e,e.ins_h,e.window[e.strstart+3-1]),i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart)}while(0!=--e.prev_length);if(e.match_available=0,e.match_length=2,e.strstart++,n&&(fn(e,!1),0===e.strm.avail_out))return 1}else if(e.match_available){if(n=Ti(e,0,e.window[e.strstart-1]),n&&fn(e,!1),e.strstart++,e.lookahead--,0===e.strm.avail_out)return 1}else e.match_available=1,e.strstart++,e.lookahead--}return e.match_available&&(n=Ti(e,0,e.window[e.strstart-1]),e.match_available=0),e.insert=e.strstart<2?e.strstart:2,t===Oi?(fn(e,!0),0===e.strm.avail_out?3:4):e.sym_next&&(fn(e,!1),0===e.strm.avail_out)?1:2};function An(e,t,i,n,r){this.good_length=e,this.max_lazy=t,this.nice_length=i,this.max_chain=n,this.func=r}const Cn=[new An(0,0,0,0,Fn),new An(4,4,8,4,vn),new An(4,5,16,8,vn),new An(4,6,32,32,vn),new An(4,4,16,16,yn),new An(8,16,32,32,yn),new An(8,16,128,128,yn),new An(8,32,128,256,yn),new An(32,128,258,1024,yn),new An(32,258,258,4096,yn)];function _n(){this.strm=null,this.status=0,this.pending_buf=null,this.pending_buf_size=0,this.pending_out=0,this.pending=0,this.wrap=0,this.gzhead=null,this.gzindex=0,this.method=en,this.last_flush=-1,this.w_size=0,this.w_bits=0,this.w_mask=0,this.window=null,this.window_size=0,this.prev=null,this.head=null,this.ins_h=0,this.hash_size=0,this.hash_bits=0,this.hash_mask=0,this.hash_shift=0,this.block_start=0,this.match_length=0,this.prev_match=0,this.match_available=0,this.strstart=0,this.match_start=0,this.lookahead=0,this.prev_length=0,this.max_chain_length=0,this.max_lazy_match=0,this.level=0,this.strategy=0,this.good_match=0,this.nice_match=0,this.dyn_ltree=new Uint16Array(1146),this.dyn_dtree=new Uint16Array(122),this.bl_tree=new Uint16Array(78),ln(this.dyn_ltree),ln(this.dyn_dtree),ln(this.bl_tree),this.l_desc=null,this.d_desc=null,this.bl_desc=null,this.bl_count=new Uint16Array(16),this.heap=new Uint16Array(573),ln(this.heap),this.heap_len=0,this.heap_max=0,this.depth=new 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Gn(t);if(i.push(e,!0),i.err)throw i.msg||Ni[i.err];return i.result}Gn.prototype.push=function(e,t){const i=this.strm,n=this.options.chunkSize;let r,s;if(this.ended)return!1;for(s=t===~~t?t:!0===t?Un:Hn,\"string\"==typeof e?i.input=Tn.string2buf(e):\"[object ArrayBuffer]\"===zn.call(e)?i.input=new Uint8Array(e):i.input=e,i.next_in=0,i.avail_in=i.input.length;;)if(0===i.avail_out&&(i.output=new Uint8Array(n),i.next_out=0,i.avail_out=n),(s===Pn||s===On)&&i.avail_out<=6)this.onData(i.output.subarray(0,i.next_out)),i.avail_out=0;else{if(r=Nn.deflate(i,s),r===Qn)return i.next_out>0&&this.onData(i.output.subarray(0,i.next_out)),r=Nn.deflateEnd(this.strm),this.onEnd(r),this.ended=!0,r===qn;if(0!==i.avail_out){if(s>0&&i.next_out>0)this.onData(i.output.subarray(0,i.next_out)),i.avail_out=0;else if(0===i.avail_in)break}else this.onData(i.output)}return!0},Gn.prototype.onData=function(e){this.chunks.push(e)},Gn.prototype.onEnd=function(e){e===qn&&(this.result=Mn.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg};var Kn=function(e,t){return(t=t||{}).raw=!0,$n(e,t)},Yn=function(e,t){return(t=t||{}).gzip=!0,$n(e,t)},Xn={Deflate:Gn,deflate:$n,deflateRaw:Kn,gzip:Yn,constants:Bi};const Zn=16209;var Jn=function(e,t){let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_,x;const k=e.state;i=e.next_in,_=e.input,n=i+(e.avail_in-5),r=e.next_out,x=e.output,s=r-(t-e.avail_out),o=r+(e.avail_out-257),a=k.dmax,c=k.wsize,l=k.whave,h=k.wnext,d=k.window,u=k.hold,f=k.bits,p=k.lencode,g=k.distcode,m=(1<<k.lenbits)-1,w=(1<<k.distbits)-1;e:do{f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=p[u&m];t:for(;;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,0===F)x[r++]=65535&b;else{if(!(16&F)){if(64&F){if(32&F){k.mode=16191;break e}e.msg=\"invalid literal/length code\",k.mode=Zn;break e}b=p[(65535&b)+(u&(1<<F)-1)];continue t}for(v=65535&b,F&=15,F&&(f<F&&(u+=_[i++]<<f,f+=8),v+=u&(1<<F)-1,u>>>=F,f-=F),f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=g[u&w];;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,16&F){if(y=65535&b,F&=15,f<F&&(u+=_[i++]<<f,f+=8,f<F&&(u+=_[i++]<<f,f+=8)),y+=u&(1<<F)-1,y>a){e.msg=\"invalid distance too far back\",k.mode=Zn;break e}if(u>>>=F,f-=F,F=r-s,y>F){if(F=y-F,F>l&&k.sane){e.msg=\"invalid distance too far back\",k.mode=Zn;break e}if(A=0,C=d,0===h){if(A+=c-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}else if(h<F){if(A+=c+h-F,F-=h,F<v){v-=F;do{x[r++]=d[A++]}while(--F);if(A=0,h<v){F=h,v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}}else if(A+=h-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}for(;v>2;)x[r++]=C[A++],x[r++]=C[A++],x[r++]=C[A++],v-=3;v&&(x[r++]=C[A++],v>1&&(x[r++]=C[A++]))}else{A=r-y;do{x[r++]=x[A++],x[r++]=x[A++],x[r++]=x[A++],v-=3}while(v>2);v&&(x[r++]=x[A++],v>1&&(x[r++]=x[A++]))}break}if(64&F){e.msg=\"invalid distance code\",k.mode=Zn;break e}b=g[(65535&b)+(u&(1<<F)-1)]}}break}}while(i<n&&r<o);v=f>>3,i-=v,f-=v<<3,u&=(1<<f)-1,e.next_in=i,e.next_out=r,e.avail_in=i<n?n-i+5:5-(i-n),e.avail_out=r<o?o-r+257:257-(r-o),k.hold=u,k.bits=f};const er=15,tr=new Uint16Array([3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0]),ir=new Uint8Array([16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78]),nr=new Uint16Array([1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0]),rr=new Uint8Array([16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64]);var sr=(e,t,i,n,r,s,o,a)=>{const c=a.bits;let l,h,d,u,f,p,g=0,m=0,w=0,b=0,F=0,v=0,y=0,A=0,C=0,_=0,x=null;const k=new Uint16Array(16),I=new Uint16Array(16);let S,E,N,B=null;for(g=0;g<=er;g++)k[g]=0;for(m=0;m<n;m++)k[t[i+m]]++;for(F=c,b=er;b>=1&&0===k[b];b--);if(F>b&&(F=b),0===b)return r[s++]=20971520,r[s++]=20971520,a.bits=1,0;for(w=1;w<b&&0===k[w];w++);for(F<w&&(F=w),A=1,g=1;g<=er;g++)if(A<<=1,A-=k[g],A<0)return-1;if(A>0&&(0===e||1!==b))return-1;for(I[1]=0,g=1;g<er;g++)I[g+1]=I[g]+k[g];for(m=0;m<n;m++)0!==t[i+m]&&(o[I[t[i+m]]++]=m);if(0===e?(x=B=o,p=20):1===e?(x=tr,B=ir,p=257):(x=nr,B=rr,p=0),_=0,m=0,g=w,f=s,v=F,y=0,d=-1,C=1<<F,u=C-1,1===e&&C>852||2===e&&C>592)return 1;for(;;){S=g-y,o[m]+1<p?(E=0,N=o[m]):o[m]>=p?(E=B[o[m]-p],N=x[o[m]-p]):(E=96,N=0),l=1<<g-y,h=1<<v,w=h;do{h-=l,r[f+(_>>y)+h]=S<<24|E<<16|N}while(0!==h);for(l=1<<g-1;_&l;)l>>=1;if(0!==l?(_&=l-1,_+=l):_=0,m++,0==--k[g]){if(g===b)break;g=t[i+o[m]]}if(g>F&&(_&u)!==d){for(0===y&&(y=F),f+=w,v=g-y,A=1<<v;v+y<b&&(A-=k[v+y],!(A<=0));)v++,A<<=1;if(C+=1<<v,1===e&&C>852||2===e&&C>592)return 1;d=_&u,r[d]=F<<24|v<<16|f-s}}return 0!==_&&(r[f+_]=g-y<<24|64<<16),a.bits=F,0};const{Z_FINISH:or,Z_BLOCK:ar,Z_TREES:cr,Z_OK:lr,Z_STREAM_END:hr,Z_NEED_DICT:dr,Z_STREAM_ERROR:ur,Z_DATA_ERROR:fr,Z_MEM_ERROR:pr,Z_BUF_ERROR:gr,Z_DEFLATED:mr}=Bi,wr=16180,br=16190,Fr=16191,vr=16192,yr=16194,Ar=16199,Cr=16200,_r=16206,xr=16209,kr=e=>(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24);function Ir(){this.strm=null,this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new Uint16Array(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}const Sr=e=>{if(!e)return 1;const t=e.state;return!t||t.strm!==e||t.mode<wr||t.mode>16211?1:0},Er=e=>{if(Sr(e))return ur;const t=e.state;return e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=wr,t.last=0,t.havedict=0,t.flags=-1,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new Int32Array(852),t.distcode=t.distdyn=new Int32Array(592),t.sane=1,t.back=-1,lr},Nr=e=>{if(Sr(e))return ur;const t=e.state;return t.wsize=0,t.whave=0,t.wnext=0,Er(e)},Br=(e,t)=>{let i;if(Sr(e))return ur;const n=e.state;return t<0?(i=0,t=-t):(i=5+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?ur:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,Nr(e))},Mr=(e,t)=>{if(!e)return ur;const i=new Ir;e.state=i,i.strm=e,i.window=null,i.mode=wr;const n=Br(e,t);return n!==lr&&(e.state=null),n};let Rr,Dr,Tr=!0;const Lr=e=>{if(Tr){Rr=new Int32Array(512),Dr=new Int32Array(32);let t=0;for(;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(sr(1,e.lens,0,288,Rr,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;sr(2,e.lens,0,32,Dr,0,e.work,{bits:5}),Tr=!1}e.lencode=Rr,e.lenbits=9,e.distcode=Dr,e.distbits=5},zr=(e,t,i,n)=>{let r;const s=e.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new Uint8Array(s.wsize)),n>=s.wsize?(s.window.set(t.subarray(i-s.wsize,i),0),s.wnext=0,s.whave=s.wsize):(r=s.wsize-s.wnext,r>n&&(r=n),s.window.set(t.subarray(i-n,i-n+r),s.wnext),(n-=r)?(s.window.set(t.subarray(i-n,i),0),s.wnext=n,s.whave=s.wsize):(s.wnext+=r,s.wnext===s.wsize&&(s.wnext=0),s.whave<s.wsize&&(s.whave+=r))),0};var Hr=(e,t)=>{let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_=0;const x=new Uint8Array(4);let k,I;const S=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(Sr(e)||!e.output||!e.input&&0!==e.avail_in)return ur;i=e.state,i.mode===Fr&&(i.mode=vr),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,d=a,u=c,C=lr;e:for(;;)switch(i.mode){case wr:if(0===i.wrap){i.mode=vr;break}for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(2&i.wrap&&35615===l){0===i.wbits&&(i.wbits=15),i.check=0,x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0),l=0,h=0,i.mode=16181;break}if(i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&l)<<8)+(l>>8))%31){e.msg=\"incorrect header check\",i.mode=xr;break}if((15&l)!==mr){e.msg=\"unknown compression method\",i.mode=xr;break}if(l>>>=4,h-=4,A=8+(15&l),0===i.wbits&&(i.wbits=A),A>15||A>i.wbits){e.msg=\"invalid window size\",i.mode=xr;break}i.dmax=1<<i.wbits,i.flags=0,e.adler=i.check=1,i.mode=512&l?16189:Fr,l=0,h=0;break;case 16181:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.flags=l,(255&i.flags)!==mr){e.msg=\"unknown compression method\",i.mode=xr;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=xr;break}i.head&&(i.head.text=l>>8&1),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0,i.mode=16182;case 16182:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.time=l),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,x[2]=l>>>16&255,x[3]=l>>>24&255,i.check=Ei(i.check,x,4,0)),l=0,h=0,i.mode=16183;case 16183:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.xflags=255&l,i.head.os=l>>8),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0,i.mode=16184;case 16184:if(1024&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length=l,i.head&&(i.head.extra_len=l),512&i.flags&&4&i.wrap&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Ei(i.check,x,2,0)),l=0,h=0}else i.head&&(i.head.extra=null);i.mode=16185;case 16185:if(1024&i.flags&&(f=i.length,f>a&&(f=a),f&&(i.head&&(A=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Uint8Array(i.head.extra_len)),i.head.extra.set(n.subarray(s,s+f),A)),512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,i.length-=f),i.length))break e;i.length=0,i.mode=16186;case 16186:if(2048&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.name+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=16187;case 16187:if(4096&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.comment+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&4&i.wrap&&(i.check=Ei(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.comment=null);i.mode=16188;case 16188:if(512&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(4&i.wrap&&l!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=xr;break}l=0,h=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=Fr;break;case 16189:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}e.adler=i.check=kr(l),l=0,h=0,i.mode=br;case br:if(0===i.havedict)return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,dr;e.adler=i.check=1,i.mode=Fr;case Fr:if(t===ar||t===cr)break e;case vr:if(i.last){l>>>=7&h,h-=7&h,i.mode=_r;break}for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}switch(i.last=1&l,l>>>=1,h-=1,3&l){case 0:i.mode=16193;break;case 1:if(Lr(i),i.mode=Ar,t===cr){l>>>=2,h-=2;break e}break;case 2:i.mode=16196;break;case 3:e.msg=\"invalid block type\",i.mode=xr}l>>>=2,h-=2;break;case 16193:for(l>>>=7&h,h-=7&h;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if((65535&l)!=(l>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=xr;break}if(i.length=65535&l,l=0,h=0,i.mode=yr,t===cr)break e;case yr:i.mode=16195;case 16195:if(f=i.length,f){if(f>a&&(f=a),f>c&&(f=c),0===f)break e;r.set(n.subarray(s,s+f),o),a-=f,s+=f,c-=f,o+=f,i.length-=f;break}i.mode=Fr;break;case 16196:for(;h<14;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.nlen=257+(31&l),l>>>=5,h-=5,i.ndist=1+(31&l),l>>>=5,h-=5,i.ncode=4+(15&l),l>>>=4,h-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=xr;break}i.have=0,i.mode=16197;case 16197:for(;i.have<i.ncode;){for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.lens[S[i.have++]]=7&l,l>>>=3,h-=3}for(;i.have<19;)i.lens[S[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,k={bits:i.lenbits},C=sr(0,i.lens,0,19,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid code lengths set\",i.mode=xr;break}i.have=0,i.mode=16198;case 16198:for(;i.have<i.nlen+i.ndist;){for(;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(b<16)l>>>=m,h-=m,i.lens[i.have++]=b;else{if(16===b){for(I=m+2;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l>>>=m,h-=m,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=xr;break}A=i.lens[i.have-1],f=3+(3&l),l>>>=2,h-=2}else if(17===b){for(I=m+3;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=3+(7&l),l>>>=3,h-=3}else{for(I=m+7;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=11+(127&l),l>>>=7,h-=7}if(i.have+f>i.nlen+i.ndist){e.msg=\"invalid bit length repeat\",i.mode=xr;break}for(;f--;)i.lens[i.have++]=A}}if(i.mode===xr)break;if(0===i.lens[256]){e.msg=\"invalid code -- missing end-of-block\",i.mode=xr;break}if(i.lenbits=9,k={bits:i.lenbits},C=sr(1,i.lens,0,i.nlen,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid literal/lengths set\",i.mode=xr;break}if(i.distbits=6,i.distcode=i.distdyn,k={bits:i.distbits},C=sr(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,k),i.distbits=k.bits,C){e.msg=\"invalid distances set\",i.mode=xr;break}if(i.mode=Ar,t===cr)break e;case Ar:i.mode=Cr;case Cr:if(a>=6&&c>=258){e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,Jn(e,u),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,i.mode===Fr&&(i.back=-1);break}for(i.back=0;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(w&&!(240&w)){for(F=m,v=w,y=b;_=i.lencode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,i.length=b,0===w){i.mode=16205;break}if(32&w){i.back=-1,i.mode=Fr;break}if(64&w){e.msg=\"invalid literal/length code\",i.mode=xr;break}i.extra=15&w,i.mode=16201;case 16201:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=16202;case 16202:for(;_=i.distcode[l&(1<<i.distbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break 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t=e.left;e.left=t.right,t.right!==Vs&&(t.right.parent=e),t.parent=e.parent,e.parent===Vs?this.root=t:e.parent.right===e?e.parent.right=t:e.parent.left=t,t.right=e,e.parent=t,Ks.call(this,e)}function Ks(e){for(;e!==Vs;){var t=e.left.max>e.right.max?e.left.max:e.right.max,i=e.interval.high;e.max=t>i?t:i;var n=e.left.min<e.right.min?e.left.min:e.right.min,r=e.interval.low;e.min=n<r?n:r,e=e.parent}}class Ys{constructor(e,t,i){this.low=e,this.high=t,this.value=i}equals(e){return!!e&&(this===e||this.low===e.low&&this.high===e.high)}compareTo(e){return this.low<e.low?-1:this.low>e.low?1:this.high<e.high?-1:this.high>e.high?1:0}overlaps(e){return this.low<=e.high&&e.low<=this.high}}function Xs(e){this.parent=Vs,this.left=Vs,this.right=Vs,this.interval=e,this.color=2}class Zs{constructor(e,t,i){e=e||[],this.treeMap=this.buildTreeMap(e,t),this.range=i,this.count=e.length}containsRange(e){return void 0===this.range||this.range.contains(e.chr,e.start,e.end)}findFeatures(e){const t=[];for(let i of Object.values(this.allFeatures))for(let n of i)e(n)&&t.push(n);return t}queryFeatures(e,t,i){const n=this.treeMap[e];if(!n)return[];const r=n.findOverlapping(t,i);if(0===r.length)return[];{const n=[],s=this.allFeatures[e];if(s){for(let e of r){const r=e.value;for(let e=r.start;e<r.end;e++){let r=s[e];if(r.start>i)break;r.end>=t&&n.push(r)}}n.sort((function(e,t){return e.start-t.start}))}return n}}getAllFeatures(){return this.allFeatures}buildTreeMap(e,t){const i={},n=[];if(this.allFeatures={},e){for(let i of e){let e=i.chr;t&&(e=t.getChromosomeName(e));let r=this.allFeatures[e];r||(n.push(e),r=[],this.allFeatures[e]=r),r.push(i)}for(let e of n){const t=this.allFeatures[e];t.sort((function(e,t){return e.start===t.start?0:e.start>t.start?1:-1})),i[e]=Js(t)}}return i}}function Js(e){const t=new js,i=e.length,n=Math.max(10,Math.round(i/10));for(let r=0;r<i;r+=n){const s=Math.min(i,r+n),o=new eo(r,s),a=e[r].start;let c=a;for(let t=r;t<s;t++)c=Math.max(c,e[t].end);t.insert(a,c,o)}return t}class eo{constructor(e,t){this.start=e,this.end=t}}const to=function(e,t,i){if(e&&0!==e.length){const n=function(e){const t=new js,i=e.length,n=Math.max(10,Math.round(i/100));e.sort((function(e,t){return e.start===t.start?0:e.start>t.start?1:-1}));for(let r=0;r<i;r+=n){const s=Math.min(i,r+n),o=e.slice(r,s),a=o[0].start;let c=a;o.forEach((function(e){c=Math.max(c,e.end)})),t.insert(a,c,o)}return t}(e),r=n.findOverlapping(t,i);return 0===r.length?[]:(e=[],r.forEach((function(n){const r=n.value,s=r.length;for(let n=0;n<s;n++){const s=r[n];if(s.start>i)break;s.end>t&&e.push(s)}})),e.sort((function(e,t){return e.start-t.start})),e)}return[]};function io(e){if(3===(e=e.replace(/^#/,\"\")).length&&(e=e.split(\"\").map((e=>e+e)).join(\"\")),6!==e.length)throw new Error(\"Invalid HEX color.\");let t=parseInt(e,16);return`rgb(${t>>16&255}, ${t>>8&255}, ${255&t})`}const no={cantaloupe:{r:255,g:206,b:110},honeydew:{r:206,g:250,b:110},spindrift:{r:104,g:251,b:208},sky:{r:106,g:207,b:255},lavender:{r:210,g:120,b:255},carnation:{r:255,g:127,b:211},licorice:{r:0,g:0,b:0},snow:{r:255,g:255,b:255},salmon:{r:255,g:114,b:110},banana:{r:255,g:251,b:109},flora:{r:104,g:249,b:110},ice:{r:104,g:253,b:255},orchid:{r:110,g:118,b:255},bubblegum:{r:255,g:122,b:255},lead:{r:30,g:30,b:30},mercury:{r:232,g:232,b:232},tangerine:{r:255,g:136,b:2},lime:{r:131,g:249,b:2},sea_foam:{r:3,g:249,b:135},aqua:{r:0,g:140,b:255},grape:{r:137,g:49,b:255},strawberry:{r:255,g:41,b:135},tungsten:{r:58,g:58,b:58},silver:{r:208,g:208,b:208},maraschino:{r:255,g:33,b:1},lemon:{r:255,g:250,b:3},spring:{r:5,g:248,b:2},turquoise:{r:0,g:253,b:255},blueberry:{r:0,g:46,b:255},magenta:{r:255,g:57,b:255},iron:{r:84,g:84,b:83},magnesium:{r:184,g:184,b:184},mocha:{r:137,g:72,b:0},fern:{r:69,g:132,b:1},moss:{r:1,g:132,b:72},ocean:{r:0,g:74,b:136},eggplant:{r:73,g:26,b:136},maroon:{r:137,g:22,b:72},steel:{r:110,g:110,b:110},aluminum:{r:160,g:159,b:160},cayenne:{r:137,g:17,b:0},aspargus:{r:136,g:133,b:1},clover:{r:2,g:132,b:1},teal:{r:0,g:134,b:136},midnight:{r:0,g:24,b:136},plum:{r:137,g:30,b:136},tin:{r:135,g:134,b:135},nickel:{r:136,g:135,b:135}};function ro(e){const{r:t,g:i,b:n}=no[e];return`rgb(${t},${i},${n})`}const so={Set1:[\"rgb(228,26,28)\",\"rgb(55,126,184)\",\"rgb(77,175,74)\",\"rgb(166,86,40)\",\"rgb(152,78,163)\",\"rgb(255,127,0)\",\"rgb(247,129,191)\",\"rgb(153,153,153)\",\"rgb(255,255,51)\"],Dark2:[\"rgb(27,158,119)\",\"rgb(217,95,2)\",\"rgb(117,112,179)\",\"rgb(231,41,138)\",\"rgb(102,166,30)\",\"rgb(230,171,2)\",\"rgb(166,118,29)\",\"rgb(102,102,102)\"],Set2:[\"rgb(102, 194,165)\",\"rgb(252,141,98)\",\"rgb(141,160,203)\",\"rgb(231,138,195)\",\"rgb(166,216,84)\",\"rgb(255,217,47)\",\"rgb(229,196,148)\",\"rgb(179,179,179)\"],Set3:[\"rgb(141,211,199)\",\"rgb(255,255,179)\",\"rgb(190,186,218)\",\"rgb(251,128,114)\",\"rgb(128,177,211)\",\"rgb(253,180,98)\",\"rgb(179,222,105)\",\"rgb(252,205,229)\",\"rgb(217,217,217)\",\"rgb(188,128,189)\",\"rgb(204,235,197)\",\"rgb(255,237,111)\"],Pastel1:[\"rgb(251,180,174)\",\"rgb(179,205,227)\",\"rgb(204,235,197)\",\"rgb(222,203,228)\",\"rgb(254,217,166)\",\"rgb(255,255,204)\",\"rgb(229,216,189)\",\"rgb(253,218,236)\"],Pastel2:[\"rgb(173,226,207)\",\"rgb(253,205,172)\",\"rgb(203,213,232)\",\"rgb(244,202,228)\",\"rgb(230,245,201)\",\"rgb(255,242,174)\",\"rgb(243,225,206)\"],Accent:[\"rgb(127,201,127)\",\"rgb(190,174,212)\",\"rgb(253,192,134)\",\"rgb(255,255,153)\",\"rgb(56,108,176)\",\"rgb(240,2,127)\",\"rgb(191,91,23)\"]};class oo{constructor(e){this.colors=so[e],Array.isArray(this.colors)||(this.colors=[]),this.colorTable=new Map,this.nextIdx=0,this.colorGenerator=new co}getColor(e){return this.colorTable.has(e)||(this.nextIdx<this.colors.length?this.colorTable.set(e,this.colors[this.nextIdx]):this.colorTable.set(e,this.colorGenerator.get()),this.nextIdx++),this.colorTable.get(e)}}class ao{constructor(e){this.colorTable=e||{},this.nextIdx=0,this.colorGenerator=new co}getColor(e){if(!this.colorTable.hasOwnProperty(e)){if(this.colorTable.hasOwnProperty(\"*\"))return this.colorTable[\"*\"];this.colorTable[e]=this.colorGenerator.get()}return this.colorTable[e]}}function co(){this.hue=Math.random(),this.goldenRatio=.618033988749895,this.hexwidth=2}function lo(e,t,i,n){return`rgba(${e=ys.clamp(e,0,255)}, ${t=ys.clamp(t,0,255)}, ${i=ys.clamp(i,0,255)}, ${n=ys.clamp(n,0,1)})`}function ho(e,t){e=ys.clamp(e,0,255),t=ys.clamp(t,0,255);return`rgb(${Math.round(Math.random()*(t-e)+e).toString(10)},${Math.round(Math.random()*(t-e)+e).toString(10)},${Math.round(Math.random()*(t-e)+e).toString(10)})`}function uo(e){if(e.startsWith(\"rgb(\")){const[t,i]=e.split(\"(\"),[n]=i.split(\")\");return n.split(\",\").map((e=>parseInt(e)))}}co.prototype.hsvToRgb=function(e,t,i){var n=Math.floor(6*e),r=6*e-n,s=i*(1-t),o=i*(1-r*t),a=i*(1-(1-r)*t),c=255,l=255,h=255;switch(n){case 0:c=i,l=a,h=s;break;case 1:c=o,l=i,h=s;break;case 2:c=s,l=i,h=a;break;case 3:c=s,l=o,h=i;break;case 4:c=a,l=s,h=i;break;case 5:c=i,l=s,h=o}return[Math.floor(256*c),Math.floor(256*l),Math.floor(256*h)]},co.prototype.padHex=function(e){return e.length>this.hexwidth?e:new Array(this.hexwidth-e.length+1).join(\"0\")+e},co.prototype.get=function(e,t){this.hue+=this.goldenRatio,this.hue%=1,\"number\"!=typeof e&&(e=.5),\"number\"!=typeof t&&(t=.95);var i=this.hsvToRgb(this.hue,e,t);return\"#\"+this.padHex(i[0].toString(16))+this.padHex(i[1].toString(16))+this.padHex(i[2].toString(16))},new co;function fo(e,t,i){if(i<.005)return e;if(i>.995)return t;{let n,r,s,o,a,c;i<.5?(i/=.5,[n,r,s]=uo(e),[o,a,c]=uo(ro(\"snow\"))):(i=(i-.5)/.5,[n,r,s]=uo(ro(\"snow\")),[o,a,c]=uo(t));const[l,h,d]=[Math.floor(ys.lerp(n,o,i)),Math.floor(ys.lerp(r,a,i)),Math.floor(ys.lerp(s,c,i))];return function(e,t,i){return`rgb(${e=ys.clamp(e,0,255)}, ${t=ys.clamp(t,0,255)}, ${i=ys.clamp(i,0,255)})`}(l,h,d)}}const po=new Set([\"bedtype\",\"alignment\",\"annotation\",\"variant\",\"wig\",\"interact\",\"shoebox\"]),go=new Set([\"alignment\",\"annotation\",\"variant\",\"eqtl\",\"qtl\",\"snp\",\"shoebox\",\"wig\"]),mo=new Set([\"sequence\",\"ruler\",\"ideogram\"]),wo={};class bo{constructor(e){this.browser=e,this.initialize()}initialize(){const e=new c;e.add(\"...\");const t={parent:this.browser.root,content:e};this.dialog=new w(t),this.browser.root.appendChild(this.dialog.elem),i(this.dialog.elem)}trackMenuItemList(e){const t=[];return\"sequence\"!==e.track.config.type&&t.push(function(){const e=Bt(\"<div>\");function t(e){const t=()=>{const e=parseInt(this.browser.inputDialog.value,10);if(void 0!==e){const t=[];this.trackView.track.selected?t.push(...this.trackView.browser.getSelectedTrackViews().map((({track:e})=>e))):t.push(this);for(const i of t)i.trackView.autoHeight=!1,void 0!==i.minHeight&&i.minHeight>e&&(i.minHeight=e),void 0!==i.maxHeight&&i.maxHeight<e&&(i.minHeight=e),i.trackView.setTrackHeight(e,!0),i.trackView.checkContentHeight(),i.trackView.repaintViews()}},i={label:\"Track Height\",value:this.height,callback:t};this.browser.inputDialog.present(i,e)}return e.text(\"Set track height\"),{object:e,dialog:t}}()),!0===function(e){const t=e.browser.getSelectedTrackViews();return t&&t.length>1&&new Set(t).has(e)}(e)?t.push(...this.multiSelectMenuItems(e)):(\"sequence\"!==e.track.config.type&&t.push(function(){const e=Bt(\"<div>\");function t(e){const t=()=>{let e=this.browser.inputDialog.value;e=\"\"===e||void 0===e?\"untitled\":e.trim(),this.name=e},i={label:\"Track Name\",value:Ao(this)||\"unnamed\",callback:t};this.browser.inputDialog.present(i,e)}return e.text(\"Set track name\"),{object:e,click:t}}()),t.push(...this.defaultMenuItems(e))),!1!==e.track.removable&&(t.push(\"<hr/>\"),t.push(function(e){const t=e.track.selected?\"Remove tracks\":\"Remove track\",i=Bt(\"<div>\");function n(e){this.trackView.browser._removeTrack(this)}return i.text(t),{object:i,click:n,menuItemType:\"removeTrack\"}}(e))),t}defaultMenuItems(e){const t=[];return Co(e.track)&&(t.push(\"<hr/>\"),t.push(Fo({trackView:e,label:\"Set track color\",option:\"color\"})),t.push(vo({trackView:e,label:\"Unset track color\"})),\"wig\"!==e.track.config.type&&\"annotation\"!==e.track.config.type||(t.push(Fo({trackView:e,label:\"Set alt color\",option:\"altColor\"})),t.push(yo({trackView:e,label:\"Unset alt color\"})))),e.track.menuItemList&&t.push(...e.track.menuItemList()),function(e){const t=e.track;return t&&t.config&&void 0!==t.config.visibilityWindow||t&&go.has(t.type)}(e)&&(t.push(\"<hr/>\"),t.push(function(e){const t=Bt(\"<div>\");function i(t){const i=()=>{let e=this.browser.inputDialog.value;e=\"\"===e||void 0===e?-1:e.trim(),this.visibilityWindow=Number.parseInt(e),this.config.visibilityWindow=Number.parseInt(e),this.trackView.updateViews()},n={label:\"wig\"===e?\"Visibility window (bp). Enter 0 for whole chromosome, -1 for whole genome.\":\"Visibility window (bp). Enter 0 for whole chromosome.\",value:this.visibilityWindow,callback:i};this.browser.inputDialog.present(n,t)}return t.text(\"Set visibility window\"),{object:t,click:i}}(e.track.type))),t}multiSelectMenuItems(e){const t=[],i=e.browser.getSelectedTrackViews();var n;return!0===(n=i.map((({track:e})=>e.type)),1===[...new Set(n)].length)?(t.push(...this.defaultMenuItems(e)),\"wig\"===e.track.type&&(t.push(\"<hr/>\"),t.push(function(){const e=Bt(\"<div>\");function t(e){const t=so.Dark2,i=Math.floor(Math.random()*t.length),n=`auto-scale-group-${s()}`;wo[n]=t[i];const r=this.browser.getSelectedTrackViews();for(const{track:e}of r)e.autoscaleGroup=n;this.browser.updateViews()}return e.text(\"Group autoscale\"),{object:e,doAllMultiSelectedTracks:!0,click:t}}()))):Co(e.track)&&(t.push(\"<hr/>\"),t.push(Fo({trackView:e,label:\"Set track color\",option:\"color\"})),t.push(vo({trackView:e,label:\"Unset track color\"})),\"wig\"!==e.track.config.type&&\"annotation\"!==e.track.config.type||(t.push(Fo({trackView:e,label:\"Set alt color\",option:\"altColor\"})),t.push(yo({trackView:e,label:\"Unset alt color\"})))),t}}function Fo({trackView:e,label:t,option:i}){const n=Bt(\"<div>\");return n.text(t),{object:n,click:()=>e.presentColorPicker(i)}}function vo({trackView:e,label:t}){const i=Bt(\"<div>\");return i.text(t),{object:i,click:()=>{e.track.color=void 0,e.repaintViews()}}}function yo({trackView:e,label:t}){const i=Bt(\"<div>\");return i.text(t),{object:i,click:()=>{e.track.altColor=void 0,e.repaintViews()}}}function Ao(e){return e.name}function Co(e){return void 0===e.type||po.has(e.type)}class _o{constructor(e,t){this.browser=e,this.$container=Bt(\"<div>\",{class:\"igv-generic-dialog-container\"}),t.append(this.$container),this.$container.offset({left:0,top:0});const i=Bt(\"<div>\",{class:\"igv-generic-dialog-header\"});this.$container.append(i),u(i[0],(()=>{this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\"),this.$container.offset({left:0,top:0}),this.$container.hide()})),this.$minimum=Bt(\"<div>\",{class:\"igv-generic-dialog-label-input\"}),this.$container.append(this.$minimum);const n=Bt(\"<div>\");n.text(\"Minimum\"),this.$minimum.append(n),this.$minimum_input=Bt(\"<input>\"),this.$minimum.append(this.$minimum_input),this.$maximum=Bt(\"<div>\",{class:\"igv-generic-dialog-label-input\"}),this.$container.append(this.$maximum);const r=Bt(\"<div>\");r.text(\"Maximum\"),this.$maximum.append(r),this.$maximum_input=Bt(\"<input>\"),this.$maximum.append(this.$maximum_input);const s=Bt(\"<div>\",{class:\"igv-generic-dialog-ok-cancel\"});this.$container.append(s),this.$ok=Bt(\"<div>\"),s.append(this.$ok),this.$ok.text(\"OK\"),this.$cancel=Bt(\"<div>\"),s.append(this.$cancel),this.$cancel.text(\"Cancel\"),this.$cancel.on(\"click\",(()=>{this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\"),this.$container.offset({left:0,top:0}),this.$container.hide()})),p(this.$container.get(0),i.get(0)),this.$container.hide()}configure(e){let t;if(Array.isArray(e)){t={min:Number.MAX_SAFE_INTEGER,max:-Number.MAX_SAFE_INTEGER};for(const i of e)i.track.dataRange&&(t.min=Math.min(i.track.dataRange.min,t.min),t.max=Math.max(i.track.dataRange.max,t.max))}else t=e.track.dataRange;t&&(this.$minimum_input.val(t.min),this.$maximum_input.val(t.max)),this.$minimum_input.unbind(),this.$minimum_input.on(\"keyup\",(t=>{13===t.keyCode&&this.processResults(e),t.stopImmediatePropagation()})),this.$maximum_input.unbind(),this.$maximum_input.on(\"keyup\",(t=>{13===t.keyCode&&(t.stopImmediatePropagation(),this.processResults(e))})),this.$ok.unbind(),this.$ok.on(\"click\",(t=>{this.processResults(e)}))}processResults(e){if(\"\"!==this.$minimum_input.val()&&\"\"!==this.$maximum_input.val()){const t=Number(this.$minimum_input.val()),i=Number(this.$maximum_input.val());if(isNaN(t)||isNaN(i))this.browser.alert.present(new Error(\"Must input numeric values\"),void 0);else{const n=Array.isArray(e)?e:[e];for(const e of n)e.track.setDataRange({min:t,max:i})}this.$minimum_input.val(\"\"),this.$maximum_input.val(\"\")}this.$container.offset({left:0,top:0}),this.$container.hide()}present(e){const 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tc{constructor(t,i,n,r){this.parent=t,this.popover=e({class:\"igv-ui-popover\"}),t.appendChild(this.popover),this.popoverHeader=e(),this.popover.appendChild(this.popoverHeader);const s=e();this.popoverHeader.appendChild(s),n&&(s.textContent=n);const o=e();this.popoverHeader.appendChild(o),o.appendChild(l(\"times\")),o.addEventListener(\"click\",(e=>{e.stopPropagation(),e.preventDefault(),r?r():this.dismiss()})),!0===i&&p(this.popover,this.popoverHeader,{minX:0,minY:0}),this.popoverContent=e(),this.popover.appendChild(this.popoverContent),this.popover.style.display=\"none\"}configure(e){if(0===e.length)return;const t=nc(e,this.popover);for(const{object:e}of t)this.popoverContent.appendChild(e)}present(e){this.popover.style.display=\"block\";const t=this.popover.parentNode,{x:i,y:n,width:r}=a(e,t);this.popover.style.top=`${n}px`;const{width:s}=this.popover.getBoundingClientRect(),o=i+s,c=o-r;this.popover.style.left=`${o>r?i-c:i}px`,this.popoverContent.style.maxWidth=`${Math.min(s,r)}px`}presentContentWithEvent(e,t){this.popover.style.display=\"block\",this.popoverContent.innerHTML=t,ic(e,this.popover,this.popoverContent)}presentMenu(e,t){if(0===t.length)return;this.popover.style.display=\"block\";const i=nc(t,this.popover);for(let e of i)this.popoverContent.appendChild(e.object);ic(e,this.popover,this.popoverContent)}dismiss(){this.popover.style.display=\"none\"}hide(){this.popover.style.display=\"none\",this.dispose()}dispose(){this.popover&&this.popover.parentNode.removeChild(this.popover);const e=Object.keys(this);for(let t of e)this[t]=void 0}}function ic(e,t,i){const{x:n,y:r,width:s}=a(e,t.parentNode);t.style.top=`${r}px`;const{width:o}=t.getBoundingClientRect(),c=n+o,l=c-s;t.style.left=`${c>s?n-l:n}px`,i.style.maxWidth=`${Math.min(o,s)}px`}function nc(t,n){const r=t.map((function(t,r){let s;if(\"string\"==typeof t)s=e(),s.innerHTML=t;else if(\"Node\"==typeof t)s=t;else{if(\"function\"==typeof t.init&&t.init(),\"checkbox\"===t.type)s=function(t,i){const n=e({class:\"igv-ui-trackgear-popover-check-container\"}),r=h(\"check\",!0===i?\"#444\":\"transparent\");r.style.borderColor=\"gray\",r.style.borderWidth=\"1px\",r.style.borderStyle=\"solid\",n.appendChild(r);let s=e();return s.textContent=t,n.appendChild(s),n}(\"Show all bases\",t.value);else if(\"color\"===t.type){const o=new Za({parent:n.parentElement,width:364,colorHandler:e=>t.click(e)});s=e(),\"string\"==typeof t.label&&(s.innerHTML=t.label);const a=e=>{o.show(),i(n),e.preventDefault(),e.stopPropagation()};s.addEventListener(\"click\",a),s.addEventListener(\"touchend\",a),s.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}else s=e(),\"string\"==typeof t.label&&(s.innerHTML=t.label);if(t.click&&\"color\"!==t.type){function c(e){t.click(),i(n),e.preventDefault(),e.stopPropagation()}s.addEventListener(\"click\",c),s.addEventListener(\"touchend\",c),s.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}}return{object:s,init:t.init}}));return r}const rc=[[\"A\",\"T\"],[\"G\",\"C\"],[\"Y\",\"R\"],[\"W\",\"S\"],[\"K\",\"M\"],[\"D\",\"H\"],[\"B\",\"V\"]],sc=new Map;for(let _A of rc){const xA=_A[0],kA=_A[1];sc.set(xA,kA),sc.set(kA,xA),sc.set(xA.toLowerCase(),kA.toLowerCase()),sc.set(kA.toLowerCase(),xA.toLowerCase())}function oc(e){return sc.has(e)?sc.get(e):e}function ac(e){let t=\"\";for(let i of e)t+=sc.has(i)?sc.get(i):i;return t}function cc(e){let t=\"\",i=e.length;for(;i-- >0;){const n=e[i];t+=sc.has(n)?sc.get(n):n}return t}class lc{constructor(e,t,i,n){this.name=e,this.order=t,this.bpLength=i,this.altNames=n}getAltName(e){return this.altNames&&this.altNames.has(e)?this.altNames.get(e):this.name}}class hc{constructor(e,t,i,n){this.chr=e,this.start=t,this.end=i,this.features=n}contains(e,t,i){return this.chr===e&&this.start<=t&&this.end>=i}containsRange(e){return this.chr===e.chr&&this.start<=e.start&&this.end>=e.end}get locusString(){return`${this.chr}:${this.start+1}-${this.end}`}}class dc extends hc{constructor(e,t,i,n){super(e,t,i,n)}getSequence(e,t){if(e<this.start||t>this.end)return null;const i=e-this.start,n=t-e;return this.features?this.features.substring(i,i+n):null}hasSequence(e,t){return e>=this.start&&t<=this.end}}const uc=Dt,fc=new Set([\"fastaURL\",\"indexURL\",\"cytobandURL\",\"indexed\"]);class pc{#e;chromosomes=new Map;sequences=new Map;constructor(e){this.fastaURL=e.fastaURL,this.withCredentials=e.withCredentials;const t={};for(let i in e)e.hasOwnProperty(i)&&!fc.has(i)&&(t[i]=e[i]);this.config=t}async init(){return this.loadAll()}getSequenceRecord(e){return this.chromosomes.get(e)}get chromosomeNames(){return this.#e||(this.#e=Array.from(this.chromosomes.keys())),this.#e}getFirstChromosomeName(){return this.chromosomeNames[0]}async getSequence(e,t,i){if(0===this.sequences.size&&await this.loadAll(),!this.sequences.has(e))return;let n=this.sequences.get(e).find((e=>e.contains(t,i)));if(!n&&(n=this.sequences.get(e).find((e=>e.overlaps(t,i))),!n))return;t-=n.offset,i-=n.offset;let r=\"\";if(t<0)for(let e=t;e<Math.min(i,0);e++)r+=\"*\";if(i<=0)return r;const s=n.sequence,o=Math.min(i,s.length);return r+s.substring(t,o)}async loadAll(){let e;if(Ga(this.fastaURL)){let t=vs(this.fastaURL);e=\"\";for(let i of t)e+=String.fromCharCode(i)}else e=await Qs.load(this.fastaURL,Ua(this.config));const t=new Set,i=uc(e),n=i.length;let r,s=0,o=0,a={};for(;s<n;){if(r=i[s++].trim(),r.startsWith(\"#\")||0===r.length);else if(r.startsWith(\">\")){a&&a.seq&&c.call(this,a,o++);const e=r.substr(1).split(/\\s+/),t=e[0].split(\":\");if(a.chr=t[0],a.seq=\"\",a.offset=0,t.length>1&&t[1].indexOf(\"-\")>0){const i=t[1].split(\"-\");2===i.length&&/^[0-9]+$/.test(i[0])&&/^[0-9]+$/.test(i[1]);const n=Number.parseInt(i[0]);if(Number.parseInt(i[1])>n&&(a.offset=n-1),e.length>1&&e[1].startsWith(\"@len=\"))try{a.length=parseInt(e[1].trim().substring(5))}catch(e){a.length=void 0,console.error(`Error parsing sequence length for ${r}`)}else a.length=void 0}}else a.seq+=r;a&&a.seq&&c.call(this,a,o)}function c(e,i){const n=e.length||e.offset+e.seq.length;if(t.has(e.chr)){const t=this.chromosomes.get(e.chr);t.bpLength=Math.max(t.bpLength,n)}else this.sequences.set(e.chr,[]),this.chromosomes.set(e.chr,new lc(e.chr,i,n)),t.add(e.chr);this.sequences.get(e.chr).push(new gc(e.offset,e.seq))}}getSequenceInterval(e,t,i){const n=this.sequences.get(e);if(n)for(let r of n){const n=r.sequence,s=r.offset,o=s+n.length;if(s<=t&&o>=i)return new dc(e,s,o,n)}}}class gc{constructor(e,t){this.offset=e,this.sequence=t}contains(e,t){return this.offset<=e&&this.end>=t}overlaps(e,t){return this.offset<t&&this.end>e}get end(){return this.offset+this.sequence.length}}const mc=Dt,wc=new Set([\"fastaURL\",\"indexURL\",\"compressedIndexURL\",\"cytobandURL\",\"indexed\"]);class bc{#e;chromosomes=new Map;constructor(e){this.file=e.fastaURL,this.indexFile=e.indexURL,this.compressedIndexFile=e.compressedIndexURL,this.withCredentials=e.withCredentials;const t={};for(let i in e)e.hasOwnProperty(i)&&!wc.has(i)&&(t[i]=e[i]);this.config=t}getSequenceRecord(e){return this.chromosomes.get(e)}async init(){return this.getIndex()}get chromosomeNames(){return this.#e||(this.#e=Array.from(this.chromosomes.keys())),this.#e}getFirstChromosomeName(){return this.chromosomeNames[0]}async getIndex(){if(this.index)return this.index;{const e=await Qs.load(this.indexFile,Ua(this.config)),t=mc(e),i=t.length;let n=0,r=0;for(this.index={};n<i;){const e=t[n++].split(\"\\t\");if(5===e.length){const t=e[0],i=parseInt(e[1]),n={size:i,position:parseInt(e[2]),basesPerLine:parseInt(e[3]),bytesPerLine:parseInt(e[4])};this.index[t]=n,this.chromosomes.set(t,new lc(t,r++,i))}}return this.index}}async getCompressedIndex(){if(this.compressedIndex)return this.compressedIndex;if(!this.compressedIndexFile)return this.compressedIndex=[],this.compressedIndex;this.compressedIndex=[];const e=await Qs.loadArrayBuffer(this.compressedIndexFile,Ua(this.config)),t=e.byteLength;if(t<8)return console.log(\"Cannot parse GZI index file: length (\"+t+\" bytes) is insufficient to determine content of index.\"),this.compressedIndex;const i=e.slice(0,8),n=Number(new DataView(i).getBigUint64(0,!0)),r=8+2*n*8;if(t!=r)return console.log(\"Incorrect file size of reference genome index. Expected : \"+r+\". Received : \"+t),this.compressedIndex;this.compressedIndex.push([0,0]);for(let t=0;t<n;t++){const i=8+2*t*8,n=8+2*t*8+16,r=e.slice(i,n),s=new DataView(r),o=Number(s.getBigUint64(0,!0)),a=Number(s.getBigUint64(8,!0));this.compressedIndex.push([o,a])}return this.compressedIndex}async getRelevantCompressedBlockNumbers(e,t){if(e<0||t<0||t<e)return console.log(\"Incompatible query positions for reference-genome. Start:\"+e+\" | End:\"+t),[];await this.getCompressedIndex();let i=[];const n=this.compressedIndex.length-1;if(0==this.compressedIndex.length)return console.log(\"Compressed index does not contain any content\"),[];if(e>this.compressedIndex[n][1])return[n];let r=0,s=n,o=Math.floor(this.compressedIndex.length/2),a=this.compressedIndex.length+1,c=!1;for(let t=0;t<a;t++){const t=this.compressedIndex[o][1],i=o<this.compressedIndex.length-1?this.compressedIndex[o+1][1]:1/0;if(t<=e&&i>e){c=!0;break}t<e?r=o+1:s=o-1,o=Math.ceil((s-r)/2)+r}if(!c)return console.log(\"No blocks within compressed index found that correspond with query positions \"+e+\",\"+t),console.log(this.compressedIndex),[];i.push(o);for(let e=o+1;e<this.compressedIndex.length;e++){i.push(e);if(this.compressedIndex[e][1]>=t)break}const l=i[i.length-1];return l===this.compressedIndex.length-1&&this.compressedIndex[l][1]<t&&i.push(-1),i}async loadAndUncompressBlocks(e,t){if(await this.getCompressedIndex(),0==e.length)return\"\";let i=Array(e.length-1);for(let t=0;t<e.length-1;t++){const n=e[t],r=this.compressedIndex[n][0],s=e[t+1];let o=[];if(-1!=s){const e=this.compressedIndex[s][0]-r;o=await Qs.loadArrayBuffer(this.file,Ua(this.config,{range:{start:r,size:e}}))}else o=await Qs.loadArrayBuffer(this.file,Ua(this.config,{range:{start:r}}));const a=await gs(o);i[t]=a}let n=\"\";for(let e=0;e<i.length;e++)for(let t=0;t<i[e].length;t++){n+=String.fromCharCode(i[e][t])}const r=t-this.compressedIndex[e[0]][1];return n=n.substring(r),n}async readSequence(e,t,i){await this.getIndex(),await this.getCompressedIndex();const n=this.index[e];if(!n)return console.log(\"No index entry for chr: \"+e),this.index[e]=null,null;const r=Math.max(0,t),s=Math.min(n.size,i),o=n.bytesPerLine,a=n.basesPerLine,c=n.position,l=o-a,h=Math.floor(r/a),d=Math.floor(s/a),u=r-h*a,f=c+h*o+u,p=c+d*o+(s-d*a)-1,g=p-f+1;if(g<=0)return console.error(\"No sequence for \"+e+\":\"+t+\"-\"+i),null;let m;if(this.compressedIndexFile){let e=await this.getRelevantCompressedBlockNumbers(f,p);if(0===e.length)return console.log(\"No blocks in the compressed index that correspond with the requested byte positions (\"+f+\",\"+p+\")\"),null;m=await this.loadAndUncompressBlocks(e,f)}else m=await Qs.load(this.file,Ua(this.config,{range:{start:f,size:g}}));if(!m)return null;let w,b=\"\",F=0,v=m.length;for(u>0&&(w=Math.min(s-r,a-u),b+=m.substr(F,w),F+=w+l);F<v;)w=Math.min(a,v-F),b+=m.substr(F,w),F+=w+l;return b}}const Fc=Dt;class vc{#e;chromosomes=new Map;constructor(e){this.url=e}async init(){return this.loadAll()}getSequenceRecord(e){return this.chromosomes.get(e)}get chromosomeNames(){this.#e||(this.#e=Array.from(this.chromosomes.keys()))}async getSequence(e,t,i){return null}async loadAll(){let e;if(Ga(this.url)){let t=vs(this.fastaURL);e=\"\";for(let i of t)e+=String.fromCharCode(i)}else e=await Qs.load(this.url,{});const t=Fc(e);let i=0;for(let e of t){const t=e.split(\"\\t\");if(t.length>1){const e=Number.parseInt(t[1]),n=new lc(t[0],i++,e);this.chromosomes.set(t[0],n)}}}}class yc{constructor(e,t=!0){this.littleEndian=t,this.position=0,this.view=e,this.length=e.byteLength}dumpBytes(e=100){const t=this.position,i=[];for(let t=0;t<=e;t++)i.push(this.getByte());console.log(i.join(\" \")),this.setPosition(t)}setPosition(e){this.position=e}available(){return this.length-this.position}remLength(){return this.length-this.position}hasNext(){return this.position<this.length-1}getByte(){const e=this.view.getUint8(this.position,this.littleEndian);return this.position++,e}getShort(){const e=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,e}getUShort(){const e=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,e}getInt(){const e=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,e}getUInt(){const e=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,e}getLong(){var e=[];e[0]=this.view.getUint8(this.position),e[1]=this.view.getUint8(this.position+1),e[2]=this.view.getUint8(this.position+2),e[3]=this.view.getUint8(this.position+3),e[4]=this.view.getUint8(this.position+4),e[5]=this.view.getUint8(this.position+5),e[6]=this.view.getUint8(this.position+6),e[7]=this.view.getUint8(this.position+7);let t=0;if(this.littleEndian)for(let i=e.length-1;i>=0;i--)t=256*t+e[i];else for(let i=0;i<e.length;i++)t=256*t+e[i];return this.position+=8,t}getString(e){let t,i=\"\";for(;0!==(t=this.view.getUint8(this.position++))&&(i+=String.fromCharCode(t),!e||i.length!==e););return i}getFixedLengthString(e){let t=\"\";for(let i=0;i<e;i++){const e=this.view.getUint8(this.position++);e>0&&(t+=String.fromCharCode(e))}return t}getFloat(){var e=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,e}getDouble(){var e=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,e}skip(e){return this.position+=e,this.position}getVPointer(){var e=this.position,t=this.view.getUint8(e+1)<<8|this.view.getUint8(e),i=4294967296*(255&this.view.getUint8(e+6))+16777216*(255&this.view.getUint8(e+5))+65536*(255&this.view.getUint8(e+4))+256*(255&this.view.getUint8(e+3))+(255&this.view.getUint8(e+2));return this.position+=8,new Ac(i,t)}}class Ac{constructor(e,t){this.block=e,this.offset=t}isLessThan(e){return this.block<e.block||this.block===e.block&&this.offset<e.offset}isGreaterThan(e){return this.block>e.block||this.block===e.block&&this.offset>e.offset}isEqualTo(e){return this.block===e.block&&this.offset===e.offset}print(){return this.block+\":\"+this.offset}}class Cc{static magic=2026540177;littleEndian=!0;nodeCache=new Map;static async loadBpTree(e,t,i){return new Cc(e,t,i).init()}constructor(e,t,i){this.path=e,this.config=t,this.startOffset=i}async init(){const e=await this.#t(this.startOffset,32);let t=e.getInt();if(t!==Cc.magic&&(e.setPosition(0),this.littleEndian=!this.littleEndian,e.littleEndian=this.littleEndian,t=e.getInt(),t!==Cc.magic))throw Error(`Bad magic number ${t}`);const i=e.getInt(),n=e.getInt(),r=e.getInt(),s=e.getLong(),o=e.getLong(),a=this.startOffset+32;return this.header={magic:t,blockSize:i,keySize:n,valSize:r,itemCount:s,reserved:o,nodeOffset:a},this}async search(e){this.header||await this.init();const{keySize:t,valSize:i}=this.header;if(16!==i&&8!==i)throw Error(`Unexpected valSize ${i}`);const n=async e=>{if(this.nodeCache.has(e))return this.nodeCache.get(e);{let n=await this.#t(e,4);const r=n.getByte();n.getByte();const s=n.getUShort(),o=[];if(1===r){const r=s*(t+i);n=await this.#t(e+4,r);for(let e=0;e<s;e++){const e=n.getFixedLengthString(t),r=n.getLong();let s;if(16===i){const e=n.getInt();n.getInt(),s={offset:r,length:e}}else s={offset:r};o.push({key:e,value:s})}}else{const i=s*(t+8);n=await this.#t(e+4,i);for(let e=0;e<s;e++){const e=n.getFixedLengthString(t),i=n.getLong();o.push({key:e,offset:i})}}const a={type:r,count:s,items:o};return this.nodeCache.set(e,a),a}},r=async t=>{const i=await n(t);if(1!==i.type){let t=i.items[0].offset;for(let n=1;n<i.items.length;n++){const r=i.items[n].key;if(e.localeCompare(r)<0)break;t=i.items[n].offset}return r(t)}for(let t of i.items)if(e===t.key)return t.value};return r(this.header.nodeOffset)}async#t(e,t){const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:t}}));return new yc(new DataView(i),this.littleEndian)}}\n",
-       "/**\n",
-       "     * Note: Some portions of this code adapated from the GMOD two-bit.js project, @Copyright (c) 2017 Robert Buels\n",
-       "     * * https://github.com/GMOD/twobit-js/blob/master/src/twoBitFile.ts*\n",
-       "     */const _c=[\"T\",\"C\",\"A\",\"G\"],xc=[];for(let IA=0;IA<256;IA++)xc.push(_c[IA>>6&3]+_c[IA>>4&3]+_c[IA>>2&3]+_c[3&IA]);const kc=xc.map((e=>e.toLowerCase()));class Ic{littleEndian;metaIndex=new Map;constructor(e){this.url=e.twoBitURL||e.fastaURL,this.config=e,e.twoBitBptURL&&(this.bptURL=e.twoBitBptURL)}async init(){if(this.bptURL)this.index=await Cc.loadBpTree(this.bptURL,this.config,0);else{const e=await this._readIndex();this.index={search:async t=>e.has(t)?{offset:e.get(t)}:void 0}}}async readSequence(e,t,i){this.index||await this.init();const n=await this.getSequenceRecord(e);if(!n)return null;if(t<0)throw new TypeError(\"regionStart cannot be less than 0\");(void 0===i||i>n.dnaSize)&&(i=n.dnaSize);const r=this._getOverlappingBlocks(t,i,n.nBlocks),s=this._getOverlappingBlocks(t,i,n.maskBlocks),o=Math.floor(t/4),a=n.packedPos+o,c=Math.floor(i/4)-o+1,l=await Qs.loadArrayBuffer(this.url,{range:{start:a,size:c}}),h=new Uint8Array(l);let d=\"\";for(let e=t;e<i;e+=1){for(;s.length&&s[0].end<=e;)s.shift();const t=s[0]&&s[0].start<=e&&s[0].end>e;if(r[0]&&e>=r[0].start&&e<r[0].end){const t=r.shift();for(;e<t.end&&e<i;)d+=\"N\",e++;e--}else{const i=e%4,n=h[Math.floor(e/4)-o];d+=t?kc[n][i]:xc[n][i]}}return d}async _readIndex(){const e=new Map;let t=await Qs.loadArrayBuffer(this.url,{range:{start:0,size:64}}),i=new DataView(t),n=0;const r=i.getUint32(n,!0),s=i.getUint32(n,!1);n+=4;const o=440477507;if(r===o)this.littleEndian=!0;else{if(s!==o)throw Error(`Bad magic number ${o}`);this.littleEndian=!1}let a,c;this.version=i.getUint32(n,this.littleEndian),n+=4,this.sequenceCount=i.getUint32(n,this.littleEndian),n+=4,this.reserved=i.getUint32(n,this.littleEndian),n+=4;let l=20;for(let t=0;t<this.sequenceCount;t++){(!c||c.available()<1)&&(a=(this.sequenceCount-t)*l,c=await this._loadBinaryBuffer(n,a));const i=c.getByte();n+=1,c.available()<i+5&&(a=(this.sequenceCount-t)*l+100,c=await this._loadBinaryBuffer(n,a));const r=c.getString(i),s=c.getUInt();n+=i+4,e.set(r,s),l=Math.floor(l*(t/(t+1))+r.length/(t+1))}return e}async getSequenceRecord(e){if(!this.metaIndex.has(e)){if(!this.index)throw Error(\"TwobitSequence object must be initialized before accessing sequence\");let t=await this.index.search(e);if(!t)return;let i=t.offset,n=8,r=await this._loadBinaryBuffer(i,n);const s=r.getUInt(),o=r.getUInt();i+=n,n=8*o+4,r=await this._loadBinaryBuffer(i,n);const a=[];for(let e=0;e<o;e++)a.push(r.getUInt());const c=[];for(let e=0;e<o;e++)c.push(r.getUInt());const l=r.getUInt();i+=n,n=8*l+4,r=await this._loadBinaryBuffer(i,n);const h=[];for(let e=0;e<l;e++)h.push(r.getUInt());const d=[];for(let e=0;e<l;e++)d.push(r.getUInt());const u=[];for(let e=0;e<o;e++)u.push(new Sc(a[e],c[e]));const f=[];for(let e=0;e<l;e++)f.push(new Sc(h[e],d[e]));if(0!=r.getUInt())throw Error(\"Bad 2-bit file\");i+=n;const p={dnaSize:s,nBlocks:u,maskBlocks:f,packedPos:i,bpLength:s};this.metaIndex.set(e,p)}return this.metaIndex.get(e)}_getOverlappingBlocks(e,t,i){const n=[];for(let r of i){if(r.start>t)break;r.end<e||n.push(r)}return n}async _loadBinaryBuffer(e,t){const i=await Qs.loadArrayBuffer(this.url,{range:{start:e,size:t}});return new yc(new DataView(i),this.littleEndian)}}class Sc{constructor(e,t){this.start=e,this.size=t}get end(){return this.start+this.size}}class Ec{static#i=1e5;#n;#r=[];#s=10;constructor(e,t){this.sequenceReader=e,this.browser=t}get chromosomes(){return this.sequenceReader.chromosomes}async getSequenceRecord(e){return this.sequenceReader.getSequenceRecord(e)}async getSequence(e,t,i){let n=this.#r.find((n=>n.contains(e,t,i)));if(n||(n=await this.#o(e,t,i),this.#a(n),this.#r.push(n)),n){const e=t-n.start,r=i-t;return n.features?n.features.substring(e,e+r):null}}#a(e){this.#r=this.#r.filter((t=>!e.contains(t))),this.#r.length===this.#s&&this.#r.shift(),this.browser&&this.browser.referenceFrameList.length<100&&(this.#r=this.#r.filter((e=>void 0!==this.browser.referenceFrameList.find((t=>t.overlaps(e))))))}getSequenceInterval(e,t,i){return this.#r.find((n=>n.contains(e,t,i)))}async#o(e,t,i){let n=t,r=i;if(i-t<Ec.#i){const e=i-t,s=Math.round(t+e/2);n=Math.max(0,s-Ec.#i/2),r=n+Ec.#i}const s=new dc(e,n,r);if(this.#n&&this.#n[0].contains(e,t,i))return this.#n[1];{const t=new Promise((async(t,i)=>{s.features=await this.sequenceReader.readSequence(e,n,r),t(s)}));return this.#n=[s,t],t}}async init(){return this.sequenceReader.init()}get chromosomeNames(){return this.sequenceReader.chromosomeNames}getFirstChromosomeName(){return\"function\"==typeof this.sequenceReader.getFirstChromosomeName?this.sequenceReader.getFirstChromosomeName():void 0}#c(e){this.browser.referenceFrameList}}async function Nc(e,t){let i;return\"chromsizes\"===e.format?i=new vc(e.fastaURL||e.url):\"2bit\"===e.format||e.twoBitURL?i=new Ec(new Ic(e),t):Ga(e.fastaURL)||!e.indexURL?i=new pc(e):\"gbk\"===e.format||e.gbkURL||(i=new Ec(new bc(e),t)),await i.init(),i}const Bc={A:\"rgb(  0, 200,   0)\",C:\"rgb(  0,0,200)\",T:\"rgb(255,0,0)\",G:\"rgb(209,113,  5)\",N:\"rgb(80,80,80)\"};function Mc(e,t){if(e.length<6)return void console.log(\"Skipping line: \"+e.join(\" \"));var i={chr1:e[0],start1:Number.parseInt(e[1]),end1:Number.parseInt(e[2]),chr2:e[3],start2:Number.parseInt(e[4]),end2:Number.parseInt(e[5])};if(isNaN(i.start1)||isNaN(i.end1)||isNaN(i.start2)||isNaN(i.end2))return;t&&void 0===t.hiccups&&(t.hiccups=!!t.columnNames&&Dc(t.columnNames));const n=t&&t.hiccups,r=n?6:10;if(n||(e.length>6&&\".\"!==e[6]&&(i.name=e[6]),e.length>7&&\".\"!==e[7]&&(i.score=Number(e[7])),e.length>8&&\".\"!==e[8]&&(i.strand1=e[8]),e.length>9&&\".\"!==e[9]&&(i.strand2=e[9])),t){const n=t.colorColumn;n&&n<e.length&&(i.color=_s.createColorString(e[n]));const s=t.thicknessColumn;s&&s<e.length&&(i.thickness=e[s]),e.length>r&&t.columnNames&&t.columnNames.length===e.length&&(i.extras=e.slice(r))}return i.chr1===i.chr2&&(i.chr=i.chr1,i.start=Math.min(i.start1,i.start2),i.end=Math.max(i.end1,i.end2)),i}function Rc(e,t){if(!(e.length<8))return{chr:e[0],start:Number.parseInt(e[1]),end:Number.parseInt(e[2]),color:_s.createColorString(e[6]),value:Number(e[7])}}function Dc(e){return e&&(e.includes(\"fdrDonut\")||e.includes(\"fdr_donut\"))}function Tc(e,t){if(!(e.length<6))return{chr:e[0],start:Number.parseInt(e[1]),end:Number.parseInt(e[2]),chr1:e[8],start1:Number.parseInt(e[9]),end1:Number.parseInt(e[10]),chr2:e[13],start2:Number.parseInt(e[14]),end2:Number.parseInt(e[15]),name:e[3],score:Number(e[4]),value:Number(e[5]),color:\".\"===e[7]?void 0:\"0\"===e[7]?\"rgb(0,0,0)\":e[7]};console.log(\"Skipping line: \"+e.join(\" \"))}class Lc{constructor(e){this.message=e}}const zc=new Map([[\"%09\",\"\\t\"],[\"%0A\",\"\\n\"],[\"%0D\",\"\\r\"],[\"%25\",\"%\"],[\"%3B\",\";\"],[\"%3D\",\"=\"],[\"%26\",\"&\"],[\"%2C\",\",\"]]);function Hc(e){if(!e.includes(\"%\"))return e;let t=\"\";for(let i=0;i<e.length;i++)if(37===e.charCodeAt(i)&&i<e.length-2){const n=e.substring(i,i+3);zc.has(n)?t+=zc.get(n):t+=n,i+=2}else t+=e.charAt(i);return t}function Pc(e,t=\"=\"){const i=\"=\"===t;var n=[];for(let r of e.split(\";\")){r=r.trim();const e=r.indexOf(t);if(e>0&&e<r.length-1){let t=Hc(r.substring(0,e).trim()),s=Hc(r.substring(e+1).trim());i||(t=Oc(t),s=Oc(s)),n.push([t,s])}}return n}function Oc(e){return e.startsWith('\"')&&e.endsWith('\"')&&(e=e.substr(1,e.length-2)),e}function Uc(e,t,i=Number.MAX_SAFE_INTEGER){if(e.length<3)return;t&&t.gffTags;const n=e[0],r=parseInt(e[1]),s=e.length>2?parseInt(e[2]):r+1;if(isNaN(r)||isNaN(s))return new Lc(\"Unparsable bed record.\");const o=new nl({chr:n,start:r,end:s,score:1e3});let a=3;try{if(e.length>3&&a++<i){if(e[3].indexOf(\";\")>0&&e[3].indexOf(\"=\")>0){const i=Pc(e[3],\"=\");o.attributes={};for(let e of i)o.attributes[e[0]]=e[1],null!=t.nameField&&e[0]===t.nameField&&(o.name=e[1])}o.name||(o.name=\".\"===e[3]?\"\":e[3])}if(e.length>4&&a++<i&&(o.score=\".\"===e[4]?0:Number(e[4]),isNaN(o.score)))return o;if(e.length>5&&a++<i&&(o.strand=e[5],\".\"!==o.strand&&\"+\"!==o.strand&&\"-\"!==o.strand))return o;if(e.length>6&&a++<i&&(o.cdStart=parseInt(e[6]),isNaN(o.cdStart)))return o;if(e.length>7&&a++<i&&(o.cdEnd=parseInt(e[7]),isNaN(o.cdEnd)))return o;if(e.length>8&&a++<i&&\".\"!==e[8]&&\"0\"!==e[8]&&(o.color=_s.createColorString(e[8])),e.length>11&&a++<i){const t=parseInt(e[9]);if(t>1e3)return o;const i=e[10].replace(/,$/,\"\").split(\",\"),n=e[11].replace(/,$/,\"\").split(\",\");if(i.length!==n.length||t!==i.length)return o;const s=[];for(let e=0;e<t;e++){const t=r+parseInt(n[e]),o=t+parseInt(i[e]);s.push({start:t,end:o})}s.length>0&&(Yc(s,o.cdStart,o.cdEnd),o.exons=s)}if(t){let i=t.thicknessColumn,n=t.colorColumn;n&&n<e.length&&(o.color=_s.createColorString(e[n])),i&&i<e.length&&(o.thickness=e[i])}}catch(e){}return o}function qc(e,t){const i=Uc(e,t);return i&&e.length>14&&(i.signal=Number(e[12]),i.pValue=Number(e[13]),i.qValue=Number(e[14])),i}function Qc(e,t){const i=Uc(e,t,9);if(i){const t=[\"Coverage\",\"% Showing Methylation\",\"N-mod\",\"N-canonical\",\"N-other mod\",\"N-delete\",\"N-fail\",\"N-dff\",\"N-nocall\"];for(let n=9;n<e.length;n++){i[t[n-9]]=e[n]}}return i}function Vc(e,t){if(e.length<=15)return;return{swScore:Number.parseInt(e[1]),milliDiv:Number.parseInt(e[2]),milliDel:Number.parseInt(e[3]),milliIns:Number.parseInt(e[4]),chr:e[5],start:Number.parseInt(e[6]),end:Number.parseInt(e[7]),strand:e[9],repName:e[10],repClass:e[11],repFamily:e[12],repStart:Number.parseInt(e[13]),repEnd:Number.parseInt(e[14]),repLeft:Number.parseInt(e[15])}}function jc(e,t){var i=void 0===t.shift?0:1;if(e.length<=9+i)return;const n=parseInt(e[5+i]),r=parseInt(e[6+i]);var s={name:e[0+i],chr:e[1+i],strand:e[2+i],start:parseInt(e[3+i]),end:parseInt(e[4+i]),cdStart:n,cdEnd:r,id:e[0+i]};const o=Kc(parseInt(e[7+i]),e[8+i],e[9+i]);return Yc(o,n,r),s.exons=o,s}function Wc(e,t){var i=void 0===t.shift?0:1;if(e.length<=11+i)return;const n=parseInt(e[5+i]),r=parseInt(e[6+i]),s={name:e[11+i],chr:e[1+i],strand:e[2+i],start:parseInt(e[3+i]),end:parseInt(e[4+i]),cdStart:n,cdEnd:r,id:e[0+i]},o=Kc(parseInt(e[7+i]),e[8+i],e[9+i],e[14+i]);return Yc(o,n,r),s.exons=o,s}function Gc(e,t){var i=void 0===t.shift?0:1;if(e.length<=10+i)return;const n=parseInt(e[6+i]),r=parseInt(e[7+i]);var s={name:e[0+i],id:e[1+i],chr:e[2+i],strand:e[3+i],start:parseInt(e[4+i]),end:parseInt(e[5+i]),cdStart:n,cdEnd:r};const o=Kc(parseInt(e[8+i]),e[9+i],e[10+i]);return Yc(o,n,r),s.exons=o,s}function $c(e,t){if(e.length<21)return;const i=e[13],n=parseInt(e[15]),r=parseInt(e[16]),s=e[8].charAt(0),o=parseInt(e[17]),a=[],c=e[20].replace(/,$/,\"\").split(\",\"),l=e[18].replace(/,$/,\"\").split(\",\");for(let e=0;e<o;e++){const t=parseInt(c[e]),i=t+parseInt(l[e]);a.push({start:t,end:i})}return new rl({chr:i,start:n,end:r,strand:s,exons:a,tokens:e})}function Kc(e,t,i,n){const r=t.replace(/,$/,\"\").split(\",\"),s=i.replace(/,$/,\"\").split(\",\"),o=n?n.replace(/,$/,\"\").split(\",\"):void 0,a=[];for(let t=0;t<e;t++){const e={start:parseInt(r[t]),end:parseInt(s[t])};if(o){const i=parseInt(o[t]);-1!=i&&(e.readingFrame=i)}a.push(e)}return a}function Yc(e,t,i){for(let n of e){const e=n.end,r=n.start;e<t||r>i?n.utr=!0:(t>=r&&t<=e&&(n.cdStart=t),i>=r&&i<=e&&(n.cdEnd=i))}}function Xc(e,t){var i,n,r,s,o,a,c;if(!(e.length<9))return i=e[0],n=parseInt(e[1]),r=parseInt(e[2]),o=e[3],a=Number(e[4]),s=e[5].trim(),c=Number(e[6]),0===a&&(a=c),{chr:i,start:n,end:r,name:o,score:a,strand:s,signal:c,pValue:Number(e[7]),qValue:Number(e[8])}}function Zc(e,t){const i=Xc(e);return e.length>9&&(i.peak=Number(e[9])),i}function Jc(e,t){if(e.length<=3)return;const i={chr:e[0],start:parseInt(e[1]),end:parseInt(e[2]),value:Number(e[3])};if(t){let n=t.colorColumn;n&&n<e.length&&(i.color=_s.createColorString(e[n]))}return i}function el(e,t){const i=t.wig;if(i&&\"fixedStep\"===i.format){const t=i.index*i.step+i.start,n=t+i.span,r=Number(e[0]);return++i.index,isNaN(r)?null:{chr:i.chrom,start:t,end:n,value:r}}if(i&&\"variableStep\"===i.format){if(e.length<2)return null;const t=parseInt(e[0],10)-1,n=t+i.span,r=Number(e[1]);return isNaN(r)?null:{chr:i.chrom,start:t,end:n,value:r}}return Jc(e)}function tl(e,t){if(e.length<6)return;const i=[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"refNCBI\",\"refUCSC\",\"observed\",\"molType\",\"class\",\"valid\",\"avHet\",\"avHetSE\",\"func\",\"locType\",\"weight\",\"exceptions\",\"submitterCount\",\"submitters\",\"alleleFreqCount\",\"alleles\",\"alleleNs\",\"alleleFreqs\",\"bitfields\"],n={chr:e[1],start:Number.parseInt(e[2]),end:Number.parseInt(e[3]),name:e[4],score:Number.parseInt(e[5])},r=Math.min(e.length,i.length);for(let t=6;t<r;t++)n[i[t]]=e[t];return n}function il(e,t,i=Number.MAX_SAFE_INTEGER){if(e.length<4)return;const n=e[0],r=parseInt(e[1]),s=e.length>2?parseInt(e[2]):r+1;if(isNaN(r)||isNaN(s))return new Lc(\"Unparsable bed record.\");const o=new nl({chr:n,start:r,end:s,score:1e3}),a=[];for(let t=3;t<e.length;t++)a.push(Number.parseInt(e[t]));return o.values=a,o}class nl{constructor(e){Object.assign(this,e)}getAttributeValue(e){return this.hasOwnProperty(e)?this[e]:this.attributes?this.attributes[e]:void 0}}class rl{constructor(e){Object.assign(this,e)}get score(){const e=this.tokens,t=parseInt(e[0]),i=parseInt(e[2]),n=parseInt(e[1]),r=parseInt(e[4]),s=parseInt(e[6]),o=parseInt(e[10]);return Math.floor(1e3*(t+i-n-r-s)/o)}get matches(){return this.tokens[0]}get misMatches(){return this.tokens[1]}get repMatches(){return this.tokens[2]}get nCount(){return this.tokens[3]}get qNumInsert(){return this.tokens[4]}get qBaseInsert(){return this.tokens[5]}get tNumInsert(){return this.tokens[6]}get tBaseInsert(){return this.tokens[7]}popupData(){return[{name:\"chr\",value:this.chr},{name:\"start\",value:this.start+1},{name:\"end\",value:this.end},{name:\"strand\",value:this.strand},{name:\"score\",value:this.score},{name:\"match\",value:this.matches},{name:\"mis-match\",value:this.misMatches},{name:\"rep. match\",value:this.repMatches},{name:\"N's\",value:this.nCount},{name:\"Q gap count\",value:this.qNumInsert},{name:\"Q gap bases\",value:this.qBaseInsert},{name:\"T gap count\",value:this.tNumInsert},{name:\"T gap bases\",value:this.tBaseInsert}]}}const sl=new Set([\"transcript\",\"primary_transcript\",\"processed_transcript\",\"mRNA\",\"mrna\",\"lnc_RNA\",\"miRNA\",\"ncRNA\",\"rRNA\",\"scRNA\",\"snRNA\",\"snoRNA\",\"tRNA\"]),ol=new Set([\"CDS\",\"cds\"]),al=new Set([\"start_codon\",\"stop_codon\"]),cl=new Set([\"5UTR\",\"3UTR\",\"UTR\",\"five_prime_UTR\",\"three_prime_UTR\",\"3'-UTR\",\"5'-UTR\"]),ll=new Set([\"exon\",\"coding-exon\"]),hl=new Set;for(let SA of[ol,al,cl,ll])for(let EA of SA)hl.add(EA);function dl(e){return e.includes(\"intron\")}function ul(e){return ol.has(e)||al.has(e)}function fl(e){return cl.has(e)}function pl(e){return sl.has(e)||e.endsWith(\"RNA\")||e.endsWith(\"transcript\")}function gl(e){return hl.has(e)||e.endsWith(\"RNA\")||dl(e)}const ml=new Set([\"id\",\"parent\",\"name\"]);class wl{constructor(e){Object.assign(this,e),void 0!==e.phase&&\".\"!==e.phase&&(this.readingFrame=(3-parseInt(e.phase))%3)}popupData(e){const t=this.geneObject?this.geneObject.popupData():[];if(this.geneObject&&t.push(\"<hr/>\"),this.name&&t.push({name:\"Name\",value:this.name}),t.push({name:\"Type\",value:this.type}),t.push({name:\"Source\",value:this.source}),void 0!==this.score&&t.push({name:\"Score\",value:this.score}),t.push({name:\"Phase\",value:this.phase}),this.attributeString){const e=Pc(this.attributeString,this.delim);for(let[i,n]of e)void 0!==n&&n.length>0&&!ml.has(i.toLowerCase())&&t.push({name:i+\":\",value:n})}return t.push({name:\"Location\",value:`${this.chr}:${Rt(this.start+1)}-${Rt(this.end)}`}),t}getAttributeValue(e){if(this.hasOwnProperty(e))return this[e];if(this._attributeCache||(this._attributeCache=new Map),this._attributeCache.has(e))return this._attributeCache.get(e);{const t=Pc(this.attributeString,this.delim);let i;for(let[n,r]of t)if(n===e){i=r;break}return this._attributeCache.set(e,i),i}}}class bl extends wl{constructor(e){super(e),this.exons=[],this.parts=[]}addExon(e){this.exons.push(e),this.start=Math.min(this.start,e.start),this.end=Math.max(this.end,e.end)}addPart(e){this.parts.push(e)}assembleParts(){if(0===this.parts.length)return;this.parts.sort((function(e,t){return e.start-t.start}));let e=this.parts[0].start,t=this.parts[0].end;for(let i=1;i<this.parts.length;i++){const n=this.parts[i];if(!dl(n.type))if(n.start<=t)t=Math.max(t,n.end);else{this.findExonContaining({start:e,end:t})||this.exons.push({start:e,end:t,psuedo:!0}),e=n.start,t=n.end}}this.findExonContaining({start:e,end:t})||(this.exons.push({start:e,end:t,psuedo:!0}),this.start=Math.min(this.start,e),this.end=Math.max(this.end,t));for(let e of this.parts){const t=e.type;ul(t)?this.addCDS(e):fl(t)&&this.addUTR(e)}}findExonContaining({start:e,end:t}){for(let i of this.exons)if(i.end>=t&&i.start<=e)return i}addCDS(e){let t;const i=this.exons;for(let n of i)if(n.start<=e.start&&n.end>=e.end){t=n;break}t?(t.cdStart=t.cdStart?Math.min(e.start,t.cdStart):e.start,t.cdEnd=t.cdEnd?Math.max(e.end,t.cdEnd):e.end,t.readingFrame=e.readingFrame):console.error(\"No exon found spanning \"+e.start+\"-\"+e.end),this.cdStart=this.cdStart?Math.min(e.start,this.cdStart):e.start,this.cdEnd=this.cdEnd?Math.max(e.end,this.cdEnd):e.end}addUTR(e){let t;const i=this.exons;for(let n=0;n<i.length;n++)if(i[n].start<=e.start&&i[n].end>=e.end){t=i[n];break}t?e.start===t.start&&e.end===t.end?t.utr=!0:(e.end<t.end&&(t.cdStart=e.end),e.start>t.start&&(t.cdEnd=e.start)):console.error(\"No exon found spanning \"+cds.start+\"-\"+cds.end)}finish(){this.assembleParts();var e=this.cdStart,t=this.cdEnd;this.exons.sort((function(e,t){return e.start-t.start})),e&&this.exons.forEach((function(i){(i.end<e||i.start>t)&&(i.utr=!0)}))}popupData(e){const t=super.popupData(e);for(let i of this.exons)if(!i.pseudo&&e>=i.start&&e<i.end&&\"function\"==typeof i.popupData){t.push(\"<hr/>\");const n=i.popupData(e);for(let e of n)t.push(e)}for(let i of this.parts)if(e>=i.start&&e<i.end&&\"function\"==typeof i.popupData){t.push(\"<hr/>\");const n=i.popupData(e);for(let e of n)t.push(e)}return t}}function Fl(e,t){const i=t.format;if(e.length<9)return;const n=\"gff3\"===i?\"=\":\" \";return new wl({source:Hc(e[1]),type:e[2],chr:e[0],start:parseInt(e[3])-1,end:parseInt(e[4]),score:\".\"===e[5]?void 0:Number(e[5]),strand:e[6],phase:\".\"===e[7]?\".\":parseInt(e[7]),attributeString:e[8],delim:n})}function vl(e,t){const i=Fl(e,t);if(!i)return;const n=Pc(i.attributeString,i.delim);for(let[e,t]of n){const n=e.toLowerCase();\"color\"===n||\"colour\"===n?i.color=_s.createColorString(t):\"ID\"===e?i.id=t:\"Parent\"===e&&(i.parent=t)}return i}function yl(e,t){const i=Fl(e,t);if(!i)return;const n=Pc(i.attributeString,i.delim);let r,s;switch(i.type){case\"gene\":r=\"gene_id\";break;case\"transcript\":r=\"transcript_id\",s=\"gene_id\";break;default:s=\"transcript_id\"}for(let[e,t]of n){const n=e.toLowerCase();\"color\"===n||\"colour\"===n?i.color=_s.createColorString(t):e===r?i.id=t:e===s&&(i.parent=t)}return i}function Al(e,t){if(!(e.length<7)){var i=e[0],n=e[1],r=parseInt(e[2]),s=parseInt(e[3]),o=parseInt(e[4]),a=parseInt(e[5]),c=e[6],l={chr:i,name:n,junction_left:r,junction_right:s,num_junction_reads:o,num_spanning_frags:a,spanning_frag_coords:[],start:-1,end:-1},h=r,d=s;if(a>0)for(var u=c.split(\",\"),f=0;f<u.length;f++){var p=u[f].split(\"-\"),g=p[0],m=p[1];g<h&&(h=g),m>d&&(d=m),l.spanning_frag_coords.push({left:g,right:m})}return l.start=h,l.end=d,l}}function Cl(e,t){if(e.length<7)return null;const i={chr:e[0],start:parseInt(e[1])-1,end:parseInt(e[2]),\"Strongest SNP-risk allele\":e[3],\"Disease/Phenotype\":e[4],\"P-value\":e[5],\"Odds ratio or beta\":e[6]};return e.length>6&&(i.PUBMEDID=`<a target = \"blank\" href = \"https://www.ncbi.nlm.nih.gov/pubmed/${e[7]}\">${e[7]}</a>`),i}function _l(e,t){const i=t.customFormat;if(e.length<i.fields.length)return;const n=i.coords||0,r=e[i.chr],s=parseInt(e[i.start])-n,o={chr:r,start:s,end:void 0!==i.end?parseInt(e[i.end]):s+1};return i.fields&&i.fields.forEach((function(t,n){n!==i.chr&&n!==i.start&&n!==i.end&&(o[t]=e[n])})),o}function xl(e,t){const i=t.columnNames;if(!i)throw Error(\"Sample names are not defined.   Missing column headers?\");const n=i.length-3,r=e[0],s=parseInt(e[1]),o=parseInt(e[2]),a=e.slice(3).map(Number);return a.length==n?{chr:r,start:s,end:o,values:a}:void console.warn(`${r}:${s}-${o} row contains ${a.length} sample columns instead of the expected ${n} columns. Skipping...`)}const kl=[\"Name\",\"transcript_id\",\"gene_name\",\"gene\",\"gene_id\",\"alias\",\"locus\",\"name\"];class Il{constructor(e){this.format=e.format,this.nameField=e.nameField,this.filterTypes=void 0===e.filterTypes?new Set([\"chromosome\"]):new Set(e.filterTypes)}combineFeatures(e,t){let i;const n=this.filterTypes;if(e=e.filter((e=>void 0===n||!n.has(e.type))),\"gff3\"===this.format){const t=this.combineFeaturesById(e);i=this.combineFeaturesByType(t)}else i=this.combineFeaturesByType(e);return this.numberExons(i,t),this.nameFeatures(i),i}combineFeaturesById(e){const t=new Map,i=[];for(let n of e)if(gl(n.type)||pl(n.type)||!n.id)i.push(n);else{let e=t.get(n.chr);e||(e=new Map,t.set(n.chr,e));let i=e.get(n.id);i?i.push(n):e.set(n.id,[n])}for(let e of t.values())for(let t of e.values())if(t.length>1){const e=t[0];e.exons=[];for(let i of t)e.start=Math.min(e.start,i.start),e.end=Math.max(e.end,i.end),e.exons.push({start:i.start,end:i.end});i.push(e)}else i.push(t[0]);return i}combineFeaturesByType(e){const t=e.filter((e=>\"gene\"===e.type||e.type.endsWith(\"_gene\"))),i=Object.create(null);for(let e of t)i[e.id]=e;const n=Object.create(null),r=[],s=new Set,o=this.filterTypes;e=e.filter((e=>void 0===o||!o.has(e.type)));for(let t of e)if(pl(t.type)){const e=t.id;if(void 0!==e){const o=new bl(t);n[e]=o,r.push(o),s.add(t);const a=i[t.parent];a&&(o.geneObject=a,s.add(a))}}for(let t of e)if(gl(t.type)){const e=l(t);if(e)for(let i of e){let o=n[i];if(!o&&\"gtf\"===this.format){const e=Object.assign({},t);e.type=\"transcript\",o=new bl(e),n[i]=o,r.push(o)}if(void 0!==o){if(a=t.type,ll.has(a))if(e.length>1){const e=new wl(t);o.addExon(e)}else o.addExon(t);else o.addPart(t);s.add(t)}}}var a;r.forEach((function(e){\"function\"==typeof e.finish&&e.finish()}));const c=e.filter((e=>!s.has(e)));for(let e of c)r.push(e);return r;function l(e){return e.parent&&\"\"!==e.parent.trim()?e.parent.trim().split(\",\"):null}}numberExons(e,t){for(let i of e)if(i.exons&&(!t||i.end<=t.end&&i.start>t.start))for(let e=0;e<i.exons.length;e++){i.exons[e].number=\"-\"===i.strand?i.exons.length-e:e+1}}nameFeatures(e){for(let t of e)if(\"function\"==typeof t.getAttributeValue)if(this.nameField)t.name=t.getAttributeValue(this.nameField);else for(let e of kl){const i=t.getAttributeValue(e);if(i){t.name=i;break}}}}const Sl={gwascatalog:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"pubMedID\",\"author\",\"pubDate\",\"journal\",\"title\",\"trait\",\"initSample\",\"replSample\",\"region\",\"genes\",\"riskAllele\",\"riskAlFreq\",\"pValue\",\"pValueDesc\",\"orOrBeta\",\"ci95\",\"platform\",\"cnv\"]},wgrna:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"thickStart\",\"thickEnd\",\"type\"]},cpgislandext:{fields:[\"bin\",\"chr\",\"start\",\"end\",\"name\",\"length\",\"cpgNum\",\"gcNum\",\"perCpg\",\"perGc\",\"obsExp\"]},clinVarMain:{fields:[\"chr1\",\"start\",\"end\",\"name\",\"score\",\"strand\",\"thickStart\",\"thickEnd\",\"reserved\",\"blockCount\",\"blockSizes\",\"chromStarts\",\"origName\",\"clinSign\",\"reviewStatus\",\"type\",\"geneId\",\"snpId\",\"nsvId\",\"rcvAcc\",\"testedInGtr\",\"phenotypeList\",\"phenotype\",\"origin\",\"assembly\",\"cytogenetic\",\"hgvsCod\",\"hgvsProt\",\"numSubmit\",\"lastEval\",\"guidelines\",\"otherIds\"]}};class El{constructor(e){this.config=e,this.header={},e.nameField&&(this.header.nameField=e.nameField),this.skipRows=0,e.decode?(this.decode=e.decode,this.delimiter=e.delimiter||\"\\t\"):e.format&&(this.header.format=e.format.toLowerCase(),this.setDecoder(this.header.format)),this.delimiter||(this.delimiter=\"\\t\")}async parseHeader(e){let t,i,n=this.header;for(;void 0!==(i=await e.nextLine());)if(i.startsWith(\"track\")||i.startsWith(\"#track\")){let e=Nl(i);Object.assign(n,e)}else if(i.startsWith(\"browser\"));else if(i.startsWith(\"#columns\")){let e=Bl(i);Object.assign(n,e)}else if(i.startsWith(\"##gff-version 3\"))n.format=\"gff3\";else if(i.startsWith(\"#gffTags\"))n.gffTags=!0;else{if(i.startsWith(\"fixedStep\")||i.startsWith(\"variableStep\"))break;if(i.startsWith(\"#\")){const e=i.split(this.delimiter||\"\\t\");e.length>1&&(t=e)}else{this.setDecoder(n.format);const e=i.split(this.delimiter||\"\\t\");try{const i=Object.assign({columnNames:t},n);if(this.decode(e,i))break;e.length>1&&(t=e)}catch(i){e.length>1&&(t=e)}}}if(t){n.columnNames=t;for(let e=0;e<t.length;e++)\"color\"===t[e]||\"colour\"===t[e]?n.colorColumn=e:\"thickness\"===t[e]&&(n.thicknessColumn=e)}return this.header=n,n}async parseFeatures(e){const t=[],i=this.decode,n=this.header.format,r=this.delimiter||\"\\t\";let s,o=0,a=0;for(;void 0!==(s=await e.nextLine());){if(o++,o<=this.skipRows)continue;if(!s||s.startsWith(\"track\")||s.startsWith(\"#\")||s.startsWith(\"browser\"))continue;if(\"wig\"===n&&s.startsWith(\"fixedStep\")){this.header.wig=Ml(s);continue}if(\"wig\"===n&&s.startsWith(\"variableStep\")){this.header.wig=Rl(s);continue}const e=s.split(r);if(e.length<1)continue;const c=i(e,this.header);c instanceof Lc?(a++,a>0&&console.error(`Error parsing line '${s}': ${c.message}`)):c&&t.push(c)}return i===Mc&&function(e){if(0==e.length)return;const t=e[0];if(void 0===t.score&&void 0!==t.name){for(let t of e)if(!Va(t.name)&&\".\"!==t.name)return;for(let t of e)t.score=Number(t.name),delete t.name}const i=e.filter((e=>e.chr1!==e.chr2));for(let t of i){const i=Object.assign({},t);i.dup=!0,e.push(i),t.chr=t.chr1,t.start=t.start1,t.end=t.end1,i.chr=i.chr2,i.start=i.start2,i.end=i.end2}}(t),\"gtf\"!==this.config.format&&\"gff3\"!==this.config.format&&\"gff\"!==this.config.format||!1===this.config.assembleGFF?t:new Il(this.config).combineFeatures(t)}setDecoder(e){switch(e){case\"broadpeak\":case\"regionpeak\":case\"peaks\":this.decode=Xc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"narrowpeak\":this.decode=Zc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedgraph\":this.decode=Jc,this.delimiter=/\\s+/;break;case\"wig\":this.decode=el,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gff3\":case\"gff\":this.decode=vl,this.delimiter=\"\\t\";break;case\"gtf\":this.decode=yl,this.delimiter=\"\\t\";break;case\"fusionjuncspan\":this.decode=Al,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gtexgwas\":this.skipRows=1,this.decode=Cl,this.delimiter=\"\\t\";break;case\"refflat\":this.decode=Gc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"genepred\":this.decode=jc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"genepredext\":this.decode=Wc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"ensgene\":this.decode=jc,this.header.shift=1,this.delimiter=this.config.delimiter||/\\s+/;break;case\"refgene\":this.decode=Wc,this.delimiter=this.config.delimiter||/\\s+/,this.header.shift=1;break;case\"bed\":this.decode=Uc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"gappedpeak\":this.decode=qc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedmethyl\":this.decode=Qc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"bedpe\":case\"hiccups\":this.decode=Mc,this.delimiter=this.config.delimiter||\"\\t\";break;case\"bedpe-domain\":this.decode=Rc,this.headerLine=!0,this.delimiter=this.config.delimiter||\"\\t\";break;case\"bedpe-loop\":this.decode=Mc,this.delimiter=this.config.delimiter||\"\\t\",this.header={colorColumn:7};break;case\"interact\":this.decode=Tc,this.delimiter=this.config.delimiter||/\\s+/;break;case\"snp\":this.decode=tl,this.delimiter=\"\\t\";break;case\"rmsk\":this.decode=Vc,this.delimiter=\"\\t\";break;case\"gcnv\":this.decode=xl,this.delimiter=\"\\t\";break;case\"shoebox\":this.decode=il,this.delimiter=\"\\t\";break;default:const t=function(e){return Sl&&Sl[e]?function(e){const t=e.fields,i=[\"chr\",\"start\",\"end\"];for(let n=0;n<t.length;n++)for(let r of i)r===t[n]&&(e[r]=n);return e}(Sl[e]):void 0}(e);void 0!==t?(this.decode=_l,this.header.customFormat=t,this.delimiter=t.delimiter||\"\\t\"):(this.decode=Uc,this.delimiter=this.config.delimiter||/\\s+/)}}}function Nl(e){const t={},i=e.split(/(?:\")([^\"]+)(?:\")|([^\\s\"]+)(?=\\s+|$)/g);let n;const r=[];for(let e of i)e&&0!==e.trim().length&&(e.endsWith(\"=\")?n=e:n?(r.push(n+e),n=void 0):r.push(e));for(let e of r){if(!e)return;var s=e.split(\"=\",2);if(2===s.length){const e=s[0].trim(),i=s[1].trim();if(t.hasOwnProperty(e)){let n=t[e];Array.isArray(n)?n.push(i):t[e]=[n,i]}else t[e]=i}}return\"interact\"==t.type?t.format=\"interact\":\"gcnv\"===t.type&&(t.format=\"gcnv\"),t}function Bl(e){let t={},i=e.split(/\\s+/);if(2===i.length){i[1].split(\";\").forEach((function(e){let i=e.split(\"=\");\"color\"===i[0]?t.colorColumn=Number.parseInt(i[1])-1:\"thickness\"===i[0]&&(t.thicknessColumn=Number.parseInt(i[1])-1)}))}return t}function Ml(e){const t=e.split(/\\s+/);return{format:\"fixedStep\",chrom:t[1].split(\"=\")[1],start:parseInt(t[2].split(\"=\")[1],10)-1,step:parseInt(t[3].split(\"=\")[1],10),span:t.length>4?parseInt(t[4].split(\"=\")[1],10):1,index:0}}function Rl(e){const t=e.split(/\\s+/);return{format:\"variableStep\",chrom:t[1].split(\"=\")[1],span:t.length>2?parseInt(t[2].split(\"=\")[1],10):1}}function Dl(t,i){const n=e({class:\"igv-menu-popup-check-container\"}),r=e();n.appendChild(r);const s=l(\"check\",!0===i?\"#444\":\"transparent\");r.appendChild(s);const o=e();return o.innerText=t,n.appendChild(o),n}function Tl(e,t){t=t||Number.MAX_SAFE_INTEGER;const i=[];e.sort((function(e,t){return e.start-t.start})),i.push(-1e3);for(let n of e){let e=0;const r=Math.min(i.length,t);for(e=0;e<r;e++)if(n.start>=i[e]){n.row=e,i[e]=n.end;break}n.row=e,i[e]=n.end}}async function Ll(e,t,i){const n=e=>{const i=Object.assign({},e);return i.chr=\"all\",i.start=t.getGenomeCoordinate(e.chr,e.start),i.end=t.getGenomeCoordinate(e.chr,e.end),i._f=e,i.exons&&delete i.exons,i},r=new Set(t.wgChromosomeNames),s=[];let o=0;for(let a of t.wgChromosomeNames){if(Array.isArray(e)){const i={};for(let n of e){const e=t.getChromosomeName(n.chr);i.hasOwnProperty(e)||(i[e]=[]),i[e].push(n)}e=i}const c=e[a];if(c){const e=i||1e4;for(let i of c){let a=t.getChromosomeName(i.chr);if(r.has(a))if(s.length<e)s.push(n(i));else{const t=e/(o+1);if(Math.random()<t){s[Math.floor(Math.random()*(e-1))]=n(i)}}o++}}}return s.sort((function(e,t){return e.start-t.start})),s}function zl(e,t){if(t=t||1e3,null==e||0===e.length)return;const i={},n=[];for(let t of e){const e=t.chr;let r=i[e];r||(r=[],i[e]=r,n.push(e)),r.push(t)}for(let e of n)Tl(i[e],t)}class Hl{static defaults={height:50,autoHeight:!1,visibilityWindow:void 0,color:void 0,altColor:void 0,supportHiDPI:!0,selected:!1};constructor(e,t){this.browser=t,this.init(e)}init(e){this.config=e,e.displayMode&&(e.displayMode=e.displayMode.toUpperCase());const t=Object.assign({},Hl.defaults);if(this.constructor.defaults)for(let e of Object.keys(this.constructor.defaults))t[e]=this.constructor.defaults[e];for(let n of Object.keys(t))this[n]=e.hasOwnProperty(n)?e[n]:t[n],\"color\"!==n&&\"altColor\"!==n||!this[n]||(this[n]=Mt(i=this[n])&&i.indexOf(\",\")>0&&!i.startsWith(\"rgb(\")&&!i.startsWith(\"rgba(\")?`rgb(${i})`:i);var i;e.name||e.label?this.name=e.name||e.label:Ht(e.url)?this.name=e.url.name:Mt(e.url)&&!e.url.startsWith(\"data:\")&&(this.name=zt(e.url)),this.url=e.url,this.config.type&&(this.type=this.config.type),this.id=void 0===this.config.id?this.name:this.config.id,this.order=e.order,this.autoscaleGroup=e.autoscaleGroup,this.removable=void 0===e.removable||e.removable,this.minHeight=e.minHeight||Math.min(25,this.height),this.maxHeight=e.maxHeight||Math.max(1e3,this.height),e.onclick&&(this.onclick=e.onclick,e.onclick=void 0),e.description&&(\"function\"==typeof e.description?this.description=e.description:this.description=()=>e.description),e.hoverTextFields?this.hoverText=Pl.bind(this):\"function\"==typeof this.config.hoverText&&(this.hoverText=this.config.hoverText)}get name(){return this._name}set name(e){this._name=e,this.trackView&&this.trackView.setTrackLabelName(e)}clearCachedFeatures(){this.trackView&&this.trackView.clearCachedFeatures()}updateViews(){this.trackView&&this.trackView.updateViews()}repaintViews(){this.trackView&&this.trackView.repaintViews()}getState(){const e={},t=Object.keys(this.config).filter((e=>{return!(void 0===(t=this.config[e])||\"function\"==typeof t||t instanceof Promise);var t}));for(const i of t)i.startsWith(\"_\")||(e[i]=this.config[i]);for(let t of Object.keys(e)){if(t.startsWith(\"_\"))continue;const i=this[t];void 0===i||!Oa(i)&&\"boolean\"!=typeof i&&\"metadata\"!==t||(e[t]=i)}const i=Object.assign({},Hl.defaults);if(this.constructor.defaults)for(let e of Object.keys(this.constructor.defaults))i[e]=this.constructor.defaults[e];for(let t of Object.keys(i))void 0!==this[t]&&i[t]!==this[t]&&(e[t]=this[t]);return!this.autoscale&&this.dataRange&&(e.min=this.dataRange.min,e.max=this.dataRange.max),this.autoscaleGroup&&(e.autoscaleGroup=this.autoscaleGroup),e}get supportsWholeGenome(){return!0===this.config.supportsWholeGenome}hasSamples(){return!1}getGenomeId(){return this.browser.genome?this.browser.genome.id:void 0}setTrackProperties(e){if(this.disposed)return;const t={};let i;for(let n of Object.keys(e))switch(n.toLowerCase()){case\"usescore\":t.useScore=1===e[n]||\"1\"===e[n]||\"on\"===e[n]||!0===e[n];break;case\"visibility\":switch(e[n]){case\"2\":case\"3\":case\"pack\":case\"full\":t.displayMode=\"EXPANDED\";break;case\"4\":case\"squish\":t.displayMode=\"SQUISHED\";break;case\"1\":case\"dense\":t.displayMode=\"COLLAPSED\"}break;case\"color\":case\"altcolor\":t[n]=e[n].startsWith(\"rgb(\")?e[n]:\"rgb(\"+e[n]+\")\";break;case\"featurevisiblitywindow\":case\"visibilitywindow\":t.visibilityWindow=Number.parseInt(e[n]);break;case\"maxheightpixels\":i=e[n].split(\":\"),3===i.length&&(t.minHeight=Number.parseInt(i[2]),t.height=Number.parseInt(i[1]),t.maxHeight=Number.parseInt(i[0]));break;case\"viewlimits\":if(!this.config.autoscale){i=e[n].split(\":\");let r,s=0;1==i.length?r=Number(i[0]):2==i.length&&(s=Number(i[0]),r=Number(i[1])),Number.isNaN(r)||Number.isNaN(s)?console.warn(`Unexpected viewLimits value in track line: ${e.viewLimits}`):(t.autoscale=!1,t.dataRange={min:s,max:r},this.viewLimitMin=s,this.viewLimitMax=r)}case\"name\":t[n]=e[n];break;case\"url\":t.infoURL=e[n];break;case\"type\":const r=e[n];Ol.has(r)?t[n]=Ol.get(r):t[n]=r;break;case\"graphtype\":t.graphType=e[n];break;default:t[n]=e[n]}for(let e of Object.keys(t))if(!this.config.hasOwnProperty(e)||\"name\"===e&&this.config._derivedName){let i=t[e];if(\"true\"===i&&(i=!0),\"false\"===i&&(i=!1),this[e]=i,\"height\"===e&&this.trackView)try{const e=Number.parseInt(i);this.trackView.setTrackHeight(e)}catch(e){console.error(e)}}}clickedFeatures(e){const t=e.viewport.cachedFeatures;if(!t||!Array.isArray(t)||0===t.length)return[];const i=e.genomicLocation,n=e.referenceFrame.bpPerPixel>.2?3*e.referenceFrame.bpPerPixel:.2;return to(t,i-n,i+n)}extractPopupData(e,t){const i=new Set([\"row\",\"color\",\"chr\",\"start\",\"end\",\"cdStart\",\"cdEnd\",\"strand\",\"alpha\"]),n=[];let r,s;for(let t in e)if(e.hasOwnProperty(t)&&!i.has(t)&&Oa(e[t])){let i=e[t];n.push({name:Lt(t),value:i}),\"alleles\"===t?r=e[t]:\"alleleFreqs\"===t&&(s=e[t])}if(r&&s){r.endsWith(\",\")&&(r=r.substr(0,r.length-1)),s.endsWith(\",\")&&(s=s.substr(0,s.length-1));let i=r.split(\",\"),o=s.split(\",\");if(o.length>1){let r=[];for(let e=0;e<o.length;e++)r.push({a:i[e],af:Number(o[e])});r.sort((function(e,t){return e.af-t.af}));let s=r[r.length-1].a;if(1===s.length)for(let i=r.length-2;i>=0;i--){let o=r[i].a;if(1===o.length){t||(t=this.getGenomeId());const i=Hl.getCravatLink(e.chr,e.start+1,s,o,t);console.log(i),i&&(n.push(\"<hr/>\"),n.push({html:i}),n.push(\"<hr/>\"))}}}}if(e.attributes)for(let t of Object.keys(e.attributes))n.push({name:t,value:e.attributes[t]});let o=`${e.chr}:${Rt(e.start+1)}-${Rt(e.end)}`;return e.strand&&(o+=` (${e.strand})`),n.push({name:\"Location\",value:o}),n}description(){const e=(e,t)=>`<div class=\"igv-track-label-popup-shim\"><b>${e}: </b>${t}</div>`;let t='<div class=\"igv-track-label-popup\">';if(this.url?Ht(this.url)?t+=e(\"Filename\",this.url.name):t+=e(\"URL\",this.url):t=this.name,this.config){if(this.config.metadata)for(let i of Object.keys(this.config.metadata)){t+=e(i,this.config.metadata[i])}for(let i of Object.keys(this.config)){if(i.startsWith(\"_\"))continue;let n=i.substr(0,1);if(n!==n.toLowerCase()){const n=this.config[i];n&&Oa(n)&&(t+=e(i,n))}}}return t+=\"</div>\",t}getColorForFeature(e){return\"function\"==typeof this.color?this.color(feature):this.color}numericDataMenuItems(){const e=[];e.push(\"<hr/>\");let t=Bt(\"<div>\");if(t.text(\"Set data range\"),e.push({object:t,dialog:function(){this.trackView.track.selected?this.browser.dataRangeDialog.configure(this.trackView.browser.getSelectedTrackViews()):this.browser.dataRangeDialog.configure(this.trackView),this.browser.dataRangeDialog.present(Bt(this.browser.columnContainer))}}),void 0!==this.logScale){function i(){this.logScale=!this.logScale,this.trackView.repaintViews()}t=Bt(Dl(\"Log scale\",this.logScale)),e.push({object:t,click:i})}return t=Bt(Dl(\"Autoscale\",this.autoscale)),e.push({object:t,click:function(){this.autoscaleGroup=void 0,this.autoscale=!this.autoscale,this.browser.updateViews()}}),e}setDataRange({min:e,max:t}){this.dataRange={min:e,max:t},this.autoscale=!1,this.autoscaleGroup=void 0,this.trackView.repaintViews()}async nextFeatureAfter(e,t,i){let n=this.trackView.viewports[0].cachedFeatures;if(n&&Array.isArray(n)&&n.length>0){if(this.browser.genome.getChromosomeName(n[0].chr)===e){const e=function(e,t,i=!0){const n=e=>(e.start+e.end)/2,r=i?(e,t)=>e.start-t.start+e.end-t.end:(e,t)=>t.start-e.start+t.end-e.end,s=Array.from(e);s.sort(r);let o=0,a=s.length;for(;o<a;){let e=Math.floor((o+a)/2);i?n(s[e])<=t?o=e+1:a=e:n(s[e])>=t?o=e+1:a=e}return s[o]}(n,t,i);if(e)return e}}if(\"function\"==typeof this.featureSource.nextFeature)return this.featureSource.nextFeature(e,t,i,this.visibilityWindow)}dispose(){this.disposed=!0;for(let e of Object.keys(this))this[e]=void 0}static getCravatLink(e,t,i,n,r){if(\"hg38\"===r||\"GRCh38\"===r){return`<a target=\"_blank\" href=\"https://run.opencravat.org/result/nocache/variant.html?chrom=${e.startsWith(\"chr\")?e:\"chr\"+e}&pos=${t}&ref_base=${i}&alt_base=${n}\"><b>Cravat ${i}->${n}</b></a>`}}static localFileInspection(e){const t=Object.assign({},e),i={url:\"file\",indexURL:\"indexFile\"};for(const e of[\"url\",\"indexURL\"])t[e]&&t[e]instanceof File&&(t[i[e]]=t[e].name,delete t[e]);return t}}function Pl(e){if(!this.hoverTextFields)return;const t=this.clickedFeatures(e);if(t&&t.length>0){let e=\"\";for(let i=0;i<t.length;i++){if(10===i){e+=\"; ...\";break}if(!t[i])continue;const n=t[i]._f||t[i];e.length>0&&(e+=\"\\n\"),e=\"\";for(let t of this.hoverTextFields)e.length>0&&(e+=\"\\n\"),n.hasOwnProperty(t)?e+=n[t]:\"function\"==typeof n.getAttribute&&(e+=n.getAttribute(t))}return e}}const Ol=new Map([[\"wiggle_0\",\"wig\"],[\"bed\",\"bed\"],[\"bigBed\",\"bigBed\"],[\"bigWig\",\"bigWig\"]]);class Ul{constructor(e){switch(this.type=e||\"seg\",this.type){case\"mut\":this.sampleColumn=3,this.chrColumn=0,this.startColumn=1,this.endColumn=2,this.dataColumn=4;break;case\"maf\":this.sampleColumn=15,this.chrColumn=4,this.startColumn=5,this.endColumn=6,this.dataColumn=8;break;default:this.sampleColumn=0,this.chrColumn=1,this.startColumn=2,this.endColumn=3}}async parseHeader(e){let t;for(;void 0!==(t=await e.nextLine());)if(!t.startsWith(\"#\")){const e=t.split(\"\\t\");this.header={headings:e};break}return this.header}async parseFeatures(e){const t=[];let i;this.header||(this.header=await this.parseHeader(e)),\"seg\"===this.type&&(this.dataColumn=this.header.headings.length-1),this.header.headings.length>5&&(i=this.extractExtraColumns(this.header.headings));const n=this.header.headings[this.dataColumn];let r;for(;void 0!==(r=await e.nextLine());){const e=r.split(\"\\t\"),s=\"seg\"===this.type?Number(e[this.dataColumn]):e[this.dataColumn];if(e.length>this.dataColumn){const r=new ql({sample:e[this.sampleColumn],chr:e[this.chrColumn],start:parseInt(e[this.startColumn])-1,end:parseInt(e[this.endColumn]),value:s,valueColumnName:n});if(i){const t=this.extractExtraColumns(e);r.setAttributes({names:i,values:t})}t.push(r)}}return t}extractExtraColumns(e){const t=[];for(let i=0;i<e.length;i++)i!==this.chrColumn&&i!==this.startColumn&&i!==this.endColumn&&i!==this.sampleColumn&&t.push(e[i]);return t}}class ql{constructor({sample:e,chr:t,start:i,end:n,value:r,valueColumnName:s}){this.sample=e,this.chr=t,this.start=i,this.end=n,this.value=r,this.valueColumnName=s}setAttributes({names:e,values:t}){this.attributeNames=e,this.attributeValues=t}getAttribute(e){if(this.attributeNames){const t=this.attributeNames.indexOf(e);if(t>=0)return this.attributeValues[t]}}popupData(e,t){const i=new Set([\"chr\",\"start\",\"end\",\"sample\",\"value\",\"row\",\"color\",\"sampleKey\",\"uniqueSampleKey\",\"sampleId\",\"chromosome\",\"uniquePatientKey\"]),n=this.chr+\":\"+Rt(this.start+1)+\"-\"+Rt(this.end),r=[{name:\"Sample\",value:this.sample},{name:\"Location\",value:n},{name:this.valueColumnName?Lt(this.valueColumnName):\"Value\",value:this.value}];if(\"mut\"===e&&\"hg38\"===t){const e=this.extractCravatLink(t);e&&(r.push(\"<hr/>\"),r.push({html:e}),r.push(\"<hr/>\"))}if(this.attributeNames&&this.attributeNames.length>0)for(let e=0;e<this.attributeNames.length;e++)!i.has(this.attributeNames[e])&this.valueColumnName!==this.attributeNames[e]&&r.push({name:Lt(this.attributeNames[e]),value:this.attributeValues[e]});return r}extractCravatLink(e){let t,i;if(this.attributeNames&&this.attributeNames.length>0)for(let n=0;n<this.attributeNames.length;n++)if(t||\"Reference_Allele\"!==this.attributeNames[n]||(t=this.attributeValues[n]),!i&&this.attributeNames[n].startsWith(\"Tumor_Seq_Allele\")&&this.attributeValues[n]!==t&&(i=this.attributeValues[n]),t&&i)return Hl.getCravatLink(this.chr,this.start+1,t,i,e)}}const Ql=new Map([[\"REF\",\"referenceBases\"],[\"ALT\",\"alternateBases\"],[\"QUAL\",\"quality\"],[\"FILTER\",\"filter\"]]);class Vl{constructor(e){this.chr=e[0],this.pos=parseInt(e[1]),this.names=e[2],this.referenceBases=e[3],this.alternateBases=e[4],this.quality=e[5],this.filter=e[6],this.info={};const t=e[7];if(t&&\".\"!==t)for(let e of t.split(\";\")){var i=e.split(\"=\");this.info[i[0]]=i[1]}this.init()}getAttributeValue(e){return Ql.has(e)&&(e=Ql.get(e)),this.hasOwnProperty(e)?this[e]:this.info[e]}init(){const e=this.referenceBases,t=this.alternateBases;if(this.info&&(this.info.VT?this.type=this.info.VT:this.info.SVTYPE?this.type=\"SV\":this.info.PERIOD&&(this.type=\"STR\")),void 0===this.type&&(this.type=function(e,t){const i=e.length;if(void 0===t)return\"UNKNOWN\";if(0===t.trim().length||\"<NON_REF>\"===t||\"<*>\"===t||\".\"===t)return\"NONVARIANT\";{const e=t.split(\",\").map((function(e){return 1===i&&1===e.length?\"SNP\":\"<NON_REF>\"===e?\"NONVARIANT\":e.length>i&&$l(e)?\"INSERTION\":e.length<i&&$l(e)?\"DELETION\":\"OTHER\"}));let n=e[0];for(let t of e)if(t!==n)return\"MIXED\";return n}}(e,t)),this.info.END)this.start=this.pos-1,this.info.CHR2&&this.info.CHR2!==this.chr?this.end=this.start+1:this.end=Number.parseInt(this.info.END);else if(\"NONVARIANT\"===this.type)this.start=this.pos-1,this.end=this.start+e.length;else{const i=t.split(\",\").filter((e=>e.length>0));this.alleles=[],this.start=void 0,this.end=void 0;for(let t of i)if(this.alleles.push(t),\"SV\"!==this.type&&$l(t)){let i=t.length,n=e.length;const r=Math.min(i,n);let s=0;for(;s<r&&e.charCodeAt(s)===t.charCodeAt(s);)s++,i--,n--;for(;i>0&&n>0;){const r=s+i-1,o=s+n-1;if(t.charCodeAt(r)!==e.charCodeAt(o))break;i--,n--}for(;i>0&&n>0;){const r=s,o=s;if(t.charCodeAt(r)!==e.charCodeAt(o))break;s++,i--,n--}const o=this.pos+s-1,a=o+n;this.start=void 0===this.start?o:Math.min(this.start,o),this.end=void 0===this.end?a:Math.max(this.end,a)}void 0===this.start&&(this.start=this.pos-1,this.end=this.pos),this.start===this.end&&(this.start-=.5,this.end+=.5)}}popupData(e,t){const i=`${Rt(this.pos)}`,n=this.start===this.end?`${Rt(this.start)} | ${Rt(this.start+1)}`:`${Rt(this.start+1)}-${Rt(this.end)}`,r=[{name:\"Chr\",value:this.chr},{name:\"Pos\",value:i},{name:\"Loc\",value:n},{name:\"ID\",value:this.names?this.names:\"\"},{name:\"Ref\",value:this.referenceBases},{name:\"Alt\",value:this.alternateBases.replace(\"<\",\"&lt;\")},{name:\"Qual\",value:this.quality},{name:\"Filter\",value:this.filter}];if(this.type&&r.push({name:\"Type\",value:this.type}),\"SNP\"===this.type){let e=this.referenceBases;if(1===e.length){let i=this.alternateBases.split(\",\");for(let n of i)if(1===n.length){let i=Hl.getCravatLink(this.chr,this.pos,e,n,t);i&&(r.push(\"<hr/>\"),r.push({html:i}))}}}const s=Object.keys(this.info);if(this.info&&s.length>0){r.push({html:'<hr style=\"border-top: dotted 1px;border-color: #c9c3ba\" />'});for(let e of s)r.push({name:e,value:Kl(decodeURIComponent(this.info[e]))})}return r}getInfo(e){return this.info?this.info[e]:void 0}isRefBlock(){return\"NONVARIANT\"===this.type}isFiltered(){return!(\".\"===this.filter||\"PASS\"===this.filter)}alleleFreq(){return this.info?this.info.AF:void 0}}class jl{constructor(e){this.mate=e,this.chr=e.info.CHR2,this.pos=Number.parseInt(e.info.END),this.start=this.pos-1,this.end=this.pos}get info(){return this.mate.info}get names(){return this.mate.names}get referenceBases(){return this.mate.referenceBases}get alternateBases(){return this.mate.alternateBases}get quality(){return this.mate.quality}get filter(){return this.mate.filter}get calls(){return this.mate.calls}getAttributeValue(e){return this.mate.getAttributeValue(e)}getInfo(e){this.mate.getInfo(e)}isFiltered(){return this.mate.isFiltered()}alleleFreq(){return this.mate.alleleFreq()}popupData(e,t){const i=[];return i.push(\"SV Breakpoint\"),i.push({name:\"Chr\",value:this.chr}),i.push({name:\"Pos\",value:`${Rt(this.pos)}`}),i.push({html:'<hr style=\"border-top: dotted 1px;border-color: #c9c3ba\" />'}),i.push(\"SV\"),i.push(...this.mate.popupData(e,t)),i}}class Wl{constructor({formatFields:e,sample:t,token:i}){this.info={},this.sample=t;const n=i.split(\":\");for(let t=0;t<n.length;t++){const i=n[t];if(t==e.genotypeIndex){this.genotype=[];for(let e of i.split(/[\\|\\/]/))this.genotype.push(\".\"===e?e:parseInt(e))}else this.info[e.fields[t]]=i}}get zygosity(){if(!this._zygosity)if(this.genotype){let e=!0,t=!0,i=!1;for(let n of this.genotype){if(\".\"===n){i=!0;break}0!==n&&(t=!1),0===n&&(e=!1)}this._zygosity=i?\"nocall\":t?\"homref\":e?\"homvar\":\"hetvar\"}else this._zygosity=\"unknown\";return this._zygosity}zygosityScore(){switch(this.zygosity){case\"homvar\":return 4;case\"hetvar\":return 3;case\"homref\":return 2;case\"nocall\":return 1;default:return 0}}#l(){switch(this.zygosity){case\"homref\":return\"Homozygous reference\";case\"homvar\":return\"Homozygous variant\";case\"hetvar\":return\"Heterozygous\";default:return\"\"}}popupData(e,t){const i=[];void 0!==this.sample&&i.push({name:\"Sample\",value:this.sample}),this.genotypeString&&i.push({name:\"Genotype\",value:this.genotypeString});const n=this.#l();n&&i.push({name:\"Zygosity\",value:n});var r=Object.keys(this.info);r.length&&i.push(\"<hr/>\");for(let e of r)i.push({name:e,value:decodeURIComponent(this.info[e])});return i}}const Gl=new Set([\"A\",\"C\",\"T\",\"G\"].map((e=>e.charCodeAt(0))));function $l(e){for(let t=0;t<e.length;t++)if(!Gl.has(e.charCodeAt(t)))return!1;return!0}function Kl(e,t){return void 0===t&&(t=\",\"),Array.isArray(e)?e.join(t):e}class Yl{construtor(){}async parseHeader(e,t){const i={};i.chrAliasTable=new Map;let n=await e.nextLine();if(!n.startsWith(\"##fileformat\"))throw new Error(\"Invalid VCF file: missing fileformat line\");for(i.version=n.substr(13);void 0!==(n=await e.nextLine())&&n.startsWith(\"#\");){let e;const s={};if(n.startsWith(\"##\")){if(n.startsWith(\"##INFO\")||n.startsWith(\"##FILTER\")||n.startsWith(\"##FORMAT\")){const t=n.indexOf(\"<\"),o=n.lastIndexOf(\">\");if(!(t>2&&o>0)){console.log(\"Malformed VCF header line: \"+n);continue}const a=n.substring(2,t-1);i[a]||(i[a]={});const c=Tt(n.substring(t+1,o-1),\",\");for(let t of c){var r=t.split(\"=\");r.length>1&&(\"ID\"===r[0]?e=r[1]:s[r[0]]=r[1])}e&&(i[a][e]=s)}else if(n.startsWith(\"##contig\")&&t){const e=n.indexOf(\"<ID=\");let r=n.indexOf(\",\",e);-1==r&&(r=n.indexOf(\">\",e));const s=n.substring(e+4,r),o=t.getChromosomeName(s);i.chrAliasTable.set(o,s)}}else if(n.startsWith(\"#CHROM\")){const e=n.split(\"\\t\");if(e.length>8){i.sampleNameMap=new Map;for(let t=9;t<e.length;t++)i.sampleNameMap.set(e[t],t-9)}}}return this.header=i,i}async parseFeatures(e){const t=[],i=this.header.sampleNameMap?Array.from(this.header.sampleNameMap.keys()):void 0,n=8+(i?i.length+1:0);let r;for(;void 0!==(r=await e.nextLine());)if(r&&!r.startsWith(\"#\")){const e=r.split(\"\\t\");if(e.length===n){const n=new Vl(e);if(n.header=this.header,t.push(n),e.length>9){const r=Xl(e[8].split(\":\"));n.calls=[];for(let t=9;t<e.length;t++){const s=i[t-9],o=e[t],a=new Wl({formatFields:r,sample:s,token:o});n.calls.push(a)}n.info&&n.info.CHR2&&n.info.END&&t.push(new jl(n))}}}return t}}function Xl(e){const t={genotypeIndex:-1,fields:e};for(let i=0;i<e.length;i++)\"GT\"===e[i]&&(t.genotypeIndex=i);return t}const Zl=Math.log10(Number.MIN_VALUE);class Jl{constructor(e){if(this.config=e,e.columns){if(void 0===e.columns.chromosome||void 0===e.columns.position||void 0===e.columns.value)throw Error(\"columns property must define chrCol, posCol, and valueCol\");this.posCol=e.columns.position-1,this.chrCol=e.columns.chromosome-1,this.valueCol=e.columns.value-1}else this.posCol=2,this.chrCol=1,this.valueCol=3}async parseHeader(e){const t=await e.nextLine();return this.parseHeaderLine(t)}parseHeaderLine(e){if(this.columns=e.split(/\\t/),!this.config.columns)for(let e=0;e<this.columns.length;e++){switch(this.columns[e].toLowerCase()){case\"chr\":case\"chromosome\":case\"chr_id\":this.chrCol=e;break;case\"bp\":case\"pos\":case\"position\":case\"chr_pos\":this.posCol=e;break;case\"p\":case\"pval\":case\"pvalue\":case\"p-value\":case\"p.value\":this.valueCol=e}}return this.columns}async parseFeatures(e){const t=[],i=e.nextLine();let n;this.columns||this.parseHeaderLine(i);const r=e=>{const t=e.indexOf(\"E\");if(t>0){if(Number.parseInt(e.substring(t+1))<Zl)return Number.MIN_VALUE}return Number(e)};for(;void 0!==(n=e.nextLine());){const e=n.split(/\\t/);if(e.length===this.columns.length){const i=e[this.posCol];if(i.indexOf(\";\")>0||0==i.length||i.indexOf(\"x\")>0)continue;const s=e[this.chrCol],o=r(e[this.valueCol]),a=parseInt(i)-1,c=a+1;t.push(new eh({chr:s,start:a,end:c,value:o,line:n,columns:this.columns}))}}return t}static isGWAS(e){const t=e.split(\"\\t\");if(t.length<5)return!1;const i=[[\"chr\",\"chromosome\",\"chr_id\",\"chrom\"],[\"bp\",\"pos\",\"position\",\"chr_pos\",\"chromEnd\"],[\"p\",\"pval\",\"p-value\",\"p.value\"]];for(let e of i)if(!t.some((t=>e.includes(t.toLowerCase()))))return!1;return!0}}class eh{constructor({chr:e,start:t,end:i,value:n,line:r,columns:s}){this.chr=e,this.start=t,this.end=i,this.value=n,this.line=r,this.columns=s}popupData(){const e=this.line.split(/\\t/);return this.columns.map((function(t,i){return{name:t,value:e[i]}}))}getAttribute(e){const t=this.line.split(/\\t/);for(let i=0;i<this.columns.length;i++)if(this.columns[i]===e)return t[i]}}var th=new RegExp(\"([^:]*)\\\\(([^)]*)\\\\)\"),ih=new RegExp(\"([^:]*):([^(]*)\\\\(([^)]*)\\\\)\");class nh{constructor(e){const t=e?e.decode:void 0;this.nameField=e?e.nameField:void 0,this.skipRows=0,this.decode=t||lh,this.delimiter=\"\\t\"}async parseHeader(e){let t,i;for(;(t=await e.nextLine())&&(t.startsWith(\"track\")||t.startsWith(\"#\")||t.startsWith(\"browser\"));)if(t.startsWith(\"track\")||t.startsWith(\"#track\")){let e=oh(t);i?Object.assign(i,e):i=e}else if(t.startsWith(\"#columns\")){let e=ah(t);i?Object.assign(i,e):i=e}else t.startsWith(\"##gff-version 3\")&&(this.format=\"gff3\",i||(i={}),i.format=\"gff3\");return this.header=i,i}async parseFeatures(e){const t=[],i=this.decode,n=this.delimiter||\"\\t\";let r,s=0;for(;void 0!==(r=e.nextLine());){if(s++,s<=this.skipRows||r.startsWith(\"track\")||r.startsWith(\"#\")||r.startsWith(\"browser\"))continue;let e=o();if(e.length<1)continue;if(!this.aed){this.aed=sh(e);continue}const n=i.call(this,e,undefined);n&&t.push(n)}return t;function o(){for(var e,t,i=[],s=\"\",o=!1;r||\"\"===r;){for(e=0;e<r.length;e++)(t=r.charAt(e))===n?o?s+=t:(i.push(s),s=\"\"):'\"'===t?e+1<r.length&&'\"'===r.charAt(e+1)?(o&&(s+='\"'),e++):o=!o:s+=t;if(!o)break;s+=\"\\n\",r=nextLine()}return i.push(s),i}}}function rh(e){var t=ih.exec(e);if(t)return{namespace:t[1],name:t[2],type:t[3]};if(t=th.exec(e))return{namespace:\"?\",name:t[1],type:t[2]};throw new Error(\"Error parsing the header row of AED file - column not in ns:name(ns:type) format\")}function sh(e){var t,i,n;for(t={columns:[],metadata:{}},i=0;i<e.length;i++)n=rh(e[i]),t.columns.push(n);return t}function oh(e){const t={},i=e.split(/(?:\")([^\"]+)(?:\")|([^\\s\"]+)(?=\\s+|$)/g);let n;const r=[];for(let e of i)e&&0!==e.trim().length&&(e.endsWith(\"=\")>0?n=e:n?(r.push(n+e),n=void 0):r.push(e));for(let e of r){if(!e)return;var s=e.split(\"=\",2);if(2===s.length){const e=s[0].trim(),i=s[1].trim();t[e]=i}}return t}function ah(e){let t={},i=e.split(/\\s+/);if(2===i.length){i[1].split(\";\").forEach((function(e){let i=e.split(\"=\");\"color\"===i[0]?t.colorColumn=Number.parseInt(i[1])-1:\"thickness\"===i[0]&&(t.thicknessColumn=Number.parseInt(i[1])-1)}))}return t}function ch(e,t){var i,n,r=e.columns;this.aed=e,this.allColumns=t,this.chr=null,this.start=null,this.end=null,this.score=1e3,this.strand=\".\",this.cdStart=null,this.cdEnd=null,this.name=null,this.color=null;for(let e=0;e<t.length;e++)if(i=t[e]){\"aed:Integer\"===(n=r[e]).type&&(i=parseInt(i));var s=[];if(n.namespace.length>0)for(let e=0;e<n.namespace.length;e++)s.push(n.namespace.charCodeAt(e));\"bio\"===n.namespace.trim()?\"sequence\"===n.name?this.chr=i:\"start\"===n.name?this.start=i:\"end\"===n.name?this.end=i:\"cdsMin\"===n.name?this.cdStart=i:\"cdsMax\"===n.name?this.cdEnd=i:\"strand\"===n.name&&(this.strand=i):\"aed\"===n.namespace?\"name\"===n.name&&(this.name=i):\"style\"===n.namespace&&\"color\"===n.name&&(this.color=_s.createColorString(i))}}function lh(e,t){var i,n,r,s,o,a,c=0,l=this.aed.columns;if(e.length===l.length){for(a=0;a<e.length;a++)s=l[a],\"\"!==(r=e[a])&&c++,\"name\"===s.name&&\"aed\"===s.namespace?i=r:\"value\"===s.name&&\"aed\"===s.namespace&&(n=r);if(2===c&&i&&n)return o=rh(i),this.aed.metadata[o.namespace]||(this.aed.metadata[o.namespace]={}),void(this.aed.metadata[o.namespace][o.name]||(this.aed.metadata[o.namespace][o.name]={type:o.type,value:n}));var h=new ch(this.aed,e);if(h.chr&&(h.start||0===h.start)&&h.end)return h;console.log(\"Cannot parse feature: \"+e.join(\",\"))}else console.log(\"Corrupted AED file row: \"+e.join(\",\"))}function hh(e,t){if(0===e.length)return e;if(e.sort((function(e,t){const i=e.minv.block-t.minv.block;return 0!==i?i:e.minv.offset-t.minv.offset})),e.length<=1)return e;t&&(e=e.filter((e=>e.maxv.isGreaterThan(t))));const i=[];let n;for(let t of e)n&&dh(n,t)?t.maxv.isGreaterThan(n.maxv)&&(n.maxv=t.maxv):(i.push(t),n=t);return i}function dh(e,t){const i=t.minv.block-e.maxv.block;return t.maxv.block-e.minv.block<5e6&&i<65e3}ch.prototype.popupData=function(){for(var e=[],t=this.aed,i=0;i<this.allColumns.length;i++){var n=this.allColumns[i],r=t.columns[i].name;\"sequence\"!==r&&\"color\"!==r&&n&&e.push({name:r,value:n})}return e};class uh{constructor(){this.tabix=!0}parse(e){const t=new yc(new DataView(e)),i=t.getInt();if(21582659!==i)throw 38359875===i?Error(\"CSI version 2 is not supported.  Please enter an issue at https://github.com/igvteam/igv.js\"):Error(\"Not a CSI index\");this.indices=[],this.blockMin=Number.MAX_SAFE_INTEGER,this.lastBlockPosition=[],this.sequenceIndexMap={},this.minShift=t.getInt(),this.depth=t.getInt();const n=[];let r=0;if(t.getInt()>=28){t.getInt(),t.getInt(),t.getInt(),t.getInt(),t.getInt(),t.getInt();const e=t.getInt(),i=t.position+e;let r=0;for(;t.position<i;){let e=t.getString();this.sequenceIndexMap[e]=r,n[r]=e,r++}}const s=this.bin_limit()+1,o=t.getInt();for(let e=0;e<o;e++){const i=[],n=[],o=t.getInt();for(let e=0;e<o;e++){const e=t.getInt();if(n[e]=t.getVPointer(),e>s)t.getInt(),t.getVPointer(),t.getVPointer(),t.getLong(),t.getLong();else{i[e]=[];const n=t.getInt();for(let s=0;s<n;s++){const n=t.getVPointer(),s=t.getVPointer();n&&s&&(n.block<this.blockMin&&(this.blockMin=n.block),s.block>r&&(r=s.block),i[e].push([n,s]))}}}o>0&&(this.indices[e]={binIndex:i,loffset:n})}this.lastBlockPosition=r}get sequenceNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(e,t,i){const n=this.indices[e];if(n){const e=this.reg2bins(t,i);if(0==e.length)return[];const r=[];for(let t of e)for(let e=t[0];e<=t[1];e++)if(n.binIndex[e]){const t=n.binIndex[e];for(let i of t){const t=i[0],n=i[1];r.push({minv:t,maxv:n,bin:e})}}let s=e[this.depth][0];do{if(n.binIndex[s])break;s>1+(this.getParentBin(s)<<3)?s--:s=this.getParentBin(s)}while(0!=s);return hh(r,n.loffset[s])}return[]}getParentBin(e){return 0==e?0:e-1>>3}reg2bins(e,t){(e-=1)<1&&(e=1),t>2**34&&(t=2**34),t-=1;let i=0,n=0,r=this.minShift+3*this.depth;const s=[];for(;i<=this.depth;r-=3,n+=1<<3*i,i+=1){const i=n+(e>>r),o=n+(t>>r);s.push([i,o])}return s}bin_limit(){return((1<<3*(this.depth+1))-1)/7}}class fh{constructor(){}async parse(e,t){const i=[];let n=Number.MAX_SAFE_INTEGER,r=0;const s=new yc(new DataView(e)),o=s.getInt(),a={};if(!(21578050===o||t&&21578324===o))throw new Error(indexURL+\" is not a \"+(t?\"tabix\":\"bai\")+\" file\");{const e=s.getInt();if(t){s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt(),s.getInt();for(let t=0;t<e;t++){a[s.getString()]=t}}for(let t=0;t<e;t++){const e={},o=[],a=s.getInt();for(let t=0;t<a;t++){const t=s.getInt();if(37450===t)s.getInt(),s.getVPointer(),s.getVPointer(),s.getLong(),s.getLong();else{e[t]=[];const i=s.getInt();for(let o=0;o<i;o++){const i=s.getVPointer(),o=s.getVPointer();i&&o&&(i.block<n&&(n=i.block),o.block>r&&(r=o.block),e[t].push([i,o]))}}}const c=s.getInt();for(let e=0;e<c;e++){const e=s.getVPointer();o.push(e)}a>0&&(i[t]={binIndex:e,linearIndex:o})}this.firstBlockPosition=n,this.lastBlockPosition=r,this.indices=i,this.sequenceIndexMap=a,this.tabix=t}}get sequenceNames(){return Object.keys(this.sequenceIndexMap)}chunksForRange(e,t,i){const n=this.indices[e];if(n){const e=function(e,t){const i=[];t>=1<<29&&(t=1<<29);return--t,i.push([0,0]),i.push([1+(e>>26),1+(t>>26)]),i.push([9+(e>>23),9+(t>>23)]),i.push([73+(e>>20),73+(t>>20)]),i.push([585+(e>>17),585+(t>>17)]),i.push([4681+(e>>14),4681+(t>>14)]),i}(t,i),r=[];for(let t of e)for(let e=t[0];e<=t[1];e++)if(n.binIndex[e]){const t=n.binIndex[e];for(let e of t){const t=e[0],i=e[1];r.push({minv:t,maxv:i})}}const s=n.linearIndex.length;let o;const a=Math.min(t>>14,s-1),c=Math.min(i>>14,s-1);for(let e=a;e<=c;e++){const t=n.linearIndex[e];if(t){o=t;break}}return hh(r,o)}return[]}}class ph{constructor(){this.tribble=!0}async parse(e){let t=0;this.chrIndex={},this.lastBlockPosition=[];const i=new yc(new DataView(e));!function(e){e.getInt(),e.getInt();const t=e.getInt();if(e.getString(),e.getLong(),e.getLong(),e.getString(),e.getInt(),t>=3){let t=e.getInt();for(;t-- >0;)e.getString(),e.getString()}}(i);let n=i.getInt();for(;n-- >0;){let e=i.getString();const n=i.getInt(),r=i.getInt(),s=i.getInt();i.getInt(),i.getInt();let o=i.getLong();const a=[];for(let e=0;e<r;e++){const e=i.getLong();a.push({min:o,max:e}),o=e,e>t&&(t=e)}this.chrIndex[e]={chr:e,blocks:a,longestFeature:s,binWidth:n}}this.lastBlockPosition=t}get sequenceNames(){return Object.keys(this.chrIndex)}chunksForRange(e,t,i){const n=this.chrIndex[e];if(n){const e=n.blocks,r=n.longestFeature,s=n.binWidth,o=Math.max(t-r,0),a=Math.floor(o/s);if(a>=e.length)return[];{const t=Math.min(Math.floor((i-1)/s),e.length-1),n=e[a].min,r=e[t].max;if(0===r-n)return[];return[{minv:{block:n,offset:0},maxv:{block:r,offset:0}}]}}}}async function gh(e,t){let i=await Qs.loadArrayBuffer(e,Ua(t)),n=new DataView(i);if(31===n.getUint8(0)&&139===n.getUint8(1)){i=gs(i).buffer,n=new DataView(i)}switch(n.getInt32(0,!0)){case 21578050:return async function(e){const t=new fh;return await t.parse(e,!1),t}(i);case 21578324:return async function(e){const t=new fh;return await t.parse(e,!0),t}(i);case 21582659:return async function(e){const t=new uh;return t.parse(e),t}(i);case 1480870228:return async function(e){const t=new ph;return t.parse(e),t}(i);case 38359875:throw Error(\"CSI version 2 is not supported.\");default:throw Error(`Unrecognized index type: ${e}`)}}function mh(e){return\"string\"==typeof e||e instanceof String?new wh(e):new bh(e)}class wh{constructor(e){this.data=e,this.ptr=0}nextLine(){var e=this.ptr,t=this.data.indexOf(\"\\n\",e),i=this.data;if(t>0)return this.ptr=t+1,t>e&&\"\\r\"===i.charAt(t-1)?i.substring(e,t-1):i.substring(e,t);var n=i.length;return this.ptr=n,e>=n?void 0:i.substring(e)}}class bh{constructor(e){this.data=e,this.length=this.data.length,this.ptr=0}nextLine(){if(this.ptr>=this.data.length)return;let e=this.ptr;const t=this.data;let i=\"\",n=!1;for(;e<t.length;){var r=t[e],s=0,o=0;if(r<=127?(s=0,o=255&r):r<=223?(s=1,o=31&r):r<=239?(s=2,o=15&r):r<=244&&(s=3,o=7&r),t.length-e-s>0)for(var a=0;a<s;)o=o<<6|63&(r=t[e+a+1]),a+=1;else o=65533,s=t.length-e;e+=s+1;const c=String.fromCodePoint(o);if(\"\\r\"===c)n=!0;else{if(\"\\n\"===c)break;n&&(i+=\"\\r\",n=!1),i+=c}}return this.ptr=e,i}}class Fh{constructor(e){this.config=e,this.filePtr=0,this.bufferPtr=0,this.buffer}async nextLine(){let e;try{for(;;){const t=this.buffer?this.buffer.length:0;for(;this.bufferPtr<t;){const t=String.fromCharCode(this.buffer[this.bufferPtr++]);if(\"\\r\"!==t){if(\"\\n\"===t)return e;e=e?e+t:t}}if(this.eof)return e;await this.readNextBlock()}}catch(t){return console.warn(t),this.eof=!0,e}}async readNextBlock(){const e=Ua(this.config,{range:{start:this.filePtr,size:26}}),t=ms(await Qs.loadArrayBuffer(this.config.url,e));if(0===t)this.eof=!0,this.buffer=void 0;else{const e=Ua(this.config,{range:{start:this.filePtr,size:t}}),i=await Qs.loadArrayBuffer(this.config.url,e);i.byteLength<t&&(this.eof=!0),this.buffer=gs(i),0==this.buffer.byteLength&&(this.eof=!0),this.bufferPtr=0,this.filePtr+=i.byteLength}}}const vh=e=>{const t=ArrayBuffer.isView(e)?e:new Uint8Array(e);return 1+(t[17]<<8|t[16])};class yh{constructor(e){this.config=e,this.cacheBlocks=0!=e.cacheBlocks,this.cache=void 0}async getData(e,t){const i=e.block,n=t.block,r=0===t.offset,s=await this.getInflatedBlocks(i,n,r);if(1===s.length)return s[0];let o=0;for(const e of s)o+=e.byteLength;const a=new Uint8Array(o);let c=0;for(const e of s)a.set(e,c),c+=e.byteLength;return a}async getInflatedBlocks(e,t,i){if(this.cacheBlocks){const n=this.cache;if(n&&n.startBlock<=e&&(n.endBlock>=t||i&&n.nextEndBlock===t)){const i=e-n.startBlock,r=t-n.startBlock;return Ch(n.buffer,i,r)}{let r;if(!n||n.startBlock>t||n.endBlock<e)r=await this.loadBLockData(e,t,{skipEnd:i});else{const s=[];if(e<n.startBlock){const t=await this.loadBLockData(e,n.startBlock,{skipEnd:!0});s.push(t)}let o;if(e<=n.startBlock&&t>=n.endBlock)o=n.buffer;else{const i=Math.max(0,e-n.startBlock);let r;if(t>=n.endBlock)r=n.buffer.byteLength;else{const e=Ah(n.buffer);for(let i=0;i<e.length-1;i++)if(n.startBlock+e[i]===t){r=e[i+1];break}}o=n.buffer.slice(i,r)}if(s.push(o),t>n.endBlock){const e=await this.loadBLockData(n.endBlock,t,{skipStart:!0,skipEnd:i});s.push(e)}r=function(e){if(1===e.length)return e[0];let t=0;for(const i of e)t+=i.byteLength;const i=new Uint8Array(t);let n=0;for(const t of e)i.set(new Uint8Array(t),n),n+=t.byteLength;return i.buffer}(s)}let s=t;if(i){const e=Ah(r);t=e[e.length-1]}return this.cache={startBlock:e,endBlock:t,nextEndBlock:s,buffer:r},Ch(r)}}return Ch(await this.loadBLockData(e,t,{skipEnd:i}))}async loadBLockData(e,t,i){const n=this.config,r=i&&i.skipStart;let s=0;if(!(i&&i.skipEnd)){const e=Ua(n,{range:{start:t,size:26}}),i=await Qs.loadArrayBuffer(n.url,e);s=vh(i)}if(r){const t=Ua(n,{range:{start:e,size:26}}),i=await Qs.loadArrayBuffer(n.url,t);e+=vh(i)}const o=Ua(n,{range:{start:e,size:t+s-e}});return Qs.loadArrayBuffer(n.url,o)}}function Ah(e){const t=e.byteLength;let i=0;const n=[0];for(;i<t;){const r=new Uint8Array(e,i);i+=1+(r[17]<<8|r[16]),i<t&&n.push(i)}return n}function Ch(e,t,i){const n=[];let r=t=t||0;const s=e.byteLength-18;for(;r<s;)try{const t=new Uint8Array(e,r,18),s=t[11]<<8|t[10],o=t[17]<<8|t[16],a=12+s+r,c=e.byteLength-a,l=o-s-18;if(c<l||l<=0)break;const h=new Uint8Array(e,a,l),d=hs(h);if(n.push(d),i===r)break;r+=o+1}catch(e){console.error(e);break}return n}const _h=Math.log10(Number.MIN_VALUE);class xh{chrCol=-1;snpCol=-1;posCol=-1;pValueCol=-1;phenotypeColumn=-1;delimiter=\"\\t\";constructor(e){this.config=e}async parseHeader(e){const t=this.config;t.delimiter&&(this.delimiter=t.delimiter);const i=await e.nextLine(),n=this.parseHeaderLine(i);return t.chrColumn&&(this.chrColumn=t.chrColumn-1),t.snpColumn&&(this.snpColumn=t.snpColumn-1),t.posColumn&&(this.posColumn=t.posColumn-1),t.pValueColumn&&(this.pValueColumn=t.pValueColumn-1),t.phenotypeColumn&&(this.phenotypeColumn=t.phenotypeColumn-1),n}parseHeaderLine(e){this.columns=e.split(this.delimiter);for(let e=0;e<this.columns.length;e++){switch(this.columns[e].toLowerCase()){case\"chr\":case\"chromosome\":case\"chr_id\":case\"chrom\":this.chrColumn=e;break;case\"bp\":case\"pos\":case\"position\":case\"chr_pos\":case\"chromEnd\":this.posColumn=e;break;case\"p\":case\"pval\":case\"pvalue\":case\"p-value\":case\"p.value\":this.pValueColumn=e;break;case\"rsid\":case\"variant\":case\"snp\":this.snpColumn=e;break;case\"phenotype\":case\"gene\":case\"gene_id\":case\"molecular_trait_id\":this.phenotypeColumn=e}}return this.columns}async parseFeatures(e){const t=[],i=e.nextLine();let n;this.columns||this.parseHeaderLine(i);const r=e=>{const t=e.indexOf(\"E\");if(t>0){if(Number.parseInt(e.substring(t+1))<_h)return Number.MIN_VALUE}return Number(e)};for(;void 0!==(n=e.nextLine());){const e=n.split(this.delimiter);if(e.length===this.columns.length){const i=e[this.posColumn];if(i.indexOf(\";\")>0||0==i.length||i.indexOf(\"x\")>0)continue;const n=e[this.chrColumn],s=r(e[this.pValueColumn]),o=parseInt(i)-1,a=o+1,c=e[this.snpColumn],l=e[this.phenotypeColumn],h=new kh({chr:n,start:o,end:a,pValue:s,snp:c,phenotype:l},this.columns,e);t.push(h)}}return t}static isQTL(e){const t=e.split(\"\\t\");if(t.length<5)return!1;const i=[[\"chr\",\"chromosome\",\"chr_id\",\"chrom\"],[\"bp\",\"pos\",\"position\",\"chr_pos\",\"chromEnd\"],[\"p\",\"pval\",\"p-value\",\"p.value\"],[\"rsid\",\"variant\",\"snp\"],[\"phenotype\",\"gene\",\"gene_id\",\"molecular_trait_id\"]];for(let e of i)if(!t.some((t=>e.includes(t.toLowerCase()))))return!1;return!0}}class kh{constructor({chr:e,start:t,end:i,pValue:n,snp:r,phenotype:s},o,a){this.chr=e,this.start=t,this.end=i,this.pValue=n,this.snp=r,this.phenotype=s,this.headers=o,this.tokens=a}popupData(){const e=[];for(let t=0;t<this.headers.length;t++)e.push({name:this.headers[t],value:this.tokens[t]});return e}}class Ih{sequenceNames;constructor(e,t){if(this.config=e||{},this.genome=t,this.indexURL=e.indexURL,this.indexed=e.indexed||void 0!==this.indexURL,this.queryable=this.indexed,Ht(this.config.url))this.filename=this.config.url.name;else if(Ga(this.config.url))this.indexed=!1,this.dataURI=e.url;else{const t=Ot(this.config.url);this.filename=e.filename||t.file}this.parser=this.getParser(this.config),\"vcf\"!==this.config.format||this.config.indexURL||console.warn(\"Warning: index file not specified.  The entire vcf file will be loaded.\")}async defaultVisibilityWindow(){if(this.config.indexURL){const e=await this.getIndex();if(e&&e.lastBlockPosition){let t=0;const i=1e4;for(let i of e.sequenceNames){const e=this.genome.getChromosome(i);e&&(t+=e.bpLength)}return Math.round(t/e.lastBlockPosition*i)}}}async readFeatures(e,t,i){let n;this.dataURI||this.header||await this.readHeader();return await this.getIndex()?(this.indexed=!0,n=await this.loadFeaturesWithIndex(e,t,i)):this.dataURI?(this.indexed=!1,n=await this.loadFeaturesFromDataURI()):\"service\"===this.config.sourceType?n=await this.loadFeaturesFromService(e,t,i):(this.indexed=!1,n=await this.loadFeaturesNoIndex()),n.sort((function(e,t){return e.chr===t.chr?e.start-t.start:e.chr.localeCompare(t.chr)})),n}async readHeader(){if(this.dataURI)return await this.loadFeaturesFromDataURI(this.dataURI),this.header;if(this.config.indexURL){const e=await this.getIndex();if(!e)throw new Error(\"Unable to load index: \"+this.config.indexURL);let t;if(this.sequenceNames=new Set(e.sequenceNames),e.tabix)this._blockLoader=new yh(this.config),t=new Fh(this.config);else{const i=Object.values(e.chrIndex).flatMap((e=>e.blocks)).map((e=>e.max)).reduce(((e,t)=>Math.min(e,t)),Number.MAX_SAFE_INTEGER),n=Ua(this.config,{bgz:e.tabix,range:{start:0,size:i}});t=mh(await Qs.loadString(this.config.url,n))}return this.header=await this.parser.parseHeader(t),this.header}if(\"service\"!==this.config.sourceType){let e;if(this.config._filecontents)e=this.config._filecontents,delete this.config._filecontents;else{const t=Ua(this.config);e=await Qs.loadByteArray(this.config.url,t)}e.length<5e8&&(e=(new TextDecoder).decode(e));let t=mh(e);this.header=await this.parser.parseHeader(t),t=mh(e),this.features=await this.parser.parseFeatures(t),this.sequenceNames=new Set;for(let e of this.features)this.sequenceNames.add(e.chr);return this.header}if(this.config.seqnamesURL){const e=Ua(this.config,{}),t=await Qs.loadString(this.config.seqnamesURL,e);t&&(this.sequenceNames=new Set(t.split(\",\").map((e=>e.trim())).filter((e=>e))))}if(this.config.headerURL){const e=Ua(this.config,{}),t=mh(await Qs.loadString(this.config.headerURL,e));return this.header=await this.parser.parseHeader(t),this.header}}getParser(e){switch(e.format){case\"vcf\":return new Yl(e);case\"seg\":return new Ul(\"seg\");case\"mut\":return new Ul(\"mut\");case\"maf\":return new Ul(\"maf\");case\"gwas\":return new Jl(e);case\"qtl\":return new xh(e);case\"aed\":return new nh(e);default:return new El(e)}}async loadFeaturesNoIndex(){if(this.features){const e=this.features;return delete this.features,e}{const e=Ua(this.config),t=await Qs.loadByteArray(this.config.url,e);if(!this.header){const e=mh(t);this.header=await this.parser.parseHeader(e)}const i=mh(t),n=[];return await this._parse(n,i),n}}async loadFeaturesWithIndex(e,t,i){const n=this.config;this.parser;const r=this.index.tabix,s=r?this.index.sequenceIndexMap[e]:e;if(void 0===s)return[];const o=this.index.chunksForRange(s,t,i);if(o&&0!==o.length){const s=[];for(let a of o){let o;if(r)o=await this._blockLoader.getData(a.minv,a.maxv);else{const e=Ua(n,{range:{start:a.minv.block,size:a.maxv.block-a.minv.block+1}});o=await Qs.loadString(n.url,e)}const c=mh(a.minv.offset?o.slice(a.minv.offset):o);await this._parse(s,c,e,i,t)}return s}return[]}async loadFeaturesFromService(e,t,i){let n;n=\"function\"==typeof this.config.url?this.config.url({chr:e,start:t,end:i}):this.config.url.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i);const r=Ua(this.config),s=mh(await Qs.loadString(n,r)),o=[];return await this._parse(o,s),o}async _parse(e,t,i,n,r){let s=await this.parser.parseFeatures(t);if(s.sort((function(e,t){return e.chr===t.chr?e.start-t.start:e.chr.localeCompare(t.chr)})),void 0===i)for(let t of s)e.push(t);else{let t=!1;for(let o=0;o<s.length;o++){const a=s[o];if(a.chr===i){if(a.start>n){e.push(a);break}a.end>=r&&a.start<=n&&(t||(t=!0,o>0&&e.push(s[o-1])),e.push(a))}}}}async getIndex(){return this.index?this.index:this.config.indexURL?(this.index=await this.loadIndex(),this.index):void 0}async loadIndex(){return gh(this.config.indexURL,this.config)}async loadFeaturesFromDataURI(){if(this.features){const e=this.features;return delete this.features,e}{const e=vs(this.dataURI);let t=mh(e);this.header=await this.parser.parseHeader(t),this.header instanceof String&&this.header.startsWith(\"##gff-version 3\")&&(this.format=\"gff3\"),t=mh(e);const i=[];return await this._parse(i,t),i}}}const Sh=Mt;class Eh{constructor(e){this.config=e}async readFeatures(e,t,i){let n;n=\"function\"==typeof this.config.url?this.config.url({chr:e,start:t,end:i}):this.config.url.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i);let r,s=Object.assign({},this.config);void 0!==this.config.body&&(\"function\"==typeof this.config.body?s.body=this.config.body({chr:e,start:t,end:i}):s.body=this.config.body.replace(\"$CHR\",e).replace(\"$START\",t).replace(\"$END\",i));const o=await Qs.load(n,s);if(o&&(r=\"function\"==typeof this.config.parser?this.config.parser(o):Sh(o)?JSON.parse(o):o),this.config.mappings){let e=Object.keys(this.config.mappings);for(let t of r)for(let i of e)t[i]=t[this.config.mappings[i]]}return r}}const Nh=function(e,t){this.config=e,this.genome=t,this.expandQueryInterval=!1};Nh.prototype.readFeatures=function(e,t,i){const n=Math.max(0,Math.floor(t));let r=Math.ceil(i);if(this.genome){const t=this.genome.getChromosome(e);t&&r>t.bpLength&&(r=t.bpLength)}const s=this.config.url+\"?db=\"+this.config.db+\"&table=\"+this.config.tableName+\"&chr=\"+e+\"&start=\"+n+\"&end=\"+r;return Qs.loadJson(s,this.config).then((function(e){return e?(e.forEach((function(e){e.hasOwnProperty(\"exonStarts\")&&e.hasOwnProperty(\"exonEnds\")&&e.hasOwnProperty(\"exonCount\")&&e.hasOwnProperty(\"cdsStart\")&&e.hasOwnProperty(\"cdsEnd\")&&function(e){var t,i,n,r,s,o;t=e.exonCount,i=e.exonStarts.split(\",\"),n=e.exonEnds.split(\",\"),r=[];for(var a=0;a<t;a++){var c={start:s=parseInt(i[a]),end:o=parseInt(n[a])};(e.cdsStart>o||e.cdsEnd<e.cdsStart)&&(c.utr=!0),e.cdsStart>=s&&e.cdsStart<=o&&(c.cdStart=e.cdsStart),e.cdsEnd>=s&&e.cdsEnd<=o&&(c.cdEnd=e.cdsEnd),r.push(c)}e.exons=r}(e)})),e):null}))};class Bh{featureCaches=[];gtexChrs=new Set([\"chr1\",\"chr10\",\"chr11\",\"chr12\",\"chr13\",\"chr14\",\"chr15\",\"chr16\",\"chr17\",\"chr18\",\"chr19\",\"chr2\",\"chr20\",\"chr21\",\"chr22\",\"chr3\",\"chr4\",\"chr5\",\"chr6\",\"chr7\",\"chr8\",\"chr9\",\"chrM\",\"chrX\",\"chrY\"]);constructor(e){this.config=e,this.url=e.url,this.tissueId=e.tissueSiteDetailId,this.datasetId=e.datasetId||\"gtex_v8\"}async readFeatures(e,t,i){const n=e.startsWith(\"chr\")?e:\"MT\"===e?\"chrM\":\"chr\"+e;if(!this.gtexChrs.has(n))return[];const r=Math.floor(t),s=Math.ceil(i),o=this.datasetId,a=this.url+\"?chromosome=\"+n+\"&start=\"+r+\"&end=\"+s+\"&tissueSiteDetailId=\"+this.tissueId+\"&datasetId=\"+o,c=await Qs.loadJson(a,{withCredentials:this.config.withCredentials});return c&&c.singleTissueEqtl?c.singleTissueEqtl.map((e=>new Mh(e))):[]}}class Mh{constructor(e){this.chr=e.chromosome,this.start=e.pos-1,this.end=this.start+1,this.snp=e.snpId,this.phenotype=e.geneSymbol,this.pValue=e.pValue,this.json=e}popupData(){return Object.keys(this.json).map((e=>({name:e,value:this.json[e]})))}}class Rh{constructor(e,t){if(this.config=e,this.genome=t,!e.format)throw Error('Format is required, and must be either \"bam\" or \"cram\"');if(this.format=e.format.toUpperCase(),\"BAM\"!==this.format&&\"VCF\"!==this.format)throw Error(`htsget format ${e.format} is not supported`)}async readHeaderData(){const e=`${Dh(this.config)}?class=header&format=${this.format}`,t=await Qs.loadJson(e,Ua(this.config));return await this.loadUrls(t.htsget.urls)}async readData(e,t,i){const n=`${Dh(this.config)}?format=${this.format}&referenceName=${e}&start=${Math.floor(t)}&end=${Math.ceil(i)}`,r=await Qs.loadJson(n,Ua(this.config));return this.loadUrls(r.htsget.urls)}async loadUrls(e){const t=[];for(let i of e)if(i.url.startsWith(\"data:\"))t.push(Promise.resolve(Th(i.url)));else{const e=Ua(this.config||{});i.headers&&(e.headers=Object.assign(e.headers||{},i.headers)),t.push(Qs.loadArrayBuffer(i.url,e))}return function(e){let t=0;for(let i of e)t+=i.byteLength;let i=0;const n=new Uint8Array(t);for(let t of e){const e=new Uint8Array(t);n.set(e,i),i+=e.length}return n}(await Promise.all(t))}static async inferFormat(e){try{const t=Dh(e),i=`${t}${t.includes(\"?\")?\"&\":\"?\"}class=header`,n=await Qs.loadJson(i,Ua(e));if(n.htsget){const t=n.htsget.format;if(\"BAM\"!==t&&\"VCF\"!==t)throw Error(`htsget format ${t} is not supported`);e.format=t.toLowerCase(),e.sourceType=\"htsget\",e.name||(e.name=await ja(e.url))}}catch(e){}}}function Dh(e){if(e.url&&e.endpoint&&e.id)return e.url+e.endpoint+e.id;if(e.endpoint&&e.id)return e.endpoint+e.id;if(e.url)return e.url.startsWith(\"htsget://\")?e.url.replace(\"htsget://\",\"https://\"):e.url;throw Error(\"Must specify either 'url', or 'endpoint' and 'id\")}function Th(e){const t=e.split(\",\"),i=t[0].split(\":\")[1];let n=t[1];n=i.indexOf(\"base64\")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s<n.length;s++)r[s]=n.charCodeAt(s);return r}class Lh extends Rh{constructor(e,t){super(e,t),this.parser=new Yl}async readHeader(){if(!this.header){let e=await this.readHeaderData();fs(e)&&(e=ps(e));const t=mh(e);this.header=await this.parser.parseHeader(t,this.genome),this.chrAliasTable=this.header.chrAliasTable}return this.header}async readFeatures(e,t,i){if(this.config.format&&\"VCF\"!==this.config.format.toUpperCase())throw Error(`htsget format ${this.config.format} is not supported`);this.chrAliasTable||await this.readHeader();let n=this.chrAliasTable.has(e)?this.chrAliasTable.get(e):e,r=await this.readData(n,t,i);fs(r)&&(r=ps(r));const s=mh(r);return this.parser.parseFeatures(s)}}class zh{chrAliasTable=new Map;constructor(e,t){this.sequenceNames=new Set(e),this.genome=t}async getAliasName(e){if(!this.genome)return e;if(!this.chrAliasTable.has(e)){const t=await this.genome.getAliasRecord(e);if(t){let i;const n=Object.keys(t).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>t[e])).filter((e=>this.sequenceNames.has(e)));n.length>0&&(i=n[0]),this.chrAliasTable.set(e,i)}else this.chrAliasTable.set(e,void 0)}return this.chrAliasTable.get(e)}}class Hh{constructor(e){this.genome=e}async nextFeature(e,t,i,n){let r=this.genome.chromosomeNames||[e],s=r.indexOf(e);if(s<0)return;const o=Math.min(1e4,n||1e4);let a=i?t:Math.max(t-o,0);for(;s<r.length&&s>=0;){e=r[s];const c=this.genome.getChromosome(e).bpLength;for(;a<c&&a>=0;){let r=i?a+o:Math.min(t,a+o);const s=await this.getFeatures({chr:e,start:a,end:r,visibilityWindow:n});if(s){const e=(e,t)=>e.start-t.start+e.end-t.end,n=Array.from(s);n.sort(e);let r=i?0:n.length-1;for(;r>=0&&r<n.length;){const e=n[r],s=(e.start+e.end)/2;if(i){if(s>t)return e;r++}else{if(s<t)return e;r--}}}a=i?r:a-o}if(i)s++,a=0,t=0;else{if(s--,s<0)break;a=(t=this.genome.getChromosome(r[s]).bpLength)-o}}}async previousFeature(e,t,i,n){let r=this.genome.chromosomeNames||[e],s=r.indexOf(e);if(s<0)return;const o=Math.min(1e4,n||1e4);let a=i?t:Math.max(t-o,0);for(;s<r.length&&s>=0;){e=r[s];const c=this.genome.getChromosome(e).bpLength;for(;a<c&&a>=0;){let r=Math.min(t,a+o);const s=await this.getFeatures({chr:e,start:a,end:r,visibilityWindow:n});if(s){const e=(e,t)=>e.start-t.start+e.end-t.end,n=Array.from(s);n.sort(e);let r=i?0:n.length-1;for(;r>=0&&r<n.length;){const e=n[r],s=(e.start+e.end)/2;if(i){if(s>t)return e;r++}else{if(s<t)return e;r--}}}a=i?r:a-o}if(i)s++,a=0,t=0;else{if(s--,s<0)break;a=(t=this.genome.getChromosome(r[s]).bpLength)-o}}}}class Ph{constructor(e,t){this.config=e,this.genome=t,this.path=e.url,this.groupCache={},this.datasetCache={}}async readHeader(){if(void 0!==this.magic)return this;let e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:0,size:64e3}})),t=new yc(new DataView(e));if(this.magic=t.getInt(),this.version=t.getInt(),this.indexPos=t.getLong(),this.indexSize=t.getInt(),t.getInt(),this.version>=2){let e=t.getInt();for(this.windowFunctions=[];e-- >0;)this.windowFunctions.push(t.getString())}this.trackType=t.getString(),this.trackLine=t.getString();let i=t.getInt();for(this.trackNames=[];i-- >0;)this.trackNames.push(t.getString());this.genomeID=t.getString(),this.flags=t.getInt(),this.compressed=!!(1&this.flags),e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:this.indexPos,size:this.indexSize}})),t=new yc(new DataView(e)),this.datasetIndex={};let n=t.getInt();for(;n-- >0;){const e=t.getString(),i=t.getLong(),n=t.getInt();this.datasetIndex[e]={position:i,size:n}}for(this.groupIndex={},n=t.getInt();n-- >0;){const e=t.getString(),i=t.getLong(),n=t.getInt();this.groupIndex[e]={position:i,size:n}}return this}async readDataset(e,t,i){const n=e+\"_\"+t+\"_\"+i;if(this.datasetCache[n])return this.datasetCache[n];{await this.readHeader();const r=this.version<2?\"\":\"/\"+t,s=\"all\"===e.toLowerCase()||void 0===i?\"0\":i.toString();let o;o=\"raw\"===t?\"/\"+e+\"/raw\":\"/\"+e+\"/z\"+s+r;const a=this.datasetIndex[o];if(void 0===a)return;const c=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:a.position,size:a.size}}));if(!c)return;const l=new yc(new DataView(c));let h=l.getInt();const d={};for(;h-- >0;)d[l.getString()]=l.getString();const u=l.getString(),f=l.getFloat();let p=l.getInt();const g=[];for(;p-- >0;)g.push({position:l.getLong(),size:l.getInt()});const m={name:o,attributes:d,dataType:u,tileWidth:f,tiles:g};return this.datasetCache[n]=m,m}}async readRootGroup(){const e=this.genome,t=this.groupCache[\"/\"];if(t)return t;{const t=await this.readGroup(\"/\"),i=t.chromosomes,n=t.maxZoom;n&&(this.maxZoom=Number(n));const r=t.totalCount;r&&(t.totalCount=Number(r));const s={};return i&&i.split(\",\").forEach((function(t){const i=e.getChromosomeName(t);s[i]=t})),this.chrAliasTable=s,this.groupCache[\"/\"]=t,t}}async readGroup(e){const t=this.groupCache[e];if(t)return t;{await this.readHeader();const t=this.groupIndex[e];if(void 0===t)return;const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:t.position,size:t.size}}));if(!i)return;const n=new yc(new DataView(i)),r={name:e};let s=n.getInt();for(;s-- >0;){const e=n.getString(),t=n.getString();r[e]=t}return this.groupCache[e]=r,r}}async readTiles(e,t){if(e.sort((function(e,t){return e.position-t.position})),0===(e=e.filter((function(e){return e.size>0}))).length)return[];const i=[];for(let n of e){const e=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:n.position,size:n.size}}));let r;try{r=this.compressed?ls(e).buffer:e}catch(e){console.error(e);continue}const s=new yc(new DataView(r)),o=s.getString();let a;switch(o){case\"fixedStep\":a=Oh(s,t);break;case\"variableStep\":a=Uh(s,t);break;case\"bed\":case\"bedWithName\":a=qh(s,t,o);break;default:throw\"Unknown tile type: \"+o}i.push(a)}return i}async readTile(e,t){let i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e.position,size:e.size}}));if(this.compressed){i=ls(i).buffer}const n=new yc(new DataView(i)),r=n.getString();switch(r){case\"fixedStep\":return Oh(n,t);case\"variableStep\":return Uh(n,t);case\"bed\":case\"bedWithName\":return qh(n,t,r);default:throw\"Unknown tile type: \"+r}}}function Oh(e,t){const i=e.getInt(),n=e.getInt(),r=e.getFloat(),s=[];let o=t;for(;o-- >0;){let t=i;const n=[];for(;t-- >0;)n.push(e.getFloat());s.push(n)}return{type:\"fixedStep\",start:n,span:r,data:s,nTracks:t,nPositions:i}}function Uh(e,t){const i=e.getInt(),n=e.getFloat(),r=e.getInt(),s=[];let o=r;for(;o-- >0;)s.push(e.getInt());e.getInt();const a=[];let c=t;for(;c-- >0;){o=r;const t=[];for(;o-- >0;)t.push(e.getFloat());a.push(t)}return{type:\"variableStep\",tileStart:i,span:n,start:s,data:a,nTracks:t,nPositions:r}}function qh(e,t,i){const n=e.getInt();let r=n;const s=[];for(;r-- >0;)s.push(e.getInt());r=n;const o=[];for(;r-- >0;)o.push(e.getInt());e.getInt();const a=[];let c=t;for(;c-- >0;){let t=n;const i=[];for(;t-- >0;)i.push(e.getFloat());a.push(i)}if(\"bedWithName\"===i){r=n;const t=[];for(;r-- >0;)t.push(e.getString())}return{type:i,start:s,end:o,data:a,nTracks:t,nPositions:n}}class Qh extends Hh{#h={};searchable=!1;constructor(e,t){super(t),this.genome=t,this.reader=new Ph(e,t),this.queryable=!0}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,windowFunction:r=\"mean\"}){return\"all\"===e.toLowerCase()?this.getWGValues(r,n):this._getFeatures(e,t,i,n,r)}async _getFeatures(e,t,i,n,r){const s=new hc(e,t,i),o=this.genome;if(!this.rootGroup&&(this.rootGroup=await this.reader.readRootGroup(),!this.normalizationFactor)){const e=this.rootGroup.totalCount;e&&(this.normalizationFactor=1e6/e)}s.bpPerPixel=n;const a=function(e,t,i){var n=i.getChromosome(e).bpLength;return Math.ceil(Math.log(Math.max(0,n/(700*t)))/Gh)}(e,n,o);let c=this.reader.chrAliasTable[e],l=this.reader.maxZoom;void 0===c&&(c=e),void 0===l&&(l=-1);const h=a>l?\"raw\":r,d=await this.reader.readDataset(c,h,a);if(null==d)return[];const u=d.tileWidth,f=Math.floor(t/u),p=Math.floor(i/u),g=await this.reader.readTiles(d.tiles.slice(f,p+1),1),m=[];for(let r of g)switch(r.type){case\"bed\":Vh(r,e,t,i,n,m);break;case\"variableStep\":jh(r,e,t,i,n,m);break;case\"fixedStep\":Wh(r,e,t,i,n,m);break;default:throw\"Unknown tile type: \"+r.type}return m.sort((function(e,t){return e.start-t.start})),m}get supportsWholeGenome(){return!0}get windowFunctions(){return this.reader.windowFunctions}async getWGValues(e,t){const i=this.#h[e];if(i&&i.bpPerPixel>.8*t&&i.bpPerPixel<1.2*t)return i.values;{const i=[],n=this.genome;if(this.genome.wgChromosomeNames)for(let r of n.wgChromosomeNames){const s=n.getChromosome(r).bpLength;t=s/1e3;const o=await this._getFeatures(r,0,s,t,e);if(o)for(let e of o){const t=Object.assign({},e);t.chr=\"all\",t.start=n.getGenomeCoordinate(e.chr,e.start),t.end=n.getGenomeCoordinate(e.chr,e.end),t._f=e,i.push(t)}}return this.#h[e]={values:i,bpPerPixel:t},i}}}function Vh(e,t,i,n,r,s){const o=e.nPositions,a=e.start,c=e.end,l=e.data[0];for(let e=0;e<o;e++){const r=a[e],o=c[e];if(!(o<i)){if(r>n)break;s.push({chr:t,start:r,end:o,value:l[e]})}}}function jh(e,t,i,n,r,s){const o=e.nPositions,a=e.start,c=e.span,l=e.data[0];for(let e=0;e<o;e++){const r=a[e],o=r+c;if(!(o<i)){if(r>n)break;s.push({chr:t,start:r,end:o,value:l[e]})}}}function Wh(e,t,i,n,r,s){const o=e.nPositions;let a=e.start;const c=e.span,l=e.data[0];for(let e=0;e<o;e++){const r=a+c;if(a>n)break;r>=i&&(Number.isNaN(l[e])||s.push({chr:t,start:a,end:r,value:l[e]})),a=r}}var Gh=Math.log(2);class $h{constructor(e,t,i,n){this.header=e,this.nameToId=t,this.idToName=i,this.sumLengths=n}static parseTree(e,t,i=!1){{const n=e.getInt(),r=e.getInt(),s=e.getInt(),o=e.getInt(),a=e.getLong(),c=e.getLong(),l={magic:n,blockSize:r,keySize:s,valSize:o,itemCount:a,reserved:c},h=new Map,d=[];let u=0;const f=n=>{n>=0&&(e.position=n);const r=e.getByte();e.getByte();const a=e.getUShort();if(1===r)for(let t=0;t<a;t++){let t,n=e.getFixedLengthString(s);if(8!==o)throw Error(`Unexpected \"valSize\" value in chromosome tree.  Expected 8, actual value is ${o}`);{t=e.getInt();const r=e.getInt();u+=r,i&&(n=i.getChromosomeName(n)),h.set(n,t),d[t]=n}}else for(let i=0;i<a;i++){e.getFixedLengthString(s);const i=e.getLong()-t,n=e.position;f(i),e.position=n}};return f(-1),new $h(l,h,d,u)}}}class Kh{static magic=610839776;littleEndian=!0;nodeCache=new Map;constructor(e,t,i){this.path=e,this.config=t,this.startOffset=i}async init(){const e=await this.#t(this.startOffset,48);let t=e.getInt();if(t!==Kh.magic&&(e.setPosition(0),this.littleEndian=!this.littleEndian,e.littleEndian=this.littleEndian,t=e.getInt(),t!==Kh.magic))throw Error(`Bad magic number ${t}`);const i=e.getUInt(),n=e.getLong(),r=e.getUInt(),s=e.getUInt(),o=e.getUInt(),a=e.getUInt(),c=e.getLong(),l=e.getUInt(),h=e.getUInt(),d=this.startOffset+48;return this.header={magic:t,blockSize:i,itemCount:n,startChromIx:r,startBase:s,endChromIx:o,endBase:a,endFileOffset:c,itemsPerSlot:l,reserved:h,rootNodeOffset:d},this}async#t(e,t){const i=await Qs.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:t}}));return new yc(new DataView(i),this.littleEndian)}async findLeafItemsOverlapping(e,t,i,n){const r=[],s=async o=>{const a=await this.readNode(o);for(let o of a.items)Yh(o,e,t,i,n)&&(1===a.type?r.push(o):await s(o.childOffset))};return await s(this.header.rootNodeOffset),r}async readNode(e){const t=e;if(this.nodeCache.has(t))return this.nodeCache.get(t);let i=await this.#t(e,4);const n=i.getByte(),r=1===n;i.getByte();const s=i.getUShort();let o=s*(r?32:24);i=await this.#t(e+4,o);const a=[];for(let e=0;e<s;e++){let e={isLeaf:r,startChrom:i.getInt(),startBase:i.getInt(),endChrom:i.getInt(),endBase:i.getInt(),childOffset:i.getLong()};r&&(e.dataSize=i.getLong(),e.dataOffset=e.childOffset),a.push(e)}const c={type:n,items:a};return this.nodeCache.set(t,c),c}}function Yh(e,t,i,n,r){return e?(n>e.startChrom||n===e.startChrom&&r>=e.startBase)&&(t<e.endChrom||t===e.endChrom&&i<=e.endBase):(console.log(\"null item for \"+t+\" \"+i+\" \"+r),!1)}class Xh{ixFile;ixxFile;bufferCache=new Map;constructor(e,t){this.ixFile=t,this.ixxFile=e}async search(e,t){const i=e.split(\" \")[0].toLowerCase(),n=await this._getBuffer(i,t);if(!n)return;const r=n.slice(0,n.lastIndexOf(\"\\n\")).split(\"\\n\").filter((e=>!!e)),s=[];for(let e of r){const t=e.split(\" \")[0];if(t.startsWith(i)&&s.push(e),t.slice(0,i.length)>i)break}if(0!==s.length){const e=new Map;for(let t of s){const[i,...n]=t.split(\" \");e.set(i,n.map((e=>e.split(\",\")[0])))}return e}}async getIndex(e){return this.index||(this.index=await this._readIndex()),this.index}async _readIndex(e){return(await Qs.loadString(this.ixxFile)).split(\"\\n\").filter((e=>!!e)).map((e=>{const t=e.length-10,i=e.slice(0,t),n=e.slice(t);return[i,Number.parseInt(n,16)]}))}async _getBuffer(e,t){let i=0,n=65536;const r=await this.getIndex(t);for(let t=0;t<r.length;t++){const[s,o]=r[t],a=Math.min(s.length,e.length);s.slice(0,a)<e&&(i=o,n=o+65536)}const s=n-i;if(!(s<0)){if(this.bufferCache.has(i))return this.bufferCache.get(i);{const e=await Qs.loadString(this.ixFile,{range:{start:i,size:s}});return this.bufferCache.set(i,e),e}}}}class Zh{chrAliasTable=new Map;rpTreeCache=new Map;constructor(e,t){this.path=e.url,this.format=e.format||\"bigwig\",this.genome=t,this.config=e,this.bufferSize=512e3,this.loader=Ga(this.path)?new sd(vs(this.path).buffer):Qs;const i=e.trixURL||e.searchTrix;i&&(this._trix=new Xh(`${i}x`,i))}async preload(){const e=await Qs.loadArrayBuffer(this.path);this.loader=new sd(e)}async readWGFeatures(e,t){await this.loadHeader();const i=this.chromTree.idToName.length-1,n=this.chromTree.idToName[0],r=this.chromTree.idToName[i];return this.readFeatures(n,0,r,Number.MAX_VALUE,e,t)}async readFeatures(e,t,i,n,r,s=\"mean\"){t||(t=0),n||(n=Number.MAX_SAFE_INTEGER),await this.loadHeader();let o,a,c=await this.#d(e),l=await this.#d(i);if(void 0===c||void 0===l)return[];if(\"bigwig\"===this.type){const e=await this.getZoomHeaders();let t=r?function(e,t){let i;for(let n=0;n<t.length;n++){const r=t[n];if(r.reductionLevel<e){i=r;break}}return i}(r,e):void 0;t&&\"none\"!=s?(o=t.indexOffset,a=rd):(o=this.header.fullIndexOffset,a=id)}else o=this.header.fullIndexOffset,a=nd.call(this);const h=await this.loadRPTree(o),d=await h.findLeafItemsOverlapping(c,t,l,n);if(d&&0!==d.length){let e=Number.MAX_VALUE,i=0;for(let t of d)e=Math.min(e,t.dataOffset),i=Math.max(i,t.dataOffset+t.dataSize);const r=i-e,o=await this.loader.loadArrayBuffer(this.config.url,Ua(this.config,{range:{start:e,size:r}})),h=[];for(let i of d){const r=new Uint8Array(o,i.dataOffset-e,i.dataSize);let d;d=this.header.uncompressBuffSize>0?ls(r):r,a.call(this,new DataView(d.buffer),c,t,l,n,h,this.chromTree.idToName,s,this.littleEndian)}return h.sort((function(e,t){return e.start-t.start})),h}return[]}async#d(e){if(this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.chromTree.nameToId.get(e);if(void 0===t&&this.genome){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>this.chromTree.nameToId.has(e)));e.length>0&&(n=e[0],t=this.chromTree.nameToId.get(e[0]))}this.chrAliasTable.set(e,n)}return t}get searchable(){return\"bigbed\"===this.type}async search(e){if(this.header||await this.loadHeader(),!this.header||!this.header.extraIndexCount)return;const t=await this._searchForRegions(e);if(t){const i=await this._loadFeaturesForRange(t.offset,t.length);if(i){const t=i.filter((t=>{for(let i of Object.keys(t)){const n=t[i];if(Mt(n)&&n.toLowerCase()===e.toLowerCase())return!0}return!1}));return t.length>0?t.reduce(((e,t)=>e.end-e.start>t.end-t.start?e:t),i[0]):void 0}}}async _searchForRegions(e){const t=await this.#u();if(t){if(this._trix){const t=e.toLowerCase(),i=await this._trix.search(t);i&&i.has(t)&&(e=i.get(t)[0])}for(let i of t){const t=await i.search(e);if(t)return t}}}async#u(){if(void 0===this._searchTrees&&this.header.extraIndexOffsets&&this.header.extraIndexOffsets.length>0){this._searchTrees=[];for(let e of this.header.extraIndexOffsets){const t=await Cc.loadBpTree(this.path,this.config,e);this._searchTrees.push(t)}}return this._searchTrees}async getZoomHeaders(){return this.zoomLevelHeaders||await this.loadHeader(),this.zoomLevelHeaders}async loadHeader(){if(this.header)return this.header;{let e,t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:0,size:64}}));this.littleEndian=!0;const i=new yc(new DataView(t),this.littleEndian);let n=i.getUInt();if(2291137574===n)this.type=\"bigwig\";else if(2273964779===n)this.type=\"bigbed\";else{this.littleEndian=!1,i.littleEndian=!1,i.position=0;let e=i.getUInt();654085990===e?this.type=\"bigwig\":3958540679===e&&(this.type=\"bigbed\")}e={bwVersion:i.getUShort(),nZoomLevels:i.getUShort(),chromTreeOffset:i.getLong(),fullDataOffset:i.getLong(),fullIndexOffset:i.getLong(),fieldCount:i.getUShort(),definedFieldCount:i.getUShort(),autoSqlOffset:i.getLong(),totalSummaryOffset:i.getLong(),uncompressBuffSize:i.getInt(),extensionOffset:i.getLong()};const r=64;let s={start:r,size:e.totalSummaryOffset>0?e.totalSummaryOffset-r+40:Math.min(e.fullDataOffset,e.chromTreeOffset)-r};t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:s}));const o=new yc(new DataView(t),this.littleEndian),a=e.nZoomLevels;this.zoomLevelHeaders=[],this.firstZoomDataOffset=Number.MAX_SAFE_INTEGER;for(let e=1;e<=a;e++){const t=a-e,i=new Jh(t,o);this.firstZoomDataOffset=Math.min(i.dataOffset,this.firstZoomDataOffset),this.zoomLevelHeaders[t]=i}if(e.autoSqlOffset>0){o.position=e.autoSqlOffset-r;const t=o.getString();t&&(this.autoSql=function(e){let t;const i=[];let n=!1;const r=e.trim().split(/\\s*[\\r\\n]+\\s*/g);for(let e of r)if(e=e.trim(),e.length>0){if(e.startsWith(\"#\"))continue;if(e.startsWith(\"table\"))t=e.split(/\\s+/)[1].trim();else if(e.startsWith(\"(\"))n=!0;else if(e.startsWith(\")\"));else if(n){const t=e.indexOf(\";\");if(t>0){const n=e.substr(0,t).split(/\\s+/),r=e.substr(t+1).replace(/\"/g,\"\").trim();i.push({type:n[0],name:n[1],description:r})}}}return{table:t,fields:i}}(t))}e.totalSummaryOffset>0&&(o.position=e.totalSummaryOffset-r,this.totalSummary=new ed(o));const c=Math.min(2e5,Math.max(1e4,e.fullDataOffset-e.chromTreeOffset));if(this.chromTree=await this.#f(e.chromTreeOffset,c),this.chrNames=new Set(this.chromTree.idToName),\"bigbed\"===this.type){const t=await this.#p(e.fullDataOffset);this.featureDensity=t/this.chromTree.sumLengths}return this.header=e,e.extensionOffset>0&&await this.loadExtendedHeader(e.extensionOffset),this.header}}async#p(e){const t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:4}}));return new yc(new DataView(t),this.littleEndian).getInt()}async#f(e,t){let i=t;const n=async()=>{const t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:i}})),n=new yc(new DataView(t),this.littleEndian);return $h.parseTree(n,e,this.genome)};let r;for(;i<1e6;)try{return await n()}catch(e){r=e,i*=2}throw r}async loadExtendedHeader(e){let t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:e,size:64}})),i=new yc(new DataView(t),this.littleEndian);i.getUShort();const n=i.getUShort(),r=i.getLong();if(0===n)return;let s=56*n;t=await this.loader.loadArrayBuffer(this.path,Ua(this.config,{range:{start:r,size:s}})),i=new yc(new DataView(t),this.littleEndian);const o=[],a=[],c=[];for(let e=0;e<n;e++){o.push(i.getUShort());const e=i.getUShort();c.push(i.getLong()),a.push(i.getInt());for(let t=0;t<e;t++)i.getUShort(),a.push(i.getUShort())}this.header.extraIndexCount=n,this.header.extraIndexOffsets=c}async loadRPTree(e){let t=this.rpTreeCache.get(e);return t||(t=new Kh(this.path,this.config,e),await t.init(),this.rpTreeCache.set(e,t),t)}async getType(){return await this.loadHeader(),this.type}async getTrackType(){return await this.loadHeader(),\"bigwig\"===this.type?\"wig\":this.autoSql&&\"chromatinInteract\"===this.autoSql.table?\"interact\":\"annotation\"}async _loadFeaturesForRange(e,t){const i=await this.loader.loadArrayBuffer(this.config.url,Ua(this.config,{range:{start:e,size:t}})),n=new Uint8Array(i),r=this.header.uncompressBuffSize>0?ls(n):n,s=[];return nd.call(this).call(this,new DataView(r.buffer),0,0,Number.MAX_SAFE_INTEGER,Number.MAX_SAFE_INTEGER,s,this.chromTree.idToName),s}}class Jh{constructor(e,t){this.index=e,this.reductionLevel=t.getInt(),this.reserved=t.getInt(),this.dataOffset=t.getLong(),this.indexOffset=t.getLong()}}class ed{constructor(e){e?(this.basesCovered=e.getLong(),this.minVal=e.getDouble(),this.maxVal=e.getDouble(),this.sumData=e.getDouble(),this.sumSquares=e.getDouble(),td.call(this)):(this.basesCovered=0,this.minVal=0,this.maxVal=0,this.sumData=0,this.sumSquares=0,this.mean=0,this.stddev=0)}}function td(){let e=this.basesCovered;if(e>0){this.mean=this.sumData/e,this.stddev=Math.sqrt(this.sumSquares/(e-1));let t=this.minVal<0?this.mean-2*this.stddev:0,i=this.maxVal>0?this.mean+2*this.stddev:0;this.defaultRange={min:t,max:i}}}function id(e,t,i,n,r,s,o,a,c){const l=new yc(e,c),h=l.getInt(),d=l.getInt();let u=d,f=l.getInt();const p=l.getInt(),g=l.getInt(),m=l.getByte();l.getByte();let w=l.getUShort();if(h>=t&&h<=n){let e=0;for(;w-- >0;){let a;switch(m){case 1:u=l.getInt(),f=l.getInt(),a=l.getFloat();break;case 2:u=l.getInt(),a=l.getFloat(),f=u+g;break;case 3:a=l.getFloat(),u=d+e*p,f=u+g,e++}if(!(h<t||h===t&&f<i)){if(h>n||h===n&&u>=r)break;if(Number.isFinite(a)){const e=o[h];s.push({chr:e,start:u,end:f,value:a})}}}}}function nd(){const e=function(e,t,i,n){if(\"biginteract\"===n||i&&(\"chromatinInteract\"===i.table||\"interact\"===i.table))return function(e,t){return e.chr1=t[5],e.start1=Number.parseInt(t[6]),e.end1=Number.parseInt(t[7]),e.chr2=t[10],e.start2=Number.parseInt(t[11]),e.end2=Number.parseInt(t[12]),e.name=t[0],e.score=Number(t[1]),e.value=Number(t[2]),e.color=\".\"===t[4]?void 0:\"0\"===t[4]?\"rgb(0,0,0)\":t[4],e};{const n=e-3;return function(r,s){if(n>0&&(r.name=s[0]),n>1&&(r.score=Number(s[1])),n>2&&(r.strand=s[2]),n>3&&(r.cdStart=parseInt(s[3])),n>4&&(r.cdEnd=parseInt(s[4])),n>5&&\".\"!==s[5]&&\"0\"!==s[5]&&\"-1\"!==s[5]){const e=_s.createColorString(s[5]);r.color=e.startsWith(\"rgb\")?e:void 0}if(n>8){const e=parseInt(s[6]),t=s[7].split(\",\"),i=s[8].split(\",\"),n=[];for(let s=0;s<e;s++){const e=r.start+parseInt(i[s]),o=e+parseInt(t[s]);n.push({start:e,end:o})}!function(e,t,i){for(let n of e){const e=n.end,r=n.start;e<t||r>i?n.utr=!0:(t>=r&&t<=e&&(n.cdStart=t),i>=r&&i<=e&&(n.cdEnd=i))}}(n,r.cdStart,r.cdEnd),r.exons=n}if(i)for(let n=e;n<t;n++)if(n<i.fields.length){const e=i.fields[n].name,t=s[n-3];r[e]=t}}}}(this.header.definedFieldCount,this.header.fieldCount,this.autoSql,this.format);return function(t,i,n,r,s,o,a,c,l){const h=new yc(t,l);for(;h.remLength()>=13;){const t=h.getInt(),c=a[t],l=h.getInt(),d=h.getInt(),u=h.getString();if(!(t<i||t===i&&d<n)){if(t>r||t===r&&l>=s)break;if(d>0){const t={chr:c,start:l,end:d};o.push(t);const i=u.split(\"\\t\");e(t,i)}}}}}function rd(e,t,i,n,r,s,o,a,c){const l=new yc(e,c);for(;l.remLength()>=32;){const e=l.getInt(),c=l.getInt(),h=l.getInt(),d=l.getInt(),u=l.getFloat(),f=l.getFloat(),p=l.getFloat();let g;switch(l.getFloat(),a){case\"min\":g=u;break;case\"max\":g=f;break;default:g=0===d?0:p/d}if(!(e<t||e===t&&h<i)){if(e>n||e===n&&c>=r)break;if(Number.isFinite(g)){const t=o[e];s.push({chr:t,start:c,end:h,value:g})}}}}class sd{constructor(e){this.data=e}loadArrayBuffer(e,t){const i=t.range;return i?this.data.slice(i.start,i.start+i.size):this.data}async dataViewForRange(e,t){const i=Math.min(this.data.byteLength-e.start,e.size);return t?new Uint8Array(this.data,e.start,i):new DataView(this.data,e.start,i)}}class od extends Hh{queryable=!0;#h={};windowFunctions=[\"mean\",\"min\",\"max\",\"none\"];constructor(e,t){super(t),this.reader=new Zh(e,t),this.genome=t,this.format=e.format||\"bigwig\"}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,windowFunction:r}){await this.reader.loadHeader();const s=\"bigwig\"===this.reader.type;let o;return o=\"all\"===e.toLowerCase()?s?await this.getWGValues(r,n):[]:await this.reader.readFeatures(e,t,e,i,n,r),s||Tl(o),o}async getHeader(){return this.reader.loadHeader()}async defaultVisibilityWindow(){return\"bigwig\"===this.reader.type?-1:this.reader.featureDensity?Math.floor(1e4/this.reader.featureDensity):-1}async getWGValues(e,t){const i=this.genome,n=this.#h[e];if(n&&n.bpPerPixel>.8*t&&n.bpPerPixel<1.2*t)return n.values;{const n=await this.reader.readWGFeatures(t,e);let r=[];for(let e of n){const t=e.chr,n=i.getCumulativeOffset(t);if(void 0===n)continue;const s=Object.assign({},e);s.chr=\"all\",s.start=n+e.start,s.end=n+e.end,s._f=e,r.push(s)}return r.sort(((e,t)=>e.start-t.start)),this.#h[e]={values:r,bpPerPixel:t},r}}supportsWholeGenome(){return\"bigwig\"===this.reader.type}async trackType(){return this.reader.getTrackType()}get searchable(){return this.reader.searchable}async search(e){return this.reader.search(e)}}const ad=.01;function cd(e,t,i,n){if(void 0===this.dataRange||void 0===this.dataRange.max||void 0===this.dataRange.min)return;xo.fillRect(e,0,0,t,i,{fillStyle:\"white\"}),n&&xo.fillRect(e,t-4-2,0,4,i,{fillStyle:n});const r=void 0!==this.flipAxis&&this.flipAxis,s=.95*t-8-5,o=.95*t-5,a={font:\"normal 10px Arial\",textAlign:\"right\",fillStyle:\"black\",strokeStyle:\"black\"};xo.strokeLine(e,s,ad*i,o,ad*i,a),xo.fillText(e,l(r?this.dataRange.min:this.dataRange.max),s+4,ad*i+12,a);const c=.99*i;function l(e){return 0===e?\"0\":Math.abs(e)>=10?e.toFixed():Math.abs(e)>=1?e.toFixed(1):Math.abs(e)>=.1?e.toFixed(2):e.toExponential(1)}xo.strokeLine(e,s,c,o,c,a),xo.fillText(e,l(r?this.dataRange.max:this.dataRange.min),s+4,c-4,a),xo.strokeLine(e,o,ad*i,o,c,a)}class ld extends Hl{static defaults={height:50,flipAxis:!1,logScale:!1,windowFunction:\"mean\",graphType:\"bar\",normalize:void 0,scaleFactor:void 0,overflowColor:\"rgb(255, 32, 255)\",baselineColor:\"lightGray\",summarize:!0,visibilityWindow:void 0};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"wig\",this.featureType=\"numeric\",this.resolutionAware=!0,this.paintAxis=cd;const t=e.format?e.format.toLowerCase():e.format;e.featureSource?(this.featureSource=e.featureSource,delete e.featureSource):this.featureSource=\"bigwig\"===t?new od(e,this.browser.genome):\"tdf\"===t?new Qh(e,this.browser.genome):Ad(e,this.browser.genome),void 0===e.max||!0===e.autoscale?this.autoscale=!0:this.dataRange={min:e.min||0,max:e.max}}async postInit(){const e=await this.getHeader();this.disposed||e&&this.setTrackProperties(e)}supportsWholeGenome(){return void 0===this.visibilityWindow||this.visibilityWindow<0}async getFeatures(e,t,i,n){const r=this.windowFunction,s=await this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow,windowFunction:r});if(this.normalize&&this.featureSource.normalizationFactor){const e=this.featureSource.normalizationFactor;for(let t of s)t.value*=e}if(this.scaleFactor){const e=this.scaleFactor;for(let t of s)t.value*=e}return!this.summarize||\"mean\"!==r&&\"min\"!==r&&\"max\"!==r?s:hd(s,t,n,r)}menuItemList(){const e=[];if(void 0!==this.flipAxis){function t(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}e.push(\"<hr>\"),e.push({label:\"Flip y-axis\",click:t})}return this.featureSource.windowFunctions&&e.push(...this.wigSummarizationItems()),e.push(...this.numericDataMenuItems()),e}wigSummarizationItems(){const e=this.featureSource.windowFunctions,t=[];t.push(\"<hr/>\"),t.push(\"<div>Windowing function</div>\");for(const i of e){const n=Bt(Dl(i,this.windowFunction===i));function r(){this.windowFunction=i,this.trackView.updateViews()}t.push({object:n,click:r})}return t}async getHeader(){return\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getScaleFactor(e,t,i,n){const r=!0===n?e<0?-Math.log10(Math.abs(e)+1):Math.log10(Math.abs(e)+1):e;return i/((!0===n?Math.log10(Math.abs(t)+1):t)-r)}computeYPixelValue(e,t){return(this.flipAxis?e-this.dataRange.min:this.dataRange.max-e)*t}computeYPixelValueInLogScale(e,t){let i=this.dataRange.max,n=this.dataRange.min;return n=n<0?-Math.log10(Math.abs(n)+1):Math.log10(Math.abs(n)+1),i=i<0?-Math.log10(Math.abs(i)+1):Math.log10(Math.abs(i)+1),e=e<0?-Math.log10(Math.abs(e)+1):Math.log10(e+1),(this.flipAxis?e-n:i-e)*t}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=e.pixelHeight-1,a=r+s*n+1,c=this.getScaleFactor(this.dataRange.min,this.dataRange.max,o,this.logScale),l=e=>this.logScale?this.computeYPixelValueInLogScale(e,c):this.computeYPixelValue(e,c);if(t&&t.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){let s,c=-1;const h=l(0);for(let d of t){if(d.end<r)continue;if(d.start>a)break;const t=(d.start-r)/n;if(isNaN(t))continue;let u=l(d.value);const f=(d.end-r)/n-t,p=e.alpha?_s.addAlpha(this.getColorForFeature(d),e.alpha):this.getColorForFeature(d);if(\"line\"===this.graphType)void 0!==s&&xo.strokeLine(i,c,s,t,u,{fillStyle:p,strokeStyle:p}),xo.strokeLine(i,t,u,t+f,u,{fillStyle:p,strokeStyle:p});else if(\"points\"===this.graphType){const e=this.config.pointSize||3,n=t+f/2;xo.fillCircle(i,n,u,e/2,{fillStyle:p,strokeStyle:p}),d.value>this.dataRange.max?xo.fillCircle(i,n,e/2,e/2,3,{fillStyle:this.overflowColor}):d.value<this.dataRange.min&&xo.fillCircle(i,n,o-e/2,e/2,3,{fillStyle:this.overflowColor})}else{const e=Math.min(o,u-h);xo.fillRect(i,t,h,f,e,{fillStyle:p}),d.value>this.dataRange.max?xo.fillRect(i,t,0,f,3,{fillStyle:this.overflowColor}):d.value<this.dataRange.min&&xo.fillRect(i,t,o-2,f,3,{fillStyle:this.overflowColor})}c=t+f,s=u}if(this.dataRange.min<0){let t=this.dataRange.max,n=this.dataRange.min;n=!0===this.logScale?n<0?-Math.log10(Math.abs(n)+1):Math.log10(Math.abs(n)+1):n,t=!0===this.logScale?t<0?-Math.log10(Math.abs(t)+1):Math.log10(Math.abs(t)+1):t;const r=t/(t-n),s=this.flipAxis?(1-r)*o:r*o;xo.strokeLine(i,0,s,e.pixelWidth,s,{strokeStyle:this.baselineColor})}}if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=l(t.y),n={strokeStyle:t.color,strokeWidth:2};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,n):xo.strokeLine(e.context,0,i,e.pixelWidth,i,n)}}popupData(e,t){if(void 0===t&&(t=this.clickedFeatures(e)),t&&t.length>0){const i=e.genomicLocation,n=[];t.sort((function(e,t){return Math.abs((e.start+e.end)/2-i)-Math.abs((t.start+t.end)/2-i)}));const r=t.length>10?t.slice(0,10):t;r.sort((function(e,t){return e.start-t.start}));for(let e of r)if(e){n.length>0&&n.push(\"<hr/>\");let t=e.end-e.start==1?Rt(Math.floor(e.start)+1):Rt(Math.floor(e.start)+1)+\"-\"+Rt(Math.floor(e.end));n.push({name:\"Position:\",value:t}),n.push({name:\"Value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;\",value:Rt(e.value.toFixed(4))})}return r.length<t.length&&n.push(\"<hr/>...\"),n}return[]}get supportsWholeGenome(){return!this.config.indexURL&&!1!==this.config.supportsWholeGenome}getColorForFeature(e){let t=e.value<0&&this.altColor?this.altColor:this.color||\"rgb(150, 150, 150)\";return\"function\"==typeof t?t(e.value):t}dispose(){this.trackView=void 0}}function hd(e,t,i,n=\"mean\"){if(i<=1||!e||0===e.length)return e;const r=e[0].chr,s=i,o=[],a=e=>{const i=t+e.bin*s,a=i+s;let c;switch(n){case\"mean\":c=e.sumData/e.count;break;case\"max\":c=e.max;break;case\"min\":c=e.min;break;default:throw Error(`Unknown window function: ${n}`)}const l=`${n} of ${e.count} values`;o.push({chr:r,start:i,end:a,value:c,description:l})};let c;for(let i of e){let e=Math.floor((i.start-t)/s);const n=Math.floor((i.end-t)/s);if(c&&e===c.bin&&(c.add(i),e++),!c||n>c.bin){if(c&&a(c),n>e){const e=t+n*s;o.push({chr:r,start:i.start,end:e,value:i.value})}c=new dd(n,i)}}c&&a(c);const l=[];let h=o[0];for(let e of o)h.value===e.value&&e.start<=h.end?h.end=e.end:(l.push(h),h=e);return l.push(h),l}class dd{constructor(e,t){this.bin=e,this.sumData=t.value,this.count=1,this.min=t.value,this.max=t.value}add(e){this.sumData+=e.value,this.max=Math.max(e.value,this.max),this.min=Math.min(e.value,this.min),this.count++}get mean(){return this.sumData/this.count}}class ud extends Hh{constructor(e,t){super(t),this.config=e||{},this.genome=t,this.sourceType=void 0===e.sourceType?\"file\":e.sourceType,this.maxWGCount=e.maxWGCount||1e4,this.windowFunctions=[\"mean\",\"min\",\"max\",\"none\"];const i=new Set([\"bigwig\",\"bw\",\"bigbed\",\"bb\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\",\"tdf\"]);if(this.queryable=e.indexURL||!0===e.queryable,e.reader)this.reader=e.reader,this.queryable=!1!==e.queryable;else{if(\"ga4gh\"===e.sourceType)throw Error(\"Unsupported source type 'ga4gh'\");\"eqtl\"!==e.type&&\"qtl\"!==e.type||\"gtex-ws\"!==e.sourceType?\"htsget\"===e.sourceType?(this.reader=new Lh(e,t),this.queryable=!0):\"ucscservice\"===e.sourceType?(this.reader=new Nh(e.source),this.queryable=!0):\"custom\"===e.sourceType?(this.reader=new Eh(e.source),this.queryable=!1!==e.source.queryable):\"service\"===e.sourceType?(this.reader=new Ih(e,t),this.queryable=!0):(this.reader=new Ih(e,t),void 0!==e.queryable?this.queryable=e.queryable:(i.has(e.format)||this.reader.indexed)&&(this.queryable=!0)):(this.reader=new Bh(e),this.queryable=!0)}this.searchable=!1!==e.searchable}async defaultVisibilityWindow(){if(this.reader&&\"function\"==typeof this.reader.defaultVisibilityWindow)return this.reader.defaultVisibilityWindow()}async trackType(){const e=await this.getHeader();return e?e.type:void 0}async getHeader(){if(!this.header)if(this.reader&&\"function\"==typeof this.reader.readHeader){const e=await this.reader.readHeader();e?(this.header=e,e.format&&(this.config.format=e.format)):this.header={}}else this.header={};return this.header}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r,windowFunction:s}){const o=\"all\"===e.toLowerCase();if(t=t||0,i=i||Number.MAX_SAFE_INTEGER,(o&&!this.wgFeatures&&this.supportsWholeGenome()||this.config.disableCache||!this.featureCache||!this.featureCache.containsRange(new hc(e,t,i)))&&await this.loadFeatures(e,t,i,r),o){if(!this.wgFeatures)if(this.supportsWholeGenome())if(\"wig\"===this.config.type){const e=await Ll(this.featureCache.getAllFeatures(),this.genome,1e6);this.wgFeatures=hd(e,0,n,s)}else this.wgFeatures=await Ll(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount);else this.wgFeatures=[];return this.wgFeatures}return this.featureCache.queryFeatures(e,t,i)}async findFeatures(e){return this.featureCache?this.featureCache.findFeatures(e):[]}supportsWholeGenome(){return!this.queryable}getAllFeatures(){return this.queryable||!this.featureCache?[]:this.featureCache.getAllFeatures()}async loadFeatures(e,t,i,n){await this.getHeader();const r=this.reader;let s=t,o=i,a=e;if(!this.chrAliasManager&&this.reader&&this.reader.sequenceNames&&(this.chrAliasManager=new zh(this.reader.sequenceNames,this.genome)),this.chrAliasManager&&(a=await this.chrAliasManager.getAliasName(e)),(!n||n<=0)&&!1!==this.config.expandQuery){const e=this.genome?this.genome.getChromosome(a):void 0;s=0,o=Math.max(e?e.bpLength:Number.MAX_SAFE_INTEGER,i)}else if(n>i-t&&!1!==this.config.expandQuery){let e=Math.min(4.1*(i-t),n);this.config.minQuerySize&&e<this.config.minQuerySize&&(e=this.config.minQuerySize),s=Math.max(0,(t+i-e)/2),o=s+e}let c=await r.readFeatures(a,s,o);void 0===this.queryable&&(this.queryable=r.indexed);const l=this.queryable?new hc(e,s,o):void 0;if(c){if(\"wig\"!==this.config.format&&\"junctions\"!==this.config.type){zl(c,this.config.maxRows||Number.MAX_SAFE_INTEGER)}this.featureCache=new Zs(c,this.genome,l),this.searchable&&this.addFeaturesToDB(c,this.config)}else this.featureCache=new Zs([],l)}addFeaturesToDB(e,t){this.featureMap||(this.featureMap=new Map);const i=t.searchableFields||[\"name\",\"transcript_id\",\"gene_id\",\"gene_name\",\"id\"];for(let t of e)for(let e of i){let i;if(t.hasOwnProperty(e)?i=t[e]:\"function\"==typeof t.getAttributeValue&&(i=t.getAttributeValue(e)),i){if(i=i.replaceAll(\" \",\"+\").toUpperCase(),this.featureMap.has(i)){const e=this.featureMap.get(i);if(t.end-t.start<e.end-e.start)continue}this.featureMap.set(i,t)}}}search(e){if(this.featureMap)return this.featureMap.get(e.toUpperCase())}}class fd extends Hh{constructor(e,t){super(t),this.config=e,this.genome=t,this.queryable=!1,this.searchable=!1!==e.searchable,this.updateFeatures(e.features)}updateFeatures(e){zl(e=function(e,t){if(t)for(let i of e)i.chr=t.getChromosomeName(i.chr);return e}(e,this.genome)),this.config.mappings&&function(e,t){let i=Object.keys(t);e.forEach((function(e){i.forEach((function(i){e[i]=e[t[i]]}))}))}(e,this.config.mappings),this.featureCache=new Zs(e,this.genome),(this.searchable||this.config.searchableFields)&&this.addFeaturesToDB(e,this.config)}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome,o=s?s.getChromosomeName(e):e;return\"all\"===o.toLowerCase()?Ll(this.featureCache.getAllFeatures(),this.genome,this.maxWGCount):this.featureCache.queryFeatures(o,t,i)}getAllFeatures(){return this.featureCache.getAllFeatures()}supportsWholeGenome(){return!0}addFeaturesToDB(e,t){this.featureMap||(this.featureMap=new Map);const i=t.searchableFields||[\"name\"];for(let t of e)for(let e of i){let i;if(\"function\"==typeof t.getAttributeValue&&(i=t.getAttributeValue(e)),i||(i=t[e]),i){i=i.replaceAll(\" \",\"+\");const e=this.featureMap.get(i.toUpperCase());if(e&&e.end-e.start>t.end-t.start)continue;this.featureMap.set(i.toUpperCase(),t)}}}search(e){if(this.featureMap)return this.featureMap.get(e.toUpperCase())}}class pd{constructor({chr:e,locus:t,accession:i,aliases:n,features:r,sequence:s}){this.chr=e,this.locus=t,this.accession=i,this.aliases=n,this.features=r,this.sequence=s,this.bpLength=s.length}toJSON(){return{gbkURL:this.url}}getSequenceRecord(e){return{chr:this.chr,bpLength:this.bpLength}}get chromosomeNames(){return[this.chr]}getFirstChromosomeName(){return this.chr}get id(){return this.accession}get name(){return this.locus}get initialLocus(){return this.chr}get description(){return this.locus}get infoURL(){return this.url}showWholeGenomeView(){return!1}getHomeChromosomeName(){return this.chr}getChromosomeName(e){return e}getChromosomeDisplayName(e){return this.chr}getChromosome(e){if(e===this.chr)return{name:this.chr,bpLength:this.bpLength}}async loadChromosome(e){return this.getChromosome(e)}async getAliasRecord(e){}getCytobands(e){return[]}getChromosomes(){return[this.getChromosome(this.chr)]}get wgChromosomeNames(){}getGenomeCoordinate(e,t){if(e===this.chr)return t}getChromosomeCoordinate(e){return{chr:this.chr,position:e}}getCumulativeOffset(e){return 0}getGenomeLength(){return this.bpLength}async getSequence(e,t,i){return e===this.chr?this.sequence.substring(t,i):void 0}getSequenceInterval(e,t,i){return e===this.chr?new dc(this.chr,0,this.sequence.length,this.sequence):void 0}}const gd=/\\s+/,md=new Map;async function wd(e){let t=md.get(e);if(!t){t=function(e){if(!e)return null;const t=mh(e);let i=t.nextLine();const n=i.split(/\\s+/);if(\"LOCUS\"!==n[0].toUpperCase())throw Error(\"Expected `LOCUS` line.  Found: \"+i);const r=n[1].trim();let s,o;do{if(i=t.nextLine(),i.startsWith(\"ACCESSION\")){const e=i.split(gd);if(e.length<2)throw Error(\"Genbank file missing ACCESSION number.\");s=e[1].trim()}else if(i.startsWith(\"ALIASES\")){const e=i.split(gd);e.length>1&&(o=e[1].split(\",\"))}}while(i&&!i.startsWith(\"FEATURES\"));const a=s||r,c=function(e,t){const i=[];let n,r,s,o=0;for(;;)if(r=t.nextLine(),\"\"!==r){if(!r||r.startsWith(\"ORIGIN\"))break;if(r.length<6)o<10&&console(\"Unexpected line in genbank file (skipping): \"+r),o++;else if(\" \"!==r.charAt(5)){let t=r.substring(5,21).trim();s={chr:e,type:t,attributes:{},getAttributeValue:function(e){return this.attributes[e]}},n=r.substring(21),\"source\"!==t.toLowerCase()&&i.push(s)}else{let t=r.substring(21).trim();if(t.length>0)if(47===t.charCodeAt(0)){if(47===n.charCodeAt(0)){let e=n.split(\"=\",2);if(e.length>1){let t=e[0].length>1?e[0].substring(1):\"\",i=Fd(e[1]);s.attributes[t]=i}}else{const t=n.includes(\"complement\")?\"-\":\"+\";s.strand=t;let i=n.replace(\"join\",\"\").replace(\"order\",\"\").replace(\"complement\",\"\").replace(\"(\",\"\").replace(\")\",\"\");if(i.includes(\"..\")){i=i.replace(\"<\",\"\").replace(\">\",\"\");const n=bd(i,e,t),r=n[0];s.start=r.start;const o=n[n.length-1];s.end=o.end,n.length>1&&(s.exons=n)}else s.start=parseInt(i)-1,s.end=s.start+1}n=t}else n+=t}}return i}(a,t),l=function(e){let t,i=\"\";for(;(t=e.nextLine())&&!t.startsWith(\"//\");){t=t.trim();const e=t.split(/\\s+/);for(let t=1;t<e.length;t++)i+=e[t]}return i}(t);return new pd({chr:a,locus:r,accession:s,aliases:o,features:c,sequence:l})}(await Qs.loadString(e,{})),t.url=e,md.set(e,t)}return t}function bd(e,t,i){const n=e.split(\",\"),r=[];e.includes(\"complement\");for(const e of n){const n=e.split(\"..\");let s=0;try{s=parseInt(n[0])-1}catch(e){console.error(e)}let o=s+1;n.length>1&&(o=parseInt(n[1])),r.push({chr:t,start:s,end:o,strand:i})}return r.sort((function(e,t){return e.start-t.start})),r}function Fd(e){return e.startsWith('\"')&&e.endsWith('\"')&&(e=e.substring(1,e.length-2)),e}class vd extends Hh{constructor(e,t){super(t),this.config=e,this.searchable=!0}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){if(!this.featureSource){const e=await wd(this.config.url);this.featureSource=new fd({genome:this.config.genome,features:e.features,searchableFields:[\"gene\",\"db_xref\",\"locus_tag\",\"transcript_id\"]})}return this.featureSource.getFeatures({chr:e,start:t,end:i})}supportsWholeGenome(){return!1}search(e){return this.featureSource.search(e)}}const yd=new Set([\"bigwig\",\"bw\",\"bigbed\",\"bb\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\"]);function Ad(e,t){const i=e.format?e.format.toLowerCase():void 0;return e.features?new fd(e,t):yd.has(i)?new od(e,t):\"tdf\"===i?new Qh(e,t):\"gbk\"===i?new vd(e,t):new ud(e,t)}function Cd(e){return(3-e.readingFrame)%3}function _d(e){return e.cdStart||e.start}function xd(e){return e.cdEnd||e.end}const kd=.25;function Id(e,t,i){let n=(e.start-t)/i,r=(e.end-t)/i,s=r-n;return s<3&&(s=3,n-=1.5),{px:n,px1:r,pw:s}}function Sd(e,t,i,n,r,s){try{r.save(),r.fillStyle=this.color,r.strokeStyle=this.color;const n=this.getColorForFeature(e);let o,a;r.fillStyle=n,r.strokeStyle=n,\"SQUISHED\"===this.displayMode&&void 0!==e.row?(o=this.featureHeight/2,a=this.margin+this.squishedRowHeight*e.row):\"EXPANDED\"===this.displayMode&&void 0!==e.row?(o=this.featureHeight,a=this.margin+this.expandedRowHeight*e.row):(o=this.featureHeight,a=this.margin);const c=s.pixelWidth,l=a+o/2,h=o/2,d=l-h/2,u=e.exons?e.exons.length:0,f=Id(e,t,i),p=this.arrowSpacing,g=\"+\"===e.strand?1:\"-\"===e.strand?-1:0;if(0===u){const e=Math.max(0,f.px),t=Math.min(c,f.px1),i=t-e;if(r.fillRect(e,a,i,o),0!==g){r.fillStyle=\"white\",r.strokeStyle=\"white\";for(let i=e+p/2;i<t;i+=p)xo.strokeLine(r,i-2*g,l-2,i,l),xo.strokeLine(r,i-2*g,l+2,i,l);r.fillStyle=n,r.strokeStyle=n}}else{xo.strokeLine(r,f.px+1,l,f.px1-1,l);const u=Math.max(0,f.px)+p/2,m=Math.min(c,f.px1);for(let e=u;e<m;e+=p)xo.strokeLine(r,e-2*g,l-2,e,l),xo.strokeLine(r,e-2*g,l+2,e,l);for(let u=0;u<e.exons.length;u++){const f=e.exons[u];let m,w=Math.round((f.start-t)/i),b=Math.round((f.end-t)/i),F=Math.max(1,b-w);if(!(w+F<0)){if(w>c)break;if(f.utr)r.fillRect(w,d,F,h);else{if(f.cdStart&&(m=Math.round((f.cdStart-t)/i),r.fillRect(w,d,m-w,h),F-=m-w,w=m),f.cdEnd&&(m=Math.round((f.cdEnd-t)/i),r.fillRect(m,d,b-m,h),F-=b-m,b=m),F=Math.max(F,1),r.fillRect(w,a,F,o),void 0!==f.readingFrame&&s.bpPerPixel<kd&&s.sequenceInterval){const i=u>0&&void 0!==e.exons[u-1].readingFrame?e.exons[u-1]:void 0,n=u<e.exons.length-1&&void 0!==e.exons[u+1].readingFrame?e.exons[u+1]:void 0;Ed.call(this,r,e.strand,i,f,n,t,s.bpPerPixel,a,o,s.sequenceInterval)}if(F>p+5&&0!==g&&s.bpPerPixel>kd){r.fillStyle=\"white\",r.strokeStyle=\"white\";for(let e=w+p/2;e<b;e+=p)xo.strokeLine(r,e-2*g,l-2,e,l),xo.strokeLine(r,e-2*g,l+2,e,l);r.fillStyle=n,r.strokeStyle=n}}}}}s.drawLabel&&\"SQUISHED\"!==this.displayMode&&Nd.call(this,r,e,f.px,f.px1,a,s.referenceFrame,s)}finally{r.restore()}}function Ed(e,t,i,n,r,s,o,a,c,l){const h=[\"rgb(124,124,204)\",\"rgb(12, 12, 120)\"];e.save();const d=(t,i,n,r,d,u)=>{const f=Math.round((i-s)/o),p=Math.round((n-s)/o)-f;let g;if(void 0===r){if(l.hasSequence(i,n)){const e=l.getSequence(i,n);if(e&&3===e.length){const i=\"+\"===t?e:ac(e.split(\"\").reverse().join(\"\"));g=Gd[i]}}}else g=r;e.fillStyle=\"M\"===r||\"M\"===g&&0===u?\"#83f902\":\"STOP\"===g?\"#ff2101\":h[d],e.fillRect(f,a,p,c),g&&(e.save(),((t,i,n,r,s)=>{\"STOP\"===s&&(s=\"*\");const o=e.measureText(s).width;xo.fillText(e,s,n+(i-o)/2,r-4,{fillStyle:\"#ffffff\"})})(0,p,f,a+c,g),e.restore());const m=n-i;return m>0&&m<3?{start:i,end:n}:void 0},u=Cd(n);let f,p,g,m,w,b=_d(n),F=xd(n),v=1;if(\"+\"===t){for(u>0&&(b+=u),v=1,w=0,f=b;f<F;w++,f+=3)m=v%2,p=Math.min(F,f+3),g=d(t,f,p,void 0,v%2,w),++v;if(u>0||g){const e=u>0?Bd.call(this,t,u,b-u,b,g,i,n,r,l):Bd.call(this,t,void 0,void 0,void 0,g,i,n,r,l);if(e){const{left:i,rite:n}=e;i&&d(t,b-u,b,i.aminoAcidLetter,0,void 0),n&&d(t,g.start,g.end,n.aminoAcidLetter,m,void 0)}}}else{for(u>0&&(F-=u),v=1,w=0,w=0,p=F;p>b;w++,p-=3)m=v%2,f=Math.max(b,p-3),g=d(t,f,p,void 0,v%2,w),++v;if(u>0||g){const e=u>0?Bd.call(this,t,u,F,F+u,g,i,n,r,l):Bd.call(this,t,void 0,void 0,void 0,g,i,n,r,l);if(e){const{left:i,rite:n}=e;n&&d(t,F,F+u,n.aminoAcidLetter,0,void 0),i&&d(t,g.start,g.end,i.aminoAcidLetter,m,void 0)}}}e.restore()}function Nd(e,t,i,n,r,s,o){try{e.save();let s=t.name;if(void 0===s&&t.gene&&(s=t.gene.name),void 0===s&&(s=t.id||t.ID),!s||\".\"===s)return;let a=o.pixelXOffset||0;const c=Math.max(i,-a);let l,h=(c+Math.min(n,-a+o.viewportWidth))/2;\"COLLAPSED\"===this.displayMode&&\"SLANT\"===this.labelDisplayMode&&(l={rotate:{angle:45}});const d=function(e,t){return t?e+20:e+25}(r,l);let u=this.getColorForFeature(t),f=this.browser.qtlSelections.hasPhenotype(t.name);const p={textAlign:\"SLANT\"===this.labelDisplayMode?void 0:\"center\",fillStyle:u,strokeStyle:u},g=e.measureText(s),m=h-g.width/2,w=h+g.width/2,b=o.rowLastLabelX[t.row]||-Number.MAX_SAFE_INTEGER;(o.labelAllFeatures||m>b||f)&&(o.rowLastLabelX[t.row]=w,\"y\"===o.axis?(e.save(),xo.labelTransformWithContext(e,h),xo.fillText(e,s,h,d,p,l),e.restore()):(e.clearRect(h-g.width/2-1,d-g.actualBoundingBoxAscent-1,g.width+2,g.actualBoundingBoxAscent+g.actualBoundingBoxDescent+2),xo.fillText(e,s,h,d,p,l)))}finally{e.restore()}}function Bd(e,t,i,n,r,s,o,a,c){let l,h,d=\"\",u=\"\",f=\"\";const p={left:void 0,rite:void 0};if(\"+\"===e){if(t){if(u=c.getSequence(i,n),!u)return;if([l,h]=[xd(s)-(3-t),xd(s)],d=c.getSequence(l,h),!d)return;f=d+u,p.left={triplet:f,aminoAcidLetter:Gd[f]}}if(r){if(d=c.getSequence(r.start,r.end),!d)return;const e=Cd(a),t=_d(a);if(u=c.getSequence(t,t+e),!u)return;f=d+u,p.rite={triplet:f,aminoAcidLetter:Gd[f]}}}else{if(t){if(d=c.getSequence(i,n),void 0===d)return;if([l,h]=[_d(a),_d(a)+(3-t)],u=c.getSequence(l,h),void 0===u)return;f=d+u,f=ac(f.split(\"\").reverse().join(\"\")),p.rite={triplet:f,aminoAcidLetter:Gd[f]}}if(r){if(u=c.getSequence(r.start,r.end),void 0===u)return;const e=Cd(s),t=xd(s);if(d=c.getSequence(t-e,t),void 0===d)return;f=d+u,f=ac(f.split(\"\").reverse().join(\"\")),p.left={triplet:f,aminoAcidLetter:Gd[f]}}}return p}const Md=new Set([\"nonsense\",\"missense\",\"stop-loss\",\"frameshift\",\"cds-indel\"]),Rd=new Set([\"coding-synon\"]),Dd=new Set([\"splice-3\",\"splice-5\"]),Td=new Set([\"untranslated-5\",\"untranslated-3\"]);function Ld(e,t,i,n,r){var s,o,a,c,l,h,d=Id(e,t,i),u=this.margin,f=this.snpColors.length;switch(s=\"squished\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight,this.colorBy){case\"function\":c=e.func,h=c.split(\",\"),l=h.map((function(e){return Md.has(e)||Dd.has(e)?f-1:Rd.has(e)?f-2:Td.has(e)?f-3:0})),o=l.reduce((function(e,t){return Math.max(e,t)}));break;case\"class\":o=\"deletion\"===(a=e.class)?f-1:\"mnp\"===a?f-2:\"microsatellite\"===a||\"named\"===a?f-3:0}r.fillStyle=this.snpColors[o],r.fillRect(d.px,u,d.pw,s)}function zd(e,t,i,n,r){const s=\"EXPANDED\"===this.displayMode?this.expandedRowHeight:this.squishedRowHeight;let o=this.margin;\"COLLAPSED\"!==this.displayMode&&void 0!==e.row&&(o+=e.row*s);const a=o+.5*s,c=a-.5*s,l=a+.5*s,h=Math.round((e.junction_left-t)/i),d=Math.round((e.junction_right-t)/i);r.beginPath(),r.moveTo(h,a),r.bezierCurveTo(h,c,d,c,d,a),r.lineWidth=1+Math.log(e.num_junction_reads)/Math.log(2),r.strokeStyle=\"blue\",r.stroke();const u=e.spanning_frag_coords;for(let e=0;e<u.length;e++){const n=u[e],s=Math.round((n.left-t)/i),o=Math.round((n.right-t)/i);r.beginPath(),r.moveTo(s,a),r.bezierCurveTo(s,l,o,l,o,a),r.lineWidth=1,r.strokeStyle=\"purple\",r.stroke()}}class Hd extends Hl{static defaults={type:\"annotation\",maxRows:1e3,displayMode:\"EXPANDED\",margin:10,featureHeight:14,useScore:!1};constructor(e,t){super(e,t)}init(e){super.init(e),this.labelDisplayMode=e.labelDisplayMode,e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):\"blat\"!==e.type&&(this.featureSource=e.featureSource?e.featureSource:Ad(e,this.browser.genome)),\"FusionJuncSpan\"===e.type?(this.render=e.render||zd,this.squishedRowHeight=e.squishedRowHeight||50,this.expandedRowHeight=e.expandedRowHeight||50,this.height=e.height||this.margin+2*this.expandedRowHeight):\"snp\"===e.type?(this.render=e.render||Ld,this.snpColors=[\"rgb(0,0,0)\",\"rgb(0,0,255)\",\"rgb(0,255,0)\",\"rgb(255,0,0)\"],this.colorBy=\"function\",this.expandedRowHeight=e.expandedRowHeight||10,this.squishedRowHeight=e.squishedRowHeight||5,this.height=e.height||30):(this.render=e.render||Sd,this.arrowSpacing=30,function(e){e.browser.on&&(e.browser.on(\"trackdragend\",t),e.browser.on(\"trackremoved\",i));function t(){e.trackView&&\"SQUISHED\"!==e.displayMode&&e.trackView.repaintViews()}function i(n){e.browser.un&&e===n&&(e.browser.un(\"trackdragend\",t),e.browser.un(\"trackremoved\",i))}}(this),this.squishedRowHeight=e.squishedRowHeight||15,this.expandedRowHeight=e.expandedRowHeight||30,this.height=e.height||this.margin+2*this.expandedRowHeight,e.colorBy&&(e.colorBy.field&&(e.colorTable=e.colorBy.pallete||e.colorBy.palette,e.colorBy=e.colorBy.field),this.colorBy=e.colorBy,e.colorTable?this.colorTable=new ao(e.colorTable):this.colorTable=new oo(\"Set1\")))}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get searchable(){return this.featureSource.searchable}async search(e){return this.featureSource&&this.featureSource.searchable?this.featureSource.search(e):void 0}get supportsWholeGenome(){return void 0!==this.config.supportsWholeGenome?this.config.supportsWholeGenome:this.featureSource&&\"function\"==typeof this.featureSource.supportsWholeGenome?this.featureSource.supportsWholeGenome():!(void 0!==this.visibilityWindow||!1!==this.config.indexed&&this.config.indexURL)||void 0}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}computePixelHeight(e){if(\"COLLAPSED\"===this.displayMode)return this.margin+this.expandedRowHeight;{let t=0;if(e&&\"function\"==typeof e.forEach)for(let i of e)i.row&&i.row>t&&(t=i.row);return this.margin+(t+1)*(\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight)}}draw(e){const{features:t,context:i,bpPerPixel:n,bpStart:r,bpEnd:s,pixelWidth:o,pixelHeight:a,referenceFrame:c}=e;if(n<kd&&(e.sequenceInterval=this.browser.genome.getSequenceInterval(c.chr,r,s)),this.isMergedTrack||xo.fillRect(i,0,e.pixelTop,o,a,{fillStyle:\"rgb(255, 255, 255)\"}),t){const c=[];e.rowLastX=[],e.rowLastLabelX=[];for(let i of t)if(i.start>r&&i.end<s){const t=\"COLLAPSED\"===this.displayMode?0:i.row||0;c[t]?c[t]++:c[t]=1,e.rowLastX[t]=-Number.MAX_SAFE_INTEGER,e.rowLastLabelX[t]=-Number.MAX_SAFE_INTEGER}const l=o/Math.max(1,Math.max(...c.filter((e=>!isNaN(e)))));let h=[];const d=[];for(let o of t){if(o.end<r)continue;if(o.start>s)break;\"COLLAPSED\"===this.displayMode&&this.browser.qtlSelections.hasPhenotype(o.name)&&d.push(o);const t=\"COLLAPSED\"===this.displayMode?0:o.row;e.drawLabel=e.labelAllFeatures||l>10;const c=Math.ceil((o.end-r)/n),u=h[t];if(!u||c>u){this.render.call(this,o,r,n,a,i,e);const s=Math.floor((o.start-r)/n);u&&s-u<=0&&(i.globalAlpha=.5,xo.strokeLine(i,s,0,s,a,{strokeStyle:\"rgb(255, 255, 255)\"}),i.globalAlpha=1),h[t]=c}}for(let t of d)e.drawLabel=!0,this.render.call(this,t,r,n,a,i,e)}else console.log(\"No feature list\")}clickedFeatures(e){const t=e.y-this.margin,i=super.clickedFeatures(e);let n;switch(this.displayMode){case\"SQUISHED\":n=Math.floor(t/this.squishedRowHeight);break;case\"EXPANDED\":n=Math.floor(t/this.expandedRowHeight);break;default:n=void 0}return i.filter((function(e){return void 0===n||void 0===e.row||n===e.row}))}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=[];for(let e of t){const t=e._f||e,r=\"function\"==typeof t.popupData?t.popupData(i):this.extractPopupData(t);if(r){n.length>0&&n.push(\"<hr/><hr/>\");const s=this.infoURL||this.config.infoURL;for(let t of r)if(n.push(t),s&&t.name&&\"name\"===t.name.toLowerCase()&&t.value&&Mt(t.value)&&!t.value.startsWith(\"<\")){const i=s.replace(\"$$\",e.name);t.value=`<a target=_blank href=${i}>${t.value}</a>`}const o=\"gff\"===this.config.format||\"gff3\"===this.config.format||\"gtf\"===this.config.format;if(t.exons&&t.exons.length>1)for(let e=0;e<t.exons.length;e++){const r=t.exons[e];if(i>=r.start&&i<=r.end){const i=o?r.number:\"-\"===t.strand?t.exons.length-e:e+1;i&&(n.push(\"<hr/>\"),n.push({name:\"Exon Number\",value:i}));break}}}}return n}menuItemList(){const e=[];if(this.render===Ld){e.push(\"<hr/>\");for(const i of[\"function\",\"class\"]){const n=Bt(Dl(`Color by ${i}`,i===this.colorBy));function r(){this.colorBy=i,this.trackView.repaintViews()}e.push({object:n,click:r})}}e.push(\"<hr/>\");const t={COLLAPSED:\"Collapse\",SQUISHED:\"Squish\",EXPANDED:\"Expand\"};for(const s of[\"COLLAPSED\",\"SQUISHED\",\"EXPANDED\"]){const o=Bt(Dl(t[s],s===this.displayMode));function a(){this.displayMode=s,this.config.displayMode=s,this.trackView.checkContentHeight(),this.trackView.repaintViews()}e.push({object:o,click:a})}return e}contextMenuItemList(e){const t=this.clickedFeatures(e);if(void 0===t||0===t.length)return;t.length>1&&t.sort(((e,t)=>t.end-t.start-(e.end-e.start)));const i=t[0];if(i.end-i.start<=1e6){const e=[{label:\"View feature sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i.chr,i.start,i.end);e?\"-\"===i.strand&&(e=cc(e)):e=\"Unknown sequence\",this.browser.alert.present(e)}}];return Xa()&&void 0!==navigator.clipboard&&e.push({label:\"Copy feature sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i.chr,i.start,i.end);e?\"-\"===i.strand&&(e=cc(e)):e=\"Unknown sequence\";try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),e.push(\"<hr/>\"),e}}description(){if(Ld===this.render){let e=\"<html>\"+this.name+\"<hr/>\";return e+=\"<em>Color By Function:</em><br>\",e+='<span style=\"color:red\">Red</span>: Coding-Non-Synonymous, Splice Site<br>',e+='<span style=\"color:green\">Green</span>: Coding-Synonymous<br>',e+='<span style=\"color:blue\">Blue</span>: Untranslated<br>',e+='<span style=\"color:black\">Black</span>: Intron, Locus, Unknown<br><br>',e+=\"<em>Color By Class:</em><br>\",e+='<span style=\"color:red\">Red</span>: Deletion<br>',e+='<span style=\"color:green\">Green</span>: MNP<br>',e+='<span style=\"color:blue\">Blue</span>: Microsatellite, Named<br>',e+='<span style=\"color:black\">Black</span>: Indel, Insertion, SNP',e+=\"</html>\",e}return super.description()}getColorForFeature(e){const t=e._f||e;let i;if(e.name&&this.browser.qtlSelections.hasPhenotype(e.name))i=this.browser.qtlSelections.colorForGene(e.name);else if(this.altColor&&\"-\"===t.strand)i=\"function\"==typeof this.altColor?this.altColor(t):this.altColor;else if(this.color)i=\"function\"==typeof this.color?this.color(t):this.color;else if(this.colorBy){const e=t.getAttributeValue?t.getAttributeValue(this.colorBy):t[this.colorBy];i=this.colorTable.getColor(e)}else t.color&&(i=t.color);if(i||(i=\"rgb(0, 0, 150)\"),t.alpha&&1!==t.alpha)i=_s.addAlpha(i,t.alpha);else if(this.useScore&&t.score&&!Number.isNaN(t.score)){const e=function(e,t,i){const n=(t-e)/9,r=Math.floor((i-e)/n);return Math.min(1,.2+.8*r/9)}(this.config.min?this.config.min:this.viewLimitMin?this.viewLimitMin:0,this.config.max?this.config.max:this.viewLimitMax?this.viewLimitMax:1e3,t.score);t.alpha=e,i=_s.addAlpha(i,e)}return i}dispose(){this.trackView=void 0}}class Pd{constructor(t){if(this.config=t,this.browser=t.browser,this.columnFormat=t.columnFormat,this.tableRowSelectionList=[],this.tableDOM=e({class:\"igv-roi-table\"}),t.width){let[e]=t.width.split(\"px\");e=parseInt(e,10),this.tableDOM.style.width=`${Math.min(e,1600)}px`}t.parent.appendChild(this.tableDOM),this.headerDOM=t,this.tableColumnTitles=this.tableDOM,this.tableRowContainer=this.tableDOM,this.footerDOM=t.gotoButtonHandler}set headerDOM({browser:t,parent:i,headerTitle:n,dismissHandler:r}){const s=e();this.tableDOM.appendChild(s);const o=e();s.appendChild(o),o.innerHTML=n;const a=e();s.appendChild(a),a.appendChild(l(\"times\")),this.boundDismissHandler=function(e){e.stopPropagation(),r()}.bind(this),a.addEventListener(\"click\",this.boundDismissHandler);const{y:c}=t.root.getBoundingClientRect(),{y:h}=i.getBoundingClientRect(),d=-(h-c);p(this.tableDOM,s,{minX:0,minY:d}),this.tableDOM.style.display=\"none\",this._headerDOM=s}set tableColumnTitles(t){const i=e({class:\"igv-roi-table-column-titles\"});t.appendChild(i);for(const{label:t,width:n}of this.columnFormat){const r=e();i.appendChild(r),r.style.width=n,r.innerText=t}this._tableColumnTitlesDOM=i}get tableColumnTitles(){return this._tableColumnTitlesDOM}set tableRowContainer(t){const i=e({class:\"igv-roi-table-row-container\"});t.appendChild(i),this._tableRowContainerDOM=i}get tableRowContainer(){return this._tableRowContainerDOM}set footerDOM(t){const i=e();this.tableDOM.appendChild(i);const n=e({class:\"igv-roi-table-button\"});i.appendChild(n),n.id=\"igv-roi-table-view-button\",n.textContent=\"Go To\",n.style.pointerEvents=\"none\",this._footerDOM=i,this.gotoButton=n,this.boundGotoButtonHandler=t.bind(this),this.gotoButton.addEventListener(\"click\",this.boundGotoButtonHandler)}tableRowDOMHelper(e){e.addEventListener(\"mousedown\",(t=>{t.stopPropagation(),e.classList.toggle(\"igv-roi-table-row-selected\"),e.classList.contains(\"igv-roi-table-row-selected\")?e.classList.remove(\"igv-roi-table-row-hover\"):e.classList.add(\"igv-roi-table-row-hover\"),this.setTableRowSelectionState(e.classList.contains(\"igv-roi-table-row-selected\"))})),e.addEventListener(\"mouseover\",(t=>{e.classList.contains(\"igv-roi-table-row-selected\")?e.classList.remove(\"igv-roi-table-row-hover\"):e.classList.add(\"igv-roi-table-row-hover\")})),e.addEventListener(\"mouseout\",(t=>{e.classList.remove(\"igv-roi-table-row-hover\")}))}clearTable(){const e=this.tableRowContainer.querySelectorAll(\".igv-roi-table-row\");for(let t of e)t.remove()}setTableRowSelectionState(e){e?this.tableRowSelectionList.push(1):this.tableRowSelectionList.pop(),this.gotoButton.style.pointerEvents=this.tableRowSelectionList.length>0?\"auto\":\"none\"}present(){this.tableDOM.style.left=\"0px\";const{y:e}=this.browser.root.getBoundingClientRect(),{y:t}=this.config.parent.getBoundingClientRect();this.tableDOM.style.top=e-t+\"px\",this.tableDOM.style.display=\"flex\"}dismiss(){this.tableDOM.style.display=\"none\"}isVisible(){return\"none\"!==this.tableDOM.style.display}dispose(){this.tableDOM.innerHTML=\"\",this.tableDOM.remove();for(const e of Object.keys(this))this[e]=void 0;document.removeEventListener(\"click\",this.boundDismissHandler)}}class Od extends Pd{constructor(e){super(Object.assign({width:\"1024px\"},e)),this.descriptionDOM=e}set descriptionDOM(t){if(t.description){let i;i=e({class:\"igv-roi-table-description\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.style.height=\"auto\",i.innerHTML=\"BLAT result for query sequence:\",i=e({class:\"igv-roi-table-description\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.style.height=\"auto\",i.style.maxHeight=\"128px\",i.innerHTML=t.description,i=e({class:\"igv-roi-table-goto-explainer\"}),this.tableDOM.insertBefore(i,this.tableColumnTitles),i.innerHTML=\"Select one or more rows and click Go To to view the regions\"}}tableRowDOM(t){const i=e({class:\"igv-roi-table-row\"}),n=t.map((e=>isFinite(e)?Rt(e):e));for(let t=0;t<n.length;t++){const r=e();i.appendChild(r);const s=this.columnFormat[t];r.style.width=s.width||\"fit-content\",r.innerText=n[t]}return this.tableRowDOMHelper(i),i}renderTable(e){if(Array.from(this.tableRowContainer.querySelectorAll(\".igv-roi-table-row\")).forEach((e=>e.remove())),e.length>0)for(let t of e){const e=this.tableRowDOM(t);this.tableRowContainer.appendChild(e)}}static getColumnFormatConfiguration(){return[{label:\"chr\",width:\"7%\"},{label:\"start\",width:\"12%\"},{label:\"end\",width:\"12%\"},{label:\"strand\",width:\"5%\"},{label:\"score\",width:\"5%\"},{label:\"match\",width:\"5%\"},{label:\"mis-match\",width:\"7%\"},{label:\"rep. match\",width:\"7%\"},{label:\"N's\",width:\"3%\"},{label:\"Q gap count\",width:\"9%\"},{label:\"Q gap bases\",width:\"9%\"},{label:\"T gap count\",width:\"9%\"},{label:\"T gap bases\",width:\"9%\"}]}static gotoButtonHandler(e){e.stopPropagation();const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\"),i=[];for(const e of t){const t=[];e.querySelectorAll(\"div\").forEach((e=>t.push(e.innerText)));const[n,r,s]=t;i.push(`${n}:${r}-${s}`)}for(const e of this.tableDOM.querySelectorAll(\".igv-roi-table-row\"))e.classList.remove(\"igv-roi-table-row-selected\");this.setTableRowSelectionState(!1),this.browser.search(i.join(\" \"))}}const Ud=\"https://igv.org/services/blatUCSC.php\";async function qd({url:e,userSeq:t,db:i}){if(e=e||Ud,!i)throw Error(\"Blat database is not defined\");const n=await async function(e=\"\",t,i){const n=new URLSearchParams;n.append(\"userSeq\",t),n.append(\"db\",i);const r=await fetch(e,{method:\"post\",body:n});return r.json()}(e,t,i);n.fields;return n.blat.map($c)}const Qd=25e3;class Vd extends Hd{constructor(e,t){super(e,t),this.name||(this.name=\"Blat Results\"),this.sequence=e.sequence,this.table=void 0,e.features&&(this._features=e.features,this.featureSource=new fd({features:e.features},this.browser.genome),delete e.features)}async postInit(){if(!this.featureSource){const e=this.browser.genome.id,t=this.browser.config.blatServerURL,i=await qd({url:t,userSeq:this.sequence,db:e});this._features=i,this.featureSource=new fd({features:i},this.browser.genome)}}openTableView(){if(void 0===this.table){const e=this._features.map((e=>[e.chr,e.start+1,e.end,e.strand,e.score,e.matches,e.misMatches,e.repMatches,e.nCount,e.qNumInsert,e.qBaseInsert,e.tNumInsert,e.tBaseInsert])),t={browser:this.browser,parent:this.browser.columnContainer,headerTitle:this.config.title,description:this.sequence,dismissHandler:()=>{this.table.dismiss(),this.table.dispose(),this.table=void 0},columnFormat:Od.getColumnFormatConfiguration(),gotoButtonHandler:Od.gotoButtonHandler};this.table=new Od(t),this.table.renderTable(e)}this.table.present()}menuItemList(){const e=super.menuItemList();return e.push(\"<hr/>\"),e.push({label:\"Open table view\",click:function(){this.openTableView()}}),e}dispose(){super.dispose(),this.table&&this.table.popover.parentElement.removeChild(this.table.popover)}}async function jd({sequence:e,browser:t,name:i,title:n}){if(e.length>Qd)t.alert.present(`Sequence size exceeds maximum allowed length (${e.length} > 25000)`);else try{const r=t.genome.id,s=t.config.blatServerURL||\"https://igv.org/services/blatUCSC.php\",o={type:\"blat\",name:i||\"blat results\",title:n||\"blat results\",sequence:e,altColor:\"rgb(176, 176, 236)\",color:\"rgb(236, 176, 176)\",searchable:!1,features:await qd({url:s,userSeq:e,db:r})};(await t.loadTrack(o)).openTableView()}catch(e){t.alert.present(`Error performing blat search:  ${e}`)}}const Wd=Number.MIN_SAFE_INTEGER,Gd={TTT:\"F\",TTC:\"F\",TTA:\"L\",TTG:\"L\",CTT:\"L\",CTC:\"L\",CTA:\"L\",CTG:\"L\",ATT:\"I\",ATC:\"I\",ATA:\"I\",ATG:\"M\",GTT:\"V\",GTC:\"V\",GTA:\"V\",GTG:\"V\",TCT:\"S\",TCC:\"S\",TCA:\"S\",TCG:\"S\",CCT:\"P\",CCC:\"P\",CCA:\"P\",CCG:\"P\",ACT:\"T\",ACC:\"T\",ACA:\"T\",ACG:\"T\",GCT:\"A\",GCC:\"A\",GCA:\"A\",GCG:\"A\",TAT:\"Y\",TAC:\"Y\",TAA:\"STOP\",TAG:\"STOP\",CAT:\"H\",CAC:\"H\",CAA:\"Q\",CAG:\"Q\",AAT:\"N\",AAC:\"N\",AAA:\"K\",AAG:\"K\",GAT:\"D\",GAC:\"D\",GAA:\"E\",GAG:\"E\",TGT:\"C\",TGC:\"C\",TGA:\"STOP\",TGG:\"W\",CGT:\"R\",CGC:\"R\",CGA:\"R\",CGG:\"R\",AGT:\"S\",AGC:\"S\",AGA:\"R\",AGG:\"R\",GGT:\"G\",GGC:\"G\",GGA:\"G\",GGG:\"G\"},$d={},Kd=[\"A\",\"G\",\"C\",\"T\",\"Y\",\"R\",\"W\",\"S\",\"K\",\"M\",\"D\",\"V\",\"H\",\"B\",\"N\",\"X\"],Yd=[\"T\",\"C\",\"G\",\"A\",\"R\",\"Y\",\"W\",\"S\",\"M\",\"K\",\"H\",\"B\",\"D\",\"V\",\"N\",\"X\"];for(let NA=0;NA<Kd.length;NA++)$d[Kd[NA]]=Yd[NA],$d[Kd[NA].toLowerCase()]=Yd[NA].toLowerCase();const Xd=115;class Zd{constructor(e,t){this.config=e,this.browser=t,this.type=\"sequence\",this.removable=!0===e.removable,this.name=e.name,this.id=e.id,this.sequenceType=e.sequenceType||\"dna\",this.disableButtons=!1,this.order=e.order||Wd,this.ignoreTrackMenu=!1,this.reversed=!0===e.reversed,this.frameTranslate=!0===e.frameTranslate,this.height=this.frameTranslate?Xd:25,e.url&&(e.fastaURL=e.url),e.fastaURL||(this.id=e.id||\"sequence\")}menuItemList(){return[{name:this.reversed?\"Forward\":\"Reverse\",click:()=>{this.reversed=!this.reversed,this.trackView.repaintViews()}},{name:this.frameTranslate?\"Close Translation\":\"Three-frame Translate\",click:()=>{if(this.frameTranslate=!this.frameTranslate,this.frameTranslate){for(let e of this.trackView.viewports)e.setContentHeight(Xd);this.trackView.setTrackHeight(Xd)}else{for(let e of this.trackView.viewports)e.setContentHeight(25);this.trackView.setTrackHeight(25)}this.trackView.repaintViews()}}]}contextMenuItemList(e){const t=e.viewport;if(t.referenceFrame.bpPerPixel<=1){const e=t.getWidth()*t.referenceFrame.bpPerPixel,i=t.referenceFrame.chr,n=Math.floor(t.referenceFrame.start),r=Math.ceil(n+e),s=[{label:this.reversed?\"View visible sequence (reversed)...\":\"View visible sequence...\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);e?this.reversed&&(e=cc(e)):e=\"Unknown sequence\",this.browser.alert.present(e)}}];return Xa()&&s.push({label:\"Copy visible sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);e?this.reversed&&(e=cc(e)):e=\"Unknown sequence\";try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),s.push({label:\"BLAT read sequence\",click:async()=>{let e=await this.browser.genome.getSequence(i,n,r);if(e){this.reversed&&(e=cc(e));const t=`blat: ${i}:${n+1}-${r}`,s=`blat: ${i}:${n+1}-${r}`;jd({sequence:e,browser:this.browser,name:t,title:s})}}}),s.push(\"<hr/>\"),s}}translateSequence(e){const t=[[],[],[]];for(let i of[0,1,2]){let n=i;for(;e.length-n>=3;){let r=e.slice(n,n+3);this.reversed&&(r=r.split(\"\").reverse().join(\"\"));const s=Gd[r.toUpperCase()]||\"\";t[i].push({codons:r,aminoA:s}),n+=3}}return t}async getSequenceSource(){return this.config.fastaURL?(this.fasta||(this.fasta=new Jd(this.config,this.browser.genome),await this.fasta.init()),this.fasta):this.browser.genome}async getFeatures(e,t,i,n){if(t=Math.floor(t),i=Math.floor(i),n&&n>10)return null;{const n=await this.getSequenceSource();return{bpStart:t,sequence:await n.getSequence(e,t,i)}}}draw(e){const t=e.context;if(e.features){let i=e.features.sequence;if(!i)return;this.reversed&&(i=i.split(\"\").map((function(e){return $d[e]})).join(\"\"));const n=e.features.bpStart,r=1+e.bpStart+e.pixelWidth*e.bpPerPixel;for(let s=Math.floor(e.bpStart);s<=r;s++){const r=Math.floor(s-n);if(r>=0&&r<i.length){const n=(s-e.bpStart)/e.bpPerPixel,o=1/e.bpPerPixel,a=i[r],c=this.fillColor(a.toUpperCase());if(e.bpPerPixel>.1)xo.fillRect(t,n,5,o,10,{fillStyle:c});else{const i=n+.5*(o-t.measureText(a).width);\"y\"===e.axis?(t.save(),xo.labelTransformWithContext(t,i),xo.strokeText(t,a,i,15,{strokeStyle:c}),t.restore()):xo.strokeText(t,a,i,15,{strokeStyle:c})}}}if(this.frameTranslate){let r=25;const s=this.translateSequence(i);for(let i=0;i<s.length;i++){const o=s[i];for(let s=0;s<o.length;s++){let a=0==s%2?\"rgb(160,160,160)\":\"rgb(224,224,224)\";const c=o[s],l=n+i+3*s-e.bpStart,h=Math.floor(l/e.bpPerPixel),d=Math.floor((l+3)/e.bpPerPixel),u=Math.round((h+d)/2);if(d<0)continue;if(h>e.pixelWidth)break;let f=c.aminoA;c.aminoA.indexOf(\"STOP\")>-1?(a=\"rgb(255, 0, 0)\",f=\"STOP\"):\"M\"===c.aminoA&&(a=\"rgb(0, 153, 0)\",f=\"START\"),xo.fillRect(t,h,r,d-h,25,{fillStyle:a}),e.bpPerPixel<=.1&&xo.strokeText(t,f,u-t.measureText(f).width/2,r+15)}r+=30}}}}get supportsWholeGenome(){return!1}computePixelHeight(e){return this.height=this.frameTranslate?Xd:25,this.height}fillColor(e){return this.color?this.color:\"dna\"===this.sequenceType?this.browser.nucleotideColors[e]||\"gray\":\"rgb(0, 0, 150)\"}getState(){const e={type:\"sequence\"};return this.order!==Wd&&(e.order=this.order),this.reversed&&(e.revealed=!0),e}}class Jd{constructor(e,t){this.config=e,this.genome=t}async init(){this.fasta=await Nc(this.config),this.chrNameMap=new Map;for(let e of this.fasta.chromosomeNames)this.chrNameMap.set(this.genome.getChromosomeName(e),e)}async getSequence(e,t,i){const n=this.chrNameMap.has(e)?this.chrNameMap.get(e):e;return this.fasta.getSequence(n,t,i)}}class eu{constructor(e,t,i,n){this.guid=s(),this.trackView=e,this.referenceFrame=i,this.browser=e.browser,this.$viewport=Bt('<div class=\"igv-viewport\">'),t.appendChild(this.$viewport.get(0)),e.track.height&&(this.$viewport.get(0).style.height=`${e.track.height}px`),e.track instanceof Zd&&(this.alert=new Ta(this.$viewport.get(0))),this.contentTop=0,this.contentHeight=this.$viewport.height(),this.$viewport.width(n),this.initializationHelper()}initializationHelper(){}showMessage(e){this.messageDiv||(this.messageDiv=document.createElement(\"div\"),this.messageDiv.className=\"igv-viewport-message\",this.$viewport.append(Bt(this.messageDiv))),this.messageDiv.textContent=e,this.messageDiv.style.display=\"inline-block\"}hideMessage(e){this.messageDiv&&(this.messageDiv.style.display=\"none\")}setTrackLabel(e){}startSpinner(){}stopSpinner(){}checkZoomIn(){return!0}shift(){}setTop(e){this.contentTop=e,this.$viewport.height()}async loadFeatures(){}clearCache(){}repaint(){}draw(e,t,i){console.log(\"Viewport - draw(drawConfiguration, features, roiFeatures)\")}checkContentHeight(e){let t=this.trackView.track;if(e=e||this.cachedFeatures,\"FILL\"===t.displayMode)this.setContentHeight(this.$viewport.height());else if(\"function\"==typeof t.computePixelHeight&&e&&e.length>0){let i=t.computePixelHeight(e);i!==this.contentHeight&&this.setContentHeight(i)}}getContentHeight(){return this.contentHeight}setContentHeight(e){this.contentHeight=e}isLoading(){return!1}saveSVG(){}isVisible(){return this.$viewport.width()}setWidth(e){this.$viewport.width(e)}getWidth(){return this.$viewport.width()}getContentTop(){return this.contentTop}containsPosition(e,t){console.log(\"Viewport - containsPosition(chr, position)\")}addMouseHandlers(){}removeMouseHandlers(){}dispose(){this.$viewport.get(0).remove();for(let e of Object.keys(this))this[e]=void 0}}\n",
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-       "     *  Canvas 2 Svg v1.0.19\n",
-       "     *  A low level canvas to SVG converter. Uses a mock canvas context to build an SVG document.\n",
-       "     *\n",
-       "     *  Licensed under the MIT license:\n",
-       "     *  http://www.opensource.org/licenses/mit-license.php\n",
-       "     *\n",
-       "     *  Author:\n",
-       "     *  Kerry Liu\n",
-       "     *\n",
-       "     *  Copyright (c) 2014 Gliffy Inc.\n",
-       "     */function tu(e,t){var i,n=Object.keys(t);for(i=0;i<n.length;i++)e=e.replace(new RegExp(\"\\\\{\"+n[i]+\"\\\\}\",\"gi\"),t[n[i]]);return e}function iu(e){var t,i,n;if(!e)throw new Error(\"cannot create a random attribute name for an undefined object\");t=\"ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz\",i=\"\";do{for(i=\"\",n=0;n<12;n++)i+=t[Math.floor(51*Math.random())]}while(e[i]);return i}function nu(e){var t={alphabetic:\"alphabetic\",hanging:\"hanging\",top:\"text-before-edge\",bottom:\"text-after-edge\",middle:\"central\"};return t[e]||t.alphabetic}function ru(e){var t=Math.sqrt(e[0]*e[0]+e[1]*e[1]);return[e[0]/t,e[1]/t]}const su=function(e,t){var i,n,r,s={};for(e=e.split(\",\"),t=t||10,i=0;i<e.length;i+=2)n=\"&\"+e[i+1]+\";\",r=parseInt(e[i],t),s[n]=\"&#\"+r+\";\";return 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Error(\"Invalid number of arguments passed to drawImage: \"+arguments.length);g=f[1],m=f[2],r=f[3],s=f[4],e=f[5],t=f[6],i=f[7],n=f[8]}o=this.__closestGroupOrSvg(),this.__currentElement;var w=\"translate(\"+e+\", \"+t+\")\";if(p instanceof lu){if((a=p.getSvg().cloneNode(!0)).childNodes&&a.childNodes.length>1){for(c=a.childNodes[0];c.childNodes.length;)u=c.childNodes[0].getAttribute(\"id\"),this.__ids[u]=u,this.__defs.appendChild(c.childNodes[0]);if(l=a.childNodes[1]){var b,F=l.getAttribute(\"transform\");b=F?F+\" \"+w:w,l.setAttribute(\"transform\",b),o.appendChild(l)}}}else\"CANVAS\"!==p.nodeName&&\"IMG\"!==p.nodeName||((h=this.__createElement(\"image\")).setAttribute(\"width\",i),h.setAttribute(\"height\",n),h.setAttribute(\"preserveAspectRatio\",\"none\"),(g||m||r!==p.width||s!==p.height)&&((d=this.__document.createElement(\"canvas\")).width=i,d.height=n,d.getContext(\"2d\").drawImage(p,g,m,r,s,0,0,i,n),p=d),h.setAttribute(\"transform\",w),h.setAttributeNS(\"http://www.w3.org/1999/xlink\",\"xlink:href\",\"CANVAS\"===p.nodeName?p.toDataURL():p.getAttribute(\"src\")),o.appendChild(h))}createPattern(e,t){let i,n=this.__document.__createElement(\"pattern\"),r=iu(this.__ids);return n.setAttribute(\"id\",r),n.setAttribute(\"width\",e.width),n.setAttribute(\"height\",e.height),\"CANVAS\"===e.nodeName||\"IMG\"===e.nodeName?(i=this.__createElement(\"image\"),i.setAttribute(\"width\",e.width),i.setAttribute(\"height\",e.height),i.setAttributeNS(\"http://www.w3.org/1999/xlink\",\"xlink:href\",\"CANVAS\"===e.nodeName?e.toDataURL():e.getAttribute(\"src\")),n.appendChild(i),this.__defs.appendChild(n)):e instanceof lu&&(n.appendChild(e.__root.childNodes[1]),this.__defs.appendChild(n)),new cu(n,this)}setLineDash(e){e&&e.length>0?this.lineDash=e.join(\",\"):this.lineDash=null}drawFocusRing(){}createImageData(){}getImageData(){}putImageData(){}globalCompositeOperation(){}setTransform(){}}function hu(e){if(e.startsWith(\"GCF\")||e.startsWith(\"GCA\")&&e.length>=13){return\"https://hgdownload.soe.ucsc.edu/hubs/\"+e.substring(0,3)+\"/\"+e.substring(4,7)+\"/\"+e.substring(7,10)+\"/\"+e.substring(10,13)+\"/\"+e+\"/hub.txt\"}}class du{static supportedTypes=new Set([\"bigBed\",\"bigWig\",\"bigGenePred\",\"vcfTabix\"]);static filterTracks=new Set([\"cytoBandIdeo\",\"assembly\",\"gap\",\"gapOverlap\",\"allGaps\",\"cpgIslandExtUnmasked\",\"windowMasker\"]);static async loadHub(e){const t=e.lastIndexOf(\"/\"),i=e.substring(0,t+1),n=await pu(e);let r;if(\"genome\"===n[1].type){const e=n[1];if(e.hasProperty(\"groups\")){const t=i+e.getProperty(\"groups\");r=await pu(t)}if(e.hasProperty(\"chromSizes\")){const t=i+e.getProperty(\"chromSizes\"),n=await async function(e){try{const t=(await fetch(e,{method:\"HEAD\"})).headers;return t.has(\"content-length\")?t.get(\"content-length\"):null}catch(e){return null}}(t);null!==n&&Number.parseInt(n)<1e6&&e.setProperty(\"chromSizesURL\",t)}}return new du(e,n,r)}constructor(e,t,i){this.url=e;const n=e.lastIndexOf(\"/\");if(this.baseURL=e.substring(0,n+1),\"hub\"!==t[0].type)throw Error(\"Unexpected hub.txt file -- does the first line start with 'hub'?\");if(this.hubStanza=t[0],\"on\"!==this.hubStanza.getProperty(\"useOneFile\"))throw Error(\"Only 'useOneFile' hubs are currently supported\");if(t.length<2)throw Error(\"Expected at least 2 stanzas, hub and genome\");if(\"genome\"!==t[1].type)throw Error(`Unexpected hub file -- expected \"genome\" stanza but found \"${t[1].type}\"`);this.genomeStanza=t[1],this.trackStanzas=[];for(let e=2;e<t.length;e++)\"track\"===t[e].type&&this.trackStanzas.push(t[e]);if(i){this.groupStanzas=i,this.groupPriorityMap=new Map;for(let e of i)e.hasProperty(\"priority\")&&this.groupPriorityMap.set(e.getProperty(\"name\"),10*Number.parseInt(e.getProperty(\"priority\")))}}getDefaultPosition(){return this.genomeStanza.getProperty(\"defaultPos\")}getGenomeConfig(e={}){const t=this.genomeStanza.getProperty(\"genome\"),i=this.hubStanza.getProperty(\"shortLabel\")||this.genomeStanza.getProperty(\"scientificName\")||this.genomeStanza.getProperty(\"organism\")||this.genomeStanza.getProperty(\"description\"),n=i+(i?` (${t})`:` ${t}`),r={hubURL:this.url,id:t,name:n,twoBitURL:this.baseURL+this.genomeStanza.getProperty(\"twoBitPath\"),nameSet:\"ucsc\"};if(this.genomeStanza.hasProperty(\"chromSizesURL\")?r.chromSizesURL=this.genomeStanza.getProperty(\"chromSizesURL\"):(r.wholeGenomeView=!1,r.showChromosomeWidget=!1),this.genomeStanza.hasProperty(\"defaultPos\")){const e=this.genomeStanza.getProperty(\"defaultPos\");if(e){const t=e.lastIndexOf(\":\");r.locus=t>0?e.substring(0,t):e}}this.genomeStanza.hasProperty(\"blat\")&&(r.blat=this.baseURL+this.genomeStanza.getProperty(\"blat\")),this.genomeStanza.hasProperty(\"chromAliasBb\")&&(r.chromAliasBbURL=this.baseURL+this.genomeStanza.getProperty(\"chromAliasBb\")),this.genomeStanza.hasProperty(\"chromAlias\")&&(r.aliasURL=this.baseURL+this.genomeStanza.getProperty(\"chromAlias\")),this.genomeStanza.hasProperty(\"twoBitBptURL\")&&(r.twoBitBptURL=this.baseURL+this.genomeStanza.getProperty(\"twoBitBptURL\")),this.genomeStanza.hasProperty(\"twoBitBptUrl\")&&(r.twoBitBptURL=this.baseURL+this.genomeStanza.getProperty(\"twoBitBptUrl\")),e.includeChromSizes&&this.genomeStanza.hasProperty(\"chromSizes\")&&(r.chromSizesURL=this.baseURL+this.genomeStanza.getProperty(\"chromSizes\")),this.hubStanza.hasProperty(\"longLabel\")?r.description=this.hubStanza.getProperty(\"longLabel\").replace(\"/\",\"\\n\"):(r.description=r.id,this.genomeStanza.hasProperty(\"description\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"description\")}`),this.genomeStanza.hasProperty(\"organism\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"organism\")}`),this.genomeStanza.hasProperty(\"scientificName\")&&(r.description+=`\\n${this.genomeStanza.getProperty(\"scientificName\")}`),this.genomeStanza.hasProperty(\"htmlPath\")&&(r.infoURL=this.baseURL+this.genomeStanza.getProperty(\"htmlPath\")));const s=this.trackStanzas.filter((e=>\"cytoBandIdeo\"===e.name&&e.hasProperty(\"bigDataUrl\")));s.length>0&&(r.cytobandBbURL=this.baseURL+s[0].getProperty(\"bigDataUrl\"));return r.tracks=this.#g((e=>!du.filterTracks.has(e.name)&&\"hide\"!==e.getProperty(\"visibility\"))),r}getGroupedTrackConfigurations(){const e=new Map;for(let t of this.#g()){if(\"cytoBandIdeo\"===t.name)continue;const i=t.group||\"other\";e.has(i)?e.get(i).push(t):e.set(i,[t])}const t=this.groupStanzas?new Map(this.groupStanzas.map((e=>[e.getProperty(\"name\"),e]))):new Map;return Array.from(e.keys()).map((i=>({label:t.has(i)?t.get(i).getProperty(\"label\"):i,tracks:e.get(i)})))}#g(e){return this.trackStanzas.filter((t=>du.supportedTypes.has(t.format)&&t.hasProperty(\"bigDataUrl\")&&(!e||e(t)))).map((e=>this.#m(e)))}#m(e){const t=e.format,i={id:e.getProperty(\"track\"),name:e.getProperty(\"shortLabel\"),format:t,url:this.baseURL+e.getProperty(\"bigDataUrl\"),displayMode:e.displayMode};if(\"vcfTabix\"===t&&(i.indexURL=i.url+\".tbi\"),e.hasProperty(\"longLabel\")&&e.hasProperty(\"html\")?(i.description&&(i.description+=\"<br/>\"),i.description=`<a target=\"_blank\" href=\"${this.baseURL+e.getProperty(\"html\")}\">${e.getProperty(\"longLabel\")}</a>`):e.hasProperty(\"longLabel\")&&(i.description=e.getProperty(\"longLabel\")),e.hasProperty(\"autoScale\")&&(i.autoscale=\"on\"===e.getProperty(\"autoScale\").toLowerCase()),e.hasProperty(\"maxHeightPixels\")){const t=e.getProperty(\"maxHeightPixels\").split(\":\");i.maxHeight=Number.parseInt(t[0]),i.height=Number.parseInt(t[1]),i.minHeight=Number.parseInt(t[2])}if(e.hasProperty(\"color\")){const t=e.getProperty(\"color\");i.color=t.indexOf(\",\")>0?`rgb(${t})`:t}if(e.hasProperty(\"altColor\")){const t=e.getProperty(\"altColor\");i.altColor=t.indexOf(\",\")>0?`rgb(${t})`:t}if(e.hasProperty(\"viewLimits\")){const t=e.getProperty(\"viewLimits\").split(\":\");let n,r;t.length>1&&(n=Number.parseInt(t[0]),r=Number.parseInt(t[1])),Number.isNaN(r)||Number.isNaN(n)?console.warn(`Unexpected viewLimits value in track line: ${properties.viewLimits}`):(i.min=n,i.max=r)}if(e.hasProperty(\"itemRgb\"),\"hide\"===e.getProperty(\"visibility\")&&(i.visible=!1),e.hasProperty(\"url\")&&(i.infoURL=e.getProperty(\"url\")),e.hasProperty(\"searchIndex\")&&(i.searchIndex=e.getProperty(\"searchIndex\")),e.hasProperty(\"searchTrix\")&&(i.trixURL=this.baseURL+e.getProperty(\"searchTrix\")),e.hasProperty(\"group\")&&(i.group=e.getProperty(\"group\"),this.groupPriorityMap&&this.groupPriorityMap.has(i.group))){const e=this.groupPriorityMap.get(i.group)+1;i.order=e,this.groupPriorityMap.set(i.group,e)}return i}}function uu(e){const t=e.indexOf(\" \");return t>0?e.substring(0,t):e}class fu{properties=new Map;constructor(e,t){this.type=e,this.name=t}setProperty(e,t){this.properties.set(e,t)}getProperty(e){return this.properties.has(e)?this.properties.get(e):this.parent?this.parent.getProperty(e):void 0}hasProperty(e){return!!this.properties.has(e)||!!this.parent&&this.parent.hasProperty(e)}get format(){const e=this.getProperty(\"type\");if(e)return uu(e)}get displayMode(){let e=this.getProperty(\"visibility\");if(!e)return\"COLLAPSED\";switch(e=e.toLowerCase(),e){case\"dense\":default:return\"COLLAPSED\";case\"pack\":return\"EXPANDED\";case\"squish\":return\"SQUISHED\"}}}async function pu(e){const t=await fetch(e),i=(await t.text()).split(/\\n|\\r\\n|\\r/g),n=[];let r,s=!0;for(let e of i){const t=gu(e),i=e.indexOf(\" \",t);if(i<0)s=!0;else{const o=e.substring(t,i).trim();if(o.startsWith(\"#\"))continue;const a=e.substring(i+1).trim();if(s){const e=new fu(o,a);n.push(e),r=e,s=!1}r.setProperty(o,a)}}return function(e){const t=new Map;for(let i of e)t.set(i.name,i);for(let i of e)if(i.properties.has(\"parent\")){const e=uu(i.properties.get(\"parent\"));i.parent=t.get(e)}return e}(n)}function gu(e){let t=0;for(t=0;t<e.length;t++){const i=e.charAt(t);if(\" \"!==i&&\"\\t\"!==i)break}return t}const mu={initializeGenomes:async function(e){if(!mu.KNOWN_GENOMES){const t={};if(!1!==e.loadDefaultGenomes){const r=\"https://igv.org/genomes/genomes.json\";n(await Qs.loadJson(r,{timeout:5e3}))}const i=e.genomeList||e.genomes;if(i)if(\"string\"==typeof i){n(await Qs.loadJson(i,{}))}else n(i);function n(e){return e.forEach((function(e){t[e.id]=e})),t}mu.KNOWN_GENOMES=t}},isWholeGenomeView:function(e){return\"all\"===e.toLowerCase()},expandReference:async function(e,t){if(Mt(t)&&t.startsWith(\"{\"))try{t=JSON.parse(t)}catch(e){}let i;if(Mt(t)?i=t:t.genome?i=t.genome:void 0===t.id||t.fastaURL||t.twobitURL||(i=t.id),i){let t=mu.KNOWN_GENOMES[i];if(!t){if((i.startsWith(\"GCA_\")||i.startsWith(\"GCF_\"))&&i.length>=13)try{const e=hu(i);t=(await du.loadHub(e)).getGenomeConfig()}catch(e){console.error(e)}t||e.present(new Error(`Unknown genome id: ${i}`),void 0)}return t}return t}};let wu,bu,Fu=0,vu=0,yu=[];class Au extends eu{constructor(e,t,i,n){super(e,t,i,n)}initializationHelper(){this.$spinner=Bt(\"<div>\",{class:\"igv-loading-spinner-container\"}),this.$viewport.append(this.$spinner),this.$spinner.append(Bt(\"<div>\"));const e=this.trackView.track;\"sequence\"!==e.type&&(this.$zoomInNotice=this.createZoomInNotice(this.$viewport)),\"sequence\"!==e.id&&(this.$trackLabel=Bt('<div class=\"igv-track-label\">'),this.$viewport.append(this.$trackLabel),this.setTrackLabel(e.name||\"\"),!1===this.browser.doShowTrackLabels&&this.$trackLabel.hide()),this.stopSpinner(),this.addMouseHandlers()}setContentHeight(e){super.setContentHeight(e),this.featureCache&&(this.featureCache.redraw=!0)}setTrackLabel(e){this.$trackLabel.empty(),this.$trackLabel.html(e);const t=this.$trackLabel.text();this.$trackLabel.attr(\"title\",t)}startSpinner(){this.$spinner.show()}stopSpinner(){this.$spinner&&this.$spinner.hide()}checkZoomIn(){if(this.trackView.track&&\"sequence\"===this.trackView.track.type&&this.referenceFrame.bpPerPixel>10)return Bt(this.canvas).remove(),this.canvas=void 0,!1;if(!this.viewIsReady())return!1;if((()=>{if(\"all\"!==this.referenceFrame.chr.toLowerCase()||this.trackView.track.supportsWholeGenome){const e=this.trackView.track.visibilityWindow;return void 0!==e&&e>0&&this.referenceFrame.bpPerPixel*this.$viewport.width()>e}return!0})()){if(this.canvas&&(Bt(this.canvas).remove(),this.canvas=void 0),this.trackView.track.autoHeight){const e=this.trackView.minHeight||0;this.setContentHeight(e)}return this.$zoomInNotice&&this.$zoomInNotice.show(),!1}return this.$zoomInNotice&&this.$zoomInNotice.hide(),!0}shift(){const e=this.referenceFrame;this.canvas&&this.canvas._data&&this.canvas._data.referenceFrame.chr===this.referenceFrame.chr&&this.canvas._data.bpPerPixel===e.bpPerPixel&&(this.canvas._data.pixelShift=Math.round((this.canvas._data.bpStart-e.start)/e.bpPerPixel),this.canvas.style.left=this.canvas._data.pixelShift+\"px\")}genomicRange(){return{start:this.referenceFrame.start,end:this.referenceFrame.start+this.referenceFrame.bpPerPixel*this.$viewport.width()}}setTop(e){if(super.setTop(e),this.canvas){const t=this.$viewport.height(),i=e+this.canvas._data.pixelTop,n=i+this.canvas._data.pixelHeight;(i>0||n<t)&&this.repaint()}else this.repaint();if(this.canvas&&this.canvas._data){let t=e+this.canvas._data.pixelTop;this.canvas.style.top=`${t}px`}}async loadFeatures(){const e=this.referenceFrame,t=e.chr,i=await this.browser.genome.loadChromosome(t),n=i?i.bpLength:Number.MAX_SAFE_INTEGER,r=this.$viewport.width()*e.bpPerPixel,s=Math.floor(Math.max(0,e.start-r)),o=Math.ceil(Math.min(n,e.start+r+r));if(!this.loading||this.loading.start!==s||this.loading.end!==o){this.loading={start:s,end:o},this.startSpinner();try{const i=this.trackView.track,n=await this.getFeatures(i,t,s,o,e.bpPerPixel);if(n){let r=[];if(i.roiSets&&i.roiSets.length>0)for(let n of i.roiSets){const i=await n.getFeatures(t,s,o,e.bpPerPixel);r.push({track:n,features:i})}const a=i&&i.resolutionAware,c=this.windowFunction;return this.featureCache=new Cu(t,s,o,e.bpPerPixel,n,r,a,c),this.loading=!1,this.hideMessage(),this.stopSpinner(),this.featureCache}}catch(e){this.trackView&&!0!==this.trackView.disposed&&(this.showMessage(\"Error loading track data\"),this.browser.alert.present(e),console.error(e))}finally{this.loading=!1,this.stopSpinner()}}}get track(){return this.trackView.track}get windowFunction(){return this.track?this.track.windowFunction:void 0}repaintDimensions(){const e=mu.isWholeGenomeView(this.referenceFrame.chr),t=e?this.$viewport.width():3*this.$viewport.width(),i=this.referenceFrame.bpPerPixel;return{bpStart:this.referenceFrame.start-(e?0:this.$viewport.width()*i),bpEnd:e?Number.MAX_SAFE_INTEGER:this.referenceFrame.start+2*this.$viewport.width()*i+1,pixelWidth:t}}repaint(){if(void 0===this.featureCache)return;const{features:e,roiFeatures:t}=this.featureCache,{bpStart:i,bpEnd:n,pixelWidth:r}=this.repaintDimensions(),s=this.$viewport.height(),o=this.getContentHeight(),a=t?Math.max(o,s):o,c=Math.min(a,3*s);if(0===r||0===c)return void(this.canvas&&Bt(this.canvas).remove());const l=Math.max(0,-this.contentTop-Math.floor(c/3)),h=this.referenceFrame.bpPerPixel,d=Math.round((i-this.referenceFrame.start)/h),u=(this.contentTop||0)+l,f=document.createElement(\"canvas\");f.style.position=\"relative\",f.style.display=\"block\",f.style.width=r+\"px\",f.style.height=c+\"px\",f.style.left=d+\"px\",f.style.top=u+\"px\";const p=\"FILL\"===this.trackView.track.displayMode||!1!==this.trackView.track.supportHiDPI?window.devicePixelRatio:1;f.width=p*r,f.height=p*c;const g=f.getContext(\"2d\");g.scale(p,p),g.translate(0,-l);const m={context:g,pixelXOffset:d,pixelWidth:r,pixelHeight:c,pixelTop:l,bpStart:i,bpEnd:n,bpPerPixel:h,pixelShift:d,windowFunction:this.windowFunction,referenceFrame:this.referenceFrame,selection:this.selection,viewport:this,viewportWidth:this.$viewport.width()};this.draw(m,e,t),this.canvas&&Bt(this.canvas).remove(),f._data=m,this.canvas=f,this.$viewport.append(Bt(f))}refresh(){if(!this.canvas||!this.featureCache)return;const e=this.canvas._data;e.context.clearRect(0,0,this.canvas.width,this.canvas.height);const{features:t,roiFeatures:i}=this.featureCache;this.draw(e,t,i)}draw(e,t,i){if(t&&(e.features=t,this.trackView.track.draw(e)),i&&i.length>0)for(let t of i)e.features=t.features,t.track.draw(e)}containsPosition(e,t){return this.referenceFrame.chr===e&&t>=this.referenceFrame.start&&t<=this.referenceFrame.calculateEnd(this.getWidth())}isLoading(){return this.loading}savePNG(){if(!this.canvas)return;const e=this.canvas._data,t=e?e.pixelTop:0,i=window.devicePixelRatio,n=this.$viewport.width()*i,r=this.$viewport.height()*i,s=-Bt(this.canvas).position().left*i,o=(-this.contentTop-t)*i,a=this.canvas.getContext(\"2d\").getImageData(s,o,n,r),c=document.createElement(\"canvas\"),l=c.getContext(\"2d\");c.width=a.width,c.height=a.height,l.putImageData(a,0,0);Pt((this.$trackLabel.text()?this.$trackLabel.text():\"image\")+\".png\",c.toDataURL(\"image/png\"))}saveSVG(){let{width:e,height:t}=this.browser.columnContainer.getBoundingClientRect();const i=new lu({width:e,height:8e3,backdropColor:\"white\",multiLocusGap:0,viewbox:{x:0,y:0,width:e,height:8e3}}),n={deltaX:32,deltaY:32};this.renderSVGContext(i,n,!1),i.setHeight(t);const r=(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\"),o=this.browser.referenceFrameList.indexOf(this.referenceFrame),a=i.getSerializedSvg(!0),c=URL.createObjectURL(new Blob([a],{type:\"application/octet-stream\"}));Pt(`${`${r}_referenceFrame_${o}_guid_${s()}`}.svg`,c)}renderSVGContext(e,{deltaX:t,deltaY:i},n=!0){if(!(this.$zoomInNotice&&this.$zoomInNotice.is(\":visible\"))){const{width:n,height:r}=this.$viewport.get(0).getBoundingClientRect(),o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${s()}`,a=t,c=i+this.contentTop,l=-this.contentTop;e.saveWithTranslationAndClipRect(o,a,c,n,r,l);const{start:h,bpPerPixel:d}=this.referenceFrame,u=Math.round((h-this.referenceFrame.start)/d),f={context:e,viewport:this,referenceFrame:this.referenceFrame,top:l,pixelTop:l,pixelWidth:n,pixelHeight:r,pixelXOffset:u,pixelShift:u,bpStart:h,bpEnd:h+n*d,bpPerPixel:d,viewportWidth:n,selection:this.selection},p=this.featureCache?this.featureCache.features:void 0,g=this.featureCache?this.featureCache.roiFeatures:void 0;this.draw(f,p,g),e.restore()}if(n&&this.$trackLabel&&this.browser.doShowTrackLabels){const{x:n,y:r,width:s,height:o}=((e,t)=>{const{x:i,y:n,width:r,height:s}=e.getBoundingClientRect(),{x:o,y:a,width:c,height:l}=t.getBoundingClientRect();return{x:o-i,y:a-n,width:c,height:l}})(this.$viewport.get(0),this.$trackLabel.get(0));this.renderTrackLabelSVG(e,t+n,i+r,s,o)}}renderTrackLabelSVG(e,t,i,n,r){const o=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_track_label_guid_${s()}`;e.saveWithTranslationAndClipRect(o,t,i,n,r,0),e.fillStyle=\"white\",e.fillRect(0,0,n,r),e.font=\"12px Arial\",e.fillStyle=\"rgb(68, 68, 68)\";const{width:a}=e.measureText(this.$trackLabel.text()),c=.25*(n-a),l=.7*(r-12);e.fillText(this.$trackLabel.text(),c,r-l),e.strokeStyle=\"rgb(68, 68, 68)\",e.strokeRect(0,0,n,r),e.restore()}get cachedFeatures(){return this.featureCache?this.featureCache.features:[]}clearCache(){this.featureCache=void 0,this.canvas&&(this.canvas._data=void 0)}async getFeatures(e,t,i,n,r){if(this.featureCache&&this.featureCache.containsRange(t,i,n,r,this.windowFunction))return this.featureCache.features;if(\"function\"==typeof e.getFeatures){const s=await e.getFeatures(t,i,n,r,this);return this.checkContentHeight(s),s}}needsRepaint(){if(!this.canvas)return!0;const e=this.canvas._data;return!e||this.referenceFrame.start<e.bpStart||this.referenceFrame.end>e.bpEnd||this.referenceFrame.chr!==e.referenceFrame.chr||this.referenceFrame.bpPerPixel!=e.bpPerPixel||this.windowFunction!=e.windowFunction}needsReload(){if(!this.featureCache)return!0;const{chr:e,bpPerPixel:t}=this.referenceFrame,{bpStart:i,bpEnd:n}=this.repaintDimensions();return!this.featureCache.containsRange(e,i,n,t,this.windowFunction)}createZoomInNotice(e){const t=Bt(\"<div>\",{class:\"igv-zoom-in-notice-container\"});e.append(t);const i=Bt(\"<div>\");return t.append(i),i.text(\"Zoom in to see features\"),t.hide(),t}viewIsReady(){return this.browser&&this.browser.referenceFrameList&&this.referenceFrame}addMouseHandlers(){const e=this.$viewport.get(0);this.addViewportContextMenuHandler(e);const t=e=>{this.enableClick=!0,this.browser.mouseDownOnViewport(e,this),r(e)};e.addEventListener(\"mousedown\",t),e.addEventListener(\"touchstart\",t);const i=e=>{this.browser.dragObject||this.browser.isScrolling?(this.browser.cancelTrackPan(),this.enableClick=!1):(this.browser.cancelTrackPan(),this.browser.endTrackDrag())};e.addEventListener(\"mouseup\",i),e.addEventListener(\"touchend\",i),\"function\"==typeof this.trackView.track.hoverText&&e.addEventListener(\"mousemove\",(e=>{if(0===e.buttons&&Date.now()-vu>100){vu=Date.now();const t=this.createClickState(e);if(t){const e=this.trackView.track.hoverText(t);e?this.$viewport[0].setAttribute(\"title\",e):this.$viewport[0].removeAttribute(\"title\")}}})),this.addViewportClickHandler(this.$viewport.get(0)),this.trackView.track.name&&\"sequence\"!==this.trackView.track.config.type&&this.addTrackLabelClickHandler(this.$trackLabel.get(0))}addViewportContextMenuHandler(e){e.addEventListener(\"contextmenu\",(e=>{if(this.browser.dragObject)return!1;const t=this.createClickState(e);if(void 0===t)return!1;e.preventDefault();let i=[];if(\"function\"==typeof this.trackView.track.contextMenuItemList){const e=this.trackView.track.contextMenuItemList(t);e&&(i=e)}i.length>0&&i.push({label:Bt(\"<HR>\")}),i.push({label:\"Save Image (PNG)\",click:()=>this.savePNG()}),i.push({label:\"Save Image (SVG)\",click:()=>this.saveSVG()}),this.browser.menuPopup.presentTrackContextMenu(e,i)}))}addViewportClickHandler(e){e.addEventListener(\"click\",(e=>{if(this.enableClick&&this.canvas){if(3===e.which||e.ctrlKey)return;if(this.browser.dragObject||this.browser.isScrolling)return;e.preventDefault();const t=a(e,this.$viewport.get(0)).x,i=a(e,this.canvas).x,n=this.referenceFrame;Math.floor(n.start+n.toBP(i));const r=Date.now();if(r-Fu<this.browser.constants.doubleClickDelay){wu&&(window.clearTimeout(wu),wu=void 0);const e=Math.round(n.start+n.toBP(t));let i;if(\"all\"===this.referenceFrame.chr.toLowerCase()){const t=this.browser.genome.getChromosomeCoordinate(e).chr;if(1===this.browser.referenceFrameList.length)i=t;else{const e=this.browser.referenceFrameList.map((({locusSearchString:e})=>e));e[this.browser.referenceFrameList.indexOf(this.referenceFrame)]=t,i=e.join(\" \")}this.browser.search(i)}else this.browser.zoomWithScaleFactor(.5,e,this.referenceFrame)}else\"function\"==typeof this.trackView.track.popupData&&(wu=setTimeout((()=>{const t=this.getPopupContent(e);if(t)if(!1===e.shiftKey){if(bu&&bu.dispose(),yu.length>0){for(const e of yu)e.dispose();yu.length=0}bu=new tc(this.$viewport.get(0).parentElement,!0,void 0,(()=>{bu.dispose()})),bu.presentContentWithEvent(e,t)}else{let i=new tc(this.$viewport.get(0).parentElement,!0,void 0,(()=>{const e=yu.indexOf(i);yu.splice(e,1),i.dispose()}));yu.push(i),i.presentContentWithEvent(e,t)}window.clearTimeout(wu),wu=void 0}),this.browser.constants.doubleClickDelay));Fu=r}}))}addTrackLabelClickHandler(e){e.addEventListener(\"click\",(e=>{e.stopPropagation();const{track:t}=this.trackView;let i;\"function\"==typeof t.description?i=t.description():t.description&&(i=`<div>${t.description}</div>`),i&&(void 0===this.popover&&(this.popover=new tc(this.browser.columnContainer,!0,t.name||\"\",void 0)),this.popover.presentContentWithEvent(e,i))}))}createClickState(e){if(!this.canvas)return;const t=this.referenceFrame,i=a(e,this.$viewport.get(0)),n=a(e,this.canvas),r=t.start+t.toBP(i.x);return{event:e,viewport:this,referenceFrame:t,genomicLocation:r,y:i.y-this.contentTop,canvasX:n.x,canvasY:n.y}}getPopupContent(e){const t=this.createClickState(e);if(void 0===t)return;let i=this.trackView.track;const n=i.popupData(t),r=this.browser.fireEvent(\"trackclick\",[i,n]);let s;return void 0===r||!0===r?n&&n.length>0&&(s=n.map((e=>{if(e.name){const t=`<span>${e.name}</span>&nbsp&nbsp&nbsp${e.value}`;return`<div title=\"${e.value}\">${t}</div>`}return\"<hr>\"===e?e:e.html?e.html:`<div title=\"${e}\">${e}</div>`})).join(\"\")):\"string\"==typeof r&&(s=r),s}dispose(){this.popover&&this.popover.dispose(),super.dispose()}}class Cu{constructor(e,t,i,n,r,s,o,a){this.chr=e,this.bpStart=t,this.bpEnd=i,this.bpPerPixel=n,this.features=r,this.roiFeatures=s,this.multiresolution=o,this.windowFunction=a}containsRange(e,t,i,n,r){if(r&&r!==this.windowFunction)return!1;const s=this.multiresolution?this.bpPerPixel/n:1;return t>=this.bpStart&&i<=this.bpEnd&&e===this.chr&&s>.5&&s<2}overlapsRange(e,t,i){return this.chr===e&&i>=this.bpStart&&t<=this.bpEnd}}const _u=function(e,t){const{r:i,g:n,b:r}=no[e];return`rgba(${i},${n},${r},${t})`}(\"nickel\",2/16),xu=_u;class ku{constructor(e,t){if(this.url=e.url,e.name&&(this.name=e.name),this.isUserDefined=e.isUserDefined,e.featureSource)this.featureSource=e.featureSource;else if(e.features)this.featureSource=new Su(e.features,t);else{if(!e.format)throw Error(\"ROI configuration must define either features or file format\");this.featureSource=Ad(e,t)}!0===this.isUserDefined?(this.color=e.color||xu,this.headerColor=\"rgba(155,185,129)\"):(this.color=e.color||_u,this.headerColor=\"rgb(190,190,190)\"),this.isVisible=void 0===e.isVisible||e.isVisible}async getFeatures(e,t,i){return this.featureSource.getFeatures({chr:e,start:t,end:i})}async getAllFeatures(){return\"function\"==typeof this.featureSource.getAllFeatures?await this.featureSource.getAllFeatures():{}}addFeature(e){this.featureSource.addFeature(e)}removeFeature(e){this.featureSource.removeFeature(e)}toJSON(){if(this.url)return{name:this.name,color:this.color,url:this.url,isUserDefined:this.isUserDefined,isVisible:this.isVisible};{const e=this.featureSource.getAllFeatures(),t=[];for(let i of Object.keys(e))for(let n of e[i])t.push(n);return{name:this.name,color:this.color,features:t,isUserDefined:this.isUserDefined,isVisible:this.isVisible}}}dispose(){for(let e of Object.keys(this))this[e]=void 0}}function Iu(e,t,i,n){let r=Math.round((e-i)/n);let s=Math.round((t-i)/n)-r;return s<3&&(s=3,r-=1),{x:r,width:s}}class Su{constructor(e,t){this.featureMap={},this.genome=t;for(let i of e){const e=t?t.getChromosomeName(i.chr):i.chr;let n=this.featureMap[e];n||(n=[],this.featureMap[e]=n),n.push(i)}for(let e of Object.keys(this.featureMap))this.featureMap[e].sort(((e,t)=>e.start-t.start))}async getFeatures({chr:e,start:t,end:i}){if(\"all\"===e.toLowerCase())return Ll(this.featureMap,this.genome);{const n=this.featureMap[e];return n?n.filter((e=>e.end>t&&e.start<i)):[]}}getAllFeatures(){return this.featureMap}supportsWholeGenome(){return!0}addFeature(e){let t=this.featureMap[e.chr];t||(t=[],this.featureMap[e.chr]=t),t.push(e),t.sort(((e,t)=>e.start-t.start))}removeFeature({chr:e,start:t,end:i}){if(this.featureMap[e]){const n=`${e}-${t}-${i}`;this.featureMap[e]=this.featureMap[e].filter((e=>n!==`${e.chr}-${e.start}-${e.end}`)),0===this.featureMap[e].length&&delete this.featureMap[e]}}}class Eu{constructor(t,i,n,r){this.rulerViewport=t,this.rulerSweeper=e({class:\"igv-ruler-sweeper\"}),i.appendChild(this.rulerSweeper),this.browser=n,this.referenceFrame=r,this.isMouseHandlers=void 0,this.addBrowserObserver()}addBrowserObserver(){this.boundObserverHandler=(()=>{this.referenceFrame&&(mu.isWholeGenomeView(this.referenceFrame.chr)?this.removeMouseHandlers():this.addMouseHandlers())}).bind(this),this.browser.on(\"locuschange\",this.boundObserverHandler)}removeBrowserObserver(){this.browser.off(\"locuschange\",this.boundObserverHandler)}addMouseHandlers(){if(!0===this.isMouseHandlers)return;let e,t,i,n,r,s;this.boundContentMouseDownHandler=function(s){e=!0,t=!0;const{x:o}=a(s,this.rulerViewport.contentDiv);n=i=o,r=1,this.rulerSweeper.style.display=\"block\",this.rulerSweeper.style.backgroundColor=!0===s.shiftKey?xu:\"rgba(68, 134, 247, 0.25)\",this.rulerSweeper.style.left=`${n}px`,this.rulerSweeper.style.width=`${r}px`}.bind(this),this.rulerViewport.contentDiv.addEventListener(\"mousedown\",this.boundContentMouseDownHandler),this.boundDocumentMouseMoveHandler=function(o){let c;if(e&&t){const{x:e}=a(o,this.rulerViewport.contentDiv);c=Math.max(Math.min(e,this.rulerViewport.contentDiv.clientWidth),0),s=c-i,r=Math.abs(s),this.rulerSweeper.style.width=`${r}px`,s<0&&(n=i+s,this.rulerSweeper.style.left=`${n}px`)}}.bind(this),document.addEventListener(\"mousemove\",this.boundDocumentMouseMoveHandler),this.boundDocumentMouseUpHandler=function(i){let s;if(!0===e&&!0===t&&(e=t=void 0,this.rulerSweeper.style.display=\"none\",r>1)){s={start:Math.floor(this.referenceFrame.calculateEnd(n)),end:Math.floor(this.referenceFrame.calculateEnd(n+r))};!0===i.shiftKey?this.browser.roiManager.updateUserDefinedROISet(Object.assign({chr:this.referenceFrame.chr},s)):(Qa(this.browser.genome.getChromosome(this.referenceFrame.chr).bpLength,s,this.browser.minimumBases()),function(e,t,i){e.start=Math.round(t.start),e.end=Math.round(t.end),e.bpPerPixel=(e.end-e.start)/i}(this.referenceFrame,s,this.rulerViewport.contentDiv.clientWidth),this.browser.updateViews(this.referenceFrame))}}.bind(this),document.addEventListener(\"mouseup\",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!0}removeMouseHandlers(){this.rulerViewport.contentDiv.removeEventListener(\"mousedown\",this.boundContentMouseDownHandler),document.removeEventListener(\"mousemove\",this.boundDocumentMouseMoveHandler),document.removeEventListener(\"mouseup\",this.boundDocumentMouseUpHandler),this.isMouseHandlers=!1}dispose(){this.removeBrowserObserver(),this.removeMouseHandlers(),this.rulerSweeper.remove()}}function Nu(e){if(Bu[e])return Bu[e];if(Bu[\"chr\"+e]){const t=Bu[\"chr\"+e];return Bu[e]=t,t}{const t=_s.randomRGB(0,255);return Bu[e]=t,t}}const Bu={chrX:\"rgb(204, 153, 0)\",chrY:\"rgb(153, 204, 0)\",chrUn:\"rgb(50, 50, 50)\",chr1:\"rgb(80, 80, 255)\",chrI:\"rgb(139, 155, 187)\",chr2:\"rgb(206, 61, 50)\",chrII:\"rgb(206, 61, 50)\",chr2a:\"rgb(216, 71, 60)\",chr2b:\"rgb(226, 81, 70)\",chr3:\"rgb(116, 155, 88)\",chrIII:\"rgb(116, 155, 88)\",chr4:\"rgb(240, 230, 133)\",chrIV:\"rgb(240, 230, 133)\",chr5:\"rgb(70, 105, 131)\",chr6:\"rgb(186, 99, 56)\",chr7:\"rgb(93, 177, 221)\",chr8:\"rgb(128, 34, 104)\",chr9:\"rgb(107, 215, 107)\",chr10:\"rgb(213, 149, 167)\",chr11:\"rgb(146, 72, 34)\",chr12:\"rgb(131, 123, 141)\",chr13:\"rgb(199, 81, 39)\",chr14:\"rgb(213, 143, 92)\",chr15:\"rgb(122, 101, 165)\",chr16:\"rgb(228, 175, 105)\",chr17:\"rgb(59, 27, 83)\",chr18:\"rgb(205, 222, 183)\",chr19:\"rgb(97, 42, 121)\",chr20:\"rgb(174, 31, 99)\",chr21:\"rgb(231, 199, 111)\",chr22:\"rgb(90, 101, 94)\",chr23:\"rgb(204, 153, 0)\",chr24:\"rgb(153, 204, 0)\",chr25:\"rgb(51, 204, 0)\",chr26:\"rgb(0, 204, 51)\",chr27:\"rgb(0, 204, 153)\",chr28:\"rgb(0, 153, 204)\",chr29:\"rgb(10, 71, 255)\",chr30:\"rgb(71, 117, 255)\",chr31:\"rgb(255, 194, 10)\",chr32:\"rgb(255, 209, 71)\",chr33:\"rgb(153, 0, 51)\",chr34:\"rgb(153, 26, 0)\",chr35:\"rgb(153, 102, 0)\",chr36:\"rgb(128, 153, 0)\",chr37:\"rgb(51, 153, 0)\",chr38:\"rgb(0, 153, 26)\",chr39:\"rgb(0, 153, 102)\",chr40:\"rgb(0, 128, 153)\",chr41:\"rgb(0, 51, 153)\",chr42:\"rgb(26, 0, 153)\",chr43:\"rgb(102, 0, 153)\",chr44:\"rgb(153, 0, 128)\",chr45:\"rgb(214, 0, 71)\",chr46:\"rgb(255, 20, 99)\",chr47:\"rgb(0, 214, 143)\",chr48:\"rgb(20, 255, 177)\"};let Mu,Ru;class Du extends Au{constructor(e,t,i,n){super(e,t,i,n)}get contentDiv(){return this.$viewport.get(0)}initializationHelper(){let e;this.$multiLocusCloseButton=Bt(\"<div>\",{class:\"igv-multi-locus-close-button\"}),this.$viewport.append(this.$multiLocusCloseButton),this.$multiLocusCloseButton.get(0).appendChild(l(\"times-circle\")),this.$multiLocusCloseButton.click((()=>{this.browser.removeMultiLocusPanel(this.referenceFrame)})),this.$rulerLabel=Bt(\"<div>\",{class:\"igv-multi-locus-ruler-label\"}),this.$viewport.append(this.$rulerLabel),e=document.createElement(\"div\"),this.$rulerLabel.append(Bt(e)),this.$rulerLabel.get(0).addEventListener(\"click\",(async e=>{e.stopPropagation(),await this.browser.gotoMultilocusPanel(this.referenceFrame)})),this.$tooltip=Bt(\"<div>\",{class:\"igv-ruler-tooltip\"}),this.$tooltip.height(this.$viewport.height()),this.$viewport.append(this.$tooltip),this.$tooltipContent=Bt(\"<div>\"),this.$tooltip.append(this.$tooltipContent),this.rulerSweeper=new Eu(this,this.$viewport.get(0).parentElement,this.browser,this.referenceFrame),this.attachMouseHandlers(mu.isWholeGenomeView(this.referenceFrame.chr)),this.$tooltip.hide(),this.dismissLocusLabel()}presentLocusLabel(e){this.$multiLocusCloseButton.show(),this.$rulerLabel.show(),this.$rulerLabel.get(0).style.backgroundColor=Nu(this.referenceFrame.chr);const t=this.$rulerLabel.get(0).querySelector(\"div\"),{width:i}=this.$rulerLabel.get(0).getBoundingClientRect();t.innerHTML=`${this.referenceFrame.getMultiLocusLabel(e)}`;const{width:n}=t.getBoundingClientRect();n/i>.5&&(t.innerHTML=`${this.referenceFrame.getMultiLocusLabelBPLengthOnly(e)}`)}dismissLocusLabel(){this.$rulerLabel.hide(),this.$multiLocusCloseButton.hide()}attachMouseHandlers(e){if(this.namespace=`.ruler_track_viewport_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}`,this.$viewport.off(this.namespace),!0===e){const e=this.browser.referenceFrameList.indexOf(this.referenceFrame),t=`click${this.namespace}`;this.$viewport.on(t,(t=>{const{x:i}=a(t,this.$viewport.get(0)),n=Math.round(this.referenceFrame.start+this.referenceFrame.toBP(i));let r;const{chr:s}=this.browser.genome.getChromosomeCoordinate(n);if(1===this.browser.referenceFrameList.length)r=s;else{let t=this.browser.referenceFrameList.map((({locusSearchString:e})=>e));t[e]=s,r=t.join(\" \")}this.browser.search(r)})),this.$viewport.get(0).style.cursor=\"pointer\"}else this.$viewport.get(0).style.cursor=\"default\"}mouseMove(e){if(!0===this.browser.doShowCursorGuide){void 0===Ru?(Ru=this,this.$tooltip.show()):Ru.guid!==this.guid?(Ru.$tooltip&&Ru.$tooltip.hide(),this.$tooltip.show(),Ru=this):this.$tooltip.show();if(this.browser.isMultiLocusWholeGenomeView()||mu.isWholeGenomeView(this.referenceFrame.chr))return void this.$tooltip.hide();const{x:t}=a(e,this.$viewport.get(0)),{start:i,end:n,bpPerPixel:r}=this.referenceFrame,s=Math.round(.5+i+Math.max(0,t)*r);this.$tooltipContent.text(Rt(s));const{width:o}=this.$tooltipContent.get(0).getBoundingClientRect(),{width:c}=this.$viewport.get(0).getBoundingClientRect();return this.$tooltip.css({left:`${ys.clamp(t,0,c-o)}px`}),clearTimeout(Mu),Mu=setTimeout((()=>{this.$tooltip&&this.$tooltip.hide()}),1e4),{start:i,bp:s,end:n}}}startSpinner(){}stopSpinner(){}dispose(){this.rulerSweeper.dispose(),super.dispose()}}class Tu extends Au{featureCache=new Lu;constructor(e,t,i,n){super(e,t,i,n)}initializationHelper(){this.canvas=document.createElement(\"canvas\"),this.canvas.className=\"igv-ideogram-canvas\",this.$viewport.append(Bt(this.canvas)),this.ideogram_ctx=this.canvas.getContext(\"2d\"),this.addMouseHandlers()}async getFeatures(e,t,i,n){return this.featureCache.containsRange(e)?this.featureCache.get(e):this.loadFeatures()}async loadFeatures(){const e=this.referenceFrame.chr,t=await this.referenceFrame.genome.getCytobands(e);return this.featureCache.set(e,t),t}repaint(){if(void 0===this.featureCache)return;const{width:e,height:t}=this.$viewport[0].getBoundingClientRect();xo.configureHighDPICanvas(this.ideogram_ctx,e,t);const i=this.referenceFrame.chr,n=this.featureCache.get(i),r={context:this.ideogram_ctx,pixelWidth:e,pixelHeight:t,referenceFrame:this.referenceFrame,features:n};this.trackView.track.draw(r)}addMouseHandlers(){this.addViewportClickHandler(this.$viewport.get(0))}addViewportClickHandler(e){this.boundClickHandler=function(e){const{xNormalized:t,width:i}=a(e,this.ideogram_ctx.canvas),{bpLength:n}=this.browser.genome.getChromosome(this.referenceFrame.chr),r=this.referenceFrame.bpPerPixel*i/n;let s=t;s-r/2<0&&(s=r/2);s+r/2>1&&(s=1-r/2);const o=Math.round((s-r/2)*n),c=Math.round((s+r/2)*n);this.referenceFrame.start=o,this.referenceFrame.end=c,this.referenceFrame.bpPerPixel=(c-o)/i,this.browser.updateViews(this.referenceFrame,this.browser.trackViews,!0)}.bind(this),e.addEventListener(\"click\",this.boundClickHandler)}setWidth(e){this.$viewport.width(e)}renderSVGContext(e,{deltaX:t,deltaY:i},n=!0){const{width:r,height:o}=this.$viewport.get(0).getBoundingClientRect(),a=`ideogram_referenceFrame_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}_guid_${s()}`,c=t,l=i+this.contentTop,h=-this.contentTop;e.saveWithTranslationAndClipRect(a,c,l,r,o,h),this.trackView.track.draw({context:e,pixelWidth:r,pixelHeight:o,referenceFrame:this.referenceFrame,features:this.featureCache.get(this.referenceFrame.chr)}),e.restore()}startSpinner(){}stopSpinner(){}}class Lu{features=new Map;containsRange(e){return this.features.has(e)}set(e,t){this.features.set(e,t)}get(e){return this.features.get(e)}}function zu(e,t,i,n){if(\"ruler\"===e.track.type)return new Du(e,t,i,n);if(\"ideogram\"===e.track.id)return new Tu(e,t,i,n);{const r=new Au(e,t,i,n);return i.viewport=r,r}}const Hu=[\"rgb(255, 0, 0)\",\"rgb(0, 255, 0)\",\"rgb(0, 0, 255)\",\"rgb(255, 0, 255)\",\"rgb(0, 255, 255)\",\"rgb(128, 0, 128)\",\"rgb(255, 165, 0)\",\"rgb(255, 105, 180)\",\"rgb(255, 127, 80)\",\"rgb(220, 20, 60)\",\"rgb(255, 99, 71)\",\"rgb(173, 216, 230)\",\"rgb(144, 238, 144)\",\"rgb(224, 255, 255)\",\"rgb(250, 250, 210)\",\"rgb(152, 251, 152)\",\"rgb(70, 130, 180)\",\"rgb(102, 205, 170)\"].map((e=>{const[t,i,n]=e.split(\",\"),[r,s]=t.split(\"(\"),[o,a]=n.split(\")\");return[s,i,o]})),Pu=ro(\"magnesium\"),Ou=[\"#sampleTable\",\"#sampleMapping\",\"#colors\"];class Uu{static emptySpaceReplacement=\"|\";sampleDictionary={};attributeNames=[];sampleMappingDictionary={};colorDictionary={};attributeRangeLUT={};constructor(e){e.tracks.some((e=>\"function\"==typeof e.getSamples)).length>0&&e.sampleInfoControl.setButtonVisibility(!0),this.initialize()}initialize(){this.sampleInfoFiles=[],this.attributeNames=[],this.sampleDictionary={},this.sampleMappingDictionary={},this.colorDictionary={},this.attributeRangeLUT={},this.initialized=!1}get attributeCount(){return this.attributeNames?this.attributeNames.length:0}isInitialized(){return this.initialized}hasAttributes(){return this.attributeCount>0}getAttributes(e){const t=0===Object.keys(this.sampleMappingDictionary)?e:this.sampleMappingDictionary[e]||e;return this.sampleDictionary[t]}async loadSampleInfoFile(e){try{const t=await Qs.loadString(e);this.#w(t),this.sampleInfoFiles.push(e)}catch(e){console.error(e.message)}}#w(e){const t=function(e){const t={},i=e.split(/\\r?\\n|\\r/).map((e=>e.trim())).filter((e=>\"\"!==e));let n;Ou.includes(i[0])||(n=\"#sampleTable\",t[n]=[]);for(const e of i)Ou.includes(e)?(n=e,t[n]=[]):n&&!1===e.startsWith(\"#\")&&t[n].push(e);return t}(e);for(const[e,i]of Object.entries(t))switch(e){case\"#sampleTable\":this.#b(i);break;case\"#sampleMapping\":this.#F(i);break;case\"#colors\":this.#v(i)}this.initialized=!0}getAttributeColor(e,t){let i;if(\"-\"===t)i=ro(\"snow\");else if(\"string\"==typeof t&&this.colorDictionary[t])i=this.colorDictionary[t]();else if(this.colorDictionary[e])i=this.colorDictionary[e](t);else if(\"string\"==typeof t)i=\"NA\"===t?Pu:function(e){let t=0;for(let i=0;i<e.length;i++)t=e.charCodeAt(i)+((t<<5)-t);let i=[];for(let e=0;e<3;e++){const n=t>>8*e&255;i.push(n)}return`rgb(${i.join(\", \")})`}(t);else{const[n,r]=this.attributeRangeLUT[e],s=.2,o=Math.max((t-n)/(r-n),s),[a,c,l]=Hu[Object.keys(this.attributeRangeLUT).indexOf(e)];i=`rgba(${a},${c},${l},${o})`}return i}getSortedSampleKeysByAttribute(e,t,i){i=i||1;const n=e.filter((e=>\"number\"==typeof this.getAttributes(e)[t])),r=e.filter((e=>\"string\"==typeof this.getAttributes(e)[t])),s=(e,n)=>{const r=this.getAttributes(e)[t],s=this.getAttributes(n)[t];return\"string\"==typeof r&&\"string\"==typeof s?i*r.localeCompare(s):\"number\"==typeof r&&\"number\"==typeof s?i*(r-s):void 0};return n.sort(s),r.sort(s),-1===i?[...n,...r]:[...r,...n]}toJSON(){const e=[];for(const t of this.sampleInfoFiles){const i={url:t},n=Hl.localFileInspection(i);e.push(n)}return e}#b(e){const t=e.shift().split(\"\\t\").filter((e=>e.length>0));t.shift();const i=t.map((e=>e.split(\" \").join(Uu.emptySpaceReplacement))),n=e.filter((e=>e.length>0));let r;for(const e of n){const t=e.split(\"\\t\"),n=t.shift();void 0===r&&(r={}),r[n]={};for(let e=0;e<t.length;e++){const s={};\"\"===t[e]?s[i[e]]=\"-\":s[i[e]]=t[e],Object.assign(r[n],s)}}for(const[e,t]of Object.entries(r))r[e]=Qu(t);const s=function(e,t){const i={};for(const n of Object.values(t))for(const t of e){let e=n[t];void 0===i[t]&&(i[t]=[]),i[t].push(e)}const n=e=>\"number\"==typeof e,r=e=>\"string\"==typeof e;for(const e of Object.keys(i)){const t=i[e],s=new Set(t),o=Array.from(s);if(!0===o.some(r)&&!0===o.some(n)?i[e]=o.filter((e=>!r(e))):i[e]=o,!i[e].some(r)){const t=i[e].slice();i[e]=[Math.min(...t),Math.max(...t)]}}return i}(i,r);qu(this.attributeRangeLUT,s);const o=new Set(this.attributeNames);for(const e of i)o.has(e)||this.attributeNames.push(e);qu(this.sampleDictionary,r)}#F(e){for(const t of e){const[e,i]=t.split(\"\\t\");this.sampleMappingDictionary[e]=i}}#v(e){const t=(e,t,i)=>{let n;switch(t){case 0:n=e.split(\" \").join(Uu.emptySpaceReplacement);break;case 1:n=e.includes(\":\")?e.split(\":\").map((e=>parseFloat(e))):e;break;case 2:case 3:n=`rgb(${e})`}return n},i=e.map((e=>e.split(\"\\t\").map(t))),n=i.filter((e=>3===e.length&&!e.includes(\"*\"))).filter((([e,t,i])=>!Array.isArray(t))),r={};for(const e of n){const[t,i,n]=e;void 0===r[t]&&(r[t]={}),r[t][i.toUpperCase()]=n}for(const[e,t]of Object.entries(r)){const i=Object.assign({},t);this.colorDictionary[e]=e=>{const t=e.toUpperCase();return i[t]||ro(\"snow\")}}const s=i.filter((e=>Array.isArray(e[1])));for(const e of s){const[t,i]=e[1],n=e[0];if(3===e.length){const[r,s,o]=uo(e[2]);this.colorDictionary[n]=e=>{e=ys.clamp(e,t,i);return lo(r,s,o,(e-t)/(i-t))}}else if(4===e.length){const[t,i]=e[1],[n,r,s,o]=e;this.colorDictionary[n]=e=>{e=ys.clamp(e,t,i);return fo(s,o,(e-t)/(i-t))}}}const o=i.filter((e=>3===e.length&&e.includes(\"*\")));for(const e of o)if(\"*\"===e[1]){const[t,i,n]=e;this.colorDictionary[t]=e=>{if(\"NA\"===e)return Pu;{const[i,r]=this.attributeRangeLUT[t],s=(e-i)/(r-i),[o,a,c]=uo(n);return lo(o,a,c,s)}}}else if(\"*\"===e[0]){const[t,i,n]=e;this.colorDictionary[i]=()=>n}}}function qu(e,t){for(const[i,n]of Object.entries(t))i in e&&e[i]===n||(e[i]=n)}function Qu(e){const t=Object.assign({},e);for(const[e,i]of Object.entries(t))\"string\"!=typeof i||isNaN(i)||(t[e]=Number(i));return t}const Vu=16,ju=Rt;class Wu{constructor(e){this.browser=e,this.height=40,this.name=\"\",this.id=\"ruler\",this.disableButtons=!0,this.ignoreTrackMenu=!0,this.order=.01*Number.MIN_SAFE_INTEGER,this.removable=!1,this.type=\"ruler\"}async getFeatures(e,t,i){return[]}computePixelHeight(e){return this.height}draw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpPerPixel:r,bpStart:s}){mu.isWholeGenomeView(t.chr)?this.drawWholeGenome({context:e,pixelWidth:i,pixelHeight:n,bpPerPixel:r}):this.doDraw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpStart:s})}drawWholeGenome({context:e,pixelWidth:t,pixelHeight:i,bpPerPixel:n}){e.save(),xo.fillRect(e,0,0,t,i,{fillStyle:\"white\"});for(let t of this.browser.genome.wgChromosomeNames){let r=this.browser.genome.getCumulativeOffset(t),s=this.browser.genome.getChromosome(t).bpLength,o=Math.round(r/n),a=Math.round(s/n);this.renderChromosomeRect(e,o,0,a,i,t)}e.restore()}doDraw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,bpStart:r}){e.clearRect(0,0,i,n);const s=function(e,t){if(e<10)return new Gu(1,\"bp\",1);const i=Math.floor(Math.log10(e));let n=\"bp\",r=1;i>9?(n=\"gb\",r=1e9):i>6?(n=\"mb\",r=1e6):i>3&&(n=\"kb\",r=1e3);const s=Math.pow(10,i-1),o=e/s,a=75,c=Math.pow(10,i-1),l=Math.pow(10,i)/2;return new Gu(o<a&&!0!==t?c:l,n,r)}(Math.floor(t.toBP(i)),e.isSVG);let o=Math.floor(r/s.majorTick)-1;const{tickDelta:a,labelLength:c}=function(e,t,i,n,r){const s=l(t,c(1+n,r),i)-l(t,c(n,r),i),o=`${Rt(Math.floor(c(n,r)/r.unitMultiplier))} ${r.majorUnit}`,a=Math.floor(e.measureText(o).width);return{tickDelta:s,labelLength:a};function c(e,t){return Math.floor(e*t.majorTick)}function l(e,t,i){return Math.round(e.toPixels(t-1-i+.5))}}(e,t,r,o,s);let l,h;this.browser.referenceFrameList.indexOf(t);let d=a;const u=.25*c;do{h=Math.floor(o*s.majorTick);const i=`${Rt(Math.floor(h/s.unitMultiplier))} ${s.majorUnit}`;l=Math.round(t.toPixels(h-1-r+.5));const n=Math.round(l-e.measureText(i).width/2);n>0&&u+c<=d&&(xo.fillText(e,i,n,this.height-8),d=0),l>0&&xo.strokeLine(e,l,this.height-6,l,this.height-2),h=Math.floor((1+o)*s.majorTick);let f=l+(Math.round(t.toPixels(h-1-r+.5))-l)/2;f>0&&xo.strokeLine(e,f,this.height-6,f,this.height-2),++o,d+=a}while(l<i);xo.strokeLine(e,0,this.height-2,i,this.height-2)}renderChromosomeRect(e,t,i,n,r,s){e.textAlign=\"center\",e.textBaseline=\"middle\",e.font=\"12px sans-serif\",xo.strokeLine(e,t+n,i,t+n,i+r,{strokeStyle:_s.greyScale(191)});const o=(s=this.browser.genome.getChromosomeDisplayName(s)).startsWith(\"chr\")?s.substring(3):s;n>e.measureText(o).width&&xo.fillText(e,o,t+n/2,i+r/2,{fillStyle:_s.greyScale(68)})}get supportsWholeGenome(){return!0}dispose(){}}class Gu{constructor(e,t,i){this.majorTick=e,this.minorTick=e/10,this.majorUnit=t,this.unitMultiplier=i}description(e){console.log((e||\"\")+\" tick \"+ju(this.majorTick)+\" label width \"+ju(this.labelWidthBP)+\" multiplier \"+this.unitMultiplier)}}class $u{constructor(t,i,n){this.guid=s(),this.trackView=t,this.browser=t.browser,this.viewport=e({class:\"igv-viewport\"}),i.appendChild(this.viewport),this.viewport.style.height=`${t.track.height}px`,null===this.viewport.previousElementSibling&&(this.viewport.style.zIndex=16,this.viewport.style.overflow=\"visible\"),this.canvas=document.createElement(\"canvas\"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext(\"2d\"),this.ctx.font=\"10px verdana\",this.contentTop=0,this.hitList=void 0,this.sortDirection=1,this.setWidth(n),this.addMouseHandlers()}resizeCanvas(){const e=window.devicePixelRatio,t=this.browser.getSampleInfoViewportWidth();let i;if(this.browser.trackViews.length>1&&null===this.viewport.previousElementSibling){const[e,t]=[this.browser.ideogramTrackView.track,this.browser.rulerTrackView.track];i=e.height+t.height}else i=this.viewport.clientHeight;if(this.canvas.width!==t*e||this.canvas.height!==i*e){const n=this.canvas;n.width=t*e,n.height=i*e,n.style.width=`${t}px`,n.style.height=`${i}px`,this.ctx=this.canvas.getContext(\"2d\"),this.ctx.scale(e,e),null===this.viewport.previousElementSibling&&xo.fillRect(this.ctx,0,0,this.ctx.canvas.width,this.ctx.canvas.height,{fillStyle:ro(\"snow\")})}}setTop(e){\"function\"==typeof this.trackView.track.getSamples&&(this.contentTop=e,this.repaint())}setWidth(e){this.viewport.innerWidth=e,this.resizeCanvas()}setHeight(e){const t=this.browser.getSampleInfoViewportWidth();this.viewport.style.width=`${t}px`,this.viewport.style.height=`${e}px`;const i=window.devicePixelRatio;this.canvas.width=t*i,this.canvas.height=e*i,this.canvas.style.width=`${t}px`,this.canvas.style.height=`${e}px`,this.ctx=this.canvas.getContext(\"2d\"),this.ctx.scale(i,i),null===this.viewport.previousElementSibling&&xo.fillRect(this.ctx,0,0,this.ctx.canvas.width,this.ctx.canvas.height,{fillStyle:ro(\"snow\")})}async repaint(){if(this.resizeCanvas(),\"function\"==typeof this.trackView.track.getSamples){const e=this.trackView.track.getSamples();e.names&&e.names.length>0&&this.draw({context:this.ctx,samples:e})}else null===this.viewport.previousElementSibling&&(this.browser.rulerTrackView&&this.browser.rulerTrackView.setTrackHeight(!0===this.browser.sampleInfoControl.showSampleInfo?this.calculateSampleInfoColumnHeight():40,!0),this.renderSampleInfoColumns(this.ctx))}calculateSampleInfoColumnHeight(){const e=this.browser.sampleInfo.attributeNames.map((e=>this.ctx.measureText(e).width));return 4+Math.min(Math.max(...e),128)}draw({context:e,samples:t}){if(e.clearRect(0,0,e.canvas.width,e.canvas.height),e.fillStyle=ro(\"snow\"),e.fillRect(0,0,e.canvas.width,e.canvas.height),t&&t.names.length>0){const i=this.browser.sampleInfo.attributeNames,n=this.viewport.getBoundingClientRect().height;let r=1;const s=t.height;r=s-2*r<=1?0:1;let o=this.contentTop+t.yOffset;this.hitList={};for(const a of t.names){if(o>n)break;if(o+s>0){const t=this.browser.sampleInfo.getAttributes(a);if(t){const n=Object.entries(t);for(const t of n){const[n,a]=t;e.fillStyle=this.browser.sampleInfo.getAttributeColor(n,a);const c=8+i.indexOf(n)*Vu,l=o+r,h=s-2*r;e.fillRect(c,l,15,h);const d=`${Math.floor(c)}#${Math.floor(l)}#16#${Math.ceil(h)}`;this.hitList[d]=`${n}#${a}`}}}o+=s}}}renderSampleInfoColumns(e){const t=(e,t,i,n,r,s)=>{e.save(),e.font=\"10px verdana\",e.translate(i+r/2,n+s),e.rotate(-Math.PI/2),e.textAlign=\"left\",e.fillStyle=ro(\"lead\"),e.fillText(t,2,2),e.restore()},i=this.browser.sampleInfo.attributeNames;this.hitList={};for(let n=0;n<i.length;n++){const r=8+n*Vu,s=15,o=Math.round(e.canvas.height/window.devicePixelRatio);xo.fillRect(e,r,0,s,o,{fillStyle:ro(\"snow\")}),t(e,i[n],r,0,s,o);const a=`${Math.floor(r)}#0#${s}#${Math.ceil(o)}`;this.hitList[a]=`${i[n]}`}}renderSVGContext(e,{deltaX:t,deltaY:i}){if(\"function\"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:o,height:a}=this.viewport.getBoundingClientRect(),c=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_sample_names_guid_${s()}`;e.saveWithTranslationAndClipRect(c,t,i+r,o,a,-r),this.draw({context:e,samples:n}),e.restore()}}addMouseHandlers(){this.addMouseMoveHandler()}addMouseMoveHandler(){this.boundMouseMoveHandler=function(e){if(this.hitList){const t=Object.entries(this.hitList);if(null===this.viewport.previousElementSibling){const i=(t,i)=>{const{marginTop:n}=window.getComputedStyle(i),{x:r,y:s}=a(e,this.browser.columnContainer.querySelector(\".igv-sample-info-column\"));return{x:Math.floor(r),y:Math.floor(s-parseInt(n,10))}},n=this.browser.columnContainer.querySelector(\".igv-sample-info-column\"),{x:r,y:s}=i(n,this.viewport);n.setAttribute(\"title\",\"\");for(const[e,i]of t){const[t,o,a,c]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(r<t||r>t+a||s<o||s>o+c)){n.setAttribute(\"title\",`${i}`);break}}}else{const{x:i,y:n}=a(e,this.viewport);this.viewport.setAttribute(\"title\",\"\");for(const[e,r]of t){const[t,s,o,a]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(i<t||i>t+o||n<s||n>s+a)){const[e,t]=r.split(\"#\");this.viewport.setAttribute(\"title\",`${e.split(Uu.emptySpaceReplacement).join(\" \")}: ${\"-\"===t?\"\":t}`);break}}}}}.bind(this),this.viewport.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandlers(){this.viewport.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}show(){this.viewport.style.display=\"block\"}hide(){this.viewport.style.display=\"none\"}}class Ku{constructor(t,i,n,r){this.guid=s(),this.trackView=t,this.browser=t.browser,this.viewport=e({class:\"igv-viewport\"}),i.appendChild(this.viewport),t.track.height&&(this.viewport.style.height=`${t.track.height}px`),this.canvas=document.createElement(\"canvas\"),this.viewport.appendChild(this.canvas),this.ctx=this.canvas.getContext(\"2d\"),this.trackScrollDelta=0,this.contentTop=0,this.hitList=void 0,this.sortDirection=1,this.setWidth(r),this.addMouseHandlers()}checkCanvas(){const e=this.browser.sampleNameViewportWidth||0;this.ctx.canvas.width=e*window.devicePixelRatio,this.ctx.canvas.style.width=`${e}px`,this.ctx.canvas.height=this.viewport.clientHeight*window.devicePixelRatio,this.ctx.canvas.style.height=`${this.viewport.clientHeight}px`,this.ctx.scale(window.devicePixelRatio,window.devicePixelRatio)}setTop(e){if(\"function\"==typeof this.trackView.track.getSamples){this.contentTop=e;const t=this.trackView.track.getSamples();this.repaint(t)}}setWidth(e){this.viewport.innerWidth=e,this.checkCanvas()}async repaint(e){if(e.names.length>0&&!0===this.browser.showSampleNames&&(this.checkCanvas(),this.draw({context:this.ctx,samples:e}),void 0===this.browser.sampleNameViewportWidth)){const t=e.names.map((e=>this.ctx.measureText(e).width));this.browser.sampleNameViewportWidth=Math.min(200,4+Math.ceil(Math.max(...t))),this.browser.layoutChange()}}draw({context:e,samples:t}){if(xo.fillRect(e,0,0,e.canvas.width,t.height,{fillStyle:ro(\"snow\")}),t&&t.names.length>0){const i=this.viewport.getBoundingClientRect().height,n=t.height,r=n-2<=1?0:1;let s=this.contentTop+t.yOffset;this.hitList={};for(const o of t.names){if(s>i)break;if(s+n>0){const t=n-2*r;Yu(e,o,0+2,s+r,e.canvas.width,t)}s+=n}}}renderSVGContext(e,{deltaX:t,deltaY:i}){if(\"function\"==typeof this.trackView.track.getSamples){const n=this.trackView.track.getSamples(),r=0,{width:o,height:a}=this.viewport.getBoundingClientRect(),c=`${(this.trackView.track.name||this.trackView.track.id).replace(/\\W/g,\"\")}_sample_names_guid_${s()}`;e.saveWithTranslationAndClipRect(c,t,i+r,o,a,-r),this.draw({context:e,samples:n}),e.restore()}}addMouseHandlers(){this.boundClickHandler=function(e){e.preventDefault();const t={label:\"Name Panel Width\",value:this.browser.sampleNameViewportWidth,callback:e=>{this.browser.sampleNameViewportWidth=parseInt(e),this.browser.layoutChange()}};this.browser.inputDialog.present(t,e)}.bind(this),this.viewport.addEventListener(\"contextmenu\",this.boundClickHandler),this.boundMouseMoveHandler=function(e){if(this.hitList){const t=Object.entries(this.hitList),{x:i,y:n}=a(e,this.viewport);this.viewport.setAttribute(\"title\",\"\");for(const[e,r]of t){const[t,s,o,a]=e.split(\"#\").map((e=>parseInt(e,10)));if(!(i<t||i>t+o||n<s||n>s+a)){this.viewport.setAttribute(\"title\",`${r}`);break}}}}.bind(this),this.viewport.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandlers(){this.viewport.removeEventListener(\"contextmenu\",this.boundClickHandler),this.viewport.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}dispose(){this.removeMouseHandlers(),this.viewport.remove()}}function Yu(e,t,i,n,r,s){const o=Math.min(s,10);e.font=`${o}px sans-serif`,e.textAlign=\"start\",e.fillStyle=ro(\"lead\");const a=i,c=e.measureText(t),l=n+s/2+(c.actualBoundingBoxAscent+c.actualBoundingBoxDescent)/2;e.fillText(t,a,l)}class Xu{constructor(t){this.popover=e({class:\"igv-menu-popup\"}),t.appendChild(this.popover),this.parent=t;const i=e({class:\"igv-menu-popup-header\"});this.popover.appendChild(i),u(i,(()=>this.popover.style.display=\"none\")),this.popoverContent=e(),this.popover.appendChild(this.popoverContent),p(this.popover,i),i.addEventListener(\"click\",(e=>{e.stopPropagation(),e.preventDefault()})),this.popover.style.display=\"none\"}presentMenuList(e,t){if(Zu(this.parent),t.length>0){this.popoverContent.innerHTML=\"\";const i=this.parseMenuList(e,t);for(let e of i){e.init&&e.init();let t=e.object;0===i.indexOf(e)&&t.removeClass(\"igv-track-menu-border-top\"),t.hasClass(\"igv-track-menu-border-top\")||t.hasClass(\"igv-menu-popup-check-container\")||t.is(\"div\")&&t.addClass(\"igv-menu-popup-shim\"),this.popoverContent.appendChild(t.get(0))}this.popover.style.display=\"flex\";const{width:n}=this.popover.getBoundingClientRect();this.popover.style.left=-n+\"px\",this.popover.style.top=\"0px\"}}parseMenuList(e,t){return t.map(((t,i)=>{let n;if(t.name?(n=Bt(\"<div>\"),n.text(t.name)):t.object?n=t.object:\"string\"==typeof t.label?(n=Bt(\"<div>\"),n.html(t.label)):\"string\"==typeof t&&(n=t.startsWith(\"<\")?Bt(t):Bt(\"<div>\"+t+\"</div>\")),0===i&&n.addClass(\"igv-track-menu-border-top\"),t.click||t.dialog){const i=i=>{if(i.preventDefault(),i.stopPropagation(),t.click)if(e.track.selected){const n=e.browser.getSelectedTrackViews();if(!0===t.doAllMultiSelectedTracks)t.click.call(e.track,i);else if(\"removeTrack\"===t.menuItemType){const r=()=>{e.browser.overlayTrackButton.setVisibility(!1);for(const{track:e}of n)t.click.call(e,i)},s={html:`Are you sure you want to delete ${n.length} tracks?`,callback:r};e.browser.menuUtils.dialog.present(s,i)}else for(const{track:e}of n)t.click.call(e,i)}else t.click.call(e.track,i);else t.dialog&&t.dialog.call(e.track,i);this.popover.style.display=\"none\"};n.on(\"click\",i),n.on(\"touchend\",(e=>i(e))),n.on(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}return{object:n,init:t.init||void 0}}))}presentTrackContextMenu(t,n){this.popoverContent.innerHTML=\"\";const r=function(t,n){return t.map((t=>{let r;if(\"string\"==typeof t&&\"<hr/>\"===t)r=document.createElement(\"hr\");else if(\"string\"==typeof t)r=e({class:\"context-menu\"}),r.innerHTML=t;else if(\"Node\"==typeof t)r=t;else{if(\"function\"==typeof t.init&&t.init(),\"checkbox\"===t.type)r=Dl(\"Show all bases\",t.value);else if(\"color\"===t.type){const s=new Ra(n.parentElement);s.configure({color:\"grey\"}),r=e({class:\"context-menu\"}),\"string\"==typeof t.label&&(r.innerHTML=t.label);const o=e=>{s.show(),i(n),e.preventDefault(),e.stopPropagation()};r.addEventListener(\"click\",o),r.addEventListener(\"touchend\",o),r.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}else r=e({class:\"context-menu\"}),\"string\"==typeof t.label&&(r.innerHTML=t.label);if(t.click&&\"color\"!==t.type){function a(e){t.click(),i(n),e.preventDefault(),e.stopPropagation()}r.addEventListener(\"click\",a),r.addEventListener(\"touchend\",a),r.addEventListener(\"mouseup\",(function(e){e.preventDefault(),e.stopPropagation()}))}}return{el:r,init:t.init}}))}(n,this.popover);for(let{el:e}of r)this.popoverContent.appendChild(e);!function(e,t){t.style.display=\"flex\";const{x:i,y:n}=a(e,t.parentNode),{width:r}=t.getBoundingClientRect(),s=i+r,{width:o}=t.parentNode.getBoundingClientRect();t.style.left=`${s>o?i-(s-o):i}px`,t.style.top=`${n}px`}(t,this.popover)}hide(){this.popover.style.display=\"none\"}dispose(){this.popoverContent.innerHTML=\"\",this.popover.innerHTML=\"\",Object.keys(this).forEach((function(e){this[e]=void 0}))}}const Zu=e=>{const t=e.querySelectorAll(\".igv-menu-popup\");for(const e of t)e.style.display=\"none\"};class Ju{constructor(t,i,n,r,s,o,a){this.browser=i,this.button=e({class:\"igv-navbar-text-button\"}),t.appendChild(this.button),Array.isArray(n)?(this.textContent=n[0],this.title=n[1]):this.textContent=this.title=n,this.buttonLabel=r,this.imageDictionary={image:`url(\"data:image/svg+xml,${encodeURIComponent(s)}\")`,imageHover:`url(\"data:image/svg+xml,${encodeURIComponent(o)}\")`},this.responsiveKey=\"text\",this.configureButton(this.textContent,this.title),this.setState(a),i.on(\"navbar-resize\",(e=>{this.navbarResizeHandler(e)}))}navbarResizeHandler(e){const t=\"igv-navbar-icon-button\"===e?\"image\":\"text\";t!==this.responsiveKey&&(this.responsiveKey=t,this.configureButton(this.textContent,this.title),this.setState(void 0))}configureButton(e,t){this.groupElement=void 0,this.button.title=t,this.button.innerHTML=\"\",this.button.style.backgroundImage=\"none\",this.button.classList.remove(\"igv-navbar-icon-button\"),this.button.classList.remove(\"igv-navbar-text-button\"),\"text\"===this.responsiveKey?this.configureTextButton(e):this.configureIconButton()}configureTextButton(e){console.log(`text ${this.title}`),this.button.classList.add(\"igv-navbar-text-button\");const t=document.createElement(\"div\");t.innerHTML=this.buttonLabel;const i=t.firstChild;this.button.appendChild(i),this.groupElement=i.querySelector(\"#igv-navbar-button-group\");i.querySelector(\"#igv-navbar-button-label\").textContent=e}configureIconButton(){console.log(`icon ${this.title}`),this.button.classList.add(\"igv-navbar-icon-button\")}setState(e){void 0!==e&&(this.doHover=e),\"text\"===this.responsiveKey?this.setTextButtonState(this.doHover):this.setIconButtonState(this.doHover)}setTextButtonState(e){this.groupElement.classList.remove(...this.groupElement.classList);const t=!0===e?\"igv-navbar-text-button-svg-hover\":\"igv-navbar-text-button-svg-inactive\";this.groupElement.classList.add(t)}setIconButtonState(e){this.button.style.backgroundImage=!0===e?this.imageDictionary.imageHover:this.imageDictionary.image}show(){this.button.style.display=\"flex\"}hide(){this.button.style.display=\"none\"}setVisibility(e){!0===e?this.show():this.hide()}}const ef='<svg width=\"80px\" height=\"18px\" viewBox=\"0 0 80 18\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"igv-navbar-button-group\">\\n            <rect id=\"Rectangle\" x=\"0.5\" y=\"0.5\" width=\"79\" height=\"17\" rx=\"6\"></rect>\\n            <text id=\"igv-text-button-label\" x=\"50%\" y=\"50%\" dy=\".1em\" font-family=\"Helvetica\" font-size=\"12\" font-weight=\"normal\" letter-spacing=\"-0.372\">\\n                <tspan id=\"igv-navbar-button-label\"></tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>';class tf extends Hl{static defaults={autoscale:void 0,alpha:.5,height:50};constructor(e,t,i){super(e,t),this.type=\"merged\",this.paintAxis=cd,this.graphType=e.graphType,this.tracks=i||[]}async postInit(){if(this.config.tracks){for(let e of this.config.tracks){const t=await this.browser.createTrack(e);t?this.tracks.push(t):console.warn(\"Could not create track \"+e),\"function\"==typeof t.postInit&&await t.postInit()}this.config.tracks.every((e=>void 0!==e.autoscale||void 0!==e.max))||(this.config.autoscale=void 0===this.config.max)}for(let e of this.tracks)e.isMergedTrack=!0;if(this.config.autoscale?this.autoscale=this.config.autoscale:void 0!==this.config.max&&this.setDataRange({min:this.config.min||0,max:this.config.max}),void 0!==this.config.flipAxis)for(let e of this.tracks)e.flipAxis=this.config.flipAxis;if(void 0!==this.config.logScale)for(let e of this.tracks)e.logScale=this.config.logScale;this.resolutionAware=this.tracks.some((e=>e.resolutionAware))}set flipAxis(e){this.config.flipAxis=e;for(let t of rf(this.tracks))t.flipAxis=e}get flipAxis(){return rf(this.tracks).every((e=>e.flipAxis))}set logScale(e){this.config.logScale=e;for(let t of rf(this.tracks))t.logScale=e}get logScale(){return rf(this.tracks).every((e=>e.logScale))}get height(){return this._height}set height(e){if(this.config.height=e,this._height=e,this.tracks)for(let t of this.tracks)t.height=e,t.config.height=e}set autoscale(e){if(this._autoscale=e,!1===e&&this.tracks)for(let e of this.tracks)e.autoscale=!1}get autoscale(){return this._autoscale}set autoscaleGroup(e){if(this.tracks)for(let t of this.tracks)t.autoscaleGroup=e}get autoscaleGroup(){if(this.tracks&&this.tracks.length>0){const e=this.tracks[0].autoscaleGroup;return this.tracks.some((t=>e!==t.autoscaleGroup))?void 0:e}}setDataRange({min:e,max:t}){this.autoscale=!1;for(const i of rf(this.tracks))i.dataRange={min:e,max:t},i.autoscale=!1,i.autoscaleGroup=!1}set dataRange({min:e,max:t}){for(const i of rf(this.tracks))i.dataRange={min:e,max:t}}get dataRange(){if(this.tracks){const e=rf(this.tracks);if(e.length>0){const t=e[0].dataRange;if(e.every((e=>e.dataRange&&e.dataRange.min===t.min&&e.dataRange.max===t.max)))return t}}}menuItemList(){const e=[];return rf(this.tracks).length>0&&(void 0!==this.flipAxis&&e.push({label:\"Flip y-axis\",click:function(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),e.push(...this.numericDataMenuItems())),e.push(\"<hr/>\"),e.push(this.overlayTrackAlphaAdjustmentMenuItem()),e.push(this.trackSeparationMenuItem()),e}async getFeatures(e,t,i,n){const r=this.tracks.map((r=>r.getFeatures(e,t,i,n))),s=await Promise.all(r);if(s.every((e=>0===e.length)))return new nf([],[]);{const e=this.tracks.map((e=>e.name));return new nf(s,e)}}draw(e){const t=e.features;for(let i=0,n=this.tracks.length;i<n;i++){const n=Object.assign({},e);n.features=t.featureArrays[i],n.alpha=this.alpha,this.graphType&&(this.tracks[i].graphType=this.graphType),this.tracks[i].draw(n)}}popupData(e){const t=this.clickedFeatures(e);if(t&&t.length===this.tracks.length){const i=[];let n=!0;for(let r=0;r<t.length;r++)if(r>0&&i.push(\"<hr/>\"),i.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${t[r].trackName}</div>`),t[r].features.length>0){n=!1;const s=this.tracks[r].popupData(e,t[r].features);i.push(...s)}else i.push(\"Missing or 0 value(s)\");return!0===n?[]:i}}clickedFeatures(e){const t=e.viewport.cachedFeatures;if(!t||!t.featureArrays||!Array.isArray(t.featureArrays)||0===t.featureArrays.length)return[];const i=e.genomicLocation,n=[],r=e.referenceFrame.bpPerPixel>.2?3*e.referenceFrame.bpPerPixel:.2,s=i-r,o=i+r;for(let e=0;e<t.featureArrays.length;e++){const i=to(t.featureArrays[e],s,o);n.push({trackName:t.trackNames[e],features:i})}return n}get supportsWholeGenome(){return this.tracks.every((e=>e.supportsWholeGenome))}getState(){const e=super.getState(),t=[];for(let e of this.tracks)t.push(e.getState());return e.tracks=t,e}updateScales(e){let t;if(this.autoscale){t=!0;let i=[];for(let t of e){if(t.featureCache&&t.featureCache.features){const e=t.referenceFrame,n=e.start,r=n+e.toBP(t.getWidth()),s=t.featureCache.features;this.autoscale&&(i.push({value:s.getMax(n,r)}),i.push({value:s.getMin(n,r)}))}const e=qa(i);for(const t of rf(this.tracks))t.dataRange=e}}else{let i=-1;for(let n of this.tracks)if(++i,n.autoscale){t=!0;let r=[];for(let t of e)if(t.featureCache&&t.featureCache.features){const e=t.referenceFrame,n=e.start,s=n+e.toBP(t.getWidth()),o=t.featureCache.features.featureArrays[i];if(o)for(let e of o)if(!(e.end<n)){if(e.start>s)break;r.push(e)}}n.dataRange=qa(r)}}return t}overlayTrackAlphaAdjustmentMenuItem(){const t=e();return t.innerText=\"Set transparency\",{object:Bt(t),dialog:function(e){const t={label:\"Transparency\",value:this.alpha,min:0,max:1,scaleFactor:1e3,callback:e=>{this.alpha=Math.max(.001,e),this.repaintViews()}};this.browser.sliderDialog.present(t,e)}}}trackSeparationMenuItem(){const e=Bt(\"<div>\");return e.text(\"Separate tracks\"),{object:e,click:function(e){const t=this.autoscale,i=this.name,n=this.tracks,r=this.browser,s=this.order;r.removeTrack(this);for(let e of n)e.order=s,t&&(e.autoscaleGroup=i),e.isMergedTrack=!1,r.addTrack(e.config,e);r.updateViews()}}}}class nf{constructor(e,t){this.featureArrays=e,this.trackNames=t}getMax(e,t){let i=-Number.MAX_VALUE;for(let n of this.featureArrays)if(Array.isArray(n))for(let r of n)if(!(void 0===r.value||Number.isNaN(r.value)||r.end<e)){if(r.start>t)break;i=Math.max(i,r.value)}return i!==-Number.MAX_VALUE?i:100}getMin(e,t){let i=0;for(let n of this.featureArrays)if(Array.isArray(n))for(let r of n)if(void 0!==r.value&&!Number.isNaN(r.value)){if(r.end<e)continue;if(r.start>t)break;i=Math.min(i,r.value)}return i}}const rf=e=>e?e.filter((e=>void 0!==e.dataRange||void 0!==e.autoscale||void 0!==e.autoscaleGroup)):[];class sf extends Ju{constructor(e,t){super(e,t,\"Overlay Tracks\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>Overlay Tracks</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"Overlay-Tracks\">\\n            <rect id=\"backdrop\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"layer-group\" transform=\"translate(3, 127)\">\\n                <rect id=\"a\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#A1A1A1\" x=\"12\" y=\"12\" width=\"332\" height=\"139\"></rect>\\n                <rect id=\"a---hold-out\" fill=\"#A1A1A1\" x=\"9\" y=\"25\" width=\"324\" height=\"115\"></rect>\\n                <rect id=\"b\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#C9C9C9\" x=\"81\" y=\"103\" width=\"474\" height=\"139\"></rect>\\n                <rect id=\"c\" stroke=\"#737373\" stroke-width=\"24\" fill=\"#ECECEC\" x=\"238\" y=\"214\" width=\"372\" height=\"139\"></rect>\\n                <rect id=\"c---hold-out\" fill=\"#ECECEC\" x=\"250\" y=\"226\" width=\"372\" height=\"115\"></rect>\\n            </g>\\n            <rect id=\"over-border\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>Overlay Tracks Hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"Overlay-Tracks-Hover\">\\n            <rect id=\"backdrop-copy\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"layer-group\" transform=\"translate(3, 127)\">\\n                <rect id=\"a\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#A1A1A1\" x=\"12\" y=\"12\" width=\"332\" height=\"139\"></rect>\\n                <rect id=\"a---hold-out\" fill=\"#A1A1A1\" x=\"9\" y=\"25\" width=\"324\" height=\"115\"></rect>\\n                <rect id=\"b\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#C9C9C9\" x=\"81\" y=\"103\" width=\"474\" height=\"139\"></rect>\\n                <rect id=\"c\" stroke=\"#FFFFFF\" stroke-width=\"24\" fill=\"#ECECEC\" x=\"238\" y=\"214\" width=\"372\" height=\"139\"></rect>\\n                <rect id=\"c---hold-out\" fill=\"#ECECEC\" x=\"250\" y=\"226\" width=\"372\" height=\"115\"></rect>\\n            </g>\\n            <rect id=\"over-border-copy\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>',!1),this.button.addEventListener(\"mouseenter\",(()=>this.setState(!0))),this.button.addEventListener(\"mouseleave\",(()=>this.setState(!1)));this.boundMouseClickHandler=(()=>{this.setVisibility(!1),of.call(this)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(!0)}}function of(e){if(!0===af(this.browser)){const e=this.browser.getSelectedTrackViews().map((({track:e})=>e));for(const t of e)t.selected=!1;const t=[];for(let i of e)\"merged\"===i.type?t.push(...i.tracks):t.push(i);const i={name:\"Overlay\",type:\"merged\",autoscale:!1,alpha:.5,height:Math.max(...e.map((({height:e})=>e))),order:Math.min(...e.map((({order:e})=>e)))},n=new tf(i,this.browser,t);for(const t of e){const e=this.browser.trackViews.indexOf(t.trackView);this.browser.trackViews.splice(e,1),t.trackView.dispose()}this.browser.addTrack(i,n),n.trackView.updateViews()}}function af(e){const t=e.getSelectedTrackViews();if(t&&t.length>1){const e=new Set([\"wig\",\"merged\"]);return t.filter((({track:t})=>e.has(t.type))).length>1}return!1}const cf=new Set([\"sequence\",\"ruler\",\"ideogram\"]),lf=new Set([\"ruler\",\"sequence\",\"ideogram\"]);class hf{constructor(e,t,i){this.namespace=`trackview-${s()}`,this.browser=e,this.track=i,i.trackView=this,this.addDOMToColumnContainer(e,t,e.referenceFrameList)}startSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].startSpinner()}stopSpinner(){this.viewports&&this.viewports.length>0&&this.viewports[0].stopSpinner()}addDOMToColumnContainer(e,t,i){this.axis=this.createAxis(e,this.track),this.createViewports(e,t,i),this.sampleInfoViewport=new $u(this,e.columnContainer.querySelector(\".igv-sample-info-column\"),e.getSampleInfoViewportWidth()),this.sampleNameViewport=new Ku(this,e.columnContainer.querySelector(\".igv-sample-name-column\"),void 0,e.getSampleNameViewportWidth()),this.createTrackScrollbar(e),this.createTrackDragHandle(e),this.createTrackGearPopup(e)}createViewports(e,t,i){this.viewports=[];const n=e.calculateViewportWidth(i.length),r=t.querySelectorAll(\".igv-column\");for(let e=0;e<r.length;e++){const t=zu(this,r[e],i[e],n);this.viewports.push(t)}}createAxis(t,i){const n=e();if(this.axis=n,t.columnContainer.querySelector(\".igv-axis-column\").appendChild(n),n.dataset.tracktype=i.type,n.style.height=`${i.height}px`,\"function\"==typeof i.paintAxis){const{width:e,height:t}=n.getBoundingClientRect();this.axisCanvas=document.createElement(\"canvas\"),this.axisCanvas.style.width=`${e}px`,this.axisCanvas.style.height=`${t}px`,n.appendChild(this.axisCanvas)}if(!1===mo.has(this.track.type)){this.trackSelectionContainer=e(),n.appendChild(this.trackSelectionContainer);const t='<input type=\"checkbox\" name=\"track-select\">',i=document.createRange().createContextualFragment(t).firstChild;this.trackSelectionContainer.appendChild(i),i.checked=this.track.selected||!1,i.addEventListener(\"change\",(e=>{e.preventDefault(),e.stopPropagation(),this.track.selected=e.target.checked,this.setDragHandleSelectionState(e.target.checked),this.browser.overlayTrackButton.setVisibility(af(this.browser))})),this.enableTrackSelection(!1)}return n}resizeAxisCanvas(e,t){this.axis.style.width=`${e}px`,this.axis.style.height=`${t}px`,\"function\"==typeof this.track.paintAxis&&(this.axisCanvas.style.width=`${e}px`,this.axisCanvas.style.height=`${t}px`)}renderSVGContext(e,{deltaX:t,deltaY:i}){!function(e,t,i,n,r){if(\"function\"==typeof t.paintAxis){const{y:o,width:a,height:c}=i.getBoundingClientRect(),l=`${(t.name||t.id).replace(/\\W/g,\"\")}_axis_guid_${s()}`;e.saveWithTranslationAndClipRect(l,n,o+r,a,c,0),t.paintAxis(e,a,c),e.restore()}}(e,this.track,this.axisCanvas,t,i);const{width:n}=this.axis.getBoundingClientRect(),{y:r}=this.viewports[0].$viewport.get(0).getBoundingClientRect();let o={deltaX:n+t,deltaY:r+i};for(let t of this.viewports){t.renderSVGContext(e,o);const{width:i}=t.$viewport.get(0).getBoundingClientRect();o.deltaX+=i}if(!0===this.browser.sampleInfo.isInitialized()&&!0===this.browser.sampleInfoControl.showSampleInfo){this.sampleInfoViewport.renderSVGContext(e,o);const{width:t}=this.sampleInfoViewport.viewport.getBoundingClientRect();o.deltaX+=t}!0===this.browser.showSampleNames&&this.sampleNameViewport.renderSVGContext(e,o)}presentColorPicker(e){if(!1===lf.has(this.track.type)){const t=[],i=this.track.color||this.track.defaultColor;Mt(i)&&t.push(i),this.track.altColor&&Mt(this.track.altColor)&&t.push(this.track.altColor);let n=t.map((e=>e.startsWith(\"#\")?e:e.startsWith(\"rgb(\")?_s.rgbToHex(e):_s.colorNameToHex(e))),r={color:e=>{this.track.color=io(e),this.repaintViews()},altColor:e=>{this.track.altColor=io(e),this.repaintViews()}};const s=this.browser.getSelectedTrackViews();s.length>0&&new Set(s).has(this)?(r={color:e=>{for(let t of s)t.track.color=e,t.repaintViews()}},this.browser.genericColorPicker.configure(n,r)):this.browser.genericColorPicker.configure(n,r),this.browser.genericColorPicker.setActiveColorHandler(e),this.browser.genericColorPicker.show()}}setTrackHeight(e,t){t||(this.track.minHeight&&(e=Math.max(this.track.minHeight,e)),this.track.maxHeight&&(e=Math.min(this.track.maxHeight,e))),this.track.height=e,this.resizeAxisCanvas(this.axis.clientWidth,this.track.height),\"function\"==typeof this.track.paintAxis&&this.paintAxis();for(let{$viewport:t}of this.viewports)t.height(e);if(this.sampleInfoViewport.setHeight(e),this.sampleNameViewport.viewport.style.height=`${e}px`,\"function\"!=typeof this.track.computePixelHeight)for(let t of this.viewports)t.setContentHeight(e);this.repaintViews(),this.updateScrollbar(),this.dragHandle.style.height=`${e}px`,this.gearContainer.style.height=`${e}px`}updateScrollbar(){const e=this.viewports[0].$viewport.height();if(this.outerScroll.style.height=`${e}px`,!1===cf.has(this.track.type)){const t=this.maxViewportContentHeight(),i=Math.round(e/t*e);t>e?(this.innerScroll.style.display=\"block\",this.innerScroll.style.height=`${i}px`):this.innerScroll.style.display=\"none\"}}moveScroller(e){const t=Bt(this.innerScroll).position().top+e,i=Math.min(Math.max(0,t),this.outerScroll.clientHeight-this.innerScroll.clientHeight);Bt(this.innerScroll).css(\"top\",`${i}px`);const n=this.maxViewportContentHeight(),r=-Math.round(i*(n/this.viewports[0].$viewport.height()));for(let e of this.viewports)e.setTop(r);this.sampleInfoViewport.setTop(r),this.sampleNameViewport.trackScrollDelta=e,this.sampleNameViewport.setTop(r)}isLoading(){for(let e of this.viewports)if(e.isLoading())return!0}repaintViews(){for(let e of this.viewports)e.isVisible()&&e.repaint();\"function\"==typeof this.track.paintAxis&&this.paintAxis(),this.repaintSampleInfo(),this.repaintSamples()}repaintSampleInfo(){this.sampleInfoViewport.repaint()}repaintSamples(){if(\"function\"==typeof this.track.getSamples){const e=this.track.getSamples();e.names&&e.names.length>0&&this.sampleNameViewport.repaint(e)}}setTrackLabelName(e){this.viewports.forEach((t=>t.setTrackLabel(e)))}resize(e){for(let t of this.viewports)t.setWidth(e)}async updateViews(){if(!this.browser||!this.browser.referenceFrameList)return;const e=this.viewports.filter((e=>e.isVisible()));if(e.forEach((e=>e.shift())),this.browser.dragObject)return;const t=e.filter((e=>e.needsRepaint())).filter((e=>e.checkZoomIn())),i=e.filter((e=>e.checkZoomIn())).filter((e=>e.needsReload()));for(let e of i)await e.loadFeatures();if(this.disposed)return;if(this.track&&\"function\"==typeof this.track.variantRowCount&&i.length>0){let e=0;for(let t of this.viewports)t.featureCache&&t.featureCache.features&&(e=Math.max(e,t.featureCache.features.reduce(((e,t)=>Math.max(e,t.row||0)),0)));if(this.track.nVariantRows!==e+1){this.track.variantRowCount(e+1);for(let e of this.viewports)e.checkContentHeight()}}let n;if(\"merged\"===this.track.type)n=this.track.updateScales(e);else if(this.track.autoscale){let t=[];for(let i of e){const e=i.referenceFrame,n=e.start,r=n+e.toBP(i.getWidth());if(i.featureCache&&i.featureCache.features)if(\"function\"==typeof i.featureCache.features.getMax){const e=i.featureCache.features.getMax(n,r);if(t.push({value:e}),\"function\"==typeof i.featureCache.features.getMin){const e=i.featureCache.features.getMin(n,r);t.push({value:e})}}else{const e=to(i.featureCache.features,n,r);for(let i of e)t.push(i)}}\"function\"==typeof this.track.doAutoscale?this.track.dataRange=this.track.doAutoscale(t):this.track.dataRange=qa(t)}const r=this.track.autoscale||this.track.autoscaleGroup||\"ruler\"===this.track.type||n||this.track.groupBy;for(let i of e)t.includes(i)?i.repaint():r&&i.refresh();this.adjustTrackHeight(),this.repaintSampleInfo(),this.repaintSamples(),this.updateRulerViewportLabels()}clearCachedFeatures(){for(let e of this.viewports)e.clearCache()}updateRulerViewportLabels(){const e=this.browser.calculateViewportWidth(this.viewports.length);for(let t of this.viewports)\"ruler\"===this.track.type&&(this.viewports.length>1?t.presentLocusLabel(e):t.dismissLocusLabel())}async getInViewFeatures(){if(!this.browser||!this.browser.referenceFrameList)return[];let e=[];const t=this.viewports.filter((e=>e.isVisible()));for(let i of t){const t=i.referenceFrame,{chr:n,start:r,bpPerPixel:s}=i.referenceFrame,o=r+t.toBP(i.getWidth());if((!i.featureCache||!i.featureCache.containsRange(n,r,o,s))&&await i.loadFeatures(),i.featureCache&&i.featureCache.features)if(\"function\"==typeof i.featureCache.features.getMax){const t=i.featureCache.features.getMax(r,o);e.push({value:t})}else{const t=\"function\"==typeof i.featureCache.queryFeatures?i.featureCache.queryFeatures(n,r,o):to(i.featureCache.features,r,o);e=e.concat(t)}}return e}checkContentHeight(){for(let e of this.viewports)e.checkContentHeight();this.adjustTrackHeight()}adjustTrackHeight(){var e=this.maxViewportContentHeight();if(this.track.autoHeight?this.setTrackHeight(e,!1):this.track.paintAxis&&this.paintAxis(),!1===cf.has(this.track.type)){const t=this.viewports[0].getContentTop(),i=this.viewports[0].$viewport.height(),n=Math.min(0,i-e);if(t<n)for(let e of this.viewports)e.setTop(n);this.updateScrollbar()}}viewportsToReload(e){return this.viewports.filter((t=>{if(!t.isVisible())return!1;if(t.checkZoomIn()){const i=t.referenceFrame,n=t.referenceFrame.chr,r=i.start,s=r+i.toBP(Bt(t.contentDiv).width()),o=i.bpPerPixel;return e||!t.tile||t.tile.invalidate||!t.tile.containsRange(n,r,s,o)}return!1}))}createTrackScrollbar(t){const i=e();if(t.columnContainer.querySelector(\".igv-scrollbar-column\").appendChild(i),i.style.height=`${this.track.height}px`,this.outerScroll=i,!1===cf.has(this.track.type)){const n=e();i.appendChild(n),this.innerScroll=n,this.addTrackScrollMouseHandlers(t)}}createTrackDragHandle(t){\"sequence\"!==this.track.type&&!0===mo.has(this.track.type)?this.dragHandle=e({class:\"igv-track-drag-shim\"}):(this.dragHandle=e({class:\"igv-track-drag-handle\"}),this.dragHandle.classList.add(\"igv-track-drag-handle-color\")),t.columnContainer.querySelector(\".igv-track-drag-column\").appendChild(this.dragHandle),this.dragHandle.style.height=`${this.track.height}px`,this.addTrackDragMouseHandlers(t)}createTrackGearPopup(t){if(this.gearContainer=e(),t.columnContainer.querySelector(\".igv-gear-menu-column\").appendChild(this.gearContainer),this.gearContainer.style.height=`${this.track.height}px`,!0===this.track.ignoreTrackMenu);else{function i(e){if(e.preventDefault(),e.stopPropagation(),\"none\"===this.trackGearPopup.popover.style.display){for(const e of t.trackViews.filter((e=>e!==this&&void 0!==e.trackGearPopup)))e.trackGearPopup.popover.style.display=\"none\";this.trackGearPopup.presentMenuList(this,t.menuUtils.trackMenuItemList(this))}else this.trackGearPopup.popover.style.display=\"none\"}this.gear=e(),this.gearContainer.appendChild(this.gear),this.gear.appendChild(l(\"cog\")),this.trackGearPopup=new Xu(this.gear),this.boundTrackGearClickHandler=i.bind(this),this.gear.addEventListener(\"click\",this.boundTrackGearClickHandler)}}addTrackScrollMouseHandlers(e){this.boundTrackScrollMouseDownHandler=function(t){t.stopPropagation();const{y:i}=r(t);Bt(this.innerScroll).data(\"yDown\",i.toString()),this.boundColumnContainerMouseMoveHandler=function(e){e.stopPropagation();const{y:t}=r(e);this.moveScroller(t-parseInt(Bt(this.innerScroll).data(\"yDown\"))),Bt(this.innerScroll).data(\"yDown\",t.toString())}.bind(this),e.columnContainer.addEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler)}.bind(this),this.innerScroll.addEventListener(\"mousedown\",this.boundTrackScrollMouseDownHandler),this.boundColumnContainerMouseUpHandler=function(t){e.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler)}.bind(this),e.columnContainer.addEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),e.columnContainer.addEventListener(\"mouseleave\",this.boundColumnContainerMouseUpHandler)}removeTrackScrollMouseHandlers(){!1===cf.has(this.track.type)&&(this.innerScroll.removeEventListener(\"mousedown\",this.boundTrackScrollMouseDownHandler),this.browser.columnContainer.removeEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.browser.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.browser.columnContainer.removeEventListener(\"mouseleave\",this.boundColumnContainerMouseMoveHandler))}addTrackDragMouseHandlers(e){if(\"sequence\"===this.track.type||!1===mo.has(this.track.type)){let t;function i(i){i.preventDefault(),t=i.target,!1===this.track.selected&&(t.classList.remove(\"igv-track-drag-handle-color\"),t.classList.add(\"igv-track-drag-handle-hover-color\")),e.startTrackDrag(this)}function n(i){e.endTrackDrag(),t&&i.target!==t&&!1===this.track.selected&&(t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.add(\"igv-track-drag-handle-color\")),t=void 0}function r(i){i.preventDefault(),void 0===t&&!1===this.track.selected&&(i.target.classList.remove(\"igv-track-drag-handle-color\"),i.target.classList.add(\"igv-track-drag-handle-hover-color\")),e.updateTrackDrag(this)}function s(e){e.preventDefault(),void 0===t&&!1===this.track.selected&&(e.target.classList.remove(\"igv-track-drag-handle-hover-color\"),e.target.classList.add(\"igv-track-drag-handle-color\"))}this.boundTrackDragMouseDownHandler=i.bind(this),this.dragHandle.addEventListener(\"mousedown\",this.boundTrackDragMouseDownHandler),this.boundDocumentTrackDragMouseUpHandler=n.bind(this),document.addEventListener(\"mouseup\",this.boundDocumentTrackDragMouseUpHandler),this.boundTrackDragMouseEnterHandler=r.bind(this),this.dragHandle.addEventListener(\"mouseenter\",this.boundTrackDragMouseEnterHandler),this.dragHandle.addEventListener(\"mouseout\",(e=>{e.preventDefault(),void 0===t&&!1===this.track.selected&&(e.target.classList.remove(\"igv-track-drag-handle-hover-color\"),e.target.classList.add(\"igv-track-drag-handle-color\"))})),this.boundTrackDragMouseOutHandler=s.bind(this),this.dragHandle.addEventListener(\"mouseout\",this.boundTrackDragMouseOutHandler)}}removeTrackDragMouseHandlers(){\"ideogram\"===this.track.type||\"ruler\"===this.track.type||(this.dragHandle.removeEventListener(\"mousedown\",this.boundTrackDragMouseDownHandler),document.removeEventListener(\"mouseup\",this.boundDocumentTrackDragMouseUpHandler),this.dragHandle.removeEventListener(\"mouseup\",this.boundTrackDragMouseEnterHandler),this.dragHandle.removeEventListener(\"mouseout\",this.boundTrackDragMouseOutHandler))}removeTrackGearMouseHandlers(){!0===this.track.ignoreTrackMenu||this.gear.removeEventListener(\"click\",this.boundTrackGearClickHandler)}removeDOMFromColumnContainer(){this.axis.remove(),this.removeViewportsFromColumnContainer(),this.sampleInfoViewport.dispose(),this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove()}removeViewportsFromColumnContainer(){for(let e of this.viewports)e.$viewport.remove()}dispose(){this.axis.remove();for(let e of this.viewports)e.dispose();this.sampleInfoViewport.dispose(),this.sampleNameViewport.dispose(),this.removeTrackScrollMouseHandlers(),this.outerScroll.remove(),this.removeTrackDragMouseHandlers(),this.dragHandle.remove(),this.removeTrackGearMouseHandlers(),this.gearContainer.remove(),\"function\"==typeof this.track.dispose&&this.track.dispose();for(let e of Object.keys(this))this[e]=void 0;this.alert&&this.alert.container.remove(),this.disposed=!0}paintAxis(){if(\"function\"==typeof this.track.paintAxis){const{width:e,height:t}=this.axisCanvas.getBoundingClientRect(),i=window.devicePixelRatio||1;this.axisCanvas.height=i*t,this.axisCanvas.width=i*e;const n=this.axisCanvas.getContext(\"2d\");if(n.scale(i,i),this.track.autoscaleGroup){if(void 0===wo[this.track.autoscaleGroup]){const e=so.Dark2,t=Math.floor(Math.random()*so.Dark2.length);wo[this.track.autoscaleGroup]=e[t]}const i=_s.addAlpha(wo[this.track.autoscaleGroup],.75);this.track.paintAxis(n,e,t,i)}else this.track.paintAxis(n,e,t,void 0)}}maxViewportContentHeight(){return Math.max(...this.viewports.map((e=>e.getContentHeight())))}enableTrackSelection(e){const t=this.trackSelectionContainer;if(t&&!mo.has(this.track.type))if(!1!==e)t.style.display=\"grid\";else{this.track.selected=!1;t.querySelector(\"[name=track-select]\").checked=this.track.selected,this.dragHandle&&this.setDragHandleSelectionState(!1),t.style.display=\"none\"}}setDragHandleSelectionState(e){const t=this.dragHandle;e?(t.classList.remove(\"igv-track-drag-handle-color\"),t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.add(\"igv-track-drag-handle-selected-color\")):(t.classList.remove(\"igv-track-drag-handle-hover-color\"),t.classList.remove(\"igv-track-drag-handle-selected-color\"),t.classList.add(\"igv-track-drag-handle-color\"))}}function df(e){this.thresholds=e.thresholds,this.colors=e.colors}function uf(e){this.scale=e,this.lowColor=\"rgb(\"+e.lowR+\",\"+e.lowG+\",\"+e.lowB+\")\",this.highColor=\"rgb(\"+e.highR+\",\"+e.highG+\",\"+e.highB+\")\",this.diff=e.high-e.low}df.prototype.getColor=function(e){for(let t of this.thresholds)if(e<t)return this.colors[this.thresholds.indexOf(t)];return this.colors[this.colors.length-1]},uf.prototype.getColor=function(e){var t,i=this.scale;return e<=i.low?this.lowColor:e>=i.high?this.highColor:(t=(e-i.low)/this.diff,\"rgb(\"+Math.floor(i.lowR+t*(i.highR-i.lowR))+\",\"+Math.floor(i.lowG+t*(i.highG-i.lowG))+\",\"+Math.floor(i.lowB+t*(i.highB-i.lowB))+\")\")};class ff{constructor(e){this.color=e}getColor(){return this.color}}const pf={threshold:2e3,r:0,g:0,b:255};class gf{constructor(e){e=e||pf,this.threshold=e.threshold,this.r=e.r,this.g=e.g,this.b=e.b,this.cache=[],this.nbins=2e3,this.binsize=this.threshold/this.nbins}setThreshold(e){this.threshold=e,this.cache=[],this.binsize=this.threshold/this.nbins}getThreshold(){return this.threshold}setColorComponents(e){this.r=e.r,this.g=e.g,this.b=e.b,this.cache=[]}getColorComponents(){return{r:this.r,g:this.g,b:this.b}}equals(e){return JSON.stringify(this)===JSON.stringify(e)}getColor(e){const t=Math.floor(Math.min(this.threshold,e)/this.binsize);if(void 0===this.cache[t]){const i=(ys.clamp(e,0,this.threshold)-0)/(this.threshold-0);this.cache[t]=`rgba(${this.r},${this.g},${this.b}, ${i})`}return this.cache[t]}stringify(){return this.threshold+\",\"+this.r+\",\"+this.g+\",\"+this.b}static parse(e){var t,i;return e.startsWith(\"R:\")?(t=e.substring(2).split(\":\"),(i=new RatioColorScale(Number.parseFloat(t[0]))).positiveScale=n(t[1]),i.negativeScale=n(t[2]),i):n(e);function n(e){var t,i;return t={threshold:(i=e.split(\",\"))[0],r:i[1],g:i[2],b:i[3]},new gf(t)}}}class mf{constructor(e){this.config=e,this.url=e.path||e.url}async read(e,t){const i={start:e,size:t};return Qs.loadArrayBuffer(this.url,{range:i})}}class wf{constructor(e){this.file=e}async read(e,t){const i=this.file;return void 0!==e?i.slice(e,e+t).arrayBuffer():i.arrayBuffer()}}class bf{constructor(e,t){this.file=e,this.rateLimiter=t}async read(e,t){const i=this.file,n=this.rateLimiter;return new Promise((function(r,s){n.limiter((async function(i){try{const n=await i.read(e,t);r(n)}catch(e){s(e)}}))(i)}))}}class Ff{constructor(e){this.file=e.file,this.size=e.size||64e3,this.position=0,this.bufferStart=0,this.bufferLength=0,this.buffer=void 0}async read(e,t){const i=e,n=e+t,r=this.bufferStart,s=this.bufferStart+this.bufferLength;if(t>this.size)return this.buffer=void 0,this.bufferStart=0,this.bufferLength=0,this.file.read(e,t);if(i>=r&&n<=s){const e=i-r,n=e+t;return this.buffer.slice(e,n)}if(i<r&&n>r){const n=r-i,s=await this.file.read(e,n),o=t-n;if(o>0){const e=this.buffer.slice(0,o);return vf(s,e)}return s}if(!(i<s&&n>s))return this.buffer=await this.file.read(e,this.size),this.bufferStart=e,this.bufferLength=this.buffer.byteLength,this.buffer.slice(0,t);{const e=s-i,n=this.bufferLength-e,r=this.buffer.slice(n,this.bufferLength),o=t-e;if(!(o>0))return r;try{this.buffer=await this.file.read(s,this.size),this.bufferStart=s,this.bufferLength=this.buffer.byteLength;const e=this.buffer.slice(0,o);return vf(r,e)}catch(e){if(e.code&&416===e.code)return r;throw e}}}}var vf=function(e,t){var i=new Uint8Array(e.byteLength+t.byteLength);return i.set(new Uint8Array(e),0),i.set(new Uint8Array(t),e.byteLength),i.buffer};const yf=function(e,t){this.littleEndian=void 0===t||t,this.position=0,this.view=e,this.length=e.byteLength};function Af(e,t){this.block=e,this.offset=t}yf.prototype.available=function(){return this.length-this.position},yf.prototype.remLength=function(){return this.length-this.position},yf.prototype.hasNext=function(){return this.position<this.length-1},yf.prototype.getByte=function(){var e=this.view.getUint8(this.position,this.littleEndian);return this.position++,e},yf.prototype.getShort=function(){var e=this.view.getInt16(this.position,this.littleEndian);return this.position+=2,e},yf.prototype.getUShort=function(){var e=this.view.getUint16(this.position,this.littleEndian);return this.position+=2,e},yf.prototype.getInt=function(){var e=this.view.getInt32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getUInt=function(){var e=this.view.getUint32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getLong=function(){var e=[];e[0]=this.view.getUint8(this.position),e[1]=this.view.getUint8(this.position+1),e[2]=this.view.getUint8(this.position+2),e[3]=this.view.getUint8(this.position+3),e[4]=this.view.getUint8(this.position+4),e[5]=this.view.getUint8(this.position+5),e[6]=this.view.getUint8(this.position+6),e[7]=this.view.getUint8(this.position+7);var t=0;if(this.littleEndian)for(var i=e.length-1;i>=0;i--)t=256*t+e[i];else for(i=0;i<e.length;i++)t=256*t+e[i];return this.position+=8,t},yf.prototype.getString=function(e){for(var t,i=\"\";0!=(t=this.view.getUint8(this.position++))&&(i+=String.fromCharCode(t),!e||i.length!=e););return i},yf.prototype.getFixedLengthString=function(e){var t,i,n=\"\";for(t=0;t<e;t++)(i=this.view.getUint8(this.position++))>0&&(n+=String.fromCharCode(i));return n},yf.prototype.getFixedLengthTrimmedString=function(e){var t,i,n=\"\";for(t=0;t<e;t++)(i=this.view.getUint8(this.position++))>32&&(n+=String.fromCharCode(i));return n},yf.prototype.getFloat=function(){var e=this.view.getFloat32(this.position,this.littleEndian);return this.position+=4,e},yf.prototype.getDouble=function(){var e=this.view.getFloat64(this.position,this.littleEndian);return this.position+=8,e},yf.prototype.skip=function(e){return this.position+=e,this.position},yf.prototype.getVPointer=function(){var e=this.position,t=this.view.getUint8(e+1)<<8|this.view.getUint8(e),i=4294967296*(255&this.view.getUint8(e+6))+16777216*(255&this.view.getUint8(e+5))+65536*(255&this.view.getUint8(e+4))+256*(255&this.view.getUint8(e+3))+(255&this.view.getUint8(e+2));return this.position+=8,new Af(i,t)},Af.prototype.isLessThan=function(e){return this.block<e.block||this.block===e.block&&this.offset<e.offset},Af.prototype.isGreaterThan=function(e){return this.block>e.block||this.block===e.block&&this.offset>e.offset},Af.prototype.print=function(){return this.block+\":\"+this.offset};class Cf{constructor(e,t){this.chr1=e,this.chr2=t}getKey(){return this.chr1.name+\"_\"+this.chr2.name+\"_\"+this.zoom.unit+\"_\"+this.zoom.binSize}getBlockNumbers(e,t,i){if(e.chr==this.chr2&&t.chr===this.chr1){const i=e;e=t,t=i}const n=this.chr1===this.chr2,r=this.zoom.binSize,s=this.blockBinCount,o=this.blockColumnCount;return i<9||!n?function(){const i=e.start/r,a=e.end/r,c=t.start/r,l=t.end/r,h=Math.floor(i/s),d=Math.floor((a-1)/s),u=Math.floor(c/s),f=Math.floor((l-1)/s),p=[];for(let e=u;e<=f;e++)for(let t=h;t<=d;t++){let i;i=n&&e<t?t*o+e:e*o+t,p.includes(i)||p.push(i)}return p}():function(){const i=e.start/r,n=e.end/r,a=t.start/r,c=t.end/r,l=Math.floor((i+a)/2/s),h=Math.floor((n+c)/2/s),d=Math.floor(Math.log2(1+Math.abs(i-c)/Math.sqrt(2)/s)),u=Math.floor(Math.log2(1+Math.abs(n-a)/Math.sqrt(2)/s)),f=(n-a)*(i-c)<0?0:Math.min(d,u),p=Math.max(d,u),g=[];for(let e=f;e<=p;e++)for(let t=l;t<=h;t++){const i=e*o+t;g.push(i)}return g}()}static parseMatrixZoomData(e,t,i){const n=new Cf(e,t),r=i.getString(),s=i.getInt(),o=i.getFloat(),a=i.getFloat(),c=i.getFloat(),l=i.getFloat(),h=i.getInt();n.blockBinCount=i.getInt(),n.blockColumnCount=i.getInt();const d=i.getInt();n.zoom={index:s,unit:r,binSize:h},n.blockIndex=new _f(d,i);const u=o/(e.size/h)/(t.size/h);return n.averageCount=u,n.sumCounts=o,n.stdDev=c,n.occupiedCellCount=a,n.percent95=l,n}}class _f{constructor(e,t){for(this.blockIndex={};e-- >0;){const e=t.getInt(),i=t.getLong(),n=t.getInt();this.blockIndex[e]={filePosition:i,size:n}}}getBlockIndexEntry(e){return this.blockIndex[e]}}class xf{constructor(e,t,i){this.chr1=e,this.chr2=t,this.bpZoomData=[],this.fragZoomData=[];for(let e of i)\"BP\"===e.zoom.unit?this.bpZoomData.push(e):this.fragZoomData.push(e)}findZoomForResolution(e,t){const i=\"FRAG\"===t?this.fragZoomData:this.bpZoomData;for(let t=1;t<i.length;t++){if(i[t].zoom.binSize<e)return t-1}return i.length-1}getZoomData(e,t){const i=\"BP\"===(t=t||\"BP\")?this.bpZoomData:this.fragZoomData;for(let t=0;t<i.length;t++){var n=i[t];if(e===n.zoom.binSize)return n}}getZoomDataByIndex(e,t){return(\"FRAG\"===t?this.fragZoomData:this.bpZoomData)[e]}static getKey(e,t){if(e>t){const i=e;e=t,t=i}return`${e}_${t}`}static parseMatrix(e,t){const i=new yf(new DataView(e)),n=i.getInt(),r=i.getInt(),s=t[n],o=t[r];let a=i.getInt();const c=[];for(;a-- >0;){const e=Cf.parseMatrixZoomData(s,o,i);c.push(e)}return new xf(n,r,c)}}class kf{constructor(e,t,i){this.bin1=e,this.bin2=t,this.counts=i}getKey(){return this.bin1+\"_\"+this.bin2}}class If{constructor(e=10){this.max=e,this.map=new Map}get(e){let t=this.map.get(e);return t&&(this.map.delete(e),this.map.set(e,t)),t}set(e,t){this.map.has(e)?this.map.delete(e):this.map.size===this.max&&this.map.delete(this.first()),this.map.set(e,t)}has(e){return this.map.has(e)}clear(){this.map.clear()}first(){return this.map.keys().next().value}}class Sf{constructor(e,t,i,n){this.file=e,this.filePosition=t,this.nValues=i,this.dataType=n,this.cache=void 0}async getValues(e,t){if(!this.cache||e<this.cache.start||t>this.cache.end){const i=Math.max(0,e-1e3),n=Math.min(this.nValues,t+1e3),r=this.filePosition+i*this.dataType,s=n-i,o=s*this.dataType,a=await this.file.read(r,o);if(!a)return;const c=new yf(new DataView(a)),l=[];for(let e=0;e<s;e++)l[e]=8===this.dataType?c.getDouble():c.getFloat();this.cache={start:i,end:n,values:l}}const i=e-this.cache.start,n=i+(t-e);return this.cache.values.slice(i,n)}getKey(){return Sf.getKey(this.type,this.chrIdx,this.unit,this.resolution)}static getNormalizationVectorKey(e,t,i,n){return e+\"_\"+t+\"_\"+i+\"_\"+n}}var 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mf(e);(t=this.url).indexOf(\"drive.google.com\")>=0||t.indexOf(\"www.googleapis.com/drive\")>0?this.file=new bf(i,Bf):this.file=i}}var t}async init(){this.initialized||(await this.readHeaderAndFooter(),this.initialized=!0)}async getVersion(){if(void 0===this.version){const e=await this.file.read(0,128);if(!e)return;const t=new yf(new DataView(e));return this.magic=t.getString(),this.version=t.getInt(),this.version}return this.version}async getMetaData(){return await this.init(),this.meta}async readHeaderAndFooter(){let e=await this.file.read(0,16);if(!e||0===e.byteLength)throw Error(\"File content is empty\");let t=new yf(new DataView(e));if(this.magic=t.getString(),this.version=t.getInt(),this.version<5)throw Error(\"Unsupported hic version: \"+this.version);this.footerPosition=t.getLong(),await this.readFooter();const i=Object.values(this.masterIndex).reduce(((e,t)=>Math.min(e,t.start)),Number.MAX_VALUE)-16;e=await this.file.read(16,i),t=new yf(new DataView(e)),this.genomeId=t.getString(),this.version>=9&&(this.normVectorIndexPosition=t.getLong(),this.normVectorIndexSize=t.getLong()),this.attributes={};let n=t.getInt();for(;n-- >0;)this.attributes[t.getString()]=t.getString();this.chromosomes=[],this.chromosomeIndexMap={};let r=t.getInt(),s=0;for(;r-- >0;){const e={index:s,name:t.getString(),size:this.version<9?t.getInt():t.getLong()};\"all\"===e.name.toLowerCase()&&(this.wholeGenomeChromosome=e,this.wholeGenomeResolution=Math.round(2*e.size)),this.chromosomes.push(e),this.chromosomeIndexMap[e.name]=e.index,s++}this.bpResolutions=[];let o=t.getInt();for(;o-- >0;)this.bpResolutions.push(t.getInt());if(this.loadFragData){this.fragResolutions=[];let e=t.getInt();if(e>0)for(;e-- >0;)this.fragResolutions.push(t.getInt())}this.chrAliasTable={};for(let e of Object.keys(this.chromosomeIndexMap))e.startsWith(\"chr\")?this.chrAliasTable[e.substr(3)]=e:\"MT\"===e?this.chrAliasTable.chrM=e:this.chrAliasTable[\"chr\"+e]=e;this.meta={version:this.version,genome:this.genomeId,chromosomes:this.chromosomes,resolutions:this.bpResolutions}}async readFooter(){const e=this.version<9?8:12;let t=await this.file.read(this.footerPosition,e);if(!t)return null;let i=new yf(new DataView(t));const n=this.version<9?i.getInt():i.getLong();let r=i.getInt();const s=196*r;for(t=await this.file.read(this.footerPosition+e,Math.min(s,n)),i=new yf(new DataView(t)),this.masterIndex={};r-- >0;){const e=i.getString(),t=i.getLong(),n=i.getInt();this.masterIndex[e]={start:t,size:n}}if(this.expectedValueVectors={},this.version>5){const e=this.version<9?4:8;this.normExpectedValueVectorsPosition=this.footerPosition+e+n}return this}async printIndexStats(){let e,t=0,i=0;await await this.init();for(let n of Object.keys(this.masterIndex)){const r=this.masterIndex[n];t+=r.size,r.size>i&&(i=r.size,e=n)}console.log(`${i}  ${e}  ${this.config.url}`)}async getMatrix(e,t){const i=xf.getKey(e,t);if(this.matrixCache.has(i))return this.matrixCache.get(i);{const n=await this.readMatrix(e,t);return this.matrixCache.set(i,n),n}}async readMatrix(e,t){if(await this.init(),e>t){const i=e;e=t,t=i}const i=xf.getKey(e,t),n=this.masterIndex[i];if(!n)return;const r=await this.file.read(n.start,n.size);return r?xf.parseMatrix(r,this.chromosomes):void 0}async getContactRecords(e,t,i,n,r,s=!1){await this.init();const o=this.chromosomeIndexMap[this.getFileChrName(t.chr)],a=this.chromosomeIndexMap[this.getFileChrName(i.chr)];if(o>a||o===a&&t.start>=i.end){const e=t;t=i,i=e}const c=await this.getBlocks(t,i,n,r);if(!c||0===c.length)return[];const l=[],h=t.start/r,d=t.end/r,u=i.start/r,f=i.end/r,p=Math.floor(h),g=Math.ceil(d),m=Math.floor(u),w=Math.ceil(f);for(let o of c)if(o){let a,c,b=e&&\"NONE\"!==e;const F=this.getFileChrName(t.chr),v=this.getFileChrName(i.chr);if(b){const t=await this.getNormalizationVector(e,F,n,r),i=F===v?t:await this.getNormalizationVector(e,v,n,r);t&&i?(a=await t.getValues(p,g),c=await i.getValues(m,w)):b=!1}for(let e of o.records)if(s||e.bin1>=h&&e.bin1<d&&e.bin2>=u&&e.bin2<f)if(b){const t=e.bin1,i=e.bin2,n=a[t-p]*c[i-m];if(0!==n&&!isNaN(n)){const r=e.counts/n;l.push(new kf(t,i,r))}}else l.push(e);void 0===this.percentile95&&o.records.length>10&&(this.percentile95=Lf(o.records,95))}return l}async getBlocks(e,t,i,n){const r=(e,t)=>`${t.getKey()}_${e}`;await this.init();const s=this.getFileChrName(e.chr),o=this.getFileChrName(t.chr),a=this.chromosomeIndexMap[s],c=this.chromosomeIndexMap[o];if(void 0===a)return console.log(\"No chromosome named: \"+e.chr),[];if(void 0===c)return console.log(\"No chromosome named: \"+t.chr),[];const l=await this.getMatrix(a,c);if(!l)return console.log(\"No matrix for \"+e.chr+\"-\"+t.chr),[];const h=l.getZoomData(n,i);if(!h){let i=`No data avalailble for resolution: ${n}  for map ${e.chr}-${t.chr}`;throw new Error(i)}const d=h.getBlockNumbers(e,t,this.version),u=[],f=[];for(let e of d){const t=r(e,h);this.blockCache.has(n,t)?u.push(this.blockCache.get(n,t)):f.push(e)}const p=f.map((e=>this.readBlock(e,h))),g=await Promise.all(p);for(let e of g)e&&this.blockCache.set(n,r(e.blockNumber,h),e);return u.concat(g)}async readBlock(e,t){const i=await t.blockIndex.getBlockIndexEntry(e);if(i){let n=await this.file.read(i.filePosition,i.size);if(!n)return;n=new ls(new Uint8Array(n)).buffer;const r=new yf(new DataView(n)),s=r.getInt(),o=[];if(this.version<7)for(let e=0;e<s;e++){const e=r.getInt(),t=r.getInt(),i=r.getFloat();o.push(new kf(e,t,i))}else{const e=r.getInt(),t=r.getInt(),i=1===r.getByte(),n=!(this.version<9)&&1==r.getByte(),s=!(this.version<9)&&1==r.getByte(),a=r.getByte();if(1===a){const a=s?r.getInt():r.getShort();for(let c=0;c<a;c++){const a=t+(s?r.getInt():r.getShort()),c=n?r.getInt():r.getShort();for(let t=0;t<c;t++){const t=e+(n?r.getInt():r.getShort()),s=i?r.getFloat():r.getShort();o.push(new kf(t,a,s))}}}else{if(2!=a)throw new Error(\"Unknown block type: \"+a);{const n=r.getInt(),s=r.getShort();for(let a=0;a<n;a++){const n=Math.floor(a/s),c=e+(a-n*s),l=t+n;if(i){const e=r.getFloat();isNaN(e)||o.push(new kf(c,l,e))}else{const e=r.getShort();-32768!=e&&o.push(new kf(c,l,e))}}}}}return new Df(e,t,o,i)}}async hasNormalizationVector(e,t,i,n){let r;if(await this.init(),Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}const s=Rf(e,r,i.toString(),n),o=await this.getNormVectorIndex();return o&&o[s]}async isNormalizationValueAvailableAtResolution(e,t,i,n){let r;if(Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}return void 0!==(await this.getNormVectorIndex())[Rf(e,r,i.toString(),n)]}async getNormalizationVector(e,t,i,n){let r;if(await this.init(),Number.isInteger(t))r=t;else{const e=this.getFileChrName(t);r=this.chromosomeIndexMap[e]}const s=Rf(e,r,i.toString(),n);if(this.normVectorCache.has(s))return this.normVectorCache.get(s);const o=await this.getNormVectorIndex();if(!o)return void console.log(\"Normalization vectors not present in this file\");if(!1===await this.isNormalizationValueAvailableAtResolution(e,t,i,n)){const t=`Normalization option ${e} not available at resolution ${n}. Will use NONE.`;return console.log(t),void(this.alert&&this.alert(t))}const a=o[s],c=await this.file.read(a.filePosition,8);if(!c)return;const l=new yf(new DataView(c)),h=this.version<9?l.getInt():l.getLong(),d=this.version<9?8:4,u=this.version<9?a.filePosition+4:a.filePosition+8,f=new Sf(this.file,u,h,d);return this.normVectorCache.set(s,f),f}async getNormVectorIndex(){if(!(this.version<6)){if(!this.normVectorIndex){if(!this.config.nvi&&this.remote&&this.url){const e=new URL(this.url),t=encodeURIComponent(e.hostname+e.pathname);Ef.hasOwnProperty(t)&&(this.config.nvi=Ef[t])}if(this.config.nvi){const e=decodeURIComponent(this.config.nvi).split(\",\"),t={start:parseInt(e[0]),size:parseInt(e[1])};return this.readNormVectorIndex(t)}try{return await this.readNormExpectedValuesAndNormVectorIndex(),this.normVectorIndex}catch(e){\"416\"===e.code||416===e.code?this.normExpectedValueVectorsPosition=void 0:console.error(e)}}return this.normVectorIndex}}async getNormalizationOptions(){return await this.getNormVectorIndex(),this.normalizationTypes}async readNormVectorIndex(e){await this.init(),this.normalizationVectorIndexRange=e;const t=await this.file.read(e.start,e.size),i=new yf(new DataView(t));this.normVectorIndex={};let n=i.getInt();for(;n-- >0;)this.parseNormVectorEntry(i);return this.normVectorIndex}async readNormExpectedValuesAndNormVectorIndex(){if(await this.init(),void 0===this.normExpectedValueVectorsPosition)return;const e=await this.skipExpectedValues(this.normExpectedValueVectorsPosition);let t=4,i=await this.file.read(e,4);if(0===i.byteLength)return;const n=new yf(new DataView(i)).getInt(),r={start:e+t,size:30*n};i=await this.file.read(r.start,r.size),this.normalizedExpectedValueVectors={},this.normVectorIndex={},await async function i(n,r){const s=new yf(new DataView(r));for(;n-- >0;){if(s.available()<100){n++,t+=s.position;const r=Math.max(1e3,30*n),o={start:e+t,size:r},a=await this.file.read(o.start,o.size);return i.call(this,n,a)}this.parseNormVectorEntry(s)}t+=s.position}.call(this,n,i),this.config.nvi=e.toString()+\",\"+t}async skipExpectedValues(e){const t=this.version,i=new Ff({file:this.file,size:256e3}),n={start:e,size:4},r=await i.read(n.start,n.size),s=new yf(new DataView(r)).getInt();return 0===s?e+4:async function e(n,r){let s={start:n,size:500},o=0,a=n,c=await i.read(s.start,s.size),l=new yf(new DataView(c));l.getString(),l.getString(),l.getInt();const h=t<9?l.getInt():l.getLong();o+=l.position+h*(t<9?8:4),s={start:n+o,size:4},c=await i.read(s.start,s.size),l=new yf(new DataView(c));const d=l.getInt();return o+=4+d*(4+(t<9?8:4)),r--,0===r?a+o:e(a+o,r)}(e+4,s)}getZoomIndexForBinSize(e,t){let i;if(\"BP\"===(t=t||\"BP\"))i=this.bpResolutions;else{if(\"FRAG\"!==t)throw new Error(\"Invalid unit: \"+t);i=this.fragResolutions}for(let t=0;t<i.length;t++)if(i[t]===e)return t;return-1}parseNormVectorEntry(e){const t=e.getString(),i=e.getInt(),n=e.getString(),r=e.getInt(),s=e.getLong(),o=this.version<9?e.getInt():e.getLong(),a=t+\"_\"+i+\"_\"+n+\"_\"+r;this.normalizationTypes.includes(t)||this.normalizationTypes.push(t),this.normVectorIndex[a]={filePosition:s,size:o}}getFileChrName(e){return this.chrAliasTable.hasOwnProperty(e)?this.chrAliasTable[e]:e}}function Rf(e,t,i,n){return e+\"_\"+t+\"_\"+i+\"_\"+n}class Df{constructor(e,t,i,n){this.blockNumber=e,this.zoomData=t,this.records=i,this.idx=n}}class Tf{constructor(){this.resolution=void 0,this.map=new If(6)}set(e,t,i){this.resolution!==e&&this.map.clear(),this.resolution=e,this.map.set(t,i)}get(e,t){return this.resolution===e?this.map.get(t):void 0}has(e,t){return this.resolution===e&&this.map.has(t)}}function Lf(e,t){const i=e.map((e=>e.counts));i.sort((function(e,t){return e-t}));return i[Math.floor(t/100*e.length)]}class zf{constructor(e,t){this.config=e,this.genome=t,this.hicFile=e._hicFile?e._hicFile:new Mf(e),e._hicFile=void 0}async getHeader(){return await this.hicFile.init(),this.hicFile}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){this.hicFile.initialized||await this.hicFile.init();const s=this.hicFile.bpResolutions,o=s[s.length-1];return(await this.hicFile.getContactRecords(void 0,{chr:e,start:t,end:i},{chr:\"celltype\",start:0,end:1e8},\"BP\",o)).map((t=>{const i=t.bin1*o;return{chr:e,start:i,end:i+o,value:t.counts,sample:t.bin2.toString()}}))}supportsWholeGenome(){return!1}}function Hf(e,t){const i=new Set(e.attributeNames),n=t[0];if(void 0===e.getAttributes(n))return!1;{const t=Object.keys(e.getAttributes(n));for(const e of t)if(!1===i.has(e))return!1}return!0}class Pf extends Hl{#y=new Map;constructor(e,t){super(e,t)}init(e){if(super.init(e),this.type=e.type||\"seg\",\"maf\"===this.type&&(this.type=\"mut\"),this.isLog=e.isLog,this.displayMode=e.displayMode||\"EXPANDED\",this.height=e.height||300,this.maxHeight=e.maxHeight||500,this.squishedRowHeight=e.sampleSquishHeight||e.squishedRowHeight||2,this.expandedRowHeight=e.sampleExpandHeight||e.expandedRowHeight||13,this.sampleHeight=this.squishedRowHeight,this.sampleKeys=[],e.samples){for(let t of e.samples)this.sampleKeys.push(t);this.explicitSamples=!0}if(e.color)this.color=e.color;else if(e.colorTable)this.colorTable=new ao(e.colorTable);else switch(this.type){case\"mut\":this.colorTable=new ao(qf);break;case\"shoebox\":e.colorScale&&(this.sbColorScale=gf.parse(e.colorScale));break;default:this.posColorScale=new uf(e.posColorScale||Of),this.negColorScale=new uf(e.negColorScale||Uf)}const t=Object.assign({},this.config);t.maxWGCount=t.maxWGCount||Number.MAX_SAFE_INTEGER,\"shoebox\"===this.type?(this.featureSource=new zf(t,this.browser.genome),this.height=e.height||500,this.maxHeight=e.maxHeight||800,this.isLog=!1,this.squishedRowHeight=e.squishedRowHeight||1,this.displayMode=e.displayMode||\"SQUISHED\",this.visibilityWindow=void 0===e.visibilityWindow?1e6:e.visibilityWindow):this.featureSource=Ad(t,this.browser.genome),this.initialSort=e.sort}async postInit(){\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader(),this.disposed)||this.header&&this.setTrackProperties(this.header)}menuItemList(){const e=[];if(!0===Hf(this.browser.sampleInfo,this.sampleKeys)){e.push(\"<hr/>\"),e.push(\"Sort by attribute:\");for(const n of this.browser.sampleInfo.attributeNames){if(this.sampleKeys.some((e=>{const t=this.browser.sampleInfo.getAttributes(e);return t&&t[n]}))){const r=Bt(\"<div>\");function s(){const e=this.#y.get(n)||1;this.sortByAttribute(n,e),this.#y.set(n,-1*e),this.config.sort={option:\"ATTRIBUTE\",attribute:n,direction:1===e?\"ASC\":\"DESC\"}}r.html(`&nbsp;&nbsp;${n.split(Uu.emptySpaceReplacement).join(\" \")}`),e.push({object:r,click:s})}}}const t={SQUISHED:\"Squish\",EXPANDED:\"Expand\",FILL:\"Fill\"};if(\"shoebox\"===this.type&&this.sbColorScale){function o(e){this.browser.inputDialog.present({label:\"Color Scale Threshold\",value:this.sbColorScale.threshold,callback:()=>{const e=Number(this.browser.inputDialog.value,10);e&&(this.sbColorScale.setThreshold(e),this.trackView.repaintViews())}},e)}e.push(\"<hr/>\"),e.push({object:Bt(\"<div>Set color scale threshold</div>\"),dialog:o})}e.push(\"<hr/>\"),e.push(\"DisplayMode:\");const i=\"seg\"===this.type||\"shoebox\"===this.type?[\"SQUISHED\",\"EXPANDED\",\"FILL\"]:[\"SQUISHED\",\"EXPANDED\"];for(let a of i){const c=Dl(t[a],a===this.displayMode);e.push({object:Bt(c),click:function(){this.displayMode=a,this.config.displayMode=a,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.trackView.moveScroller(this.trackView.sampleNameViewport.trackScrollDelta)}})}return e}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys,height:this.sampleHeight,yOffset:0}}async getFeatures(e,t,i){const n=await this.featureSource.getFeatures({chr:e,start:t,end:i});if(this.updateSampleKeys(n),this.initialSort){const e=this.initialSort;if(void 0===e.option||\"VALUE\"===e.option.toUpperCase())this.sortByValue(e,n);else if(\"ATTRIBUTE\"===e.option.toUpperCase()&&e.attribute){const t=\"DESC\"===e.direction?1:-1;this.sortByAttribute(e.attribute,t)}this.initialSort=void 0}return n}draw({context:e,pixelTop:t,pixelWidth:i,pixelHeight:n,features:r,bpPerPixel:s,bpStart:o}){if(xo.fillRect(e,0,t,i,n,{fillStyle:\"rgb(255, 255, 255)\"}),r&&r.length>0){if(this.checkForLog(r),\"shoebox\"===this.type&&!this.sbColorScale){const e=this.featureSource.hicFile.percentile95||2e3;this.sbColorScale=new gf({threshold:e,r:0,g:0,b:255})}const a={};let c;switch(this.sampleKeys.forEach((function(e,t){a[e]=t})),this.displayMode){case\"FILL\":this.sampleHeight=n/this.sampleKeys.length,c=0;break;case\"SQUISHED\":this.sampleHeight=this.squishedRowHeight,c=0;break;default:this.sampleHeight=this.expandedRowHeight,c=1}const l=this.sampleHeight;for(let e of r)e.pixelRect=void 0;const h=t+n,d=o+i*s+1,u=s;this.sampleYStart=void 0;for(let i of r){if(i.end<o||i.start>d)continue;const n=i.sampleKey||i.sample;i.row=a[n];const r=i.row*l+c;void 0===this.sampleYStart&&(this.sampleYStart=r);if(r+l<t||r>h)continue;const s=Math.max(i.start,o);let f=Math.round((s-o)/u);const p=Math.min(i.end,d),g=Math.round((p-o)/u);let m,w,b=Math.max(1,g-f);if(this.color?m=\"function\"==typeof this.color?this.color(i):this.color:this.colorTable&&(m=this.colorTable.getColor(i.value.toLowerCase())),\"mut\"===this.type)w=l-2*c,b<3&&(b=3,f-=1);else if(\"shoebox\"===this.type){m=this.sbColorScale.getColor(i.value);let e=l;if(l<.25){const t=.1+2*Math.abs(t.value);e=Math.min(1,t*l)}w=e-2*c}else{let e=i.value;this.isLog||(e=ys.log2(e/2)),m=e<-.1?this.negColorScale.getColor(e):e>.1?this.posColorScale.getColor(e):\"white\";let t=l;if(l<.25){const i=.1+2*Math.abs(e);t=Math.min(1,i*l)}w=t-2*c}i.pixelRect={x:f,y:r,w:b,h:w},e.fillStyle=m,e.fillRect(f,r,b,w)}}}checkForLog(e){if(void 0===this.isLog){this.isLog=!1;for(let t of e)if(t.value<0)return void(this.isLog=!0)}}computePixelHeight(e){if(!e)return 0;const t=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.expandedRowHeight;return this.updateSampleKeys(e),this.sampleKeys.length*t}async sortByValue(e,t){const i=e.chr;let n,r;if(e.position?(n=e.position-1,r=n+1):(n=e.start,r=e.end),t||(t=await this.featureSource.getFeatures({chr:i,start:n,end:r})),!t)return;this.updateSampleKeys(t);const s={},o=\"ASC\"===e.direction?1:-1,a=()=>{const e=r-n+1;for(let i of t){if(i.end<n)continue;if(i.start>r)break;const t=Math.max(n,i.start),o=(Math.min(r,i.end)-t)/e,a=i.sampleKey||i.sample,c=s[a]||0;s[a]=c+o*i.value}this.sampleKeys.sort((function(e,t){let i=s[e],n=s[t];return i||(i=o*Number.MAX_VALUE),n||(n=o*Number.MAX_VALUE),i===n?0:i>n?o:-1*o}))},c=()=>{for(let e of t){if(e.end<n)continue;if(e.start>r)break;const t=e.sampleKey||e.sample;(!s.hasOwnProperty(t)||e.value.localeCompare(s[t])>0)&&(s[t]=e.value)}this.sampleKeys.sort((function(e,t){let i=s[e]||\"\",n=s[t]||\"\";return o*i.localeCompare(n)}))};\"mut\"===this.type?c():a(),this.trackView.repaintViews()}sortByAttribute(e,t){this.sampleKeys=this.browser.sampleInfo.getSortedSampleKeysByAttribute(this.sampleKeys,e,t),this.trackView.repaintViews()}clickedFeatures(e){const t=super.clickedFeatures(e),i=e.y;return t.filter((function(e){const t=e.pixelRect;return t&&i>=t.y&&i<=t.y+t.h}))}hoverText(e){const t=this.clickedFeatures(e);if(t&&t.length>0)return`${t[0].sample}: ${t[0].value}`}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){i.length>0&&(i.push(\"<hr/>\"),i.push(\"<hr/>\"));const t=e._f||e,n=\"function\"==typeof t.popupData?t.popupData(this.type,this.browser.genome.id):this.extractPopupData(t);Array.prototype.push.apply(i,n)}return i}contextMenuItemList(e){const t=e.genomicLocation,i=t=>{const i=e.viewport.cachedFeatures;this.sortByValue(t,i)},n=e.referenceFrame.toBP(2.5);return[\"DESC\",\"ASC\"].map((r=>{const s=\"DESC\"===r?\"descending\":\"ascending\";return{label:\"seg\"===this.type||\"shoebox\"===this.type?`Sort by value (${s})`:`Sort by type (${s})`,click:()=>{const s={option:\"VALUE\",direction:r,chr:e.referenceFrame.chr,start:Math.floor(t-n),end:Math.floor(t+n)};i(s),this.config.sort=s}}}))}get supportsWholeGenome(){return(!1===this.config.indexed||!this.config.indexURL)&&!1!==this.config.supportsWholeGenome}updateSampleKeys(e){if(this.explicitSamples)return;const t=new Set(this.sampleKeys);for(let i of e){const e=i.sampleKey||i.sample;t.has(e)||(this.sampleKeys.push(e),t.add(e))}}}const Of={low:.1,lowR:255,lowG:255,lowB:255,high:1.5,highR:255,highG:0,highB:0},Uf={low:-1.5,lowR:0,lowG:0,lowB:255,high:-.1,highR:255,highG:255,highB:255},qf={indel:\"rgb(0,200,0)\",\"targeted region\":\"rgb(236,155,43)\",truncating:\"rgb(\\t150,0,0)\",\"non-coding transcript\":\"rgb(0,0,150)\",synonymous:\"rgb(109,165,95)\",silent:\"rgb(109,135,80)\",missense_mutation:\"rgb(72,130,187)\",missense:\"rgb(72,130,187)\",\"splice site\":\"rgb(143,83,155)\",splice_region:\"rgb(143,83,155)\",nonsense:\"rgb(216, 57,81)\",nonsense_mutation:\"rgb(216, 57,81)\",frame_shift_del:\"rgb(226,135,65)\",frame_shift_ins:\"rgb(226,135,65)\",in_frame_del:\"rgb(247,235,94)\",in_frame_ins:\"rgb(247,235,94)\",\"*other*\":\"rgb(159,91,50)\"};class Qf{constructor(e){this.paired=!0,this.firstAlignment=e,this.chr=e.chr,this.readName=e.readName,e.start<e.mate.position?(this.start=e.start,this.scStart=e.scStart,this.connectingStart=e.start+e.lengthOnRef,this.connectingEnd=e.mate.position):(this.start=e.mate.position,this.scStart=this.start,this.connectingStart=e.mate.position,this.connectingEnd=e.start),this.end=Math.max(e.mate.position,e.start+e.lengthOnRef),this.lengthOnRef=this.end-this.start;let t=Math.max(this.end,e.scStart+e.scLengthOnRef);this.scLengthOnRef=t-this.scStart}setSecondAlignment(e){this.secondAlignment=e;const t=this.firstAlignment;e.start>t.start?this.connectingEnd=e.start:this.connectingStart=e.start+e.lengthOnRef,this.start=Math.min(t.start,e.start),this.end=Math.max(t.start+t.lengthOnRef,e.start+e.lengthOnRef),this.lengthOnRef=this.end-this.start,this.scStart=Math.min(t.scStart,e.scStart);const i=Math.max(t.scStart+t.scLengthOnRef,e.scStart+e.scLengthOnRef);this.scLengthOnRef=i-this.scStart}containsLocation(e,t){const i=t?this.scStart:this.start,n=t?this.scLengthOnRef:this.lengthOnRef;return e>=i&&e<=i+n}alignmentContaining(e,t){return this.firstAlignment.containsLocation(e,t)?this.firstAlignment:this.secondAlignment&&this.secondAlignment.containsLocation(e,t)?this.secondAlignment:void 0}popupData(e){let t=this.firstAlignment.popupData(e);return this.secondAlignment&&(t.push(\"-------------------------------\"),t=t.concat(this.secondAlignment.popupData(e))),t}isPaired(){return!0}isMateMapped(){return!0}isProperPair(){return this.firstAlignment.isProperPair()}get fragmentLength(){return Math.abs(this.firstAlignment.fragmentLength)}get firstOfPairStrand(){return this.firstAlignment.firstOfPairStrand}get pairOrientation(){return this.firstAlignment.pairOrientation}hasTag(e){return this.firstAlignment.hasTag(e)||this.secondAlignment&&this.secondAlignment.hasTag(e)}getGroupValue({option:e,tag:t}){switch(e){case\"strand\":return this.isNegativeStrand()?\"-\":\"+\";case\"FIRST_IN_PAIR_STRAND\":return this.isPaired()?this.isFirstOfPair()?this.isNegativeStrand()?\"-\":\"+\":this.isSecondOfPair()?this.isNegativeStrand()?\"+\":\"-\":void 0:void 0;case\"START\":return this.start;case\"INSERT_SIZE\":return this.fragmentLength;case\"MATE_CHR\":return this.mate?this.mate.chr:void 0;case\"MQ\":return this.mq;case\"ALIGNED_READ_LENGTH\":return this.lengthOnRef;case\"TAG\":return this.tags()[t];case\"PHASE\":return this.tags().HP;case\"READ_ORDER\":return this.isPaired()&&this.isFirstOfPair()?\"FIRST\":this.isPaired()&&this.isSecondOfPair()?\"SECOND\":\"\";default:return}}}class Vf{static instances=new Map;static getKey(e,t,i){const n=\"\"+e+t+i;return Vf.instances.has(n)||Vf.instances.set(n,new Vf(e,t,i)),Vf.instances.get(n)}constructor(e,t,i){this.base=e,this.strand=t,this.modification=i,this.canonicalBase=\"+\"===this.strand?this.base:oc(this.base)}getCanonicalBase(){}toString(){return\"\"+this.base+this.strand+this.modification}static compare(e,t){const i=e.modification,n=t.modification;return i===n?e.strand.charAt(0)-t.strand.charAt(0):jf.has(i)&jf.has(n)?jf.get(i)-jf.get(n):jf.has(i)?1:jf.has(n)?-1:i>n?1:-1}}const jf=new Map([\"NONE_C\",\"NONE_T\",\"NONE_G\",\"NONE_A\",\"m\",\"h\",\"f\",\"c\",\"C\",\"g\",\"e\",\"b\",\"T\",\"U\",\"a\",\"A\",\"o\",\"G\",\"n\",\"N\"].map(((e,t)=>[e,t])));class Wf{constructor(e,t,i,n){this.base=e,this.modification=i,this.strand=t,this.likelihoods=n,this.canonicalBase=\"+\"==this.strand?this.base:oc(this.base),this.key=Vf.getKey(e,t,i)}containsPosition(e){return this.likelihoods.has(e)}is5mC(){return this.modification.equals(\"m\")&&(\"C\"===this.base&&\"+\"===this.strand||\"G\"===this.base&&\"-\"===this.strand)}fullName(){return Gf.get(this.modification)||this.modification}}const Gf=new Map;Gf.set(\"m\",\"5mC\"),Gf.set(\"h\",\"5hmC\"),Gf.set(\"f\",\"5fC\"),Gf.set(\"c\",\"5caC\"),Gf.set(\"g\",\"5hmU\"),Gf.set(\"e\",\"5fU\"),Gf.set(\"b\",\"5caU\"),Gf.set(\"a\",\"6mA\"),Gf.set(\"o\",\"8xoG\"),Gf.set(\"n\",\"Xao\"),Gf.set(\"C\",\"Unknown C\"),Gf.set(\"T\",\"Unknown T\"),Gf.set(\"A\",\"Unknown A\"),Gf.set(\"G\",\"Unknown G\"),Gf.set(\"N\",\"Unknown\");const $f=new Map([[\"m\",\"5mC\"],[\"h\",\"5hmC\"],[\"f\",\"5fC\"],[\"c\",\"5caC\"],[\"g\",\"5hmU\"],[\"e\",\"5fU\"],[\"b\",\"5caU\"],[\"a\",\"6mA\"],[\"o\",\"8xoG\"],[\"n\",\"Xao\"],[\"C\",\"Unknown C\"],[\"T\",\"Unknown T\"],[\"A\",\"Unknown A\"],[\"G\",\"Unknown G\"],[\"N\",\"Unknown\"]]);function Kf(e){return $f.has(e)?$f.get(e):\"Uknown\"}function Yf(e){if(!e)return!1;const t=e.length;if(0==t)return!1;for(let i=0;i<t;i++){const t=e.charAt(i);if(t<\"0\"||t>\"9\")return!1}return!0}function Xf(e){return e<0?e+256:e}class Zf{allModifications=new Set;simplexModifications=new Set;maxLikelihoods=new Map;nomodLikelihoods=new Map;lastThreshold;incrementCounts(e){if(!e.blocks)return;const t=e.getBaseModificationSets();if(t)for(let i of e.blocks)if(\"S\"!==i.type)for(let e=0;e<i.len;e++){let n,r=e+i.seqOffset,s=0,o=-1,a=255;for(let e of t){const t=Vf.getKey(e.base,e.strand,e.modification);this.allModifications.add(t);const i=e.likelihoods;if(e.containsPosition(r)){const c=Xf(i.get(r));a-=c,c>o&&(s=e.canonicalBase,o=c,n=t)}}if(0!=s){const t=i.start+e,r=Vf.getKey(s,\"+\",\"NONE_\"+s);this.allModifications.add(r);const c=(e,t,i,n)=>{let r=n.get(i);r||(r=new Map,n.set(i,r));let s=r.get(e);s||(s=[],r.set(e,s)),s.push(t)};c(t,o,n,this.maxLikelihoods),a>o?c(t,a,r,this.nomodLikelihoods):c(t,o,n,this.nomodLikelihoods)}}}getCount(e,t,i,n){this.lastThreshold=i;const r=255*i,s=n?this.nomodLikelihoods.get(t):this.maxLikelihoods.get(t);if(!s)return 0;const o=s.get(e);if(o){let e=0;for(let t of o){Xf(t)>=r&&e++}return e}return 0}getLikelihoodSum(e,t,i,n){this.lastThreshold=i;const r=255*i,s=(n?this.nomodLikelihoods.get(t):this.maxLikelihoods.get(t)).get(e);if(s){let e=0;for(let t of s){const i=Xf(t);i>=r&&(e+=i)}return e}return 0}popupData(e,t){const i=[];i.push(\"<b>Modifications with likelihood > \"+100*this.lastThreshold+\"%</b>\");for(let n of this.maxLikelihoods.keys()){if(this.maxLikelihoods.get(n).has(e)){let r=\"basemod2\"===t;const s=this.getCount(e,n,this.lastThreshold,r);if(s>0){const t=this.getLikelihoodSum(e,n,this.lastThreshold,r)/s*.3921568,o=Kf(n.modification);i.push(o+\" (\"+n.base+n.strand+\"): \"+s+\"  @ average likelihood \"+Math.round(t)+\"%\")}}}return i}computeSimplex(){const e=new Set(Array.from(this.allModifications).filter((e=>\"-\"===e.strand)).map((e=>e.modification)));for(let t of this.allModifications)\"+\"!==t.strand||e.has(t.modification)||(this.simplexModifications.add(t.modification),this.simplexModifications.add(\"NONE_\"+t.getCanonicalBase()))}}class Jf{constructor(){this.alignments=[],this.score=void 0}findAlignment(e,t=!1){const i=(e,i)=>i>=e.start&&i<e.start+(t?e.fragmentLength:e.lengthOnRef);let n;for(let r=0;r<this.alignments.length;r++){const s=this.alignments[r];if(e>=s.start&&e<s.start+(t?s.fragmentLength:s.lengthOnRef)){s.paired?s.firstAlignment&&i(s.firstAlignment,e)?n=s.firstAlignment:s.secondAlignment&&i(s.secondAlignment,e)&&(n=s.secondAlignment):n=s;break}}return n}getSortValue({position:e,option:t,tag:i,sortAsPairs:n},r){t||(t=\"BASE\");const s=this.findAlignment(e,n);if(void 0===s)return Number.MAX_VALUE;switch(t){case\"NUCLEOTIDE\":case\"BASE\":return function(e,t,i){let n;const r=Math.floor(i)-t.start;r<t.sequence.length&&(n=t.sequence.charAt(r));if(!n)return 0;const s=e.readBaseAt(i),o=e.readBaseQualityAt(i),a=t.coverageMap,c=Math.floor(i-a.bpStart),l=a.coverage[c];let h=0;if(e.insertions)for(let t of e.insertions)t.start===i&&(h=-l.ins);if(s)if(n=n.toUpperCase(),\"N\"===s&&0===h)h=2;else if(n!==s&&\"=\"!==s||0!==h){if(\"X\"===s||n!==s){h-=l[\"pos\"+s]+l[\"neg\"+s]+o/1e3}}else h=4-o/1e3;else{const e=l.del;e>0?h-=e:0===h&&(h=1)}return h}(s,r,e);case\"strand\":return s.strand?1:-1;case\"START\":return s.start;case\"TAG\":return s.tags()[i];case\"READ_NAME\":return s.readName;case\"INSERT_SIZE\":return-Math.abs(s.fragmentLength);case\"GAP_SIZE\":return-s.gapSizeAt(e);case\"MATE_CHR\":return s.mate?s.mate.chr:Number.MAX_VALUE;case\"MQ\":return void 0===s.mq?Number.MAX_VALUE:-s.mq;case\"ALIGNED_READ_LENGTH\":return-s.lengthOnRef;default:return Number.MAX_VALUE}}}var ep={fr:{F1R2:\"LR\",F2R1:\"LR\",F1F2:\"LL\",F2F1:\"LL\",R1R2:\"RR\",R2R1:\"RR\",R1F2:\"RL\",R2F1:\"RL\"},rf:{R1F2:\"LR\",R2F1:\"LR\",R1R2:\"LL\",R2R1:\"LL\",F1F2:\"RR\",F2F1:\"RR\",F1R2:\"RL\",F2R1:\"RL\"},ff:{F2F1:\"LR\",R1R2:\"LR\",F2R1:\"LL\",R1F2:\"LL\",R2F1:\"RR\",F1R2:\"RR\",R2R1:\"RL\",F1F2:\"RL\"}};class tp{#A=[];baseModificationKeys=new Set;constructor(e,t,i,{samplingWindowSize:n,samplingDepth:r,alleleFreqThreshold:s,colorBy:o}){this.alleleFreqThreshold=void 0===s?.2:s,this.samplingWindowSize=n||100,this.samplingDepth=r||1e3,this.chr=e,this.start=Math.floor(t),this.end=Math.ceil(i),this.length=i-t,this.coverageMap=new np(e,t,i,this.alleleFreqThreshold),this.downsampledIntervals=[],o&&o.startsWith(\"basemod\")&&(this.baseModCounts=new Zf),this.alignments=[],this.pairsCache=new Map,this.downsampledReads=new Set,this.currentBucket=new ip(this.start,this.start+this.samplingWindowSize,this),this.hasPairs=!1}pack({viewAsPairs:e,showSoftClips:t,expectedPairOrientation:i,groupBy:n,displayMode:r}){let s=this.allAlignments();s=e?function(e){const t=new Map,i=e.map((e=>{if(ap(e)){let i=t.get(e.readName);return i?(i.setSecondAlignment(e),t.delete(e.readName),i):(i=new Qf(e),t.set(e.readName,i),i)}return e}));return i}(s):function(e){return e.flatMap((e=>e instanceof Qf?[e.firstAlignment,e.secondAlignment].filter(Boolean):[e]))}(s),this.packAlignmentRows(s,t,i,n,r),this.alignments&&delete this.alignments}packAlignmentRows(e,t,i,n,r){this.#A=[];const s=(e,i)=>{e.sort((function(e,i){return t?e.scStart-i.scStart:e.start-i.start}));const n=new op(i);let r,s=0,o=0;const a=new Set,c=()=>{r=new Jf,n.push(r),s=0,o=0,a.clear()};for(c();e.length>0;)if(o>=0&&o<e.length){const i=e[o];a.add(i),r.alignments.push(i),s=t?i.scStart+i.scLengthOnRef+2:i.start+i.lengthOnRef+2,o=cp(e,(e=>(t?e.scStart:e.start)>s),o)}else e=e.filter((e=>!a.has(e))),c();return n},o=(e,t)=>{e.sort((function(e,t){return e.start-t.start}));const i=new op(t),{start:n,end:r}=this.viewport.genomicRange();for(let t of e)if(t.end<n||t.start>r)this.#A.push(t);else{const e=new Jf;e.alignments.push(t),i.push(e)}return i};if(!e||0===e.length)return new Map;{const t=new Map;if(n)for(let r of e){const e=lp(r,n,i)||\"\";t.has(e)||t.set(e,[]),t.get(e).push(r)}else t.set(\"\",e);const a=new Map,c=Array.from(t.keys()).sort(function(e,t){switch(e){case\"pairOrientation\":return function(e){const t=[\"LL\",\"RR\",\"RL\",\"LR\",\"\"];return(e,i)=>t.indexOf(e)-t.indexOf(i)}();case\"strand\":case\"firstOfPairStrand\":return up;default:return e&&e.startsWith(\"base:\")?dp:fp}}(n));for(let e of c){const i=t.get(e),n=\"FULL\"===r?o(i,e):s(i,e);a.set(e,n)}this.packedGroups=a}}push(e){this.hasPairs=this.hasPairs||e.isPaired(),this.coverageMap.incCounts(e);const t=e.getBaseModificationSets();if(t)for(let e of t)this.baseModificationKeys.add(e.key);this.baseModCounts&&this.baseModCounts.incrementCounts(e),this.downsampledReads.has(e.readName)?this.currentBucket.downsampledCount++:(e.start>=this.currentBucket.end&&(this.finishBucket(),this.currentBucket=new ip(e.start,e.start+this.samplingWindowSize,this)),this.currentBucket.addAlignment(e))}finish(){void 0!==this.currentBucket&&this.finishBucket(),this.hasAlignments=this.alignments.length>0,this.alignments.sort((function(e,t){return e.start-t.start})),this.baseModCounts&&this.baseModCounts.computeSimplex(),delete this.currentBucket,delete this.pairsCache,delete this.downsampledReads}contains(e,t,i){return this.chr===e&&this.start<=t&&this.end>=i}hasDownsampledIntervals(){return this.downsampledIntervals&&this.downsampledIntervals.length>0}finishBucket(){this.alignments=this.alignments.concat(this.currentBucket.alignments),this.currentBucket.downsampledCount>0&&this.downsampledIntervals.push(new sp(this.currentBucket.start,this.currentBucket.end,this.currentBucket.downsampledCount))}allAlignments(){if(this.alignments)return this.alignments;if(this.packedGroups){const e=Array.from(this.packedGroups.values()).flatMap((e=>e.rows.flatMap((e=>e.alignments))));if(this.#A&&this.#A.length>0)for(let t of this.#A)e.push(t);return e}return[]}getMax(e,t){return this.coverageMap.getMax(e,t)}sortRows(e){if(this.packedGroups)for(let t of this.packedGroups.values())t.sortRows(e,this)}}class ip{constructor(e,t,{samplingDepth:i,downsampledReads:n,pairsCache:r}){this.start=e,this.end=t,this.alignments=[],this.downsampledCount=0,this.samplingDepth=i,this.downsampledReads=n,this.pairsCache=r,this.hasPairs=!1}addAlignment(e){this.hasPairs=this.hasPairs||e.isPaired();const t=this.hasPairs?Math.ceil(this.samplingDepth/2):this.samplingDepth;if(ap(e)){const t=this.pairsCache.get(e.readName);if(t)return t.setSecondAlignment(e),void this.pairsCache.delete(e.readName)}if(this.alignments.length<t)if(ap(e)){const t=new Qf(e);this.pairsCache.set(e.readName,t),this.alignments.push(t)}else this.alignments.push(e);else{const i=Math.floor(Math.random()*(t+this.downsampledCount-1));if(i<t){const t=this.alignments[i];if(this.pairsCache.has(t.readName)&&this.pairsCache.delete(t.readName),ap(e)){const t=new Qf(e);this.pairsCache.set(e.readName,t),this.alignments[i]=t}else this.alignments[i]=e;this.downsampledReads.add(t.readName)}else this.downsampledReads.add(e.readName);this.downsampledCount++}}}class np{constructor(e,t,i,n){this.chr=e,this.bpStart=t,this.length=i-t,this.coverage=new Array(this.length),this.maximum=0,this.threshold=n,this.qualityWeight=!0}getMax(e,t){let i=0;const n=this.coverage.length;for(let r=0;r<n;r++){const n=this.bpStart+r;if(n>t)break;const s=this.coverage[r];n>=e&&s&&(i=Math.max(i,s.total))}return i}incCounts(e){var t=this;if(void 0===e.blocks?i(e):e.blocks.forEach((function(e){i(e)})),e.gaps)for(let i of e.gaps)if(\"D\"===i.type){const e=i.start-t.bpStart;for(let n=e;n<e+i.len;n++)n<0||(this.coverage[n]||(this.coverage[n]=new rp(t.threshold)),this.coverage[n].del++)}if(e.insertions)for(let i of e.insertions){const e=i.start-this.bpStart;e<0||(this.coverage[e]||(this.coverage[e]=new rp(t.threshold)),this.coverage[e].ins++)}function i(i){if(\"S\"===i.type)return;const n=e.seq,r=e.qual,s=i.seqOffset;for(let o=i.start-t.bpStart,a=0;a<i.len;o++,a++){t.coverage[o]||(t.coverage[o]=new rp(t.threshold));const i=null==n?\"N\":n.charAt(s+a),c=e.strand?\"pos\"+i:\"neg\"+i,l=r&&s+a<r.length?r[s+a]:30;t.coverage[o][c]+=1,t.coverage[o][\"qual\"+i]+=l,t.coverage[o].total+=1,t.coverage[o].qual+=l,t.maximum=Math.max(t.coverage[o].total,t.maximum)}}}getPosCount(e,t){const i=e-this.bpStart;if(i<0||i>=this.coverage.length)return 0;const n=this.coverage[i];switch(t){case\"A\":case\"a\":return n.posA;case\"C\":case\"c\":return n.posC;case\"T\":case\"t\":return n.posT;case\"G\":case\"g\":return n.posG;case\"N\":case\"n\":return n.posN;default:return 0}}getNegCount(e,t){const i=e-this.bpStart;if(i<0||i>=this.coverage.length)return 0;const n=this.coverage[i];switch(t){case\"A\":case\"a\":return n.negA;case\"C\":case\"c\":return n.negC;case\"T\":case\"t\":return n.negT;case\"G\":case\"g\":return n.negG;case\"N\":case\"n\":return n.negN;default:return 0}}getCount(e,t){return this.getPosCount(e,t)+this.getNegCount(e,t)}getTotalCount(e){const t=e-this.bpStart;return t>=0&&t<this.coverage.length?this.coverage[t].total:0}}class rp{constructor(e){this.qualityWeight=!0,this.posA=0,this.negA=0,this.posT=0,this.negT=0,this.posC=0,this.negC=0,this.posG=0,this.negG=0,this.posN=0,this.negN=0,this.pos=0,this.neg=0,this.qualA=0,this.qualT=0,this.qualC=0,this.qualG=0,this.qualN=0,this.qual=0,this.total=0,this.del=0,this.ins=0,this.threshold=e}hoverText(){const e=this.posA+this.posT+this.posC+this.posG+this.posN,t=this.negA+this.negT+this.negC+this.negG+this.negN;return`${this.total} (${e}+, ${t}-)`}isMismatch(e){const t=this.threshold*(this.qualityWeight&&this.qual?this.qual:this.total);let i=0;for(let t of[\"A\",\"T\",\"C\",\"G\"])t!==e&&(i+=this.qualityWeight&&this.qual?this[\"qual\"+t]:this[\"pos\"+t]+this[\"neg\"+t]);return i>=t}}class sp{constructor(e,t,i){this.start=e,this.end=t,this.counts=i}popupData(e){return[{name:\"start\",value:Math.floor(this.start+1)},{name:\"end\",value:this.end},{name:\"# downsampled:\",value:this.counts}]}}class op{pixelTop=0;pixelBottom=0;rows=[];constructor(e){this.name=this.name}push(e){this.rows.push(e)}get length(){return this.rows.length}sortRows(e,t){const i=[],n=[];for(let t of this.rows){void 0!==t.findAlignment(e.position,e.sortAsPairs)?i.push(t):n.push(t)}i.sort(((i,n)=>{const r=e.direction,s=i.getSortValue(e,t),o=n.getSortValue(e,t);if(void 0===o&&void 0!==o)return 1;if(void 0!==s&&void 0===o)return-1;const a=s>o?1:s<o?-1:0;return!0===r?a:-a}));for(let e of n)i.push(e);this.rows=i}}function ap(e){return e.isPaired()&&e.mate&&e.isMateMapped()&&e.chr===e.mate.chr&&(e.isFirstOfPair()||e.isSecondOfPair())&&!(e.isSecondary()||e.isSupplementary())}function cp(e,t,i){let n=i-1,r=e.length;for(;1+n<r;){const i=n+(r-n>>1);t(e[i])?r=i:n=i}return r}function lp(e,t,i){let n,r,s;if(t.startsWith(\"tag:\"))n=t.substring(4),t=\"tag\";else if(t.startsWith(\"base:\")){const e=t.split(\":\");3===e.length&&(t=\"base\",r=e[1],s=Number.parseInt(e[2].replaceAll(\",\",\"\"))-1)}switch(t){case\"strand\":return e.strand?\"+\":\"-\";case\"firstOfPairStrand\":const t=e.firstOfPairStrand;return void 0===t?\"\":t?\"+\":\"-\";case\"mateChr\":return e.mate&&e.isMateMapped()?e.mate.chr:\"\";case\"pairOrientation\":return ep[i][e.pairOrientation]||\"\";case\"chimeric\":return e.tags().SA?\"chimeric\":\"\";case\"supplementary\":return e.isSupplementary?\"supplementary\":\"\";case\"readOrder\":return e.isPaired()&&e.isFirstOfPair()?\"first\":e.isPaired()&&e.isSecondOfPair()?\"second\":\"\";case\"phase\":return e.tags().HP||\"\";case\"tag\":return e.tags()[n]||\"\";case\"base\":if(e.chr===r&&e.start<=s&&e.end>s){const t=e.readBaseAt(s);return t||\"GAP\"}return\"\";default:return}}const hp=new Map([[\"A\",1],[\"T\",2],[\"C\",3],[\"G\",4],[\"N\",5],[\"GAP\",5],[\"\",7]]);function dp(e,t){return hp.has(e)&&hp.has(t)?hp.get(e)-hp.get(t):e.localeCompare(t,void 0,{sensitivity:\"base\"})}function up(e,t){return e===t?0:e&&t?-e.localeCompare(t):e?1:-1}function fp(e,t){if(e||t){if(e){if(t){if(e===t)return 0;if(Va(e)&&(Va(t),1))return Number.parseFloat(e)-Number.parseFloat(t);{let i=e.toString(),n=t.toString();return i.localeCompare(n,void 0,{sensitivity:\"base\"})}}return-1}return 1}return 0}class pp{constructor(e){const t=e.split(\",\");this.chr=t[0],this.start=parseInt(t[1]),this.strand=t[2].charAt(0),this.mapQ=parseInt(t[4]),this.numMismatches=parseInt(t[5]),this.lenOnRef=function(e){let t=0,i=\"\";for(let n=0;n<e.length;n++){const r=e.charCodeAt(n);if(r>47&&r<58)i+=e.charAt(n);else{switch(r){case 78:case 68:case 77:case 61:case 88:t+=parseInt(i.toString())}i=\"\"}}return t}(t[3])}printString(){return this.chr+\":\"+Rt(this.start)+\"-\"+Rt(this.start+this.lenOnRef)+\" (\"+this.strand+\") = \"+Rt(this.lenOnRef)+\"bp @MAPQ: \"+this.mapQ+\" NM: \"+this.numMismatches}}function gp(e){return e.split(\";\").filter((e=>e.length>0)).map((e=>new pp(e)))}const mp={c:1,C:1,s:2,S:2,i:4,I:4,f:4};class wp{constructor(){this.hidden=!1}isMapped(){return!(4&this.flags)}isPaired(){return!!(1&this.flags)}isProperPair(){return!!(2&this.flags)}isFirstOfPair(){return!!(64&this.flags)}isSecondOfPair(){return!!(128&this.flags)}isSecondary(){return!!(256&this.flags)}isSupplementary(){return!!(2048&this.flags)}isFailsVendorQualityCheck(){return!!(512&this.flags)}isDuplicate(){return!!(1024&this.flags)}isMateMapped(){return!(8&this.flags)}isNegativeStrand(){return!!(16&this.flags)}isMateNegativeStrand(){return!!(32&this.flags)}hasTag(e){const t=this.tagDict||function(e){let t=0;const i=e.length,n={};for(;t<i;){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const s=String.fromCharCode(e[t++]);let o;if(\"A\"===s)o=String.fromCharCode(e[t]),t++;else if(\"i\"===s||\"I\"===s)o=vp(e,t),t+=4;else if(\"c\"===s)o=Cp(e,t),t++;else if(\"C\"===s)o=_p(e,t),t++;else if(\"s\"===s||\"S\"===s)o=yp(e,t),t+=2;else if(\"f\"===s)o=Ap(e,t),t+=4;else if(\"Z\"===s)for(o=\"\";;){var r=e[t++];if(0===r)break;o+=String.fromCharCode(r)}else{if(\"B\"!==s){o=\"Error unknown type: \"+s,n[i]=o;break}{const r=String.fromCharCode(e[t++]);let s=mp[r];if(void 0===s){n[i]=`Error: unknown element type '${r}'`;break}const a=vp(e,t);t+=4;const c=t+a*s;o=[];const l=new DataView(e.buffer);for(;t<c;){switch(r){case\"c\":o.push(l.getInt8(t));break;case\"C\":o.push(l.getUint8(t));break;case\"s\":o.push(l.getInt16(t));break;case\"S\":o.push(l.getUint16(t));break;case\"i\":o.push(l.getInt32(t));break;case\"I\":o.push(l.getUint32(t));break;case\"f\":o.push(l.getFloat32(t))}t+=s}}}n[i]=o}return n}(this.tagBA);return t.hasOwnProperty(e)}tags(){return this.tagDict}getTag(e){return this.tags()[e]}get firstOfPairStrand(){if(this.isPaired()){if(this.isFirstOfPair())return this.strand;if(this.isMateMapped())return this.mate.strand}}containsLocation(e,t){const i=t?this.scStart:this.start,n=t?this.scLengthOnRef:this.lengthOnRef;return e>=i&&e<=i+n}popupData(e){const t=[];if(e=Math.floor(e),this.insertions){const n=this.seq;for(let r of this.insertions){var i=r.start;if(e===i||e===i-1)return t.push({name:\"Insertion\",value:n.substr(r.seqOffset,r.len)}),t.push({name:\"Location\",value:i}),t}}t.push({name:\"Read Name\",value:this.readName}),t.push(\"<hr/>\"),t.push({name:\"Alignment Start\",value:Rt(1+this.start),borderTop:!0}),t.push({name:\"Read Strand\",value:!0===this.strand?\"(+)\":\"(-)\",borderTop:!0});let n=this.cigar;if(n&&n.length>50){const e=25;n=`${n.substring(0,e-2)} ... ${n.substring(n.length-e+2)}`}t.push({name:\"Cigar\",value:n}),t.push({name:\"Mapping Quality\",value:this.mq}),t.push({name:\"Secondary\",value:a(this.isSecondary())}),t.push({name:\"Supplementary\",value:a(this.isSupplementary())}),t.push({name:\"Duplicate\",value:a(this.isDuplicate())}),t.push({name:\"Failed QC\",value:a(this.isFailsVendorQualityCheck())}),this.isPaired()&&(t.push(\"<hr/>\"),t.push({name:\"First in Pair\",value:!this.isSecondOfPair(),borderTop:!0}),t.push({name:\"Mate is Mapped\",value:a(this.isMateMapped())}),this.pairOrientation&&t.push({name:\"Pair Orientation\",value:this.pairOrientation}),this.isMateMapped()&&(t.push({name:\"Mate Chromosome\",value:this.mate.chr}),t.push({name:\"Mate Start\",value:this.mate.position+1}),t.push({name:\"Mate Strand\",value:!0===this.mate.strand?\"(+)\":\"(-)\"}),t.push({name:\"Insert Size\",value:this.fragmentLength})));const r=this.tags();if(r.hasOwnProperty(\"SA\")){t.push(\"<hr/>\"),t.push({name:\"Supplementary Alignments\",value:\"\"});const e=gp(r.SA);if(e){t.push(\"<ul>\");for(let i of e)t.push(`<li>${i.printString()}</li>`);t.push(\"</ul>\")}}const s=new Set([\"SA\",\"MD\"]);t.push(\"<hr/>\");for(let e in r)s.has(e)||t.push({name:e,value:r[e]});t.push({name:\"Hidden Tags\",value:\"SA, MD\"}),t.push(\"<hr/>\"),t.push({name:\"Genomic Location: \",value:Rt(1+e)}),t.push({name:\"Read Base:\",value:this.readBaseAt(e)}),t.push({name:\"Base Quality:\",value:this.readBaseQualityAt(e)});const o=this.getBaseModificationSets();if(o){const i=this.positionToReadIndex(e);if(void 0!==i){let e=!1;for(let n of o)if(n.containsPosition(i)){e||(t.push(\"<hr/>\"),t.push(\"<b>Base modifications:</b>\"),e=!0);const r=Math.round(100/255*Xf(n.likelihoods.get(i)));t.push(`${n.fullName()} @ likelihood =  ${r}%`)}}}return t;function a(e){return e?\"Yes\":\"No\"}}readBaseAt(e){const t=Fp(this.blocks,e);if(t){if(\"*\"===this.seq)return\"*\";{const i=t.seqIndexAt(e);return this.seq[i]}}}readBaseQualityAt(e){const t=Fp(this.blocks,e);if(t){if(\"*\"===this.qual)return 30;{const i=t.seqIndexAt(e);return i>=0&&this.qual&&i<this.qual.length?this.qual[i]:30}}}gapSizeAt(e){if(this.gaps)for(let t of this.gaps)if(e>=t.start&&e<t.start+t.len)return t.len;return 0}softClippedBlocks(){let e,t,i;for(let n of this.blocks)\"S\"===n.type?i?t=n:e=n:\"H\"!==n.type&&(i=!0);return{left:e,right:t}}getBaseModificationSets(){if(!this.baseModificationSets&&(this.tagDict.MM||this.tagDict.Mm)){const e=this.tagDict.MM||this.tagDict.Mm,t=this.tagDict.ML||this.tagDict.Ml;!Mt(e)||t&&!Array.isArray(t)||(0===e.length?this.baseModificationSets=bp:this.baseModificationSets=function(e,t,i,n){n&&(i=cc(i));const r=[],s=e.split(\";\");let o=0;for(let e of s){const s=e.split(\",\"),a=s[0].charAt(0),c=s[0].charAt(1),l=s[0].endsWith(\".\");if(1==s.length);else{const e=s[0].endsWith(\".\")||s[0].endsWith(\"?\")?s[0].substring(2,s[0].length-1):s[0].substring(2);let h=[];if(e.length>1)if(Yf(e))h.push(e);else for(let t=0;t<e.length;t++)h.push(e.substring(t,t+1));else h.push(e);const d=new Map;for(let e of h)d.set(e,new Map);let u=1,f=Number.parseInt(s[u++]),p=0,g=0;for(;p<i.length;){if(\"N\"===a||i[p]===a){const e=n?i.length-1-p:p;if(g===f){for(let i of h){const n=t?t[o++]:255;d.get(i).set(e,n)}if(u<s.length)f=Number.parseInt(s[u++]),g=0;else{if(!l)break;f=-1}}else{if(l)for(let t of h)d.get(t).set(e,0);g++}}p++}for(let e of h)r.push(new Wf(a,c,e,d.get(e)))}}return r}(e,t,this.seq,this.isNegativeStrand()))}return this.baseModificationSets}getGroupValue(e,t,i){const n=this;switch(e){case\"strand\":return n.strand?\"+\":\"-\";case\"firstOfPairStrand\":const e=n.firstOfPairStrand;return void 0===e?\"\":e?\"+\":\"-\";case\"mateChr\":return n.mate&&n.isMateMapped()?n.mate.chr:\"\";case\"pairOrientation\":return ep[i][n.pairOrientation]||\"\";case\"chimeric\":return n.tags().SA?\"chimeric\":\"\";case\"supplementary\":return n.isSupplementary?\"supplementary\":\"\";case\"readOrder\":return n.isPaired()&&n.isFirstOfPair()?\"first\":n.isPaired()&&n.isSecondOfPair()?\"second\":\"\";case\"phase\":return n.tags().HP||\"\";case\"tag\":return n.tags()[t]||\"\";default:return}}positionToReadIndex(e){const t=Fp(this.blocks,e);return t?e-t.start+t.seqOffset:void 0}}const bp=new Set;function Fp(e,t){for(let i=0;i<e.length;i++){const n=e[i];if(t>=n.start&&t<n.start+n.len)return n}}function vp(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function yp(e,t){return e[t+1]<<8|e[t]}function Ap(e,t){return new DataView(e.buffer).getFloat32(t)}function Cp(e,t){return new DataView(e.buffer).getInt8(t)}function _p(e,t){return new DataView(e.buffer).getUint8(t)}class xp{constructor(e){e&&Object.assign(this,e)}seqIndexAt(e){return Math.floor(e)-this.start+this.seqOffset}}class kp{constructor(e){e||(e={}),this.vendorFailed=e.vendorFailed=!1!==e.vendorFailed,this.duplicate=e.duplicate=!1!==e.duplicate,this.secondary=e.secondary||!1,this.supplementary=e.supplementary||!1,this.mq=e.mq||0,e.readgroups&&(this.readgroups=new Set(e.readgroups))}pass(e){if(!e.isMapped())return!1;if(this.vendorFailed&&e.isFailsVendorQualityCheck())return!1;if(this.duplicate&&e.isDuplicate())return!1;if(this.secondary&&e.isSecondary())return!1;if(this.supplementary&&e.isSupplementary())return!1;if(e.mq<this.mq)return!1;if(this.readgroups){const t=e.tags().RG;return this.readgroups.has(t)}return!0}}const Ip=Dp(new Uint8Array([66,65,77,1]),0),Sp=[\"=\",\"A\",\"C\",\"M\",\"G\",\"R\",\"S\",\"V\",\"T\",\"W\",\"Y\",\"H\",\"K\",\"D\",\"B\",\"N\"],Ep=[\"M\",\"I\",\"D\",\"N\",\"S\",\"H\",\"P\",\"=\",\"X\",\"?\",\"?\",\"?\",\"?\",\"?\",\"?\",\"?\"],Np={c:1,C:1,s:2,S:2,i:4,I:4,f:4},Bp=1e4,Mp={readHeader:async function(e,t,i){const n=gs(await Qs.loadArrayBuffer(e,t));return Mp.decodeBamHeader(n,i)},decodeBamHeader:function(e){const t=Dp(e,0);if(t!==Ip)throw new Error(\"BAM header errror: bad magic number.  This could be caused by either a corrupt or missing file.\");const i=Dp(e,4);let n=\"\";for(var r=0;r<i;++r)n+=String.fromCharCode(e[r+8]);const s=Dp(e,i+8);let o=i+12;const a={},c=[];for(r=0;r<s;++r){const t=Dp(e,o);let i=\"\";for(var l=0;l<t-1;++l)i+=String.fromCharCode(e[o+4+l]);a[i]=r,c[r]=i,o=o+8+t}return{magicNumber:t,size:o,chrNames:c,chrToIndex:a}},bam_tag2cigar:function(e,t,i,n,r,s){function o(e){return\"C\"===e||\"c\"===e||\"A\"===e?1:\"S\"===e||\"s\"===e?2:\"I\"===e||\"i\"===e||\"f\"===e?4:0}if(1!==s.length||r.start<0)return!1;for(var a=i+(n+1>>1)+n;a+4<t;){if(\"CG\"===String.fromCharCode(e[a])+String.fromCharCode(e[a+1]))break;var c=String.fromCharCode(e[a+2]);if(\"B\"===c)a+=8+o(c=String.fromCharCode(e[a+3]))*Dp(e,a+4);else if(\"Z\"===c||\"H\"===c)for(a+=3;0!==e[a++];);else a+=3+o(c)}if(a>=t)return!1;if(\"B\"!==String.fromCharCode(e[a+2])||\"I\"!==String.fromCharCode(e[a+3]))return!1;var l=Dp(e,a+4),h=a+8;if(h+4*l>t)return!1;var d=\"\",u=0;s.length=0,a=h;for(var f=0;f<l;++f,a+=4){var p=Dp(e,a),g=p>>4,m=Ep[15&p];\"M\"!==m&&\"EQ\"!==m&&\"X\"!==m&&\"D\"!==m&&\"N\"!==m&&\"=\"!==m||(u+=g),d=d+g+m,s.push({len:g,ltr:m})}return r.cigar=d,r.lengthOnRef=u,!0},decodeBamRecords:function(e,t,i,n,r,s,o,a){for(;t<e.length;){const u=t+Dp(e,t)+4,f=new wp,p=Dp(e,t+4),g=Dp(e,t+8);if(u>e.length)return;if(p<0){t=u;continue}if(void 0!==r&&(p>r||g>o))return!0;if(void 0!==r&&p<r){t=u;continue}const m=Dp(e,t+12),w=(65280&m)>>8,b=255&m,F=Dp(e,t+16),v=(4294901760&F)>>16,y=65535&F,A=Dp(e,t+20),C=Dp(e,t+24),_=Dp(e,t+28),x=Dp(e,t+32);let k=[];for(let i=0;i<b-1;++i)k.push(String.fromCharCode(e[t+36+i]));k=k.join(\"\");let I=0,S=\"\",E=t+36+b;const N=[];let B;for(let t=0;t<y;++t){var c=Dp(e,E),l=c>>4,h=Ep[15&c];\"M\"!==h&&\"EQ\"!==h&&\"X\"!==h&&\"D\"!==h&&\"N\"!==h&&\"=\"!==h||(I+=l),S=S+l+h,E+=4,B={len:l,ltr:h},N.push(B)}if(f.chr=n[p],f.start=g,f.flags=v,f.strand=!(16&v),f.readName=k,f.cigar=S,f.lengthOnRef=I,f.fragmentLength=x,f.mq=w,Mp.bam_tag2cigar(e,u,E,A,f,N),f.end=f.start+f.lengthOnRef,f.end<s){t=u;continue}let M=[];const R=A+1>>1;for(let t=0;t<R;++t){var d=e[E+t];M.push(Sp[(240&d)>>4]),M.push(Sp[15&d])}M=M.slice(0,A).join(\"\"),E+=R;const D=[];for(let t=0;t<A;++t)D.push(e[E+t]);E+=A,C>=0&&(f.mate={chr:n[C],position:_,strand:!(32&v)}),f.seq=M,f.qual=D;const T=new Uint8Array(e.buffer.slice(E,u));f.tagDict=zp(T),this.setPairOrientation(f),(void 0===a||a.pass(f))&&(Rp(f,N),i.push(f)),t=u}},decodeSamRecords:function(e,t,i,n,r,s){var o,a,c,l,h,d,u,f,p,g;for(l=(o=Dt(e)).length,!1,a=0;a<l;a++)if(h=o[a].split(\"\\t\"),(p=new wp).chr=h[2],p.start=Number.parseInt(h[3])-1,p.flags=Number.parseInt(h[1]),p.readName=h[0],p.strand=!(16&p.flags),p.mq=Number.parseInt(h[4]),p.cigar=h[5],p.fragmentLength=Number.parseInt(h[8]),p.seq=h[9],\"*\"!==p.chr&&p.isMapped()&&p.chr===i){if(p.start>r)break;if(f=0,(g=Tp(p.cigar)).forEach((function(e){var t=e.len,i=e.ltr;\"M\"!==i&&\"EQ\"!==i&&\"X\"!==i&&\"D\"!==i&&\"N\"!==i&&\"=\"!==i||(f+=t)})),p.lengthOnRef=f,!(p.start+f<n)){for(d=h[10],p.qual=[],c=0;c<d.length;c++)p.qual[c]=d.charCodeAt(c)-33;p.tagDict=h.length<11?{}:Lp(h.slice(11)),p.isMateMapped()&&(u=h[6],p.mate={chr:\"=\"===u?p.chr:u,position:Number.parseInt(h[7]),strand:!(32&p.flags)}),this.setPairOrientation(p),(void 0===s||s.pass(p))&&(Rp(p,g),t.push(p))}}},setReaderDefaults:function(e,t){e.filter=\"function\"==typeof t.filter?{pass:t.filter}:new kp(t.filter),t.readgroup&&(e.filter.readgroups=new Set([t.readgroup])),e.alleleFreqThreshold=void 0===t.alleleFreqThreshold?.2:t.alleleFreqThreshold,e.samplingWindowSize=void 0===t.samplingWindowSize?100:t.samplingWindowSize,e.samplingDepth=void 0===t.samplingDepth?500:t.samplingDepth,e.samplingDepth>Bp&&(console.log(\"Warning: attempt to set sampling depth > maximum value of \"+Bp),e.samplingDepth=Bp)},setPairOrientation:function(e){if(e.isMapped()&&e.mate&&e.isMateMapped()&&e.mate.chr===e.chr){var t=e.strand?\"F\":\"R\",i=e.mate,n=i.strand?\"F\":\"R\",r=\" \",s=\" \";e.isFirstOfPair()?(r=\"1\",s=\"2\"):e.isSecondOfPair()&&(r=\"2\",s=\"1\");var o=[],a=e.fragmentLength,c=e.end-e.start;if(0===a)a=(e.start<i.position?i.position+c:i.position-c)-e.start;a>0?(o[0]=t,o[1]=r,o[2]=n,o[3]=s):(o[2]=t,o[3]=r,o[0]=n,o[1]=s),e.pairOrientation=o.join(\"\")}}};function Rp(e,t){const i=[];let n,r,s=0,o=e.start;e.scStart=e.start,e.scLengthOnRef=e.lengthOnRef;for(let a of t){let t;switch(a.ltr){case\"H\":case\"P\":break;case\"S\":t=o,e.scLengthOnRef+=a.len,0===i.length&&(e.scStart-=a.len,t-=a.len),i.push(new xp({start:t,seqOffset:s,len:a.len,type:\"S\"})),s+=a.len;break;case\"N\":case\"D\":void 0===r&&(r=[]),r.push({start:o,len:a.len,type:a.ltr}),o+=a.len;break;case\"I\":void 0===n&&(n=[]),n.push(new xp({start:o,len:a.len,seqOffset:s,type:\"I\"})),s+=a.len;break;case\"M\":case\"EQ\":case\"=\":case\"X\":i.push(new xp({start:o,seqOffset:s,len:a.len,type:\"M\"})),s+=a.len,o+=a.len;break;default:console.log(\"Error processing cigar element: \"+a.len+a.ltr)}}e.blocks=i,e.insertions=n,e.gaps=r}function Dp(e,t){return e[t+3]<<24|e[t+2]<<16|e[t+1]<<8|e[t]}function Tp(e){var t,i,n,r,s,o,a,c,l;for(t=[],i=[],s=null,r=e.length,n=0;n<r;n++)o=e.charAt(n),l=void 0,(l=o.charCodeAt(0))>=48&&l<=57?i.push(o):(a=o,c=Number.parseInt(i.join(\"\")),i=[],null!==s&&s.ltr===a?s.len+=c:(s={len:c,ltr:a},t.push(s)));return t}function Lp(e){var t={};return e.forEach((function(e){var i=e.split(\":\");t[i[0]]=i[2]})),t}function zp(e){let t=0;const i=e.length,n={},r=new DataView(e.buffer);for(;t<i;){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const o=String.fromCharCode(e[t++]);let a;if(\"A\"===o)a=String.fromCharCode(e[t]),t++;else if(\"i\"===o||\"I\"===o)a=r.getInt32(t,!0),t+=4;else if(\"c\"===o)a=r.getInt8(t,!0),t++;else if(\"C\"===o)a=r.getUint8(t,!0),t++;else if(\"s\"===o||\"S\"===o)a=r.getInt16(t,!0),t+=2;else if(\"f\"===o)a=r.getFloat32(t,!0),t+=4;else if(\"Z\"===o)for(a=\"\";;){var s=e[t++];if(0===s)break;a+=String.fromCharCode(s)}else{if(\"B\"!==o){a=\"Error unknown type: \"+o,n[i]=a;break}{const s=String.fromCharCode(e[t++]);let o=Np[s];if(void 0===o){n[i]=`Error: unknown element type '${s}'`;break}const c=r.getInt32(t,!0);t+=4;const l=t+c*o;for(a=[];t<l;){switch(s){case\"c\":a.push(r.getInt8(t,!0));break;case\"C\":a.push(r.getUint8(t,!0));break;case\"s\":a.push(r.getInt16(t,!0));break;case\"S\":a.push(r.getUint16(t,!0));break;case\"i\":a.push(r.getInt32(t,!0));break;case\"I\":a.push(r.getUint32(t,!0));break;case\"f\":a.push(r.getFloat32(t,!0))}t+=o}}}n[i]=a}return n}class Hp{chrAliasTable=new Map;constructor(e,t){this.config=e,this.genome=t,this.bamPath=e.url,this.isDataUri=Ga(e.url),Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(!this.alignmentCache){let e;if(this.isDataUri){const t=function(e){const t=e.split(\",\"),i=t[0].split(\":\")[1];let n=t[1];n=i.indexOf(\"base64\")>=0?atob(n):decodeURI(n);const r=new Uint8Array(n.length);for(var s=0;s<n.length;s++)r[s]=n.charCodeAt(s);return r}(this.bamPath);e=gs(t.buffer)}else{e=gs(await Qs.loadArrayBuffer(this.bamPath,Ua(this.config)))}this.alignmentCache=this.#C(e)}const n=await this.#_(e),r=this.alignmentCache.queryFeatures(n,t,i),s=new tp(e,t,i,this.config);for(let e of r)s.push(e);return s.finish(),s}#C(e){const t=[];return this.header=Mp.decodeBamHeader(e),Mp.decodeBamRecords(e,this.header.size,t,this.header.chrNames,void 0,0,Number.MAX_SAFE_INTEGER,this.filter),new Zs(t,this.genome)}async#_(e){const t=new Set(this.header.chrNames);if(t.has(e))return e;if(this.chrAliasTable.has(e))return this.chrAliasTable.get(e);if(this.genome){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>t.has(e)));e.length>0&&(n=e[0])}return this.chrAliasTable.set(e,n),n}return e}}class Pp{chrAliasTable=new Map;constructor(e,t){this.config=e,this.genome=t,this.bamPath=e.url,this.baiPath=e.indexURL,Mp.setReaderDefaults(this,e),this._blockLoader=new yh(e)}async readAlignments(e,t,i){const n=await this.#x(e),r=new tp(e,t,i,this.config);if(void 0===n)return r;{const e=(await this.getIndex()).chunksForRange(n,t,i);if(!e||0===e.length)return r;for(let s of e){const e=await this._blockLoader.getData(s.minv,s.maxv);if(Mp.decodeBamRecords(e,s.minv.offset,r,this.header.chrNames,n,t,i,this.filter))break}return r.finish(),r}}async#x(e){if(await this.getHeader(),this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.header.chrToIndex[e];if(void 0===t){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>void 0!==this.header.chrToIndex[e]));e.length>0&&(n=e[0],t=this.header.chrToIndex[e[0]])}this.chrAliasTable.set(e,n)}return t}async getHeader(){if(!this.header){const e=this.genome,t=await this.getIndex();let i;if(t.firstBlockPosition){const e=Ua(this.config,{range:{start:t.firstBlockPosition,size:26}}),n=ms(await Qs.loadArrayBuffer(this.bamPath,e));i=t.firstBlockPosition+n}else i=64e3;const n=Ua(this.config,{range:{start:0,size:i}});this.header=await Mp.readHeader(this.bamPath,n,e)}return this.header}async getIndex(){return this.index||(this.index=await gh(this.baiPath,this.config)),this.index}async getChrIndex(){if(this.chrToIndex)return this.chrToIndex;{const e=await this.getHeader();return this.chrToIndex=e.chrToIndex,this.indexToChr=e.chrNames,this.chrNames=new Set(e.chrNames),this.chrToIndex}}}class Op{constructor(e,t){this.config=e,this.genome=t;const i={};e.sources.sequences.forEach((function(n){const r=t?t.getChromosomeName(n):n;i[r]=function(e,t,i){const n={url:e.sources.url.replace(\"$CHR\",i)};e.sources.indexURL&&(n.indexURL=e.sources.indexURL.replace(\"$CHR\",i));const r=Object.assign(e,n);return new Pp(r,t)}(e,t,n)})),this.bamReaders=i,Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(this.bamReaders.hasOwnProperty(e)){let n=this.bamReaders[e];return await n.readAlignments(e,t,i)}return new tp(e,t,i,this.config)}}const Up=function(e,t){this.config=e,this.genome=t,Mp.setReaderDefaults(this,e)};function qp(){const e=this,t=this.genome;if(this.header)return Promise.resolve(this.header);{const i=this.config.url+\"?file=\"+this.config.alignmentFile+\"&options=-b,-H\",n=Ua(this.config);return Mp.readHeader(i,n,t).then((function(t){return e.header=t,t}))}}Up.prototype.readAlignments=function(e,t,i){var n=this;return qp.call(n).then((function(r){var s,o;return s=r.chrAliasTable.hasOwnProperty(e)?r.chrAliasTable[e]:e,o=n.config.url+\"?reference=\"+n.config.referenceFile+\"&file=\"+n.config.alignmentFile+\"&region=\"+s+\":\"+t+\"-\"+i,Qs.loadString(o,Ua(n.config)).then((function(o){var a;return r.chrToIndex[s],a=new tp(e,t,i,n.config),Mp.decodeSamRecords(o,a,s,t,i,n.filter),a}))}))};class Qp extends Rh{constructor(e,t){super(e,t),Mp.setReaderDefaults(this,e)}async readAlignments(e,t,i){if(!this.header){const e=gs((await this.readHeaderData()).buffer);this.header=Mp.decodeBamHeader(e,this.genome),this.chrAliasTable=new Map;for(let e of this.header.chrNames)this.chrAliasTable.set(e,this.genome.getChromosomeName(e))}let n=this.chrAliasTable.has(e)?this.chrAliasTable.get(e):e;const r=gs((await this.readData(n,t,i)).buffer);this.header=Mp.decodeBamHeader(r,this.genome);const s=this.header.chrToIndex[e],o=new tp(e,t,i,this.config);return Mp.decodeBamRecords(r,this.header.size,o,this.header.chrNames,s,t,i,this.filter),o.finish(),o}}\n",
-       "/*! For license information please see cram-bundle.js.LICENSE.txt */for(var Vp=(()=>{var e={4923:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(8712),s=i(5931),o=i(9747);function a(e,t){const[i,n,r,s,o,a]=t,c=i;e[c]||(e[c]=[]),e[c].push({start:n,span:r,containerStart:s,sliceStart:o,sliceBytes:a})}t.default=class{constructor(e){this.filehandle=(0,s.open)(e.url,e.path,e.filehandle)}parseIndex(){return n(this,void 0,void 0,(function*(){const e={},t=31===(i=yield this.filehandle.readFile())[0]&&139===i[1]?(0,r.unzip)(i):i;var i;if(t.length>4&&21578050===t.readUInt32LE(0))throw new o.CramMalformedError(\"invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support\");let n=[],s=\"\";for(const i of t)if(i>=48&&i<=57||!s&&45===i)s+=String.fromCharCode(i);else if(9===i)n.push(Number.parseInt(s,10)),s=\"\";else if(10===i)n.push(Number.parseInt(s,10)),s=\"\",a(e,n),n=[];else if(13!==i&&32!==i)throw new o.CramMalformedError(\"invalid .crai index file\");return s&&n.push(Number.parseInt(s,10)),6===n.length&&a(e,n),Object.entries(e).forEach((([t,i])=>{const n=i;e[t]=n.sort(((e,t)=>e.start-t.start||e.span-t.span))})),e}))}getIndex(){return this.parseIndexP||(this.parseIndexP=this.parseIndex().catch((e=>{throw this.parseIndexP=void 0,e}))),this.parseIndexP}hasDataForReferenceSequence(e){return n(this,void 0,void 0,(function*(){return!!(yield this.getIndex())[e]}))}getEntriesForRange(e,t,i){return n(this,void 0,void 0,(function*(){const n=(yield this.getIndex())[e];if(!n)return[];const r=e=>{const n=e.start,r=e.start+e.span;return n>i?-1:r<=t?1:0},s=[];for(const e of n)0===r(e)&&s.push(e);return s}))}}},9508:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=class{constructor(e,t){this.parameters=e,this.dataType=t}}},368:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`)}decode(e,t,i,n){return(0,o.getBits)(t.content,n.coreBlock,this.parameters.length)-this.parameters.offset}}t.default=a},8635:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=n(i(9508)),s=i(400);class o extends r.default{constructor(e,t,i){super(e,t),this.instantiateCodec=i}decode(e,t,i,n){const r=this._getLengthCodec().decode(e,t,i,n),s=this._getDataCodec(),o=new Uint8Array(r);for(let a=0;a<r;a+=1)o[a]=s.decode(e,t,i,n);return o}_getLengthCodec(){const e=this.parameters.lengthsEncoding;return this.instantiateCodec(e,\"int\")}_getDataCodec(){const e=this.parameters.valuesEncoding;return this.instantiateCodec(e,\"byte\")}}t.default=o,\"_getLengthCodec _getDataCodec\".split(\" \").forEach((e=>{(0,s.tinyMemoize)(o,e)}))},4839:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{decode(e,t,i,n){const{blockContentId:s}=this.parameters,o=i[s];if(!o)throw new r.CramMalformedError(`no block found with content ID ${s}`);const a=n.externalBlocks.getCursor(s);return this._decodeByteArray(o,a)}_decodeByteArray(e,t){const i=e.content,{stopByte:n}=this.parameters,r=t.bytePosition;let s=t.bytePosition;for(;i[s]!==n&&s<i.length;){if(s===i.length)throw new o.CramBufferOverrunError(\"byteArrayStop reading beyond length of data buffer?\");s+=1}return t.bytePosition=s+1,i.subarray(r,s)}}t.default=a},8153:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(400),a=i(612);class c extends s.default{constructor(e,t){if(super(e,t),\"int\"===this.dataType)this._decodeData=this._decodeInt;else{if(\"byte\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by EXTERNAL codec`);this._decodeData=this._decodeByte}}decode(e,t,i,n){const{blockContentId:s}=this.parameters,o=i[s];if(!o)throw new r.CramMalformedError(`no block found with content ID ${s}}`);const a=n.externalBlocks.getCursor(s);return this._decodeData(o,a)}_decodeInt(e,t){const[i,n]=(0,o.parseItf8)(e.content,t.bytePosition);return t.bytePosition=t.bytePosition+n,i}_decodeByte(e,t){if(t.bytePosition>=e.content.length)throw new a.CramBufferOverrunError(\"attempted to read beyond end of block. this file seems truncated.\");return e.content[t.bytePosition++]}}t.default=c},8185:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new r.CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`)}decode(e,t,i,n){let r=1;for(;0===(0,o.getBits)(t.content,n.coreBlock,1);)r+=1;return((0,o.getBits)(t.content,n.coreBlock,r-1)|1<<r-1)-this.parameters.offset}}t.default=a},612:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.CramBufferOverrunError=void 0,t.getBits=function(e,t,n){let r=0;if(t.bytePosition+(7-t.bitPosition+n)/8>e.length)throw new i(\"read error during 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t=0;t<this.parameters.numCodes;t++)e[t]={symbol:this.parameters.symbols[t],bitLength:this.parameters.bitLengths[t]};e=e.sort(((e,t)=>e.bitLength-t.bitLength||e.symbol-t.symbol)),this.codeBook={},e.forEach((e=>{this.codeBook[e.bitLength]||(this.codeBook[e.bitLength]=[]),this.codeBook[e.bitLength].push(e.symbol)}))}buildCodes(){this.codes={};let e=0,t=-1;Object.entries(this.codeBook).forEach((([i,n])=>{const s=Number.parseInt(i,10);n.forEach((i=>{const n={bitLength:s,value:i,bitCode:0};t+=1;const o=s-e;if(t<<=o,n.bitCode=t,e+=o,function(e){let t=e-(e>>1)&1431655765;return t=(858993459&t)+(t>>2&858993459),16843009*(t+(t>>4)&252645135)>>24}(t)>s)throw new r.CramMalformedError(\"Symbol out of range\");this.codes[i]=n}))}))}buildCaches(){this.sortedCodes=Object.values(this.codes).sort(((e,t)=>e.bitLength-t.bitLength||e.bitCode-t.bitCode)),this.sortedValuesByBitCode=this.sortedCodes.map((e=>e.value)),this.sortedBitCodes=this.sortedCodes.map((e=>e.bitCode)),this.sortedBitLengthsByBitCode=this.sortedCodes.map((e=>e.bitLength));const e=Math.max(...this.sortedBitCodes);this.bitCodeToValue=new Array(e+1).fill(-1);for(let e=0;e<this.sortedBitCodes.length;e+=1)this.bitCodeToValue[this.sortedCodes[e].bitCode]=e}decode(e,t,i,n){return this._decode(e,t,n.coreBlock)}_decodeZeroLengthCode(){return this.sortedCodes[0].value}_decode(e,t,i){const n=t.content;let s=0,a=0;for(let e=0;e<this.sortedCodes.length;e+=1){const t=this.sortedCodes[e].bitLength;a<<=t-s,a|=(0,o.getBits)(n,i,t-s),s=t;{const i=this.bitCodeToValue[a];if(i>-1&&this.sortedBitLengthsByBitCode[i]===t)return this.sortedValuesByBitCode[i];for(let i=e;this.sortedCodes[i+1].bitLength===t&&i<this.sortedCodes.length;i+=1)e+=1}}throw new r.CramMalformedError(\"Huffman symbol not found.\")}}t.default=a},6524:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.instantiateCodec=function e(t,i){const n=(s=\"ignore\"===i?0:t.codecId,u[s]);var s;if(!n)throw new r.CramUnimplementedError(`no codec implemented for codec ID ${t.codecId}`);return new n(t.parameters,i,e)};const r=i(9747),s=n(i(4341)),o=n(i(8153)),a=n(i(4839)),c=n(i(8635)),l=n(i(368)),h=n(i(8185)),d=n(i(99)),u={1:o.default,3:s.default,4:c.default,5:a.default,6:l.default,7:d.default,9:h.default}},99:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const r=i(9747),s=n(i(9508)),o=i(612);class a extends s.default{constructor(e,t){if(super(e,t),\"int\"!==this.dataType)throw new 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0===a?(r=this.parameters.K,s=(0,o.getBits)(t.content,n.coreBlock,r)):(r=a+this.parameters.K-1,s=1<<r|(0,o.getBits)(t.content,n.coreBlock,r)),s-this.parameters.offset}}t.default=a},7295:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default={CRAM_FLAG_PRESERVE_QUAL_SCORES:1,CRAM_FLAG_DETACHED:2,CRAM_FLAG_MATE_DOWNSTREAM:4,CRAM_FLAG_NO_SEQ:8,CRAM_FLAG_MASK:15,CRAM_M_REVERSE:1,CRAM_M_UNMAP:2,BAM_FPAIRED:1,BAM_FPROPER_PAIR:2,BAM_FUNMAP:4,BAM_FMUNMAP:8,BAM_FREVERSE:16,BAM_FMREVERSE:32,BAM_FREAD1:64,BAM_FREAD2:128,BAM_FSECONDARY:256,BAM_FQCFAIL:512,BAM_FDUP:1024,BAM_FSUPPLEMENTARY:2048,BAM_CMATCH:0,BAM_CINS:1,BAM_CDEL:2,BAM_CREF_SKIP:3,BAM_CSOFT_CLIP:4,BAM_CHARD_CLIP:5,BAM_CPAD:6,BAM_CEQUAL:7,BAM_CDIFF:8,BAM_CBACK:9,BAM_CIGAR_STR:\"MIDNSHP:XB\",BAM_CIGAR_SHIFT:4,BAM_CIGAR_MASK:15,BAM_CIGAR_TYPE:246183}},7219:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0});const 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t[0][e[0]>>6&3]=\"C\",t[0][e[0]>>4&3]=\"G\",t[0][e[0]>>2&3]=\"T\",t[0][3&e[0]]=\"N\",t[1][e[1]>>6&3]=\"A\",t[1][e[1]>>4&3]=\"G\",t[1][e[1]>>2&3]=\"T\",t[1][3&e[1]]=\"N\",t[2][e[2]>>6&3]=\"A\",t[2][e[2]>>4&3]=\"C\",t[2][e[2]>>2&3]=\"T\",t[2][3&e[2]]=\"N\",t[3][e[3]>>6&3]=\"A\",t[3][e[3]>>4&3]=\"C\",t[3][e[3]>>2&3]=\"G\",t[3][3&e[3]]=\"N\",t[4][e[4]>>6&3]=\"A\",t[4][e[4]>>4&3]=\"C\",t[4][e[4]>>2&3]=\"G\",t[4][3&e[4]]=\"T\",t}(e.preservation.SM),this.dataSeriesEncoding=e.dataSeriesEncoding,this.tagEncoding=e.tagEncoding}getCodecForTag(e){const t=this.tagCodecCache[e];if(t)return t;{const t=this.tagEncoding[e];if(!t)throw new Error(\"Error, no tag encoding\");const i=(0,n.instantiateCodec)(t,\"byteArray\");return this.tagCodecCache[e]=i,i}}getTagNames(e){return this.tagIdsDictionary[e]}getCodecForDataSeries(e){let t=this.dataSeriesCodecCache[e];if(void 0===t){const i=this.dataSeriesEncoding[e];if(i){const o=s[e];if(!o)throw new r.CramMalformedError(`data series name ${e} not defined in 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0:e.numRecords))return null;const{majorVersion:t}=yield this.file.getDefinition(),i=(0,h.getSectionParsers)(t),n=yield this.getFirstBlock();if(void 0===n)return;if(\"COMPRESSION_HEADER\"!==n.contentType)throw new o.CramMalformedError(`invalid content type ${n.contentType} in compression header block`);const r=(0,a.parseItem)(n.content,i.cramCompressionHeader.parser,0,n.contentPosition);return Object.assign(Object.assign({},n),{parsedContent:r})}))}getFirstBlock(){return n(this,void 0,void 0,(function*(){const e=yield this.getHeader();if(e)return this.file.readBlock(e._endPosition)}))}getCompressionScheme(){return n(this,void 0,void 0,(function*(){const e=yield this.getCompressionHeaderBlock();if(e)return new l.default(e.parsedContent)}))}getSlice(e,t){return new c.default(this,e,t)}_readContainerHeader(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield 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\").forEach((e=>{(0,a.tinyMemoize)(d,e)}))},6794:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(8287),o=r(i(928)),a=r(i(7392)),c=r(i(6960)),l=r(i(235)),h=i(1307),d=i(9747),u=i(8712),f=r(i(9989)),p=i(3165),g=r(i(78)),m=i(5931),w=i(400),b=i(5417);class F{constructor(e){var t;if(this.file=(0,m.open)(e.url,e.path,e.filehandle),this.validateChecksums=!0,this.fetchReferenceSequenceCallback=e.seqFetch,this.options={checkSequenceMD5:e.checkSequenceMD5,cacheSize:null!==(t=e.cacheSize)&&void 0!==t?t:2e4},this.featureCache=new a.default({maxSize:this.options.cacheSize}),function(){const e=new Uint32Array([287454020]),t=new Uint8Array(e.buffer);return 68===t[0]?0:17===t[0]?1:2}()>0)throw new Error(\"Detected big-endian machine, may be unable to run\")}read(e,t,i,n){return this.file.read(e,t,i,n)}stat(){return this.file.stat()}getDefinition(){return n(this,void 0,void 0,(function*(){const{maxLength:e,parser:t}=(0,p.cramFileDefinition)(),i=s.Buffer.allocUnsafe(e);yield this.file.read(i,0,e,0);const n=t(i).value;if(2!==n.majorVersion&&3!==n.majorVersion)throw new d.CramUnimplementedError(`CRAM version ${n.majorVersion} not supported`);return n}))}getSamHeader(){return n(this,void 0,void 0,(function*(){const e=yield this.getContainerById(0);if(!e)throw new d.CramMalformedError(\"file contains no containers\");const t=yield e.getFirstBlock();if(void 0===t)return(0,b.parseHeaderText)(\"\");const i=t.content,n=i.readInt32LE(0),r=i.toString(\"utf8\",4,4+n);return this.header=r,(0,b.parseHeaderText)(r)}))}getHeaderText(){return n(this,void 0,void 0,(function*(){return yield this.getSamHeader(),this.header}))}getContainerById(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t);let n=i.cramFileDefinition.maxLength;const{size:r}=yield this.file.stat(),{cramContainerHeader1:s}=i;let o;for(let t=0;t<=e;t++){if(n+s.maxLength+8>=r)return;o=this.getContainerAtPosition(n);const i=yield o.getHeader();if(!i)throw new d.CramMalformedError(`container ${e} not found in file`);if(0===t){n=i._endPosition;for(let e=0;e<i.numBlocks;e++){const e=yield this.readBlock(n);if(void 0===e)return;n=e._endPosition}}else n+=i._size+i.length}return o}))}checkCrc32(e,t,i,r){return n(this,void 0,void 0,(function*(){const n=s.Buffer.allocUnsafe(t);yield this.file.read(n,0,t,e);const a=o.default.unsigned(n);if(a!==i)throw new d.CramMalformedError(`crc mismatch in ${r}: recorded CRC32 = ${i}, but calculated CRC32 = ${a}`)}))}containerCount(){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.getDefinition(),t=(0,p.getSectionParsers)(e),{size:i}=yield this.file.stat(),{cramContainerHeader1:n}=t;let r=0,s=t.cramFileDefinition.maxLength;for(;s+n.maxLength+8<i;){const e=yield this.getContainerAtPosition(s).getHeader();if(!e)break;if(0===r){s=e._endPosition;for(let t=0;t<e.numBlocks;t++){const e=yield this.readBlock(s);if(void 0===e)return;s=e._endPosition}}else s+=e._size+e.length;r+=1}return r}))}getContainerAtPosition(e){return new g.default(this,e)}readBlockHeader(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t),{cramBlockHeader:n}=i,{size:r}=yield this.file.stat();if(e+n.maxLength>=r)return;const o=s.Buffer.allocUnsafe(n.maxLength);return yield this.file.read(o,0,n.maxLength,e),(0,w.parseItem)(o,n.parser,0,e)}))}_parseSection(e,t){return n(this,arguments,void 0,(function*(e,t,i=e.maxLength,n){let r;if(n)r=n;else{const{size:e}=yield this.file.stat();if(t+i>=e)return;r=s.Buffer.allocUnsafe(i),yield this.file.read(r,0,i,t)}const o=(0,w.parseItem)(r,e.parser,0,t);if(o._size!==i)throw new d.CramMalformedError(`section read error: requested size ${i} does not equal parsed size ${o._size}`);return o}))}_uncompress(e,t,i){return n(this,void 0,void 0,(function*(){if(\"gzip\"===e)(0,u.unzip)(t).copy(i);else if(\"bzip2\"===e){const e=l.default.array(t);let n,r=l.default.header(e),o=0;do{n=l.default.decompress(e,r),-1!==n&&(s.Buffer.from(n).copy(i,o),o+=n.length,r-=n.length)}while(-1!==n)}else if(\"lzma\"===e){const e=new Response(new h.XzReadableStream((n=t,new ReadableStream({start(e){e.enqueue(n),e.close()}}))));s.Buffer.from(yield e.arrayBuffer()).copy(i)}else if(\"rans\"===e)(0,f.default)(t,i);else if(\"rans4x16\"===e)c.default.r4x16_uncompress(t,i);else if(\"arith\"===e)c.default.arith_uncompress(t,i);else if(\"fqzcomp\"===e)c.default.fqzcomp_uncompress(t,i);else{if(\"tok3\"!==e)throw new d.CramUnimplementedError(`${e} decompression not yet implemented`);c.default.tok3_uncompress(t,i)}var n}))}readBlock(e){return n(this,void 0,void 0,(function*(){const{majorVersion:t}=yield this.getDefinition(),i=(0,p.getSectionParsers)(t),n=yield this.readBlockHeader(e);if(void 0===n)return;const r=n._endPosition,o=s.Buffer.allocUnsafe(n.uncompressedSize),a=Object.assign(Object.assign({},n),{_endPosition:r,contentPosition:r,content:o});if(\"raw\"!==n.compressionMethod){const e=s.Buffer.allocUnsafe(n.compressedSize);yield this.read(e,0,n.compressedSize,r),yield this._uncompress(n.compressionMethod,e,o)}else yield this.read(o,0,n.uncompressedSize,r);if(t>=3){const t=yield this._parseSection(i.cramBlockCrc32,r+n.compressedSize);if(void 0===t)return;a.crc32=t.crc32,this.validateChecksums&&(yield this.checkCrc32(e,n._size+n.compressedSize,t.crc32,\"block data\")),a._endPosition=t._endPosition,a._size=a.compressedSize+i.cramBlockCrc32.maxLength}else a._endPosition=r+a.compressedSize,a._size=a.compressedSize;return a}))}}t.default=F,\"getDefinition getSectionParsers getSamHeader\".split(\" \").forEach((e=>{(0,w.tinyMemoize)(F,e)}))},7390:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=t.CramRecord=void 0;var r=i(8401);Object.defineProperty(t,\"CramRecord\",{enumerable:!0,get:function(){return n(r).default}});var s=i(6794);Object.defineProperty(t,\"default\",{enumerable:!0,get:function(){return n(s).default}})},8401:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.MateFlagsDecoder=t.CramFlagsDecoder=t.BamFlagsDecoder=t.MateFlags=t.CramFlags=t.BamFlags=void 0;const r=n(i(7295)),s={a:0,A:0,c:1,C:1,g:2,G:2,t:3,T:3,n:4,N:4};function o(e){const t={};for(const[i,n]of e)t[`is${n}`]=e=>!!(e&i),t[`set${n}`]=e=>e|i;return t}t.BamFlags=[[1,\"Paired\"],[2,\"ProperlyPaired\"],[4,\"SegmentUnmapped\"],[8,\"MateUnmapped\"],[16,\"ReverseComplemented\"],[32,\"MateReverseComplemented\"],[64,\"Read1\"],[128,\"Read2\"],[256,\"Secondary\"],[512,\"FailedQc\"],[1024,\"Duplicate\"],[2048,\"Supplementary\"]],t.CramFlags=[[1,\"PreservingQualityScores\"],[2,\"Detached\"],[4,\"WithMateDownstream\"],[8,\"DecodeSequenceAsStar\"]],t.MateFlags=[[1,\"OnNegativeStrand\"],[2,\"Unmapped\"]],t.BamFlagsDecoder=o(t.BamFlags),t.CramFlagsDecoder=o(t.CramFlags),t.MateFlagsDecoder=o(t.MateFlags),t.default=class{constructor({flags:e,cramFlags:t,readLength:i,mappingQuality:n,lengthOnRef:r,qualityScores:s,mateRecordNumber:o,readBases:a,readFeatures:c,mateToUse:l,readGroupId:h,readName:d,sequenceId:u,uniqueId:f,templateSize:p,alignmentStart:g,tags:m}){this.flags=e,this.cramFlags=t,this.readLength=i,this.mappingQuality=n,this.lengthOnRef=r,this.qualityScores=s,a&&(this.readBases=a),this.readGroupId=h,this.readName=d,this.sequenceId=u,this.uniqueId=f,this.templateSize=p,this.alignmentStart=g,this.tags=m,c&&(this.readFeatures=c),l&&(this.mate={flags:l.mateFlags,readName:l.mateReadName,sequenceId:l.mateSequenceId,alignmentStart:l.mateAlignmentStart}),o&&(this.mateRecordNumber=o)}isPaired(){return!!(this.flags&r.default.BAM_FPAIRED)}isProperlyPaired(){return!!(this.flags&r.default.BAM_FPROPER_PAIR)}isSegmentUnmapped(){return!!(this.flags&r.default.BAM_FUNMAP)}isMateUnmapped(){return!!(this.flags&r.default.BAM_FMUNMAP)}isReverseComplemented(){return!!(this.flags&r.default.BAM_FREVERSE)}isMateReverseComplemented(){return!!(this.flags&r.default.BAM_FMREVERSE)}isRead1(){return!!(this.flags&r.default.BAM_FREAD1)}isRead2(){return!!(this.flags&r.default.BAM_FREAD2)}isSecondary(){return!!(this.flags&r.default.BAM_FSECONDARY)}isFailedQc(){return!!(this.flags&r.default.BAM_FQCFAIL)}isDuplicate(){return!!(this.flags&r.default.BAM_FDUP)}isSupplementary(){return!!(this.flags&r.default.BAM_FSUPPLEMENTARY)}isDetached(){return!!(this.cramFlags&r.default.CRAM_FLAG_DETACHED)}hasMateDownStream(){return!!(this.cramFlags&r.default.CRAM_FLAG_MATE_DOWNSTREAM)}isPreservingQualityScores(){return!!(this.cramFlags&r.default.CRAM_FLAG_PRESERVE_QUAL_SCORES)}isUnknownBases(){return!!(this.cramFlags&r.default.CRAM_FLAG_NO_SEQ)}getReadBases(){if(!this.readBases&&this._refRegion){const e=function(e,t){if(!e.lengthOnRef&&!e.readLength)return null;if(e.isUnknownBases())return null;const i=e.alignmentStart-t.start;if(!e.readFeatures)return t.seq.slice(i,i+(e.lengthOnRef||0)).toUpperCase();let n=\"\",r=i,s=0;for(;n.length<e.readLength;)if(s<e.readFeatures.length){const i=e.readFeatures[s];if(\"Q\"===i.code||\"q\"===i.code)s+=1;else if(i.pos===n.length+1)if(s+=1,\"b\"===i.code){const e=i.data;n+=e,r+=e.length}else\"B\"===i.code?(n+=i.data[0],r+=1):\"X\"===i.code?(n+=i.sub,r+=1):\"I\"===i.code?n+=i.data:\"D\"===i.code?r+=i.data:\"i\"===i.code?n+=i.data:\"N\"===i.code?r+=i.data:\"S\"===i.code?n+=i.data:\"P\"===i.code||i.code;else if(s<e.readFeatures.length){const e=t.seq.slice(r,r+i.pos-n.length-1);n+=e,r+=e.length}}else{const i=t.seq.slice(r,r+e.readLength-n.length);n+=i,r+=i.length}return n.toUpperCase()}(this,this._refRegion);e&&(this.readBases=e)}return this.readBases}getPairOrientation(){if(!this.isSegmentUnmapped()&&this.isPaired()&&!this.isMateUnmapped()&&this.mate&&this.sequenceId===this.mate.sequenceId){const e=this.isReverseComplemented()?\"R\":\"F\",t=this.isMateReverseComplemented()?\"R\":\"F\";let i=\" \",n=\" \";this.isRead1()?(i=\"1\",n=\"2\"):this.isRead2()&&(i=\"2\",n=\"1\");const r=[];let s=this.templateLength||this.templateSize;if(void 0===s)throw new Error(\"One of templateSize and templateLength must be set\");return this.alignmentStart>this.mate.alignmentStart&&s>0&&(s=-s),s>0?(r[0]=e,r[1]=i,r[2]=t,r[3]=n):(r[2]=e,r[3]=i,r[0]=t,r[1]=n),r.join(\"\")}return null}addReferenceSequence(e,t){this.readFeatures&&this.readFeatures.forEach((i=>{\"X\"===i.code&&function(e,t,i,n){const r=n.refPos-t.start,o=t.seq.charAt(r);o&&(n.ref=o);let a=s[o];void 0===a&&(a=4);const c=i.substitutionMatrix[a][n.data];c&&(n.sub=c)}(0,e,t,i)})),!this.readBases&&e.start<=this.alignmentStart&&e.end>=this.alignmentStart+(this.lengthOnRef||this.readLength)-1&&(this._refRegion=e)}toJSON(){const e={};return Object.keys(this).forEach((t=>{t.startsWith(\"_\")||(e[t]=this[t])})),e.readBases=this.getReadBases(),e}}},3165:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.cramFileDefinition=r,t.cramBlockHeader=s,t.cramBlockCrc32=o,t.cramTagDictionary=c,t.cramPreservationMap=l,t.isMappedSliceHeader=function(e){return\"number\"==typeof e.refSeqId},t.getSectionParsers=function(e){return{cramFileDefinition:r(),cramBlockHeader:s(),cramBlockCrc32:o(),cramDataSeriesEncodingMap:p(),cramTagEncodingMap:g(),cramCompressionHeader:{parser:(e,t)=>{const{value:i,offset:n}=l().parser(e,t);t=n;const{value:r,offset:s}=p().parser(e,t);t=s;const{value:o,offset:a}=g().parser(e,t);return t=a,{value:{dataSeriesEncoding:h(r),preservation:h(i),tagEncoding:h(o)},offset:t}}},cramEncoding:{parser:(e,t)=>f(e,t)},cramUnmappedSliceHeader:d(e),cramMappedSliceHeader:u(e),cramContainerHeader1:m(e),cramContainerHeader2:w(e)}};const n=i(400);function r(){return{parser:(e,t=0)=>{const i=e,n=new DataView(i.buffer,i.byteOffset,i.length);let r=0;const s=e.subarray(r,r+4).toString();r+=4;const o=n.getUint8(r);r+=1;const a=n.getUint8(r);r+=1;const c=i.subarray(r,r+20).toString().replaceAll(\"\\0\",\"\");return r+=20,{value:{magic:s,majorVersion:o,minorVersion:a,fileId:c},offset:r}},maxLength:26}}function s(){return{parser:(e,t=0)=>{const i=e,r=new DataView(i.buffer,i.byteOffset,i.length);let s=0;const o=r.getUint8(s),a=[\"raw\",\"gzip\",\"bzip2\",\"lzma\",\"rans\",\"rans4x16\",\"arith\",\"fqzcomp\",\"tok3\"][o];if(!a)throw new Error(`compression method number ${o} not implemented`);s+=1;const c=r.getUint8(s),l=[\"FILE_HEADER\",\"COMPRESSION_HEADER\",\"MAPPED_SLICE_HEADER\",\"UNMAPPED_SLICE_HEADER\",\"EXTERNAL_DATA\",\"CORE_DATA\"][c];if(!l)throw new Error(`invalid block content type id ${c}`);s+=1;const[h,d]=(0,n.parseItf8)(e,s);s+=d;const[u,f]=(0,n.parseItf8)(e,s);s+=f;const[p,g]=(0,n.parseItf8)(e,s);return s+=g,{offset:s,value:{uncompressedSize:p,compressedSize:u,contentId:h,contentType:l,compressionMethod:a}}},maxLength:17}}function o(){return{parser:(e,t)=>{const i=e,n=new DataView(i.buffer,i.byteOffset,i.length).getUint32(t,!0);return{offset:t+=4,value:{crc32:n}}},maxLength:4}}function a(e,t,i){const n=e.toString(\"utf8\",t,i),r=[];for(let e=0;e<n.length;e+=3)r.push(n.slice(e,e+3));return r}function c(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const s=e.subarray(t,t+i);t+=i;const o=[];let c=0,l=0;for(;l<s.length;l++)s[l]||(o.push(a(s,c,l)),c=l+1);return l>c&&o.push(a(s,c,l)),{value:{size:i,ents:o},offset:t}}}}function l(){return{parser:(e,t)=>{const i=e,r=new DataView(i.buffer,i.byteOffset,i.length),[s,o]=(0,n.parseItf8)(e,t);t+=o;const[a,l]=(0,n.parseItf8)(e,t);t+=l;const h=[];for(let i=0;i<a;i++){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);if(t+=2,\"MI\"===i||\"UI\"===i||\"PI\"===i||\"RN\"===i||\"AP\"===i||\"RR\"===i)h.push({key:i,value:!!r.getUint8(t)}),t+=1;else if(\"SM\"===i)h.push({key:i,value:[r.getUint8(t),r.getUint8(t+1),r.getUint8(t+2),r.getUint8(t+3),r.getUint8(t+4)]}),t+=5;else{if(\"TD\"!==i)throw new Error(`unknown key ${i}`);{const{offset:n,value:r}=c().parser(e,t);h.push({key:i,value:r.ents}),t=n}}}return{value:{mapSize:s,mapCount:a,ents:h},offset:t}}}}function h(e){const t={};for(const{key:i,value:n}of e.ents)t[i]&&console.warn(`duplicate key ${i} in map`),t[i]=n;return t}function d(e){return{parser:(t,i)=>{const[r,s]=(0,n.parseItf8)(t,i);i+=s;let o=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);i+=r,o=e}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);i+=r,o=e}else console.warn(\"recordCounter=0\");const[a,c]=(0,n.parseItf8)(t,i);i+=c;const[l,h]=(0,n.parseItf8)(t,i);i+=h;const d=[];for(let e=0;e<l;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,d.push(e)}let u;return e>=2&&(u=[...t.subarray(i,i+16)],i+=16),{value:{recordCounter:o,md5:u,contentIds:d,numContentIds:l,numBlocks:a,numRecords:r},offset:i}},maxLength:e=>40+5*e}}function u(e){return{parser:(t,i)=>{const[r,s]=(0,n.parseItf8)(t,i);i+=s;const[o,a]=(0,n.parseItf8)(t,i);i+=a;const[c,l]=(0,n.parseItf8)(t,i);i+=l;const[h,d]=(0,n.parseItf8)(t,i);i+=d;let u=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);i+=r,u=e}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);i+=r,u=e}else console.warn(\"majorVersion is <2, recordCounter set to 0\");const[f,p]=(0,n.parseItf8)(t,i);i+=p;const[g,m]=(0,n.parseItf8)(t,i);i+=m;const w=[];for(let e=0;e<g;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,w.push(e)}const[b,F]=(0,n.parseItf8)(t,i);let v;return i+=F,e>=2&&(v=[...t.subarray(i,i+16)],i+=16),{value:{md5:v,numBlocks:f,numRecords:h,numContentIds:g,refSeqSpan:c,refSeqId:r,refSeqStart:o,recordCounter:u,refBaseBlockId:b,contentIds:w},offset:i}},maxLength:e=>60+5*e}}function f(e,t){const i=e,r=new DataView(i.buffer,i.byteOffset,i.length),[s,o]=(0,n.parseItf8)(e,t);t+=o;const[a,c]=(0,n.parseItf8)(e,t);t+=c;const l={};if(0===s);else if(1===s){const[i,r]=(0,n.parseItf8)(e,t);l.blockContentId=i,t+=r}else if(2===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.M=s,t+=o}else if(3===s){const i=(0,n.parseItf8)(e,t),r=i[0];t+=i[1];const s=[];for(let i=0;i<r;i++){const i=(0,n.parseItf8)(e,t);s.push(i[0]),t+=i[1]}l.symbols=s;const o=(0,n.parseItf8)(e,t),a=i[0];l.numLengths=a,l.numCodes=r,l.numLengths=a,t+=o[1];const c=[];for(let i=0;i<a;i++){const i=(0,n.parseItf8)(e,t);t+=i[1],c.push(i[0])}l.bitLengths=c}else if(4===s){const{value:i,offset:n}=f(e,t);l.lengthsEncoding=i,t=n;const{value:r,offset:s}=f(e,t);l.valuesEncoding=r,t=s}else if(5===s){l.stopByte=r.getUint8(t),t+=1;const[i,s]=(0,n.parseItf8)(e,t);l.blockContentId=i,t+=s}else if(6===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.length=s,t+=o}else if(7===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.K=s,t+=o}else if(8===s){const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r;const[s,o]=(0,n.parseItf8)(e,t);l.log2m=s,t+=o}else{if(9!==s)throw new Error(`unknown codecId ${s}`);{const[i,r]=(0,n.parseItf8)(e,t);l.offset=i,t+=r}}return{value:{codecId:s,parametersBytes:a,parameters:l},offset:t}}function p(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const[s,o]=(0,n.parseItf8)(e,t);t+=o;const a=[];for(let i=0;i<s;i++){const i=String.fromCharCode(e[t])+String.fromCharCode(e[t+1]);t+=2;const{value:n,offset:r}=f(e,t);t=r,a.push({key:i,value:n})}return{value:{mapSize:i,ents:a,mapCount:s},offset:t}}}}function g(){return{parser:(e,t)=>{const[i,r]=(0,n.parseItf8)(e,t);t+=r;const[s,o]=(0,n.parseItf8)(e,t);t+=o;const a=[];for(let i=0;i<s;i++){const[i,r]=(0,n.parseItf8)(e,t);t+=r;const s=String.fromCharCode(i>>16&255)+String.fromCharCode(i>>8&255)+String.fromCharCode(255&i),{value:o,offset:c}=f(e,t);t=c,a.push({key:s,value:o})}return{value:{mapSize:i,ents:a,mapCount:s},offset:t}}}}function m(e){return{maxLength:52,parser:(t,i)=>{const r=t,s=new DataView(r.buffer,r.byteOffset,r.length).getInt32(i,!0);i+=4;const[o,a]=(0,n.parseItf8)(t,i);i+=a;const[c,l]=(0,n.parseItf8)(t,i);i+=l;const[h,d]=(0,n.parseItf8)(t,i);i+=d;const[u,f]=(0,n.parseItf8)(t,i);i+=f;let p,g=0;if(e>=3){const[e,r]=(0,n.parseLtf8)(t,i);g=e,i+=r}else if(2===e){const[e,r]=(0,n.parseItf8)(t,i);g=e,i+=r}else console.warn(\"setting recordCounter=0\");if(e>1){const[e,r]=(0,n.parseLtf8)(t,i);p=e,i+=r}const[m,w]=(0,n.parseItf8)(t,i);i+=w;const[b,F]=(0,n.parseItf8)(t,i);return{value:{length:s,refSeqId:o,refSeqStart:c,alignmentSpan:h,numBlocks:m,numLandmarks:b,numBases:p,recordCounter:g,numRecords:u},offset:i+=F}}}}function w(e){return{parser:(t,i)=>{const r=t,s=new DataView(r.buffer,r.byteOffset,r.length),[o,a]=(0,n.parseItf8)(t,i);i+=a;const c=[];for(let e=0;e<o;e++){const[e,r]=(0,n.parseItf8)(t,i);i+=r,c.push(e)}let l;return e>=3&&(l=s.getUint32(i,!0),i+=4),{value:Object.assign(Object.assign({},void 0===l?{}:{crc32:l}),{numLandmarks:o,landmarks:c}),offset:i}},maxLength:e=>5+5*e+4}}},6484:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,c,l,h,d,u,f){let p=t(\"BF\");const g=t(\"CF\");if(!(0,s.isMappedSliceHeader)(c.parsedContent))throw new Error(\"slice header not mapped\");const m=u>1&&-2===c.parsedContent.refSeqId?t(\"RI\"):c.parsedContent.refSeqId,w=t(\"RL\");let b=t(\"AP\");i.APdelta&&(b+=d.lastAlignmentStart),d.lastAlignmentStart=b;const F=t(\"RG\");let v,y,A,C;if(i.readNamesIncluded&&(v=o(t(\"RN\"))),r.CramFlagsDecoder.isDetached(g)){const e=t(\"MF\");let n;i.readNamesIncluded||(n=o(t(\"RN\")),v=n);const s=t(\"NS\"),a=t(\"NP\");(e||s>-1)&&(y={mateFlags:e,mateSequenceId:s,mateAlignmentStart:a,mateReadName:n}),A=t(\"TS\"),r.MateFlagsDecoder.isUnmapped(e)&&(p=r.BamFlagsDecoder.setMateUnmapped(p)),r.MateFlagsDecoder.isOnNegativeStrand(e)&&(p=r.BamFlagsDecoder.setMateReverseComplemented(p))}else r.CramFlagsDecoder.isWithMateDownstream(g)&&(C=t(\"NF\")+f+1);const _=t(\"TL\");if(_<0)throw new n.CramMalformedError(\"invalid TL index\");const x={},k=i.getTagNames(_),I=k.length;for(let t=0;t<I;t+=1){const n=k[t],r=n.slice(0,2),s=n.slice(2,3),o=i.getCodecForTag(n).decode(e,l,h,d);x[r]=\"number\"==typeof o?o:a(s,o)}let S,E,N,B,M;if(r.BamFlagsDecoder.isSegmentUnmapped(p))if(r.CramFlagsDecoder.isDecodeSequenceAsStar(g))M=null,B=null;else{const e=new Array(w);for(let i=0;i<e.length;i+=1)e[i]=t(\"BA\");if(M=String.fromCharCode(...e),r.CramFlagsDecoder.isPreservingQualityScores(g)){B=new Array(w);for(let i=0;i<e.length;i+=1)B[i]=t(\"QS\")}}else{const e=t(\"FN\");if(e&&(S=function(e,t,i,r,s){let o=0,a=e-1;const c=new Array(t);function l([e,t]){const n=i(t);if(\"character\"===e)return String.fromCharCode(n);if(\"string\"===e){let e=\"\";for(let t=0;t<n.byteLength;t++)e+=String.fromCharCode(n[t]);return e}return\"numArray\"===e?n.toArray():n}for(let e=0;e<t;e+=1){const t=String.fromCharCode(i(\"FC\")),r=i(\"FP\"),h={B:[\"character\",\"BA\"],S:[\"string\",s>1?\"SC\":\"IN\"],X:[\"number\",\"BS\"],D:[\"number\",\"DL\"],I:[\"string\",\"IN\"],i:[\"character\",\"BA\"],b:[\"string\",\"BB\"],q:[\"numArray\",\"QQ\"],Q:[\"number\",\"QS\"],H:[\"number\",\"HC\"],P:[\"number\",\"PD\"],N:[\"number\",\"RS\"]}[t];if(!h)throw new n.CramMalformedError(`invalid read feature code \"${t}\"`);let d=l(h);const u={B:[\"number\",\"QS\"]}[t];u&&(d=[d,l(u)]),o+=r;const f=o;a+=r;const p=a;\"D\"===t||\"N\"===t?a+=d:\"I\"===t||\"S\"===t?a-=d.length:\"i\"===t&&(a-=1),c[e]={code:t,pos:f,refPos:p,data:d}}return c}(b,e,t,0,u)),E=w,S)for(const{code:e,data:t}of S)\"D\"===e||\"N\"===e?E+=t:\"I\"===e||\"S\"===e?E-=t.length:\"i\"===e&&(E-=1);if(Number.isNaN(E)&&(console.warn(`${v||`${m}:${b}`} record has invalid read features`),E=w),N=t(\"MQ\"),r.CramFlagsDecoder.isPreservingQualityScores(g)){B=new Array(w);for(let e=0;e<B.length;e++)B[e]=t(\"QS\")}}return{readLength:w,sequenceId:m,cramFlags:g,flags:p,alignmentStart:b,readGroupId:F,readName:v,mateToUse:y,templateSize:A,mateRecordNumber:C,readFeatures:S,lengthOnRef:E,mappingQuality:N,qualityScores:B,readBases:M,tags:x}};const n=i(9747),r=i(8401),s=i(3165);function o(e){let t=\"\";for(let i=0;i<e.length&&0!==e[i];i++)t+=String.fromCharCode(e[i]);return t}function a(e,t){if(\"Z\"===e)return o(t);if(\"A\"===e)return String.fromCharCode(t[0]);if(\"I\"===e)return new Uint32Array(t.buffer)[0];if(\"i\"===e)return new Int32Array(t.buffer)[0];if(\"s\"===e)return new Int16Array(t.buffer)[0];if(\"S\"===e)return new Uint16Array(t.buffer)[0];if(\"c\"===e)return new Int8Array(t.buffer)[0];if(\"C\"===e)return t[0];if(\"f\"===e)return new Float32Array(t.buffer)[0];if(\"H\"===e)return Number.parseInt(o(t).replace(/^0x/,\"\"),16);if(\"B\"===e)return function(e){const t=String.fromCharCode(e[0]),i=new DataView(e.buffer).getUint32(1,!0),n=new Array(i);if(e=e.slice(5),\"c\"===t){const t=new Int8Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"C\"===t){const t=new Uint8Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"s\"===t){const t=new Int16Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"S\"===t){const t=new Uint16Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"i\"===t){const t=new Int32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else if(\"I\"===t){const t=new Uint32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}else{if(\"f\"!==t)throw new Error(`unknown type: ${t}`);{const t=new Float32Array(e.buffer);for(let e=0;e<i;e+=1)n[e]=t[e]}}return n}(t);throw new n.CramMalformedError(`Unrecognized tag type ${e}`)}},6771:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(9747),o=i(400),a=r(i(7295)),c=r(i(6484)),l=r(i(8401)),h=i(3165),d=i(612);function u(e,t,i,n){const r=!!(n.mate||void 0!==n.mateRecordNumber&&n.mateRecordNumber!==t);i.readName||(i.readName=String(i.uniqueId),n.readName=i.readName),i.mate={sequenceId:n.sequenceId,alignmentStart:n.alignmentStart,uniqueId:n.uniqueId},n.readName&&(i.mate.readName=n.readName),n.mate||void 0!==n.mateRecordNumber||(n.mate={sequenceId:i.sequenceId,alignmentStart:i.alignmentStart,uniqueId:i.uniqueId},i.readName&&(n.mate.readName=i.readName)),i.flags|=a.default.BAM_FPAIRED,n.flags&a.default.BAM_FUNMAP&&(i.flags|=a.default.BAM_FMUNMAP),i.flags&a.default.BAM_FUNMAP&&(n.flags|=a.default.BAM_FMUNMAP),n.flags&a.default.BAM_FREVERSE&&(i.flags|=a.default.BAM_FMREVERSE),i.flags&a.default.BAM_FREVERSE&&(n.flags|=a.default.BAM_FMREVERSE),void 0===i.templateLength&&(r?function(e,t,i){const n=function t(i){const n=[i];if(void 0!==i.mateRecordNumber&&i.mateRecordNumber>=0){const r=e[i.mateRecordNumber];if(!r)throw new s.CramMalformedError(\"intra-slice mate record not found, this file seems malformed\");n.push(...t(r))}return n}(i),r=n.map((e=>e.alignmentStart)),o=n.map((e=>e.alignmentStart+e.readLength-1)),a=Math.max(...o)-Math.min(...r)+1;a>=0&&n.forEach((e=>{if(void 0!==e.templateLength)throw new s.CramMalformedError(\"mate pair group has some members that have template lengths already, this file seems malformed\");e.templateLength=a}))}(e,0,i):function(e,t){const i=Math.min(e.alignmentStart,t.alignmentStart),n=Math.max(e.alignmentStart+e.readLength-1,t.alignmentStart+t.readLength-1)-i+1;e.templateLength=n,t.templateLength=n}(i,n)),i.mateRecordNumber=void 0}class f{constructor(e,t,i){this.container=e,this.containerPosition=t,this.sliceSize=i,this.file=e.file}getHeader(){return n(this,void 0,void 0,(function*(){const{majorVersion:e}=yield this.file.getDefinition(),t=(0,h.getSectionParsers)(e),i=yield this.container.getHeader();if(!i)throw new Error(\"no container header detected\");const n=yield this.file.readBlock(i._endPosition+this.containerPosition);if(void 0===n)throw new Error(\"block header undefined\");if(\"MAPPED_SLICE_HEADER\"===n.contentType){const e=(0,o.parseItem)(n.content,t.cramMappedSliceHeader.parser,0,i._endPosition);return Object.assign(Object.assign({},n),{parsedContent:e})}if(\"UNMAPPED_SLICE_HEADER\"===n.contentType){const e=(0,o.parseItem)(n.content,t.cramUnmappedSliceHeader.parser,0,i._endPosition);return Object.assign(Object.assign({},n),{parsedContent:e})}throw new s.CramMalformedError(`error reading slice header block, invalid content type ${n.contentType}`)}))}getBlocks(){return n(this,void 0,void 0,(function*(){const e=yield this.getHeader();let t=e._endPosition;const i=new Array(e.parsedContent.numBlocks);for(let e=0;e<i.length;e++){const n=yield this.file.readBlock(t);if(void 0===n)throw new Error(\"block undefined\");i[e]=n,t=i[e]._endPosition}return i}))}getCoreDataBlock(){return n(this,void 0,void 0,(function*(){return(yield this.getBlocks())[0]}))}_getBlocksContentIdIndex(){return n(this,void 0,void 0,(function*(){const e=yield this.getBlocks(),t={};return e.forEach((e=>{\"EXTERNAL_DATA\"===e.contentType&&(t[e.contentId]=e)})),t}))}getBlockByContentId(e){return n(this,void 0,void 0,(function*(){return(yield this._getBlocksContentIdIndex())[e]}))}getReferenceRegion(){return n(this,void 0,void 0,(function*(){const e=(yield this.getHeader()).parsedContent;if(!(0,h.isMappedSliceHeader)(e))throw new Error(\"slice header not mapped\");if(e.refSeqId<0)return;const t=yield this.container.getCompressionScheme();if(void 0===t)throw new Error(\"compression scheme undefined\");if(e.refBaseBlockId>=0){const t=yield this.getBlockByContentId(e.refBaseBlockId);if(!t)throw new s.CramMalformedError(\"embedded reference specified, but reference block does not exist\");return{seq:t.data.toString(\"utf8\"),start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan}}if(t.referenceRequired||this.file.fetchReferenceSequenceCallback){if(!this.file.fetchReferenceSequenceCallback)throw new Error(\"reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence\");const t=yield this.file.fetchReferenceSequenceCallback(e.refSeqId,e.refSeqStart,e.refSeqStart+e.refSeqSpan-1);if(t.length!==e.refSeqSpan)throw new s.CramArgumentError(\"seqFetch callback returned a reference sequence of the wrong length\");return{seq:t,start:e.refSeqStart,end:e.refSeqStart+e.refSeqSpan-1,span:e.refSeqSpan}}}))}getAllRecords(){return this.getRecords((()=>!0))}_fetchRecords(){return n(this,void 0,void 0,(function*(){var e,t;const{majorVersion:i}=yield this.file.getDefinition(),n=yield this.container.getCompressionScheme();if(void 0===n)throw new Error(\"compression scheme undefined\");const r=yield this.getHeader(),a=yield this._getBlocksContentIdIndex();if(i>1&&this.file.options.checkSequenceMD5&&(0,h.isMappedSliceHeader)(r.parsedContent)&&r.parsedContent.refSeqId>=0&&\"0000000000000000\"!==(null===(e=r.parsedContent.md5)||void 0===e?void 0:e.join(\"\"))){const e=yield this.getReferenceRegion();if(e){const{seq:i,start:n,end:a}=e,c=(0,o.sequenceMD5)(i),l=null===(t=r.parsedContent.md5)||void 0===t?void 0:t.map((e=>(e<16?\"0\":\"\")+e.toString(16))).join(\"\");if(c!==l)throw new s.CramMalformedError(`MD5 checksum reference mismatch for ref ${r.parsedContent.refSeqId} pos ${n}..${a}. recorded MD5: ${l}, calculated MD5: ${c}`)}}const f=yield this.getCoreDataBlock(),p={lastAlignmentStart:(0,h.isMappedSliceHeader)(r.parsedContent)?r.parsedContent.refSeqStart:0,coreBlock:{bitPosition:7,bytePosition:0},externalBlocks:{map:new Map,getCursor(e){let t=this.map.get(e);return void 0===t&&(t={bitPosition:7,bytePosition:0},this.map.set(e,t)),t}}},g=e=>{const t=n.getCodecForDataSeries(e);if(!t)throw new s.CramMalformedError(`no codec defined for ${e} data series`);return t.decode(this,f,a,p)},m=new Array(r.parsedContent.numRecords);for(let t=0;t<m.length;t+=1)try{const e=(0,c.default)(this,g,n,r,f,a,p,i,t);m[t]=new l.default(Object.assign(Object.assign({},e),{uniqueId:r.contentPosition+r.parsedContent.recordCounter+t+1}))}catch(e){if(e instanceof d.CramBufferOverrunError){console.warn(\"read attempted beyond end of buffer, file seems truncated.\");break}throw e}for(let e=0;e<m.length;e+=1){const{mateRecordNumber:t}=m[e];void 0!==t&&t>=0&&u(m,e,m[e],m[t])}return m}))}getRecords(e){return n(this,void 0,void 0,(function*(){const t=this.container.filePosition+this.containerPosition;let i=this.file.featureCache.get(t.toString());i||(i=this._fetchRecords(),this.file.featureCache.set(t.toString(),i));const r=(yield i).filter(e);if(r.length&&this.file.fetchReferenceSequenceCallback){const e=yield this.getHeader();if((0,h.isMappedSliceHeader)(e.parsedContent)&&(e.parsedContent.refSeqId>=0||-2===e.parsedContent.refSeqId)){const t=e.parsedContent.refSeqId>=0?e.parsedContent.refSeqId:void 0,i=yield this.container.getCompressionScheme();if(void 0===i)throw new Error(\"compression scheme undefined\");const s={};for(const e of r){const i=void 0!==t?t:e.sequenceId;let n=s[i];n||(n={id:i,start:e.alignmentStart,end:Number.NEGATIVE_INFINITY,seq:null},s[i]=n);const r=e.alignmentStart+(e.lengthOnRef||e.readLength)-1;r>n.end&&(n.end=r),e.alignmentStart<n.start&&(n.start=e.alignmentStart)}yield Promise.all(Object.values(s).map((e=>n(this,void 0,void 0,(function*(){-1!==e.id&&e.start<=e.end&&this.file.fetchReferenceSequenceCallback&&(e.seq=yield this.file.fetchReferenceSequenceCallback(e.id,e.start,e.end))})))));for(const e of r){const n=s[void 0!==t?t:e.sequenceId];if(null==n?void 0:n.seq){const t=n.seq;e.addReferenceSequence(Object.assign(Object.assign({},n),{seq:t}),i)}}}}return r}))}}t.default=f,\"getHeader getBlocks _getBlocksContentIdIndex\".split(\" \").forEach((e=>{(0,o.tinyMemoize)(f,e)}))},400:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.itf8Size=function(e){return-128&e?-16384&e?-2097152&e?-268435456&e?5:4:3:2:1},t.parseItf8=function(e,t){let i=t;const n=e[i];let r;if(n<128?(r=n,i+=1):n<192?(r=16383&(n<<8|e[i+1]),i+=2):n<224?(r=2097151&(n<<16|e[i+1]<<8|e[i+2]),i+=3):n<240?(r=268435455&(n<<24|e[i+1]<<16|e[i+2]<<8|e[i+3]),i+=4):(r=(15&n)<<28|e[i+1]<<20|e[i+2]<<12|e[i+3]<<4|15&e[i+4],i+=5),i>e.length)throw new o.CramBufferOverrunError(\"Attempted to read beyond end of buffer; this file seems truncated.\");return[r,i-t]},t.parseLtf8=function(e,t){let i=t;const n=e[i];let r;if(n<128)r=n,i+=1;else if(n<192)r=16383&(e[i]<<8|e[i+1]),i+=2;else if(n<224)r=2097151&(e[i]<<16|e[i+1]<<8|e[i+2]),r=(63&n)<<16|e.readUInt16LE(i+1),i+=3;else if(n<240)r=268435455&(e[i]<<24|e[i+1]<<16|e[i+2]<<8|e[i+3]),i+=4;else if(n<248)r=(15&e[i])*Math.pow(2,32)+(e[i+1]<<24)|e[i+2]<<16|e[i+3]<<8|e[i+4],i+=5;else if(n<252)r=((7&e[i])<<8|e[i+1])*Math.pow(2,32)+(e[i+2]<<24)|e[i+3]<<16|e[i+4]<<8|e[i+5],i+=6;else if(n<254)r=((3&e[i])<<16|e[i+1]<<8|e[i+2])*Math.pow(2,32)+(e[i+3]<<24)|e[i+4]<<16|e[i+5]<<8|e[i+6],i+=7;else if(n<255){if(r=s.default.fromBytesBE(e.slice(i+1,i+8)),r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new Error(\"integer overflow\");r=r.toNumber(),i+=8}else{if(r=s.default.fromBytesBE(e.slice(i+1,i+9)),r.greaterThan(Number.MAX_SAFE_INTEGER)||r.lessThan(Number.MIN_SAFE_INTEGER))throw new Error(\"integer overflow\");r=r.toNumber(),i+=9}return[r,i-t]},t.parseItem=function(e,t,i=0,n=0){const{offset:r,value:s}=t(e,i);return Object.assign(Object.assign({},s),{_endPosition:r+n,_size:r-i})},t.tinyMemoize=function(e,t){const i=e.prototype[t],n=`_memo_${t}`;e.prototype[t]=function(){if(!(n in this)){const e=i.call(this);this[n]=e,Promise.resolve(e).catch((()=>{delete this[n]}))}return this[n]}},t.sequenceMD5=function(e){return(0,r.default)(e.toUpperCase().replaceAll(/[^\\u0021-\\u007e]/g,\"\"))};const r=n(i(3503)),s=n(i(8570)),o=i(612)},9747:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.CramArgumentError=t.CramSizeLimitError=t.CramMalformedError=t.CramUnimplementedError=t.CramError=void 0;class i extends Error{}t.CramError=i;class n extends Error{}t.CramUnimplementedError=n,t.CramMalformedError=class extends i{},t.CramSizeLimitError=class extends i{},t.CramArgumentError=class extends i{}},7806:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.IndexedCramFile=t.CraiIndex=t.CramRecord=t.CramFile=void 0;var r=i(7390);Object.defineProperty(t,\"CramFile\",{enumerable:!0,get:function(){return n(r).default}}),Object.defineProperty(t,\"CramRecord\",{enumerable:!0,get:function(){return r.CramRecord}});var s=i(4923);Object.defineProperty(t,\"CraiIndex\",{enumerable:!0,get:function(){return n(s).default}});var o=i(6014);Object.defineProperty(t,\"IndexedCramFile\",{enumerable:!0,get:function(){return n(o).default}})},6014:function(e,t,i){var n=this&&this.__awaiter||function(e,t,i,n){return new(i||(i=Promise))((function(r,s){function o(e){try{c(n.next(e))}catch(e){s(e)}}function a(e){try{c(n.throw(e))}catch(e){s(e)}}function c(e){var t;e.done?r(e.value):(t=e.value,t instanceof i?t:new i((function(e){e(t)}))).then(o,a)}c((n=n.apply(e,t||[])).next())}))},r=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0});const s=i(9747),o=r(i(7390));t.default=class{constructor(e){var t;if(this.cram=null!==(t=e.cram)&&void 0!==t?t:new o.default({url:e.cramUrl,path:e.cramPath,filehandle:e.cramFilehandle,seqFetch:e.seqFetch,checkSequenceMD5:e.checkSequenceMD5,cacheSize:e.cacheSize}),!(this.cram instanceof o.default))throw new Error(\"invalid arguments: no cramfile\");this.index=e.index}getRecordsForRange(e,t,i){return n(this,arguments,void 0,(function*(e,t,i,n={}){if(n.viewAsPairs=n.viewAsPairs||!1,n.pairAcrossChr=n.pairAcrossChr||!1,n.maxInsertSize=n.maxInsertSize||2e5,\"string\"==typeof e)throw new s.CramUnimplementedError(\"string sequence names not yet supported\");const r=e,o=yield this.index.getEntriesForRange(r,t,i),a=n=>n.sequenceId===e&&n.alignmentStart<=i&&void 0!==n.lengthOnRef&&n.alignmentStart+n.lengthOnRef-1>=t,c=yield Promise.all(o.map((e=>this.getRecordsInSlice(e,a))));let l=Array.prototype.concat(...c);if(n.viewAsPairs){const e={},t={};for(const i of l){const n=i.readName;if(void 0===n)throw new Error(\"readName undefined\");const r=i.uniqueId;e[n]||(e[n]=0),e[n]+=1,t[r]=1}const i={};Object.entries(e).forEach((([e,t])=>{1===t&&(i[e]=!0)}));const s=[];for(const e of l){const t=e.readName;if(void 0===t)throw new Error(\"readName undefined\");if(i[t]&&e.mate&&(e.mate.sequenceId===r||n.pairAcrossChr)&&Math.abs(e.alignmentStart-e.mate.alignmentStart)<n.maxInsertSize){const t=this.index.getEntriesForRange(e.mate.sequenceId,e.mate.alignmentStart,e.mate.alignmentStart+1);s.push(t)}}const o=yield Promise.all(s);let a=[];for(const e of o)a.push(...e);a=a.sort(((e,t)=>e.toString().localeCompare(t.toString()))).filter(((e,t,i)=>!t||e.toString()!==i[t-1].toString()));const c=[];for(const e of a){let n=this.cram.featureCache.get(e.toString());n||(n=this.getRecordsInSlice(e,(()=>!0)),this.cram.featureCache.set(e.toString(),n));const r=n.then((e=>{const n=[];for(const r of e){if(void 0===r.readName)throw new Error(\"readName undefined\");i[r.readName]&&!t[r.uniqueId]&&n.push(r)}return n}));c.push(r)}const h=yield Promise.all(c);if(h.length){const e=h.reduce(((e,t)=>e.concat(t)));l=l.concat(e)}}return l}))}getRecordsInSlice({containerStart:e,sliceStart:t,sliceBytes:i},n){return this.cram.getContainerAtPosition(e).getSlice(t,i).getRecords(n)}hasDataForReferenceSequence(e){return this.index.hasDataForReferenceSequence(e)}}},5931:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.RemoteFile=t.LocalFile=void 0,t.open=function(e,t,i){if(i)return i;if(e)return new n.RemoteFile(e);if(t)return new n.LocalFile(t);throw new Error(\"no url, path, or filehandle provided, cannot open\")};const n=i(1113);var r=i(1113);Object.defineProperty(t,\"LocalFile\",{enumerable:!0,get:function(){return r.LocalFile}}),Object.defineProperty(t,\"RemoteFile\",{enumerable:!0,get:function(){return r.RemoteFile}})},6476:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.RANS_BYTE_L=t.TOTFREQ=t.TF_SHIFT=void 0,t.TF_SHIFT=12,t.TOTFREQ=4096,t.RANS_BYTE_L=1<<23},997:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,n){let a=e.getInt(),c=e.getInt(),l=e.getInt(),h=e.getInt();const d=n.remaining(),u=-4&d;for(let r=0;r<u;r+=4){const d=t.R[o.default.get(a,s.TF_SHIFT)],u=t.R[o.default.get(c,s.TF_SHIFT)],f=t.R[o.default.get(l,s.TF_SHIFT)],p=t.R[o.default.get(h,s.TF_SHIFT)];n.putAt(r,d),n.putAt(r+1,u),n.putAt(r+2,f),n.putAt(r+3,p),a=o.default.advanceSymbolStep(a,i[255&d],s.TF_SHIFT),c=o.default.advanceSymbolStep(c,i[255&u],s.TF_SHIFT),l=o.default.advanceSymbolStep(l,i[255&f],s.TF_SHIFT),h=o.default.advanceSymbolStep(h,i[255&p],s.TF_SHIFT),a=o.default.renormalize(a,e),c=o.default.renormalize(c,e),l=o.default.renormalize(l,e),h=o.default.renormalize(h,e)}let f;switch(n.setPosition(u),3&d){case 0:break;case 1:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f);break;case 2:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(c,s.TF_SHIFT)],o.default.advanceSymbol(c,e,i[255&f],s.TF_SHIFT),n.put(f);break;case 3:f=t.R[o.default.get(a,s.TF_SHIFT)],o.default.advanceSymbol(a,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(c,s.TF_SHIFT)],o.default.advanceSymbol(c,e,i[255&f],s.TF_SHIFT),n.put(f),f=t.R[o.default.get(l,s.TF_SHIFT)],o.default.advanceSymbol(l,e,i[255&f],s.TF_SHIFT),n.put(f);break;default:throw new r.CramMalformedError(\"invalid output size encountered during rANS decoding\")}n.setPosition(0)};const r=i(9747),s=i(6476),o=n(i(488))},7960:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i,n){const o=t.remaining();let a=e.getInt(),c=e.getInt(),l=e.getInt(),h=e.getInt();const d=o>>2;let u=0,f=d,p=2*d,g=3*d,m=0,w=0,b=0,F=0;for(;u<d;u+=1,f+=1,p+=1,g+=1){const o=255&i[m].R[s.default.get(a,r.TF_SHIFT)],d=255&i[w].R[s.default.get(c,r.TF_SHIFT)],v=255&i[b].R[s.default.get(l,r.TF_SHIFT)],y=255&i[F].R[s.default.get(h,r.TF_SHIFT)];t.putAt(u,o),t.putAt(f,d),t.putAt(p,v),t.putAt(g,y),a=s.default.advanceSymbolStep(a,n[m][o],r.TF_SHIFT),c=s.default.advanceSymbolStep(c,n[w][d],r.TF_SHIFT),l=s.default.advanceSymbolStep(l,n[b][v],r.TF_SHIFT),h=s.default.advanceSymbolStep(h,n[F][y],r.TF_SHIFT),a=s.default.renormalize(a,e),c=s.default.renormalize(c,e),l=s.default.renormalize(l,e),h=s.default.renormalize(h,e),m=o,w=d,b=v,F=y}for(;g<o;g+=1){const o=255&i[F].R[s.default.get(h,r.TF_SHIFT)];t.putAt(g,o),h=s.default.advanceSymbol(h,e,n[F][o],r.TF_SHIFT),F=o}};const r=i(6476),s=n(i(488))},488:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0});const n=i(9747),r=i(6476);class s{constructor(){this.F=void 0,this.C=void 0}}function o(e,t,i,n){return i*(e>>n)+(e&(1<<n)-1)-t}t.default={FC:s,AriDecoder:class{constructor(){this.fc=new Array(256);for(let e=0;e<this.fc.length;e+=1)this.fc[e]=new s;this.R=null}},DecodingSymbol:class{constructor(){this.start=void 0,this.freq=void 0}},symbolInit:function(e,t,i){if(!(t<=65536))throw new n.CramMalformedError(\"assertion failed: start <= 1<<16\");if(!(i<=65536-t))throw new n.CramMalformedError(\"assertion failed: freq <= 1<<16\");e.start=t,e.freq=i},advanceStep:o,advanceSymbolStep:function(e,t,i){return o(e,t.start,t.freq,i)},get:function(e,t){return e&(1<<t)-1},advanceSymbol:function(e,t,i,n){return function(e,t,i,n,s){if((e=n*(e>>s)+(e&(1<<s)-1)-i)<r.RANS_BYTE_L)do{e=e<<8|255&t.get()}while(e<r.RANS_BYTE_L);return e}(e,t,i.start,i.freq,n)},renormalize:function(e,t){if(e<r.RANS_BYTE_L)do{e=e<<8|255&t.get()}while(e<r.RANS_BYTE_L);return e}}},1971:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.readStatsO0=function(e,t,i){let n=0,r=0,c=255&e.get();do{null==t.fc[c]&&(t.fc[c]=new o.default.FC),t.fc[c].F=255&e.get(),t.fc[c].F>=128&&(t.fc[c].F&=-129,t.fc[c].F=(127&t.fc[c].F)<<8|255&e.get()),t.fc[c].C=r,o.default.symbolInit(i[c],t.fc[c].C,t.fc[c].F),t.R||(t.R=new Array(s.TOTFREQ)),t.R.fill(c,r,r+t.fc[c].F),r+=t.fc[c].F,0===n&&c+1===(255&e.getByteAt(e.position()))?(c=255&e.get(),n=255&e.get()):0!==n?(n-=1,c+=1):c=255&e.get()}while(0!==c);a(r<s.TOTFREQ)},t.readStatsO1=function(e,t,i){let n=0,r=255&e.get();do{let c=0,l=0,h=255&e.get();null==t[r]&&(t[r]=new o.default.AriDecoder);do{null==t[r].fc[h]&&(t[r].fc[h]=new o.default.FC),t[r].fc[h].F=255&e.get(),t[r].fc[h].F>=128&&(t[r].fc[h].F&=-129,t[r].fc[h].F=(127&t[r].fc[h].F)<<8|255&e.get()),t[r].fc[h].C=l,0===t[r].fc[h].F&&(t[r].fc[h].F=s.TOTFREQ),null==i[r][h]&&(i[r][h]=new o.default.RansDecSymbol),o.default.symbolInit(i[r][h],t[r].fc[h].C,t[r].fc[h].F),null==t[r].R&&(t[r].R=new Array(s.TOTFREQ)),t[r].R.fill(h,l,l+t[r].fc[h].F),l+=t[r].fc[h].F,a(l<=s.TOTFREQ),0===c&&h+1===(255&e.getByteAt(e.position()))?(h=255&e.get(),c=255&e.get()):0!==c?(c-=1,h+=1):h=255&e.get()}while(0!==h);0===n&&r+1===(255&e.getByteAt(e.position()))?(r=255&e.get(),n=255&e.get()):0!==n?(n-=1,r+=1):r=255&e.get()}while(0!==r)};const r=i(9747),s=i(6476),o=n(i(488));function a(e){if(!e)throw new r.CramMalformedError(\"assertion failed\")}},9989:function(e,t,i){var n=this&&this.__importDefault||function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(t,\"__esModule\",{value:!0}),t.default=function(e,t,i=0){if(0===e.length)return t.fill(0),t;const n=new d(e,i),u=n.get();if(0!==u&&1!==u)throw new s.CramMalformedError(`Invalid rANS order ${u}`);if(n.getInt()!==n.remaining()-h)throw new s.CramMalformedError(\"Incorrect input length.\");const f=n.getInt(),p=new d(t||r.Buffer.allocUnsafe(f));if(p.length<f)throw new s.CramMalformedError(`Output buffer too small to fit ${f} bytes.`);switch(u){case 0:return function(e,t){const i=new o.default.AriDecoder,n=new Array(256);for(let e=0;e<n.length;e+=1)n[e]=new o.default.DecodingSymbol;return(0,a.readStatsO0)(e,i,n),(0,c.default)(e,i,n,t),t}(n,p);case 1:return function(e,t){const i=new Array(256);for(let e=0;e<i.length;e+=1)i[e]=new o.default.AriDecoder;const n=new Array(256);for(let e=0;e<n.length;e+=1){n[e]=new Array(256);for(let t=0;t<n[e].length;t+=1)n[e][t]=new o.default.DecodingSymbol}return(0,a.readStatsO1)(e,i,n),(0,l.default)(e,t,i,n),t}(n,p);default:throw new s.CramMalformedError(`Invalid rANS order: ${u}`)}};const r=i(8287),s=i(9747),o=n(i(488)),a=i(1971),c=n(i(997)),l=n(i(7960)),h=4;class d{constructor(e,t=0){this._buffer=e,this._position=t,this.length=e.length}get(){const e=this._buffer[this._position];return this._position+=1,e}getByte(){return this.get()}getByteAt(e){return this._buffer[e]}position(){return this._position}put(e){return this._buffer[this._position]=e,this._position+=1,e}putAt(e,t){return this._buffer[e]=t,t}setPosition(e){return this._position=e,e}getInt(){const e=this._buffer.readInt32LE(this._position);return this._position+=4,e}remaining(){return this._buffer.length-this._position}}},5417:(e,t)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.parseHeaderText=function(e){const t=e.split(/\\r?\\n/),i=[];for(const e of t){const[t,...n]=e.split(/\\t/);t&&i.push({tag:t.slice(1),data:n.map((e=>{const t=e.indexOf(\":\");return-1!==t?{tag:e.slice(0,t),value:e.slice(t+1)}:{tag:e,value:\"\"}}))})}return i}},8712:(e,t,i)=>{Object.defineProperty(t,\"__esModule\",{value:!0}),t.unzip=function(e){return r.Buffer.from((0,n.inflate)(e))};const n=i(1668),r=i(8287)},635:(e,t,i)=>{var n=i(8287).Buffer;const r=i(4646),s=i(8706),o=i(9614),a=i(235),c=128;e.exports=class{decode(e){return this.stream=new s(e),this.decodeStream(this.stream)}decodeStream(e,t=0){var i=this.stream.ReadByte();16&i||(t=this.stream.ReadUint7());var n,r=t,s=1&i;if(8&i)return this.decodeStripe(this.stream,t);if(i&c&&([n,r]=this.decodePackMeta(this.stream)),32&i)var o=this.decodeCat(this.stream,r);else o=4&i?this.decodeExt(this.stream,r):64&i?s?this.decodeRLE1(this.stream,r):this.decodeRLE0(this.stream,r):s?this.decode1(this.stream,r):this.decode0(this.stream,r);return i&c&&(o=this.decodePack(o,n,t)),o}encode(e,t){if(this.stream=new s(\"\",0,1.1*e.length+100),this.stream.WriteByte(t),16&t||this.stream.WriteUint7(e.length),8&t)return n.concat([this.stream.buf.slice(0,this.stream.pos),this.encodeStripe(this.stream,e,t>>8)]);var i,r=1&t,o=e.length;return t&c&&([i,e,o]=this.encodePack(e)),t&c&&this.stream.WriteStream(i),64&t?r?this.encodeRLE1(e,o,this.stream):this.encodeRLE0(e,o,this.stream):r?this.encode1(e,o,this.stream):this.encode0(e,o,this.stream)}decode0(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);var a=new o(s),c=new r(e);c.RangeStartDecode(e);for(var l=0;l<t;l++)i[l]=a.ModelDecode(e,c);return i}encode0(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new o(n);i.WriteByte(n);var c=new r(i);for(s=0;s<t;s++)a.ModelEncode(i,c,e[s]);return c.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decode1(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new Array(s),c=0;c<s;c++)a[c]=new o(s);var l=new r(e);l.RangeStartDecode(e);var h=0;for(c=0;c<t;c++)i[c]=a[h].ModelDecode(e,l),h=i[c];return i}encode1(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new Array(n);for(s=0;s<n;s++)a[s]=new o(n);i.WriteByte(n);var c=new r(i),l=0;for(s=0;s<t;s++)a[l].ModelEncode(i,c,e[s]),l=e[s];return c.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeExt(e,t){var i=new n.allocUnsafe(t),r=a.array(e.buf.slice(e.pos)),s=a.header(r),o=0;do{var c=a.decompress(r,s);-1!=c&&(n.from(c).copy(i,o),o+=c.length,s-=c.length)}while(-1!=c);return i}encodeExt(e,t){}decodeRLE0(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new o(s),c=new Array(258),l=0;l<=257;l++)c[l]=new o(4);var h=new r(e);for(h.RangeStartDecode(e),l=0;l<t;){i[l]=a.ModelDecode(e,h);for(var d=c[i[l]].ModelDecode(e,h),u=d,f=256;3==d;)d=c[f].ModelDecode(e,h),f=257,u+=d;for(var p=1;p<=u;p++)i[l+p]=i[l];l+=u+1}return i}encodeRLE0(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new o(n),c=new Array(258);for(s=0;s<=257;s++)c[s]=new o(4);i.WriteByte(n);var l=new r(i);for(s=0;s<t;){a.ModelEncode(i,l,e[s]);for(var h=1;s+h<t&&e[s+h]==e[s];)h++;h--;var d=e[s];e[s],s+=h+1;var u=h>=3?3:h;for(c[d].ModelEncode(i,l,u),h-=u,d=256;3==u;)u=h>=3?3:h,c[d].ModelEncode(i,l,u),d=257,h-=u}return l.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodeRLE1(e,t){var i=new n.allocUnsafe(t),s=e.ReadByte();0==s&&(s=256);for(var a=new Array(s),c=0;c<s;c++)a[c]=new o(s);var l=new Array(258);for(c=0;c<=257;c++)l[c]=new o(4);var h=new r(e);h.RangeStartDecode(e);var d=0;for(c=0;c<t;){i[c]=a[d].ModelDecode(e,h),d=i[c];for(var u=l[i[c]].ModelDecode(e,h),f=u,p=256;3==u;)u=l[p].ModelDecode(e,h),p=257,f+=u;for(var g=1;g<=f;g++)i[c+g]=i[c];c+=f+1}return i}encodeRLE1(e,t,i){for(var n=0,s=0;s<t;s++)n<e[s]&&(n=e[s]);n++;var a=new Array(n);for(s=0;s<n;s++)a[s]=new o(n);var c=new Array(258);for(s=0;s<=257;s++)c[s]=new o(4);i.WriteByte(n);for(var l=new r(i),h=(s=0,0);s<t;){a[h].ModelEncode(i,l,e[s]);for(var d=1;s+d<t&&e[s+d]==e[s];)d++;d--;var u=e[s];h=e[s],s+=d+1;var f=d>=3?3:d;for(c[u].ModelEncode(i,l,f),d-=f,u=256;3==f;)f=d>=3?3:d,c[u].ModelEncode(i,l,f),u=257,d-=f}return l.RangeFinishEncode(i),i.buf.slice(0,i.pos)}decodePackMeta(e){this.nsym=e.ReadByte();for(var t=new Array(this.nsym),i=0;i<this.nsym;i++)t[i]=e.ReadByte();return[t,e.ReadUint7()]}decodePack(e,t,i){var r=new n.allocUnsafe(i);if(this.nsym<=1)for(var s=0;s<i;s++)r[s]=t[0];else if(this.nsym<=2){s=0;for(var o=0;s<i;s++){if(s%8==0)var a=e[o++];r[s]=t[1&a],a>>=1}}else if(this.nsym<=4)for(s=0,o=0;s<i;s++)s%4==0&&(a=e[o++]),r[s]=t[3&a],a>>=2;else{if(!(this.nsym<=16))return e;for(s=0,o=0;s<i;s++)s%2==0&&(a=e[o++]),r[s]=t[15&a],a>>=4}return r}packMeta(e){for(var t=new s(\"\",0,1024),i=new Array(256),n=0;n<e.length;n++)i[e[n]]=1;var r=0;for(n=0;n<256;n++)i[n]&&(i[n]=++r);for(t.WriteByte(r),n=0;n<256;n++)i[n]&&(t.WriteByte(n),i[n]--);return[t,i,r]}encodePack(e){var t,i,r;[t,i,r]=this.packMeta(e);var s=e.length,o=0;if(r<=1)return t.WriteUint7(0),[t,new n.allocUnsafe(0),0];if(r<=2){for(var a=new n.allocUnsafe(Math.floor((s+7)/8)),c=(o=0,0);o<(-8&s);o+=8,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<1)+(i[e[o+2]]<<2)+(i[e[o+3]]<<3)+(i[e[o+4]]<<4)+(i[e[o+5]]<<5)+(i[e[o+6]]<<6)+(i[e[o+7]]<<7);if(o<s){a[c]=0;for(var l=0;o<s;)a[c]|=i[e[o++]]<<l,l++;c++}return t.WriteUint7(c),[t,a,a.length]}if(r<=4){for(a=new n.allocUnsafe(Math.floor((s+3)/4)),o=0,c=0;o<(-4&s);o+=4,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<2)+(i[e[o+2]]<<4)+(i[e[o+3]]<<6);if(o<s){for(a[c]=0,l=0;o<s;)a[c]|=i[e[o++]]<<l,l+=2;c++}return t.WriteUint7(c),[t,a,a.length]}if(r<=16){for(a=new n.allocUnsafe(Math.floor((s+1)/2)),o=0,c=0;o<(-2&s);o+=2,c++)a[c]=(0|i[e[o+0]])+(i[e[o+1]]<<4);return o<s&&(a[c++]=i[e[o++]]),t.WriteUint7(c),[t,a,a.length]}return t.WriteUint7(e.length),[t,e,e.length]}encodeStripe(e,t,i){0==i&&(i=4);for(var n=new Array(i),r=new Array(i),o=0;o<i;o++)r[o]=Math.floor(t.length/i)+(t.length%i>o),n[o]=new Array(r[o]);for(var a=0,c=0;c<t.length;c+=i,a++)for(var l=0;l<i;l++)a<n[l].length&&(n[l][a]=t[c+l]);var h=new Array(i),d=0;for(o=0;o<i;o++){var u=this.encode(n[o],0),f=this.encode(n[o],1);h[o]=f.length<u.length?f:u,d+=h[o].length}var p=new s(\"\",0,d+5*i+1);for(p.WriteByte(i),o=0;o<i;o++)p.WriteUint7(h[o].length);for(o=0;o<i;o++)p.WriteData(h[o],h[o].length);return p.buf.slice(0,p.buf.pos)}decodeStripe(e,t){for(var i=e.ReadByte(),r=new Array(i),s=new Array(i),o=0;o<i;o++)r[o]=e.ReadUint7();var a=new Array(i);for(o=0;o<i;o++)s[o]=Math.floor(t/i)+(t%i>o),a[o]=this.decodeStream(e,s[o]);var c=new n.allocUnsafe(t);for(o=0;o<i;o++)for(var l=0;l<s[o];l++)c[l*i+o]=a[o][l];return c}decodeCat(e,t){for(var i=new n.allocUnsafe(t),r=0;r<t;r++)i[r]=e.ReadByte();return i}}},4646:e=>{e.exports=class{constructor(e){this.low=0,this.range=4294967295,this.code=0,this.FFnum=0,this.carry=0,this.cache=0}RangeStartDecode(e){for(var t=0;t<5;t++)this.code=(this.code<<8)+e.ReadByte();this.code&=4294967295,this.code>>>=0}RangeGetFrequency(e){return this.range=Math.floor(this.range/e),Math.floor(this.code/this.range)}RangeDecode(e,t,i,n){for(this.code-=t*this.range,this.range*=i;this.range<1<<24;)this.range*=256,this.code=256*this.code+e.ReadByte()}RangeShiftLow(e){if(this.low<4278190080|this.carry){for(e.WriteByte(this.cache+this.carry);this.FFnum;)e.WriteByte(this.carry-1),this.FFnum--;this.cache=this.low>>>24,this.carry=0}else this.FFnum++;this.low<<=8,this.low>>>=0}RangeEncode(e,t,i,n){var r=this.low;for(this.range=Math.floor(this.range/n),this.low+=t*this.range,this.low>>>=0,this.range*=i,this.low<r&&(0!=this.carry&&console.log(\"ERROR: Multiple carry\"),this.carry=1);this.range<1<<24;)this.range*=256,this.RangeShiftLow(e)}RangeFinishEncode(e){for(var t=0;t<5;t++)this.RangeShiftLow(e)}}},9614:e=>{e.exports=class{constructor(e=256){this.total_freq=e,this.max_sym=e-1,this.S=new Array,this.F=new Array;for(var t=0;t<=this.max_sym;t++)this.S[t]=t,this.F[t]=1}ModelDecode(e,t){for(var i=t.RangeGetFrequency(this.total_freq),n=0,r=0;n+this.F[r]<=i;)n+=this.F[r++];t.RangeDecode(e,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise();var s=this.S[r];if(r>0&&this.F[r]>this.F[r-1]){var o=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=o,o=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=o}return s}ModelRenormalise(){this.total_freq=0;for(var e=0;e<=this.max_sym;e++)this.F[e]-=Math.floor(this.F[e]/2),this.total_freq+=this.F[e]}ModelEncode(e,t,i){for(var n=0,r=0;this.S[r]!=i;r++)n+=this.F[r];if(t.RangeEncode(e,n,this.F[r],this.total_freq),this.F[r]+=16,this.total_freq+=16,this.total_freq>65519&&this.ModelRenormalise(),i=this.S[r],r>0&&this.F[r]>this.F[r-1]){var s=this.F[r];this.F[r]=this.F[r-1],this.F[r-1]=s,s=this.S[r],this.S[r]=this.S[r-1],this.S[r-1]=s}}}},6038:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706),s=i(9614),o=i(4646);function a(e,t,i){for(var n=0,r=0,s=-1,o=new Array(1024);r<i;){var a=e.ReadByte();if(o[n++]=a,r+=a,a==s){var c=e.ReadByte();for(r+=a*c;c--;)o[n++]=a}s=a}var l=0;for(n=0,r=0;r<i;){var h=0;do{var d=o[n++];h+=d}while(255==d);for(;h--;)t[r++]=l;l++}}function c(e,t,i){var n=e.context;return t.qctx=(t.qctx<<e.qshift)+e.qtab[i],n+=(t.qctx&(1<<e.qbits)-1)<<e.qloc,e.do_pos&&(n+=e.ptab[Math.min(t.p,1023)]<<e.ploc),e.do_delta&&(n+=e.dtab[Math.min(t.delta,255)]<<e.dloc,t.delta+=t.prevq!=i?1:0,t.prevq=i),e.do_sel&&(n+=t.s<<e.sloc),t.p--,65535&n}function l(e){var t={};t.context=e.ReadUint16(),t.pflags=e.ReadByte(),t.do_dedup=2&t.pflags,t.fixed_len=4&t.pflags,t.do_sel=8&t.pflags,t.do_qmap=16&t.pflags,t.do_pos=32&t.pflags,t.do_delta=64&t.pflags,t.do_qtab=128&t.pflags,t.max_sym=e.ReadByte();var i=e.ReadByte();if(t.qbits=i>>4,t.qshift=15&i,i=e.ReadByte(),t.qloc=i>>4,t.sloc=15&i,i=e.ReadByte(),t.ploc=i>>4,t.dloc=15&i,t.qmap=new Array(256),16&t.pflags)for(var n=0;n<t.max_sym;n++)t.qmap[n]=e.ReadByte();else for(n=0;n<256;n++)t.qmap[n]=n;if(t.qtab=new Array(1024),t.qbits>0&&128&t.pflags)a(e,t.qtab,256);else for(n=0;n<256;n++)t.qtab[n]=n;return t.ptab=new Array(1024),32&t.pflags&&a(e,t.ptab,1024),t.dtab=new Array(256),64&t.pflags&&a(e,t.dtab,256),t}function h(e,t,i,n,r,s){i.max_sel>0?r.s=n.sel.ModelDecode(e,t):r.s=0,r.x=i.stab[r.s];var o=i.params[r.x];if(o.fixed_len>=0){var a=n.len[0].ModelDecode(e,t);a|=n.len[1].ModelDecode(e,t)<<8,a|=n.len[2].ModelDecode(e,t)<<16,a|=n.len[3].ModelDecode(e,t)<<24,o.fixed_len>0&&(o.fixed_len=-a)}else a=-o.fixed_len;r.len=a,i.do_rev&&(s[r.rec]=n.rev.ModelDecode(e,t)),r.is_dup=0,2&o.pflags&&n.dup.ModelDecode(e,t)&&(r.is_dup=1),r.p=a,r.delta=0,r.qctx=0,r.prevq=0,r.rec++}function d(e,t,i){for(var n=0,r=0,s=new Array(2*i),o=0;n<i;){for(var a=n;n<i&&t[n]==r;)n++;var c=n-a;do{var l=Math.min(255,c);s[o++]=l,c-=l}while(255==l);r++}var h=-1,d=new Array(2*i),u=0;for(n=0;n<o;){var f=s[n++];if(d[u++]=f,f==h){for(a=n;n<o&&s[n]==h&&n-a<255;)n++;d[u++]=n-a}else h=f}e.WriteData(d,u)}e.exports={decode:function(e,t){return function(e,t){var i=e.ReadUint7(),r=function(e){var t={max_sym:0};if(5==e.ReadByte()){var i=e.ReadByte(),n=1&i?e.ReadByte():1,r=i.nparam>1?i.nparam-1:0,s=new Array(256);if(2&i)r=e.ReadByte(),a(e,s,256);else{for(var o=0;o<n;o++)s[o]=o;for(;o<256;o++)s[o]=n-1}t.do_rev=4&i,t.stab=s,t.max_sel=r,t.params=new Array(t.nparam);for(var c=0;c<n;c++)t.params[c]=l(e),t.max_sym<t.params[c].max_sym&&(t.max_sym=t.params[c].max_sym);return t}console.error(\"Invalid FQZComp version number\")}(e);if(r){var d=r.params,u=new Array(t.length),f=function(e){var t={};t.qual=new Array(65536);for(var i=0;i<65536;i++)t.qual[i]=new s(e.max_sym+1);for(t.len=new Array(4),i=0;i<4;i++)t.len[i]=new s(256);return t.rev=new s(2),t.dup=new s(2),e.max_sel>0&&(t.sel=new s(e.max_sel+1)),t}(r),p=new o(e);p.RangeStartDecode(e);for(var g=new n.allocUnsafe(i),m={qctx:0,prevq:0,delta:0,p:0,s:0,x:0,len:0,is_dup:0,rec:0},w=0;w<i;){if(0==m.p){if(h(e,p,r,f,m,u),m.is_dup>0&&f.dup.ModelDecode(e,p)){for(var b=0;b<len;b++)g[w+b]=g[w+b-m.len];w+=m.len,m.p=0;continue}t.push(m.len);var F=(d=r.params[m.x]).context}var v=f.qual[F].ModelDecode(e,p);g[w++]=d.qmap[v],F=c(d,m,v)}return r.do_rev&&function(e,t,i,n){for(var r=0,s=0;s<t;){if(i[r])for(var o=0,a=n[r]-1;o<a;){var c=e[s+o];e[s+o]=e[s+a],e[s+a]=c,o++,a--}s+=n[r++]}}(g,i,u,t),g}}(new r(e),t)},encode:function(e,t,i){for(var n=new Array(2),a=new Array(2),c=new Array(2),l=new Array(2),h=new Array(256),u=0;u<2;u++)n[u]=new Array(256),a[u]=new Array(256),c[u]=new Array(1024),l[u]=new Array(256);(p=new r(\"\",0,1.1*e.length+100)).WriteUint7(e.length);var f=function(e,t,i,n){for(var r=i[0],s=0;s<i.length&&i[s]==r;s++);var o=s==i.length?1:0,a=0,c=0;for(s=0;s<256;s++)n[0][s]=0;var l=0,h=0;for(s=0;s<e.length;s++)0==h&&(h=t[l<t.length-1?l++:l]),n[0][e[s]]++,h--;for(s=0;s<256;s++)n[0][s]&&(c<s&&(c=s),a++);var d=5,u=0;return a<=16&&(u=1,d=a<=2?1:a<=4?2:a<=8?3:4),[{qbits:8+(d>4),qshift:d,qloc:7,pbits:7,pshift:t[0]>128?1:0,ploc:0,dbits:d>4?0:1,dshift:3,dloc:15,sbits:0,sloc:15,do_stab:0,context:0,max_sym:c,nsym:a,do_qmap:u,do_dedup:0,fixed_len:1==t.length?1:0,do_sel:0,do_rev:0,do_pos:1,do_delta:d<=4?1:0,do_qtab:0,qbits:8+(d>4)-(0==o),sbits:1,sloc:15-(d<=4),do_stab:1,do_sel:1}]}(e,t,i,n),p=function(e,t,i,n,r,s,o){for(var a=[0,1,1,1,2,2,2,2,2,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7],c=0;c<t.length;c++)o[c]=c;for(;c<256;c++)o[c]=t.length-1;e.WriteByte(5);var l=(t.length>1?1:0)|(t[0].do_stab?2:0);if(e.WriteByte(l),1&l&&e.WriteByte(t.length),2&l){var h=1<<t[0].sbits;h>0&&h--,e.WriteByte(h),d(e,o,256)}for(var u=0;u<t.length;u++){if(e.WriteUint16(t[u].context),e.WriteByte((t[u].do_qtab?128:0)|(t[u].do_delta?64:0)|(t[u].do_pos?32:0)|(t[u].do_qmap?16:0)|(t[u].do_sel?8:0)|(t[u].fixed_len?4:0)|(t[u].do_dedup?2:0)),t[u].do_qmap?e.WriteByte(t[u].nsym):e.WriteByte(t[u].max_sym),e.WriteByte(t[u].qbits<<4|t[u].qshift),e.WriteByte(t[u].qloc<<4|t[u].sloc),e.WriteByte(t[u].ploc<<4|t[u].dloc),t[u].do_qmap){t[u].max_sym=t[u].nsym;var f=0;for(c=0;c<256;c++)i[u][c]&&(e.WriteByte(c),i[u][c]=f++);for(;f<t[u].nsym;f++)e.WriteByte(0)}else for(c=0;c<256;c++)i[u][c]=c;if(t[u].qbits>0){for(c=0;c<256;c++)n[u][c]=c;t[u].do_qtab&&d(e,n[u],256)}if(t[u].pbits>0){for(c=0;c<1024;c++)r[u][c]=Math.min((1<<t[u].pbits)-1,c>>t[u].pshift);d(e,r[u],1024)}if(t[u].dbits>0){for(c=0;c<256;c++)a[c]>(1<<t[u].dbits)-1&&(a[c]=(1<<t[u].dbits)-1);for(c=0;c<256;c++)s[u][c]=a[Math.min(a.length-1,c>>t[u].dshift)];d(e,s[u],256)}}return e}(p,f,n,a,c,l,h);return function(e,t,i,n,r,a,c,l,h,d){var u=1<<r[0].sbits;u>0&&u--;for(var f=t.length,p=0,g=0;g<r.length;g++)p<r[g].max_sym&&(p=r[g].max_sym);for(var m=new Array(65536),w=0;w<65536;w++)m[w]=new s(p+1);var b=new Array(4);for(w=0;w<4;w++)b[w]=new s(256);new s(2),new s(2);for(var F=new s(u+1),v=new o(t),y=(g=0,w=0,0);w<f;){if(0==g){var A=n[y];r[0].sbits>0&&F.ModelEncode(e,v,A);var C=d[A],_=i[Math.min(i.length-1,y++)];r[C].fixed_len?r[C].fixed_len>0&&(b[0].ModelEncode(e,v,255&_),b[1].ModelEncode(e,v,_>>8&255),b[2].ModelEncode(e,v,_>>16&255),b[3].ModelEncode(e,v,_>>24&255),r[C].fixed_len=-1):(b[0].ModelEncode(e,v,255&_),b[1].ModelEncode(e,v,_>>8&255),b[2].ModelEncode(e,v,_>>16&255),b[3].ModelEncode(e,v,_>>24&255)),r[C].do_dedup&&process.exit(1),g=_;var x=0,k=r[C].context,I=0,S=0}var E=t[w++],N=a[C][E];m[k].ModelEncode(e,v,N),I=(I<<r[C].qshift)+c[C][N],k=r[C].context,k+=(I&(1<<r[C].qbits)-1)<<r[C].qloc,r[C].pbits>0&&(k+=l[C][Math.min(g,1023)]<<r[C].ploc),r[C].dbits>0&&(k+=h[C][Math.min(x,255)]<<r[C].dloc,x+=S!=N?1:0,S=N),r[C].do_sel&&(k+=A<<r[C].sloc),k&=65535,g--}return v.RangeFinishEncode(e),e.buf.slice(0,e.pos)}(p,e,t,i,f,n,a,c,l,h)}}},6960:(e,t,i)=>{var n=i(8287).Buffer,r=i(5460),s=i(8223),o=i(635),a=i(6038),c=i(5997);e.exports={r4x8_uncompress:function(e,t){r.decode(e).copy(t,0,0)},r4x16_uncompress:function(e,t){s.decode(e).copy(t,0,0)},arith_uncompress:function(e,t){o.decode(e).copy(t,0,0)},fqzcomp_uncompress:function(e,t){var i=new Array;a.decode(e,i).copy(t,0,0)},tok3_uncompress:function(e,t){var i=c.decode(e,0,\"\\0\");n.from(i,\"binary\").copy(t,0,0)}}},8706:(e,t,i)=>{var n=i(8287).Buffer;e.exports=class{constructor(e,t=0,i=0){0!=i?(this.buf=n.allocUnsafe(i),this.length=i):(this.buf=e,this.length=e.length),this.pos=t}EOF(){return this.pos>=this.length}ReadData(e){var t=this.buf.slice(this.pos,this.pos+e);return this.pos+=e,t}ReadByte(){const e=this.buf[this.pos];return this.pos++,e}ReadChar(){const e=this.buf[this.pos];return this.pos++,String.fromCharCode(e)}ReadUint16(){return this.ReadByte()|this.ReadByte()<<8}ReadUint32(){const e=this.buf.readInt32LE(this.pos);return this.pos+=4,e}ReadString(){var e=\"\";do{var t=this.buf[this.pos++];t&&(e+=String.fromCharCode(t))}while(t);return e}ReadUint7(){var e=0;do{var t=this.ReadByte();e=e<<7|127&t}while(128&t);return e}ReadITF8(){var e=this.buf[this.pos];return this.pos++,e>=240?(e=(15&e)<<28,e+=(this.buf[this.pos+0]<<20)+(this.buf[this.pos+1]<<12)+(this.buf[this.pos+2]<<4)+(this.buf[this.pos+3]>>4),this.pos+=4):e>=224?(e=(15&e)<<24,e+=(this.buf[this.pos+0]<<16)+(this.buf[this.pos+1]<<8)+(0|this.buf[this.pos+2]),this.pos+=3):e>=192?(e=(31&e)<<16,e+=(this.buf[this.pos+0]<<8)+(0|this.buf[this.pos+1]),this.pos+=2):e>=128&&(e=(63&e)<<8,e+=this.buf[this.pos],this.pos++),e}WriteByte(e){this.buf[this.pos++]=e}WriteChar(e){this.buf[this.pos++]=e.charCodeAt(0)}WriteString(e){for(var t=0;t<e.length;t++)this.buf[this.pos++]=e.charCodeAt(t);this.buf[this.pos++]=0}WriteData(e,t){for(var i=0;i<t;i++)this.buf[this.pos++]=e[i]}WriteStream(e){this.WriteData(e.buf,e.pos)}WriteUint16(e){this.WriteByte(255&e),this.WriteByte(e>>8&255)}WriteUint32(e){this.buf.writeInt32LE(e,this.pos),this.pos+=4}WriteUint7(e){var t=0,i=e;do{t+=7,i>>=7}while(i>0);do{t-=7,this.WriteByte((e>>t&127)+((t>0)<<7))}while(t>0)}WriteITF8(e){e<0&&(e=1+e),e<=127?this.buf[this.pos++]=e:e<=16383?(this.buf[this.pos++]=128|Math.floor(e/256),this.buf[this.pos++]=255&e):e<131071?(this.buf[this.pos++]=192|Math.floor(e/65536),this.buf[this.pos++]=255&Math.floor(e/256),this.buf[this.pos++]=255&e):e<268435455?(this.buf[this.pos++]=224|Math.floor(e/16777216),this.buf[this.pos++]=255&Math.floor(e/65536),this.buf[this.pos++]=255&Math.floor(e/256),this.buf[this.pos++]=255&e):(this.buf[this.pos++]=240|Math.floor(e/268435456),this.buf[this.pos++]=255&Math.floor(e/1048576),this.buf[this.pos++]=255&Math.floor(e/4096),this.buf[this.pos++]=255&Math.floor(e/4),this.buf[this.pos++]=15&e)}WriteByteNeg(e){this.buf[--this.pos]=e}}},5460:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706);function s(e){return 4095&e}function o(e,t){for(var i=0;t>=e[i+1];)i++;return i}function a(e){for(var t=new 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o=0,a=0,c=0;for(i=0,n=0;n<256;n++)0!=e[n]&&(o<e[n]&&(o=e[n],a=n),e[n]=Math.floor(e[n]*s),0==e[n]&&(e[n]=1),i+=e[n]);i<r?e[a]+=r-i:i-r<e[a]/2&&e[a]>2?e[a]-=i-r:i!=r&&(s=r/i,c=1)}while(c)}function b(e,t){for(var i=0,n=0;n<256;n++)i+=e[n];if(0!=i&&i!=1<<t){for(var r=0;i<1<<t;)i*=2,r++;for(n=0;n<256;n++)e[n]<<=r}}function F(e,t){for(var i=0,n=0;n<256;n++)if(t[n])if(i>0)i--;else if(e.WriteByte(n),n>0&&t[n-1]>0){for(i=n+1;i<256&&t[i];i++);i-=n+1,e.WriteByte(i)}e.WriteByte(0)}function v(e){const t=e.length;var i=new r(\"\",0,780),s=new Array(256);!function(e,t){for(var i=0;i<256;i++)t[i]=0;for(i=0;i<e.length;i++)t[e[i]]++}(e,s);var o=Math.ceil(Math.log2(t));o>12&&(o=12),w(s,o),function(e,t){F(e,t);for(var i=0;i<256;i++)t[i]&&e.WriteUint7(t[i])}(i,s),w(s,12);var a=new Array(256);a[0]=0;for(var c=1;c<256;c++)a[c]=a[c-1]+s[c-1];var l=new Array(4);for(c=0;c<4;c++)l[c]=32768;var u=new r(\"\",1.05*t+100|0,1.05*t+100|0);for(c=t-1;c>=0;c--)l[c%4]=d(l[c%4],u,a[e[c]],s[e[c]],12);for(c=3;c>=0;c--)h(l[c],u);return n.concat([i.buf.slice(0,i.pos),u.buf.slice(u.pos,u.length)],i.pos+u.length-u.pos)}e.exports={decode:function(e){return f(new r(e),0)},encode:p}},5997:(e,t,i)=>{var n=i(8287).Buffer;const r=i(8706),s=i(8223);var o=new(i(635));function a(e,t){for(var i=e+\"\";i.length<t;)i=\"0\"+i;return i}function c(e,t,i,n){var r=e[0][0].ReadByte(),s=n-e[0][r].ReadUint32();if(5==r)return t[n]=t[s],i[n]=i[s],t[n];var o=1;t[n]=\"\",i[n]=new Array(256);do{switch(r=e[o][0].ReadByte()){case 2:i[n][o]=e[o][2].ReadChar();break;case 1:i[n][o]=e[o][1].ReadString();break;case 7:i[n][o]=e[o][7].ReadUint32();break;case 3:var c=e[o][3].ReadUint32(),l=e[o][4].ReadByte();i[n][o]=a(c,l);break;case 8:i[n][o]=(0|i[s][o])+e[o][8].ReadByte();break;case 9:c=(0|i[s][o])+e[o][9].ReadByte(),l=i[s][o].length,i[n][o]=a(c,l);break;case 10:i[n][o]=i[s][o];break;default:i[n][o]=\"\"}t[n]+=i[n][o++]}while(12!=r);return t[n]}function l(e,t,i,n,r,s){for(var o=0;o<n.length;o++)if(!(i>0&&5==t[o][0].type)&&t[o][i])switch(e[0].WriteByte(t[o][i].type),t[o][i].type){case 6:e[6].WriteUint32(t[o][i].val);break;case 5:e[5].WriteUint32(t[o][i].val);break;case 1:e[1].WriteString(t[o][i].val);break;case 2:e[2].WriteChar(t[o][i].val);break;case 7:e[7].WriteUint32(t[o][i].val);break;case 3:e[3].WriteUint32(t[o][i].val),e[4].WriteByte(t[o][i].val.length);break;case 8:case 9:e[t[o][i].type].WriteByte(t[o][i].val)}}function h(e,t,i,n){for(var r=0;r<=12;r++)if(!(e[r].pos<=0)){n.WriteByte(r+(0==r?128:0)),e[r]=e[r].buf.slice(0,e[r].pos);var s=d(e[r],i);n.WriteUint7(s.length),n.WriteData(s,s.length)}}function d(e,t){var i,n=1<<30,r=[0,1,64,65,128,129,201];for(var a in r){var c=r[a];if(!(1&c&&e.length<100||8&c&&e.length%4!=0)){try{var l=t?o.encode(e,c):s.encode(e,c)}catch(e){l=0}l&&n>l.length&&(n=l.length,i=l)}}return i}function u(e,t,i,n,r){var s=0,o=r-1;e[r]=new Array(256),t[n]?e[r][0]={type:5,val:r-t[n]}:e[r][0]={type:6,val:0==r?0:1},t[n]=r;for(var a=n.match(/([a-zA-Z0-9]{1,9})|([^a-zA-Z0-9]+)/g),c=0;c<a.length;c++){var l=c+1,h=1,d=a[c];if(a[c].match(/^0+[0-9]*$/g)?h=3:a[c].match(/^[0-9]+$/g)?h=7:1==a[c].length&&(h=2),o>=0&&e[o][l])if(e[o][l].str==a[c])h=10,d=\"\";else if(7==e[o][l].type||8==e[o][l].type){var u=d-e[o][l].str;i[l]++,u>=0&&u<256&&i[l]>r/2&&(h=8,d=u)}else 3!=e[o][l].type&&9!=e[o][l].type||e[o][l].str.length!=d.length||(u=d-e[o][l].str,i[l]++,u>=0&&u<256&&i[l]>r/2&&(h=9,d=u));e[r][l]={str:a[c],val:d,type:h},s<e[r][l].val.length+3&&(s=e[r][l].val.length+3)}return e[r][++l]={type:12},[l+1,s]}e.exports={encode:function(e,t){var i=e.toString();\"\\n\"==i[i.length-1]&&(i=i.substring(0,i.length-1));var n=i.split(\"\\n\"),s=new r(\"\",0,2*i.length+1e4);s.WriteUint32(i.length),s.WriteUint32(n.length),s.WriteByte(t);for(var o=new Array(n.length),a={},c=new Array(256).fill(0),d=0,f=0,p=0;p<n.length;p++){var[g,m]=u(o,a,c,n[p],p);d<g&&(d=g),f<m&&(f=m)}for(var w=0;w<d;w++){for(var b=new Array(13),F=0;F<=12;F++)b[F]=new r(\"\",0,n.length*f);l(b,o,w,n),h(b,0,t,s)}return s.buf.slice(0,s.pos)},decode:function(e,t,i){(e=new r(e)).ReadUint32();var a=e.ReadUint32(),l=e.ReadByte(),h=function(e,t,i,a){for(var c=-1,l=new Array(256);!e.EOF();){var h=e.ReadByte(),d=128&h,u=64&h,f=63&h;if(d&&(l[++c]=new Array(13)),0!=f&&d){var p=new Array(a-1).fill(10);l[c][0]=new r(n.from([f].concat(p)))}if(u){var g=e.ReadByte(),m=e.ReadByte();l[c][f]=new r(l[g][m].buf)}else{var w=e.ReadUint7(),b=e.ReadData(w);l[c][f]=i?o.decode(b):s.decode(b),l[c][f]=new r(l[c][f])}}return l}(e,0,l,a),d=new Array(a),u=new Array(a),f=\"\";void 0===i&&(i=\"\\n\");for(var p=0;p<a;p++)f+=c(h,d,u,p)+i;return f}}},7526:(e,t)=>{t.byteLength=function(e){var t=a(e),i=t[0],n=t[1];return 3*(i+n)/4-n},t.toByteArray=function(e){var t,i,s=a(e),o=s[0],c=s[1],l=new r(function(e,t,i){return 3*(t+i)/4-i}(0,o,c)),h=0,d=c>0?o-4:o;for(i=0;i<d;i+=4)t=n[e.charCodeAt(i)]<<18|n[e.charCodeAt(i+1)]<<12|n[e.charCodeAt(i+2)]<<6|n[e.charCodeAt(i+3)],l[h++]=t>>16&255,l[h++]=t>>8&255,l[h++]=255&t;return 2===c&&(t=n[e.charCodeAt(i)]<<2|n[e.charCodeAt(i+1)]>>4,l[h++]=255&t),1===c&&(t=n[e.charCodeAt(i)]<<10|n[e.charCodeAt(i+1)]<<4|n[e.charCodeAt(i+2)]>>2,l[h++]=t>>8&255,l[h++]=255&t),l},t.fromByteArray=function(e){for(var t,n=e.length,r=n%3,s=[],o=16383,a=0,l=n-r;a<l;a+=o)s.push(c(e,a,a+o>l?l:a+o));return 1===r?(t=e[n-1],s.push(i[t>>2]+i[t<<4&63]+\"==\")):2===r&&(t=(e[n-2]<<8)+e[n-1],s.push(i[t>>10]+i[t>>4&63]+i[t<<2&63]+\"=\")),s.join(\"\")};for(var i=[],n=[],r=\"undefined\"!=typeof Uint8Array?Uint8Array:Array,s=\"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/\",o=0;o<64;++o)i[o]=s[o],n[s.charCodeAt(o)]=o;function a(e){var t=e.length;if(t%4>0)throw new Error(\"Invalid string. 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Received type number');return d(e)}return l(e,t,i)}function l(e,t,i){if(\"string\"==typeof e)return function(e,t){if(\"string\"==typeof t&&\"\"!==t||(t=\"utf8\"),!c.isEncoding(t))throw new TypeError(\"Unknown encoding: \"+t);const i=0|g(e,t);let n=a(i);const r=n.write(e,t);return r!==i&&(n=n.slice(0,r)),n}(e,t);if(ArrayBuffer.isView(e))return function(e){if(K(e,Uint8Array)){const t=new Uint8Array(e);return f(t.buffer,t.byteOffset,t.byteLength)}return u(e)}(e);if(null==e)throw new TypeError(\"The first argument must be one of type string, Buffer, ArrayBuffer, Array, or Array-like Object. Received type \"+typeof e);if(K(e,ArrayBuffer)||e&&K(e.buffer,ArrayBuffer))return f(e,t,i);if(\"undefined\"!=typeof SharedArrayBuffer&&(K(e,SharedArrayBuffer)||e&&K(e.buffer,SharedArrayBuffer)))return f(e,t,i);if(\"number\"==typeof e)throw new TypeError('The \"value\" argument must not be of type number. Received type number');const n=e.valueOf&&e.valueOf();if(null!=n&&n!==e)return c.from(n,t,i);const r=function(e){if(c.isBuffer(e)){const t=0|p(e.length),i=a(t);return 0===i.length||e.copy(i,0,0,t),i}return void 0!==e.length?\"number\"!=typeof e.length||Y(e.length)?a(0):u(e):\"Buffer\"===e.type&&Array.isArray(e.data)?u(e.data):void 0}(e);if(r)return r;if(\"undefined\"!=typeof Symbol&&null!=Symbol.toPrimitive&&\"function\"==typeof e[Symbol.toPrimitive])return c.from(e[Symbol.toPrimitive](\"string\"),t,i);throw new TypeError(\"The first argument must be one of type string, Buffer, ArrayBuffer, Array, or Array-like Object. 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reading blob\"))},t.onabort=()=>{n(new Error(\"blob reading was aborted\"))},t.onload=()=>{t.result&&\"string\"!=typeof t.result?i(t.result):n(new Error(\"unknown error reading blob\"))},t.readAsArrayBuffer(e)}))}class l{constructor(e){this.blob=e,this.size=e.size}async read(e,t=0,i,n=0){if(!i)return{bytesRead:0,buffer:e};const r=n,o=r+i,a=await c(this.blob.slice(r,o)),l=s.Buffer.from(a);return{bytesRead:l.copy(e,t),buffer:l}}async readFile(e){const t=\"string\"==typeof e?e:null==e?void 0:e.encoding;if(\"utf8\"===t)return function(e){const t=new FileReader;return new Promise(((i,n)=>{t.onerror=()=>{t.abort(),n(new Error(\"problem reading blob\"))},t.onabort=()=>{n(new Error(\"blob reading was aborted\"))},t.onload=()=>{t.result&&\"string\"==typeof t.result?i(t.result):n(new Error(\"unknown error reading blob\"))},t.readAsText(e)}))}(this.blob);if(t)throw new Error(`unsupported encoding: ${t}`);const i=await c(this.blob);return s.Buffer.from(i)}async stat(){return{size:this.size}}async close(){}}function h(e,t={}){return new a(e,t)}function d(e,t,i,n={}){if(void 0!==i)return i;if(void 0!==e)return h(e,n);if(void 0!==t)return new(r())(t,n);throw new Error(\"no url, path, or filehandle provided, cannot open\")}},251:(e,t)=>{t.read=function(e,t,i,n,r){var s,o,a=8*r-n-1,c=(1<<a)-1,l=c>>1,h=-7,d=i?r-1:0,u=i?-1:1,f=e[t+d];for(d+=u,s=f&(1<<-h)-1,f>>=-h,h+=a;h>0;s=256*s+e[t+d],d+=u,h-=8);for(o=s&(1<<-h)-1,s>>=-h,h+=n;h>0;o=256*o+e[t+d],d+=u,h-=8);if(0===s)s=1-l;else{if(s===c)return o?NaN:1/0*(f?-1:1);o+=Math.pow(2,n),s-=l}return(f?-1:1)*o*Math.pow(2,s-n)},t.write=function(e,t,i,n,r,s){var o,a,c,l=8*s-r-1,h=(1<<l)-1,d=h>>1,u=23===r?Math.pow(2,-24)-Math.pow(2,-77):0,f=n?0:s-1,p=n?1:-1,g=t<0||0===t&&1/t<0?1:0;for(t=Math.abs(t),isNaN(t)||t===1/0?(a=isNaN(t)?1:0,o=h):(o=Math.floor(Math.log(t)/Math.LN2),t*(c=Math.pow(2,-o))<1&&(o--,c*=2),(t+=o+d>=1?u/c:u*Math.pow(2,1-d))*c>=2&&(o++,c/=2),o+d>=h?(a=0,o=h):o+d>=1?(a=(t*c-1)*Math.pow(2,r),o+=d):(a=t*Math.pow(2,d-1)*Math.pow(2,r),o=0));r>=8;e[i+f]=255&a,f+=p,a/=256,r-=8);for(o=o<<r|a,l+=r;l>0;e[i+f]=255&o,f+=p,o/=256,l-=8);e[i+f-p]|=128*g}},8570:e=>{e.exports=i;var t=null;try{t=new WebAssembly.Instance(new WebAssembly.Module(new Uint8Array([0,97,115,109,1,0,0,0,1,13,2,96,0,1,127,96,4,127,127,127,127,1,127,3,7,6,0,1,1,1,1,1,6,6,1,127,1,65,0,11,7,50,6,3,109,117,108,0,1,5,100,105,118,95,115,0,2,5,100,105,118,95,117,0,3,5,114,101,109,95,115,0,4,5,114,101,109,95,117,0,5,8,103,101,116,95,104,105,103,104,0,0,10,191,1,6,4,0,35,0,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,126,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,127,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,128,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,129,34,4,66,32,135,167,36,0,32,4,167,11,36,1,1,126,32,0,173,32,1,173,66,32,134,132,32,2,173,32,3,173,66,32,134,132,130,34,4,66,32,135,167,36,0,32,4,167,11])),{}).exports}catch(e){}function i(e,t,i){this.low=0|e,this.high=0|t,this.unsigned=!!i}function n(e){return!0===(e&&e.__isLong__)}i.prototype.__isLong__,Object.defineProperty(i.prototype,\"__isLong__\",{value:!0}),i.isLong=n;var r={},s={};function o(e,t){var i,n,o;return t?(o=0<=(e>>>=0)&&e<256)&&(n=s[e])?n:(i=c(e,(0|e)<0?-1:0,!0),o&&(s[e]=i),i):(o=-128<=(e|=0)&&e<128)&&(n=r[e])?n:(i=c(e,e<0?-1:0,!1),o&&(r[e]=i),i)}function a(e,t){if(isNaN(e))return t?w:m;if(t){if(e<0)return w;if(e>=f)return A}else{if(e<=-p)return C;if(e+1>=p)return y}return e<0?a(-e,t).neg():c(e%u|0,e/u|0,t)}function c(e,t,n){return new i(e,t,n)}i.fromInt=o,i.fromNumber=a,i.fromBits=c;var l=Math.pow;function h(e,t,i){if(0===e.length)throw Error(\"empty string\");if(\"NaN\"===e||\"Infinity\"===e||\"+Infinity\"===e||\"-Infinity\"===e)return m;if(\"number\"==typeof t?(i=t,t=!1):t=!!t,(i=i||10)<2||36<i)throw RangeError(\"radix\");var n;if((n=e.indexOf(\"-\"))>0)throw Error(\"interior hyphen\");if(0===n)return h(e.substring(1),t,i).neg();for(var r=a(l(i,8)),s=m,o=0;o<e.length;o+=8){var c=Math.min(8,e.length-o),d=parseInt(e.substring(o,o+c),i);if(c<8){var u=a(l(i,c));s=s.mul(u).add(a(d))}else s=(s=s.mul(r)).add(a(d))}return s.unsigned=t,s}function d(e,t){return\"number\"==typeof e?a(e,t):\"string\"==typeof e?h(e,t):c(e.low,e.high,\"boolean\"==typeof t?t:e.unsigned)}i.fromString=h,i.fromValue=d;var u=4294967296,f=u*u,p=f/2,g=o(1<<24),m=o(0);i.ZERO=m;var w=o(0,!0);i.UZERO=w;var b=o(1);i.ONE=b;var F=o(1,!0);i.UONE=F;var v=o(-1);i.NEG_ONE=v;var y=c(-1,2147483647,!1);i.MAX_VALUE=y;var A=c(-1,-1,!0);i.MAX_UNSIGNED_VALUE=A;var C=c(0,-2147483648,!1);i.MIN_VALUE=C;var _=i.prototype;_.toInt=function(){return this.unsigned?this.low>>>0:this.low},_.toNumber=function(){return this.unsigned?(this.high>>>0)*u+(this.low>>>0):this.high*u+(this.low>>>0)},_.toString=function(e){if((e=e||10)<2||36<e)throw RangeError(\"radix\");if(this.isZero())return\"0\";if(this.isNegative()){if(this.eq(C)){var t=a(e),i=this.div(t),n=i.mul(t).sub(this);return i.toString(e)+n.toInt().toString(e)}return\"-\"+this.neg().toString(e)}for(var r=a(l(e,6),this.unsigned),s=this,o=\"\";;){var c=s.div(r),h=(s.sub(c.mul(r)).toInt()>>>0).toString(e);if((s=c).isZero())return h+o;for(;h.length<6;)h=\"0\"+h;o=\"\"+h+o}},_.getHighBits=function(){return this.high},_.getHighBitsUnsigned=function(){return this.high>>>0},_.getLowBits=function(){return this.low},_.getLowBitsUnsigned=function(){return this.low>>>0},_.getNumBitsAbs=function(){if(this.isNegative())return this.eq(C)?64:this.neg().getNumBitsAbs();for(var e=0!=this.high?this.high:this.low,t=31;t>0&&!(e&1<<t);t--);return 0!=this.high?t+33:t+1},_.isZero=function(){return 0===this.high&&0===this.low},_.eqz=_.isZero,_.isNegative=function(){return!this.unsigned&&this.high<0},_.isPositive=function(){return this.unsigned||this.high>=0},_.isOdd=function(){return!(1&~this.low)},_.isEven=function(){return!(1&this.low)},_.equals=function(e){return n(e)||(e=d(e)),(this.unsigned===e.unsigned||this.high>>>31!=1||e.high>>>31!=1)&&this.high===e.high&&this.low===e.low},_.eq=_.equals,_.notEquals=function(e){return!this.eq(e)},_.neq=_.notEquals,_.ne=_.notEquals,_.lessThan=function(e){return this.comp(e)<0},_.lt=_.lessThan,_.lessThanOrEqual=function(e){return this.comp(e)<=0},_.lte=_.lessThanOrEqual,_.le=_.lessThanOrEqual,_.greaterThan=function(e){return this.comp(e)>0},_.gt=_.greaterThan,_.greaterThanOrEqual=function(e){return this.comp(e)>=0},_.gte=_.greaterThanOrEqual,_.ge=_.greaterThanOrEqual,_.compare=function(e){if(n(e)||(e=d(e)),this.eq(e))return 0;var t=this.isNegative(),i=e.isNegative();return t&&!i?-1:!t&&i?1:this.unsigned?e.high>>>0>this.high>>>0||e.high===this.high&&e.low>>>0>this.low>>>0?-1:1:this.sub(e).isNegative()?-1:1},_.comp=_.compare,_.negate=function(){return!this.unsigned&&this.eq(C)?C:this.not().add(b)},_.neg=_.negate,_.add=function(e){n(e)||(e=d(e));var t=this.high>>>16,i=65535&this.high,r=this.low>>>16,s=65535&this.low,o=e.high>>>16,a=65535&e.high,l=e.low>>>16,h=0,u=0,f=0,p=0;return f+=(p+=s+(65535&e.low))>>>16,u+=(f+=r+l)>>>16,h+=(u+=i+a)>>>16,h+=t+o,c((f&=65535)<<16|(p&=65535),(h&=65535)<<16|(u&=65535),this.unsigned)},_.subtract=function(e){return n(e)||(e=d(e)),this.add(e.neg())},_.sub=_.subtract,_.multiply=function(e){if(this.isZero())return m;if(n(e)||(e=d(e)),t)return c(t.mul(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned);if(e.isZero())return m;if(this.eq(C))return e.isOdd()?C:m;if(e.eq(C))return this.isOdd()?C:m;if(this.isNegative())return e.isNegative()?this.neg().mul(e.neg()):this.neg().mul(e).neg();if(e.isNegative())return this.mul(e.neg()).neg();if(this.lt(g)&&e.lt(g))return a(this.toNumber()*e.toNumber(),this.unsigned);var i=this.high>>>16,r=65535&this.high,s=this.low>>>16,o=65535&this.low,l=e.high>>>16,h=65535&e.high,u=e.low>>>16,f=65535&e.low,p=0,w=0,b=0,F=0;return b+=(F+=o*f)>>>16,w+=(b+=s*f)>>>16,b&=65535,w+=(b+=o*u)>>>16,p+=(w+=r*f)>>>16,w&=65535,p+=(w+=s*u)>>>16,w&=65535,p+=(w+=o*h)>>>16,p+=i*f+r*u+s*h+o*l,c((b&=65535)<<16|(F&=65535),(p&=65535)<<16|(w&=65535),this.unsigned)},_.mul=_.multiply,_.divide=function(e){if(n(e)||(e=d(e)),e.isZero())throw Error(\"division by zero\");var i,r,s;if(t)return this.unsigned||-2147483648!==this.high||-1!==e.low||-1!==e.high?c((this.unsigned?t.div_u:t.div_s)(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned):this;if(this.isZero())return this.unsigned?w:m;if(this.unsigned){if(e.unsigned||(e=e.toUnsigned()),e.gt(this))return w;if(e.gt(this.shru(1)))return F;s=w}else{if(this.eq(C))return e.eq(b)||e.eq(v)?C:e.eq(C)?b:(i=this.shr(1).div(e).shl(1)).eq(m)?e.isNegative()?b:v:(r=this.sub(e.mul(i)),s=i.add(r.div(e)));if(e.eq(C))return this.unsigned?w:m;if(this.isNegative())return e.isNegative()?this.neg().div(e.neg()):this.neg().div(e).neg();if(e.isNegative())return this.div(e.neg()).neg();s=m}for(r=this;r.gte(e);){i=Math.max(1,Math.floor(r.toNumber()/e.toNumber()));for(var o=Math.ceil(Math.log(i)/Math.LN2),h=o<=48?1:l(2,o-48),u=a(i),f=u.mul(e);f.isNegative()||f.gt(r);)f=(u=a(i-=h,this.unsigned)).mul(e);u.isZero()&&(u=b),s=s.add(u),r=r.sub(f)}return s},_.div=_.divide,_.modulo=function(e){return n(e)||(e=d(e)),t?c((this.unsigned?t.rem_u:t.rem_s)(this.low,this.high,e.low,e.high),t.get_high(),this.unsigned):this.sub(this.div(e).mul(e))},_.mod=_.modulo,_.rem=_.modulo,_.not=function(){return c(~this.low,~this.high,this.unsigned)},_.and=function(e){return n(e)||(e=d(e)),c(this.low&e.low,this.high&e.high,this.unsigned)},_.or=function(e){return n(e)||(e=d(e)),c(this.low|e.low,this.high|e.high,this.unsigned)},_.xor=function(e){return n(e)||(e=d(e)),c(this.low^e.low,this.high^e.high,this.unsigned)},_.shiftLeft=function(e){return 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e=this.high,t=this.low;return[e>>>24,e>>>16&255,e>>>8&255,255&e,t>>>24,t>>>16&255,t>>>8&255,255&t]},i.fromBytes=function(e,t,n){return n?i.fromBytesLE(e,t):i.fromBytesBE(e,t)},i.fromBytesLE=function(e,t){return new i(e[0]|e[1]<<8|e[2]<<16|e[3]<<24,e[4]|e[5]<<8|e[6]<<16|e[7]<<24,t)},i.fromBytesBE=function(e,t){return new i(e[4]<<24|e[5]<<16|e[6]<<8|e[7],e[0]<<24|e[1]<<16|e[2]<<8|e[3],t)}},3503:(e,t,i)=>{var n,r,s,o,a;n=i(3939),r=i(2151).utf8,s=i(652),o=i(2151).bin,(a=function(e,t){e.constructor==String?e=t&&\"binary\"===t.encoding?o.stringToBytes(e):r.stringToBytes(e):s(e)?e=Array.prototype.slice.call(e,0):Array.isArray(e)||e.constructor===Uint8Array||(e=e.toString());for(var i=n.bytesToWords(e),c=8*e.length,l=1732584193,h=-271733879,d=-1732584194,u=271733878,f=0;f<i.length;f++)i[f]=16711935&(i[f]<<8|i[f]>>>24)|4278255360&(i[f]<<24|i[f]>>>8);i[c>>>5]|=128<<c%32,i[14+(c+64>>>9<<4)]=c;var p=a._ff,g=a._gg,m=a._hh,w=a._ii;for(f=0;f<i.length;f+=16){var 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e.state=c,c.strm=e,c.wrap=a,c.gzhead=null,c.w_bits=n,c.w_size=1<<c.w_bits,c.w_mask=c.w_size-1,c.hash_bits=s+7,c.hash_size=1<<c.hash_bits,c.hash_mask=c.hash_size-1,c.hash_shift=~~((c.hash_bits+F-1)/F),c.window=new r.Buf8(2*c.w_size),c.head=new r.Buf16(c.hash_size),c.prev=new r.Buf16(c.w_size),c.lit_bufsize=1<<s+6,c.pending_buf_size=4*c.lit_bufsize,c.pending_buf=new r.Buf8(c.pending_buf_size),c.d_buf=1*c.lit_bufsize,c.l_buf=3*c.lit_bufsize,c.level=t,c.strategy=o,c.method=i,U(e)}n=[new H(0,0,0,0,(function(e,t){var i=65535;for(i>e.pending_buf_size-5&&(i=e.pending_buf_size-5);;){if(e.lookahead<=1){if(T(e),0===e.lookahead&&t===l)return 1;if(0===e.lookahead)break}e.strstart+=e.lookahead,e.lookahead=0;var n=e.block_start+i;if((0===e.strstart||e.strstart>=n)&&(e.lookahead=e.strstart-n,e.strstart=n,N(e,!1),0===e.strm.avail_out))return 1;if(e.strstart-e.block_start>=e.w_size-y&&(N(e,!1),0===e.strm.avail_out))return 1}return 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1;if(0===e.lookahead)break}if(e.match_length=0,e.lookahead>=F&&e.strstart>0&&(n=a[r=e.strstart-1])===a[++r]&&n===a[++r]&&n===a[++r]){o=e.strstart+v;do{}while(n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&n===a[++r]&&r<o);e.match_length=v-(o-r),e.match_length>e.lookahead&&(e.match_length=e.lookahead)}if(e.match_length>=F?(i=s._tr_tally(e,1,e.match_length-F),e.lookahead-=e.match_length,e.strstart+=e.match_length,e.match_length=0):(i=s._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++),i&&(N(e,!1),0===e.strm.avail_out))return 1}return e.insert=0,4===t?(N(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(N(e,!1),0===e.strm.avail_out)?1:2}(r,t):n[r.level].func(r,t);if(3!==p&&4!==p||(r.status=x),1===p||3===p)return 0===e.avail_out&&(r.last_flush=-1),h;if(2===p&&(1===t?s._tr_align(r):5!==t&&(s._tr_stored_block(r,0,0,!1),3===t&&(S(r.head),0===r.lookahead&&(r.strstart=0,r.block_start=0,r.insert=0))),E(e),0===e.avail_out))return r.last_flush=-1,h}return 4!==t?h:r.wrap<=0?1:(2===r.wrap?(B(r,255&e.adler),B(r,e.adler>>8&255),B(r,e.adler>>16&255),B(r,e.adler>>24&255),B(r,255&e.total_in),B(r,e.total_in>>8&255),B(r,e.total_in>>16&255),B(r,e.total_in>>24&255)):(M(r,e.adler>>>16),M(r,65535&e.adler)),E(e),r.wrap>0&&(r.wrap=-r.wrap),0!==r.pending?h:1)},t.deflateEnd=function(e){var t;return e&&e.state?(t=e.state.status)!==A&&69!==t&&73!==t&&91!==t&&t!==C&&t!==_&&t!==x?k(e,d):(e.state=null,t===_?k(e,-3):h):d},t.deflateSetDictionary=function(e,t){var i,n,s,a,c,l,u,f,p=t.length;if(!e||!e.state)return d;if(2===(a=(i=e.state).wrap)||1===a&&i.status!==A||i.lookahead)return d;for(1===a&&(e.adler=o(e.adler,t,p,0)),i.wrap=0,p>=i.w_size&&(0===a&&(S(i.head),i.strstart=0,i.block_start=0,i.insert=0),f=new r.Buf8(i.w_size),r.arraySet(f,t,p-i.w_size,i.w_size,0),t=f,p=i.w_size),c=e.avail_in,l=e.next_in,u=e.input,e.avail_in=p,e.next_in=0,e.input=t,T(i);i.lookahead>=F;){n=i.strstart,s=i.lookahead-(F-1);do{i.ins_h=(i.ins_h<<i.hash_shift^i.window[n+F-1])&i.hash_mask,i.prev[n&i.w_mask]=i.head[i.ins_h],i.head[i.ins_h]=n,n++}while(--s);i.strstart=n,i.lookahead=F-1,T(i)}return i.strstart+=i.lookahead,i.block_start=i.strstart,i.insert=i.lookahead,i.lookahead=0,i.match_length=i.prev_length=F-1,i.match_available=0,e.next_in=l,e.input=u,e.avail_in=c,i.wrap=a,h},t.deflateInfo=\"pako deflate (from Nodeca project)\"},7414:e=>{e.exports=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name=\"\",this.comment=\"\",this.hcrc=0,this.done=!1}},7293:e=>{e.exports=function(e,t){var i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_,x,k;i=e.state,n=e.next_in,x=e.input,r=n+(e.avail_in-5),s=e.next_out,k=e.output,o=s-(t-e.avail_out),a=s+(e.avail_out-257),c=i.dmax,l=i.wsize,h=i.whave,d=i.wnext,u=i.window,f=i.hold,p=i.bits,g=i.lencode,m=i.distcode,w=(1<<i.lenbits)-1,b=(1<<i.distbits)-1;e:do{p<15&&(f+=x[n++]<<p,p+=8,f+=x[n++]<<p,p+=8),F=g[f&w];t:for(;;){if(f>>>=v=F>>>24,p-=v,0==(v=F>>>16&255))k[s++]=65535&F;else{if(!(16&v)){if(64&v){if(32&v){i.mode=12;break e}e.msg=\"invalid literal/length code\",i.mode=30;break e}F=g[(65535&F)+(f&(1<<v)-1)];continue t}for(y=65535&F,(v&=15)&&(p<v&&(f+=x[n++]<<p,p+=8),y+=f&(1<<v)-1,f>>>=v,p-=v),p<15&&(f+=x[n++]<<p,p+=8,f+=x[n++]<<p,p+=8),F=m[f&b];;){if(f>>>=v=F>>>24,p-=v,16&(v=F>>>16&255)){if(A=65535&F,p<(v&=15)&&(f+=x[n++]<<p,(p+=8)<v&&(f+=x[n++]<<p,p+=8)),(A+=f&(1<<v)-1)>c){e.msg=\"invalid distance too far back\",i.mode=30;break e}if(f>>>=v,p-=v,A>(v=s-o)){if((v=A-v)>h&&i.sane){e.msg=\"invalid distance too far back\",i.mode=30;break e}if(C=0,_=u,0===d){if(C+=l-v,v<y){y-=v;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}}else if(d<v){if(C+=l+d-v,(v-=d)<y){y-=v;do{k[s++]=u[C++]}while(--v);if(C=0,d<y){y-=v=d;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}}}else if(C+=d-v,v<y){y-=v;do{k[s++]=u[C++]}while(--v);C=s-A,_=k}for(;y>2;)k[s++]=_[C++],k[s++]=_[C++],k[s++]=_[C++],y-=3;y&&(k[s++]=_[C++],y>1&&(k[s++]=_[C++]))}else{C=s-A;do{k[s++]=k[C++],k[s++]=k[C++],k[s++]=k[C++],y-=3}while(y>2);y&&(k[s++]=k[C++],y>1&&(k[s++]=k[C++]))}break}if(64&v){e.msg=\"invalid distance code\",i.mode=30;break e}F=m[(65535&F)+(f&(1<<v)-1)]}}break}}while(n<r&&s<a);n-=y=p>>3,f&=(1<<(p-=y<<3))-1,e.next_in=n,e.next_out=s,e.avail_in=n<r?r-n+5:5-(n-r),e.avail_out=s<a?a-s+257:257-(s-a),i.hold=f,i.bits=p}},1447:(e,t,i)=>{var n=i(9805),r=i(3269),s=i(4823),o=i(7293),a=i(1998),c=0,l=-2,h=1,d=12,u=30,f=852,p=592;function g(e){return(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24)}function m(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new n.Buf16(320),this.work=new n.Buf16(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}function w(e){var t;return e&&e.state?(t=e.state,e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=h,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new n.Buf32(f),t.distcode=t.distdyn=new n.Buf32(p),t.sane=1,t.back=-1,c):l}function b(e){var t;return e&&e.state?((t=e.state).wsize=0,t.whave=0,t.wnext=0,w(e)):l}function F(e,t){var i,n;return e&&e.state?(n=e.state,t<0?(i=0,t=-t):(i=1+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?l:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,b(e))):l}function v(e,t){var i,n;return e?(n=new m,e.state=n,n.window=null,(i=F(e,t))!==c&&(e.state=null),i):l}var y,A,C=!0;function _(e){if(C){var t;for(y=new n.Buf32(512),A=new n.Buf32(32),t=0;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(a(1,e.lens,0,288,y,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;a(2,e.lens,0,32,A,0,e.work,{bits:5}),C=!1}e.lencode=y,e.lenbits=9,e.distcode=A,e.distbits=5}function x(e,t,i,r){var s,o=e.state;return null===o.window&&(o.wsize=1<<o.wbits,o.wnext=0,o.whave=0,o.window=new n.Buf8(o.wsize)),r>=o.wsize?(n.arraySet(o.window,t,i-o.wsize,o.wsize,0),o.wnext=0,o.whave=o.wsize):((s=o.wsize-o.wnext)>r&&(s=r),n.arraySet(o.window,t,i-r,s,o.wnext),(r-=s)?(n.arraySet(o.window,t,i-r,r,0),o.wnext=r,o.whave=o.wsize):(o.wnext+=s,o.wnext===o.wsize&&(o.wnext=0),o.whave<o.wsize&&(o.whave+=s))),0}t.inflateReset=b,t.inflateReset2=F,t.inflateResetKeep=w,t.inflateInit=function(e){return v(e,15)},t.inflateInit2=v,t.inflate=function(e,t){var i,f,p,m,w,b,F,v,y,A,C,k,I,S,E,N,B,M,R,D,T,L,z,H,P=0,O=new n.Buf8(4),U=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15];if(!e||!e.state||!e.output||!e.input&&0!==e.avail_in)return l;(i=e.state).mode===d&&(i.mode=13),w=e.next_out,p=e.output,F=e.avail_out,m=e.next_in,f=e.input,b=e.avail_in,v=i.hold,y=i.bits,A=b,C=F,L=c;e:for(;;)switch(i.mode){case h:if(0===i.wrap){i.mode=13;break}for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(2&i.wrap&&35615===v){i.check=0,O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0),v=0,y=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&v)<<8)+(v>>8))%31){e.msg=\"incorrect header check\",i.mode=u;break}if(8!=(15&v)){e.msg=\"unknown compression method\",i.mode=u;break}if(y-=4,T=8+(15&(v>>>=4)),0===i.wbits)i.wbits=T;else if(T>i.wbits){e.msg=\"invalid window size\",i.mode=u;break}i.dmax=1<<T,e.adler=i.check=1,i.mode=512&v?10:d,v=0,y=0;break;case 2:for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(i.flags=v,8!=(255&i.flags)){e.msg=\"unknown compression method\",i.mode=u;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=u;break}i.head&&(i.head.text=v>>8&1),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0,i.mode=3;case 3:for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.head&&(i.head.time=v),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,O[2]=v>>>16&255,O[3]=v>>>24&255,i.check=s(i.check,O,4,0)),v=0,y=0,i.mode=4;case 4:for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.head&&(i.head.xflags=255&v,i.head.os=v>>8),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0,i.mode=5;case 5:if(1024&i.flags){for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.length=v,i.head&&(i.head.extra_len=v),512&i.flags&&(O[0]=255&v,O[1]=v>>>8&255,i.check=s(i.check,O,2,0)),v=0,y=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&((k=i.length)>b&&(k=b),k&&(i.head&&(T=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Array(i.head.extra_len)),n.arraySet(i.head.extra,f,m,k,T)),512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,i.length-=k),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===b)break e;k=0;do{T=f[m+k++],i.head&&T&&i.length<65536&&(i.head.name+=String.fromCharCode(T))}while(T&&k<b);if(512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,T)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===b)break e;k=0;do{T=f[m+k++],i.head&&T&&i.length<65536&&(i.head.comment+=String.fromCharCode(T))}while(T&&k<b);if(512&i.flags&&(i.check=s(i.check,f,k,m)),b-=k,m+=k,T)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;y<16;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=u;break}v=0,y=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=d;break;case 10:for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}e.adler=i.check=g(v),v=0,y=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=w,e.avail_out=F,e.next_in=m,e.avail_in=b,i.hold=v,i.bits=y,2;e.adler=i.check=1,i.mode=d;case d:if(5===t||6===t)break e;case 13:if(i.last){v>>>=7&y,y-=7&y,i.mode=27;break}for(;y<3;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}switch(i.last=1&v,y-=1,3&(v>>>=1)){case 0:i.mode=14;break;case 1:if(_(i),i.mode=20,6===t){v>>>=2,y-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg=\"invalid block type\",i.mode=u}v>>>=2,y-=2;break;case 14:for(v>>>=7&y,y-=7&y;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if((65535&v)!=(v>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=u;break}if(i.length=65535&v,v=0,y=0,i.mode=15,6===t)break e;case 15:i.mode=16;case 16:if(k=i.length){if(k>b&&(k=b),k>F&&(k=F),0===k)break e;n.arraySet(p,f,m,k,w),b-=k,m+=k,F-=k,w+=k,i.length-=k;break}i.mode=d;break;case 17:for(;y<14;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(i.nlen=257+(31&v),v>>>=5,y-=5,i.ndist=1+(31&v),v>>>=5,y-=5,i.ncode=4+(15&v),v>>>=4,y-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=u;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;y<3;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.lens[U[i.have++]]=7&v,v>>>=3,y-=3}for(;i.have<19;)i.lens[U[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,z={bits:i.lenbits},L=a(0,i.lens,0,19,i.lencode,0,i.work,z),i.lenbits=z.bits,L){e.msg=\"invalid code lengths set\",i.mode=u;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;N=(P=i.lencode[v&(1<<i.lenbits)-1])>>>16&255,B=65535&P,!((E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(B<16)v>>>=E,y-=E,i.lens[i.have++]=B;else{if(16===B){for(H=E+2;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v>>>=E,y-=E,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=u;break}T=i.lens[i.have-1],k=3+(3&v),v>>>=2,y-=2}else if(17===B){for(H=E+3;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}y-=E,T=0,k=3+(7&(v>>>=E)),v>>>=3,y-=3}else{for(H=E+7;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}y-=E,T=0,k=11+(127&(v>>>=E)),v>>>=7,y-=7}if(i.have+k>i.nlen+i.ndist){e.msg=\"invalid bit length 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e;b--,v+=f[m++]<<y,y+=8}if(N&&!(240&N)){for(M=E,R=N,D=B;N=(P=i.lencode[D+((v&(1<<M+R)-1)>>M)])>>>16&255,B=65535&P,!(M+(E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}v>>>=M,y-=M,i.back+=M}if(v>>>=E,y-=E,i.back+=E,i.length=B,0===N){i.mode=26;break}if(32&N){i.back=-1,i.mode=d;break}if(64&N){e.msg=\"invalid literal/length code\",i.mode=u;break}i.extra=15&N,i.mode=22;case 22:if(i.extra){for(H=i.extra;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.length+=v&(1<<i.extra)-1,v>>>=i.extra,y-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;N=(P=i.distcode[v&(1<<i.distbits)-1])>>>16&255,B=65535&P,!((E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(!(240&N)){for(M=E,R=N,D=B;N=(P=i.distcode[D+((v&(1<<M+R)-1)>>M)])>>>16&255,B=65535&P,!(M+(E=P>>>24)<=y);){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}v>>>=M,y-=M,i.back+=M}if(v>>>=E,y-=E,i.back+=E,64&N){e.msg=\"invalid distance code\",i.mode=u;break}i.offset=B,i.extra=15&N,i.mode=24;case 24:if(i.extra){for(H=i.extra;y<H;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}i.offset+=v&(1<<i.extra)-1,v>>>=i.extra,y-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=u;break}i.mode=25;case 25:if(0===F)break e;if(k=C-F,i.offset>k){if((k=i.offset-k)>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=u;break}k>i.wnext?(k-=i.wnext,I=i.wsize-k):I=i.wnext-k,k>i.length&&(k=i.length),S=i.window}else S=p,I=w-i.offset,k=i.length;k>F&&(k=F),F-=k,i.length-=k;do{p[w++]=S[I++]}while(--k);0===i.length&&(i.mode=21);break;case 26:if(0===F)break e;p[w++]=i.length,F--,i.mode=21;break;case 27:if(i.wrap){for(;y<32;){if(0===b)break e;b--,v|=f[m++]<<y,y+=8}if(C-=F,e.total_out+=C,i.total+=C,C&&(e.adler=i.check=i.flags?s(i.check,p,C,w-C):r(i.check,p,C,w-C)),C=F,(i.flags?v:g(v))!==i.check){e.msg=\"incorrect data check\",i.mode=u;break}v=0,y=0}i.mode=28;case 28:if(i.wrap&&i.flags){for(;y<32;){if(0===b)break e;b--,v+=f[m++]<<y,y+=8}if(v!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=u;break}v=0,y=0}i.mode=29;case 29:L=1;break e;case u:L=-3;break e;case 31:return-4;default:return l}return e.next_out=w,e.avail_out=F,e.next_in=m,e.avail_in=b,i.hold=v,i.bits=y,(i.wsize||C!==e.avail_out&&i.mode<u&&(i.mode<27||4!==t))&&x(e,e.output,e.next_out,C-e.avail_out)?(i.mode=31,-4):(A-=e.avail_in,C-=e.avail_out,e.total_in+=A,e.total_out+=C,i.total+=C,i.wrap&&C&&(e.adler=i.check=i.flags?s(i.check,p,C,e.next_out-C):r(i.check,p,C,e.next_out-C)),e.data_type=i.bits+(i.last?64:0)+(i.mode===d?128:0)+(20===i.mode||15===i.mode?256:0),(0===A&&0===C||4===t)&&L===c&&(L=-5),L)},t.inflateEnd=function(e){if(!e||!e.state)return l;var t=e.state;return t.window&&(t.window=null),e.state=null,c},t.inflateGetHeader=function(e,t){var i;return e&&e.state&&2&(i=e.state).wrap?(i.head=t,t.done=!1,c):l},t.inflateSetDictionary=function(e,t){var i,n=t.length;return e&&e.state?0!==(i=e.state).wrap&&11!==i.mode?l:11===i.mode&&r(1,t,n,0)!==i.check?-3:x(e,t,n,n)?(i.mode=31,-4):(i.havedict=1,c):l},t.inflateInfo=\"pako inflate (from Nodeca project)\"},1998:(e,t,i)=>{var n=i(9805),r=[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0],s=[16,16,16,16,16,16,16,16,17,17,17,17,18,18,18,18,19,19,19,19,20,20,20,20,21,21,21,21,16,72,78],o=[1,2,3,4,5,7,9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577,0,0],a=[16,16,16,16,17,17,18,18,19,19,20,20,21,21,22,22,23,23,24,24,25,25,26,26,27,27,28,28,29,29,64,64];e.exports=function(e,t,i,c,l,h,d,u){var f,p,g,m,w,b,F,v,y,A=u.bits,C=0,_=0,x=0,k=0,I=0,S=0,E=0,N=0,B=0,M=0,R=null,D=0,T=new n.Buf16(16),L=new n.Buf16(16),z=null,H=0;for(C=0;C<=15;C++)T[C]=0;for(_=0;_<c;_++)T[t[i+_]]++;for(I=A,k=15;k>=1&&0===T[k];k--);if(I>k&&(I=k),0===k)return l[h++]=20971520,l[h++]=20971520,u.bits=1,0;for(x=1;x<k&&0===T[x];x++);for(I<x&&(I=x),N=1,C=1;C<=15;C++)if(N<<=1,(N-=T[C])<0)return-1;if(N>0&&(0===e||1!==k))return-1;for(L[1]=0,C=1;C<15;C++)L[C+1]=L[C]+T[C];for(_=0;_<c;_++)0!==t[i+_]&&(d[L[t[i+_]]++]=_);if(0===e?(R=z=d,b=19):1===e?(R=r,D-=257,z=s,H-=257,b=256):(R=o,z=a,b=-1),M=0,_=0,C=x,w=h,S=I,E=0,g=-1,m=(B=1<<I)-1,1===e&&B>852||2===e&&B>592)return 1;for(;;){F=C-E,d[_]<b?(v=0,y=d[_]):d[_]>b?(v=z[H+d[_]],y=R[D+d[_]]):(v=96,y=0),f=1<<C-E,x=p=1<<S;do{l[w+(M>>E)+(p-=f)]=F<<24|v<<16|y}while(0!==p);for(f=1<<C-1;M&f;)f>>=1;if(0!==f?(M&=f-1,M+=f):M=0,_++,0==--T[C]){if(C===k)break;C=t[i+d[_]]}if(C>I&&(M&m)!==g){for(0===E&&(E=I),w+=x,N=1<<(S=C-E);S+E<k&&!((N-=T[S+E])<=0);)S++,N<<=1;if(B+=1<<S,1===e&&B>852||2===e&&B>592)return 1;l[g=M&m]=I<<24|S<<16|w-h}}return 0!==M&&(l[w+M]=C-E<<24|64<<16),u.bits=I,0}},4674:e=>{e.exports={2:\"need dictionary\",1:\"stream end\",0:\"\",\"-1\":\"file error\",\"-2\":\"stream error\",\"-3\":\"data error\",\"-4\":\"insufficient memory\",\"-5\":\"buffer error\",\"-6\":\"incompatible version\"}},3665:(e,t,i)=>{var n=i(9805);function r(e){for(var t=e.length;--t>=0;)e[t]=0}var s=15,o=16,a=[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0],c=[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13],l=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7],h=[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15],d=new Array(576);r(d);var u=new Array(60);r(u);var f=new Array(512);r(f);var p=new Array(256);r(p);var g=new Array(29);r(g);var m,w,b,F=new Array(30);function v(e,t,i,n,r){this.static_tree=e,this.extra_bits=t,this.extra_base=i,this.elems=n,this.max_length=r,this.has_stree=e&&e.length}function y(e,t){this.dyn_tree=e,this.max_code=0,this.stat_desc=t}function A(e){return e<256?f[e]:f[256+(e>>>7)]}function C(e,t){e.pending_buf[e.pending++]=255&t,e.pending_buf[e.pending++]=t>>>8&255}function 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M(e,t,i){var n,r,s,o,l=0;if(0!==e.last_lit)do{n=e.pending_buf[e.d_buf+2*l]<<8|e.pending_buf[e.d_buf+2*l+1],r=e.pending_buf[e.l_buf+l],l++,0===n?x(e,r,t):(x(e,(s=p[r])+256+1,t),0!==(o=a[s])&&_(e,r-=g[s],o),x(e,s=A(--n),i),0!==(o=c[s])&&_(e,n-=F[s],o))}while(l<e.last_lit);x(e,256,t)}function R(e,t){var i,n,r,o=t.dyn_tree,a=t.stat_desc.static_tree,c=t.stat_desc.has_stree,l=t.stat_desc.elems,h=-1;for(e.heap_len=0,e.heap_max=573,i=0;i<l;i++)0!==o[2*i]?(e.heap[++e.heap_len]=h=i,e.depth[i]=0):o[2*i+1]=0;for(;e.heap_len<2;)o[2*(r=e.heap[++e.heap_len]=h<2?++h:0)]=1,e.depth[r]=0,e.opt_len--,c&&(e.static_len-=a[2*r+1]);for(t.max_code=h,i=e.heap_len>>1;i>=1;i--)B(e,o,i);r=l;do{i=e.heap[1],e.heap[1]=e.heap[e.heap_len--],B(e,o,1),n=e.heap[1],e.heap[--e.heap_max]=i,e.heap[--e.heap_max]=n,o[2*r]=o[2*i]+o[2*n],e.depth[r]=(e.depth[i]>=e.depth[n]?e.depth[i]:e.depth[n])+1,o[2*i+1]=o[2*n+1]=r,e.heap[1]=r++,B(e,o,1)}while(e.heap_len>=2);e.heap[--e.heap_max]=e.heap[1],function(e,t){var i,n,r,o,a,c,l=t.dyn_tree,h=t.max_code,d=t.stat_desc.static_tree,u=t.stat_desc.has_stree,f=t.stat_desc.extra_bits,p=t.stat_desc.extra_base,g=t.stat_desc.max_length,m=0;for(o=0;o<=s;o++)e.bl_count[o]=0;for(l[2*e.heap[e.heap_max]+1]=0,i=e.heap_max+1;i<573;i++)(o=l[2*l[2*(n=e.heap[i])+1]+1]+1)>g&&(o=g,m++),l[2*n+1]=o,n>h||(e.bl_count[o]++,a=0,n>=p&&(a=f[n-p]),c=l[2*n],e.opt_len+=c*(o+a),u&&(e.static_len+=c*(d[2*n+1]+a)));if(0!==m){do{for(o=g-1;0===e.bl_count[o];)o--;e.bl_count[o]--,e.bl_count[o+1]+=2,e.bl_count[g]--,m-=2}while(m>0);for(o=g;0!==o;o--)for(n=e.bl_count[o];0!==n;)(r=e.heap[--i])>h||(l[2*r+1]!==o&&(e.opt_len+=(o-l[2*r+1])*l[2*r],l[2*r+1]=o),n--)}}(e,t),I(o,h,e.bl_count)}function D(e,t,i){var n,r,s=-1,o=t[1],a=0,c=7,l=4;for(0===o&&(c=138,l=3),t[2*(i+1)+1]=65535,n=0;n<=i;n++)r=o,o=t[2*(n+1)+1],++a<c&&r===o||(a<l?e.bl_tree[2*r]+=a:0!==r?(r!==s&&e.bl_tree[2*r]++,e.bl_tree[32]++):a<=10?e.bl_tree[34]++:e.bl_tree[36]++,a=0,s=r,0===o?(c=138,l=3):r===o?(c=6,l=3):(c=7,l=4))}function 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v(d,a,257,286,s),w=new v(u,c,0,30,s),b=new v(new Array(0),l,0,19,7)}(),L=!0),e.l_desc=new y(e.dyn_ltree,m),e.d_desc=new y(e.dyn_dtree,w),e.bl_desc=new y(e.bl_tree,b),e.bi_buf=0,e.bi_valid=0,S(e)},t._tr_stored_block=z,t._tr_flush_block=function(e,t,i,n){var r,s,o=0;e.level>0?(2===e.strm.data_type&&(e.strm.data_type=function(e){var t,i=4093624447;for(t=0;t<=31;t++,i>>>=1)if(1&i&&0!==e.dyn_ltree[2*t])return 0;if(0!==e.dyn_ltree[18]||0!==e.dyn_ltree[20]||0!==e.dyn_ltree[26])return 1;for(t=32;t<256;t++)if(0!==e.dyn_ltree[2*t])return 1;return 0}(e)),R(e,e.l_desc),R(e,e.d_desc),o=function(e){var t;for(D(e,e.dyn_ltree,e.l_desc.max_code),D(e,e.dyn_dtree,e.d_desc.max_code),R(e,e.bl_desc),t=18;t>=3&&0===e.bl_tree[2*h[t]+1];t--);return e.opt_len+=3*(t+1)+5+5+4,t}(e),r=e.opt_len+3+7>>>3,(s=e.static_len+3+7>>>3)<=r&&(r=s)):r=s=i+5,i+4<=r&&-1!==t?z(e,t,i,n):4===e.strategy||s===r?(_(e,2+(n?1:0),3),M(e,d,u)):(_(e,4+(n?1:0),3),function(e,t,i,n){var r;for(_(e,t-257,5),_(e,i-1,5),_(e,n-4,4),r=0;r<n;r++)_(e,e.bl_tree[2*h[r]+1],3);T(e,e.dyn_ltree,t-1),T(e,e.dyn_dtree,i-1)}(e,e.l_desc.max_code+1,e.d_desc.max_code+1,o+1),M(e,e.dyn_ltree,e.dyn_dtree)),S(e),n&&E(e)},t._tr_tally=function(e,t,i){return e.pending_buf[e.d_buf+2*e.last_lit]=t>>>8&255,e.pending_buf[e.d_buf+2*e.last_lit+1]=255&t,e.pending_buf[e.l_buf+e.last_lit]=255&i,e.last_lit++,0===t?e.dyn_ltree[2*i]++:(e.matches++,t--,e.dyn_ltree[2*(p[i]+256+1)]++,e.dyn_dtree[2*A(t)]++),e.last_lit===e.lit_bufsize-1},t._tr_align=function(e){_(e,2,3),x(e,256,d),function(e){16===e.bi_valid?(C(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=255&e.bi_buf,e.bi_buf>>=8,e.bi_valid-=8)}(e)}},4442:e=>{e.exports=function(){this.input=null,this.next_in=0,this.avail_in=0,this.total_in=0,this.output=null,this.next_out=0,this.avail_out=0,this.total_out=0,this.msg=\"\",this.state=null,this.data_type=2,this.adler=0}},7392:e=>{class t{constructor(e={}){if(!(e.maxSize&&e.maxSize>0))throw new TypeError(\"`maxSize` must be a number greater than 0\");this.maxSize=e.maxSize,this.cache=new Map,this.oldCache=new Map,this._size=0}_set(e,t){this.cache.set(e,t),this._size++,this._size>=this.maxSize&&(this._size=0,this.oldCache=this.cache,this.cache=new Map)}get(e){if(this.cache.has(e))return this.cache.get(e);if(this.oldCache.has(e)){const t=this.oldCache.get(e);return this.oldCache.delete(e),this._set(e,t),t}}set(e,t){return this.cache.has(e)?this.cache.set(e,t):this._set(e,t),this}has(e){return this.cache.has(e)||this.oldCache.has(e)}peek(e){return this.cache.has(e)?this.cache.get(e):this.oldCache.has(e)?this.oldCache.get(e):void 0}delete(e){const t=this.cache.delete(e);return t&&this._size--,this.oldCache.delete(e)||t}clear(){this.cache.clear(),this.oldCache.clear(),this._size=0}*keys(){for(const[e]of this)yield e}*values(){for(const[,e]of this)yield e}*[Symbol.iterator](){for(const e of this.cache)yield e;for(const e of this.oldCache){const[t]=e;this.cache.has(t)||(yield e)}}get size(){let e=0;for(const t of this.oldCache.keys())this.cache.has(t)||e++;return this._size+e}}e.exports=t},1307:function(e,t,i){var n;n=e=>(()=>{var 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\"},t=>{t.exports=e}],i={};function 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-       "/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */var Jp={read:function(e,t,i,n,r){var s,o,a=8*r-n-1,c=(1<<a)-1,l=c>>1,h=-7,d=i?r-1:0,u=i?-1:1,f=e[t+d];for(d+=u,s=f&(1<<-h)-1,f>>=-h,h+=a;h>0;s=256*s+e[t+d],d+=u,h-=8);for(o=s&(1<<-h)-1,s>>=-h,h+=n;h>0;o=256*o+e[t+d],d+=u,h-=8);if(0===s)s=1-l;else{if(s===c)return o?NaN:1/0*(f?-1:1);o+=Math.pow(2,n),s-=l}return(f?-1:1)*o*Math.pow(2,s-n)},write:function(e,t,i,n,r,s){var o,a,c,l=8*s-r-1,h=(1<<l)-1,d=h>>1,u=23===r?Math.pow(2,-24)-Math.pow(2,-77):0,f=n?0:s-1,p=n?1:-1,g=t<0||0===t&&1/t<0?1:0;for(t=Math.abs(t),isNaN(t)||t===1/0?(a=isNaN(t)?1:0,o=h):(o=Math.floor(Math.log(t)/Math.LN2),t*(c=Math.pow(2,-o))<1&&(o--,c*=2),(t+=o+d>=1?u/c:u*Math.pow(2,1-d))*c>=2&&(o++,c/=2),o+d>=h?(a=0,o=h):o+d>=1?(a=(t*c-1)*Math.pow(2,r),o+=d):(a=t*Math.pow(2,d-1)*Math.pow(2,r),o=0));r>=8;e[i+f]=255&a,f+=p,a/=256,r-=8);for(o=o<<r|a,l+=r;l>0;e[i+f]=255&o,f+=p,o/=256,l-=8);e[i+f-p]|=128*g}};\n",
-       "/*!\n",
-       "     * The buffer module from node.js, for the browser.\n",
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-       "     * @author   Feross Aboukhadijeh <https://feross.org>\n",
-       "     * @license  MIT\n",
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e>>>=0,t||Ig(e,4,this.length),Jp.read(this,e,!1,23,4)},ng.prototype.readDoubleLE=function(e,t){return e>>>=0,t||Ig(e,8,this.length),Jp.read(this,e,!0,52,8)},ng.prototype.readDoubleBE=function(e,t){return e>>>=0,t||Ig(e,8,this.length),Jp.read(this,e,!1,52,8)},ng.prototype.writeUintLE=ng.prototype.writeUIntLE=function(e,t,i,n){if(e=+e,t>>>=0,i>>>=0,!n){Sg(this,e,t,i,Math.pow(2,8*i)-1,0)}let r=1,s=0;for(this[t]=255&e;++s<i&&(r*=256);)this[t+s]=e/r&255;return t+i},ng.prototype.writeUintBE=ng.prototype.writeUIntBE=function(e,t,i,n){if(e=+e,t>>>=0,i>>>=0,!n){Sg(this,e,t,i,Math.pow(2,8*i)-1,0)}let r=i-1,s=1;for(this[t+r]=255&e;--r>=0&&(s*=256);)this[t+r]=e/s&255;return t+i},ng.prototype.writeUint8=ng.prototype.writeUInt8=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,1,255,0),this[t]=255&e,t+1},ng.prototype.writeUint16LE=ng.prototype.writeUInt16LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,65535,0),this[t]=255&e,this[t+1]=e>>>8,t+2},ng.prototype.writeUint16BE=ng.prototype.writeUInt16BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,65535,0),this[t]=e>>>8,this[t+1]=255&e,t+2},ng.prototype.writeUint32LE=ng.prototype.writeUInt32LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,4294967295,0),this[t+3]=e>>>24,this[t+2]=e>>>16,this[t+1]=e>>>8,this[t]=255&e,t+4},ng.prototype.writeUint32BE=ng.prototype.writeUInt32BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,4294967295,0),this[t]=e>>>24,this[t+1]=e>>>16,this[t+2]=e>>>8,this[t+3]=255&e,t+4},ng.prototype.writeBigUInt64LE=Gg((function(e,t=0){return Eg(this,e,t,BigInt(0),BigInt(\"0xffffffffffffffff\"))})),ng.prototype.writeBigUInt64BE=Gg((function(e,t=0){return Ng(this,e,t,BigInt(0),BigInt(\"0xffffffffffffffff\"))})),ng.prototype.writeIntLE=function(e,t,i,n){if(e=+e,t>>>=0,!n){const n=Math.pow(2,8*i-1);Sg(this,e,t,i,n-1,-n)}let r=0,s=1,o=0;for(this[t]=255&e;++r<i&&(s*=256);)e<0&&0===o&&0!==this[t+r-1]&&(o=1),this[t+r]=(e/s|0)-o&255;return t+i},ng.prototype.writeIntBE=function(e,t,i,n){if(e=+e,t>>>=0,!n){const n=Math.pow(2,8*i-1);Sg(this,e,t,i,n-1,-n)}let r=i-1,s=1,o=0;for(this[t+r]=255&e;--r>=0&&(s*=256);)e<0&&0===o&&0!==this[t+r+1]&&(o=1),this[t+r]=(e/s|0)-o&255;return t+i},ng.prototype.writeInt8=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,1,127,-128),e<0&&(e=255+e+1),this[t]=255&e,t+1},ng.prototype.writeInt16LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,32767,-32768),this[t]=255&e,this[t+1]=e>>>8,t+2},ng.prototype.writeInt16BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,2,32767,-32768),this[t]=e>>>8,this[t+1]=255&e,t+2},ng.prototype.writeInt32LE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,2147483647,-2147483648),this[t]=255&e,this[t+1]=e>>>8,this[t+2]=e>>>16,this[t+3]=e>>>24,t+4},ng.prototype.writeInt32BE=function(e,t,i){return e=+e,t>>>=0,i||Sg(this,e,t,4,2147483647,-2147483648),e<0&&(e=4294967295+e+1),this[t]=e>>>24,this[t+1]=e>>>16,this[t+2]=e>>>8,this[t+3]=255&e,t+4},ng.prototype.writeBigInt64LE=Gg((function(e,t=0){return Eg(this,e,t,-BigInt(\"0x8000000000000000\"),BigInt(\"0x7fffffffffffffff\"))})),ng.prototype.writeBigInt64BE=Gg((function(e,t=0){return Ng(this,e,t,-BigInt(\"0x8000000000000000\"),BigInt(\"0x7fffffffffffffff\"))})),ng.prototype.writeFloatLE=function(e,t,i){return Mg(this,e,t,!0,i)},ng.prototype.writeFloatBE=function(e,t,i){return Mg(this,e,t,!1,i)},ng.prototype.writeDoubleLE=function(e,t,i){return Rg(this,e,t,!0,i)},ng.prototype.writeDoubleBE=function(e,t,i){return Rg(this,e,t,!1,i)},ng.prototype.copy=function(e,t,i,n){if(!ng.isBuffer(e))throw new TypeError(\"argument should be a Buffer\");if(i||(i=0),n||0===n||(n=this.length),t>=e.length&&(t=e.length),t||(t=0),n>0&&n<i&&(n=i),n===i)return 0;if(0===e.length||0===this.length)return 0;if(t<0)throw new RangeError(\"targetStart out of bounds\");if(i<0||i>=this.length)throw new RangeError(\"Index out of range\");if(n<0)throw new RangeError(\"sourceEnd out of bounds\");n>this.length&&(n=this.length),e.length-t<n-i&&(n=e.length-t+i);const r=n-i;return this===e&&\"function\"==typeof Uint8Array.prototype.copyWithin?this.copyWithin(t,i,n):Uint8Array.prototype.set.call(e,this.subarray(i,n),t),r},ng.prototype.fill=function(e,t,i,n){if(\"string\"==typeof e){if(\"string\"==typeof t?(n=t,t=0,i=this.length):\"string\"==typeof i&&(n=i,i=this.length),void 0!==n&&\"string\"!=typeof n)throw new TypeError(\"encoding must be a string\");if(\"string\"==typeof n&&!ng.isEncoding(n))throw new TypeError(\"Unknown encoding: \"+n);if(1===e.length){const t=e.charCodeAt(0);(\"utf8\"===n&&t<128||\"latin1\"===n)&&(e=t)}}else\"number\"==typeof e?e&=255:\"boolean\"==typeof e&&(e=Number(e));if(t<0||this.length<t||this.length<i)throw new RangeError(\"Out of range index\");if(i<=t)return this;let r;if(t>>>=0,i=void 0===i?this.length:i>>>0,e||(e=0),\"number\"==typeof e)for(r=t;r<i;++r)this[r]=e;else{const s=ng.isBuffer(e)?e:ng.from(e,n),o=s.length;if(0===o)throw new TypeError('The value \"'+e+'\" is invalid for argument \"value\"');for(r=0;r<i-t;++r)this[r+t]=s[r%o]}return this};const Dg={};function Tg(e,t,i){Dg[e]=class extends i{constructor(){super(),Object.defineProperty(this,\"message\",{value:t.apply(this,arguments),writable:!0,configurable:!0}),this.name=`${this.name} [${e}]`,this.stack,delete this.name}get code(){return e}set code(e){Object.defineProperty(this,\"code\",{configurable:!0,enumerable:!0,value:e,writable:!0})}toString(){return`${this.name} [${e}]: ${this.message}`}}}function Lg(e){let t=\"\",i=e.length;const n=\"-\"===e[0]?1:0;for(;i>=n+4;i-=3)t=`_${e.slice(i-3,i)}${t}`;return`${e.slice(0,i)}${t}`}function zg(e,t,i,n,r,s){if(e>i||e<t){const n=\"bigint\"==typeof t?\"n\":\"\";let r;throw r=s>3?0===t||t===BigInt(0)?`>= 0${n} and < 2${n} ** ${8*(s+1)}${n}`:`>= -(2${n} ** 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Received ${r}`,n}),RangeError);const Og=/[^+/0-9A-Za-z-_]/g;function Ug(e,t){let i;t=t||1/0;const n=e.length;let r=null;const s=[];for(let o=0;o<n;++o){if(i=e.charCodeAt(o),i>55295&&i<57344){if(!r){if(i>56319){(t-=3)>-1&&s.push(239,191,189);continue}if(o+1===n){(t-=3)>-1&&s.push(239,191,189);continue}r=i;continue}if(i<56320){(t-=3)>-1&&s.push(239,191,189),r=i;continue}i=65536+(r-55296<<10|i-56320)}else r&&(t-=3)>-1&&s.push(239,191,189);if(r=null,i<128){if((t-=1)<0)break;s.push(i)}else if(i<2048){if((t-=2)<0)break;s.push(i>>6|192,63&i|128)}else if(i<65536){if((t-=3)<0)break;s.push(i>>12|224,i>>6&63|128,63&i|128)}else{if(!(i<1114112))throw new Error(\"Invalid code point\");if((t-=4)<0)break;s.push(i>>18|240,i>>12&63|128,i>>6&63|128,63&i|128)}}return s}function qg(e){return Zp.toByteArray(function(e){if((e=(e=e.split(\"=\")[0]).trim().replace(Og,\"\")).length<2)return\"\";for(;e.length%4!=0;)e+=\"=\";return e}(e))}function Qg(e,t,i,n){let r;for(r=0;r<n&&!(r+i>=t.length||r>=e.length);++r)t[r+i]=e[r];return r}function Vg(e,t){return e instanceof t||null!=e&&null!=e.constructor&&null!=e.constructor.name&&e.constructor.name===t.name}function jg(e){return e!=e}const Wg=function(){const e=\"0123456789abcdef\",t=new Array(256);for(let i=0;i<16;++i){const n=16*i;for(let r=0;r<16;++r)t[n+r]=e[i]+e[r]}return t}();function Gg(e){return\"undefined\"==typeof BigInt?$g:e}function $g(){throw new Error(\"BigInt not supported\")}class Kg{constructor(e,t){this.position=0,this.url=e,this.config=t,Ht(e)||!1===t.cacheFetches?this.useCache=!1:(this.useCache=!0,this.cache=new Yg({fetch:(e,t)=>this._fetch(e,t),fetchSize:t.fetchSize||1e4}))}async _fetch(e,t){const i={start:e,size:t};this._stat={size:void 0};const n=await Qs.loadArrayBuffer(this.url,Ua(this.config,{range:i}));return ng.from(n)}async read(e,t=0,i=1/0,n=0){if(this.useCache)await this.cache.get(e,t,n,i);else{(await this._fetch(n,i)).copy(e,t)}return{bytesRead:i,buffer:e}}async readFile(){const e=await Qs.loadArrayBuffer(this.url,Ua(this.config));return ng.from(e)}async stat(){if(!this._stat){const e=ng.allocUnsafe(10);if(await this.read(e,0,10,0),!this._stat)throw new Error(`unable to determine size of file at ${this.url}`)}return this._stat}}class Yg{constructor({fetch:e,fetchSize:t=3e4}){this.fetch=e,this.position=0,this.buffer=ng.allocUnsafe(0),this.fetchSize=t}async get(e,t,i,n){if(e.length<t+n)throw new Error(\"output buffer not big enough for request\");if(i>=this.position&&i+n<=this.position+this.buffer.length);else{const e=Math.max(n,this.fetchSize);this.buffer=await this.fetch(i,e),this.position=i}const r=t,s=i-this.position,o=s+n;this.buffer.copy(e,r,s,o)}}class Xg{chrAliasTable=new Map;constructor(e,t,i){this.config=e,this.browser=i,this.genome=t,this.cramFile=new Vp.CramFile({filehandle:e.fileHandle?e.fileHandle:new Kg(e.url,e),seqFetch:e.seqFetch||async function(e,t,i){const n=this.genome,r=await this.getHeader(),s=n.getChromosomeName(r.indexToChr[e]);return this.genome.getSequence(s,t-1,i)}.bind(this),checkSequenceMD5:void 0===e.checkSequenceMD5||e.checkSequenceMD5});const n=e.indexFileHandle?e.indexFileHandle:new Kg(e.indexURL,e);this.indexedCramFile=new Vp.IndexedCramFile({cram:this.cramFile,index:new Vp.CraiIndex({filehandle:n}),fetchSizeLimit:e.fetchSizeLimit||1e9}),Mp.setReaderDefaults(this,e)}async getHeader(){if(!this.header){const e=await this.cramFile.getSamHeader(),t={},i=[],n=[];for(let r of e)if(\"SQ\"===r.tag){for(let e of r.data)if(\"SN\"===e.tag){const n=e.value;t[n]=i.length,i.push(n);break}}else\"RG\"===r.tag&&n.push(r.data);this.header={indexToChr:i,chrToIndex:t,chrNames:Object.keys(t),readGroups:n}}return this.header}async#x(e){if(await this.getHeader(),this.chrAliasTable.has(e)&&void 0===(e=this.chrAliasTable.get(e)))return;let t=this.header.chrToIndex[e];if(void 0===t){const i=await this.genome.getAliasRecord(e);let n;if(i){const e=Object.keys(i).filter((e=>\"start\"!==e&&\"end\"!==e)).map((e=>i[e])).filter((e=>void 0!==this.header.chrToIndex[e]));e.length>0&&(n=e[0],t=this.header.chrToIndex[e[0]])}this.chrAliasTable.set(e,n)}return t}async readAlignments(e,t,i){const n=await this.getHeader(),r=await this.#x(e),s=new tp(e,t,i,this.config);if(void 0===r)return s;try{const e=await this.indexedCramFile.getRecordsForRange(r,t,i);for(let a of e){const e=a.sequenceId,c=a.alignmentStart,l=c+a.lengthOnRef;if(e<0)continue;if(e>r||c>i)return;if(e<r)continue;if(l<t)continue;const h=o(a,n.chrNames);this.filter.pass(h)&&s.push(h)}return s.finish(),s}catch(e){let t=e.message;throw t&&t.indexOf(\"MD5\")>=0&&(t=\"Sequence mismatch. Is this the correct genome for the loaded CRAM?\"),this.browser.alert.present(new Error(t)),e}function o(e,t){const i=new wp;if(i.chr=t[e.sequenceId],i.start=e.alignmentStart-1,i.lengthOnRef=e.lengthOnRef,i.flags=e.flags,i.strand=!(16&e.flags),i.fragmentLength=e.templateLength||e.templateSize,i.mq=e.mappingQuality,i.end=e.alignmentStart+e.lengthOnRef,i.readGroupId=e.readGroupId,e.mate&&void 0!==e.mate.sequenceId){const n=void 0!==e.mate.flags?!(1&e.mate.flags):!(32&e.flags);i.mate={chr:t[e.mate.sequenceId],position:e.mate.alignmentStart,strand:n}}return i.seq=e.getReadBases(),i.qual=e.qualityScores,i.tagDict=e.tags,i.readName=e.readName,function(e,t){const i=[];let n,r,s=0,o=\"\";if(t.scStart=t.start,t.scLengthOnRef=t.lengthOnRef,e.readFeatures)for(let a of e.readFeatures){const e=a.code,c=a.data,l=a.pos-1,h=a.refPos-1;switch(e){case\"S\":case\"I\":case\"i\":case\"N\":case\"D\":if(l>s){const e=l-s;i.push(new xp({start:h-e,seqOffset:s,len:e,type:\"M\"})),s+=e,o+=e+\"M\"}if(\"S\"===e){let n=h;t.scLengthOnRef+=c.length,0===l&&(t.scStart-=c.length,n-=c.length);const r=c.length;i.push(new xp({start:n,seqOffset:s,len:r,type:\"S\"})),s+=r,o+=r+e}else if(\"I\"===e||\"i\"===e){void 0===n&&(n=[]);const t=\"i\"===e?1:c.length;n.push(new xp({start:h,len:t,seqOffset:s,type:\"I\"})),s+=t,o+=t+e}else\"D\"!==e&&\"N\"!==e||(r||(r=[]),r.push({start:h,len:c,type:e}),o+=c+e);break;case\"H\":case\"P\":o+=c+e}}const a=e.readLength-s;a>0&&(i.push(new xp({start:e.alignmentStart+e.lengthOnRef-a-1,seqOffset:s,len:a,type:\"M\"})),o+=a+\"M\");t.blocks=i,t.insertions=n,t.gaps=r,t.cigar=o}(e,i),i.mate&&i.start>i.mate.position&&i.fragmentLength>0&&(i.fragmentLength=-i.fragmentLength),Mp.setPairOrientation(i),i}}}const Zg=2291137574,Jg=2273964779,em=[84,68,70,52],tm=new Uint8Array([66,65,77,1]),im=[67,82,65,77],nm=[31,139],rm=4,sm=new Set([\"narrowpeak\",\"broadpeak\",\"regionpeak\",\"peaks\",\"bedgraph\",\"wig\",\"gff3\",\"gff\",\"gtf\",\"fusionjuncspan\",\"refflat\",\"seg\",\"aed\",\"bed\",\"bedMethyl\",\"vcf\",\"bb\",\"bigbed\",\"biginteract\",\"biggenepred\",\"bignarrowpeak\",\"bw\",\"bigwig\",\"bam\",\"tdf\",\"refgene\",\"genepred\",\"genepredext\",\"bedpe\",\"bp\",\"snp\",\"rmsk\",\"cram\",\"gwas\",\"maf\",\"mut\",\"hiccups\",\"fasta\",\"fa\",\"fna\",\"pytor\",\"hic\",\"qtl\"]);function om(e,t){const i=Math.min(e.length,t.length);if(0==i)return!1;for(let n=0;n<i;n++)if(e[n]!==t[n])return!1;return!0}async function am(e){let t;const i=e.filename||await ja(e.url);return i&&(t=await function(e){if(!e)return;if((e=e.toLowerCase()).endsWith(\"refgene.txt.gz\")||e.endsWith(\"refgene.txt.bgz\")||e.endsWith(\"refgene.txt\")||e.endsWith(\"refgene.sorted.txt.gz\")||e.endsWith(\"refgene.sorted.txt.bgz\"))return\"refgene\";e.endsWith(\".gz\")&&(e=e.substring(0,e.length-3));e.endsWith(\".bgz\")&&(e=e.substring(0,e.length-4));(e.endsWith(\".txt\")||e.endsWith(\".tab\")||e.endsWith(\".tsv\"))&&(e=e.substring(0,e.length-4));const t=e.lastIndexOf(\".\"),i=t<0?e:e.substring(t+1);switch(i){case\"bw\":return\"bigwig\";case\"bb\":return\"bigbed\";case\"fasta\":case\"fa\":case\"fna\":return\"fasta\";default:return sm.has(i)?i:void 0}}(i)),t||(t=await async function(e){const t=e.url;let i=Ua(e,{range:{start:0,size:1e3}}),n=await Qs.loadArrayBuffer(t,i),r=new Uint8Array(n);if(om(r,nm)){if(0!==(r[3]&rm)&&66===r[12]&&67===r[13]){i=Ua(e,{range:{start:0,size:ms(n)}}),n=await Qs.loadArrayBuffer(t,i),r=gs(n)}else i=Ua(e,{}),n=await Qs.loadArrayBuffer(t,i),r=ps(n),e._filecontents=r}if(om(r,tm))return\"bam\";if(om(r,im))return\"cram\";const s=!0;let o=new yc(new DataView(n),s).getUInt();if(o===Zg)return\"bigwig\";if(o===Jg)return\"bigbed\";if(om(r,em))return\"tdf\";const a=new TextDecoder(\"utf-8\").decode(r),c=a.split(/\\r?\\n/)[0];if(c.startsWith(\"##fileformat=VCF\"))return\"vcf\";if(c.startsWith(\"##gff-version 3\"))return\"gff3\";if(c.startsWith(\"##gff-version\"))return\"gff\";if(c.startsWith(\"##fileformat=\"))return c.substring(13).toLowerCase();if(xh.isQTL(c))return\"qtl\";if(Jl.isGWAS(c))return\"gwas\";if(Dc(c.split(\"\\t\")))return\"hiccups\";return null}(e)),t}class cm{constructor(e,t){const i=t.genome;if(this.config=e,this.genome=i,Ga(e.url)&&(this.config.indexed=!1),\"ga4gh\"===e.sourceType)throw Error(\"Unsupported source type 'ga4gh'\");if(\"pysam\"===e.sourceType)this.bamReader=new Up(e,i);else if(\"htsget\"===e.sourceType)this.bamReader=new Qp(e,i);else if(\"shardedBam\"===e.sourceType)this.bamReader=new Op(e,i);else if(\"cram\"===e.format)this.bamReader=new Xg(e,i,t);else{if(!this.config.indexURL&&!1!==e.indexed)if(Mt(this.config.url)){const e=function(e,t){if(Mt(e)){if(e.includes(\"?\")){const i=e.indexOf(\"?\");return e.substring(0,i)+\".\"+t+e.substring(i)}return e+\".\"+t}}(this.config.url,\"bai\");e?(console.warn(`Warning: no indexURL specified for ${this.config.url}.  Guessing ${e}`),this.config.indexURL=e):(console.warning(`Warning: no indexURL specified for ${this.config.url}.`),this.config.indexed=!1)}else console.warning(`Warning: no indexURL specified for ${this.config.name}.`),this.config.indexed=!1;!1!==this.config.indexed?this.bamReader=new Pp(e,i):this.bamReader=new Hp(e,i)}}async getAlignments(e,t,i){const n=this.genome,r=await this.bamReader.readAlignments(e,t,i);if(r.hasAlignments){const t=await n.getSequence(e,r.start,r.end);if(t)return r.coverageMap.refSeq=t,r.sequence=t,r;console.error(\"No sequence for: \"+e+\":\"+r.start+\"-\"+r.end)}return r}}class lm{constructor({chr:e,start:t,end:i}){this.chr=e,this.start=t,this.end=i}contains(e){return e.chr===this.chr&&e.start>=this.start&&e.end<=this.end}overlaps(e){return e.chr===this.chr&&!(e.end<this.start||e.start>this.end)}extend(e){e.chr===this.chr&&(this.start=Math.min(e.start,this.start),this.end=Math.max(e.end,this.end))}getLocusString(){if(\"all\"===this.chr)return\"all\";{const e=Rt(Math.floor(this.start)+1),t=Rt(Math.round(this.end));return`${this.chr}:${e}-${t}`}}static fromLocusString(e){if(\"all\"===e)return new lm({chr:\"all\"});const t=e.split(\":\"),i=t[0],n=t[1].split(\"-\"),r=Number.parseInt(n[0].replace(/,/g,\"\"))-1,s=Number.parseInt(n[1].replace(/,/g,\"\"));return new lm({chr:i,start:r,end:s})}}\n",
-       "/*!\n",
-       "     * vanilla-picker v2.12.1\n",
-       "     * https://vanilla-picker.js.org\n",
-       "     *\n",
-       "     * Copyright 2017-2021 Andreas Borgen (https://github.com/Sphinxxxx), Adam Brooks (https://github.com/dissimulate)\n",
-       "     * Released under the ISC license.\n",
-       "     */var hm=function(e,t){if(!(e instanceof t))throw new TypeError(\"Cannot call a class as a function\")},dm=function(){function e(e,t){for(var i=0;i<t.length;i++){var n=t[i];n.enumerable=n.enumerable||!1,n.configurable=!0,\"value\"in n&&(n.writable=!0),Object.defineProperty(e,n.key,n)}}return function(t,i,n){return i&&e(t.prototype,i),n&&e(t,n),t}}(),um=function(e,t){if(Array.isArray(e))return e;if(Symbol.iterator in Object(e))return function(e,t){var i=[],n=!0,r=!1,s=void 0;try{for(var o,a=e[Symbol.iterator]();!(n=(o=a.next()).done)&&(i.push(o.value),!t||i.length!==t);n=!0);}catch(e){r=!0,s=e}finally{try{!n&&a.return&&a.return()}finally{if(r)throw s}}return i}(e,t);throw new TypeError(\"Invalid attempt to destructure non-iterable instance\")};String.prototype.startsWith=String.prototype.startsWith||function(e){return 0===this.indexOf(e)},String.prototype.padStart=String.prototype.padStart||function(e,t){for(var i=this;i.length<e;)i=t+i;return i};var fm={cb:\"0f8ff\",tqw:\"aebd7\",q:\"-ffff\",qmrn:\"7fffd4\",zr:\"0ffff\",bg:\"5f5dc\",bsq:\"e4c4\",bck:\"---\",nch:\"ebcd\",b:\"--ff\",bvt:\"8a2be2\",brwn:\"a52a2a\",brw:\"deb887\",ctb:\"5f9ea0\",hrt:\"7fff-\",chcT:\"d2691e\",cr:\"7f50\",rnw:\"6495ed\",crns:\"8dc\",crms:\"dc143c\",cn:\"-ffff\",Db:\"--8b\",Dcn:\"-8b8b\",Dgnr:\"b8860b\",Dgr:\"a9a9a9\",Dgrn:\"-64-\",Dkhk:\"bdb76b\",Dmgn:\"8b-8b\",Dvgr:\"556b2f\",Drng:\"8c-\",Drch:\"9932cc\",Dr:\"8b--\",Dsmn:\"e9967a\",Dsgr:\"8fbc8f\",DsTb:\"483d8b\",DsTg:\"2f4f4f\",Dtrq:\"-ced1\",Dvt:\"94-d3\",ppnk:\"1493\",pskb:\"-bfff\",mgr:\"696969\",grb:\"1e90ff\",rbrc:\"b22222\",rwht:\"af0\",stg:\"228b22\",chs:\"-ff\",gnsb:\"dcdcdc\",st:\"8f8ff\",g:\"d7-\",gnr:\"daa520\",gr:\"808080\",grn:\"-8-0\",grnw:\"adff2f\",hnw:\"0fff0\",htpn:\"69b4\",nnr:\"cd5c5c\",ng:\"4b-82\",vr:\"0\",khk:\"0e68c\",vnr:\"e6e6fa\",nrb:\"0f5\",wngr:\"7cfc-\",mnch:\"acd\",Lb:\"add8e6\",Lcr:\"08080\",Lcn:\"e0ffff\",Lgnr:\"afad2\",Lgr:\"d3d3d3\",Lgrn:\"90ee90\",Lpnk:\"b6c1\",Lsmn:\"a07a\",Lsgr:\"20b2aa\",Lskb:\"87cefa\",LsTg:\"778899\",Lstb:\"b0c4de\",Lw:\"e0\",m:\"-ff-\",mgrn:\"32cd32\",nn:\"af0e6\",mgnt:\"-ff\",mrn:\"8--0\",mqm:\"66cdaa\",mmb:\"--cd\",mmrc:\"ba55d3\",mmpr:\"9370db\",msg:\"3cb371\",mmsT:\"7b68ee\",\"\":\"-fa9a\",mtr:\"48d1cc\",mmvt:\"c71585\",mnLb:\"191970\",ntc:\"5fffa\",mstr:\"e4e1\",mccs:\"e4b5\",vjw:\"dead\",nv:\"--80\",c:\"df5e6\",v:\"808-0\",vrb:\"6b8e23\",rng:\"a5-\",rngr:\"45-\",rch:\"da70d6\",pgnr:\"eee8aa\",pgrn:\"98fb98\",ptrq:\"afeeee\",pvtr:\"db7093\",ppwh:\"efd5\",pchp:\"dab9\",pr:\"cd853f\",pnk:\"c0cb\",pm:\"dda0dd\",pwrb:\"b0e0e6\",prp:\"8-080\",cc:\"663399\",r:\"--\",sbr:\"bc8f8f\",rb:\"4169e1\",sbrw:\"8b4513\",smn:\"a8072\",nbr:\"4a460\",sgrn:\"2e8b57\",ssh:\"5ee\",snn:\"a0522d\",svr:\"c0c0c0\",skb:\"87ceeb\",sTb:\"6a5acd\",sTgr:\"708090\",snw:\"afa\",n:\"-ff7f\",stb:\"4682b4\",tn:\"d2b48c\",t:\"-8080\",thst:\"d8bfd8\",tmT:\"6347\",trqs:\"40e0d0\",vt:\"ee82ee\",whT:\"5deb3\",wht:\"\",hts:\"5f5f5\",w:\"-\",wgrn:\"9acd32\"};function pm(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:1;return(t>0?e.toFixed(t).replace(/0+$/,\"\").replace(/\\.$/,\"\"):e.toString())||\"0\"}var gm=function(){function e(t,i,n,r){hm(this,e);var s=this;if(void 0===t);else if(Array.isArray(t))this.rgba=t;else if(void 0===n){var o=t&&\"\"+t;o&&function(t){if(t.startsWith(\"hsl\")){var i=t.match(/([\\-\\d\\.e]+)/g).map(Number),n=um(i,4),r=n[0],o=n[1],a=n[2],c=n[3];void 0===c&&(c=1),r/=360,o/=100,a/=100,s.hsla=[r,o,a,c]}else if(t.startsWith(\"rgb\")){var l=t.match(/([\\-\\d\\.e]+)/g).map(Number),h=um(l,4),d=h[0],u=h[1],f=h[2],p=h[3];void 0===p&&(p=1),s.rgba=[d,u,f,p]}else t.startsWith(\"#\")?s.rgba=e.hexToRgb(t):s.rgba=e.nameToRgb(t)||e.hexToRgb(t)}(o.toLowerCase())}else this.rgba=[t,i,n,void 0===r?1:r]}return dm(e,[{key:\"printRGB\",value:function(e){var t=(e?this.rgba:this.rgba.slice(0,3)).map((function(e,t){return pm(e,3===t?3:0)}));return e?\"rgba(\"+t+\")\":\"rgb(\"+t+\")\"}},{key:\"printHSL\",value:function(e){var t=[360,100,100,1],i=[\"\",\"%\",\"%\",\"\"],n=(e?this.hsla:this.hsla.slice(0,3)).map((function(e,n){return pm(e*t[n],3===n?3:1)+i[n]}));return e?\"hsla(\"+n+\")\":\"hsl(\"+n+\")\"}},{key:\"printHex\",value:function(e){var t=this.hex;return e?t:t.substring(0,7)}},{key:\"rgba\",get:function(){if(this._rgba)return this._rgba;if(!this._hsla)throw new Error(\"No color is set\");return this._rgba=e.hslToRgb(this._hsla)},set:function(e){3===e.length&&(e[3]=1),this._rgba=e,this._hsla=null}},{key:\"rgbString\",get:function(){return this.printRGB()}},{key:\"rgbaString\",get:function(){return this.printRGB(!0)}},{key:\"hsla\",get:function(){if(this._hsla)return this._hsla;if(!this._rgba)throw new Error(\"No color is set\");return this._hsla=e.rgbToHsl(this._rgba)},set:function(e){3===e.length&&(e[3]=1),this._hsla=e,this._rgba=null}},{key:\"hslString\",get:function(){return this.printHSL()}},{key:\"hslaString\",get:function(){return this.printHSL(!0)}},{key:\"hex\",get:function(){var e=this.rgba.map((function(e,t){return t<3?e.toString(16):Math.round(255*e).toString(16)}));return\"#\"+e.map((function(e){return e.padStart(2,\"0\")})).join(\"\")},set:function(t){this.rgba=e.hexToRgb(t)}}],[{key:\"hexToRgb\",value:function(e){var t=(e.startsWith(\"#\")?e.slice(1):e).replace(/^(\\w{3})$/,\"$1F\").replace(/^(\\w)(\\w)(\\w)(\\w)$/,\"$1$1$2$2$3$3$4$4\").replace(/^(\\w{6})$/,\"$1FF\");if(!t.match(/^([0-9a-fA-F]{8})$/))throw new Error(\"Unknown hex color; \"+e);var i=t.match(/^(\\w\\w)(\\w\\w)(\\w\\w)(\\w\\w)$/).slice(1).map((function(e){return parseInt(e,16)}));return i[3]=i[3]/255,i}},{key:\"nameToRgb\",value:function(t){var i=t.toLowerCase().replace(\"at\",\"T\").replace(/[aeiouyldf]/g,\"\").replace(\"ght\",\"L\").replace(\"rk\",\"D\").slice(-5,4),n=fm[i];return void 0===n?n:e.hexToRgb(n.replace(/\\-/g,\"00\").padStart(6,\"f\"))}},{key:\"rgbToHsl\",value:function(e){var t=um(e,4),i=t[0],n=t[1],r=t[2],s=t[3];i/=255,n/=255,r/=255;var o=Math.max(i,n,r),a=Math.min(i,n,r),c=void 0,l=void 0,h=(o+a)/2;if(o===a)c=l=0;else{var d=o-a;switch(l=h>.5?d/(2-o-a):d/(o+a),o){case i:c=(n-r)/d+(n<r?6:0);break;case n:c=(r-i)/d+2;break;case r:c=(i-n)/d+4}c/=6}return[c,l,h,s]}},{key:\"hslToRgb\",value:function(e){var t=um(e,4),i=t[0],n=t[1],r=t[2],s=t[3],o=void 0,a=void 0,c=void 0;if(0===n)o=a=c=r;else{var l=function(e,t,i){return i<0&&(i+=1),i>1&&(i-=1),i<1/6?e+6*(t-e)*i:i<.5?t:i<2/3?e+(t-e)*(2/3-i)*6:e},h=r<.5?r*(1+n):r+n-r*n,d=2*r-h;o=l(d,h,i+1/3),a=l(d,h,i),c=l(d,h,i-1/3)}var u=[255*o,255*a,255*c].map(Math.round);return u[3]=s,u}}]),e}(),mm=function(){function e(){hm(this,e),this._events=[]}return dm(e,[{key:\"add\",value:function(e,t,i){e.addEventListener(t,i,!1),this._events.push({target:e,type:t,handler:i})}},{key:\"remove\",value:function(t,i,n){this._events=this._events.filter((function(r){var s=!0;return t&&t!==r.target&&(s=!1),i&&i!==r.type&&(s=!1),n&&n!==r.handler&&(s=!1),s&&e._doRemove(r.target,r.type,r.handler),!s}))}},{key:\"destroy\",value:function(){this._events.forEach((function(t){return e._doRemove(t.target,t.type,t.handler)})),this._events=[]}}],[{key:\"_doRemove\",value:function(e,t,i){e.removeEventListener(t,i,!1)}}]),e}();function wm(e,t,i){var n=!1;function r(e,t,i){return Math.max(t,Math.min(e,i))}function s(e,s,o){if(o&&(n=!0),n){e.preventDefault();var a=t.getBoundingClientRect(),c=a.width,l=a.height,h=s.clientX,d=s.clientY,u=r(h-a.left,0,c),f=r(d-a.top,0,l);i(u/c,f/l)}}function o(e,t){1===(void 0===e.buttons?e.which:e.buttons)?s(e,e,t):n=!1}function a(e,t){1===e.touches.length?s(e,e.touches[0],t):n=!1}e.add(t,\"mousedown\",(function(e){o(e,!0)})),e.add(t,\"touchstart\",(function(e){a(e,!0)})),e.add(window,\"mousemove\",o),e.add(t,\"touchmove\",a),e.add(window,\"mouseup\",(function(e){n=!1})),e.add(t,\"touchend\",(function(e){n=!1})),e.add(t,\"touchcancel\",(function(e){n=!1}))}var bm=\"keydown\",Fm=\"mousedown\",vm=\"focusin\";function ym(e,t){return(t||document).querySelector(e)}function Am(e){e.preventDefault(),e.stopPropagation()}function Cm(e,t,i,n,r){e.add(t,bm,(function(e){i.indexOf(e.key)>=0&&(r&&Am(e),n(e))}))}var _m=function(){function e(t){hm(this,e),this.settings={popup:\"right\",layout:\"default\",alpha:!0,editor:!0,editorFormat:\"hex\",cancelButton:!1,defaultColor:\"#0cf\"},this._events=new mm,this.onChange=null,this.onDone=null,this.onOpen=null,this.onClose=null,this.setOptions(t)}return dm(e,[{key:\"setOptions\",value:function(e){var t=this;if(e){var i=this.settings;if(e instanceof HTMLElement)i.parent=e;else{i.parent&&e.parent&&i.parent!==e.parent&&(this._events.remove(i.parent),this._popupInited=!1),function(e,t,i){for(var n in e)i&&i.indexOf(n)>=0||(t[n]=e[n])}(e,i),e.onChange&&(this.onChange=e.onChange),e.onDone&&(this.onDone=e.onDone),e.onOpen&&(this.onOpen=e.onOpen),e.onClose&&(this.onClose=e.onClose);var n=e.color||e.colour;n&&this._setColor(n)}var r=i.parent;if(r&&i.popup&&!this._popupInited){var s=function(e){return t.openHandler(e)};this._events.add(r,\"click\",s),Cm(this._events,r,[\" \",\"Spacebar\",\"Enter\"],s),this._popupInited=!0}else e.parent&&!i.popup&&this.show()}}},{key:\"openHandler\",value:function(e){if(this.show()){e&&e.preventDefault(),this.settings.parent.style.pointerEvents=\"none\";var t=e&&e.type===bm?this._domEdit:this.domElement;setTimeout((function(){return t.focus()}),100),this.onOpen&&this.onOpen(this.colour)}}},{key:\"closeHandler\",value:function(e){var t=e&&e.type,i=!1;if(e)if(t===Fm||t===vm){var n=(this.__containedEvent||0)+100;e.timeStamp>n&&(i=!0)}else Am(e),i=!0;else i=!0;i&&this.hide()&&(this.settings.parent.style.pointerEvents=\"\",t!==Fm&&this.settings.parent.focus(),this.onClose&&this.onClose(this.colour))}},{key:\"movePopup\",value:function(e,t){this.closeHandler(),this.setOptions(e),t&&this.openHandler()}},{key:\"setColor\",value:function(e,t){this._setColor(e,{silent:t})}},{key:\"_setColor\",value:function(e,t){if(\"string\"==typeof e&&(e=e.trim()),e){t=t||{};var i=void 0;try{i=new gm(e)}catch(e){if(t.failSilently)return;throw e}if(!this.settings.alpha){var n=i.hsla;n[3]=1,i.hsla=n}this.colour=this.color=i,this._setHSLA(null,null,null,null,t)}}},{key:\"setColour\",value:function(e,t){this.setColor(e,t)}},{key:\"show\",value:function(){if(!this.settings.parent)return!1;if(this.domElement){var e=this._toggleDOM(!0);return this._setPosition(),e}var t=function(e){var t=document.createElement(\"div\");return t.innerHTML=e,t.firstElementChild}(this.settings.template||'<div class=\"picker_wrapper\" tabindex=\"-1\"><div class=\"picker_arrow\"></div><div class=\"picker_hue picker_slider\"><div class=\"picker_selector\"></div></div><div class=\"picker_sl\"><div class=\"picker_selector\"></div></div><div class=\"picker_alpha picker_slider\"><div class=\"picker_selector\"></div></div><div class=\"picker_editor\"><input aria-label=\"Type a color name or hex value\"/></div><div class=\"picker_sample\"></div><div class=\"picker_done\"><button>Ok</button></div><div class=\"picker_cancel\"><button>Cancel</button></div></div>');return this.domElement=t,this._domH=ym(\".picker_hue\",t),this._domSL=ym(\".picker_sl\",t),this._domA=ym(\".picker_alpha\",t),this._domEdit=ym(\".picker_editor input\",t),this._domSample=ym(\".picker_sample\",t),this._domOkay=ym(\".picker_done button\",t),this._domCancel=ym(\".picker_cancel button\",t),t.classList.add(\"layout_\"+this.settings.layout),this.settings.alpha||t.classList.add(\"no_alpha\"),this.settings.editor||t.classList.add(\"no_editor\"),this.settings.cancelButton||t.classList.add(\"no_cancel\"),this._ifPopup((function(){return t.classList.add(\"popup\")})),this._setPosition(),this.colour?this._updateUI():this._setColor(this.settings.defaultColor),this._bindEvents(),!0}},{key:\"hide\",value:function(){return this._toggleDOM(!1)}},{key:\"destroy\",value:function(){this._events.destroy(),this.domElement&&this.settings.parent.removeChild(this.domElement)}},{key:\"_bindEvents\",value:function(){var e=this,t=this,i=this.domElement,n=this._events;function r(e,t,i){n.add(e,t,i)}r(i,\"click\",(function(e){return e.preventDefault()})),wm(n,this._domH,(function(e,i){return t._setHSLA(e)})),wm(n,this._domSL,(function(e,i){return t._setHSLA(null,e,1-i)})),this.settings.alpha&&wm(n,this._domA,(function(e,i){return t._setHSLA(null,null,null,1-i)}));var s=this._domEdit;r(s,\"input\",(function(e){t._setColor(this.value,{fromEditor:!0,failSilently:!0})})),r(s,\"focus\",(function(e){var t=this;t.selectionStart===t.selectionEnd&&t.select()})),this._ifPopup((function(){var t=function(t){return e.closeHandler(t)};r(window,Fm,t),r(window,vm,t),Cm(n,i,[\"Esc\",\"Escape\"],t);var s=function(t){e.__containedEvent=t.timeStamp};r(i,Fm,s),r(i,vm,s),r(e._domCancel,\"click\",t)}));var o=function(t){e._ifPopup((function(){return e.closeHandler(t)})),e.onDone&&e.onDone(e.colour)};r(this._domOkay,\"click\",o),Cm(n,i,[\"Enter\"],o)}},{key:\"_setPosition\",value:function(){var e=this.settings.parent,t=this.domElement;e!==t.parentNode&&e.appendChild(t),this._ifPopup((function(i){\"static\"===getComputedStyle(e).position&&(e.style.position=\"relative\");var n=!0===i?\"popup_right\":\"popup_\"+i;[\"popup_top\",\"popup_bottom\",\"popup_left\",\"popup_right\"].forEach((function(e){e===n?t.classList.add(e):t.classList.remove(e)})),t.classList.add(n)}))}},{key:\"_setHSLA\",value:function(e,t,i,n,r){r=r||{};var s=this.colour,o=s.hsla;[e,t,i,n].forEach((function(e,t){(e||0===e)&&(o[t]=e)})),s.hsla=o,this._updateUI(r),this.onChange&&!r.silent&&this.onChange(s)}},{key:\"_updateUI\",value:function(e){if(this.domElement){e=e||{};var t=this.colour,i=t.hsla,n=\"hsl(\"+360*i[0]+\", 100%, 50%)\",r=t.hslString,s=t.hslaString,o=this._domH,a=this._domSL,c=this._domA,l=ym(\".picker_selector\",o),h=ym(\".picker_selector\",a),d=ym(\".picker_selector\",c);b(0,l,i[0]),this._domSL.style.backgroundColor=this._domH.style.color=n,b(0,h,i[1]),F(0,h,1-i[2]),a.style.color=r,F(0,d,1-i[3]);var u=r,f=u.replace(\"hsl\",\"hsla\").replace(\")\",\", 0)\"),p=\"linear-gradient(\"+[u,f]+\")\";if(this._domA.style.background=p+\", linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0 / 2em 2em,\\n                   linear-gradient(45deg, lightgrey 25%,       white 25%,       white 75%, lightgrey 75%) 1em 1em / 2em 2em\",!e.fromEditor){var g=this.settings.editorFormat,m=this.settings.alpha,w=void 0;switch(g){case\"rgb\":w=t.printRGB(m);break;case\"hsl\":w=t.printHSL(m);break;default:w=t.printHex(m)}this._domEdit.value=w}this._domSample.style.color=s}function b(e,t,i){t.style.left=100*i+\"%\"}function F(e,t,i){t.style.top=100*i+\"%\"}}},{key:\"_ifPopup\",value:function(e,t){this.settings.parent&&this.settings.popup?e&&e(this.settings.popup):t&&t()}},{key:\"_toggleDOM\",value:function(e){var t=this.domElement;if(!t)return!1;var i=e?\"\":\"none\",n=t.style.display!==i;return n&&(t.style.display=i),n}}]),e}(),xm=document.createElement(\"style\");function km(e){if(Im[e])return Im[e];if(Im[\"chr\"+e]){const t=Im[\"chr\"+e];return Im[e]=t,t}{const r=(t=Math.round(255*Math.random()).toString(10),i=Math.round(255*Math.random()).toString(10),n=Math.round(255*Math.random()).toString(10),\"rgb(\"+t+\",\"+i+\",\"+n+\")\");return Im[e]=r,r}var t,i,n}xm.textContent='.picker_wrapper.no_alpha .picker_alpha{display:none}.picker_wrapper.no_editor .picker_editor{position:absolute;z-index:-1;opacity:0}.picker_wrapper.no_cancel .picker_cancel{display:none}.layout_default.picker_wrapper{display:flex;flex-flow:row wrap;justify-content:space-between;align-items:stretch;font-size:10px;width:25em;padding:.5em}.layout_default.picker_wrapper input,.layout_default.picker_wrapper button{font-size:1rem}.layout_default.picker_wrapper>*{margin:.5em}.layout_default.picker_wrapper::before{content:\"\";display:block;width:100%;height:0;order:1}.layout_default .picker_slider,.layout_default .picker_selector{padding:1em}.layout_default .picker_hue{width:100%}.layout_default .picker_sl{flex:1 1 auto}.layout_default .picker_sl::before{content:\"\";display:block;padding-bottom:100%}.layout_default .picker_editor{order:1;width:6.5rem}.layout_default .picker_editor input{width:100%;height:100%}.layout_default .picker_sample{order:1;flex:1 1 auto}.layout_default .picker_done,.layout_default .picker_cancel{order:1}.picker_wrapper{box-sizing:border-box;background:#f2f2f2;box-shadow:0 0 0 1px silver;cursor:default;font-family:sans-serif;color:#444;pointer-events:auto}.picker_wrapper:focus{outline:none}.picker_wrapper button,.picker_wrapper input{box-sizing:border-box;border:none;box-shadow:0 0 0 1px silver;outline:none}.picker_wrapper button:focus,.picker_wrapper button:active,.picker_wrapper input:focus,.picker_wrapper input:active{box-shadow:0 0 2px 1px #1e90ff}.picker_wrapper button{padding:.4em .6em;cursor:pointer;background-color:#f5f5f5;background-image:linear-gradient(0deg, gainsboro, transparent)}.picker_wrapper button:active{background-image:linear-gradient(0deg, transparent, gainsboro)}.picker_wrapper button:hover{background-color:#fff}.picker_selector{position:absolute;z-index:1;display:block;-webkit-transform:translate(-50%, -50%);transform:translate(-50%, -50%);border:2px solid #fff;border-radius:100%;box-shadow:0 0 3px 1px #67b9ff;background:currentColor;cursor:pointer}.picker_slider .picker_selector{border-radius:2px}.picker_hue{position:relative;background-image:linear-gradient(90deg, red, yellow, lime, cyan, blue, magenta, red);box-shadow:0 0 0 1px silver}.picker_sl{position:relative;box-shadow:0 0 0 1px silver;background-image:linear-gradient(180deg, white, rgba(255, 255, 255, 0) 50%),linear-gradient(0deg, black, rgba(0, 0, 0, 0) 50%),linear-gradient(90deg, #808080, rgba(128, 128, 128, 0))}.picker_alpha,.picker_sample{position:relative;background:linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%) 0 0/2em 2em,linear-gradient(45deg, lightgrey 25%, white 25%, white 75%, lightgrey 75%) 1em 1em/2em 2em;box-shadow:0 0 0 1px silver}.picker_alpha .picker_selector,.picker_sample .picker_selector{background:none}.picker_editor input{font-family:monospace;padding:.2em .4em}.picker_sample::before{content:\"\";position:absolute;display:block;width:100%;height:100%;background:currentColor}.picker_arrow{position:absolute;z-index:-1}.picker_wrapper.popup{position:absolute;z-index:2;margin:1.5em}.picker_wrapper.popup,.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{background:#f2f2f2;box-shadow:0 0 10px 1px rgba(0,0,0,.4)}.picker_wrapper.popup .picker_arrow{width:3em;height:3em;margin:0}.picker_wrapper.popup .picker_arrow::before,.picker_wrapper.popup .picker_arrow::after{content:\"\";display:block;position:absolute;top:0;left:0;z-index:-99}.picker_wrapper.popup .picker_arrow::before{width:100%;height:100%;-webkit-transform:skew(45deg);transform:skew(45deg);-webkit-transform-origin:0 100%;transform-origin:0 100%}.picker_wrapper.popup .picker_arrow::after{width:150%;height:150%;box-shadow:none}.popup.popup_top{bottom:100%;left:0}.popup.popup_top .picker_arrow{bottom:0;left:0;-webkit-transform:rotate(-90deg);transform:rotate(-90deg)}.popup.popup_bottom{top:100%;left:0}.popup.popup_bottom .picker_arrow{top:0;left:0;-webkit-transform:rotate(90deg) scale(1, -1);transform:rotate(90deg) scale(1, -1)}.popup.popup_left{top:0;right:100%}.popup.popup_left .picker_arrow{top:0;right:0;-webkit-transform:scale(-1, 1);transform:scale(-1, 1)}.popup.popup_right{top:0;left:100%}.popup.popup_right .picker_arrow{top:0;left:0}',document.documentElement.firstElementChild.appendChild(xm),_m.StyleElement=xm;const Im={chrX:\"rgb(204, 153, 0)\",chrY:\"rgb(153, 204, 0\",chrUn:\"rgb(50, 50, 50)\",chr1:\"rgb(80, 80, 255)\",chrI:\"rgb(139, 155, 187)\",chr2:\"rgb(206, 61, 50)\",chrII:\"rgb(206, 61, 50)\",chr2a:\"rgb(216, 71, 60)\",chr2b:\"rgb(226, 81, 70)\",chr3:\"rgb(116, 155, 88)\",chrIII:\"rgb(116, 155, 88)\",chr4:\"rgb(240, 230, 133)\",chrIV:\"rgb(240, 230, 133)\",chr5:\"rgb(70, 105, 131)\",chr6:\"rgb(186, 99, 56)\",chr7:\"rgb(93, 177, 221)\",chr8:\"rgb(128, 34, 104)\",chr9:\"rgb(107, 215, 107)\",chr10:\"rgb(213, 149, 167)\",chr11:\"rgb(146, 72, 34)\",chr12:\"rgb(131, 123, 141)\",chr13:\"rgb(199, 81, 39)\",chr14:\"rgb(213, 143, 92)\",chr15:\"rgb(122, 101, 165)\",chr16:\"rgb(228, 175, 105)\",chr17:\"rgb(59, 27, 83)\",chr18:\"rgb(205, 222, 183)\",chr19:\"rgb(97, 42, 121)\",chr20:\"rgb(174, 31, 99)\",chr21:\"rgb(231, 199, 111)\",chr22:\"rgb(90, 101, 94)\",chr23:\"rgb(204, 153, 0)\",chr24:\"rgb(153, 204, 0)\",chr25:\"rgb(51, 204, 0)\",chr26:\"rgb(0, 204, 51)\",chr27:\"rgb(0, 204, 153)\",chr28:\"rgb(0, 153, 204)\",chr29:\"rgb(10, 71, 255)\",chr30:\"rgb(71, 117, 255)\",chr31:\"rgb(255, 194, 10)\",chr32:\"rgb(255, 209, 71)\",chr33:\"rgb(153, 0, 51)\",chr34:\"rgb(153, 26, 0)\",chr35:\"rgb(153, 102, 0)\",chr36:\"rgb(128, 153, 0)\",chr37:\"rgb(51, 153, 0)\",chr38:\"rgb(0, 153, 26)\",chr39:\"rgb(0, 153, 102)\",chr40:\"rgb(0, 128, 153)\",chr41:\"rgb(0, 51, 153)\",chr42:\"rgb(26, 0, 153)\",chr43:\"rgb(102, 0, 153)\",chr44:\"rgb(153, 0, 128)\",chr45:\"rgb(214, 0, 71)\",chr46:\"rgb(255, 20, 99)\",chr47:\"rgb(0, 214, 143)\",chr48:\"rgb(20, 255, 177)\"};class Sm{constructor(e){this.tracks=[],this.chordSets=[]}addChordSet(e){this.chordSets=this.chordSets.filter((t=>t.name!==e.name)),this.chordSets.push(e);let t=this.tracks.find((t=>e.trackName===t.name));t&&(t.chordSets=t.chordSets.filter((t=>t.name!==e.name)),t.chordSets.push(e)),t||(t=new Em(e),this.tracks.push(t))}clearChords(){this.tracks=[],this.chordSets=[]}getTrack(e){return this.tracks.find((t=>e===t.name))}getChordSet(e){return this.chordSets.find((t=>e===t.name))}}class Em{constructor(e){this.name=e.trackName,this.color=e.trackColor,this.visible=!0,this.chordSets=[e],this.id=(\"0000\"+(Math.random()*Math.pow(36,4)|0).toString(36)).slice(-4)}get chords(){if(1===this.chordSets.length)return this.chordSets[0].chords;const e=[];for(let t of this.chordSets)for(let i of t.chords)e.push(i);return e}}const Nm=Math.exp(5);class Bm{static isInstalled(){return void 0!==window.JBrowseReactCircularGenomeView&&void 0!==window.React&&void 0!==window.ReactDOM}constructor(e,t){if(t=t||{},this.config=t,Bm.isInstalled()){this.parent=e,this.groupByTrack=!0===t.groupByTrack,this.chordManager=new Sm(t);const i=document.createElement(\"div\");i.className=\"igv-circview-container\",e.appendChild(i),this.createControls(i),this.resetControlPanel();const n=document.createElement(\"div\");n.className=\"igv-circview-circular-genome-view\",i.appendChild(n),this.container=n,t.assembly&&this.setAssembly(t.assembly),this.width=t.width||500,this.height=t.height||500,this.setSize(this.width,this.height)}else console.error(\"JBrowse circular view is not installed\")}createControls(e){const t=document.createElement(\"div\");t.className=\"igv-circview-toolbar\",e.appendChild(t),this.toolbar=t;const i=document.createElement(\"div\");i.className=\"igv-circview-track-panel\",e.appendChild(i),this.controlPanel=i,this.controlPanel.style.display=\"none\";const n=document.createElement(\"div\");n.className=\"igv-circview-toolbar-button-container\",this.toolbar.appendChild(n),this.showControlsButton=document.createElement(\"div\"),this.showControlsButton.className=\"igv-circview-button\",n.appendChild(this.showControlsButton),this.showControlsButton.innerText=\"none\"===this.controlPanel.style.display?\"Show Controls\":\"Hide Controls\",this.showControlsButton.addEventListener(\"click\",(e=>{this.controlPanel.querySelectorAll(\"div\").length>0&&(\"none\"===this.controlPanel.style.display?(this.controlPanel.style.display=\"flex\",e.target.innerText=\"Hide Controls\"):(this.controlPanel.style.display=\"none\",e.target.innerText=\"Show Controls\"))}));let r=document.createElement(\"div\");r.className=\"igv-circview-button\",n.appendChild(r),r.innerText=\"Clear All\",r.addEventListener(\"click\",(()=>{this.clearChords()})),!1!==this.config.showCloseButton&&(r=document.createElement(\"div\"),r.className=\"igv-circview-button\",n.appendChild(r),r.innerText=\"Close\",r.addEventListener(\"click\",(()=>{this.visible=!1})))}resetControlPanel(){this.controlPanel.innerHTML=\"\",this.controlPanel.appendChild(this.createGroupByCB());const e=this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets;for(let t of e)this.addToControlPanel(t)}createGroupByCB(){const e=document.createElement(\"input\");e.type=\"checkbox\",e.id=\"groupByCB\",e.style.width=\"1.4em\",e.style.height=\"1.4em\",e.checked=this.groupByTrack,e.onclick=e=>{this.groupByTrack=e.target.checked,this.resetControlPanel(),this.render()};const t=document.createElement(\"label\");t.for=\"groupByCB\",t.innerText=\"Group by track\",t.style.color=\"black\",t.style.paddingLeft=\"10px\";const i=document.createElement(\"div\");return i.style.width=\"100%\",i.style.paddingTop=\"5px\",i.style.paddingBottom=\"5px\",i.style.background=\"rgb(216, 230, 234)\",i.appendChild(e),i.appendChild(t),i}addToControlPanel(e){const t=document.createElement(\"div\");this.controlPanel.appendChild(t);const i=document.createElement(\"div\");i.className=\"igv-circview-button\",t.appendChild(i),i.innerText=!0===e.visible?\"Hide\":\"Show\",i.addEventListener(\"click\",(t=>{!0===e.visible?(this.hideChordSet(e.name),t.target.innerText=\"Show\"):(this.showChordSet(e.name),t.target.innerText=\"Hide\")}));const n=document.createElement(\"input\"),r=e=>200*Math.log(e*Nm),s=document.createElement(\"div\");s.className=\"igv-circview-button\",s.innerHTML=\"&nbsp;&nbsp;&nbsp;&nbsp;\",t.appendChild(s),s.style.backgroundColor=Mm(e.color,1);const o={parent:s,popup:\"right\",editorFormat:\"rgb\",color:e.color,onChange:({rgbaString:t})=>{s.style.backgroundColor=Mm(t,1),this.setColor(e.name,t),n.value=r(Rm(e.color))}},a=new _m(o);n.setAttribute(\"title\",\"Adjust transparency of arcs\"),n.type=\"range\",n.style.width=\"100px\",n.style.marginRight=\"10px\",n.setAttribute(\"class\",\"range\"),n.setAttribute(\"min\",\"0\"),n.setAttribute(\"max\",\"1000\"),n.value=r(Rm(e.color)),n.oninput=()=>{const t=(i=n.value,Math.exp(i/200)/Nm);var i;this.setColor(e.name,Mm(e.color,t)),a.setColor(e.color)},t.appendChild(n);const c=document.createElement(\"div\");c.style.color=\"black\",t.appendChild(c),c.innerText=c.title=e.name}setAssembly(e){const t=this.genomeId||Lm();if(this.genomeId===t)return;this.chordManager.clearChords(),this.genomeId=t,this.chrNames=new Set(e.chromosomes.map((e=>Dm(e.name))));const i=[],n=[];for(let t of e.chromosomes){const e=Dm(t.name);n.push(t.color||km(e)),i.push({refName:e,uniqueId:e,start:0,end:t.bpLength})}this.assembly={name:e.name,sequence:{trackId:t,type:\"ReferenceSequenceTrack\",adapter:{type:\"FromConfigSequenceAdapter\",features:i}},refNameColors:n},this.render()}addChords(e,t={}){const i=t.name||t.track||\"*\",n=i.split(\" \")[0].replaceAll(\"%20\",\" \"),r={name:i.replaceAll(\"%20\",\" \"),trackName:n,chords:e,color:t.color||\"black\",trackColor:t.trackColor||t.color||\"black\",visible:!0,id:t.id||Lm()};this.chordManager.addChordSet(r),this.resetControlPanel(),this.render()}setSize(e,t){if(t=t||e,this.width=e,this.height=t,this.viewState){const i=this.viewState.session.view;i.setWidth(e),i.setHeight(t),i.setBpPerPx(i.minBpPerPx)}}getSize(){return Math.min(this.width,this.height)}clearChords(){this.chordManager.clearChords(),this.resetControlPanel(),this.render()}clearSelection(){this.viewState.pluginManager.rootModel.session.clearSelection()}show(){this.parent.style.display=\"block\"}hide(){this.parent.style.display=\"none\"}get visible(){return\"none\"!==this.parent.style.display}set visible(e){this.parent.style.display=e?\"block\":\"none\"}hideChordSet(e){let t=this.getChordSet(e);t?(t.visible=!1,this.render()):console.warn(`No track with name: ${name}`)}showChordSet(e){let t=this.getChordSet(e);t?(t.visible=!0,this.render()):console.warn(`No track with name: ${e}`)}deleteTrack(e){let t=this.tracks.findIndex((t=>e===t.name));t>=0&&this.tracks.splice(t,1),this.render()}getChordSet(e){return this.groupByTrack?this.chordManager.getTrack(e):this.chordManager.getChordSet(e)}setColor(e,t){const i=this.getChordSet(e);if(i){i.color=t;const e=i.id;for(let i of this.viewState.config.tracks)if(e===i.trackId){i.displays[0].renderer.strokeColor.set(t);break}}}render(){const{createViewState:e,JBrowseCircularGenomeView:t}=JBrowseReactCircularGenomeView;ReactDOM.unmountComponentAtNode(this.container);const i=(this.groupByTrack?this.chordManager.tracks:this.chordManager.chordSets).filter((e=>e.visible)),n=[],r=[];for(let e of i)n.push({trackId:e.id,name:e.name,assemblyNames:[\"forIGV\"],type:\"VariantTrack\",adapter:{type:\"FromConfigAdapter\",features:e.chords}}),r.push(e.color);this.viewState=e({assembly:this.assembly,tracks:n});for(let e=0;e<i.length;e++)this.viewState.config.tracks[e].displays[0].renderer.strokeColor.set(r[e]);this.element=React.createElement(t,{viewState:this.viewState}),this.setSize(this.width,this.height),ReactDOM.render(this.element,this.container);const s=this.config.onChordClick||Tm;for(let e=0;e<i.length;e++)this.viewState.session.view.showTrack(this.viewState.config.tracks[e].trackId),s&&(this.viewState.pluginManager.jexl.addFunction(\"onChordClick\",s),this.viewState.config.tracks[e].displays[0].onChordClick.set(\"jexl:onChordClick(feature, track, pluginManager)\"))}}function Mm(e,t){const[i,n,r,s]=e.split(\",\");return`${i},${n},${r},${t})`}function Rm(e){return e.startsWith(\"rgba(\")?Number(e.split(\",\")[3].replace(\")\",\"\")):1}function Dm(e){return e.startsWith(\"chr\")?e.substring(3):e}function Tm(e,t,i){console.log(e)}function Lm(){return(\"0000\"+(Math.random()*Math.pow(36,4)|0).toString(36)).slice(-4)}if(\"undefined\"!=typeof document){function BA(e){for(let t of document.styleSheets)if(t=t.href?t.href.replace(/^.*[\\\\\\/]/,\"\"):\"\",t===e)return!0;return!1}BA(\"circular-view.css\")||function(){const e=document.createElement(\"style\");e.setAttribute(\"type\",\"text/css\"),e.innerHTML='.igv-circview-container {\\n  width: fit-content;\\n  height: fit-content;\\n  box-sizing: content-box;\\n  color: dimgray;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  background-color: white;\\n  border-color: dimgray;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-circview-toolbar {\\n  position: relative;\\n  width: 100%;\\n  height: 32px;\\n  background-color: lightgrey;\\n  border-bottom-style: solid;\\n  border-bottom-color: dimgray;\\n  border-bottom-width: thin;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n\\n.igv-circview-toolbar-button-container {\\n  height: 100%;\\n  width: fit-content;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-circview-toolbar-button-container > div {\\n  margin: 4px;\\n}\\n\\n.igv-circview-track-panel {\\n  z-index: 1024;\\n  position: absolute;\\n  top: 33px;\\n  left: 0;\\n  width: 100%;\\n  height: fit-content;\\n  border-bottom-style: solid;\\n  border-bottom-color: dimgray;\\n  border-bottom-width: thin;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n.igv-circview-track-panel > div {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-circview-track-panel > div > div {\\n  margin: 4px;\\n}\\n\\n.igv-circview-swatch-button {\\n  cursor: pointer;\\n  padding: 5px;\\n  width: 8px;\\n  height: 8px;\\n  border: 1px solid #8d8b8b;\\n  border-radius: 16px;\\n}\\n\\n.igv-circview-button {\\n  cursor: pointer;\\n  padding: 5px;\\n  color: #444;\\n  vertical-align: middle;\\n  text-align: center;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  border: 1px solid #8d8b8b;\\n  border-radius: 4px;\\n  background: #efefef;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.2);\\n}\\n\\n.igv-circview-button:hover {\\n  background: #efefef;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\\n}\\n\\n.igv-circview-button:active {\\n  color: #007bff;\\n  box-shadow: 0 0 5px -1px rgba(0, 0, 0, 0.6);\\n}\\n\\n/*# sourceMappingURL=circular-view.css.map */\\n',document.head.insertBefore(e,document.head.childNodes[document.head.childNodes.length-1])}()}const zm=e=>e.startsWith(\"chr\")?e.substring(3):e;function Hm(e){const t=[],i=[];if(e.wgChromosomeNames)for(let n of e.wgChromosomeNames){const r=e.getChromosome(n);i.push(Nu(r.name)),t.push({name:r.name,bpLength:r.bpLength})}return t}function Pm(e,t,i,n){const r=t.color||\"rgb(0,0,255)\",s=_s.addAlpha(\"all\"===i.chr?r:Nu(i.chr),n),o=_s.addAlpha(r,n),a=t.name.replaceAll(\" \",\"%20\"),c=\"all\"===i.chr?a:`${a}  ${i.chr}:${i.start}-${i.end}`;t.browser.circularView.addChords(e,{track:c,color:s,trackColor:o}),t.browser.circularViewVisible||(t.browser.circularViewVisible=!0)}class Om{constructor(e,{minTLENPercentile:t,maxTLENPercentile:i}){this.totalCount=0,this.frCount=0,this.rfCount=0,this.ffCount=0,this.sumF=0,this.sumF2=0,this.lp=void 0===t?.1:t,this.up=void 0===i?99.5:i,this.isizes=[],this.compute(e)}compute(e){for(let n of e)if(n.isProperPair()){var t=Math.abs(n.fragmentLength);this.sumF+=t,this.sumF2+=t*t,this.isizes.push(t);var i=n.pairOrientation;if(\"string\"==typeof i&&4===i.length)switch(\"\"+i.charAt(0)+i.charAt(2)){case\"FF\":case\"RR\":this.ffCount++;break;case\"FR\":this.frCount++;break;case\"RF\":this.rfCount++}this.totalCount++}this.ffCount/this.totalCount>.9?this.orienation=\"ff\":this.frCount/this.totalCount>.9?this.orienation=\"fr\":this.rfCount/this.totalCount>.9&&(this.orienation=\"rf\"),this.minTLEN=0===this.lp?0:Um(this.isizes,this.lp),this.maxTLEN=Um(this.isizes,this.up)}}function Um(e,t){if(0!==e.length){var i=Math.floor(e.length*(t/100));return e.sort((function(e,t){return e-t})),e[i]}}const qm=\"rgb(255,0,255)\",Qm=\"rgb(0,0,255)\",Vm=\"rgb(132, 178, 158)\",jm=new Map;jm.set(\"m\",\"rgb(255,0,0)\"),jm.set(\"h\",qm),jm.set(\"o\",\"rgb(111, 78, 129)\"),jm.set(\"f\",\"rgb(246, 200, 95)\"),jm.set(\"c\",\"rgb(157, 216, 102)\"),jm.set(\"g\",\"rgb(255, 160, 86)\"),jm.set(\"e\",\"rgb(141, 221, 208)\"),jm.set(\"b\",\"rgb(202, 71, 47)\"),jm.set(\"h\",qm),jm.set(\"a\",\"rgb(51,0,111)\"),jm.set(\"NONE_A\",Qm),jm.set(\"NONE_C\",Qm),jm.set(\"NONE_T\",Qm),jm.set(\"NONE_G\",Qm),jm.set(\"NONE_N\",Qm);const Wm=new Map;function Gm(e,t,i){let n=function(e,t){return jm.has(e)?jm.get(e):Vm}(e),r=Xf(t);if(r>255)return n;const s=e+r+i;if(r<0&&(r=0),!Wm.has(s)){const e=\"basemod2\"===i?Math.max(20,Math.min(255,r*r/50-4*r+200+20)):Math.max(20,Math.min(255,.006127*r*r)),[t,o,a]=_s.rgbComponents(n);Wm.set(s,`rgba(${t},${o},${a},${e/255})`)}return Wm.get(s)}class $m{constructor(e){this.alignmentTrack=e}updateContext(e){this.context=e}drawModifications(e,t,i,n,r,s){const{ctx:o,pixelEnd:a,bpStart:c,bpPerPixel:l}=n,h=e.getBaseModificationSets();if(h){let n;const d=r.split(\":\");2==d.length&&(r=d[0],n=d[1]);for(let d of e.blocks){if(\"S\"===d.type)continue;const e=t,u=i;let f=Math.max(1,1/l);for(let t=d.seqOffset;t<d.seqOffset+d.len;t++){let i=(d.start+(t-d.seqOffset)-c)/l;if(i>a)break;if(i+f<0)continue;let p,g=-1,m=255,w=0;for(let e of h)if((!n||e.modification===n)&&e.containsPosition(t)){const i=Xf(e.likelihoods.get(t));m-=i,(!p||i>g)&&(p=e.modification,w=e.canonicalBase,g=i)}if(p){const t=255*s;let n;m>g&&\"basemod2\"===r&&m>=t?n=Gm(\"NONE_\"+w,m,r):g>=t&&(n=Gm(p,g,r)),o.fillStyle=n,f<3&&(f=3,i--),o.fillRect(i,e,f,Math.max(1,u-2))}}}}}}const Km=new Set([\"firstOfPairStrand\"]);class Ym extends Hl{static defaults={viewAsPairs:!1,showSoftClips:!1,showAllBases:!1,showInsertions:!0,showMismatches:!0,colorBy:void 0,groupBy:void 0,displayMode:\"EXPANDED\",alignmentRowHeight:14,squishedRowHeight:3,negStrandColor:\"rgba(150, 150, 230, 0.75)\",posStrandColor:\"rgba(230, 150, 150, 0.75)\",baseModPosStrandColor:\"rgb(195, 195, 195)\",baseModNegStrandColor:\"rgb(195, 210, 195)\",insertionColor:\"rgb(138, 94, 161)\",insertionTextColor:\"white\",showInsertionText:!1,deletionColor:\"black\",deletionTextColor:\"black\",showDeletionText:!1,skippedColor:\"rgb(150, 170, 170)\",pairConnectorColor:void 0,smallTLENColor:\"rgb(0, 0, 150)\",largeTLENColor:\"rgb(200, 0, 0)\",expectedPairOrientation:\"fr\",rlColor:\"rgb(0, 150, 0)\",rrColor:\"rgb(20, 50, 200)\",llColor:\"rgb(0, 150, 150)\",bamColorTag:\"YC\",hideSmallIndels:!1,indelSizeThreshold:1,highlightColor:void 0,minTLEN:void 0,maxTLEN:void 0,tagColorPallete:\"Set1\"};_colorTables=new Map;_baseModifications=new Set;constructor(e,t){super(e,t),(e.colorTable||e.tagColorTable)&&(this.colorTable=new ao(e.tagColorTable)),e.largeFragmentLengthColor&&(this.largeTLENColor=e.largeFragmentLengthColor),e.pairOrienation&&(this.expectedPairOrientation=e.pairOrientation),e.smallFragmentLengthColor&&(this.smallTLENColor=e.smallFragmentLengthColor),e.largeFragmentLengthColor&&(this.largeTLENColor=e.largeFragmentLengthColor),e.minFragmentLength&&(this.minTLEN=e.minFragmentLength),e.maxFragmentLength&&(this.maxTLEN=e.maxFragmentLength),e.displayMode&&(this.displayMode=e.displayMode.toUpperCase()),e.colorBy&&e.colorByTag&&(this.colorBy=e.colorBy+\":\"+e.colorByTag),this.featureSource=this.parent.featureSource,this.top=0===e.coverageTrackHeight?0:e.coverageTrackHeight+5,this.pairColors={RL:this.rlColor,RR:this.rrColor,LL:this.llColor},e.highlightedReads&&this.setHighlightedReads(e.highlightedReads),this.hasPairs=!1,this.hasSupplemental=!1,this._groupByTags=[],this._groupByPositions=[],e.groupBy&&(this.groupBy=e.groupBy,e.groupBy.startsWith(\"base:\")&&this._groupByPositions.push(e.groupBy.substring(5)),e.groupBy.startsWith(\"tag:\")&&this._groupByTags.push(e.groupBy.substring(4))),this._locusChange=Zm.bind(this),this.browser.on(\"locuschange\",this._locusChange)}init(e){this.parent=e.parent,delete e.parent,super.init(e)}dispose(){this.browser.off(\"locuschage\",this._locusChange)}get baseModRenderer(){return this._baseModRenderer||(this._baseModRenderer=new $m(this)),this._baseModRenderer}get baseModificationThreshold(){return this.parent.baseModificationThreshold}setTop(e,t){this.top=0===e.height||!1===t?0:5+e.height}setHighlightedReads(e,t){if(!Array.isArray(e)||!e.every((e=>\"string\"==typeof e)))throw new Error(\"AlignmentTrack.setHighlightedReads() only accept array of strings\");t&&(this.highlightColor=t),this.highlightedReads=new Set(e)}computePixelHeight(e){if(e.packedGroups){let t=e.hasDownsampledIntervals()?15:0;const i=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;for(let n of e.packedGroups.values())t+=i*n.length+10;return t+5}return 0}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=r+s*n+1,a=this.showSoftClips,c=this.showAllBases,l=this.browser.nucleotideColors;i.save();for(let e of t.baseModificationKeys)this._baseModifications.add(e.modification);let h=t.sequence;h&&(h=h.toUpperCase());let d=0;this.colorBy||(this.colorBy=this.hasPairs?\"unexpectedPair\":\"none\");let u=e.pixelTop;this.top&&i.translate(0,this.top);const f=u+e.pixelHeight;t.hasDownsampledIntervals()?(d=15,t.downsampledIntervals.forEach((function(e){var t=(e.start-r)/n,s=(e.end-r)/n;s-t>5&&(t+=1,s-=1),xo.fillRect(i,t,2,s-t,8,{fillStyle:\"black\"})}))):d=0,this.alignmentsYOffset=d;const p=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight,g=t.packedGroups;if(g){let t=d;for(let n of g.keys()){const a=g.get(n),c=a.rows,l=c.length;a.pixelTop=t;for(let e=0;e<l;e++){const i=c[e],n=p<=4?p:p-2;if(t>f)break;if(t+n<u)t+=p;else{for(let e of i.alignments)if(this.browser.circularView&&(this.hasSupplemental=this.hasSupplemental||e.hasTag(\"SA\")),!(e.start+e.lengthOnRef<r)){if(e.start>o)break;!0!==e.hidden&&(e instanceof Qf?(m.call(this,e,t,n),w.call(this,e.firstAlignment,t,n),e.secondAlignment&&w.call(this,e.secondAlignment,t,n)):w.call(this,e,t,n))}t+=p}}if(a.pixelBottom=t,this.groupBy&&n){i.save(),i.font=\"400 12px sans-serif\";const r=i.measureText(n),o=r.width+10,c=-e.pixelShift+e.viewportWidth-o-10,l=r.actualBoundingBoxAscent+r.actualBoundingBoxDescent+10,h=Math.min(a.pixelTop+l-1,a.pixelBottom);i.textAlign=\"center\",i.fillStyle=\"white\",i.strokeStyle=\"lightGray\",xo.roundRect(i,c,h-r.actualBoundingBoxAscent-5,o,l,2,1,1),i.fillStyle=\"black\",i.fillText(n,c+o/2,h),xo.dashedLine(i,0,t,s,t),i.restore(),t+=10}}}function m(e,t,s){var a=this.getConnectorColor(e.firstAlignment),c=(e.connectingStart-r)/n,l=(e.connectingEnd-r)/n,h=t+s/2;e.connectingEnd<r||e.connectingStart>o||(e.mq<=0&&(a=_s.addAlpha(a,.15)),xo.setProperties(i,{fillStyle:a,strokeStyle:a}),xo.strokeLine(i,c,h,l,h))}function w(e,d,u){if(e.start+e.lengthOnRef<r||e.start>o)return;const f=a?e.blocks:e.blocks.filter((e=>\"S\"!==e.type));let g=this.getAlignmentColor(e);const m=g;e.mq<=0&&(g=_s.addAlpha(g,.15)),xo.setProperties(i,{fillStyle:g,strokeStyle:m});const w=[];for(let e=0;e<f.length;e++){const t=f[e];if(!(e!==f.length-1&&f[e+1].start<r)&&(w.push(...b.call(this,t,e)),t.start+t.len>o))break}if(e.gaps){const t=d+u/2;for(let s of e.gaps){const e=(s.start-r)/n,o=(s.start+s.len-r)/n,a=o-e,c=s.len.toString(),l=6*c.length,h=e+a/2,u=\"D\"===s.type?this.deletionColor:this.skippedColor;if(xo.strokeLine(i,e,t,o,t,{strokeStyle:u,lineWidth:2}),this.showDeletionText&&s.len>1&&a>=l+8){const e=h-l/2;xo.fillRect(i,e-1,d-1,l+2,12,{fillStyle:\"white\"}),xo.fillText(i,c,e,d+10,{font:\"normal 10px monospace\",fillStyle:this.deletionTextColor})}}}if(e.insertions&&this.showInsertions){let t=-1;for(let s of e.insertions){if(this.hideSmallIndels&&s.len<=this.indelSizeThreshold)continue;if(s.start<r)continue;if(s.start>o)break;const e=s.start-r,a=s.len.toString(),c=2+6*a.length,l=this.showInsertionText&&1!==s.len?Math.round(s.len/n):2,h=Math.max(Math.min(c,l),2),f=e/n-h/2;if(f-t>2){const e={fillStyle:this.insertionColor};xo.fillRect(i,f-2,d,h+4,2,e),xo.fillRect(i,f,d+2,h,u-4,e),xo.fillRect(i,f-2,d+u-2,h+4,2,e),this.showInsertionText&&s.len>1&&l>c&&xo.fillText(i,a,f+1,d+10,{font:\"normal 10px monospace\",fillStyle:this.insertionTextColor}),t=f}}}for(let{bbox:e,baseColor:t,readChar:r}of w){if(n<=.1&&e.height>=8){const n=Math.min(10,e.height);i.font=n+\"px sans-serif\";const s=e.x+e.width/2;xo.strokeText(i,r,s-i.measureText(r).width/2,n-1+e.y,{strokeStyle:t})}else xo.fillRect(i,e.x,e.y,e.width,e.height,{fillStyle:t})}if(this.colorBy&&this.colorBy.startsWith(\"basemod\")){const t={ctx:i,bpPerPixel:n,bpStart:r,bpEnd:o,pixelEnd:s};this.baseModRenderer.drawModifications(e,d,u,t,this.colorBy,this.baseModificationThreshold)}function b(o,a){const w=[],b=o.start-t.start,F=(o.start-r)/n,v=(o.start+o.len-r)/n,y=Math.max(1,v-F),A=100/n,C=Math.min(p/2,A/6),_=\"S\"===o.type,x=e.mq<=0||this.selectedReadName===e.readName||_||this.highlightedReads&&this.highlightedReads.has(e.readName);let k=m;this.selectedReadName===e.readName?k=\"red\":_?k=\"rgb(50,50,50)\":this.highlightedReads&&this.highlightedReads.has(e.readName)&&(k=this.highlightColor||\"#00ff00\");const I=!0===e.strand&&a===f.length-1,S=!1===e.strand&&0===a;if(I|S){let e,t;I?(e=[F,v,v+C,v,F,F],t=[d,d,d+u/2,d+u,d+u,d]):S&&(e=[v,F,F-C,F,v,v],t=[d,d,d+u/2,d+u,d+u,d]),xo.fillPolygon(i,e,t,{fillStyle:g}),x&&xo.strokePolygon(i,e,t,{strokeStyle:k})}else xo.fillRect(i,F,d,y,u,{fillStyle:g}),x&&(i.save(),i.strokeStyle=k,i.strokeRect(F,d,y,u),i.restore());if(_||c||this.showMismatches&&h&&e.seq&&\"*\"!==e.seq){const t=e.seq?e.seq.toUpperCase():void 0,i=e.qual,a=o.seqOffset,f=Math.max(1,1/n);for(let e=0,p=o.len;e<p;e++){const p=(o.start+e-r)/n;if(p+f<0)continue;if(p>s)break;let g=t?t.charAt(a+e):\"\";const m=b+e>=0?h.charAt(b+e):\"\";if(\"=\"===g&&(g=m),\"X\"===g||m!==g||_||c){let t=l[g]||\"rgb(0,0,0)\";if(!_&&void 0!==i&&i.length>a+e){t=Xm(i[a+e],t)}w.push({bbox:{x:p,y:d,width:f,height:u},baseColor:t,readChar:g})}}}return w}}i.restore()}popupData(e){const t=this.getClickedObject(e);return t?t.popupData(e.genomicLocation):void 0}menuItemList(){let e=[];e.push(\"<hr/>\");const t=Bt('<div class=\"igv-track-menu-category\">');t.text(\"Color by:\"),e.push({name:void 0,object:t,click:void 0,init:void 0});const i=[];i.push({key:\"none\",label:\"none\"}),i.push({key:\"strand\",label:\"read strand\"}),this.hasPairs&&(i.push({key:\"firstOfPairStrand\",label:\"first-of-pair strand\"}),i.push({key:\"pairOrientation\",label:\"pair orientation\"}),i.push({key:\"tlen\",label:\"insert size (TLEN)\"}),i.push({key:\"unexpectedPair\",label:\"pair orientation & insert size (TLEN)\"})),i.push({key:\"tag\",label:\"tag\"});for(let t of i){const i=void 0===this.colorBy&&\"none\"===t.key||this.colorBy===t.key;e.push(this.colorByCB(t,i))}const n=this._baseModifications.size;if(n>0){e.push('<hr style=\"border-top:1px dotted;border-bottom: none;\">');let t=1===n?\"base modification\":\"base modification (all)\";if(e.push(this.basemodColorByCB({key:\"basemod\",label:t})),n>1)for(let t of this._baseModifications)e.push(this.basemodColorByCB({key:\"basemod:\"+t,label:`base modification (${Kf(t)})`}));if(e.push('<hr style=\"border-top:1px dotted;border-bottom: none;\">'),t=1===n?\"base modification 2-color\":\"base modification 2-color (all)\",e.push(this.basemodColorByCB({key:\"basemod2\",label:t})),n>1)for(let t of this._baseModifications)e.push(this.basemodColorByCB({key:\"basemod2:\"+t,label:`base modification 2-color (${Kf(t)})`}))}e.push(\"<hr/>\");const r=Bt('<div class=\"igv-track-menu-category\">');r.text(\"Group by:\"),e.push({name:void 0,object:r,click:void 0,init:void 0});const s=[];s.push({key:\"none\",label:\"none\"}),s.push({key:\"strand\",label:\"read strand\"}),this.hasPairs&&(s.push({key:\"firstOfPairStrand\",label:\"first-of-pair strand\"}),s.push({key:\"pairOrientation\",label:\"pair orientation\"}),s.push({key:\"mateChr\",label:\"chromosome of mate\"})),s.push({key:\"chimeric\",label:\"chimeric\"}),s.push({key:\"supplementary\",label:\"supplementary flag\"}),s.push({key:\"readOrder\",label:\"read order\"});for(let e of this._groupByTags)s.push({key:`tag:${e}`,label:`tag:${e}`});for(let e of this._groupByPositions)s.push({key:`base:${e}`,label:`base:${e}`});s.push({key:\"tag\",label:\"tag...\"});for(let t of s){const i=void 0===this.groupBy&&\"none\"===t.key||this.groupBy===t.key;e.push(this.groupByCB(t,i))}e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"Show all bases\",this.showAllBases)),click:function(){this.alignmentTrack.showAllBases=!this.alignmentTrack.showAllBases,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show mismatches\",this.showMismatches)),click:function(){this.alignmentTrack.showMismatches=!this.alignmentTrack.showMismatches,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show insertions\",this.showInsertions)),click:function(){this.alignmentTrack.showInsertions=!this.alignmentTrack.showInsertions,this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show soft clips\",this.showSoftClips)),click:function(){this.alignmentTrack.showSoftClips=!this.alignmentTrack.showSoftClips;const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this);this.trackView.repaintViews()}}),this.hasPairs&&(e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"View as pairs\",this.viewAsPairs)),click:function(){const e=!this.alignmentTrack.viewAsPairs;if(e&&this.groupBy&&!Km.has(this.groupBy))return void this.browser.alert.present(`'View as Pairs' is incompatible with 'Group By ${this.groupBy}'`);this.alignmentTrack.viewAsPairs=e;const t=this.getCachedAlignmentContainers();for(let e of t)e.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(e.push(\"<hr/>\"),this.hasPairs&&e.push({label:\"Add discordant pairs to circular view\",click:function(){for(let e of this.trackView.viewports)this.addPairedChordsForViewport(e)}}),this.hasSupplemental&&e.push({label:\"Add split reads to circular view\",click:function(){for(let e of this.trackView.viewports)this.addSplitChordsForViewport(e)}})),e.push(\"<hr/>\");const o=Bt('<div class=\"igv-track-menu-category\">');o.text(\"Display mode:\"),e.push({name:void 0,object:o,click:void 0,init:void 0});for(let t of[\"EXPANDED\",\"SQUISHED\",\"FULL\"])e.push({object:Bt(Dl(t.toLowerCase(),this.displayMode===t)),click:function(){this.alignmentTrack.setDisplayMode(t)}});return e}setDisplayMode(e){const t=\"FULL\"===this.displayMode||\"FULL\"===e;if(this.displayMode=e,t){const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this)}this.trackView.checkContentHeight(),this.trackView.repaintViews()}colorByCB(e,t){const i=Bt(Dl(e.label,t));if(\"tag\"!==e.key){function n(){this.alignmentTrack.colorBy=e.key,this.trackView.repaintViews()}return{name:void 0,object:i,click:n,init:void 0}}{function r(e){const t=this.alignmentTrack.colorBy.startsWith(\"tag:\")?this.alignmentTrack.colorBy.substring(4):\"\";this.browser.inputDialog.present({label:\"Tag Name\",value:t,callback:e=>{const t=this.alignmentTrack;e?(t.colorBy=\"tag:\"+e,t.colorTable||(t.colorTable=new oo(\"Set1\"))):t.colorBy=void 0,this.trackView.repaintViews()}},e)}return{name:void 0,object:i,dialog:r,init:void 0}}}basemodColorByCB(e){const t=this.colorBy===e.key;return{name:void 0,object:Bt(Dl(e.label,t)),click:function(){this.alignmentTrack.colorBy=e.key,this.trackView.repaintViews()},init:void 0}}groupByCB(e,t){return{name:void 0,object:Bt(Dl(e.label,t)),dialog:function(t){const i=()=>this.alignmentTrack.repackAlignments();if(\"tag\"===e.key){let e=\"\";this.alignmentTrack.groupBy&&this.alignmentTrack.groupBy.startsWith(\"tag:\")&&(e=this.alignmentTrack.groupBy.substring(4)),this.browser.inputDialog.present({label:\"Tag Name\",value:e,callback:e=>{e&&(this.alignmentTrack.groupBy=\"tag:\"+e,this.alignmentTrack._groupByTags.push(e),i())}},t)}else\"none\"===e.key?this.alignmentTrack.groupBy=void 0:this.alignmentTrack.groupBy=e.key,i()},init:void 0}}repackAlignments(){const e=this.getCachedAlignmentContainers();for(let t of e)\"function\"==typeof t.pack&&t.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}contextMenuItemList(e){const t=e.viewport,i=[],n=i=>{const n=this.sortObject,r=!n||n.position!==Math.floor(e.genomicLocation)||!n.direction,s={chr:t.referenceFrame.chr,position:Math.floor(e.genomicLocation),option:i,direction:r,sortAsPairs:t.trackView.track.viewAsPairs};this.sortObject=s,t.cachedFeatures.sortRows(s),t.repaint()};i.push(\"<b>Sort by...</b>\"),i.push({label:\"&nbsp; base\",click:()=>n(\"BASE\")}),i.push({label:\"&nbsp; read strand\",click:()=>n(\"strand\")}),i.push({label:\"&nbsp; start location\",click:()=>n(\"START\")}),i.push({label:\"&nbsp; insert size\",click:()=>n(\"INSERT_SIZE\")}),i.push({label:\"&nbsp; gap size\",click:()=>n(\"GAP_SIZE\")}),i.push({label:\"&nbsp; chromosome of mate\",click:()=>n(\"MATE_CHR\")}),i.push({label:\"&nbsp; mapping quality\",click:()=>n(\"MQ\")}),i.push({label:\"&nbsp; read name\",click:()=>n(\"READ_NAME\")}),i.push({label:\"&nbsp; aligned read length\",click:()=>n(\"ALIGNED_READ_LENGTH\")}),i.push({label:\"&nbsp; tag\",click:()=>{const i=this.sortObject,n=!i||i.position!==Math.floor(e.genomicLocation)||!i.direction,r={label:\"Tag Name\",value:this.sortByTag?this.sortByTag:\"\",callback:i=>{if(i){const r={chr:t.referenceFrame.chr,position:Math.floor(e.genomicLocation),option:\"TAG\",tag:i,direction:n};this.sortByTag=i,this.sortObject=r,t.cachedFeatures.sortRows(r),t.repaint()}}};this.browser.inputDialog.present(r,e.event)}}),i.push(\"<hr/>\");const r=`${t.referenceFrame.chr}:${Rt(Math.floor(e.genomicLocation)+1)}`;i.push({label:`Group by base @${r}`,click:()=>{this._groupByPositions.push(r),this.groupBy=`base:${r}`;const e=this.getCachedAlignmentContainers();for(let t of e)t.pack(this);this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),i.push(\"<hr/>\");const s=this.getClickedObject(e);if(s){const t=this.showSoftClips,n=\"function\"==typeof s.alignmentContaining?s.alignmentContaining(e.genomicLocation,t):s;if(n){n.isPaired()&&n.isMateMapped()&&i.push({label:\"View mate in split screen\",click:()=>{if(n.mate){const t=e.viewport.referenceFrame,i=this.browser.genome.getChromosome(n.mate.chr);if(i){this.selectedReadName=n.readName;const r=t.bpPerPixel*e.viewport.getWidth(),s=n.mate.position-r/2,o=n.mate.position+r/2;this.browser.addMultiLocusPanel(i.name,s,o,t)}else this.browser.alert.present(`Reference does not contain chromosome: ${n.mate.chr}`)}},init:void 0}),i.push({label:\"View read sequence\",click:()=>{const e=n.seq;e&&\"*\"!==e?this.browser.alert.present(e):this.browser.alert.present(\"Read sequence: *\")}}),Xa()&&i.push({label:\"Copy read sequence\",click:async()=>{const e=n.seq;try{await navigator.clipboard.writeText(e)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}});const t=n.seq;if(t&&\"*\"!==t){t.length<Qd&&i.push({label:\"BLAT read sequence\",click:()=>{const e=n.isNegativeStrand()?cc(t):t,i=`${n.readName} - blat`,r=`${this.name} - ${i}`;jd({sequence:e,browser:this.browser,name:i,title:r})}});const e=n.softClippedBlocks();e.left&&e.left.len>20&&e.left.len<Qd&&i.push({label:\"BLAT left soft-clipped sequence\",click:()=>{const i=t.substr(e.left.seqOffset,e.left.len),r=n.isNegativeStrand()?cc(i):i,s=`${n.readName} - blat left clip`,o=`${this.name} - ${s}`;jd({sequence:r,browser:this.browser,name:s,title:o})}}),e.right&&e.right.len>20&&e.right.len<Qd&&i.push({label:\"BLAT right soft-clipped sequence\",click:()=>{const i=t.substr(e.right.seqOffset,e.right.len),r=n.isNegativeStrand()?cc(i):i,s=`${n.readName} - blat right clip`,o=`${this.name} - ${s}`;jd({sequence:r,browser:this.browser,name:s,title:o})}})}i.push(\"<hr/>\")}}return this.browser.circularView&&(this.hasPairs||this.hasSupplemental)&&(this.hasPairs&&i.push({label:\"Add discordant pairs to circular view\",click:()=>{this.addPairedChordsForViewport(t)}}),this.hasSupplemental&&i.push({label:\"Add split reads to circular view\",click:()=>{this.addSplitChordsForViewport(t)}}),i.push(\"<hr/>\")),i}getClickedObject(e){let t=e.viewport.cachedFeatures;if(!t)return;const i=e.y-this.top,n=e.genomicLocation;if(t.packedGroups){let e=Number.MAX_VALUE;for(let r of t.packedGroups.values())if(e=Math.min(e,r.pixelTop),i>r.pixelTop&&i<=r.pixelBottom){const e=\"SQUISHED\"===this.displayMode?this.squishedRowHeight:this.alignmentRowHeight;let t=Math.floor((i-r.pixelTop)/e);if(t>=0&&t<r.length){const e=r.rows[t].alignments.filter((e=>e.containsLocation(n,this.showSoftClips)));if(e.length>0)return e[0]}}}if(i<minGroupY&&t.downsampledIntervals)for(const e of t.downsampledIntervals)if(e.start<=n&&e.end>=n)return e}getConnectorColor(e){if(this.pairConnectorColor)return this.pairConnectorColor;let t=this.colorBy;switch(t&&t.startsWith(\"tag:\")&&(t.substring(4),t=\"tag\"),t){case\"strand\":case\"firstOfPairStrand\":case\"pairOrientation\":case\"tag\":return this.color?\"function\"==typeof this.color?this.color(e):this.color:\"rgb(200, 200, 200)\";default:return this.getAlignmentColor(e)}}getAlignmentColor(e){let t;t=this.color?\"function\"==typeof this.color?this.color(e):this.color:\"rgb(185, 185, 185)\";let i,n=this.colorBy;switch(n&&n.startsWith(\"tag:\")&&(i=n.substring(4),n=\"tag\"),n){case\"basemod\":case\"basemod2\":t=e.strand?this.baseModPosStrandColor:this.baseModNegStrandColor;break;case\"strand\":t=e.strand?this.posStrandColor:this.negStrandColor;break;case\"firstOfPairStrand\":const r=e.firstOfPairStrand;void 0!==r&&(t=r?this.posStrandColor:this.negStrandColor);break;case\"unexpectedPair\":case\"pairOrientation\":if(e.pairOrientation){const i=ep[this.expectedPairOrientation];if(i){const n=this.pairColors[i[e.pairOrientation]];if(n){t=n;break}}}if(\"pairOrientation\"===n)break;case\"tlen\":case\"fragmentLength\":e.mate&&e.isMateMapped()&&(e.mate.chr!==e.chr?t=Nu(e.mate.chr):this.minTemplateLength&&Math.abs(e.fragmentLength)<this.minTemplateLength?t=this.smallTLENColor:this.maxTemplateLength&&Math.abs(e.fragmentLength)>this.maxTemplateLength&&(t=this.largeTLENColor));break;case\"tag\":const s=e.tags()[i];void 0!==s&&(this.bamColorTag===i&&(t=_s.createColorStringSafe(s)),this.colorTable||(this.colorTable=new oo(this.tagColorPallete)),t=this.colorTable.getColor(s))}return t}get nucleotideColors(){return this.browser.nucleotideColors}get minTemplateLength(){return void 0!==this.minTLEN?this.minTLEN:this.parent._pairedEndStats?this.parent._pairedEndStats.minTLEN:0}get maxTemplateLength(){return void 0!==this.maxTLEN?this.maxTLEN:this.parent._pairedEndStats?this.parent._pairedEndStats.maxTLEN:1e3}getState(){const e=super.getState();return this.highlightedReads&&(e.highlightedReads=Array.from(this.highlightedReads)),e}get name(){return this.parent.name}set name(e){this.parent.name=e}get color(){return this.parent.color}set color(e){this.parent.color=e}get trackView(){return this.parent.trackView}get getCachedAlignmentContainers(){return this.parent.getCachedAlignmentContainers}get sortObject(){return this.parent.sortObject}set sortObject(e){this.parent.sortObject=e}addPairedChordsForViewport(e){return this.parent.addPairedChordsForViewport(e)}addSplitChordsForViewport(e){return this.parent.addSplitChordsForViewport(e)}}function Xm(e,t){let i;return i=e<5?.1:Math.max(.1,Math.min(1,.1+.9*(e-5)/15)),i=Math.round(10*i)/10,i<1&&(t=_s.addAlpha(t,i)),t}function Zm(){\"FULL\"!==this.displayMode||this.browser.isTrackPanning()||this.repackAlignments()}function Jm(e,t,i,n,r,s,o,a,c){const l=o.baseModCounts,h=o.coverageMap;if(l){let o;const d=a.split(\":\");2==d.length&&(a=d[0],o=d[1]);const u=Array.from(l.allModifications);u.sort(Vf.compare);const f=h.getTotalCount(s);if(!u.filter((e=>o?o===e.modification:!e.modification.startsWith(\"NONE_\"))).find((e=>l.getCount(s,e,0,!1)>0)))return;for(let d of u){if(d.modification.startsWith(\"NONE_\")&&\"basemod2\"!==a)continue;if(o&&o!==d.modification&&!d.modification.startsWith(\"NONE_\"))continue;const u=d.base,p=oc(u),g=h.getCount(s,u)+h.getCount(s,p),m=l.simplexModifications.has(d.modification)?h.getPosCount(s,u)+h.getNegCount(s,p):g;if(0==m)continue;const w=\"basemod2\"===a,b=l.getCount(s,d,c,w);if(0==b)continue;const F=g/f*(b/m),v=Math.round(F*r),y=l.getLikelihoodSum(s,d,c,w)/b,A=i-v,C=Gm(d.modification,y,a);e.fillStyle=C,e.fillRect(t,A,n,v),i=A}}}class ew{constructor(e,t){this.featureType=\"numeric\",this.parent=t,this.featureSource=t.featureSource,this.paintAxis=cd,this.top=0,this.autoscale=e.autoscale||void 0===e.max,e.coverageColor&&(this.color=e.coverageColor),this.autoscale||(this.dataRange={min:e.min||0,max:e.max})}get height(){return this.parent.coverageTrackHeight}draw(e){const t=e.pixelTop;e.pixelHeight;const i=this.parent.browser.nucleotideColors;if(t>this.height)return;const n=e.context,r=e.features,s=r.coverageMap;let o;s.refSeq&&(o=s.refSeq.toUpperCase());const a=e.bpPerPixel,c=e.bpStart,l=c+e.pixelWidth*a+1;let h;h=this.color?this.color:this.parent.color&&\"function\"!=typeof this.parent.color?_s.darkenLighten(this.parent.color,-35):\"rgb(150, 150, 150)\",xo.setProperties(n,{fillStyle:h,strokeStyle:h});const d=Math.max(1,1/a);for(let e=0,t=s.coverage.length;e<t;e++){const t=s.bpStart+e;if(t<c)continue;if(t>l)break;const i=s.coverage[e];if(!i)continue;const r=i.total/this.dataRange.max*this.height,o=this.height-r,h=(t-c)/a;xo.fillRect(n,h,o,d,r)}if(o)for(let e=0,t=s.coverage.length;e<t;e++){const t=s.bpStart+e;if(t<c)continue;if(t>l)break;const h=s.coverage[e];if(!h)continue;const u=h.total/this.dataRange.max*this.height;let f=this.height-u;const p=Math.floor((t-c)/a),g=o[e];if(this.parent.colorBy&&this.parent.colorBy.startsWith(\"basemod\"))Jm(n,p,this.height,d,u,t,r,this.parent.colorBy,this.parent.baseModificationThreshold);else if(h.isMismatch(g)){xo.setProperties(n,{fillStyle:i[g]}),xo.fillRect(n,p,f,d,u);let e=0;for(let t of[\"A\",\"C\",\"T\",\"G\"]){const r=(h[\"pos\"+t]+h[\"neg\"+t])/this.dataRange.max*this.height;f=this.height-r-e,e+=r,xo.setProperties(n,{fillStyle:i[t]}),xo.fillRect(n,p,f,d,r)}}}}getClickedObject(e){let t=e.viewport.cachedFeatures;if(!t||0===t.length)return;const i=Math.floor(e.genomicLocation),n=t.coverageMap,r=Math.floor(i-n.bpStart),s=n.coverage[r];return s?{coverage:s,baseModCounts:t.baseModCounts,hoverText:()=>n.coverage[r].hoverText()}:void 0}popupData(e){const t=[],{coverage:i,baseModCounts:n}=this.getClickedObject(e);if(i){const r=Math.floor(e.genomicLocation),s=e.viewport.referenceFrame;t.push(s.chr+\":\"+Rt(1+r)),t.push({name:\"Total Count\",value:i.total});let o=i.posA+i.negA;o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posA+\"+, \"+i.negA+\"- )\"),t.push({name:\"A\",value:o}),o=i.posC+i.negC,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posC+\"+, \"+i.negC+\"- )\"),t.push({name:\"C\",value:o}),o=i.posG+i.negG,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posG+\"+, \"+i.negG+\"- )\"),t.push({name:\"G\",value:o}),o=i.posT+i.negT,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posT+\"+, \"+i.negT+\"- )\"),t.push({name:\"T\",value:o}),o=i.posN+i.negN,o>0&&(o=o.toString()+\" (\"+Math.round(o/i.total*100)+\"%, \"+i.posN+\"+, \"+i.negN+\"- )\"),t.push({name:\"N\",value:o}),t.push(\"<HR/>\"),t.push({name:\"DEL\",value:i.del.toString()}),t.push({name:\"INS\",value:i.ins.toString()}),n&&(t.push(\"<hr/>\"),t.push(...n.popupData(r,this.parent.colorBy)))}return t}}class tw extends Hl{static defaults={alleleFreqThreshold:.2,visibilityWindow:3e4,showCoverage:!0,showAlignments:!0,height:300,coverageTrackHeight:50,baseModificationThreshold:0};constructor(e,t){super(e,t)}init(e){this.type=\"alignment\",this.featureSource=new cm(e,this.browser);const t=Object.assign({parent:this},e);this.coverageTrack=new ew(t,this);const i=Object.assign({parent:this},e);this.alignmentTrack=new Ym(i,this.browser),super.init(e),this.showAlignments||(this._height=this.coverageTrackHeight),e.sort&&(Array.isArray(e.sort)?this.assignSort(e.sort[0]):this.assignSort(e.sort))}dispose(){this.alignmentTrack.dispose()}setHighlightedReads(e,t){this.alignmentTrack.setHighlightedReads(e,t),this.updateViews()}get expectedPairOrientation(){return this.alignmentTrack.expectedPairOrientation}get viewAsPairs(){return this.alignmentTrack.viewAsPairs}get colorBy(){return this.alignmentTrack.colorBy}set height(e){this._height=e,this.showAlignments&&(this.alignmentTrack.height=this.showCoverage?e-this.coverageTrackHeight:e)}get height(){return this._height}sort(e){e=this.assignSort(e);for(let t of this.trackView.viewports)if(t.containsPosition(e.chr,e.position)){const i=t.cachedFeatures;i&&(i.sortRows(e),t.repaint())}}assignSort(e){if(e.locus){const t=function(e){const t=e.split(\":\"),i=t[1].split(\"-\"),n={chr:t[0],start:Number.parseInt(i[0].replace(/,/g,\"\"))-1};return i.length>1?n.end=Number.parseInt(i[1].replace(/,/g,\"\")):n.end=n.start+1,n}(e.locus);e.chr=t.chr,e.position=t.start}else e.position--;return e.direction=\"ASC\"===e.direction||!0===e.direction,e.chr=this.browser.genome.getChromosomeName(e.chr),this.sortObject=e,this.sortObject}async getFeatures(e,t,i,n,r){const s=await this.featureSource.getAlignments(e,t,i);if(s.viewport=r,s.hasPairs&&!this._pairedEndStats&&!this.config.maxFragmentLength){const e=new Om(s.allAlignments(),this.config);e.totalCount>99&&(this._pairedEndStats=e)}s.pack(this.alignmentTrack);const o=this.sortObject;return o&&o.chr===e&&o.position>=t&&o.position<=i&&s.sortRows(o),this.alignmentTrack.hasPairs=this.alignmentTrack.hasPairs||s.hasPairs,s}computePixelHeight(e){return(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.computePixelHeight(e):0)}draw(e){xo.fillRect(e.context,0,e.pixelTop,e.pixelWidth,e.pixelHeight,{fillStyle:\"rgb(255, 255, 255)\"}),!0===this.showCoverage&&this.coverageTrackHeight>0?(this.trackView.axisCanvas.style.display=\"block\",this.coverageTrack.draw(e)):this.trackView.axisCanvas.style.display=\"none\",!0===this.showAlignments&&(this.alignmentTrack.setTop(this.coverageTrack,this.showCoverage),this.alignmentTrack.draw(e))}paintAxis(e,t,i){this.coverageTrack.paintAxis(e,t,this.coverageTrackHeight)}contextMenuItemList(e){return this.alignmentTrack.contextMenuItemList(e)}popupData(e){return!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight?this.coverageTrack.popupData(e):this.alignmentTrack.popupData(e)}clickedFeatures(e){let t;return t=!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight?this.coverageTrack.getClickedObject(e):this.alignmentTrack.getClickedObject(e),t?[t]:void 0}hoverText(e){if(!0===this.showCoverage&&e.y>=this.coverageTrack.top&&e.y<this.coverageTrackHeight){const t=this.coverageTrack.getClickedObject(e);if(t)return t.hoverText()}}menuItemList(){let e=[];e=e.concat(this.numericDataMenuItems()),e=e.concat(this.alignmentTrack.menuItemList());const t=()=>{if(!this.autoHeight){const e=(this.showCoverage?this.coverageTrackHeight:0)+(this.showAlignments?this.alignmentTrack.height:0);this.trackView.setTrackHeight(e)}};return e.push(\"<hr/>\"),e.push({object:Bt(Dl(\"Show Coverage\",this.showCoverage)),click:function(){this.showCoverage=!this.showCoverage,t(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),e.push({object:Bt(Dl(\"Show Alignments\",this.showAlignments)),click:function(){this.showAlignments=!this.showAlignments,t(),this.trackView.checkContentHeight(),this.trackView.repaintViews()}}),e}getState(){const e=super.getState();return this.sortObject&&(e.sort={chr:this.sortObject.chr,position:this.sortObject.position+1,option:this.sortObject.option,direction:this.sortObject.direction?\"ASC\":\"DESC\"}),Object.assign(e,this.alignmentTrack.getState()),e}getCachedAlignmentContainers(){return this.trackView.viewports.map((e=>e.cachedFeatures))}get dataRange(){return this.coverageTrack.dataRange}set dataRange(e){this.coverageTrack.dataRange=e}get logScale(){return this.coverageTrack.logScale}set logScale(e){this.coverageTrack.logScale=e}get autoscale(){return this.coverageTrack.autoscale}set autoscale(e){this.coverageTrack.autoscale=e}addPairedChordsForViewport(e){const t=this.maxTemplateLength,i=[],n=e.referenceFrame;for(let r of e.cachedFeatures.allAlignments())r.end>=n.start&&r.start<=n.end&&(r.paired?r.end-r.start>t&&i.push(r):r.mate&&r.mate.chr&&(r.mate.chr!==r.chr||Math.max(r.fragmentLength)>t)&&i.push(r));Pm((e=>{const t=[];for(let i of e)if(i.paired)i.firstAlignment&&i.secondAlignment&&t.push({uniqueId:i.readName,refName:zm(i.firstAlignment.chr),start:i.firstAlignment.start,end:i.firstAlignment.end,mate:{refName:zm(i.secondAlignment.chr),start:i.secondAlignment.start,end:i.secondAlignment.end}});else{const e=i.mate;e&&e.chr&&e.position&&t.push({uniqueId:i.readName,refName:zm(i.chr),start:i.start,end:i.end,mate:{refName:zm(e.chr),start:e.position-1,end:e.position}})}return t})(i),this,n,.02)}addSplitChordsForViewport(e){const t=[],i=e.referenceFrame;for(let n of e.cachedFeatures.allAlignments()){const e=n.hasTag(\"SA\");n.end>=i.start&&n.start<=i.end&&e&&t.push(n)}Pm((e=>{const t=e=>{const t=gp(e.tags().SA);let n=0;for(let r of t)r.start!==e.start&&i.push({uniqueId:`${e.readName}_${n++}`,refName:zm(e.chr),start:e.start,end:e.end,mate:{refName:zm(r.chr),start:r.start,end:r.start+r.lenOnRef}})},i=[];for(let i of e)i.paired?(t(i.firstAlignment),i.secondAlignment&&t(i.secondAlignment)):t(i);return i})(t),this,i,.02)}}class iw extends Hl{static defaults={height:250,theta:Math.PI/4,arcOrientation:\"UP\",showBlocks:!0,blockHeight:3,thickness:1,color:\"rgb(180,25,137)\",alpha:.02,logScale:!0};constructor(e,t){super(e,t)}init(e){super.init(e),!1===e.arcOrientation?this.arcOrientation=\"DOWN\":!0===e.arcOrientation?this.arcOrientation=\"UP\":e.arcOrientation?this.arcOrientation=e.arcOrientation.toUpperCase():this.arcOrientation=\"UP\",this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta),this.arcType=function(e){if(!e.arcType)return\"nested\";switch(e.arcType){case\"chiapet\":return\"inView\";case\"chiapetoutbound\":return\"partialInView\";default:return e.arcType}}(e),this.painter={flipAxis:\"DOWN\"===this.arcOrientation,dataRange:this.dataRange,paintAxis:cd},e.valueColumn?(this.valueColumn=e.valueColumn,this.hasValue=!0):e.useScore&&(this.hasValue=!0,this.valueColumn=\"score\"),e.max?(this.dataRange={min:e.min||0,max:e.max},this.autoscale=!1):this.autoscale=!0,e.featureSource?(this.featureSource=e.featureSource,delete e._featureSource):(this.featureSource=Ad(e,this.browser.genome),this.featureSource.getWGFeatures=aw)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow(),this.featureSource.visibilityWindow=this.visibilityWindow),this}get supportsWholeGenome(){return!0}async getFeatures(e,t,i){const n=this.visibilityWindow,r=await this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n});return void 0===this.hasValue&&r&&r.length>0&&(this.hasValue=void 0!==r[0].score),r}draw(e){\"proportional\"===this.arcType||\"inView\"===this.arcType||\"partialInView\"===this.arcType?this.drawProportional(e):this.drawNested(e)}drawNested(e){const t=e.context,i=e.pixelWidth,n=e.pixelHeight,r=e.viewportWidth,s=e.bpPerPixel,o=e.bpStart,a=s;xo.fillRect(t,0,e.pixelTop,i,n,{fillStyle:\"rgb(255, 255, 255)\"});const c=e.features;if(c){(function(){let e=0;for(let t of c){let n=(t.start-o)/a,r=(t.end-o)/a;n>=0&&r<=i&&(e=Math.max(e,r-n))}let t=Math.min(r,e)/2;if(e>0){let e=(n-10)/t;this.theta=function(e){let t,i=[.01570925532366355,.15838444032453644,.3249196962329063,.5095254494944288,.7265425280053609,.9999999999999999],n=[.031415926535897934,.3141592653589793,.6283185307179586,.9424777960769379,1.2566370614359172,1.5707963267948966];for(t=0;t<i.length&&!(i[t]>e);t++);let r=0===t?0:i[t-1],s=t<i.length?i[t]:1,o=(e-r)/(s-r),a=0===t?0:n[t-1],c=t<n.length?n[t]:Math.PI/2;return Math.min(Math.PI/2,a+o*(c-a))}(e),this.sinTheta=Math.sin(this.theta),this.cosTheta=Math.cos(this.theta)}}).call(this);const s=\"UP\"===this.arcOrientation,h=s?e.pixelHeight:0;t.font=\"8px sans-serif\",t.textAlign=\"center\";for(let e of c){let n;if(e.drawState=void 0,\"function\"==typeof this.color?n=this.color(e):(n=this.color||e.color||\"rgb(180,25,137)\",n&&this.config.useScore&&(n=ow(n,(l=e.score,Math.min(1,.11+l/779*.89).toString())))),t.lineWidth=e.thickness||this.thickness||1,e.chr1===e.chr2||\"all\"===e.chr){const{m1:c,m2:l}=nw(e,this.browser.genome);let d=Math.round((c-o)/a),u=Math.round((l-o)/a);if(u<0||d>i)continue;let f=u-d;f<3&&(f=3,d--);const p=f/2,g=p/this.sinTheta,m=this.cosTheta*g,w=d+p;let b,F,v;if(s?(b=this.height+m,F=Math.PI+Math.PI/2-this.theta,v=Math.PI+Math.PI/2+this.theta):(b=-m,F=Math.PI/2-this.theta,v=Math.PI/2+this.theta),this.showBlocks&&\"all\"!==e.chr){const i=(e.start1-o)/a,n=(e.end1-o)/a,r=(e.start2-o)/a,c=(e.end2-o)/a,l=s?-this.blockHeight:this.blockHeight;t.fillRect(i,h,n-i,l),t.fillRect(r,h,c-r,l)}n&&!this.config.useScore&&f>r&&(n=ow(n,this.alpha)),t.strokeStyle=n,t.fillStyle=n,t.beginPath(),t.arc(w,b,g,F,v,!1),t.stroke(),e.drawState={xc:w,yc:b,r:g}}else{let r=Math.round((e.start-o)/a),c=Math.round((e.end-o)/a);if(c<0||r>i)continue;let l=c-r;l<3&&(l=3,r--);const h=e.chr===e.chr1?e.chr2:e.chr1;t.strokeStyle=n,t.fillStyle=ow(Nu(h),.5),s?(t.fillRect(r,this.height/2,l,this.height/2),t.fillText(h,r+l/2,this.height/2-5),e.drawState={x:r,y:this.height/2,w:l,h:this.height/2}):(t.fillRect(r,0,l,this.height/2),t.fillText(h,r+l/2,this.height/2+13),e.drawState={x:r,y:0,w:l,h:this.height/2})}}}var l}getScaleFactor(e,t,i,n){return n?i/(Math.log10(t+1)-(e<=0?0:Math.log10(e+1))):i/(t-e)}drawProportional(e){const t=e.context,i=e.pixelWidth,n=e.pixelHeight,r=e.bpPerPixel,s=e.bpStart,o=r,a=e.referenceFrame.start,c=e.referenceFrame.end,l=\"UP\"===this.arcOrientation;xo.fillRect(t,0,e.pixelTop,i,n,{fillStyle:\"rgb(255, 255, 255)\"});const h=e.features;if(h&&h.length>0){const n=0,r=this.getScaleFactor(n,this.dataRange.max,e.pixelHeight-1,this.logScale),d=l?e.pixelHeight:0;for(let e of h){e.drawState=void 0;const n=this.valueColumn?e[this.valueColumn]:e.score;if(void 0===n||Number.isNaN(n))continue;const h=Math.round((this.logScale?Math.log10(n+1):n)*r);if(e.chr1===e.chr2||\"all\"===e.chr){const{m1:i,m2:r}=nw(e,this.browser.genome);let u=Math.round((i-s)/o),f=Math.round((r-s)/o)-u;if(f<3&&(f=3,u--),n<this.dataRange.min||n>this.dataRange.max)continue;if(\"proportional\"!==this.arcType){const e=\"partialInView\"===this.arcType,t=i>=a&&r<=c;let n=!1,s=!1;if(!t&&e&&(n=a<=i&&i<=c,n||(s=a<=r&&r<=c)),!(t||n||s))continue}const p=f/2,g=u+f/2;e.drawState={xc:g,yc:d,radiusX:p,radiusY:h};const m=l,w=e.color||this.color;if(t.strokeStyle=w,t.lineWidth=e.thickness||this.thickness||1,!0===t.isSVG?t.strokeEllipse(g,d,p,h,0,0,Math.PI,m):(t.beginPath(),t.ellipse(g,d,p,h,0,0,Math.PI,m),t.stroke()),this.alpha&&(t.fillStyle=ow(w,this.alpha),!0===t.isSVG?t.fillEllipse(g,d,p,h,0,0,Math.PI,m):t.fill()),this.showBlocks&&\"all\"!==e.chr){t.fillStyle=w;const i=(e.start1-s)/o,n=(e.end1-s)/o,r=(e.start2-s)/o,a=(e.end2-s)/o,c=l?-this.blockHeight:this.blockHeight;t.fillRect(i,d,n-i,c),t.fillRect(r,d,a-r,c)}}else{let r=Math.round((e.start-s)/o),a=Math.round((e.end-s)/o);if(a<0||r>i||n<this.dataRange.min||n>this.dataRange.max)continue;const c=Math.min(h,this.height-13);let d=a-r;d<3&&(d=3,r--);const u=e.chr===e.chr1?e.chr2:e.chr1;if(t.font=\"8px sans-serif\",t.textAlign=\"center\",t.fillStyle=ow(Nu(u),.5),l){const i=this.height-c;t.fillRect(r,i,d,c),t.fillText(u,r+d/2,i-5),e.drawState={x:r,y:i,w:d,h:c}}else t.fillRect(r,0,d,c),t.fillText(u,r+d/2,c+13),e.drawState={x:r,y:0,w:d,h:c}}}}}clearAxis(e,t,i){xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"})}paintAxis(e,t,i){const n={min:0,max:this.dataRange.max};\"proportional\"===this.arcType||\"inView\"===this.arcType||\"partialInView\"===this.arcType?(this.painter.flipAxis=\"DOWN\"===this.arcOrientation,this.painter.dataRange=n,this.painter.paintAxis(e,t,i)):this.clearAxis(e,t,i)}menuItemList(){let e=[];if(this.hasValue){e.push(\"<hr/>\");const t={nested:\"Nested\",proportional:\"Proportional - All\",inView:\"Proportional - Both Ends in View\",partialInView:\"Proportional - One End in View\"};e.push(\"<b>Arc Type</b>\");for(let i of[\"nested\",\"proportional\",\"inView\",\"partialInView\"])e.push({object:Bt(Dl(t[i],i===this.arcType)),click:function(){this.arcType=i,this.trackView.repaintViews()}})}return e.push(\"<hr/>\"),e.push({name:\"Toggle arc direction\",click:function(){this.arcOrientation=\"UP\"===this.arcOrientation?\"DOWN\":\"UP\",this.trackView.repaintViews()}}),e.push({name:this.showBlocks?\"Hide Blocks\":\"Show Blocks\",click:function(){this.showBlocks=!this.showBlocks,this.trackView.repaintViews()}}),\"proportional\"!==this.arcType&&\"inView\"!==this.arcType&&\"partialInView\"!==this.arcType||(e=e.concat(this.numericDataMenuItems())),this.browser.circularView&&(e.push(\"<hr/>\"),e.push({label:\"Add interactions to circular view\",click:function(){for(let e of this.trackView.viewports)this.addChordsForViewport(e.referenceFrame)}})),e}contextMenuItemList(e){if(this.browser.circularView){const t=e.viewport,i=[];return i.push({label:\"Add interactions to circular view\",click:()=>{const e=t.referenceFrame;this.addChordsForViewport(e)}}),i.push(\"<hr/>\"),i}}addChordsForViewport(e){let t;if(\"all\"===e.chr)t=Object.values(this.featureSource.getAllFeatures()).flat();else{t=this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end).filter((e=>e.drawState))}if(0===t.length)return;Pm(t.map((e=>{const t=e._f||e;return{uniqueId:`${t.chr1}:${t.start1}-${t.end1}_${t.chr2}:${t.start2}-${t.end2}`,refName:zm(t.chr1),start:t.start1,end:t.end1,mate:{refName:zm(t.chr2),start:t.start2,end:t.end2}}})),this,e,.5)}doAutoscale(e){let t=0;if(e)for(let i of e){const e=this.valueColumn?i[this.valueColumn]:i.score;Number.isNaN(e)||(t=Math.max(t,e))}return{min:0,max:t}}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){const t=e._||e;if(i.push({name:\"Region 1\",value:rw(t.chr1,t.start1,t.end1,t.strand1)}),i.push({name:\"Region 2\",value:rw(t.chr2,t.start2,t.end2,t.strand2)}),t.name&&i.push({name:\"Name\",value:t.name}),void 0!==t.value&&i.push({name:\"Value\",value:t.value}),void 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i})(s,r)},utf8border:(e,t)=>{(t=t||e.length)>e.length&&(t=e.length);let i=t-1;for(;i>=0&&128==(192&e[i]);)i--;return i<0||0===i?t:i+Kw[e[i]]>t?i:t}};var Xw=function(){this.input=null,this.next_in=0,this.avail_in=0,this.total_in=0,this.output=null,this.next_out=0,this.avail_out=0,this.total_out=0,this.msg=\"\",this.state=null,this.data_type=2,this.adler=0},Zw=function(e,t){let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_,x;const k=e.state;i=e.next_in,_=e.input,n=i+(e.avail_in-5),r=e.next_out,x=e.output,s=r-(t-e.avail_out),o=r+(e.avail_out-257),a=k.dmax,c=k.wsize,l=k.whave,h=k.wnext,d=k.window,u=k.hold,f=k.bits,p=k.lencode,g=k.distcode,m=(1<<k.lenbits)-1,w=(1<<k.distbits)-1;e:do{f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=p[u&m];t:for(;;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,0===F)x[r++]=65535&b;else{if(!(16&F)){if(64&F){if(32&F){k.mode=12;break e}e.msg=\"invalid literal/length code\",k.mode=30;break e}b=p[(65535&b)+(u&(1<<F)-1)];continue t}for(v=65535&b,F&=15,F&&(f<F&&(u+=_[i++]<<f,f+=8),v+=u&(1<<F)-1,u>>>=F,f-=F),f<15&&(u+=_[i++]<<f,f+=8,u+=_[i++]<<f,f+=8),b=g[u&w];;){if(F=b>>>24,u>>>=F,f-=F,F=b>>>16&255,16&F){if(y=65535&b,F&=15,f<F&&(u+=_[i++]<<f,f+=8,f<F&&(u+=_[i++]<<f,f+=8)),y+=u&(1<<F)-1,y>a){e.msg=\"invalid distance too far back\",k.mode=30;break e}if(u>>>=F,f-=F,F=r-s,y>F){if(F=y-F,F>l&&k.sane){e.msg=\"invalid distance too far back\",k.mode=30;break e}if(A=0,C=d,0===h){if(A+=c-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}else if(h<F){if(A+=c+h-F,F-=h,F<v){v-=F;do{x[r++]=d[A++]}while(--F);if(A=0,h<v){F=h,v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}}}else if(A+=h-F,F<v){v-=F;do{x[r++]=d[A++]}while(--F);A=r-y,C=x}for(;v>2;)x[r++]=C[A++],x[r++]=C[A++],x[r++]=C[A++],v-=3;v&&(x[r++]=C[A++],v>1&&(x[r++]=C[A++]))}else{A=r-y;do{x[r++]=x[A++],x[r++]=x[A++],x[r++]=x[A++],v-=3}while(v>2);v&&(x[r++]=x[A++],v>1&&(x[r++]=x[A++]))}break}if(64&F){e.msg=\"invalid distance code\",k.mode=30;break 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0!==_&&(r[f+_]=g-y<<24|64<<16),a.bits=F,0},{Z_FINISH:sb,Z_BLOCK:ob,Z_TREES:ab,Z_OK:cb,Z_STREAM_END:lb,Z_NEED_DICT:hb,Z_STREAM_ERROR:db,Z_DATA_ERROR:ub,Z_MEM_ERROR:fb,Z_BUF_ERROR:pb,Z_DEFLATED:gb}=jw,mb=12,wb=30,bb=e=>(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24);function Fb(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new Uint16Array(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}var vb,yb,Ab=e=>{if(!e||!e.state)return db;const t=e.state;return e.total_in=e.total_out=t.total=0,e.msg=\"\",t.wrap&&(e.adler=1&t.wrap),t.mode=1,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new Int32Array(852),t.distcode=t.distdyn=new Int32Array(592),t.sane=1,t.back=-1,cb},Cb=e=>{if(!e||!e.state)return db;const t=e.state;return t.wsize=0,t.whave=0,t.wnext=0,Ab(e)},_b=(e,t)=>{let i;if(!e||!e.state)return db;const n=e.state;return t<0?(i=0,t=-t):(i=1+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?db:(null!==n.window&&n.wbits!==t&&(n.window=null),n.wrap=i,n.wbits=t,Cb(e))},xb=(e,t)=>{if(!e)return db;const i=new Fb;e.state=i,i.window=null;const n=_b(e,t);return n!==cb&&(e.state=null),n},kb=!0,Ib=e=>{if(kb){vb=new Int32Array(512),yb=new Int32Array(32);let t=0;for(;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(rb(1,e.lens,0,288,vb,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;rb(2,e.lens,0,32,yb,0,e.work,{bits:5}),kb=!1}e.lencode=vb,e.lenbits=9,e.distcode=yb,e.distbits=5},Sb=(e,t,i,n)=>{let r;const s=e.state;return null===s.window&&(s.wsize=1<<s.wbits,s.wnext=0,s.whave=0,s.window=new Uint8Array(s.wsize)),n>=s.wsize?(s.window.set(t.subarray(i-s.wsize,i),0),s.wnext=0,s.whave=s.wsize):(r=s.wsize-s.wnext,r>n&&(r=n),s.window.set(t.subarray(i-n,i-n+r),s.wnext),(n-=r)?(s.window.set(t.subarray(i-n,i),0),s.wnext=n,s.whave=s.wsize):(s.wnext+=r,s.wnext===s.wsize&&(s.wnext=0),s.whave<s.wsize&&(s.whave+=r))),0},Eb=(e,t)=>{let i,n,r,s,o,a,c,l,h,d,u,f,p,g,m,w,b,F,v,y,A,C,_=0;const x=new Uint8Array(4);let k,I;const S=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]);if(!e||!e.state||!e.output||!e.input&&0!==e.avail_in)return db;i=e.state,i.mode===mb&&(i.mode=13),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,d=a,u=c,C=cb;e:for(;;)switch(i.mode){case 1:if(0===i.wrap){i.mode=13;break}for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(2&i.wrap&&35615===l){i.check=0,x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0),l=0,h=0,i.mode=2;break}if(i.flags=0,i.head&&(i.head.done=!1),!(1&i.wrap)||(((255&l)<<8)+(l>>8))%31){e.msg=\"incorrect header check\",i.mode=wb;break}if((15&l)!==gb){e.msg=\"unknown compression method\",i.mode=wb;break}if(l>>>=4,h-=4,A=8+(15&l),0===i.wbits)i.wbits=A;else if(A>i.wbits){e.msg=\"invalid window size\",i.mode=wb;break}i.dmax=1<<i.wbits,e.adler=i.check=1,i.mode=512&l?10:mb,l=0,h=0;break;case 2:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.flags=l,(255&i.flags)!==gb){e.msg=\"unknown compression method\",i.mode=wb;break}if(57344&i.flags){e.msg=\"unknown header flags set\",i.mode=wb;break}i.head&&(i.head.text=l>>8&1),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0,i.mode=3;case 3:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.time=l),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,x[2]=l>>>16&255,x[3]=l>>>24&255,i.check=Qw(i.check,x,4,0)),l=0,h=0,i.mode=4;case 4:for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.head&&(i.head.xflags=255&l,i.head.os=l>>8),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0,i.mode=5;case 5:if(1024&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length=l,i.head&&(i.head.extra_len=l),512&i.flags&&(x[0]=255&l,x[1]=l>>>8&255,i.check=Qw(i.check,x,2,0)),l=0,h=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&(f=i.length,f>a&&(f=a),f&&(i.head&&(A=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Uint8Array(i.head.extra_len)),i.head.extra.set(n.subarray(s,s+f),A)),512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,i.length-=f),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.name+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===a)break e;f=0;do{A=n[s+f++],i.head&&A&&i.length<65536&&(i.head.comment+=String.fromCharCode(A))}while(A&&f<a);if(512&i.flags&&(i.check=Qw(i.check,n,f,s)),a-=f,s+=f,A)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;h<16;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l!==(65535&i.check)){e.msg=\"header crc mismatch\",i.mode=wb;break}l=0,h=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=mb;break;case 10:for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}e.adler=i.check=bb(l),l=0,h=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,hb;e.adler=i.check=1,i.mode=mb;case mb:if(t===ob||t===ab)break e;case 13:if(i.last){l>>>=7&h,h-=7&h,i.mode=27;break}for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}switch(i.last=1&l,l>>>=1,h-=1,3&l){case 0:i.mode=14;break;case 1:if(Ib(i),i.mode=20,t===ab){l>>>=2,h-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg=\"invalid block type\",i.mode=wb}l>>>=2,h-=2;break;case 14:for(l>>>=7&h,h-=7&h;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if((65535&l)!=(l>>>16^65535)){e.msg=\"invalid stored block lengths\",i.mode=wb;break}if(i.length=65535&l,l=0,h=0,i.mode=15,t===ab)break e;case 15:i.mode=16;case 16:if(f=i.length,f){if(f>a&&(f=a),f>c&&(f=c),0===f)break e;r.set(n.subarray(s,s+f),o),a-=f,s+=f,c-=f,o+=f,i.length-=f;break}i.mode=mb;break;case 17:for(;h<14;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(i.nlen=257+(31&l),l>>>=5,h-=5,i.ndist=1+(31&l),l>>>=5,h-=5,i.ncode=4+(15&l),l>>>=4,h-=4,i.nlen>286||i.ndist>30){e.msg=\"too many length or distance symbols\",i.mode=wb;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;h<3;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.lens[S[i.have++]]=7&l,l>>>=3,h-=3}for(;i.have<19;)i.lens[S[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,k={bits:i.lenbits},C=rb(0,i.lens,0,19,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid code lengths set\",i.mode=wb;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(b<16)l>>>=m,h-=m,i.lens[i.have++]=b;else{if(16===b){for(I=m+2;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l>>>=m,h-=m,0===i.have){e.msg=\"invalid bit length repeat\",i.mode=wb;break}A=i.lens[i.have-1],f=3+(3&l),l>>>=2,h-=2}else if(17===b){for(I=m+3;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=3+(7&l),l>>>=3,h-=3}else{for(I=m+7;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=m,h-=m,A=0,f=11+(127&l),l>>>=7,h-=7}if(i.have+f>i.nlen+i.ndist){e.msg=\"invalid bit length repeat\",i.mode=wb;break}for(;f--;)i.lens[i.have++]=A}}if(i.mode===wb)break;if(0===i.lens[256]){e.msg=\"invalid code -- missing end-of-block\",i.mode=wb;break}if(i.lenbits=9,k={bits:i.lenbits},C=rb(1,i.lens,0,i.nlen,i.lencode,0,i.work,k),i.lenbits=k.bits,C){e.msg=\"invalid literal/lengths set\",i.mode=wb;break}if(i.distbits=6,i.distcode=i.distdyn,k={bits:i.distbits},C=rb(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,k),i.distbits=k.bits,C){e.msg=\"invalid distances set\",i.mode=wb;break}if(i.mode=20,t===ab)break e;case 20:i.mode=21;case 21:if(a>=6&&c>=258){e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,Zw(e,u),o=e.next_out,r=e.output,c=e.avail_out,s=e.next_in,n=e.input,a=e.avail_in,l=i.hold,h=i.bits,i.mode===mb&&(i.back=-1);break}for(i.back=0;_=i.lencode[l&(1<<i.lenbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(w&&!(240&w)){for(F=m,v=w,y=b;_=i.lencode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,i.length=b,0===w){i.mode=26;break}if(32&w){i.back=-1,i.mode=mb;break}if(64&w){e.msg=\"invalid literal/length code\",i.mode=wb;break}i.extra=15&w,i.mode=22;case 22:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.length+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}i.was=i.length,i.mode=23;case 23:for(;_=i.distcode[l&(1<<i.distbits)-1],m=_>>>24,w=_>>>16&255,b=65535&_,!(m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(!(240&w)){for(F=m,v=w,y=b;_=i.distcode[y+((l&(1<<F+v)-1)>>F)],m=_>>>24,w=_>>>16&255,b=65535&_,!(F+m<=h);){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}l>>>=F,h-=F,i.back+=F}if(l>>>=m,h-=m,i.back+=m,64&w){e.msg=\"invalid distance code\",i.mode=wb;break}i.offset=b,i.extra=15&w,i.mode=24;case 24:if(i.extra){for(I=i.extra;h<I;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}i.offset+=l&(1<<i.extra)-1,l>>>=i.extra,h-=i.extra,i.back+=i.extra}if(i.offset>i.dmax){e.msg=\"invalid distance too far back\",i.mode=wb;break}i.mode=25;case 25:if(0===c)break e;if(f=u-c,i.offset>f){if(f=i.offset-f,f>i.whave&&i.sane){e.msg=\"invalid distance too far back\",i.mode=wb;break}f>i.wnext?(f-=i.wnext,p=i.wsize-f):p=i.wnext-f,f>i.length&&(f=i.length),g=i.window}else g=r,p=o-i.offset,f=i.length;f>c&&(f=c),c-=f,i.length-=f;do{r[o++]=g[p++]}while(--f);0===i.length&&(i.mode=21);break;case 26:if(0===c)break e;r[o++]=i.length,c--,i.mode=21;break;case 27:if(i.wrap){for(;h<32;){if(0===a)break e;a--,l|=n[s++]<<h,h+=8}if(u-=c,e.total_out+=u,i.total+=u,u&&(e.adler=i.check=i.flags?Qw(i.check,r,u,o-u):Uw(i.check,r,u,o-u)),u=c,(i.flags?l:bb(l))!==i.check){e.msg=\"incorrect data check\",i.mode=wb;break}l=0,h=0}i.mode=28;case 28:if(i.wrap&&i.flags){for(;h<32;){if(0===a)break e;a--,l+=n[s++]<<h,h+=8}if(l!==(4294967295&i.total)){e.msg=\"incorrect length check\",i.mode=wb;break}l=0,h=0}i.mode=29;case 29:C=lb;break e;case wb:C=ub;break e;case 31:return fb;default:return db}return e.next_out=o,e.avail_out=c,e.next_in=s,e.avail_in=a,i.hold=l,i.bits=h,(i.wsize||u!==e.avail_out&&i.mode<wb&&(i.mode<27||t!==sb))&&Sb(e,e.output,e.next_out,u-e.avail_out),d-=e.avail_in,u-=e.avail_out,e.total_in+=d,e.total_out+=u,i.total+=u,i.wrap&&u&&(e.adler=i.check=i.flags?Qw(i.check,r,u,e.next_out-u):Uw(i.check,r,u,e.next_out-u)),e.data_type=i.bits+(i.last?64:0)+(i.mode===mb?128:0)+(20===i.mode||15===i.mode?256:0),(0===d&&0===u||t===sb)&&C===cb&&(C=pb),C},Nb={inflateReset:Cb,inflateReset2:_b,inflateResetKeep:Ab,inflateInit:e=>xb(e,15),inflateInit2:xb,inflate:Eb,inflateEnd:e=>{if(!e||!e.state)return db;let t=e.state;return t.window&&(t.window=null),e.state=null,cb},inflateGetHeader:(e,t)=>{if(!e||!e.state)return db;const i=e.state;return 2&i.wrap?(i.head=t,t.done=!1,cb):db},inflateSetDictionary:(e,t)=>{const i=t.length;let n,r,s;return e&&e.state?(n=e.state,0!==n.wrap&&11!==n.mode?db:11===n.mode&&(r=1,r=Uw(r,t,i,0),r!==n.check)?ub:(s=Sb(e,t,i,i),s?(n.mode=31,fb):(n.havedict=1,cb))):db},inflateInfo:\"pako inflate (from Nodeca project)\"};var Bb=function(){this.text=0,this.time=0,this.xflags=0,this.os=0,this.extra=null,this.extra_len=0,this.name=\"\",this.comment=\"\",this.hcrc=0,this.done=!1},Mb=Object.prototype.toString,{Z_NO_FLUSH:Rb,Z_FINISH:Db,Z_OK:Tb,Z_STREAM_END:Lb,Z_NEED_DICT:zb,Z_STREAM_ERROR:Hb,Z_DATA_ERROR:Pb,Z_MEM_ERROR:Ob}=jw;function Ub(e){this.options=Gw.assign({chunkSize:65536,windowBits:15,to:\"\"},e||{});const t=this.options;t.raw&&t.windowBits>=0&&t.windowBits<16&&(t.windowBits=-t.windowBits,0===t.windowBits&&(t.windowBits=-15)),!(t.windowBits>=0&&t.windowBits<16)||e&&e.windowBits||(t.windowBits+=32),t.windowBits>15&&t.windowBits<48&&(15&t.windowBits||(t.windowBits|=15)),this.err=0,this.msg=\"\",this.ended=!1,this.chunks=[],this.strm=new Xw,this.strm.avail_out=0;let i=Nb.inflateInit2(this.strm,t.windowBits);if(i!==Tb)throw new Error(Vw[i]);if(this.header=new Bb,Nb.inflateGetHeader(this.strm,this.header),t.dictionary&&(\"string\"==typeof t.dictionary?t.dictionary=Yw.string2buf(t.dictionary):\"[object ArrayBuffer]\"===Mb.call(t.dictionary)&&(t.dictionary=new Uint8Array(t.dictionary)),t.raw&&(i=Nb.inflateSetDictionary(this.strm,t.dictionary),i!==Tb)))throw new Error(Vw[i])}function qb(e,t){const i=new Ub(t);if(i.push(e),i.err)throw i.msg||Vw[i.err];return i.result}Ub.prototype.push=function(e,t){const i=this.strm,n=this.options.chunkSize,r=this.options.dictionary;let s,o,a;if(this.ended)return!1;for(o=t===~~t?t:!0===t?Db:Rb,\"[object ArrayBuffer]\"===Mb.call(e)?i.input=new Uint8Array(e):i.input=e,i.next_in=0,i.avail_in=i.input.length;;){for(0===i.avail_out&&(i.output=new Uint8Array(n),i.next_out=0,i.avail_out=n),s=Nb.inflate(i,o),s===zb&&r&&(s=Nb.inflateSetDictionary(i,r),s===Tb?s=Nb.inflate(i,o):s===Pb&&(s=zb));i.avail_in>0&&s===Lb&&i.state.wrap>0&&0!==e[i.next_in];)Nb.inflateReset(i),s=Nb.inflate(i,o);switch(s){case Hb:case Pb:case zb:case Ob:return this.onEnd(s),this.ended=!0,!1}if(a=i.avail_out,i.next_out&&(0===i.avail_out||s===Lb))if(\"string\"===this.options.to){let e=Yw.utf8border(i.output,i.next_out),t=i.next_out-e,r=Yw.buf2string(i.output,e);i.next_out=t,i.avail_out=n-t,t&&i.output.set(i.output.subarray(e,e+t),0),this.onData(r)}else this.onData(i.output.length===i.next_out?i.output:i.output.subarray(0,i.next_out));if(s!==Tb||0!==a){if(s===Lb)return s=Nb.inflateEnd(this.strm),this.onEnd(s),this.ended=!0,!0;if(0===i.avail_in)break}}return!0},Ub.prototype.onData=function(e){this.chunks.push(e)},Ub.prototype.onEnd=function(e){e===Tb&&(\"string\"===this.options.to?this.result=this.chunks.join(\"\"):this.result=Gw.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg};var Qb=function(e,t){return(t=t||{}).raw=!0,qb(e,t)},Vb={Inflate:Ub,inflate:qb,inflateRaw:Qb,ungzip:qb,constants:jw},{Inflate:jb,inflate:Wb,inflateRaw:Gb,ungzip:$b}=Vb,Kb=Wb,Yb=$b;var Xb=new Map([[1,function(e,t){let i=new Uint8Array(e);return Kb(i).buffer}],[2,function(e,t){let i=e.byteLength,n=new Uint8Array(i),r=Math.floor(i/t),s=new DataView(e);for(var o=0;o<t;o++)for(var a=0;a<r;a++)n[o+a*t]=s.getUint8(o*r+a);return n.buffer}],[3,function(e,t){return function(e){for(var t=e.byteLength%2!=0,i=e.byteLength-4,n=new DataView(e),r=0,s=0,o=0;o<i-1;o+=2){s=(s+(r=(r+n.getUint16(o,!0))%65535))%65535}if(t){s=(s+(r=(r+n.getUint8(i-1))%65535))%65535}var[a,c]=Aw.unpack_from(\">HH\",e,i);if(c%=65535,r!=(a%=65535)||s!=c)throw'ValueError(\"fletcher32 checksum invalid\")'}(e),e.slice(0,-4)}]]),Zb=class{constructor(e,t){this.fh=e,this.offset=t,this.depth=null}async init(){this.all_nodes=new Map,await this._read_root_node(),await this._read_children()}async _read_children(){let e=this.depth;for(;e>0;){for(var t of this.all_nodes.get(e))for(var i of t.get(\"addresses\"))this._add_node(await this._read_node(i,e-1));e--}}async _read_root_node(){let e=await this._read_node(this.offset,null);this._add_node(e),this.depth=e.get(\"node_level\")}_add_node(e){let t=e.get(\"node_level\");this.all_nodes.has(t)?this.all_nodes.get(t).push(e):this.all_nodes.set(t,[e])}async _read_node(e,t){let i=await this._read_node_header(e,t);return i.set(\"keys\",[]),i.set(\"addresses\",[]),i}async _read_node_header(e){throw\"NotImplementedError: must define _read_node_header in implementation class\"}},Jb=class extends Zb{constructor(){super(...arguments),pw(this,\"B_LINK_NODE\",new Map([[\"signature\",\"4s\"],[\"node_type\",\"B\"],[\"node_level\",\"B\"],[\"entries_used\",\"H\"],[\"left_sibling\",\"Q\"],[\"right_sibling\",\"Q\"]]))}async _read_node_header(e,t){let i=await gw(this.B_LINK_NODE,this.fh,e);if(null!=t&&i.get(\"node_level\")!=t)throw\"node level does not match\";return i}},eF=class extends Jb{constructor(e,t){super(e,t),pw(this,\"NODE_TYPE\",0),this.ready=this.init()}async _read_node(e,t){let i=await this._read_node_header(e,t);e+=bw(this.B_LINK_NODE);let n=[],r=[],s=i.get(\"entries_used\");for(var o=0;o<s;o++){let t=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8;let i=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8,n.push(t),r.push(i)}return n.push((await Aw.unpack_from_async(\"<Q\",this.fh,e))[0]),i.set(\"keys\",n),i.set(\"addresses\",r),i}symbol_table_addresses(){var e=[],t=this.all_nodes.get(0);for(var i of t)e=e.concat(i.get(\"addresses\"));return e}},tF=class extends Jb{constructor(e,t,i){super(e,t),pw(this,\"NODE_TYPE\",1),this.dims=i,this.ready=this.init()}async _read_node(e,t){let i=await this._read_node_header(e,t);e+=bw(this.B_LINK_NODE);var n=[],r=[];let s=i.get(\"entries_used\");for(var o=0;o<s;o++){let[t,i]=await Aw.unpack_from_async(\"<II\",this.fh,e);e+=8;let s=\"<\"+this.dims.toFixed()+\"Q\",o=Aw.calcsize(s),a=await Aw.unpack_from_async(s,this.fh,e);e+=o;let c=(await Aw.unpack_from_async(\"<Q\",this.fh,e))[0];e+=8,n.push(new Map([[\"chunk_size\",t],[\"filter_mask\",i],[\"chunk_offset\",a]])),r.push(c)}return i.set(\"keys\",n),i.set(\"addresses\",r),i}async construct_data_from_chunks(e,t,i,n){var r,s,o;if(i instanceof Array){let e=i[0];if(\"REFERENCE\"==e){if(8!=i[1])throw\"NotImplementedError('Unsupported Reference type')\";i=\"<u8\",r=\"getUint64\",s=!1,o=8}else{if(\"VLEN_STRING\"!=e&&\"VLEN_SEQUENCE\"!=e)throw\"NotImplementedError('datatype not implemented')\";r=\"getVLENStruct\",s=!1,o=16}}else[r,s,o]=yw(i);var a=t.reduce((function(e,t){return e*t}),1),c=e.reduce((function(e,t){return e*t}),1);let l=t.length;var h=1;e.slice().map((function(e){let t=h;return h*=e,t}));h=1;var d=t.slice().reverse().map((function(e){let t=h;return h*=e,t})).reverse(),u=new Array(a);let f=c*o;for(var p of this.all_nodes.get(0)){let i=p.get(\"keys\"),a=p.get(\"addresses\"),h=i.length;for(var g=0;g<h;g++){let h=i[g],p=a[g];var m;if(null==n)m=await this.fh.slice(p,p+f);else{m=await this.fh.slice(p,p+h.get(\"chunk_size\"));let e=h.get(\"filter_mask\");m=this._filter_chunk(m,e,n,o)}for(var w=h.get(\"chunk_offset\").slice(),b=w.slice(),F=b.map((function(){return 0})),v=new Cw(m),y=0;y<c;y++){for(var A=l-1;A>=0&&F[A]>=e[A];A--)F[A]=0,b[A]=w[A],A>0&&(F[A-1]+=1,b[A-1]+=1);if(b.slice(0,-1).every((function(e,i){return e<t[i]}))){let e=y*o,t=v[r](e,!s,o),i=b.slice(0,-1).reduce((function(e,t,i){return t*d[i]+e}),0);u[i]=t}F[l-1]+=1,b[l-1]+=1}}}return u}_filter_chunk(e,t,i,n){let r=i.length,s=e.slice();for(var o=r-1;o>=0;o--){if(t&1<<o)continue;let e=i[o],r=e.get(\"filter_id\"),a=e.get(\"client_data\");if(!Xb.has(r))throw'NotImplementedError(\"Filter with id:'+r.toFixed()+' not supported\")';s=Xb.get(r)(s,n,a)}return s}},iF=class extends Zb{constructor(e,t){super(e,t),pw(this,\"B_TREE_HEADER\",new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"node_type\",\"B\"],[\"node_size\",\"I\"],[\"record_size\",\"H\"],[\"depth\",\"H\"],[\"split_percent\",\"B\"],[\"merge_percent\",\"B\"],[\"root_address\",\"Q\"],[\"root_nrecords\",\"H\"],[\"total_nrecords\",\"Q\"]])),pw(this,\"B_LINK_NODE\",new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"node_type\",\"B\"]])),this.ready=this.init()}async _read_root_node(){let e=await this._read_tree_header(this.offset);this.address_formats=this._calculate_address_formats(e),this.header=e,this.depth=e.get(\"depth\");let t=[e.get(\"root_address\"),e.get(\"root_nrecords\"),e.get(\"total_nrecords\")],i=await this._read_node(t,this.depth);this._add_node(i)}async _read_tree_header(e){return await gw(this.B_TREE_HEADER,this.fh,this.offset)}_calculate_address_formats(e){let t=e.get(\"node_size\"),i=e.get(\"record_size\"),n=0,r=0,s=new Map,o=e.get(\"depth\");for(var a=0;a<=o;a++){let e,c,l,h=\"\",d=\"\",u=\"\";if(0==a?(e=0,c=0,l=0):1==a?(e=8,h=\"<Q\",c=this._required_bytes(n),d=this._int_format(c),l=0):(e=8,h=\"<Q\",c=this._required_bytes(n),d=this._int_format(c),l=this._required_bytes(r),u=this._int_format(l)),s.set(a,[e,c,l,h,d,u]),a<o){let s=e+c+l;n=this._nrecords_max(t,i,s),r>0?r*=n:r=n}}return s}_nrecords_max(e,t,i){return Math.floor((e-10-i)/(t+i))}_required_bytes(e){return Math.ceil(_w(e)/8)}_int_format(e){return[\"<B\",\"<H\",\"<I\",\"<Q\"][e-1]}async _read_node(e,t){let[i,n,r]=e,s=this._read_node_header(i,t);i+=bw(this.B_LINK_NODE);let o=this.header.get(\"record_size\"),a=[];for(let e=0;e<n;e++){let e=await this._parse_record(this.fh,i,o);i+=o,a.push(e)}let c=[],l=this.address_formats.get(t);if(0!=t){let[e,t,r,s,o,a]=l;for(let l=0;l<=n;l++){let n=(await Aw.unpack_from_async(s,this.fh,i))[0];i+=e;let l=(await Aw.unpack_from_async(o,this.fh,i))[0];i+=t;let h=l;r>0&&(h=(await Aw.unpack_from_async(a,this.fh,i))[0],i+=r),c.push([n,l,h])}}return s.set(\"keys\",a),s.set(\"addresses\",c),s}async _read_node_header(e,t){let i=await gw(this.B_LINK_NODE,this.fh,e);return i.set(\"node_level\",t),i}*iter_records(){for(let e of this.all_nodes.values())for(let t of e)for(let e of t.get(\"keys\"))yield e}_parse_record(e){throw\"NotImplementedError\"}},nF=class extends iF{constructor(){super(...arguments),pw(this,\"NODE_TYPE\",5)}async _parse_record(e,t,i){let n=(await Aw.unpack_from_async(\"<I\",e,t))[0];t+=4;const r=await e.slice(t,t+7);return new Map([[\"namehash\",n],[\"heapid\",r]])}},rF=class extends iF{constructor(){super(...arguments),pw(this,\"NODE_TYPE\",6)}async _parse_record(e,t,i){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];t+=8;const r=await e.slice(t,t+7);return new Map([[\"creationorder\",n],[\"heapid\",r]])}},sF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await Aw.unpack_from_async(\"<B\",e,t+8);var n;if(0==i)n=await gw(uF,e,t),this._end_of_sblock=t+fF;else{if(2!=i&&3!=i)throw\"unsupported superblock version: \"+i.toFixed();n=await gw(pF,e,t),this._end_of_sblock=t+gF}if(n.get(\"format_signature\")!=hF)throw\"Incorrect file signature: \"+n.get(\"format_signature\");if(8!=n.get(\"offset_size\")||8!=n.get(\"length_size\"))throw\"File uses non-64-bit addressing\";this.version=n.get(\"superblock_version\"),this._contents=n,this._root_symbol_table=null,this._fh=e}async get_offset_to_dataobjects(){if(0==this.version){var e=new aF(this._fh,this._end_of_sblock,!0);return await e.ready,this._root_symbol_table=e,e.group_offset}if(2==this.version||3==this.version)return this._contents.get(\"root_group_address\");throw\"Not implemented version = \"+this.version.toFixed()}},oF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await gw(vF,e,t);ww(\"HEAP\"==i.get(\"signature\")),ww(0==i.get(\"version\"));let n=i.get(\"address_of_data_segment\"),r=await e.slice(n,n+i.get(\"data_segment_size\"));i.set(\"heap_data\",r),this._contents=i,this.data=r}get_object_name(e){let t=new Uint8Array(this.data).indexOf(0,e)-e;return Aw.unpack_from(\"<\"+t.toFixed()+\"s\",this.data,e)[0]}},aF=class{constructor(e,t,i=!1){this.ready=this.init(e,t,i)}async init(e,t,i){var n;if(i)n=new Map([[\"symbols\",1]]);else{if(\"SNOD\"!=(n=await gw(bF,e,t)).get(\"signature\"))throw\"incorrect node type\";t+=FF}for(var r=[],s=n.get(\"symbols\"),o=0;o<s;o++)r.push(await gw(mF,e,t)),t+=wF;return i&&(this.group_offset=r[0].get(\"object_header_address\")),this.entries=r,this._contents=n,this}assign_name(e){this.entries.forEach((function(t){let i=t.get(\"link_name_offset\"),n=e.get_object_name(i);t.set(\"link_name\",n)}))}get_links(e){var t={};return this.entries.forEach((function(i){let n=i.get(\"cache_type\"),r=i.get(\"link_name\");if(0==n||1==n)t[r]=i.get(\"object_header_address\");else if(2==n){let n=i.get(\"scratch\"),o=new ArrayBuffer(4),a=new Uint8Array(o);for(var s=0;s<4;s++)a[s]=n.charCodeAt(s);let c=Aw.unpack_from(\"<I\",o,0)[0];t[r]=e.get_object_name(c)}})),t}},cF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=await gw(yF,e,t);t+=AF;let n=i.get(\"collection_size\")-AF,r=await e.slice(t,t+n);this.heap_data=r,this._header=i,this._objects=null}get objects(){if(null==this._objects){this._objects=new Map;for(var e=0;e<=this.heap_data.byteLength-_F;){let t=mw(CF,this.heap_data,e);if(0==t.get(\"object_index\"))break;e+=_F;let i=this.heap_data.slice(e,e+t.get(\"object_size\"));this._objects.set(t.get(\"object_index\"),i),e+=Fw(t.get(\"object_size\"))}}return this._objects}},lF=class{constructor(e,t){this.fh=e,this.ready=this.init(t)}async init(e){let t=await gw(xF,this.fh,e);if(e+=bw(xF),ww(\"FRHP\"==t.get(\"signature\")),ww(0==t.get(\"version\")),t.get(\"filter_info_size\")>0)throw\"Filter info size not supported on FractalHeap\";if(t.get(\"btree_address_huge_objects\")!=dF)throw\"Huge objects not implemented in FractalHeap\";t.set(\"btree_address_huge_objects\",null),t.get(\"root_block_address\")==dF&&t.set(\"root_block_address\",null);let i=t.get(\"log2_maximum_heap_size\"),n=this._min_size_nbits(i),r=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"heap_header_adddress\",\"Q\"],[\"block_offset\",`${n}B`]]);this.indirect_block_header=new Map(r),this.indirect_block_header_size=bw(r),2&~t.get(\"flags\")||r.set(\"checksum\",\"I\"),this.direct_block_header=r,this.direct_block_header_size=bw(r);let s=t.get(\"maximum_direct_block_size\");this._managed_object_offset_size=this._min_size_nbits(i);let o=Math.min(s,t.get(\"max_managed_object_size\"));this._managed_object_length_size=this._min_size_integer(o);let a=t.get(\"starting_block_size\"),c=t.get(\"table_width\");if(!(a>0))throw\"Starting block size == 0 not implemented\";let l=Number(Math.floor(Math.log2(s)));ww(1n<<BigInt(l)==s);let h=Number(Math.floor(Math.log2(a)));ww(1n<<BigInt(h)==a),this._max_direct_nrows=l-h+2;let d=Math.floor(Math.log2(c));ww(1<<d==c),this._indirect_nrows_sub=d+h-1,this.header=t,this.nobjects=t.get(\"managed_object_count\")+t.get(\"huge_object_count\")+t.get(\"tiny_object_count\");let u=[],f=t.get(\"root_block_address\"),p=0;if(null!=f&&(p=t.get(\"indirect_current_rows_count\")),p>0)for await(let e of this._iter_indirect_block(this.fh,f,p))u.push(e);else{let e=await this._read_direct_block(this.fh,f,a);u.push(e)}let g=u.reduce(((e,t)=>e+t.byteLength),0),m=new Uint8Array(g),w=0;u.forEach((e=>{m.set(new Uint8Array(e),w),w+=e.byteLength})),this.managed=m.buffer}async _read_direct_block(e,t,i){let n=await e.slice(t,t+i);return ww(\"FHDB\"==mw(this.direct_block_header,n).get(\"signature\")),n}get_data(e){let t=Aw.unpack_from(\"<B\",e,0)[0],i=t>>4&3,n=1;if(0==i){ww(0==t>>6);let i=this._managed_object_offset_size,r=xw(i,e,n);n+=i,i=this._managed_object_length_size;let s=xw(i,e,n);return this.managed.slice(r,r+s)}throw 1==i?\"tiny objectID not supported in FractalHeap\":2==i?\"huge objectID not supported in FractalHeap\":\"unknown objectID type in FractalHeap\"}_min_size_integer(e){return this._min_size_nbits(_w(e))}_min_size_nbits(e){return Math.ceil(e/8)}async*_iter_indirect_block(e,t,i){let n=await gw(this.indirect_block_header,e,t);t+=this.indirect_block_header_size,ww(\"FHIB\"==n.get(\"signature\"));let r=n.get(\"block_offset\").reduce(((e,t,i)=>e+(t<<8*i)),0);n.set(\"block_offset\",r);let[s,o]=this._indirect_info(i),a=[];for(let i=0;i<s;i++){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];if(t+=8,n==dF)break;let r=this._calc_block_size(i);a.push([n,r])}let c=[];for(let i=s;i<s+o;i++){let n=(await Aw.unpack_from_async(\"<Q\",e,t))[0];if(t+=8,n==dF)break;let r=this._calc_block_size(i),s=this._iblock_nrows_from_block_size(r);c.push([n,s])}for(let[t,i]of a){let n=await this._read_direct_block(e,t,i);yield n}for(let[t,i]of c)for await(let n of this._iter_indirect_block(e,t,i))yield n}_calc_block_size(e){let t=Math.floor(e/this.header.get(\"table_width\"));return 2**Math.max(t-1,0)*this.header.get(\"starting_block_size\")}_iblock_nrows_from_block_size(e){let t=Math.floor(Math.log2(e));return ww(2**t==e),t-this._indirect_nrows_sub}_indirect_info(e){let t,i,n=this.header.get(\"table_width\"),r=e*n,s=this._max_direct_nrows*n;return e<=s?(t=r,i=0):(t=s,i=r-s),[t,i]}_int_format(e){return[\"B\",\"H\",\"I\",\"Q\"][e-1]}},hF=Aw.unpack_from(\"8s\",new Uint8Array([137,72,68,70,13,10,26,10]).buffer)[0],dF=Aw.unpack_from(\"<Q\",new Uint8Array([255,255,255,255,255,255,255,255]).buffer)[0],uF=new Map([[\"format_signature\",\"8s\"],[\"superblock_version\",\"B\"],[\"free_storage_version\",\"B\"],[\"root_group_version\",\"B\"],[\"reserved_0\",\"B\"],[\"shared_header_version\",\"B\"],[\"offset_size\",\"B\"],[\"length_size\",\"B\"],[\"reserved_1\",\"B\"],[\"group_leaf_node_k\",\"H\"],[\"group_internal_node_k\",\"H\"],[\"file_consistency_flags\",\"L\"],[\"base_address_lower\",\"Q\"],[\"free_space_address\",\"Q\"],[\"end_of_file_address\",\"Q\"],[\"driver_information_address\",\"Q\"]]),fF=bw(uF),pF=new Map([[\"format_signature\",\"8s\"],[\"superblock_version\",\"B\"],[\"offset_size\",\"B\"],[\"length_size\",\"B\"],[\"file_consistency_flags\",\"B\"],[\"base_address\",\"Q\"],[\"superblock_extension_address\",\"Q\"],[\"end_of_file_address\",\"Q\"],[\"root_group_address\",\"Q\"],[\"superblock_checksum\",\"I\"]]),gF=bw(pF),mF=new Map([[\"link_name_offset\",\"Q\"],[\"object_header_address\",\"Q\"],[\"cache_type\",\"I\"],[\"reserved\",\"I\"],[\"scratch\",\"16s\"]]),wF=bw(mF),bF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved_0\",\"B\"],[\"symbols\",\"H\"]]),FF=bw(bF),vF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved\",\"3s\"],[\"data_segment_size\",\"Q\"],[\"offset_to_free_list\",\"Q\"],[\"address_of_data_segment\",\"Q\"]]),yF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"reserved\",\"3s\"],[\"collection_size\",\"Q\"]]),AF=bw(yF),CF=new Map([[\"object_index\",\"H\"],[\"reference_count\",\"H\"],[\"reserved\",\"I\"],[\"object_size\",\"Q\"]]),_F=bw(CF),xF=new Map([[\"signature\",\"4s\"],[\"version\",\"B\"],[\"object_index_size\",\"H\"],[\"filter_info_size\",\"H\"],[\"flags\",\"B\"],[\"max_managed_object_size\",\"I\"],[\"next_huge_object_index\",\"Q\"],[\"btree_address_huge_objects\",\"Q\"],[\"managed_freespace_size\",\"Q\"],[\"freespace_manager_address\",\"Q\"],[\"managed_space_size\",\"Q\"],[\"managed_alloc_size\",\"Q\"],[\"next_directblock_iterator_address\",\"Q\"],[\"managed_object_count\",\"Q\"],[\"huge_objects_total_size\",\"Q\"],[\"huge_object_count\",\"Q\"],[\"tiny_objects_total_size\",\"Q\"],[\"tiny_object_count\",\"Q\"],[\"table_width\",\"H\"],[\"starting_block_size\",\"Q\"],[\"maximum_direct_block_size\",\"Q\"],[\"log2_maximum_heap_size\",\"H\"],[\"indirect_starting_rows_count\",\"H\"],[\"root_block_address\",\"Q\"],[\"indirect_current_rows_count\",\"H\"]]),kF=class{constructor(e,t){this.ready=this.init(e,t)}async init(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];if(1==i)var[n,r,s]=await this._parse_v1_objects(e,t);else{if(i!=\"O\".charCodeAt(0))throw\"InvalidHDF5File('unknown Data Object Header')\";var[n,r,s]=await this._parse_v2_objects(e,t)}this.fh=e,this.msgs=n,this.msg_data=r,this.offset=t,this._global_heaps={},this._header=s,this._filter_pipeline=null,this._chunk_params_set=!1,this._chunks=null,this._chunk_dims=null,this._chunk_address=null}get dtype(){let e=this.find_msg_type(ev)[0].get(\"offset_to_message\");return new kw(this.fh,e).dtype}get chunks(){return this._get_chunk_params().then((()=>this._chunks))}get shape(){let e=this.find_msg_type(ZF)[0].get(\"offset_to_message\");return async function(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];var n;if(1==i)ww(1==(n=await gw(TF,e,t)).get(\"version\")),t+=LF;else{if(2!=i)throw\"InvalidHDF5File('unknown dataspace message version')\";ww(2==(n=await gw(zF,e,t)).get(\"version\")),t+=HF}let r=n.get(\"dimensionality\");return(await Aw.unpack_from_async(\"<\"+(2*r).toFixed()+\"I\",e,t)).filter((function(e,t){return t%2==0}))}(this.fh,e)}async get_filter_pipeline(){if(null!=this._filter_pipeline)return this._filter_pipeline;let e=this.find_msg_type(rv);if(!e.length)return this._filter_pipeline=null,this._filter_pipeline;var t=e[0].get(\"offset_to_message\");let[i,n]=await Aw.unpack_from_async(\"<BB\",this.fh,t);t+=Aw.calcsize(\"<BB\");var r=[];if(1==i){await Aw.unpack_from_async(\"<HI\",this.fh,t),t+=Aw.calcsize(\"<HI\");for(var s=0;s<n;s++){let e=await gw(YF,this.fh,t);t+=XF;let i=Fw(e.get(\"name_length\"),8),n=\"<\"+i.toFixed()+\"s\",s=(await Aw.unpack_from_async(n,this.fh,t))[0];e.set(\"filter_name\",s),t+=i,n=\"<\"+e.get(\"client_data_values\").toFixed()+\"I\";let o=await Aw.unpack_from_async(n,this.fh,t);e.set(\"client_data\",o),t+=4*e.get(\"client_data_values\"),e.get(\"client_data_values\")%2&&(t+=4),r.push(e)}}else{if(2!=i)throw`version ${i} is not supported`;for(let e=0;e<n;e++){let e=new Map,i=this.fh,n=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2,e.set(\"filter_id\",n);let s=0;n>255&&(s=(await Aw.unpack_from_async(\"<H\",i,t))[0],t+=2);let o=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2;let a=(1&o)>0;e.set(\"optional\",a);let c,l=(await Aw.unpack_from_async(\"<H\",i,t))[0];t+=2,s>0&&(c=(await Aw.unpack_from_async(`${s}s`,i,t))[0],t+=s),e.set(\"name\",c);let h=await Aw.unpack_from_async(`<${l}i`,i,t);t+=4*l,e.set(\"client_data_values\",h),r.push(e)}}return this._filter_pipeline=r,this._filter_pipeline}find_msg_type(e){return this.msgs.filter((function(t){return t.get(\"type\")==e}))}async get_attributes(){let e={},t=this.find_msg_type(sv);for(let i of t){let t=i.get(\"offset_to_message\"),[n,r]=await this.unpack_attribute(t);e[n]=r}return e}async get_fillvalue(){var e,t=this.find_msg_type(tv)[0].get(\"offset_to_message\");let i=(await Aw.unpack_from_async(\"<B\",this.fh,t))[0];var n,r,s;if(1==i||2==i)n=await gw(WF,this.fh,t),t+=GF,e=n.get(\"fillvalue_defined\");else{if(3!=i)throw'InvalidHDF5File(\"Unknown fillvalue msg version: \"'+String(i);n=await gw($F,this.fh,t),t+=KF,e=32&n.get(\"flags\")}if(e?(r=(await Aw.unpack_from_async(\"<I\",this.fh,t))[0],t+=4):r=0,r){let[e,i,n]=yw(await this.dtype);s=new Cw(await this.fh.slice(t,t+n))[e](t,!i,n)}else s=0;return s}async unpack_attribute(e){let t=(await Aw.unpack_from_async(\"<B\",this.fh,e))[0];var i,n;if(1==t)ww(1==(i=await gw(EF,this.fh,e)).get(\"version\")),e+=NF,n=8;else{if(3!=t)throw\"unsupported attribute message version: \"+t;ww(3==(i=await gw(BF,this.fh,e)).get(\"version\")),e+=MF,n=1}let r=i.get(\"name_size\"),s=(await Aw.unpack_from_async(\"<\"+r.toFixed()+\"s\",this.fh,e))[0];var o;s=s.replace(/\\x00$/,\"\"),e+=Fw(r,n);try{o=await new kw(this.fh,e).dtype}catch(e){return console.warn(\"Attribute \"+s+\" type not implemented, set to null.\"),[s,null]}e+=Fw(i.get(\"datatype_size\"),n);let a=await this.determine_data_shape(this.fh,e),c=a.reduce((function(e,t){return e*t}),1);if(e+=Fw(i.get(\"dataspace_size\"),n),5===o.datatype_class)l=await this.fh.slice(e,e+o.size);else{var l=await this._attr_value(o,this.fh,c,e);0==a.length&&(l=l[0])}return[s,l]}async determine_data_shape(e,t){let i=(await Aw.unpack_from_async(\"<B\",e,t))[0];var n;if(1==i)ww(1==(n=await gw(TF,e,t)).get(\"version\")),t+=LF;else{if(2!=i)throw\"unknown dataspace message version\";ww(2==(n=await gw(zF,e,t)).get(\"version\")),t+=HF}let r=n.get(\"dimensionality\");return await Aw.unpack_from_async(\"<\"+r.toFixed()+\"Q\",e,t)}async _attr_value(e,t,i,n){var r=new Array(i);if(e instanceof Array){let l=e[0];for(var s=0;s<i;s++)if(\"VLEN_STRING\"==l){let i=e[2];var[o,a]=await this._vlen_size_and_data(t,n);const c=new TextDecoder(0==i?\"ascii\":\"utf-8\");r[s]=c.decode(a),n+=16}else if(\"REFERENCE\"==l){var c=await Aw.unpack_from_async(\"<Q\",t,n);r[s]=c,n+=8}else{if(\"VLEN_SEQUENCE\"!=l)throw\"NotImplementedError\";{let i=e[1];var[o,a]=this._vlen_size_and_data(t,n);r[s]=this._attr_value(i,a,o,0),n+=16}}}else{let[o,a,c]=yw(e);const l=await t.slice(n,n+i*c);let h=new Cw(l,0),d=0;for(s=0;s<i;s++)r[s]=h[o](d,!a,c),d+=c}return r}async _vlen_size_and_data(e,t){let i=(await Aw.unpack_from_async(\"<I\",e,t))[0],n=await gw(SF,e,t+4),r=n.get(\"collection_address\");var s;return ww(n.get(\"collection_address\")<Number.MAX_SAFE_INTEGER),r in this._global_heaps||(s=new cF(this.fh,r),await s.ready,this._global_heaps[r]=s),[i,(s=this._global_heaps[r]).objects.get(n.get(\"object_index\"))]}async _parse_v1_objects(e,t){let i=await gw(RF,e,t);ww(1==i.get(\"version\"));let n=i.get(\"total_header_messages\");for(var r=i.get(\"object_header_size\"),s=t+bw(RF),o=await e.slice(s,s+r),a=[[s,r]],c=0,l=0,h=new Array(n),d=0;d<n;d++){l>=r&&([s,r]=a[++c],l=0);let t=await gw(PF,e,s+l),i=s+l+OF;if(t.set(\"offset_to_message\",i),t.get(\"type\")==ov){var[u,f]=await Aw.unpack_from_async(\"<QQ\",e,i);a.push([u,f])}l+=OF+t.get(\"size\"),h[d]=t}return[h,o,i]}async _parse_v2_objects(e,t){var[i,n,r]=await this._parse_v2_header(e,t);t=r;for(var s=[],o=i.get(\"size_of_chunk_0\"),a=e.slice(t,t+=o),c=[[r,o]],l=0,h=0;;){if(h>=o-qF){let e=c[++l];if(null==e)break;[r,o]=e,h=0}let t=await gw(UF,e,r+h),i=r+h+qF+n;if(t.set(\"offset_to_message\",i),t.get(\"type\")==ov){var[d,u]=await Aw.unpack_from_async(\"<QQ\",e,i);c.push([d+4,u-4])}h+=qF+t.get(\"size\")+n,s.push(t)}return[s,a,i]}async _parse_v2_header(e,t){let i=await gw(DF,e,t);var n;if(t+=bw(DF),ww(2==i.get(\"version\")),n=4&i.get(\"flags\")?2:0,ww(!(16&i.get(\"flags\"))),32&i.get(\"flags\")){let n=await Aw.unpack_from_async(\"<4I\",e,t);t+=16,i.set(\"access_time\",n[0]),i.set(\"modification_time\",n[1]),i.set(\"change_time\",n[2]),i.set(\"birth_time\",n[3])}let r=[\"<B\",\"<H\",\"<I\",\"<Q\"][3&i.get(\"flags\")];return i.set(\"size_of_chunk_0\",(await Aw.unpack_from_async(r,e,t))[0]),[i,n,t+=Aw.calcsize(r)]}async find_link(e){if(this._links){for(link of this._links)if(e===link[0])return link}else{const t=[];for await(const i of this.iter_links()){if(e===i[0])return i;t.push(i)}this._links=t}}async get_links(){const e=[];for await(const t of this.iter_links())e.push(t);return Object.fromEntries(e)}async*iter_links(){for(let e of this.msgs)e.get(\"type\")==av?yield*this._iter_links_from_symbol_tables(e):e.get(\"type\")==iv?yield this._get_link_from_link_msg(e):e.get(\"type\")==JF&&(yield*this._iter_link_from_link_info_msg(e))}async*_iter_links_from_symbol_tables(e){ww(16==e.get(\"size\"));let t=await gw(QF,this.fh,e.get(\"offset_to_message\"));yield*this._iter_links_btree_v1(t.get(\"btree_address\"),t.get(\"heap_address\"))}async*_iter_links_btree_v1(e,t){let i=new eF(this.fh,e);await i.ready;let n=new oF(this.fh,t);await n.ready;for(let e of 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t=e.get(\"offset_to_message\"),i=await this._decode_link_info_msg(this.fh,t),n=i.get(\"heap_address\"),r=i.get(\"name_btree_address\"),s=i.get(\"order_btree_address\");null!=r&&(yield*this._iter_links_btree_v2(r,s,n))}async*_iter_links_btree_v2(e,t,i){let n,r=new lF(this.fh,i);await r.ready;const s=null!=t;s?(n=new rF(this.fh,t),await n.ready):(n=new nF(this.fh,e),await n.ready);let o=new Map;for(let e of n.iter_records()){let t=r.get_data(e.get(\"heapid\")),[i,n]=await this._decode_link_msg(t,0);const a=s?i:n[0];o.set(a,n)}let a=Array.from(o.keys()).sort();for(let e of a)yield o.get(e)}async _decode_link_info_msg(e,t){let[i,n]=await Aw.unpack_from_async(\"<BB\",e,t);ww(0==i),t+=2,(1&n)>0&&(t+=8);let r=(2&n)>0?jF:VF,s=await gw(r,e,t),o=new Map;for(let[e,t]of s.entries())o.set(e,t==IF?null:t);return o}get is_dataset(){return this.find_msg_type(ZF).length>0}async get_data(){let e=this.find_msg_type(nv)[0].get(\"offset_to_message\");var[t,i,n,r]=await 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wv(this.pytor_keys),n=i.get_rd_bins(),r=i.get_snp_bins();this.available_bins=[...new Set(n,r)],this.available_bins.includes(e)||(e=this.available_bins.at(-1));const s=await t.get(\"rd_chromosomes\");await s.dtype;let o=await s.value,a=await this.rd_stat(e);var c=[],l=[],h=[],d=[],u=[],f=[];for(let t of o){let i=new gv(t,e);var p=i.signals.raw_RD;let n=await this.get_chr_signal(t,e,p,a);c=c.concat(n);var g=i.signals.gc_RD;let r=await this.get_chr_signal(t,e,g,a);l=l.concat(r);let s=i.signals.gc_partition,o=await this.get_chr_signal(t,e,s,a);h=h.concat(o);let m=await this.rd_call_combined(t,e,a,i);d=d.concat(m);let w=i.signals.baf_i1,b=await this.get_baf_signals_v2(t,e,w);u=u.concat(b[0]),f=f.concat(b[1])}this.callers=[],0!=d.length&&this.callers.push(\"ReadDepth\"),0!=d.length&&this.callers.push(\"2D\");var m={},w={RD_Raw:c,RD_Raw_gc_coor:l,ReadDepth:h,\"2D\":d,BAF1:u,BAF2:f};return m[e]=w,m}decode_segments(e){let t=[],i=[];for(let n of e)4294967295==n?(t.push(i),i=[]):i.push(n);return t}async rd_call_combined(e,t,i,n){let r,s=[],o=n.signals.Mosaic_segments;if(this.pytor_keys.includes(o)){const e=await this.h5_obj.get(o);let t=await e.value;r=this.decode_segments(t)}let a=n.signals.Mosaic_calls;if(this.pytor_keys.includes(a)){const n=await this.h5_obj.get(a);let o=await n.to_array();r.forEach(((n,r)=>{n.forEach(((n,a)=>{s.push({chr:e,start:n*t,end:(n+1)*t,value:o[0][r]/i[4]*2})}))}))}return s}async rd_stat(e){let t,i=`rd_stat_${e}_auto`;if(this.pytor_keys.includes(i)){const e=await this.h5_obj.get(i);t=await e.value}return t}async get_chr_signal(e,t,i,n){let r=[];if(this.pytor_keys.includes(i)){const s=await this.h5_obj.get(i);(await s.value).forEach(((i,s)=>{r.push({chr:e,start:s*t,end:(s+1)*t,value:i/n[4]*2})}))}return r}async get_baf_signals(e,t,i,n=-1){let r=[],s=[];if(this.pytor_keys.includes(i)){let o=await this.h5_obj.get(i);(await o.to_array()).forEach(((i,o)=>{let a=Math.max(...i);const c=i.indexOf(a);let l=Math.max(c/200,1-c/200);r.push({chr:e,start:o*t,end:(o+1)*t,value:n*l}),.5!=l&&s.push({chr:e,start:o*t,end:(o+1)*t,value:n*(1-l)})}))}return[r,s]}async get_baf_signals_v2(e,t,i,n=-1){let r=[],s=[];if(this.pytor_keys.includes(i)){let o=await this.h5_obj.get(i);(await o.to_array()).forEach(((i,o)=>{isNaN(i)||(r.push({chr:e,start:o*t,end:(o+1)*t,value:n*(.5-i)}),.5!=i&&s.push({chr:e,start:o*t,end:(o+1)*t,value:n*(.5+i)}))}))}return[r,s]}}class wv{constructor(e){this.signals=e}get_rd_bins(){let e=[];this.signals.forEach((t=>{let i=t.match(/^his_rd_p_(.*)_(\\d+)$/);i&&e.push({chr:i[1],bin_size:i[2]})}));return[...new Set(e.map((e=>Number(e.bin_size))))]}get_snp_bins(){let e=[];this.signals.forEach((t=>{let i=t.match(/^snp_likelihood_(.*)_(\\d+)_mask$/);i&&e.push({chr:i[1],bin_size:i[2]})}));return[...new Set(e.map((e=>Number(e.bin_size))))]}}function bv(e){let t=function(e){if(e.length<4)return e;let t,i,n,r,s,o;return t=e.slice().sort(((e,t)=>e-t)),t.length/4%1==0?(i=.5*(t[t.length/4]+t[t.length/4+1]),n=.5*(t[t.length*(3/4)]+t[t.length*(3/4)+1])):(i=t[Math.floor(t.length/4+1)],n=t[Math.ceil(t.length*(3/4)+1)]),r=n-i,s=n+1.5*r,o=i-1.5*r,t.filter((e=>e>=o&&e<=s))}(e);const i=t.length,n=t.reduce(((e,t)=>e+t))/i,r=Math.sqrt(t.map((e=>Math.pow(e-n,2))).reduce(((e,t)=>e+t))/i);return[n,r]}var Fv={range_function:function(e,t,i){return Array(Math.ceil((t-e)/i)).fill(e).map(((e,t)=>e+t*i))},getDistParams:bv,linspace:function(e,t,i){if(void 0===i&&(i=Math.max(Math.round(t-e)+1,1)),i<2)return 1===i?[e]:[];var n=Array(i);for(let r=--i;r>=0;r--)n[r]=(r*t+(i-r)*e)/i;return n},GetFit:class{constructor(e){this.allBins=e}getValues(){return Object.values(this.allBins).reduce(((e,t)=>e.concat(t.filter((e=>e.binScore>0)).map((e=>e.binScore)))),[])}getMean(e){return e.reduce((function(e,t){return e+t}))/e.length}fit_data(){return bv(this.getValues())}histogram(e,t){const i=t[1]-t[0],n=[];e.forEach(((e,r)=>{t.forEach(((t,r)=>{if(n[t]||(n[t]={count:0}),t<=e&&e<t+i)return n[t].count++,!1}))}));const r=[];return n.forEach(((e,t)=>{r.push(e.count)})),r}}};function vv(e,t){return isNaN(e)||isNaN(t)||t<=0?NaN:0===e?.5:.5+.5*(yv(.5*t,.5,1)-yv(.5*t,.5,t/(t+e*e)))*Math.sign(e)}function yv(e,t,i){if(0==i)return 0;if(1==i)return 1;{let n=xv(e+t)-xv(e)-xv(t)+e*Math.log(i)+t*Math.log(1-i);return i<(e+1)/(e+t+2)?Math.exp(n)*Av(e,t,i)/e:1-Math.exp(n)*Av(t,e,1-i)/t}}function Av(e,t,i,n=1e3){let r=1,s=1,o=1,a=e+t,c=e+1,l=e-1,h=1-a*i/c;for(let d=0;d<=n;d++){let n=parseFloat(d+1),u=n+n,f=n*(t-n)*i/((l+u)*(e+u)),p=r+f*s,g=h+f*o;f=-(e+n)*(a+n)*i/((c+u)*(e+u));let m=g+f*h,w=r;if(s=p/m,o=g/m,r=(p+f*r)/m,h=1,Math.abs(r-w)<3e-7*Math.abs(r))return r}}function Cv(e){if(0==e||1==e)return 1;return e*Cv(e-1)}function _v(e){let t;var i=[75122.633153,80916.6278952,36308.2951477,8687.24529705,1168.92649479,83.8676043424,2.50662827511],n=0,r=1;if(0==e)t=1e99;else if(e%1==0)t=Cv(e-1);else{for(let t=0;t<i.length;t++)n+=i[t]*Math.pow(e,t),r*=e+t;t=n*Math.pow(e+5.5,e+.5)*Math.exp(-(e+5.5))/r}return t}function xv(e){return Math.log(_v(e))}var kv={TdistributionCDF:vv,gamma:_v,t_test_1_sample:function(e,t,i,n){0==i&&(i=1);var r=(e-t)/i*Math.sqrt(n);return 1-vv(Math.abs(r),n-1)},t_test_2_samples:function(e,t,i,n,r,s){0==t&&(t=1),0==r&&(r=1);var o=(e-n)/Math.sqrt(t**2/i+r**2/s),a=(t**2/i+r**2/s)**2*(i-1)*(s-1)/(t**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-vv(Math.abs(o),parseInt(a+.5))}};function Iv(e){return e.reduce((function(e,t){return e>t?e:t}))}function Sv(e,t,i,n){return t*Math.exp(-1*(e-i)**2/(2*n**2))/Math.sqrt(2*Math.PI)/n}function Ev(e,t,i,n){return Math.exp(-1*(e-i)**2/(t**2+n**2))}function Nv(e,t){let i;try{i=e.reduce(((e,i,n)=>e+Math.min(i,t[n])))}catch{return console.log(\"Failed to find likelihood overlap: \",e,t),0}return i}function Bv(e,t,i,n){return 0==t&&0==n?{nl:.5*(e+i),ne:0}:{nl:(e*n*n+i*t*t)/(t*t+n*n),ne:Math.sqrt(t*t*n*n/(t*t+n*n))}}function Mv(e,t){let i=parseInt(t*(e.length-1)),n=t*(e.length-1)-i;return i<e.length-1?e[i]*(1-n)+e[i+1]*n:e[i]}function Rv(e){const t=e.length,i=Math.max(...e);let n=e.indexOf(i);n>Math.floor(t/2)&&(n=t-1-n);const r=(t/2-n)/(t+1),s=Math.floor((t/2+n)/2),o=t-1-s;let a=e.slice(s,o+1).reduce(((e,t)=>e+t),0)/e.reduce(((e,t)=>e+t),0);return n===Math.floor(t/2)&&(a=1),{mean:r,p:a}}var Dv=class{constructor(e,t){this.wigFeatures=e,this.binSize=t}get_fit(){var e=new Fv.GetFit(this.wigFeatures),[t,i]=e.fit_data();return{globalMean:t,globalStd:i}}async call_2d(e=null,t=null,i=\"both\",n=.1,r=0,s=10,o=0){let a=this.get_fit();this.globalMean=a.globalMean,this.globalStd=a.globalStd;let c=null==e?.05*this.binSize/3e9:e,l=null==t?parseInt(this.binSize/1e4):t,h=[],d=[],u=[],f=[],p=[],g=[];for(const[e,t]of Object.entries(this.wigFeatures)){let e=[],i=[],s=[];t.forEach(((t,n)=>{t.hets_count>4&&t.dp_count>l&&(e.push([n]),i.push(t.binScore),s.push(t.likelihood_score),delete t.likelihood_score)}));let o=[];for(let e=1;e<i.length;e++)o.push(Math.abs(i[e]-i[e-1]));let a=[0];for(let e=1;e<o.length;e++)a.push(Math.min(o[e-1],o[e]));a.push(0);let g=i.map(((e,t)=>Math.sqrt(Math.sqrt(e)**2+this.globalStd**2+Math.pow(a[t]/2,2)))),m=[];for(let t=0;t<e.length-1;t++){let n=0;try{n=Nv(s[t],s[t+1])}catch{console.log(\"Overlap failed: \",t,s[t],e[t+1],s[t+1])}let r=Ev(i[t],g[t],i[t+1],g[t+1]);m.push(r*n)}for(;m.length>0;){m=m.filter((e=>\"number\"==typeof e));let t=Iv(m);if(isNaN(t)&&console.log(\"NaN value\",m),t<c)break;let n,r,o=m.indexOf(t),a=Bv(i[o],g[o],i[o+1],g[o+1]);try{n=s[o].map(((e,t)=>e*s[o+1][t])),r=n.reduce(((e,t)=>e+t))}catch{console.log(s),console.log(\"max_overlap:\",t,o,m.length),console.log(\"likelihood: \",o,s[o],s[o+1]),console.log(\"nlh: \",r)}if(i[o]=a.nl,g[o]=a.ne,s[o]=n.map((function(e){return e/r})),e[o].push(...e[o+1]),i.splice(o+1,1),g.splice(o+1,1),e.splice(o+1,1),s.splice(o+1,1),m.splice(o,1),o<m.length){let e=Ev(i[o],g[o],i[o+1],g[o+1])*Nv(s[o],s[o+1]);m[o]=e}if(o>0){let e=Ev(i[o-1],g[o-1],i[o],g[o])*Nv(s[o-1],s[o]);m[o-1]=e}}let w=-1;for(;;){m=[];for(let t=0;t<i.length;t++)for(let r=t;r<i.length;r++)e[r][0]-e[t].at(-1)<n*(e[t].length+e[r].length)&&m.push(Ev(i[t],g[t],i[r],g[r])*Nv(s[t],s[r]));if(0==m.length)break;let t=Iv(m);if(t<c)break;let r=0,o=1;for(;r<e.length-1;){let a=Ev(i[r],g[r],i[o],g[o])*Nv(s[r],s[o]);if(e[o][0]-e[r].at(-1)<n*(e[r].length+e[o].length)&&a==t){let t=Bv(i[r],g[r],i[r+1],g[r+1]);i[r]=t.nl,g[r]=t.ne;let n=s[r].map(((e,t)=>e*s[r+1][t])),a=n.reduce(((e,t)=>e+t));s[r]=n.map((function(e){return e/a})),e[r].push(...e[r+1]),e[r]=e[r].sort(((e,t)=>e-t)),i.splice(o,1),g.splice(o,1),e.splice(o,1),s.splice(o,1),o>=e.length&&(r+=1,o=r+1)}else o+=1,o>=e.length&&(r+=1,o=r+1)}if(w==e.length)break;w=e.length}e.forEach(((e,n)=>{let o=Rv(s[n]);e.length>1&&(e.forEach(((e,s)=>{d.push(t[e]),o.mean<=r&&h.push(t[e]),t[e].segment_score=i[n]})),u.push(i[n]),f.push(g[n]),p.push(s[n]))}))}let m=parseInt(1e3*(1-o));0==m&&(m=1);let w=Fv.linspace(o,1,m),b={},F={};for(let e=10;e>-1;e--)for(let t=0;t<e/2+1;t++){let n,r,s=e-t,o=w.map(((t,i)=>1-t+t*e/2)),a=e/2;e>0?(n=.5-t/(t+s),r=w.map(((e,i)=>.5-(1-e+e*t)/(2-2*e+(t+s)*e)))):(n=0,r=w.map(((e,t)=>0*e)));for(let i=0;i<u.length;i++){let c=Sv(a*this.globalMean,1,u[i],f[i])*Mv(p[i],.5+n);i in F?F[i].push([e,t,s,c,1]):F[i]=[e,t,s,c,1];let l=0,h=0,d=0;o.forEach(((e,t)=>{if(!isNaN(r[t])){let n=Sv(e*this.globalMean,1,u[i],f[i])*Mv(p[i],.5+r[t]);l+=n,n>h&&(h=n,d=w[t])}})),i in b?b[i].push([e,t,s,l/w.length,d]):b[i]=[e,t,s,l/w.length,d]}for(let e=0;e<u.length;e++)if(\"germline\"==i)b[e].sort(((e,t)=>e[3]-t[3]));else if(b[e].sort(((e,t)=>e[3]-t[3])),\"both\"==i&&(F[e].sort(((e,t)=>e[3]-t[3])),F[e][0][3]>b[e][0][3])){let t=b[e].filter((t=>t[0]!=F[e][0][0]&&t[1]<=F[e][0][1]));b[e]=[F[e][0]].push(...t)}for(let e=0;e<u.length;e++)b[e][0][0],b[e][0][0],u[e],this.globalMean,kv.t_test_1_sample(this.globalMean,u[e],f[e],g[e])}return{binScore:this.formatDataStructure(this.wigFeatures,\"binScore\",this.globalMean),segment_score:this.formatDataStructure(this.wigFeatures,\"segment_score\",this.globalMean)}}formatDataStructure(e,t,i=1){const n=[];for(const[r,s]of Object.entries(e))s.forEach((e=>{var r={...e};1!=i&&(r.value=e[t]/i*2),n.push(r)}));return n}formatDataStructure_BAF(e,t=-1){const i=[],n=[];for(const[r,s]of Object.entries(this.wigFeatures))s.forEach((r=>{var s={...r},o={...r};let a=r[e];.5!=a&&(o.value=t*(1-a),n.push(o)),s.value=t*a,i.push(s)}));return[i,n]}};const Tv=2871e6;function Lv(e){for(var t=1,i=1,n=1*e,r=1;r<50;r++)t*=r,n+=(i*=-1)*Math.pow(e,2*r+1)/(t*(2*r+1));return 2*n/Math.sqrt(3.14159265358979)}function zv(e,t,i,n,r){var s=new Ov(i.slice(n,r));return 0==s.std&&(s.std=t>0?t*s.mean/e:1),Uv(e,s.mean,s.std,r-n)/(r-n)}function Hv(e,t,i,n,r){var s=new Ov(i.slice(n,r));if(s.mean<e){var o=(s.max-s.mean)/(t*Math.sqrt(2));return Math.pow(.5*(1+Lv(o)),r-n)}o=(s.min-s.mean)/(t*Math.sqrt(2));return Math.pow(.5*(1-Lv(o)),r-n)}function Pv(e,t,i,n,r,s,o=1e3){for(var a=zv(e,t,i,n,r),c=0,l=!1;a>s&!l&c<o;){l=!0,c+=1;var[h,d,u,f]=[1e10,1e10,1e10,1e10];if(n>0&&(h=zv(e,t,i,n-1,r)),r-n>2)var d=zv(e,t,i,n+1,r),u=zv(e,t,i,n,r-1);if(r<i.length)var f=zv(e,t,i,n,r+1);Math.min[f]<a&&(l=!1,h==Math.min[f]&&(n-=1,a=h),elif(d==Math.min[f]),n+=1,a=d,elif(u==Math.min[f]),r-=1,a=u,elif(f==Math.min[f]),r+=1,a=f)}return a<=s?r:0}class Ov{constructor(e){this.data=e,this.mean=e.reduce(((e,t)=>e+t))/e.length,this.std=Math.sqrt(e.reduce(((e,t)=>(t-this.mean)**2))/e.length)}}function Uv(e,t,i,n){0==i&&(i=1);var r=(e-t)/i*Math.sqrt(n);return 1-kv.TdistributionCDF(Math.abs(r),n-1)}function qv(e,t,i,n,r,s){0==t&&(t=1),0==r&&(r=1);var o=(e-n)/Math.sqrt(t**2/i+r**2/s),a=(t**2/i+r**2/s)**2*(i-1)*(s-1)/(t**4*(s-1)/i**2+r**4*(i-1)/s**2);return 1-kv.TdistributionCDF(Math.abs(o),parseInt(a+.5))}var Qv=class{constructor(e,t,i){this.rd=e,this.mean=t,this.std=i,this.bin_bands=[2,3,4,5,6,7,8,10,12,14,16,20,24,28,32,40,48,56,64,80,96,112,128]}get_rd_signal_bandwidth(e){var t=[];return e.forEach(((e,i)=>{var n=0;n=e>this.mean/4?this.mean/(this.std**2*e):4/this.std**2,t.push(n)})),t}meanShiftCaller(e,t=3){var i={};return Object.entries(this.rd).forEach((([e,n])=>{var r=new Array(n.length).fill(!1),s=new Array(n.length);for(let e=0;e<n.length;e++)r[e]||(s[e]=n[e]);this.bin_bands.forEach(((e,i)=>{var o=r.map(((e,t)=>!e)),a=[];Object.entries(n).forEach((([e,t])=>{a.push(t.binScore)}));var c=[0],l=0;for(let e=0;e<r.length;e++)r[e]?l>0&&(c.push(c[c.length-1]+l-1),l=0):l+=1;c.shift();for(let i=0;i<t;i++){var h=this.get_rd_signal_bandwidth(a),d=new Array(a.length).fill(0);for(let t=0;t<a.length;t++)for(let i=t-3*e;i<=t+3*e+1;i++)if(!(i<0||i>=a.length||Math.abs(t-i)>=a.length)){var u=(i-t)*Math.exp(-.5*(i-t)**2/e**2)*Math.exp(-.5*(a[t]-a[i])**2*h[t]);d[t]+=u}for(var f=new Array,p=0;p<d.length-1;p++)d[p]<0&d[p+1]>=0&&f.push(p);f.push(d.length-1),f=f.concat(c).sort(((e,t)=>e-t)),f=Array.from(new Set(f));var g=0;for(p=0;p<f.length;p++){var m=a.slice(g,f[p]+1),w=m.reduce(((e,t)=>e+t))/m.length;a.fill(w,g,f[p]+1),g=f[p]+1}}p=0;for(var b=0;p<s.length;p++)o[p]&&(s[p]=a[b],b++);for(f=new Array,p=0;p<s.length-1;p++){Math.abs(s[p+1]-s[p])>.01&&f.push(p+1)}f.unshift(0),f.push(s.length),r=new Array(this.rd.length).fill(!1);for(p=1;p<f.length;p++){var F=[f[p-1],f[p]],v=[f[p-1],f[p-1]];if(!(p>1))continue;v[0]=f[p-2];var y=[f[p],f[p]];if(!(p<f.length-1))continue;y[1]=f[p+1];var A=F[1]-F[0],C=v[1]-v[0],_=y[1]-y[0];if(A<=1)continue;var x=new Ov(s.slice(F[0],F[1]));if(_<=15||C<=15||A<=15){var k=1.8*Math.sqrt(s[v[0]]/this.mean)*this.std;if(Math.abs(s[v[0]]-s[F[0]])<k)continue;if(k=1.8*Math.sqrt(s[y[0]]/this.mean)*this.std,Math.abs(s[y[0]]-s[F[0]])<k)continue}else{var I=s.slice(v[0],v[1]),S=new Ov(I),E=s.slice(y[0],y[1]),N=new Ov(E);if(qv(x.mean,x.std,x.data.length,S.mean,S.std,S.data.length)>.01/Tv*bin_size*(A+C))continue;if(qv(x.mean,x.std,x.data.length,N.mean,N.std,N.data.length)>.01/Tv*bin_size*(A+_))continue}if(Uv(this.mean,x.mean,x.std,x.data.length)>.05)continue;let e=a.slice(F[0],F[1]);var B=new Ov(e);r.fill(!0,F[0],F[1]),s.fill(B.mean,F[0],F[1])}})),i[e]=s})),i}call_mean_shift(e=3){for(var t=new Array(this.rd.length).fill(!1),i=new Array(this.rd.length),n=0;n<this.rd.length;n++)t[n]||(i[n]=this.rd[n]);return this.bin_bands.forEach(((n,r)=>{var s=t.map(((e,t)=>!e)),o=[];s.forEach(((e,t)=>{e&&o.push(this.rd[t])}));for(var a=[0],c=0,l=0;l<t.length;l++)t[l]?c>0&&(a.push(a[a.length-1]+c-1),c=0):c+=1;a.shift();for(var h=0;h<e;h++){var d=this.get_rd_signal_bandwidth(o),u=new Array(o.length).fill(0);for(l=0;l<o.length;l++)for(var f=l-3*n;f<=l+3*n+1;f++)if(!(f<0||f>=o.length||Math.abs(l-f)>=o.length)){var p=(f-l)*Math.exp(-.5*(f-l)**2/n**2)*Math.exp(-.5*(o[l]-o[f])**2*d[l]);u[l]+=p}var g=new Array;for(l=0;l<u.length-1;l++)u[l]<0&u[l+1]>=0&&g.push(l);g.push(u.length-1),g=g.concat(a).sort(((e,t)=>e-t)),g=Array.from(new Set(g));var m=0;for(l=0;l<g.length;l++){var w=o.slice(m,g[l]+1),b=w.reduce(((e,t)=>e+t))/w.length;o.fill(b,m,g[l]+1),m=g[l]+1}}for(l=0,f=0;l<i.length;l++)s[l]&&(i[l]=o[f],f++);for(g=new Array,l=0;l<i.length-1;l++){Math.abs(i[l+1]-i[l])>.01&&g.push(l+1)}g.unshift(0),g.push(i.length),t=new Array(this.rd.length).fill(!1);for(l=1;l<g.length;l++){var F=[g[l-1],g[l]],v=[g[l-1],g[l-1]];if(l>1){v[0]=g[l-2];var y=[g[l],g[l]];if(l<g.length-1){y[1]=g[l+1];var A=F[1]-F[0],C=v[1]-v[0],_=y[1]-y[0];if(!(A<=1)){var x=new Ov(i.slice(F[0],F[1]));if(_<=15||C<=15||A<=15){var k=1.8*Math.sqrt(i[v[0]]/this.mean)*this.std;if(Math.abs(i[v[0]]-i[F[0]])<k)continue;if(k=1.8*Math.sqrt(i[y[0]]/this.mean)*this.std,Math.abs(i[y[0]]-i[F[0]])<k)continue}else{var I=i.slice(v[0],v[1]),S=new Ov(I),E=i.slice(y[0],y[1]),N=new Ov(E);if(qv(x.mean,x.std,x.data.length,S.mean,S.std,S.data.length)>3.483106931382794e-9*(A+C))continue;if(qv(x.mean,x.std,x.data.length,N.mean,N.std,N.data.length)>3.483106931382794e-9*(A+_))continue}if(!(Uv(this.mean,x.mean,x.std,x.data.length)>.05)){var B=new Ov(this.rd.slice(F[0],F[1]));t.fill(!0,F[0],F[1]),i.fill(B.mean,F[0],F[1])}}}}}})),i}cnv_calling(e=1e5){var t=.25*this.mean,i=this.mean-t,n=this.mean+t,r=2971e6,s=this.meanShiftCaller(e),o={},a=[];return Object.entries(s).forEach((([c,l])=>{for(var h=!1;!h;){h=!0;var d=new Array(1).fill(0);for(let e=0;e<l.length-1;e++){Math.abs(l[e+1]-l[e])>.01&&d.push(e+1)}d.push(l.length);for(let e=0;e<d.length-2;e++){var u=Math.abs(l[d[e]]-l[d[e+1]]);if(u<t){var f=u+1,p=u+1;if(e>0&&(f=Math.abs(l[d[e]]-l[d[e-1]])),e<d.length-3&&(p=Math.abs(s[d[e+1]]-l[d[e+2]])),u<f&&u<p){h=!1;var g=new Ov(l.slice(d[e],d[e+2]));l.fill(g.mean,d[e],d[e+2]),d.splice(e+1,e+1)}}}}var m=[];Object.entries(this.rd[c]).forEach((([e,t])=>{m.push(t.binScore)}));for(var w,b=new Array(l.length).fill(\"\"),F=0,v=.05*e/r;F<l.length;){for(var y=F,A=F;F<l.length&l[F]<i;)F+=1;if((_=F)>A+1){var C=Pv(this.mean,this.std,m,A,_,v);if(C){var _=C;b.fill(\"D\",A,_)}}for(A=F;F<l.length&l[F]>n;)F+=1;(_=F)>A+1&&(C=Pv(this.mean,this.std,m,A,_,v))&&(_=C,b.fill(\"A\",A,_)),F==y&&(F+=1)}for(F=0;F<l.length;){for(;F<l.length&\"\"!=b[F];)F+=1;for(A=F;F<l.length&l[F]<i;)F+=1;(_=F)>A+1&&(Hv(this.mean,this.std,m,A,_)<1682935038707506e-26&&b.fill([\"d\"]*(_-A),A,_),F-=1),F+=1}(F=0)<l.length&&(w=b[F]),A=0;for(var x=[...m];F<l.length;){for(;b[F]==w&&!((F+=1)>=b.length););if(F>A){var k=new Ov(x.slice(A,F));x.fill(k.mean,A,F)}F<l.length&&(w=b[F]),A=F}for(o[c]=x,F=0;F<l.length;){if(\"\"==(w=b[F])){F+=1;continue}for(A=F;F<l.length&w==b[F];)F+=1;let t,i=new Ov(x.slice(A,F)).mean/this.mean;t=\"D\"==w?\"deletion\":\"duplication\";let n={chr:c,start:e*A+1,end:e*F,size:e*(F-A+1),value:2*i,event_type:t};a.push(n)}})),[o,a]}};class Vv{constructor(e,t){this.allVariants=e,this.rowBinSize=1e4,this.binSize=t,this.binFactor=parseInt(t/this.rowBinSize)}async read_rd_baf(e=\"ReadDepth\"){var t={};for(let e=this.allVariants.length-1;e>=0;e--){var i;let n=this.allVariants[e];this.allVariants.splice(e,1);let r=n.chr;i=Math.max(Math.floor(n.start/this.rowBinSize),0),t[r]||(t[r]=[]),t[r][i]||(t[r][i]={chr:r,start:i*this.rowBinSize,end:(i+1)*this.rowBinSize,dp_sum_score:0,dp_count:0,hets_count:0,hets:[]});const s=Object.values(n.calls);if(1!==s.length)throw Error(`Unexpected number of genotypes: ${s.length}.  CNVPytor expects 1 and only 1 genotype`);const o=s[0],a=o.info.DP;a&&(t[r][i].dp_sum_score+=Number.parseInt(a),t[r][i].dp_count++);let c=o.info.AD.split(\",\"),l=o.genotype;if(0==l[0]&&1==l[1]||1==l[0]&&0==l[1]){t[r][i].hets_count++;let e=parseInt(c[0]),n=parseInt(c[1]);t[r][i].hets.push({ref:e,alt:n})}}this.chromosomes=Object.keys(t);var n,r=this.adjust_bin_size(t);if(\"ReadDepth\"==e){n=new Wv(r,this.binSize).ReadDepth_caller();var s=this.formatDataStructure_BAF(r,\"max_likelihood\")}else if(\"2D\"==e){let e=new Dv(r,this.binSize),t=await e.call_2d();n=[t.binScore,[],t.segment_score];s=e.formatDataStructure_BAF(\"max_likelihood\",-1)}return[n,s]}formatDataStructure(e,t,i=1){const n=[];for(const[s,o]of Object.entries(e))for(let e of o){var r={...e};1!=i&&(r.value=e[t]/i*2),n.push(r)}return n}format_BAF_likelihood(e){const t=[];for(const[n,r]of Object.entries(e))for(let e of r){var i={...e};.5!=e.value&&(i.value=1-e.value,t.push(i))}return t}get_max_min_score(e){if(e.likelihood_score.length>0){const t=Math.max(...e.likelihood_score),i=e.likelihood_score.indexOf(t);e.value=Math.max(i/100,1-i/100),e.min_score=Math.min(i/100,1-i/100)}else e.score=0;return e}async getAllbins(){const e=await this.computeDepthFeatures();return new Fv.GetFit(e).fit_data(),e}formatDataStructure_BAF(e,t,i=-1){const n=[],r=[];for(const[a,c]of Object.entries(e))for(let e of c){var s={...e},o={...e};let a=e[t];.5!=a&&(o.value=i*(1-a),r.push(o)),s.value=i*a,n.push(s)}return[n,r]}adjust_bin_size(e){var t={};for(let r of this.chromosomes){t[r]||(t[r]=[]);for(let s=0;s<e[r].length/this.binFactor;s++){const o=s;t[r][s]||(t[r][s]={chr:r,start:o*this.binSize,end:(o+1)*this.binSize,dp_count:0,hets_count:0,binScore:0,likelihood_score:[],dp_sum_score:0});for(var i=s*this.binFactor;i<this.binFactor*s+this.binFactor;i++)if(e[r][i]&&(t[r][s].dp_sum_score+=e[r][i].dp_sum_score,t[r][s].dp_count+=e[r][i].dp_count,t[r][s].hets_count+=e[r][i].hets_count,0!=e[r][i].hets.length))for(let o of e[r][i].hets)if(0==t[r][s].likelihood_score.length)t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,t)=>jv(o.ref,o.alt,e)));else{var n=0;t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,i)=>{var a=t[r][s].likelihood_score[i]*jv(o.ref,o.alt,e);return n+=a,a})),t[r][s].likelihood_score=Fv.linspace(0,1,100).map(((e,i)=>t[r][s].likelihood_score[i]/n))}t[r][s].binScore=100*parseInt(t[r][s].dp_sum_score/t[r][s].dp_count);const a=this.get_max_min_score(t[r][s]);t[r][s].max_likelihood=a.value}}return t}}function jv(e,t,i,n=!0){return Math.pow(i,e)*Math.pow(1-i,t)+Math.pow(i,t)*Math.pow(1-i,e)}class Wv{constructor(e,t){this.wigFeatures=e,this.binSize=t}ReadDepth_caller(){var e=new Fv.GetFit(this.wigFeatures),[t,i]=e.fit_data(),n=new Qv(this.wigFeatures,t,i),r=n.meanShiftCaller(this.binSize),s=n.cnv_calling();return Object.entries(this.wigFeatures).forEach((([e,t])=>{t.forEach(((t,i)=>{t.partition_level=parseInt(r[e][i]),t.partition_call=parseInt(s[0][e][i])}))})),[this.formatDataStructure(\"binScore\",t),this.formatDataStructure(\"partition_level\",t),this.formatDataStructure(\"partition_call\",t),s[1]]}formatDataStructure(e,t=1){const i=[];for(const[r,s]of Object.entries(this.wigFeatures))for(let r of s){var n={...r};1!=t&&(n.value=r[e]/t*2),i.push(n)}return i}}class Gv extends Hl{static DEFAULT_TRACK_HEIGHT=250;constructor(e,t){super(e,t)}init(e){this.featureType=\"numeric\",this.type=\"cnvpytor\",e.max||(this.defaultScale=!0,this.autoscale=!1),e.height||(e.height=Gv.DEFAULT_TRACK_HEIGHT),this.type=\"cnvpytor\",this.graphType=e.graphType||\"points\",this.bin_size=e.bin_size||1e5,this.signal_name=e.signal_name||\"rd_snp\",this.cnv_caller=e.cnv_caller||\"2D\",this.colors=e.colors||[\"gray\",\"black\",\"green\",\"blue\"],super.init(e)}get supportsWholeGenome(){return!0}get_signals(){let e=[];return\"rd_snp\"==this.signal_name?e=[\"RD_Raw\",\"RD_Raw_gc_coor\",this.cnv_caller,\"BAF1\",\"BAF2\"]:\"rd\"==this.signal_name?e=[\"RD_Raw\",\"RD_Raw_gc_coor\",this.cnv_caller]:\"snp\"==this.signal_name?e=[\"BAF1\",\"BAF2\"]:\"cnh\"==this.signal_name&&(e=[this.cnv_caller]),e}get_signal_colors(){return[{singal_name:\"RD_Raw\",color:this.colors[0]},{singal_name:\"RD_Raw_gc_coor\",color:this.colors[1]},{singal_name:\"ReadDepth\",color:this.colors[2]},{singal_name:\"2D\",color:this.colors[2]},{singal_name:\"BAF1\",color:this.colors[3]},{singal_name:\"BAF2\",color:this.colors[3]}]}async postInit(){if(\"vcf\"==this.config.format){let e;this.featureSource?e=Object.values(this.featureSource.getAllFeatures()).flat():(this.featureSource=this.featureSource||Ad(this.config,this.browser.genome),this.header=await this.getHeader(),e=this.featureSource.reader.features);const t=new Vv(e,this.bin_size);let i,n,r;this.wigFeatures_obj={},this.wigFeatures_obj[this.bin_size]={},\"2D\"==this.cnv_caller?(r=await t.read_rd_baf(\"2D\"),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size][\"2D\"]=i[2],this.available_callers=[\"2D\"]):(r=await t.read_rd_baf(),i=r[0],n=r[1],this.wigFeatures_obj[this.bin_size].ReadDepth=i[2],this.available_callers=[\"ReadDepth\"]),this.wigFeatures_obj[this.bin_size].RD_Raw=i[0],this.wigFeatures_obj[this.bin_size].RD_Raw_gc_coor=i[1],this.wigFeatures_obj[this.bin_size].BAF1=n[0],this.wigFeatures_obj[this.bin_size].BAF2=n[1],this.available_bins=[this.bin_size],this.set_available_callers()}else this.cnvpytor_obj=new mv(this.config.url,this.bin_size),this.wigFeatures_obj=await this.cnvpytor_obj.get_rd_signal(this.bin_size),this.available_bins=this.cnvpytor_obj.available_bins,this.available_callers=this.cnvpytor_obj.callers,this.set_available_callers();this.tracks=[];const e=[];this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(let t in this.wigFeatures_obj)for(const[i,n]of Object.entries(this.wigFeatures_obj[t]))if(this.signals.includes(i)){let t={type:\"wig\"};t.features=n,t.name=i,t.color=this.signal_colors.filter((e=>e.singal_name===i)).map((e=>e.color));const r=await this.browser.createTrack(t);r?(r.isMergedTrack=!0,r.autoscale=!1,this.tracks.push(r)):console.warn(\"Could not create track \"+t),\"function\"==typeof r.postInit&&e.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let e of this.tracks)e.autoscale=!1,e.dataRange=this.dataRange;return Promise.all(e)}set_available_callers(){this.available_callers.includes(this.cnv_caller)||(this.available_callers.length>0?this.cnv_caller=this.available_callers[0]:this.cnv_caller=null)}async getHeader(){if(!this.header){if(\"function\"==typeof this.featureSource.getHeader){const e=await this.featureSource.getHeader();e&&(this.callSets=e.callSets||[]),this.header=e}this.sampleKeys=this.callSets?this.callSets.map((e=>e.sample)):[],this.sampleNames=this.sampleKeys}return this.header}get height(){return this._height}set height(e){if(this._height=e,this.tracks)for(let t of this.tracks)t.height=e,t.config.height=e}menuItemList(){let e=[];void 0!==this.flipAxis&&e.push({label:\"Flip y-axis\",click:function(){this.flipAxis=!this.flipAxis,this.trackView.repaintViews()}}),e=e.concat(this.numericDataMenuItems()),e.push(\"<hr/>\"),e.push(\"Bin Sizes\");for(let t of this.available_bins){const i=Dl(t,t===this.bin_size);e.push({object:Bt(i),click:async function(){this.bin_size=t,this.trackView.startSpinner(),await this.recreate_tracks(t),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}e.push(\"<hr/>\"),e.push(\"Signal Type\");let t={rd_snp:\"RD and BAF Likelihood\",rd:\"RD Signal\",snp:\"BAF Likelihood\"};for(let i in t){const n=Dl(t[i],i===this.signal_name);e.push({object:Bt(n),click:async function(){this.signal_name=i,await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}e.push(\"<hr/>\"),e.push(\"CNV caller\");for(let t of this.available_callers){const i=Dl(t,t===this.cnv_caller);e.push({object:Bt(i),click:async function(){this.cnv_caller=t,this.trackView.startSpinner(),await this.recreate_tracks(this.bin_size),this.clearCachedFeatures(),this.trackView.updateViews(),this.trackView.repaintViews()}})}if(this.variantState){e.push(\"<hr/>\");for(let t of this.available_callers)e.push({label:\"Convert to variant track\",click:()=>{this.convertToVariant()}})}return e}async recreate_tracks(e){this.tracks=[];const t=[];e in this.wigFeatures_obj||(this.wigFeatures_obj={...this.wigFeatures_obj,...await this.cnvpytor_obj.get_rd_signal(e)}),this.signals=this.get_signals(),this.signal_colors=this.get_signal_colors();for(const[i,n]of Object.entries(this.wigFeatures_obj[e]))if(this.signals.includes(i)){let e={type:\"wig\"};e.features=n,e.name=i,e.color=this.signal_colors.filter((e=>e.singal_name===i)).map((e=>e.color));const r=await this.browser.createTrack(e);r?(r.isMergedTrack=!0,r.autoscale=!1,this.tracks.push(r)):console.warn(\"Could not create track \"+e),\"function\"==typeof r.postInit&&t.push(r.postInit())}this.flipAxis=!!this.config.flipAxis&&this.config.flipAxis,this.logScale=!!this.config.logScale&&this.config.logScale,this.autoscale=this.config.autoscale,this.autoscale||(this.dataRange={min:this.config.min||0,max:this.config.max});for(let e of this.tracks)e.autoscale=!1,e.dataRange=this.dataRange;return Promise.all(t)}async getFeatures(e,t,i,n){if(this.tracks){const r=this.tracks.map((r=>r.getFeatures(e,t,i,n)));return Promise.all(r)}}getScaleFactor(e,t,i,n){return n?i/(Math.log10(t+1)-(e<=0?0:Math.log10(e+1))):i/(t-e)}computeYPixelValue(e,t){return(this.flipAxis?e-this.dataRange.min:this.dataRange.max-e)*t}computeYPixelValueInLogScale(e,t){let i=this.dataRange.max,n=this.dataRange.min;return i<=0?0:(n<=-1&&(n=0),n=n<=0?0:Math.log10(n+1),i=Math.log10(i+1),e=Math.log10(e+1),(this.flipAxis?e-n:i-e)*t)}draw(e){const t=e.features;if(!t)return;if(this.defaultScale&&(\"rd_snp\"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||-1,max:this.config.max||this.dataRange.max||5}:\"rd\"==this.signal_name?this.dataRange={min:this.config.min||this.dataRange.min||0,max:this.config.max||this.dataRange.max||5}:\"snp\"==this.signal_name&&(this.dataRange={min:this.config.min||this.dataRange.min||-1,max:this.config.max||this.dataRange.max||0})),this.autoscale&&(this.dataRange=function(e,t){let i=0,n=-Number.MAX_VALUE;for(let e of t)for(let t of e)void 0===t.value||Number.isNaN(t.value)||(i=Math.min(i,t.value),n=Math.max(n,t.value));return{min:i,max:n}}(e.referenceFrame.chr,t)),this.tracks)for(let i=0,n=this.tracks.length;i<n;i++){const n=Object.assign({},e);n.features=t[i],this.tracks[i].dataRange=this.dataRange,this.tracks[i].flipAxis=this.flipAxis,this.tracks[i].logScale=this.logScale,this.graphType&&(this.tracks[i].graphType=this.graphType),this.tracks[i].draw(n)}const i=this.getScaleFactor(this.dataRange.min,this.dataRange.max,e.pixelHeight,this.logScale),n=e=>this.logScale?this.computeYPixelValueInLogScale(e,i):this.computeYPixelValue(e,i);if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=n(t.y),r={strokeStyle:t.color,strokeWidth:1};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,r):xo.strokeLine(e.context,0,i,e.pixelWidth,i,r)}let r=n(2);xo.dashedLine(e.context,0,r,e.pixelWidth,r,5,{strokeStyle:\"lightgray\",strokeWidth:.5})}paintAxis(e,t,i){var n,r,s,o,a,c,l,h={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};if(void 0===this.dataRange||void 0===this.dataRange.max||void 0===this.dataRange.min)return;let d=void 0!==this.flipAxis&&this.flipAxis;function u(e){return e<0?Math.abs(e):0===e?\"0\":Math.abs(e)>=10||e%1==0?e.toFixed():Math.abs(e)>=1?e.toFixed(1):e.toFixed(2)}xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"}),n=(l=.95*t)-8,a={x:r=l,y:s=o=.01*i},xo.strokeLine(e,n,s,r,o,h),xo.fillText(e,u(d?this.dataRange.min:this.dataRange.max),n+4,s+12,h),c={x:r,y:s=o=.99*i},xo.strokeLine(e,n,s,r,o,h),xo.fillText(e,u(d?this.dataRange.max:this.dataRange.min),n+4,s-4,h),xo.strokeLine(e,a.x,a.y,c.x,c.y,h);const f=this.getScaleFactor(this.dataRange.min,this.dataRange.max,i,this.logScale),p=e=>this.logScale?this.computeYPixelValueInLogScale(e,f):this.computeYPixelValue(e,f),g=Math.ceil((this.dataRange.max-this.dataRange.min)/10);for(let t=Math.ceil(this.dataRange.min+1);t<Math.round(this.dataRange.max-.4);t+=g){const i=p(t);xo.strokeLine(e,45,i,50,i,h),xo.fillText(e,u(d?this.dataRange.max-t:t),44,i+4,h)}}popupData(e,t){const i=t||e.viewport.cachedFeatures;if(i&&i.length===this.tracks.length){const t=[];for(let n=0;n<this.tracks.length;n++){n>0&&t.push(\"<hr/>\"),t.push(`<div style=background-color:rgb(245,245,245);border-bottom-style:dashed;border-bottom-width:1px;padding-bottom:5px;padding-top:10px;font-weight:bold;font-size:larger >${this.tracks[n].name}</div>`);const r=this.tracks[n].popupData(e,i[n]);t.push(...r)}return t}}async convertToVariant(){this.variantState&&(Object.setPrototypeOf(this,Yv.prototype),this.init(this.variantState),await this.postInit(),this.trackView.clearCachedFeatures(),this.variantState.trackHeight&&this.trackView.setTrackHeight(this.variantState.trackHeight),this.trackView.checkContentHeight(),this.trackView.updateViews(),delete this.variantState)}}const $v=Mt,Kv=10;class Yv extends Hl{static defaults={displayMode:\"EXPANDED\",sortDirection:\"ASC\",showGenotypes:!0,expandedVariantHeight:10,squishedVariantHeight:2,squishedCallHeight:1,expandedCallHeight:10,expandedVGap:2,squishedVGap:1,expandedGroupGap:10,squishedGroupGap:5,featureHeight:14,noGenotypeColor:\"rgb(200,180,180)\",noCallColor:\"rgb(225, 225, 225)\",nonRefColor:\"rgb(200, 200, 215)\",mixedColor:\"rgb(200, 220, 200)\",homrefColor:\"rgb(200, 200, 200)\",homvarColor:\"rgb(17,248,254)\",hetvarColor:\"rgb(34,12,253)\",refColor:\"rgb(0,0,220)\",altColor:\"rgb(255,0,0)\",visibilityWindow:void 0,labelDisplayMode:void 0,type:\"variant\"};_sortDirections=new Map;constructor(e,t){super(e,t)}init(e){if(super.init(e),e.variantHeight&&(this.expandedVariantHeight=e.variantHeight),this.featureSource=Ad(e,this.browser.genome),this.colorTables=new Map,e.colorTable){const t=e.colorBy||\"*\";this.colorTables.set(t,new ao(e.colorTable))}if(this.strokecolor=e.strokecolor,this._context_hook=e.context_hook,e.color&&(this.colorBy=void 0),this.nVariantRows=1,e.samples)for(let t of e.samples)this.sampleKeys=e.samples;e.sort&&(this.initialSort=e.sort),this._colorByItems=new Map([[\"none\",\"None\"]])}async postInit(){if(this.header=await this.getHeader(),this.header.INFO){const e=new Set(Object.keys(this.header.INFO));this.config.colorBy?this.colorBy=this.config.colorBy:!this.config.color&&e.has(\"AF\")&&(this.colorBy=\"AF\"),e.has(\"AF\")&&this._colorByItems.set(\"AF\",\"Allele frequency\"),e.has(\"VT\")&&this._colorByItems.set(\"VT\",\"Variant Type\"),e.has(\"SVTYPE\")&&this._colorByItems.set(\"SVTYPE\",\"SV Type\")}if(this.config.colorBy&&!this._colorByItems.has(this.config.colorBy)&&this._colorByItems.set(this.config.colorBy,this.config.colorBy),!this.disposed){if(this.header&&!this.sampleKeys&&(this.sampleKeys=this.header.sampleNameMap?Array.from(this.header.sampleNameMap.keys()):[]),void 0===this.visibilityWindow&&!1!==this.config.indexed){const e=Ht(this.config.url)?this.config.url.name:this.config.url;$v(e)&&e.toLowerCase().includes(\"gnomad\")?this.visibilityWindow=1e3:\"function\"==typeof this.featureSource.defaultVisibilityWindow?this.visibilityWindow=await this.featureSource.defaultVisibilityWindow():this.visibilityWindow=1e6}return this}}get supportsWholeGenome(){return!this.config.indexURL||!0===this.config.supportsWholeGenome}get color(){return this._color||\"rgb(0,0,150)\"}set color(e){this._color=e,e&&(this.colorBy=void 0)}async getHeader(){return this.header||\"function\"==typeof this.featureSource.getHeader&&(this.header=await this.featureSource.getHeader()),this.header}getSampleCount(){return this.sampleKeys?this.sampleKeys.length:0}async getFeatures(e,t,i,n){void 0===this.header&&(this.header=await this.getHeader());const r=await this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:this.visibilityWindow});if(this.initialSort){const e=this.initialSort;if(void 0===e.option||\"GENOTYPE\"===e.option.toUpperCase())this.sortSamplesByGenotype(e,r);else if(\"ATTRIBUTE\"===e.option.toUpperCase()&&e.attribute){const t=\"ASC\"===e.direction?1:-1;this.sortByAttribute(e.attribute,t)}this.initialSort=void 0}return r}hasSamples(){return this.getSampleCount()>0}getSamples(){const e=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,i=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=t*((\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight)+e),r=Kv+t*(i+e);return{names:this.sampleKeys,yOffset:r,height:n}}computePixelHeight(e){if(!e||0===e.length)return Kv;const t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,i=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,n=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,r=\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s=!1===this.showGenotypes?0:this.getSampleCount()*t;return Kv+t*(n+i)+i+(s+1)*(r+i)}variantRowCount(e){this.nVariantRows=e}draw({context:e,pixelWidth:t,pixelHeight:i,bpPerPixel:n,bpStart:r,pixelTop:s,features:o}){xo.fillRect(e,0,s,t,i,{fillStyle:\"rgb(255, 255, 255)\"});const a=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,c=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows,l=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=Kv+c*(l+a);let h=this.sampleColumns;const d=this.hasSamples();if(h&&d&&!1!==this.showGenotypes&&xo.strokeLine(e,0,this.variantBandHeight,t,this.variantBandHeight,{strokeStyle:\"rgb(224,224,224) \"}),o){const i=\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,s=\"SQUISHED\"===this.displayMode?this.squishedVGap:this.expandedVGap,a=r+t*n+1;for(let t of o){if(t.end<r)continue;if(t.start>a)break;const o=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,c=Kv+(\"COLLAPSED\"===this.displayMode?0:t.row*(o+s)),l=o;let h=(t.start-r)/n,u=(t.end-r)/n,f=Math.max(1,u-h);f<3?(f=3,h-=1):f>5&&(h+=1,f-=2);const p=t._f||t;let g;try{g=p.alleleFreq()}catch(e){console.log(e)}if(\"AF\"===this.colorBy&&g){const t=Math.min(1,g)*l,i=l-t;e.fillStyle=p.isFiltered()?this.refColorFiltered:this.refColor,e.fillRect(h,c,f,i),e.fillStyle=p.isFiltered()?this.altColorFiltered:this.altColor,e.fillRect(h,c+i,f,t)}else e.fillStyle=this.getColorForFeature(p),e.fillRect(h,c,f,l);let m=this.getVariantStrokecolor(p);if(m&&(e.strokeStyle=m,e.strokeRect(h,c,f,l)),this.callContextHook(p,e,h,c,f,l),d&&!1!==this.showGenotypes){const t=\"COLLAPSED\"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+s,this.sampleHeight=t*(i+s);let n=0;for(let t of this.sampleKeys){const r=this.header.sampleNameMap.get(t),o=p.calls[r];if(o){const t=\"COLLAPSED\"===this.displayMode?0:p.row,r=this.sampleYOffset+n*this.sampleHeight+t*(i+s);let a=!0,c=!0,l=!1;if(o.genotype)for(let e of o.genotype){if(\".\"===e){l=!0;break}0!==e&&(c=!1),0===e&&(a=!1)}o.genotype?e.fillStyle=l?this.noCallColor:c?this.homrefColor:a?this.homvarColor:this.hetvarColor:e.fillStyle=this.noGenotypeColor,e.fillRect(h,r,f,i)}n++}}}}else console.log(\"No feature list\")}get refColorFiltered(){return this._refColorFiltered||(this._refColorFiltered=_s.addAlpha(this.refColor,.2)),this._refColorFiltered}get altColorFiltered(){return this._altColorFiltered||(this._altColorFiltered=_s.addAlpha(this.altColor,.2)),this._altColorFiltered}getColorForFeature(e){const t=e._f||e;let i;if(this.colorBy&&\"none\"!==this.colorBy){const e=t.getAttributeValue(this.colorBy);i=void 0!==e?this.getVariantColorTable(this.colorBy).getColor(e):\"gray\"}else i=this.color?\"function\"==typeof this.color?this.color(e):this.color:\"NONVARIANT\"===t.type?this.nonRefColor:\"MIXED\"===t.type?this.mixedColor:this.color;return t.isFiltered()&&(i=_s.addAlpha(i,.2)),i}getVariantStrokecolor(e){const t=e._f||e;let i;return i=this.strokecolor?\"function\"==typeof this.strokecolor?this.strokecolor(t):this.strokecolor:void 0,i}callContextHook(e,t,i,n,r,s){if(this._context_hook&&\"function\"==typeof this._context_hook){const o=e._f||e;t.save(),this._context_hook(o,t,i,n,r,s),t.restore()}}clickedFeatures(e){let t=super.clickedFeatures(e);const i=\"EXPANDED\"===this.displayMode?this.expandedVGap:this.squishedVGap,n=i+(\"SQUISHED\"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),r=e.y;if(r<=this.variantBandHeight){const e=\"SQUISHED\"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,n=Math.floor((r-Kv)/(e+i));\"COLLAPSED\"!==this.displayMode&&(t=t.filter((e=>e.row===n)))}else if(this.sampleKeys){const e=r-this.variantBandHeight,i=Math.floor(e/this.sampleHeight);if(i>=0&&i<this.sampleKeys.length){const r=Math.floor((e-i*this.sampleHeight)/n),s=\"COLLAPSED\"===this.displayMode?t:t.filter((e=>e.row===r)),o=this.sampleKeys[i],a=this.header.sampleNameMap.get(o);t=s.map((e=>{const t=e.calls[a];return t.genotypeString=function(e,t){if(e.genotype){let i=\"\";if(\".\"===t.alternateBases)i=\"No Call\";else{const n=t.alternateBases.split(\",\");for(let r of e.genotype)if(i.length>0&&(i+=\" | \"),\".\"===r)i+=\".\";else if(0===r)i+=t.referenceBases;else{i+=n[r-1].replace(\"<\",\"&lt;\")}}return i}}(t,e),t}))}}return t}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=this.browser.genome.id;let r=[];for(let e of t){const t=e._f||e;if(r.length>0&&r.push({html:'<hr style=\"border-top-width:2px ;border-color: #c9c3ba\" />'}),\"function\"==typeof t.popupData){const e=t.popupData(i,n);Array.prototype.push.apply(r,e)}}return r}menuItemList(){const e=[];if(this.header.INFO&&this.header.INFO){const t=this._colorByItems;e.push(\"<hr/>\");const i=Bt('<div class=\"igv-track-menu-category igv-track-menu-border-top\">');i.text(\"Color by:\"),e.push({name:void 0,object:i,click:void 0,init:void 0});for(let n of t.keys()){const r=this.colorBy===n;e.push(this.colorByCB({key:n,label:t.get(n)},r))}e.push(this.colorByCB({key:\"info\",label:\"Info field...\"}))}if(!0===Hf(this.browser.sampleInfo,this.sampleKeys)){e.push(\"<hr/>\"),e.push(\"Sort by attribute:\");for(const s of this.browser.sampleInfo.attributeNames)if(this.sampleKeys.some((e=>{const t=this.browser.sampleInfo.getAttributes(e);return t&&t[s]}))){const o=Bt(\"<div>\");function a(){const e=this._sortDirections.get(s)||1;this.sortByAttribute(s,e),this.config.sort={option:\"ATTRIBUTE\",attribute:s,direction:e>0?\"ASC\":\"DESC\"},this._sortDirections.set(s,-1*e)}o.html(`&nbsp;&nbsp;${s.split(Uu.emptySpaceReplacement).join(\" \")}`),e.push({object:o,click:a})}}e.push(\"<hr/>\"),this.getSampleCount()>0&&(e.push({object:Bt('<div class=\"igv-track-menu-border-top\">')}),e.push({object:Bt(Dl(\"Show Genotypes\",this.showGenotypes)),click:function(){this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews(),this.browser.sampleNameControl.performClickWithState(this.browser,this.showGenotypes),this.browser.sampleInfoControl.performClickWithState(this.browser,this.showGenotypes)}})),e.push({object:Bt('<div class=\"igv-track-menu-border-top\">')});for(let c of[\"COLLAPSED\",\"SQUISHED\",\"EXPANDED\"]){e.push({object:Bt(Dl({COLLAPSED:\"Collapse\",SQUISHED:\"Squish\",EXPANDED:\"Expand\"}[c],c===this.displayMode)),click:function(){this.displayMode=c,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})}return this.browser.circularView&&(e.push(\"<hr>\"),e.push({label:\"Add SVs to circular view\",click:function(){for(let e of this.trackView.viewports)this.sendChordsForViewport(e)}})),this.canCovertToPytor()&&(e.push(\"<hr>\"),e.push({label:\"Convert to CNVpytor track\",click:function(){this.convertToPytor()}})),e}contextMenuItemList(e){const t=[];if(this.hasSamples()&&this.showGenotypes){const i=e.viewport.referenceFrame,n=e.genomicLocation,r=i.toBP(2.5),s=this._sortDirections.get(\"genotype\")||1;this._sortDirections.set(\"genotype\",-1*s),t.push({label:\"Sort by genotype\",click:t=>{const i={direction:s,option:\"genotype\",chr:e.viewport.referenceFrame.chr,start:Math.floor(n-r),end:Math.ceil(n+r)},o=e.viewport.cachedFeatures;this.sortSamplesByGenotype(i,o),this.config.sort=i}}),t.push(\"<hr/>\")}if(this.browser.circularView){const i=e.viewport;t.push({label:\"Add SVs to Circular View\",click:()=>{this.sendChordsForViewport(i)}}),t.push(\"<hr/>\")}return t}async sortSamplesByGenotype({chr:e,position:t,start:i,end:n,direction:r},s){if(void 0===i&&(i=t-1),void 0===n&&(n=t),s||(s=await this.featureSource.getFeatures({chr:e,start:i,end:n})),!s)return;const o=new Map,a=\"ASC\"===r?1:-1;for(let e of s)if(!(e.end<i)){if(e.start>n)break;for(let t of e.calls){const e=t.sample,i=t.zygosityScore();o.set(e,o.has(e)?o.get(e)+i:i)}}this.sampleKeys.sort((function(e,t){let i=o.get(e)||0,n=o.get(t)||0;return a*(i-n)})),this.trackView.repaintViews()}sortByAttribute(e,t){this.config.sort={option:\"ATTRIBUTE\",attribute:e,direction:1===t?\"ASC\":\"DESC\"},this.sampleKeys=this.browser.sampleInfo.getSortedSampleKeysByAttribute(this.sampleKeys,e,t),this.trackView.repaintViews()}sendChordsForViewport(e){const t=e.referenceFrame;let i;if(\"all\"===t.chr){const e=this.featureSource.getAllFeatures(),t=Object.keys(e).map((t=>e[t]));i=[].concat(...t)}else i=this.featureSource.featureCache.queryFeatures(t.chr,t.start,t.end);Pm(i.filter((e=>{const t=e._f||e;return t.info&&t.info.CHR2&&t.info.END&&(t.info.CHR2!==t.chr||Math.abs(Number.parseInt(t.info.END)-t.pos)>1e6)})).map((e=>{const t=e._f||e,i=Number.parseInt(t.info.END),n=i-100,r=i+100;return{uniqueId:`${t.chr}:${t.start}-${t.end}_${t.info.CHR2}:${t.info.END}`,refName:zm(t.chr),start:t.start,end:t.end,mate:{refName:zm(t.info.CHR2),start:n,end:r}}})),this,t,.5)}colorByCB(e,t){const i=Bt(Dl(e.label,t));if(\"info\"!==e.key){function n(){const t=\"none\"===e.key?void 0:e.key;this.colorBy=t,this.config.colorBy=t,this.trackView.repaintViews()}return{name:void 0,object:i,click:n,init:void 0}}{function r(e){this.browser.inputDialog.present({label:\"Info field\",value:\"\",callback:e=>{e?(this.colorBy=e,this._colorByItems.set(e,e)):this.colorBy=void 0,this.trackView.repaintViews()}},e)}return{name:void 0,object:i,dialog:r,init:void 0}}}getState(){const e=super.getState();return this.color&&\"function\"!=typeof this.color&&(e.color=this.color),e}getVariantColorTable(e){if(this.colorTables.has(e))return this.colorTables.get(e);if(this.colorTables.has(\"*\"))return this.colorTables.get(\"*\");{let t;if(\"SVTYPE\"===e)t=Xv;else t=new oo(\"Set1\");return this.colorTables.set(e,t),t}}paintAxis(){}canCovertToPytor(){return!this.config.indexURL&&(!!this.header&&(1===Object.keys(this.sampleKeys).length&&this.header.FORMAT&&this.header.FORMAT.AD&&this.header.FORMAT.DP))}async convertToPytor(){this.variantState={...this.config,...this.getState()},this.variantState.trackHeight=this.height,this.trackView.startSpinner(),setTimeout((async()=>{try{const e=Object.assign({},this.config);Object.setPrototypeOf(this,Gv.prototype),this.init(e),await this.postInit(),this.trackView.clearCachedFeatures(),this.trackView.setTrackHeight(this.config.height||Gv.DEFAULT_TRACK_HEIGHT),this.trackView.checkContentHeight(),this.trackView.updateViews()}finally{this.trackView.stopSpinner()}}),100)}}const Xv=new ao({DEL:\"#ff2101\",INS:\"#001888\",DUP:\"#028401\",INV:\"#008688\",CNV:\"#8931ff\",BND:\"#891100\",\"*\":\"#002eff\"}),Zv={timeout:5e3,type:\"plain\",url:\"https://igv.org/genomes/locus.php?genome=$GENOME$&name=$FEATURE$\",coords:0};async function Jv(e,t){const i=e.searchConfig||Zv;let n;t=t.toUpperCase();const r=e.tracks.filter((e=>e.searchable));for(let e of r){const i=await e.search(t);if(i)return i}if(e.config&&!1!==e.config.search)try{return n=await async function(e,t,i){let n=i.url.replace(\"$FEATURE$\",t.toUpperCase());n.indexOf(\"$GENOME$\")>-1&&(n=n.replace(\"$GENOME$\",e.genome.id?e.genome.id:\"hg19\"));const r=i.timeout?{timeout:i.timeout}:void 0,s=await Qs.loadString(n,r);return function(e,t,i){let n;n=\"plain\"===i.type?function(e,t){const i=[],n=Dt(t);for(let t of n){const n=t.split(\"\\t\");if(n.length>=3){const t=n[1].split(\":\"),r=t[1].split(\"-\");i.push({chromosome:e.genome.getChromosomeName(t[0].trim()),start:parseInt(r[0].replace(/,/g,\"\")),end:parseInt(r[1].replace(/,/g,\"\")),name:n[0].toUpperCase()})}}return i}(e,t):JSON.parse(t);i.resultsField&&(n=n[i.resultsField]);if(n&&0!==n.length){const e=i.chromosomeField||\"chromosome\",t=i.startField||\"start\",r=i.endField||\"end\",s=i.coords||1;let o;o=Array.isArray(n)?n[0]:n,o.hasOwnProperty(e)&&o.hasOwnProperty(t)||console.error(\"Search service results must include chromosome and start fields: \"+o);const a=o[e];let c=o[t]-s,l=o[r];void 0===l&&(l=c+1);const h={chr:a,start:c,end:l};if(!o.type||o.type,i.geneField&&i.snpField){const e=o[i.geneField]||o[i.snpField];e&&(h.name=e.toUpperCase())}return h}return}(e,s,i)}(e,t,i),n}catch(e){console.log(\"Search service not available \"+e)}}function ey(e,t=!1){const i=e.split(\"\\t\");if(i.length>2)try{const e=i[0],t=parseInt(i[1].replace(/,/g,\"\"),10)-1,n=parseInt(i[2].replace(/,/g,\"\"),10);if(!isNaN(t)&&!isNaN(n))return{chr:e,start:t,end:n}}catch(e){}const n=e.split(\":\"),r={chr:n[0]};if(n.length>1){let e,i=n[1].split(\"-\");if(i.length>2){if(!n[1].startsWith(\"-\"))return;{const e=n[1].indexOf(\"-\",1);if(e>0){i=[n[1].substring(0,e),n[1].substring(e+1)]}}}if(e=i[0].replace(/,/g,\"\"),isNaN(e))return;if(r.start=parseInt(e,10)-1,r.end=r.start+1,1===i.length&&(r.start-=20,r.end+=20),2===i.length){if(e=i[1].replace(/,/g,\"\"),isNaN(e))return;if(r.end=parseInt(e,10),r.start<0&&!t){const e=-extent.start;r.start+=e,r.end+=e}}}return r}class ty extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"qtl\",this.name=e.name;const t=e.minLogP||e.min,i=e.maxLogP||e.max;this.dataRange={min:void 0!==t?t:3.5,max:i||25},this.autoscale=!i||e.autoscale,this.autoscalePercentile=void 0===e.autoscalePercentile?98:e.autoscalePercentile,this.background=e.background,this.divider=e.divider||\"rgb(225,225,225)\",this.dotSize=e.dotSize||2,this.height=e.height||100,this.disableButtons=e.disableButtons,this.featureSource=Ad(e,this.browser.genome)}paintAxis(e,t,i){const n=(this.dataRange.max-this.dataRange.min)/i,r={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"});const s=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let o=4;o<=this.dataRange.max;o+=s){const s=.85*t,a=s-5,c=s,l=i-(o-this.dataRange.min)/n;xo.strokeLine(e,a,l,c,l,r),l>8&&xo.fillText(e,o,a-1,l+2,r)}r.textAlign=\"center\",xo.fillText(e,\"-log10(pvalue)\",t/4,i/2,r,{rotate:{angle:-90}})}async getFeatures(e,t,i){const n=this.visibilityWindow;return await this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const{context:t,referenceFrame:i,pixelWidth:n,pixelHeight:r}=e;this.background&&xo.fillRect(t,0,0,n,r,{fillStyle:this.background}),xo.strokeLine(t,0,r-1,n,r-1,{strokeStyle:this.divider}),i.feature&&i.feature.match(/RS[0-9]+/);const s=i=>{const s=i?2*this.dotSize:this.dotSize,o=e.bpStart,a=(this.dataRange.max-this.dataRange.min)/r;for(let d of e.features){const u=(d.start-o+.5)/e.bpPerPixel;if(u<0)continue;if(u>n)break;const f=d.phenotype;let p;if(this.browser.qtlSelections.qtl?(l=this.browser.qtlSelections.qtl,h=d,p=l.chr===h.chr&&l.start===h.start&&l.pValue===h.pValue):p=this.browser.qtlSelections.snps.size>0?this.browser.qtlSelections.hasSnp(d.snp)&&this.browser.qtlSelections.hasPhenotype(f):this.browser.qtlSelections.hasPhenotype(f),!i||p){var c=-Math.log(d.pValue)/Math.LN10;if(c>=this.dataRange.min){let e;c>this.dataRange.max?(c=this.dataRange.max,e=!0):e=!1;const n=Math.max(0+s,r-Math.round((c-this.dataRange.min)/a));let o;d.px=u,d.py=n,d.radius=s,i&&p?(o=this.browser.qtlSelections.colorForGene(f),xo.setProperties(t,{fillStyle:o,strokeStyle:\"black\"})):(o=e?\"rgb(150, 150, 150)\":\"rgb(180, 180, 180)\",xo.setProperties(t,{fillStyle:o,strokeStyle:o})),xo.fillCircle(t,u,n,s),xo.strokeCircle(t,u,n,s)}}}var l,h};s(!1),s(!0)}popupData(e,t){if(void 0===t&&(t=e.viewport.cachedFeatures),!t||0===t.length)return[];const i=this.name,n=[];for(let r of this._clickedFeatures(e,t))n.length>0&&n.push(\"<hr/>\"),\"function\"==typeof r.popupData?n.push(...r.popupData(e)):n.push({name:\"snp id\",value:r.snp},{name:\"gene id\",value:r.gencodeId},{name:\"gene name\",value:r.geneSymbol},{name:\"p value\",value:r.pValue},{name:\"tissue\",value:i});return n}_clickedFeatures(e,t){const i=(e,t)=>Math.sqrt((e.px-t.canvasX)*(e.px-t.canvasX)+(e.py-t.canvasY)*(e.py-t.canvasY)),n=t.filter((t=>i(t,e)<6));if(n.length>1){n.sort(((t,n)=>i(t,e)-i(n,e)));const t=i(n[0],e);return n.filter((n=>i(n,e)<=t))}return n}contextMenuItemList(e){const t=[],i=e.viewport.cachedFeatures;if(i){const n=this._clickedFeatures(e,i);n.length>0&&(t.push({label:\"Highlight associated features\",click:async()=>{this.browser.qtlSelections.clear();for(let e of n)this.browser.qtlSelections.qtl=e,this.browser.qtlSelections.addPhenotype(e.phenotype);this.browser.repaintViews()}}),t.push(\"<hr>\"))}return t}menuItemList(){const e=[];return e.push(...this.numericDataMenuItems()),e.push(\"<hr/>\"),e.push({label:\"Search for...\",dialog:function(e){this.browser.inputDialog.present({label:\"Search for snp or phenotype\",value:\"\",callback:async e=>{if(e){e=e.trim().toUpperCase();const t=t=>((t.phenotype&&t.phenotype.toUpperCase())===e||t.snp&&t.snp.toUpperCase()===e)&&-Math.log(t.pValue)/Math.LN10>this.dataRange.min;let i,n,r,s=await this.featureSource.findFeatures(t);if(0==s.length){await this.browser.search(e)&&(s=await this.featureSource.findFeatures(t))}if(s.length>0){this.browser.qtlSelections.clear();const t=new Set;i=s[0].chr,n=s[0].start,r=s[0].end;for(let o of s)o.snp&&o.snp.toUpperCase()===e&&this.browser.qtlSelections.addSnp(o.snp),this.browser.qtlSelections.addPhenotype(o.phenotype),t.add(o.phenotype),o.chr===i&&(n=Math.min(n,o.start),r=Math.max(r,o.end));const o=this.browser.genome.getChromosomeName(i);for(let e of t){const t=await Jv(this.browser,e);t&&o===this.browser.genome.getChromosomeName(t.chr)&&(n=Math.min(n,t.start),r=Math.max(r,t.end))}const a=Math.floor(.1*(r-n));n=Math.max(0,n-a),r+=a,await this.browser.search(`${i}:${n}-${r}`)}}}},e)}}),e}doAutoscale(e){let t=this.config.max||25;if(e.length>0){const i=e.map((e=>-Math.log(e.pValue)/Math.LN10));i.sort(((e,t)=>e-t));t=i[Math.floor(i.length*(this.autoscalePercentile/100))]}return this.dataRange.max=Math.max(t,10),this.dataRange}}const iy={X:\"rgb(204, 153, 0)\",Y:\"rgb(153, 204, 0)\",Un:\"darkGray)\",1:\"rgb(80, 80, 255)\",2:\"rgb(206, 61, 50)\",\"2a\":\"rgb(210, 65, 55)\",\"2b\":\"rgb(215, 70, 60)\",3:\"rgb(116, 155, 88)\",4:\"rgb(240, 230, 133)\",5:\"rgb(70, 105, 131)\",6:\"rgb(186, 99, 56)\",7:\"rgb(93, 177, 221)\",8:\"rgb(128, 34, 104)\",9:\"rgb(107, 215, 107)\",10:\"rgb(213, 149, 167)\",11:\"rgb(146, 72, 34)\",12:\"rgb(131, 123, 141)\",13:\"rgb(199, 81, 39)\",14:\"rgb(213, 143, 92)\",15:\"rgb(122, 101, 165)\",16:\"rgb(228, 175, 105)\",17:\"rgb(59, 27, 83)\",18:\"rgb(205, 222, 183)\",19:\"rgb(97, 42, 121)\",20:\"rgb(174, 31, 99)\",21:\"rgb(231, 199, 111)\",22:\"rgb(90, 101, 94)\",23:\"rgb(204, 153, 0)\",24:\"rgb(153, 204, 0)\",25:\"rgb(51, 204, 0)\",26:\"rgb(0, 204, 51)\",27:\"rgb(0, 204, 153)\",28:\"rgb(0, 153, 204)\",29:\"rgb(10, 71, 255)\",30:\"rgb(71, 117, 255)\",31:\"rgb(255, 194, 10)\",32:\"rgb(255, 209, 71)\",33:\"rgb(153, 0, 51)\",34:\"rgb(153, 26, 0)\",35:\"rgb(153, 102, 0)\",36:\"rgb(128, 153, 0)\",37:\"rgb(51, 153, 0)\",38:\"rgb(0, 153, 26)\",39:\"rgb(0, 153, 102)\",40:\"rgb(0, 128, 153)\",41:\"rgb(0, 51, 153)\",42:\"rgb(26, 0, 153)\",43:\"rgb(102, 0, 153)\",44:\"rgb(153, 0, 128)\",45:\"rgb(214, 0, 71)\",46:\"rgb(255, 20, 99)\",47:\"rgb(0, 214, 143)\",48:\"rgb(20, 255, 177)\"};for(let DA of Object.keys(iy)){iy[\"chr\"+DA]=iy[DA]}for(let TA=1;TA<=48;TA++){if(10===TA)continue;const LA=ny(TA);iy[LA]=iy[TA.toString()]}function ny(e){if(!+e)return!1;for(var t=String(+e).split(\"\"),i=[\"\",\"C\",\"CC\",\"CCC\",\"CD\",\"D\",\"DC\",\"DCC\",\"DCCC\",\"CM\",\"\",\"X\",\"XX\",\"XXX\",\"XL\",\"L\",\"LX\",\"LXX\",\"LXXX\",\"XC\",\"\",\"I\",\"II\",\"III\",\"IV\",\"V\",\"VI\",\"VII\",\"VIII\",\"IX\"],n=\"\",r=3;r--;)n=(i[+t.pop()+10*r]||\"\")+n;return Array(+t.join(\"\")+1).join(\"M\")+n}class ry extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.useChrColors=void 0===e.useChrColors||e.useChrColors,this.trait=e.trait,this.posteriorProbability=e.posteriorProbability,this.valueProperty=\"bed\"===e.format?\"score\":\"value\",this.height=e.height||100,this.autoscale=e.autoscale,this.autoscalePercentile=void 0===e.autoscalePercentile?98:e.autoscalePercentile,this.background=e.background,this.divider=e.divider||\"rgb(225,225,225)\",this.dotSize=e.dotSize||3,this.popoverWindow=void 0===e.popoverWindow?1e8:e.popoverWindow,this.useChrColors?this.colorScale=new ao(e.colorTable||iy):e.color?this.colorScale=new ff(e.color):this.colorScale=new df(e.colorScale||{thresholds:[5e-8,5e-4,.5],colors:[\"rgb(255,50,50)\",\"rgb(251,100,100)\",\"rgb(251,170,170)\",\"rgb(227,238,249)\"]}),this.featureSource=Ad(e,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),this.autoscale||(this.posteriorProbability?this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?1:this.config.max}:this.dataRange={min:void 0===this.config.min?0:this.config.min,max:void 0===this.config.max?25:this.config.max}),this}get supportsWholeGenome(){return!0}async getFeatures(e,t,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const t=e.features,i=e.context,n=e.pixelWidth,r=e.pixelHeight;if(this.background&&xo.fillRect(i,0,0,n,r,{fillStyle:this.background}),xo.strokeLine(i,0,r-1,n,r-1,{strokeStyle:this.divider}),t){const s=e.bpPerPixel,o=e.bpStart,a=o+n*s+1;for(let e of t){const t=e.start;if(t<o)continue;if(t>a)break;let n;if(this.posteriorProbability)n=e[this.valueProperty];else{const t=e[this.valueProperty];if(!t)continue;n=-Math.log10(t)}const c=this.useChrColors?e._f?e._f.chr:e.chr:n,l=this.colorScale.getColor(c),h=(this.dataRange.max-this.dataRange.min)/r,d=Math.round((t-o)/s),u=Math.max(this.dotSize,r-Math.round((n-this.dataRange.min)/h));l&&xo.setProperties(i,{fillStyle:l,strokeStyle:\"black\"}),xo.fillCircle(i,d,u,this.dotSize),e.px=d,e.py=u}}}paintAxis(e,t,i){xo.fillRect(e,0,0,t,i,{fillStyle:\"rgb(255, 255, 255)\"});var n={font:\"normal 10px Arial\",textAlign:\"right\",strokeStyle:\"black\"};const r=(this.dataRange.max-this.dataRange.min)/i;if(this.posteriorProbability){const t=.1;for(let s=this.dataRange.min;s<this.dataRange.max;s+=t){const t=i-Math.round((s-this.dataRange.min)/r);xo.strokeLine(e,45,t-2,50,t-2,n),xo.fillText(e,s.toFixed(1),44,t+2,n)}}else{const t=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/i);for(let s=this.dataRange.min;s<this.dataRange.max;s+=t){const t=i-Math.round((s-this.dataRange.min)/r);xo.strokeLine(e,45,t,50,t,n),xo.fillText(e,Math.floor(s),44,t+4,n)}}n.textAlign=\"center\",this.posteriorProbability?xo.fillText(e,\"PPA\",t/2,i/2,n,{rotate:{angle:-90}}):xo.fillText(e,\"-log10(pvalue)\",t/2,i/2,n,{rotate:{angle:-90}})}popupData(e,t){void 0===t&&(t=e.viewport.cachedFeatures);let i=[];const n=e.viewport.trackView.track;if(t){let r=0;for(let s of t){const t=Math.abs(e.canvasX-s.px),o=Math.abs(e.canvasY-s.py);if(t<this.dotSize&&o<this.dotSize){if(r>0&&i.push(\"<HR/>\"),5==r){i.push(\"...\");break}if(s=s._f||s,\"function\"==typeof s.popupData)i=i.concat(s.popupData());else{const e=s[this.valueProperty],t=s.chr,r=Rt(s.start+1);i.push({name:\"chromosome\",value:t}),i.push({name:\"position\",value:r}),i.push({name:\"name\",value:s.name}),n.posteriorProbability?i.push({name:\"posterior probability\",value:e}):i.push({name:\"pValue\",value:e})}r++}}}return i}menuItemList(){return this.numericDataMenuItems()}doAutoscale(e){if(e.length>0){const t=this.valueProperty,i=this.posteriorProbability,n=e.map((function(e){const n=e[t];return{value:i?n:-Math.log(n)/Math.LN10}}));this.dataRange=qa(n)}else this.posteriorProbability?this.dataRange={min:this.config.min||0,max:this.config.max||1}:this.dataRange={min:this.config.max||25,max:this.config.min||0};return this.dataRange}}class sy extends Hl{constructor(e,t){super(e,t)}init(e){super.init(e),this.autoscale=e.autoscale||void 0===e.max,this.dataRange={min:e.min||0,max:e.max},this.windowFunction=e.windowFunction||\"mean\",this.paintAxis=cd,this.graphType=e.graphType||\"bar\",e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):this.featureSource=Ad(this.config,this.browser.genome),this.visibilityWindow=-1,this.featureSource.visibilityWindow=this.visibilityWindow}async postInit(){if(\"function\"==typeof this.featureSource.getHeader){if(this.header=await this.featureSource.getHeader(),this.disposed)return;if(this.sampleKeys=this.header.columnNames.slice(3),this.setTrackProperties(this.header),this.header.hasOwnProperty(\"clickToHighlight\")){let e=this.header.clickToHighlight;this.config.clickToHighlight=e,this.config.samplesClickedToHighlight={}}if(this.header.hasOwnProperty(\"highlight\")){this.config.highlightSamples={};let e=this.header.highlight;Array.isArray(e)||(e=[e]);for(let t of e){const e=t.split(\";\");2===e.length&&(this.config.highlightSamples[e[0]]=e[1])}}}}menuItemList(){return this.numericDataMenuItems()}async getFeatures(e,t,i){const n=await this.featureSource.getFeatures({chr:e,start:0,end:Number.MAX_SAFE_INTEGER,visibilityWindow:this.visibilityWindow});let r,s;for(let e=1;e<n.length-1;e++)if(void 0===r&&n[e].end>t&&(r=e-1),void 0===s&&n[e].start>i){s=e+1;break}return void 0===r&&(r=0),void 0===s&&(s=n.length),n.slice(r,s)}draw(e){const{features:t,context:i,bpPerPixel:n,bpStart:r,pixelWidth:s,pixelHeight:o}=e,a=e=>(this.dataRange.max-e)/(this.dataRange.max-this.dataRange.min)*o,c=function(e){let t=Math.floor((e-r)/n);return isNaN(t)&&console.warn(\"isNaN(x). feature start \"+Rt(e)+\" bp start \"+Rt(r)),t};if(t&&t.length>0&&(void 0===this.dataRange.min&&(this.dataRange.min=0),this.dataRange.max>this.dataRange.min)){const e=this.config.highlightSamples,n=this.config.onlyHandleClicksForHighlightedSamples,r=this.config.clickToHighlight;let s=-1,o={},l=[],h=[];this.clickDetectorCache={};for(let d of t){const t=c(d.start),u=c(d.end),f=s>=0?c(s):t;if(!isNaN(t)&&!isNaN(u)){this.clickDetectorCache[t]=[],this.clickDetectorCache[u]=[];for(let s=0;s<d.values.length;s++){const c=this.sampleKeys[s],p=d.values[s],g=a(p);if(t-f>=1){const s=o[c],h=a(s),d=e&&e[c];d?l.push([f,h,t,g,d]):r&&c in this.config.samplesClickedToHighlight?l.push([f,h,t,g,this.config.samplesClickedToHighlight[c]]):xo.strokeLine(i,f,h,t,g,{strokeStyle:\"#D9D9D9\"}),n&&!(c in e)||this.clickDetectorCache[t].push([f,h,t,g,c,d||\"gray\"])}if(u-t>=1){const s=e&&e[c];s?h.push([t,g,u,g,s]):r&&c in this.config.samplesClickedToHighlight?h.push([t,g,u,g,this.config.samplesClickedToHighlight[c]]):xo.strokeLine(i,t,g,u,g,{strokeStyle:\"gray\"}),n&&!(c in e)||this.clickDetectorCache[u].push([t,g,u,g,c,s||\"gray\"])}o[c]=p}s=d.end}}for(let e of l)xo.strokeLine(i,e[0],e[1],e[2],e[3],{strokeStyle:e[4],lineWidth:1.3});for(let e of h)xo.strokeLine(i,e[0],e[1],e[2],e[3],{strokeStyle:e[4],lineWidth:2})}(e=>{if(this.config.hasOwnProperty(\"guideLines\"))for(let t of this.config.guideLines)if(t.hasOwnProperty(\"color\")&&t.hasOwnProperty(\"y\")&&t.hasOwnProperty(\"dotted\")){let i=a(t.y),n={strokeStyle:t.color,strokeWidth:2};t.dotted?xo.dashedLine(e.context,0,i,e.pixelWidth,i,5,n):xo.strokeLine(e.context,0,i,e.pixelWidth,i,n)}})(e)}doAutoscale(e){let t,i;return e.length>0?(t=Number.MAX_VALUE,i=-Number.MAX_VALUE,e.forEach((function(e){t=Math.min(t,...e.values),i=Math.max(i,...e.values)})),t-=.01,i+=.01):(t=0,i=100),{min:t,max:i}}clickedFeatures(e){const t=e.canvasX,i=e.canvasY;let n=null;for(n of Object.keys(this.clickDetectorCache))if(n=parseInt(n),n>=t)break;if(n){let e=Number.MAX_VALUE,o=[];const a=this.clickDetectorCache[n];for(let n of a){const r=n[0],s=n[2];if(t<r||t>s)return[];const a=n[1],c=n[3];if(i<Math.min(a,c)-10||i>Math.max(a,c)+10)continue;const l=oy(t,i,r,a,s,c);l<e&&(o=[{name:n[4],color:n[5]}],e=l)}if(e<5){if(this.config.clickToHighlight){if(o[0].name in this.config.samplesClickedToHighlight)delete this.config.samplesClickedToHighlight[o[0].name];else if(\"any\"===this.config.clickToHighlight){var r=[\"red\",\"darkblue\",\"green\",\"teal\",\"olivedrab\",\"orange\",\"maroon\",\"purple\",\"blue\",\"gold\"],s=r[Math.floor(Math.random()*(r.length+1))];this.config.samplesClickedToHighlight[o[0].name]=s}else this.config.samplesClickedToHighlight[o[0].name]=this.config.clickToHighlight;this.trackView.repaintViews()}return o}}return[]}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];return t.forEach((function(e){for(let t of Object.keys(e))Oa(e[t])&&i.push({name:t,value:e[t]})})),i}get supportsWholeGenome(){return!1}}function oy(e,t,i,n,r,s){const o=r-i,a=s-n,c=Math.abs(o*(n-t)-(i-e)*a),l=Math.sqrt(o*o+a*a);return l>0?c/l:0}class ay extends Hl{static defaults={height:300,theta:Math.PI/2,arcOrientation:\"UP\"};constructor(e,t){super(e,t),!1===e.arcOrientation?this.arcOrientation=\"DOWN\":!0===e.arcOrientation?this.arcOrientation=\"UP\":e.arcOrientation?this.arcOrientation=e.arcOrientation.toUpperCase():this.arcOrientation=\"UP\",\"bp\"===e.format?this.featureSource=new ly(e,t.genome):this.featureSource=new ud(e,t.genome)}async getFeatures(e,t,i){const n=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,visibilityWindow:n})}draw(e){const t=e.context,i=Math.PI/2,n=e.pixelWidth,r=e.pixelHeight;e.viewportWidth;const s=e.bpPerPixel,o=e.bpStart,a=s,c=\"UP\"===this.arcOrientation;xo.fillRect(t,0,e.pixelTop,n,r,{fillStyle:\"rgb(255, 255, 255)\"});const l=e.features;if(l){cy(l,1);for(let e of l)if(e.startLeft){let n=Math.round((e.startLeft-o)/a),r=Math.round((e.startRight-o)/a),s=Math.round((e.endLeft-o)/a),l=Math.round((e.endRight-o)/a);t.fillStyle=e.color,t.strokeStyle=e.color,t.beginPath();let h=(n+l)/2,d=(l-n)/2,u=this.height,f=Math.PI+(Math.PI/2-i),p=2*Math.PI-(Math.PI/2-i);c?(t.arc(h,u,d,f,p),t.lineTo(s,u)):(u=0,t.arc(h,u,d,p,f),t.lineTo(l,u));const g=(r+s)/2,m=(s-r)/2,w=u;c?(t.arc(g,w,m,p,f,!0),t.lineTo(n,w)):(t.arc(g,w,m,f,p,!0),t.lineTo(s,w)),t.stroke(),t.fill(),e.drawState={x1:h,y1:u,r1:d,x2:g,y2:w,r2:m,sa:f,ea:p}}else{let n=Math.round((e.start-o)/a),r=Math.round((e.end-o)/a);t.strokeStyle=e.color,t.beginPath();let s=(n+r)/2,l=(r-n)/2,h=this.height,d=Math.PI+(Math.PI/2-i),u=2*Math.PI-(Math.PI/2-i);c?t.arc(s,h,l,d,u):(h=0,t.arc(s,h,l,u,d)),t.stroke(),e.drawState={x1:s,y1:h,r1:l,sa:d,ea:u}}}}clickedFeatures(e){const t=super.clickedFeatures(e),i=[];cy(t,-1);for(let n of t){const t=n.drawState,r=e.canvasX-t.x1,s=e.canvasY-t.y1,o=Math.sqrt(r*r+s*s),a=t.r1+3;let c,l;if(void 0===t.x2)c=o,l=t.r1-3;else{const i=e.canvasX-t.x2,n=e.canvasY-t.y2;c=Math.sqrt(i*i+n*n),l=t.r2-3}if(o<a&&c>l){i.push(n);break}}return i}popupData(e,t){if(void 0===t&&(t=this.clickedFeatures(e)),t&&t.length>0)return this.extractPopupData(t[0],this.getGenomeId())}menuItemList(){return[{name:\"Toggle arc direction\",click:function(){this.arcOrientation=\"UP\"===this.arcOrientation?\"DOWN\":\"UP\",this.trackView.repaintViews()}}]}}function cy(e,t){e.sort((function(e,i){const n=void 0===e.score?-Number.MAX_VALUE:e.score,r=void 0===i.score?-Number.MAX_VALUE:i.score;return(void 0===t?1:t)*(n-r)}))}class ly{constructor(e,t){this.config=e,this.genome=t}async getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r}){const s=this.genome;if(this.featureCache)return this.featureCache.queryFeatures(e,t,i);{const n=Ua(this.config),r=await Qs.loadByteArray(this.config.url,n);return this.featureCache=new Zs(function(e){if(!e)return null;const t=mh(e);let i,n=!0;const r=[],s=[],o=[];for(;void 0!==(i=t.nextLine());){const e=i.split(\"\\t\");if(n&&i.startsWith(\"color:\")){const t=\"rgb(\"+e[1]+\",\"+e[2]+\",\"+e[3]+\")\";r.push(t),e.length>4&&s.push(e[4])}else{n=!1;const t=e[0],i=Number.parseInt(e[1])-1,c=Number.parseInt(e[2])-1,l=Number.parseInt(e[3]),h=Number.parseInt(e[4]);var a=Number.parseInt(e[5]);const d=r[a];let u;u=i<=h?{chr:t,startLeft:Math.min(i,c),startRight:Math.max(i,c),endLeft:Math.min(l,h),endRight:Math.max(l,h),color:d,score:a}:{chr:t,startLeft:Math.min(l,h),startRight:Math.max(l,h),endLeft:Math.min(i,c),endRight:Math.max(i,c),color:d,score:a},u.start=u.startLeft,u.end=u.endRight,s.length>a&&(u.description=s[a]),o.push(u)}}return o}(r),s),this.featureCache.queryFeatures(e,t,i)}}}class hy{constructor(e){this.browser=e,this.type=\"ideogram\",this.height=16,this.order=Number.MIN_SAFE_INTEGER,this.disableButtons=!0,this.ignoreTrackMenu=!0}computePixelHeight(e){return this.height}draw({context:e,referenceFrame:t,pixelWidth:i,pixelHeight:n,features:r}){const s=t.chr,o=t.genome.getChromosome(s);if(void 0===o||i<=0||n<=0||\"all\"===s.toLowerCase())return;!function({ctx:e,chr:t,referenceFrame:i,genome:n,width:r,height:s,stainColors:o,features:a}){const c=1,l=.5*c,h=0;if(void 0===n)return;xo.fillRect(e,0,0,r,s,{fillStyle:_s.greyScale(255)});const d=a;if(d){const t=h+s/2,i=[],n=[];if(0===d.length)return;const a=r/d[d.length-1].end;e.beginPath(),xo.roundRect(e,l,l+h,r-2*l,s-2*l,(s-2*l)/2,0,1),e.clip();for(let r=0;r<d.length;r++){const l=d[r],u=a*l.start,f=a*l.end;\"c\"===l.type?(\"p\"===l.name.charAt(0)?(i[0]=u,n[0]=s+h,i[1]=u,n[1]=h,i[2]=f,n[2]=t):(i[0]=f,n[0]=s+h,i[1]=f,n[1]=h,i[2]=u,n[2]=t),e.fillStyle=\"rgb(150, 0, 0)\",e.strokeStyle=\"rgb(150, 0, 0)\",xo.polygon(e,i,n,1,0)):(e.fillStyle=dy(o,l),xo.fillRect(e,u,c+h,f-u,s-2*c))}}e.strokeStyle=_s.greyScale(41),xo.roundRect(e,l,l+h,r-2*l,s-2*l,(s-2*l)/2,0,1)}({ctx:e,features:r,chr:s,referenceFrame:t,genome:t.genome,width:i,height:n,stainColors:[]});const a=Math.round(t.bpPerPixel*i),c=t.start;let l=o.bpLength;const h=t.genome.getCytobands(s);if(h&&h.length>0&&h[h.length-1].end&&(l=Math.max(l,h[h.length-1].end),o.bpLength=l),a<l){const t=a/l,r=c/l;let s=Math.floor(r*i),o=Math.floor(t*i);s=Math.max(0,s),s=Math.min(i-o,s),e.save(),e.strokeStyle=\"red\",e.lineWidth=o<2?1:2;const h=s+e.lineWidth/2;o=o<2?1:o-e.lineWidth;const d=e.lineWidth/2,u=n-e.lineWidth;e.strokeRect(h,d,o,u),e.restore()}}dispose(){this.trackView=void 0}}function dy(e,t){if(\"c\"===t.type)return\"rgb(150, 10, 10)\";var i=t.stain,n=230;\"p\"===t.type&&(n=Math.floor(230-i/100*230));var r=e[n];return r||(r=\"rgb(\"+n+\",\"+n+\",\"+n+\")\",e[n]=r),r}let uy=new oo(\"Dark2\");[\"GT/AG\",\"CT/AC\",\"GC/AG\",\"CT/GC\",\"AT/AC\",\"GT/AT\",\"non-canonical\"].forEach((e=>{uy.getColor(e)}));class fy extends Hl{static defaults={margin:10,colorByNumReadsThreshold:5,height:100};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=e.type||\"junctions\",e._featureSource?(this.featureSource=e._featureSource,delete e._featureSource):this.featureSource=e.featureSource?e.featureSource:Ad(e,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))return this.header&&this.setTrackProperties(this.header),void 0===this.visibilityWindow&&\"function\"==typeof this.featureSource.defaultVisibilityWindow&&(this.visibilityWindow=await this.featureSource.defaultVisibilityWindow()),this}get supportsWholeGenome(){return!1}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}computePixelHeight(e){return this.height}draw(e){const t=e.features,i=e.context,n=e.bpPerPixel,r=e.bpStart,s=e.pixelWidth,o=e.pixelHeight,a=r+s*n+1;if(this.isMergedTrack||xo.fillRect(i,0,e.pixelTop,s,o,{fillStyle:\"rgb(255, 255, 255)\"}),t){const s={};s.referenceFrame=e.viewport.referenceFrame,s.referenceFrameStart=s.referenceFrame.start,s.referenceFrameEnd=s.referenceFrameStart+s.referenceFrame.toBP(e.viewport.getWidth()),s.featureZoomOutTracker={};for(let e of t)if(!(e.end<r)){if(e.start>a)break;this.renderJunction(e,r,n,o,i,s)}}else console.log(\"No feature list\")}renderJunction(e,t,i,n,r,s){e.isVisible=!1;const o=Math.round((e.start-t)/i),a=Math.round((e.end-t)/i),c=(o+a)/2;if(a-o<=3){if(c in s.featureZoomOutTracker)return;s.featureZoomOutTracker[c]=!0}if(this.config.hideAnnotatedJunctions&&\"true\"===e.attributes.annotated_junction)return;if(this.config.hideUnannotatedJunctions&&\"false\"===e.attributes.annotated_junction)return;if(this.config.hideMotifs&&this.config.hideMotifs.includes(e.attributes.motif))return;if(this.config.hideStrand===e.strand)return;if(this.config.minJunctionEndsVisible){let t=0;if(e.start>=s.referenceFrameStart&&e.start<=s.referenceFrameEnd&&(t+=1),e.end>=s.referenceFrameStart&&e.end<=s.referenceFrameEnd&&(t+=1),t<this.config.minJunctionEndsVisible)return}let l,h,d,u;if(e.attributes.uniquely_mapped){if(l=parseInt(e.attributes.uniquely_mapped),l<this.config.minUniquelyMappedReads)return;if(h=parseInt(e.attributes.multi_mapped),d=l+h,d<this.config.minTotalReads)return;if(d>0&&h/d>this.config.maxFractionMultiMappedReads)return;if(e.attributes.maximum_spliced_alignment_overhang&&parseInt(e.attributes.maximum_spliced_alignment_overhang)<this.config.minSplicedAlignmentOverhang)return}if(e.attributes.num_samples_with_this_junction){if(u=parseInt(e.attributes.num_samples_with_this_junction),this.config.minSamplesWithThisJunction&&u<this.config.minSamplesWithThisJunction)return;if(this.config.maxSamplesWithThisJunction&&u>this.config.maxSamplesWithThisJunction)return;if(e.attributes.num_samples_total&&(e.attributes.percent_samples_with_this_junction=100*u/Number(e.attributes.num_samples_total),this.config.minPercentSamplesWithThisJunction&&(e.attributes.percent_samples_with_this_junction<this.config.minPercentSamplesWithThisJunction||e.attributes.percent_samples_with_this_junction>this.config.maxPercentSamplesWithThisJunction)))return}const f=this.margin,p=n,g=f+.5*p;let m=f;const w=f+p-10,b=(o+c)/2,F=(c+a)/2;let v,y,A=1;e.attributes.line_width?A=Number(e.attributes.line_width):(void 0===this.config.thicknessBasedOn||\"numUniqueReads\"===this.config.thicknessBasedOn?A=l:\"numReads\"===this.config.thicknessBasedOn?A=d:\"numSamplesWithThisJunction\"===this.config.thicknessBasedOn&&void 0!==u&&(A=u),A=1+Math.log(A+1)/Math.log(12)),void 0===this.config.bounceHeightBasedOn||\"random\"===this.config.bounceHeightBasedOn?v=(e.start+e.end)%7:\"distance\"===this.config.bounceHeightBasedOn?v=6*(e.end-e.start)/(s.referenceFrameEnd-s.referenceFrameStart):\"thickness\"===this.config.bounceHeightBasedOn&&(v=2*A),m+=p*Math.max(7-v,0)/10,y=e.attributes.color?e.attributes.color:void 0===this.config.colorBy||\"numUniqueReads\"===this.config.colorBy?l>this.config.colorByNumReadsThreshold?\"blue\":\"#AAAAAA\":\"numReads\"===this.config.colorBy?d>this.config.colorByNumReadsThreshold?\"blue\":\"#AAAAAA\":\"isAnnotatedJunction\"===this.config.colorBy?\"true\"===e.attributes.annotated_junction?\"#b0b0ec\":\"orange\":\"strand\"===this.config.colorBy?\"+\"===e.strand?\"#b0b0ec\":\"#ecb0b0\":\"motif\"===this.config.colorBy?uy.getColor(e.attributes.motif):\"#AAAAAA\";let C=\"\";e.attributes.label?C=e.attributes.label.replace(/_/g,\" \"):void 0===this.config.labelWith||\"uniqueReadCount\"===this.config.labelWith?C=l:\"totalReadCount\"===this.config.labelWith?C=d:\"numSamplesWithThisJunction\"===this.config.labelWith?void 0!==u&&(C=u):\"percentSamplesWithThisJunction\"===this.config.labelWith?void 0!==e.attributes.percent_samples_with_this_junction&&(C=e.attributes.percent_samples_with_this_junction.toFixed(0)+\"%\"):\"motif\"===this.config.labelWith&&void 0!==e.attributes.motif&&(C+=e.attributes.motif),\"uniqueReadCount\"===this.config.labelWithInParen?C+=\" (\"+l+\")\":\"totalReadCount\"===this.config.labelWithInParen?C+=\" (\"+d+\")\":\"multiMappedReadCount\"===this.config.labelWithInParen?h>0&&(C+=\" (+\"+h+\")\"):\"numSamplesWithThisJunction\"===this.config.labelWithInParen?void 0!==u&&(C+=\" (\"+u+\")\"):\"percentSamplesWithThisJunction\"===this.config.labelWithInParen?void 0!==e.attributes.percent_samples_with_this_junction&&(C+=\" (\"+e.attributes.percent_samples_with_this_junction.toFixed(0)+\"%)\"):\"motif\"===this.config.labelWithInParen&&void 0!==e.attributes.motif&&(C+=` ${e.attributes.motif}`),e.isVisible=!0,r.beginPath(),r.moveTo(o,w),r.bezierCurveTo(b,m,F,m,a,w),r.lineWidth=A,r.strokeStyle=y,r.stroke();const _=(e,t,i,n)=>{e.beginPath(),e.moveTo(t,i),e.lineTo(t-n/2,i-n),e.lineTo(t+n/2,i-n),e.lineTo(t,i),e.closePath(),e.fill()};if(e.attributes.left_shape||e.attributes.right_shape){r.fillStyle=y;const t=r.lineWidth>2?10:7;e.attributes.left_shape&&_(r,o,w,t),e.attributes.right_shape&&_(r,a,w,t)}r.fillText(C,c-r.measureText(C).width/2,(7*m+g)/8)}clickedFeatures(e){return super.clickedFeatures(e).filter((function(e){return e.isVisible&&e.attributes}))}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=e.genomicLocation,n=[];for(let e of t){const t=\"function\"==typeof e.popupData?e.popupData(i):this.extractPopupData(e._f||e,this.getGenomeId());t&&(n.length>0&&n.push(\"<hr/><hr/>\"),Array.prototype.push.apply(n,t))}return n}dispose(){this.trackView=void 0}}const py={min:0,max:3e3,color:\"rgb(0,0,255)\"};class gy{constructor(e){e=e||py,this.max=e.max,this.min=e.min||0,this.cache=[],this.nbins=1e3,this.binsize=(this.max-this.min)/this.nbins,this.updateColor(e.color||\"rgb(0,0,255)\")}updateColor(e){const t=e.substring(4).replace(\")\",\"\").split(\",\");3===t.length&&(this.r=Number.parseInt(t[0].trim()),this.g=Number.parseInt(t[1].trim()),this.b=Number.parseInt(t[2].trim())),this.cache=[]}setMinMax(e,t){this.min=e,this.max=t,this.cache=[],this.binsize=(this.max-this.min)/this.nbins}getColor(e){if(e<this.min)return\"white\";const t=Math.floor((Math.min(this.max,e)-this.min)/this.binsize);if(void 0===this.cache[t]){const i=(ys.clamp(e,0,this.max)-0)/(this.max-0);this.cache[t]=`rgba(${this.r},${this.g},${this.b}, ${i})`}return this.cache[t]}toJson(){return{min:this.min,max:this.max,color:`rgb(${this.r},${this.g},${this.b})`}}static parse(e){const t=e.split(\",\"),i={min:Number.parseFloat(t[0]),max:Number.parseFloat(t[1]),color:`${t[2]},${t[3]},${t[4]}`};return new gy(i)}}class my extends Hl{static defaults={height:300,rowHeight:3,max:3e3,visibilityWindow:1e4};constructor(e,t){super(e,t)}init(e){super.init(e),this.type=\"shoebox\",this.height=e.height||300,this.rowHeight=e.rowHeight||3,this.max=e.max||3e3,this.sampleKeys=[];for(let e=1;e<=100;e++)this.sampleKeys.push(e);const t=Object.assign({},this.config);t.format=\"shoebox\",this.featureSource=Ad(t,this.browser.genome)}async postInit(){if(\"function\"!=typeof this.featureSource.getHeader||(this.header=await this.featureSource.getHeader(),!this.disposed))if(this.header&&this.setTrackProperties(this.header),this.config.colorScale&&this.config.colorScale.max&&this.config.colorScale.color)this.colorScale=new gy(this.config.colorScale);else{const e=this.dataRange.min,t=this.dataRange.max;this.colorScale=new gy({min:e,max:t,color:this.color})}}get color(){return this._color||\"rgb(0,0,255)\"}set color(e){this._color=e,this.colorScale&&this.colorScale.updateColor(e)}menuItemList(){const e=[];e.push(\"<hr/>\");let t=Bt(\"<div>\");return t.text(\"Set data range\"),e.push({object:t,dialog:function(){this.trackView.track.selected?this.browser.dataRangeDialog.configure(this.trackView.browser.getSelectedTrackViews()):this.browser.dataRangeDialog.configure(this.trackView),this.browser.dataRangeDialog.present(Bt(this.browser.columnContainer))}}),e}setDataRange({min:e,max:t}){this.dataRange.min=e,this.dataRange.max=t,this.colorScale.min=e,this.colorScale.max=t,this.trackView.repaintViews()}hasSamples(){return!0}getSamples(){return{names:this.sampleKeys,height:this.rowHeight,yOffset:0}}async getFeatures(e,t,i,n){const r=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:t,end:i,bpPerPixel:n,visibilityWindow:r})}draw({context:e,pixelTop:t,pixelWidth:i,pixelHeight:n,features:r,bpPerPixel:s,bpStart:o}){if(xo.fillRect(e,0,t,i,n,{fillStyle:\"rgb(255, 255, 255)\"}),r&&r.length>0){const a=this.rowHeight,c=t+n,l=o+i*s+1,h=a;for(let i of r){if(i.end<o||i.start>l)continue;const n=Math.round((i.start-o)/s),r=Math.round((i.end-o)/s),d=Math.max(1,r-n);let u=0;for(let r=i.values.length-1;r>=0;r--){const s=i.values[r],o=u*a;if(o+a<t||o>c)continue;const l=this.colorScale.getColor(s);e.fillStyle=l,e.fillRect(n,o,d,h),u++}}}}computePixelHeight(e){return e&&0!==e.length?e[0].values.length*this.rowHeight:0}clickedFeatures(e){const t=super.clickedFeatures(e),i=e.y;return t.filter((function(e){const t=e.pixelRect;return t&&i>=t.y&&i<=t.y+t.h}))}hoverText(e){const t=this.clickedFeatures(e);if(t&&t.length>0)return`${t[0].sample}: ${t[0].value}`}popupData(e,t){void 0===t&&(t=this.clickedFeatures(e));const i=[];for(let e of t){i.length>0&&(i.push(\"<hr/>\"),i.push(\"<hr/>\"));const t=e._f||e,n=\"function\"==typeof t.popupData?t.popupData(this.type,this.browser.genome.id):this.extractPopupData(t);Array.prototype.push.apply(i,n)}return i}get supportsWholeGenome(){return!1}getState(){const e=super.getState();return e.colorScale=this.colorScale.toJson(),e}}const wy=new Map([[\"ideogram\",(e,t)=>new hy(e,t)],[\"sequence\",(e,t)=>new Zd(e,t)],[\"feature\",(e,t)=>new Hd(e,t)],[\"seg\",(e,t)=>new Pf(e,t)],[\"mut\",(e,t)=>new Pf(e,t)],[\"maf\",(e,t)=>new Pf(e,t)],[\"shoebox\",(e,t)=>new my(e,t)],[\"wig\",(e,t)=>new ld(e,t)],[\"merged\",(e,t)=>new tf(e,t)],[\"alignment\",(e,t)=>new tw(e,t)],[\"interaction\",(e,t)=>new iw(e,t)],[\"interact\",(e,t)=>new iw(e,t)],[\"variant\",(e,t)=>new Yv(e,t)],[\"qtl\",(e,t)=>new ty(e,t)],[\"eqtl\",(e,t)=>new ty(e,t)],[\"gwas\",(e,t)=>new ry(e,t)],[\"arc\",(e,t)=>new ay(e,t)],[\"gcnv\",(e,t)=>new sy(e,t)],[\"junction\",(e,t)=>new fy(e,t)],[\"blat\",(e,t)=>new Vd(e,t)],[\"cnvpytor\",(e,t)=>new Gv(e,t)]]);class by{constructor(e,t){const i=(new DOMParser).parseFromString(e,\"text/xml\");this.processRootNode(i,t);const n=i.getElementsByTagName(\"Resource\"),r=i.getElementsByTagName(\"Track\"),s=r&&r.length>0,o=[];this.tracks=o;const a=new Map;Array.from(n).forEach((function(e,t){var i={url:e.getAttribute(\"path\"),indexURL:e.getAttribute(\"index\"),order:t};a.set(i.url,i),s||o.push(i)})),s&&Array.from(r).forEach((function(e){const t=e.getElementsByTagName(\"Track\");if(t&&t.length>0){const i={type:\"merged\",tracks:[]};Fy(e,i),o.push(i),Array.from(t).forEach((function(e){e.processed=!0;const t=e.getAttribute(\"id\"),n=a.get(t);n&&(i.tracks.push(n),Fy(e,n),n.autoscale=!1,i.height=n.height)}))}else if(!e.processed){const t=e.getAttribute(\"id\"),i=a.get(t);i&&(o.push(i),Fy(e,i))}}))}processRootNode(e,t){const i=e.getElementsByTagName(\"Session\");!i||i.length;const n=i.item(0),r=n.getAttribute(\"genome\"),s=n.getAttribute(\"locus\"),o=n.getAttribute(\"ucscID\");t&&t.hasOwnProperty(r)?this.genome=r:(this.reference={fastaURL:r},o&&(this.reference.id=o)),s&&(this.locus=s)}}function Fy(e,t){t.name=e.getAttribute(\"name\");const i=e.getAttribute(\"color\");i&&(t.color=\"rgb(\"+i+\")\");const n=e.getAttribute(\"altColor\");i&&(t.altColor=\"rgb(\"+n+\")\");const r=e.getAttribute(\"height\");r&&(t.height=parseInt(r));const s=e.getAttribute(\"autoScale\");s&&(t.autoscale=\"true\"===s);const o=e.getAttribute(\"autoscaleGroup\");o&&(t.autoscaleGroup=o);const a=e.getAttribute(\"windowFunction\");a&&(t.windowFunction=a);const c=e.getAttribute(\"visibilityWindow\")||e.getAttribute(\"featureVisibilityWindow\");c&&(t.visibilityWindow=c);const l=e.getAttribute(\"indexed\");l&&(t.indexed=\"true\"===l);const h=e.getAttribute(\"normalize\");h&&(t.normalize=\"true\"===h);const d=e.getElementsByTagName(\"DataRange\");if(d.length>0){const e=d.item(0);t.min=Number(e.getAttribute(\"minimum\")),t.max=Number(e.getAttribute(\"maximum\")),t.logScale=\"LOG\"===e.getAttribute(\"type\")}}class vy{constructor(e,t,i,n,r){this.genome=e,this.chr=t,this.start=i,this.end=n,this.bpPerPixel=r,this.id=s()}get center(){return(this.start+this.end)/2}get locusSearchString(){return`${this.chr}:${this.start+1}-${this.end}`}extend(e){const t=Math.min(e.start,this.start),i=Math.max(e.end,this.end),n=(i-t)/(this.end-this.start);this.start=t,this.end=i,this.bpPerPixel*=n}calculateEnd(e){return this.start+this.bpPerPixel*e}calculateCenter(e){return this.start+this.bpPerPixel*e/2}calculateBPP(e,t){return(e-this.start)/t}set(e){this.chr=e.chr,this.start=e.start,this.bpPerPixel=e.bpPerPixel}toPixels(e){return e/this.bpPerPixel}toBP(e){return this.bpPerPixel*e}shift(e){this.start+=e,this.end+=e}shiftPixels(e,t,i){const n=this.start,r=e*this.bpPerPixel;return this.start+=r,i&&this.clampStart(t),this.end=this.start+t*this.bpPerPixel,n!==this.start}clampStart(e){const t=this.genome.getChromosome(this.chr).bpStart||0;if(this.start=Math.max(t,this.start),e){const{bpLength:t}=this.genome.getChromosome(this.chr),i=t-e*this.bpPerPixel;this.start>i&&(this.start=i)}}async zoomWithScaleFactor(e,t,i,n){const r=void 0===n?this.start+this.toBP(i/2):n,s=this.start,o=this.bpPerPixel,a=this.getChromosome().bpLength,c=t<1?e.minimumBases()/i:a/i;this.bpPerPixel=t<1?Math.max(this.bpPerPixel*t,c):Math.min(this.bpPerPixel*t,c);const l=this.bpPerPixel*i;this.start=r-.5*l,this.clampStart(i),this.end=this.start+l;(s!==this.start||o!==this.bpPerPixel)&&await e.updateViews(!0)}getChromosome(){return this.genome.getChromosome(this.chr)}getMultiLocusLabelBPLengthOnly(e){const t=\"&nbsp\",i=Math.floor(this.start)+1,n=Math.round(this.start+this.bpPerPixel*e);return`${t}${this.chr}${t}${Wa(n-i)}${t}`}getMultiLocusLabelLocusOnly(e){const t=\"&nbsp\",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(e);return`${t}${i}:${n}-${r}${t}`}getMultiLocusLabel(e){const t=\"&nbsp\",{chr:i,start:n,end:r}=this.getPresentationLocusComponents(e),s=Math.floor(this.start)+1;return`${t}${i}:${n}-${r}${t}${t}(${Wa(Math.round(this.start+this.bpPerPixel*e)-s)})${t}`}getPresentationLocusComponents(e){if(\"all\"===this.chr)return{chr:this.chr};{const t=Rt(Math.floor(this.start)+1),i=Rt(Math.round(this.start+this.bpPerPixel*e));return{chr:this.chr,start:t,end:i}}}getLocusString(){if(\"all\"===this.chr)return\"all\";return`${this.genome.getChromosomeDisplayName(this.chr)}:${Rt(Math.floor(this.start)+1)}-${Rt(Math.round(this.end))}`}description(e){console.log(` ${e||\"\"} referenceFrame - ${this.chr} bpp ${this.bpPerPixel.toFixed(3)} start ${Rt(Math.round(this.start))} end ${Rt(Math.round(this.end))} `)}overlaps(e){return this.chr===e.chr&&this.end>=e.start&&e.end>=this.start}}function yy(){return\"3.0.9\"}const Ay=\"Maximum sequence count exceeded\";class Cy{constructor(t,i){this.container=e({class:\"igv-chromosome-select-widget-container\"}),i.appendChild(this.container),this.select=document.createElement(\"select\"),this.select.setAttribute(\"name\",\"chromosome-select-widget\"),this.container.appendChild(this.select),this.select.addEventListener(\"change\",(()=>{this.select.blur(),\"\"!==this.select.value&&Ay!==this.select.value&&t.search(this.select.value)})),this.showAllChromosomes=!1!==t.config.showAllChromosomes,this.genome=t.genome}show(){this.container.style.display=\"flex\"}hide(){this.container.style.display=\"none\"}setValue(e){this.select.value=this.genome.getChromosomeDisplayName(e)}update(e){this.genome=e;const t=e.wgChromosomeNames.map((t=>e.getChromosomeDisplayName(t)))||[];if(this.showAllChromosomes&&e.chromosomeNames.length>1){const i=new Set(t);let n=0;for(let r of e.chromosomeNames){if(1e3==++n){t.push(Ay);break}i.has(r)||(r=e.getChromosomeDisplayName(r),t.push(r))}}this.select.innerHTML=\"\",e.showWholeGenomeView()&&t.unshift(\"all\");for(let i of t){const t=document.createElement(\"option\");t.setAttribute(\"value\",i),t.innerText=e.getChromosomeDisplayName(i),this.select.appendChild(t)}}}class _y{constructor(t,i){this.container=e({class:\"igv-windowsize-panel-container\"}),t.appendChild(this.container),i.on(\"locuschange\",(e=>{this.updatePanel(e)})),this.browser=i}show(){this.container.style.display=\"block\"}hide(){this.container.style.display=\"none\"}updatePanel(e){const t=this.browser.calculateViewportWidth(this.browser.referenceFrameList.length);this.container.innerText=1===e.length?Wa(Math.round(t*e[0].bpPerPixel)):\"\"}}class xy extends Ju{constructor(e,t,i,n){super(e,t,\"Select Tracks\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>multi select</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"multi-select\">\\n            <rect id=\"backdrop-copy-3\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-copy-3\" transform=\"translate(81, 427)\" fill=\"#737373\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy-2\" transform=\"translate(82, 277)\">\\n                <rect id=\"Rectangle\" fill-opacity=\"0.33\" fill=\"#CFCECE\" x=\"133\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke-opacity=\"0.32659528\" stroke=\"#CFCECE\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy\" transform=\"translate(81, 119)\" fill=\"#737373\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-17\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>multi select hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"multi-select-hover\">\\n            <rect id=\"backdrop-copy-4\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-copy-3\" transform=\"translate(81, 427)\" fill=\"#FFFFFF\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke=\"#FFFFFF\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy-2\" transform=\"translate(82, 277)\">\\n                <rect id=\"Rectangle\" fill-opacity=\"0.33\" fill=\"#CFCECE\" x=\"133\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-16\" stroke-opacity=\"0.33\" stroke=\"#CFCECE\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n            <g id=\"row-copy\" transform=\"translate(81, 119)\" fill=\"#FFFFFF\">\\n                <rect id=\"Rectangle\" x=\"134\" y=\"0\" width=\"329\" height=\"70\"></rect>\\n                <rect id=\"Rectangle-Copy-17\" stroke=\"#FFFFFF\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"58\" height=\"58\"></rect>\\n            </g>\\n        </g>\\n    </g>\\n</svg>',!1),this.navbar=i,this.enableMultiTrackSelection=!1,this.button.addEventListener(\"mouseenter\",(e=>{!1===n&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(e=>{!1===n&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{this.setMultiTrackSelection(!this.enableMultiTrackSelection)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler)}setMultiTrackSelection(e){this.enableMultiTrackSelection=e,this.setState(this.enableMultiTrackSelection),!1===this.enableMultiTrackSelection&&this.navbar.overlayTrackButton.setVisibility(!1);for(const t of this.browser.trackViews)t.enableTrackSelection(e)}}class ky{constructor(t,i){this.browser=i,this.columnContainer=t,this.horizontalGuide=e({class:\"igv-cursor-guide-horizontal\"}),t.appendChild(this.horizontalGuide),this.verticalGuide=e({class:\"igv-cursor-guide-vertical\"}),t.appendChild(this.verticalGuide),this.addMouseHandler(i),this.setVisibility(i.config.showCursorGuide)}addMouseHandler(e){this.boundMouseMoveHandler=function(t){t.target.tagName;const{x:i,y:n}=a(t,this.columnContainer);if(this.horizontalGuide.style.top=`${n}px`,\"CANVAS\"===t.target.tagName){const n=function(e,t){for(;e.parentElement;){if(e.parentElement.classList.contains(t))return e.parentElement;e=e.parentElement}return}(t.target,\"igv-viewport\");if(n&&e.getRulerTrackView()){this.verticalGuide.style.left=`${i}px`;const r=e.root.querySelectorAll(\".igv-column\");let s;const o=n.parentElement;for(let e=0;e<r.length;e++)void 0===s&&o===r[e]&&(s=e);if(void 0!==s){const i=e.getRulerTrackView().viewports[s].mouseMove(t);if(i){const{start:e,bp:t,end:n}=i,r=(t-e)/(n-e);this.customMouseHandler&&this.customMouseHandler({start:e,bp:t,end:n,interpolant:r})}}}}}.bind(this),this.columnContainer.addEventListener(\"mousemove\",this.boundMouseMoveHandler)}removeMouseHandler(){this.columnContainer.removeEventListener(\"mousemove\",this.boundMouseMoveHandler)}setVisibility(e){!0===e?this.show():this.hide()}show(){this.verticalGuide.style.display=\"block\",this.horizontalGuide.style.display=\"block\"}hide(){if(this.verticalGuide.style.display=\"none\",this.horizontalGuide.style.display=\"none\",this.browser.getRulerTrackView())for(let e of this.browser.getRulerTrackView().viewports)e.$tooltip.hide()}}class Iy extends Ju{constructor(e,t){super(e,t,\"Crosshairs\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>cursor</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"cursor\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-3\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group\" transform=\"translate(5, 9)\" stroke-width=\"24\">\\n                <line x1=\"0.5\" y1=\"212.5\" x2=\"614.5\" y2=\"212.5\" id=\"Line\"></line>\\n                <line x1=\"-115.5\" y1=\"303.5\" x2=\"490.5\" y2=\"303.5\" id=\"Line-Copy\" transform=\"translate(187.5, 303.5) scale(-1, 1) rotate(90) translate(-187.5, -303.5)\"></line>\\n            </g>\\n            <circle id=\"Oval\" stroke-width=\"24\" cx=\"191.5\" cy=\"221.5\" r=\"88.5\"></circle>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>cursor hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"cursor-hover\">\\n            <rect id=\"Rectangle-Copy-5\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group-Copy-2\" transform=\"translate(5, 9)\" stroke=\"#FFFFFF\" stroke-width=\"24\">\\n                <line x1=\"0.5\" y1=\"212.5\" x2=\"614.5\" y2=\"212.5\" id=\"Line\"></line>\\n                <line x1=\"-115.5\" y1=\"303.5\" x2=\"490.5\" y2=\"303.5\" id=\"Line-Copy\" transform=\"translate(187.5, 303.5) scale(-1, 1) rotate(90) translate(-187.5, -303.5)\"></line>\\n            </g>\\n            <circle id=\"Oval\" stroke=\"#FFFFFF\" stroke-width=\"24\" cx=\"191.5\" cy=\"221.5\" r=\"88.5\"></circle>\\n        </g>\\n    </g>\\n</svg>',t.doShowCursorGuide),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowCursorGuide&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowCursorGuide&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowCursorGuide=!t.doShowCursorGuide,t.setCursorGuideVisibility(t.doShowCursorGuide),this.setState(t.doShowCursorGuide)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showCursorTrackingGuideButton)}}class Sy extends Ju{constructor(e,t){super(e,t,\"Center Line\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>centerline</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"centerline\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-2\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"6.5\" y1=\"312.5\" x2=\"618.5\" y2=\"312.5\" id=\"Line-Copy\" stroke-width=\"31\" transform=\"translate(312.5, 312.5) scale(-1, 1) rotate(90) translate(-312.5, -312.5)\"></line>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>centerline hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"centerline-hover\">\\n            <rect id=\"Rectangle-Copy-9\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"6.5\" y1=\"312.5\" x2=\"618.5\" y2=\"312.5\" id=\"Line-Copy\" stroke=\"#FFFFFF\" stroke-width=\"31\" transform=\"translate(312.5, 312.5) scale(-1, 1) rotate(90) translate(-312.5, -312.5)\"></line>\\n        </g>\\n    </g>\\n</svg>',t.config.showCenterGuide),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowCenterLine&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowCenterLine&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowCenterLine=!t.doShowCenterLine,t.setCenterLineVisibility(t.doShowCenterLine),this.setState(t.doShowCenterLine)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showCenterGuideButton)}}class Ey extends Ju{constructor(e,t){super(e,t,\"Track Labels\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>track labels</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"track-labels\" fill=\"#FFFFFF\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-27\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"group\" transform=\"translate(52.2778, 149.7248)\" stroke-width=\"24\">\\n                <path d=\"M448.444444,87.1189616 L448.444444,322.431462 L166.619398,322.431462 L19.2344421,204.775212 L166.619398,87.1189616 L448.444444,87.1189616 Z M244.028212,163.997434 C232.925565,163.997434 222.874656,168.493347 215.598982,175.760254 C208.318067,183.032394 203.815972,193.079106 203.815972,204.175675 C203.815972,215.272243 208.318067,225.318955 215.598982,232.591095 C222.874656,239.858002 232.925565,244.353915 244.028212,244.353915 C255.130858,244.353915 265.181767,239.858002 272.457442,232.591095 C279.738356,225.318955 284.240451,215.272243 284.240451,204.175675 C284.240451,193.079106 279.738356,183.032394 272.457442,175.760254 C265.181767,168.493347 255.130858,163.997434 244.028212,163.997434 Z\" id=\"backdrop\"></path>\\n                <path d=\"M495.232604,12 L495.232604,264.550423 L193.616935,264.550423 L35.4455183,138.275212 L193.616935,12 L495.232604,12 Z M168.133512,95.1660194 C156.441871,95.1660194 145.858581,99.8943121 138.197214,107.534302 C130.523695,115.18641 125.780417,125.758499 125.780417,137.434423 C125.780417,149.110347 130.523695,159.682435 138.197214,167.334543 C145.858581,174.974533 156.441871,179.702826 168.133512,179.702826 C179.825153,179.702826 190.408443,174.974533 198.06981,167.334543 C205.743329,159.682435 210.486607,149.110347 210.486607,137.434423 C210.486607,125.758499 205.743329,115.18641 198.06981,107.534302 C190.408443,99.8943121 179.825153,95.1660194 168.133512,95.1660194 Z\" id=\"hero\"></path>\\n            </g>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>track labels hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"track-labels-hover\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-29\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"group\" transform=\"translate(52.2778, 149.7248)\" fill=\"#FFFFFF\" stroke-width=\"24\">\\n                <path d=\"M448.444444,85.1189616 L448.444444,320.431462 L166.619398,320.431462 L19.2344421,202.775212 L166.619398,85.1189616 L448.444444,85.1189616 Z M244.028212,161.997434 C232.925565,161.997434 222.874656,166.493347 215.598982,173.760254 C208.318067,181.032394 203.815972,191.079106 203.815972,202.175675 C203.815972,213.272243 208.318067,223.318955 215.598982,230.591095 C222.874656,237.858002 232.925565,242.353915 244.028212,242.353915 C255.130858,242.353915 265.181767,237.858002 272.457442,230.591095 C279.738356,223.318955 284.240451,213.272243 284.240451,202.175675 C284.240451,191.079106 279.738356,181.032394 272.457442,173.760254 C265.181767,166.493347 255.130858,161.997434 244.028212,161.997434 Z\" id=\"backdrop\"></path>\\n                <path d=\"M495.232604,12 L495.232604,264.550423 L193.616935,264.550423 L35.4455183,138.275212 L193.616935,12 L495.232604,12 Z M168.133512,95.1660194 C156.441871,95.1660194 145.858581,99.8943121 138.197214,107.534302 C130.523695,115.18641 125.780417,125.758499 125.780417,137.434423 C125.780417,149.110347 130.523695,159.682435 138.197214,167.334543 C145.858581,174.974533 156.441871,179.702826 168.133512,179.702826 C179.825153,179.702826 190.408443,174.974533 198.06981,167.334543 C205.743329,159.682435 210.486607,149.110347 210.486607,137.434423 C210.486607,125.758499 205.743329,115.18641 198.06981,107.534302 C190.408443,99.8943121 179.825153,95.1660194 168.133512,95.1660194 Z\" id=\"hero\"></path>\\n            </g>\\n        </g>\\n    </g>\\n</svg>',t.config.showTrackLabels),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowTrackLabels&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowTrackLabels&&this.setState(!1)}));this.boundMouseClickHandler=(()=>{t.doShowTrackLabels=!t.doShowTrackLabels,t.setTrackLabelVisibility(t.doShowTrackLabels),this.setState(t.doShowTrackLabels)}).bind(this),this.button.addEventListener(\"click\",this.boundMouseClickHandler),this.setVisibility(t.config.showTrackLabelButton)}}class Ny extends Ju{constructor(e,t){super(e,t,[\"ROI\",\"Regions of Interest Table\"],ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>roi</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"roi\">\\n            <rect id=\"Rectangle-Copy-23\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <text id=\"ROI\" font-family=\"HelveticaNeue-Bold, Helvetica Neue\" font-size=\"258\" font-weight=\"bold\" fill=\"#737373\">\\n                <tspan x=\"81.445\" y=\"389\">ROI</tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>roi hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"roi-hover\">\\n            <rect id=\"Rectangle-Copy-24\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <text id=\"ROI\" font-family=\"HelveticaNeue-Bold, Helvetica Neue\" font-size=\"258\" font-weight=\"bold\" fill=\"#FFFFFF\">\\n                <tspan x=\"81.445\" y=\"389\">ROI</tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>',!1),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.doShowROITable&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.doShowROITable&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>this.buttonHandler(!t.doShowROITable))),this.setVisibility(!1)}buttonHandler(e){this.setState(e),this.browser.setROITableVisibility(e)}}class By extends Ju{constructor(e,t){super(e,t,\"Sample Info\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample info</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-info\">\\n            <rect id=\"Rectangle-Copy-6\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"Group-2\" transform=\"translate(8, 149)\">\\n                <rect id=\"Rectangle\" fill=\"#8DD3C7\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#FBB4AE\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#7FC97F\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#E41A1C\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#3F70AE\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"Group-2-Copy\" transform=\"translate(8, 251)\">\\n                <rect id=\"Rectangle\" fill=\"#E41A1C\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BC80BD\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#FFFFB3\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"Group-2-Copy-2\" transform=\"translate(314, 404) scale(-1, 1) translate(-314, -404)translate(8, 353)\">\\n                <rect id=\"Rectangle\" fill=\"#1B9E77\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BAD1E9\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#4DAF4A\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#CBF03E\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <rect id=\"Rectangle-Copy-10\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample info hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-info-hover\">\\n            <rect id=\"Rectangle-Copy-14\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"row-2\" transform=\"translate(314, 404) scale(-1, 1) translate(-314, -404)translate(8, 353)\">\\n                <rect id=\"Rectangle\" fill=\"#1B9E77\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BAD1E9\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#4DAF4A\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#CBF03E\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"row-1\" transform=\"translate(8, 251)\">\\n                <rect id=\"Rectangle\" fill=\"#E41A1C\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#377EB8\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#FDB46B\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#BC80BD\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#FFFFB3\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <g id=\"row-0\" transform=\"translate(8, 149)\">\\n                <rect id=\"Rectangle\" fill=\"#8DD3C7\" x=\"0\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy\" fill=\"#FBB4AE\" x=\"102\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-8\" fill=\"#7FC97F\" x=\"204\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#ADE2CF\" x=\"306\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#E41A1C\" x=\"408\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n                <rect id=\"Rectangle-Copy-7\" fill=\"#3F70AE\" x=\"510\" y=\"0\" width=\"102\" height=\"102\"></rect>\\n            </g>\\n            <rect id=\"Rectangle-Copy-15\" stroke=\"#737373\" stroke-width=\"12\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <rect id=\"scrim\" fill=\"#000000\" style=\"mix-blend-mode: hue;\" x=\"8\" y=\"149\" width=\"612\" height=\"306\"></rect>\\n        </g>\\n    </g>\\n</svg>',!1),this.showSampleInfo=!1,this.button.addEventListener(\"mouseenter\",(()=>{!1===this.showSampleInfo&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===this.showSampleInfo&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>{this.performClickWithState(t,void 0)}))}performClickWithState(e,t){this.showSampleInfo=void 0===t?!this.showSampleInfo:t;e.columnContainer.querySelector(\".igv-sample-info-column\").style.display=!1===this.showSampleInfo?\"none\":\"flex\",this.setState(this.showSampleInfo),e.layoutChange()}setButtonVisibility(e){this.showSampleInfo=e,this.setState(this.showSampleInfo),!0===this.showSampleInfo?this.show():this.hide()}}class My extends Ju{constructor(e,t){super(e,t,\"Sample Names\",'<svg width=\"90px\" height=\"20px\" viewBox=\"0 0 90 20\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"igv-navbar-button-group\">\\n            <rect id=\"Rectangle\" x=\"0.5\" y=\"0.5\" width=\"89\" height=\"18\" rx=\"6\"></rect>\\n            <text id=\"igv-text-button-label\" x=\"50%\" y=\"50%\" dy=\".1em\" font-family=\"Helvetica\" font-size=\"12\" font-weight=\"normal\" letter-spacing=\"-0.372\">\\n                <tspan id=\"igv-navbar-button-label\"></tspan>\\n            </text>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample names</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-names\" stroke=\"#737373\">\\n            <rect id=\"Rectangle-Copy-13\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"80\" y1=\"465\" x2=\"541\" y2=\"464.5\" id=\"Line-3-Copy-3\" stroke-width=\"32\"></line>\\n            <line x1=\"80\" y1=\"312.5\" x2=\"542\" y2=\"313\" id=\"Line-3\" stroke-width=\"32\"></line>\\n            <line x1=\"80\" y1=\"158\" x2=\"541\" y2=\"158\" id=\"Line-3-Copy\" stroke-width=\"32\"></line>\\n        </g>\\n    </g>\\n</svg>','<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>sample names hover</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"sample-names-hover\">\\n            <rect id=\"Rectangle-Copy-18\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#737373\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <line x1=\"80\" y1=\"465\" x2=\"541\" y2=\"464.5\" id=\"Line-3-Copy-3\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n            <line x1=\"80\" y1=\"312.5\" x2=\"542\" y2=\"313\" id=\"Line-3\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n            <line x1=\"80\" y1=\"158\" x2=\"541\" y2=\"158\" id=\"Line-3-Copy\" stroke=\"#FFFFFF\" stroke-width=\"32\" fill=\"#FFFFFF\"></line>\\n        </g>\\n    </g>\\n</svg>',t.config.showSampleNames),this.button.addEventListener(\"mouseenter\",(()=>{!1===t.showSampleNames&&this.setState(!0)})),this.button.addEventListener(\"mouseleave\",(()=>{!1===t.showSampleNames&&this.setState(!1)})),this.button.addEventListener(\"click\",(()=>{this.performClickWithState(t,void 0)})),!0===t.config.showSampleNameButton?this.show():this.hide()}performClickWithState(e,t){e.showSampleNames=void 0===t?!e.showSampleNames:t;e.columnContainer.querySelector(\".igv-sample-name-column\").style.display=!1===e.showSampleNames?\"none\":\"flex\",this.setState(e.showSampleNames),e.layoutChange()}}class Ry{constructor(t,i){this.parent=t,this.popover=e({class:\"igv-ui-dropdown\"}),t.appendChild(this.popover),this.popoverContent=e(),this.popover.appendChild(this.popoverContent),this.popover.style.display=\"none\",this.shim=i}configure(e){if(0===e.length)return;const t=nc(e,this.popover);for(const{object:e}of t)this.popoverContent.appendChild(e)}present(e){this.popover.style.display=\"block\";let{x:t,y:i}=a(e,this.parent);this.popover.style.left=`${t+this.shim.left}px`,this.popover.style.top=`${i+this.shim.top}px`}_present(e){this.popover.style.display=\"block\";let{x:t,y:i,width:n}=a(e,this.parent);t+=this.shim.left,i+=this.shim.top,this.popover.style.top=`${i}px`;const{width:r}=this.popover.getBoundingClientRect(),s=t+r,o=s-n;this.popover.style.left=`${s>n?t-o:t}px`}dismiss(){this.popover.style.display=\"none\"}}class Dy extends Ju{constructor(e,t){super(e,t,\"Save Image\",ef,'<svg width=\"625px\" height=\"625px\" viewBox=\"0 0 625 625\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\\n    <title>save image</title>\\n    <g id=\"Page-1\" stroke=\"none\" stroke-width=\"1\" fill=\"none\" fill-rule=\"evenodd\">\\n        <g id=\"save-image\">\\n            <rect id=\"border\" stroke=\"#737373\" stroke-width=\"12\" fill=\"#FFFFFF\" x=\"6\" y=\"6\" width=\"613\" height=\"613\" rx=\"135\"></rect>\\n            <g id=\"frame\" transform=\"translate(66, 66)\" fill=\"#737373\" fill-rule=\"nonzero\">\\n                <path d=\"M54.75,493 C39.69375,493 26.8046875,487.639062 16.0828125,476.917187 C5.3609375,466.195312 0,453.30625 0,438.25 L0,274 L54.75,274 L54.75,438.25 L219,438.25 L219,493 L54.75,493 Z\" id=\"Path\"></path>\\n                <path d=\"M274,493 L274,438.25 L438.25,438.25 L438.25,274 L493,274 L493,438.25 C493,453.30625 487.639062,466.195312 476.917187,476.917187 C466.195312,487.639062 453.30625,493 438.25,493 L274,493 Z\" id=\"Path\"></path>\\n                <path d=\"M0,219 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Hy(t,i,u.get(0)),!1===t.showNavigation&&this.$navigation.hide()}navbarDidResize(){const e=this.$navigation.width(),t=this.currentNavbarButtonClass();\"igv-navbar-text-button\"===t&&(this.textButtonContainerWidth=this.navbarRightContainer.getBoundingClientRect().width);const i=this.browser,n=i.isMultiLocusWholeGenomeView()||i.referenceFrameList&&mu.isWholeGenomeView(i.referenceFrameList[0].chr);n?this.windowSizePanel.hide():this.windowSizePanel.show();const{x:r,width:s}=this.navbarLeftContainer.getBoundingClientRect(),o=r+s,{x:a}=this.navbarRightContainer.getBoundingClientRect();let c;if(\"igv-navbar-text-button\"===t&&a-o<8)c=\"igv-navbar-icon-button\";else if(this.textButtonContainerWidth&&\"igv-navbar-icon-button\"===t){e-o-this.textButtonContainerWidth>8&&(c=\"igv-navbar-text-button\")}let l;c&&t!==c&&(this.currentClass=c,this.browser.fireEvent(\"navbar-resize\",[c])),l=n?\"igv-zoom-widget-hidden\":e>860?\"igv-zoom-widget\":\"igv-zoom-widget-900\",Bt(this.zoomWidget.zoomContainer).removeClass(),Bt(this.zoomWidget.zoomContainer).addClass(l)}setCenterLineButtonVisibility(e){e?this.centerLineButton.setVisibility(!e):this.centerLineButton.setVisibility(this.config.showCenterGuideButton)}setCursorGuideVisibility(e){e?this.cursorGuide.show():this.cursorGuide.hide()}updateGenome(e){let t=e.id&&e.id.length<20?e.id:`${e.id.substring(0,8)}...${e.id.substring(e.id.length-8)}`;this.$current_genome.text(t),this.$current_genome.attr(\"title\",e.description);!1!==this.config.showChromosomeWidget&&!1!==e.showChromosomeWidget&&e.chromosomeNames&&e.chromosomeNames.length>1?(this.chromosomeSelectWidget.update(e),this.chromosomeSelectWidget.show()):this.chromosomeSelectWidget.hide()}updateLocus(e,t){this.$searchInput&&this.$searchInput.val(e),this.chromosomeSelectWidget&&(this.chromosomeSelectWidget.select.value=t)}currentNavbarButtonClass(){return this.currentClass}setEnableTrackSelection(e){this.multiTrackSelectButton.setMultiTrackSelection(e)}getEnableTrackSelection(){return this.multiTrackSelectButton.enableMultiTrackSelection}hide(){this.$navigation.hide()}show(){this.$navigation.show()}}const Oy=(e,t)=>{const i=0===e?t.nextElementSibling:t.previousElementSibling;t.remove(),i.remove()},Uy=t=>{const i=e({class:\"igv-column-shim\"});Ya(i,t);const 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Vy=function(t,i){this.button=e({class:\"igv-navbar-button\"}),t.appendChild(this.button),this.button.textContent=\"circular view\",this.button.addEventListener(\"click\",(()=>{i.circularViewVisible=!i.circularViewVisible})),this.browser=i,this.setVisibility(i.config.showCircularViewButton),this.setState(i.circularViewVisible)};Vy.prototype.setVisibility=function(e){!0===e?this.show():this.hide()},Vy.prototype.setState=function(e){!0===e?this.button.classList.add(\"igv-navbar-button-clicked\"):this.button.classList.remove(\"igv-navbar-button-clicked\")},Vy.prototype.show=function(){this.button.style.display=\"block\",this.setState(this.browser.circularViewVisible)},Vy.prototype.hide=function(){this.button.style.display=\"none\"};class jy{constructor(t,i){this.browser=t,this.container=e({class:\"igv-roi-menu\"}),i.appendChild(this.container);const n=e();this.container.appendChild(n),u(n,(()=>this.container.style.display=\"none\")),this.body=e(),this.container.appendChild(this.body),this.container.style.display=\"none\"}async present(e,t,i,n,r,s){const o=this.menuItems(e,t,i,n,r,s);this.browser.menuPopup.presentTrackContextMenu(i,o)}menuItems(e,t,i,n,r,s){const o=e.name?[`<b>${e.name}</b><br/>`]:[];return\"name\"in t&&o.push(`<b>ROI Set: ${t.name}</b>`),o.length>0&&o.push(\"<hr/>\"),t.isUserDefined&&o.push({label:\"Set description ...\",click:()=>{const t={label:\"Description\",value:e.name||\"\",callback:()=>{const t=this.browser.inputDialog.value||\"\";e.name=t.trim(),this.browser.roiManager.repaintTable()}};this.browser.inputDialog.present(t,i)}}),Xa()&&e.end-e.start<1e6&&o.push({label:\"Copy reference sequence\",click:async()=>{this.container.style.display=\"none\";let t=await this.browser.genome.getSequence(e.chr,e.start,e.end);t||(t=\"Unknown sequence\");try{await navigator.clipboard.writeText(t)}catch(e){console.error(e),this.browser.alert.present(`error copying sequence to clipboard ${e}`)}}}),e.end-e.start<=25e3&&o.push({label:\"BLAT reference sequence\",click:async()=>{this.container.style.display=\"none\";const{chr:t,start:i,end:n}=e;let r=await this.browser.genome.getSequence(t,i,n);if(r){const e=`blat: ${t}:${i+1}-${n}`,s=`blat: ${t}:${i+1}-${n}`;jd({sequence:r,browser:this.browser,name:e,title:s})}}}),t.isUserDefined&&o.push(\"<hr/>\",{label:\"Delete\",click:async()=>{t.removeFeature(e);const i=await t.getAllFeatures();0===Object.keys(i).length&&n.deleteUserDefinedROISet(),n.deleteRegionWithKey(s.dataset.region,r),n.repaintTable()}}),o}dispose(){this.container.innerHTML=\"\"}}class Wy extends Pd{constructor(e){const t={browser:e,parent:e.columnContainer,headerTitle:\"Regions of 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n=e({class:\"igv-roi-table-button\"});this._footerDOM.appendChild(n),n.id=\"igv-roi-hide-show-button\",n.textContent=\"Hide all ROIs\",this.toggleROIButton=n,this.boundToggleDisplayButtonHandler=function(e){e.preventDefault(),e.stopPropagation(),this.browser.roiManager.toggleROIs()}.bind(this),this.toggleROIButton.addEventListener(\"click\",this.boundToggleDisplayButtonHandler)}setROIVisibility(e){const t=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let i=0;i<t.length;i++){const n=t[i];!1===e?$y(n,0):n.style.backgroundColor=n.dataset.color}this.toggleROIButton.textContent=!1===e?\"Show all ROIs\":\"Hide all ROIs\"}setTableRowSelectionState(e){super.setTableRowSelectionState(e);const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\");if(t.length>0&&t.length<2){const{locus:e}=Jy(t[0].dataset.region),{chr:i,start:n,end:r}=ey(e,this.browser.isSoftclipped());Gy(this.copySequenceButton,r-n<1e6)}else Gy(this.copySequenceButton,!1)}dispose(){document.removeEventListener(\"click\",this.boundGotoButtonHandler),document.removeEventListener(\"click\",this.boundCopySequenceButtonHandler),document.removeEventListener(\"click\",this.boundToggleDisplayButtonHandler),this.browser.roiTableControl.buttonHandler(!1),super.dispose()}static getColumnFormatConfiguration(e){return!0===e?[{label:\"Chr\",width:\"20%\"},{label:\"Start\",width:\"15%\"},{label:\"End\",width:\"15%\"},{label:\"Description\",width:\"30%\"},{label:\"ROI Set\",width:\"20%\"}]:[{label:\"Chr\",width:\"25%\"},{label:\"Start\",width:\"20%\"},{label:\"End\",width:\"20%\"},{label:\"Description\",width:\"35%\"}]}static gotoButtonHandler(e){e.stopPropagation();const t=this.tableDOM.querySelectorAll(\".igv-roi-table-row-selected\"),i=[];for(let e of t){const{locus:t}=Jy(e.dataset.region);i.push(t)}for(let e of this.tableDOM.querySelectorAll(\".igv-roi-table-row\"))e.classList.remove(\"igv-roi-table-row-selected\");this.setTableRowSelectionState(!1),i.length>0&&this.browser.search(i.join(\" \"))}}function Gy(e,t){e.style.pointerEvents=t?\"auto\":\"none\",e.style.color=ro(t?\"licorice\":\"silver\"),e.style.borderColor=ro(t?\"licorice\":\"silver\")}function $y(e,t){const i=window.getComputedStyle(e).backgroundColor.match(/[\\d.]+/g);3===i.length&&i.push(1),i[3]=t,e.style.backgroundColor=`rgba(${i.join(\", \")})`}class Ky{constructor(e){this.browser=e,this.roiMenu=new jy(e,e.columnContainer),this.roiTable=new Wy(e,e.columnContainer),this.top=0,this.roiSets=[],this.boundLocusChangeHandler=Yy.bind(this),e.on(\"locuschange\",this.boundLocusChangeHandler);this.observer=new MutationObserver((()=>{const t=e.findTracks((e=>new Set([\"ideogram\",\"ruler\"]).has(e.type))),[i,n]=t.map((e=>e.trackView.viewports[0].$viewport.get(0))).map((e=>function(e){const t=window.getComputedStyle(e),i=parseInt(t.marginTop),n=parseInt(t.marginBottom),{top:r,bottom:s,height:o}=e.getBoundingClientRect();return{top:Math.floor(r)-i,bottom:Math.floor(s)+n,height:Math.floor(o)+i+n}}(e))),r=i?i.height:0,s=n?n.height:0,o=e.columnContainer.querySelectorAll(\".igv-roi-region\");if(o)for(const e of o)e.style.marginTop=`${r+s+-.5}px`})),this.observer.observe(e.columnContainer,{attributes:!0,childList:!0,subtree:!0})}async reset(){this.roiSets.length>0&&this.browser.roiTableControl.setVisibility(!0);const e=this.roiSets.map((e=>this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e})));e.length>0&&await Promise.all(e);const t=await this.getTableRecords();if(this.roiTable.renderTable(t),this.roiSets.length>0){const e=this.roiSets[0].isVisible;this.roiTable.setROIVisibility(e)}}async loadROI(e,t){const i=Array.isArray(e)?e:[e];for(let e of i)!e.name&&e.url&&(e.name=await ja(e.url)),e.url&&!e.format&&(e.format=await am(e)),this.roiSets.push(new ku(e,t));await this.reset()}clearROIs(){this.roiTable.clearTable();const e=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let t of e)t.remove();for(let e of this.roiSets)e.dispose();this.roiSets=[]}async getTableRecords(){const e=[];for(let t of this.roiSets){const i=t.name||\"\",n=await t.getAllFeatures();for(let t of Object.keys(n))for(let r of n[t])e.push({setName:i,feature:r})}return e}presentTable(){this.roiTable.present()}async repaintTable(){const e=await this.getTableRecords();this.roiTable.renderTable(e)}dismissTable(){this.roiTable.dismiss()}roiTableIsVisible(){return this.roiTable.isVisible()}async updateUserDefinedROISet(e){let t=await this.getUserDefinedROISet();void 0===t&&(t=this.initializeUserDefinedROISet()),t.addFeature(e),this.setROITableButtonVisibility(!0),await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:t});const i=await this.getTableRecords();this.roiTable.renderTable(i)}setROITableButtonVisibility(e){this.browser.roiTableControl.setVisibility(e)}toggleROIs(){const e=!this.roiSets[0].isVisible;this.roiTable.setROIVisibility(e);for(const t of this.roiSets)t.isVisible=e}async renderAllROISets(){for(let e of this.roiSets)await this.renderROISet({browser:this.browser,pixelTop:this.top,roiSet:e})}async renderROISet({browser:e,pixelTop:t,roiSet:i}){const n=e.columnContainer.querySelectorAll(\".igv-column\");for(let r=0;r<n.length;r++){let{chr:s,start:o,end:a,bpPerPixel:c}=e.referenceFrameList[r];const l=n[r].querySelectorAll(\".igv-roi-region\");for(let e of l){const t=e.dataset.region,{chr:i,start:n,end:r}=Jy(t);(i!==s||r<o||n>a)&&e.remove()}const h=await i.getFeatures(s,o,a);if(h)for(let l of h){const h=Xy(s,l.start,l.end),{x:d,width:u}=Iu(Math.max(o,l.start),Math.min(a,l.end),o,c),f=n[r].querySelector(Zy(h));if(f)f.style.left=`${d}px`,f.style.width=`${u}px`;else{const s=this.createRegionElement(e.columnContainer,t,d,u,i,h,l);n[r].appendChild(s)}}}}createRegionElement(t,i,n,r,s,o,c){const l=e({class:\"igv-roi-region\"});l.style.top=`${i}px`,l.style.left=`${n}px`,l.style.width=`${r}px`,l.style.backgroundColor=s.color,l.dataset.color=s.color,l.dataset.region=o;const h=e();return l.appendChild(h),h.style.backgroundColor=s.headerColor,h.addEventListener(\"click\",(e=>{e.preventDefault(),e.stopPropagation(),a(e,t),this.roiMenu.present(c,s,e,this,t,l)})),l}renderSVGContext(e,t,{deltaX:i,deltaY:n}){for(const r of e.querySelectorAll(\".igv-roi-region\")){const{x:e,y:s,width:o,height:a}=r.getBoundingClientRect();t.fillStyle=r.style.backgroundColor,t.fillRect(e-i,s+n,o,a);const c=r.querySelector(\"div\"),{x:l,y:h,width:d,height:u}=c.getBoundingClientRect();t.fillStyle=c.style.backgroundColor,t.fillRect(l-i,h+n,d,u)}}getUserDefinedROISet(){return this.roiSets.find((e=>!0===e.isUserDefined))}deleteUserDefinedROISet(){this.roiSets=this.roiSets.filter((e=>!0!==e.isUserDefined))}initializeUserDefinedROISet(){const e=new ku({name:\"user defined\",isUserDefined:!0,features:[]},this.browser.genome);return this.roiSets.push(e),e}async deleteRegionWithKey(e,t){t.querySelectorAll(Zy(e)).forEach((e=>e.remove()));0===(await this.getTableRecords()).length&&(this.browser.roiTableControl.buttonHandler(!1),this.setROITableButtonVisibility(!1))}toJSON(){return this.roiSets.map((e=>e.toJSON()))}dispose(){this.browser.off(\"locuschange\",this.boundLocusChangeHandler);const e=this.browser.columnContainer.querySelectorAll(\".igv-roi-region\");for(let t of e)t.remove();this.roiMenu&&this.roiMenu.dispose(),this.roiTable&&this.roiTable.dispose();for(let e of this.roiSets)e.dispose();for(let e of Object.keys(this))this[e]=void 0}}function Yy(){this.renderAllROISets()}function Xy(e,t,i){return`${e}-${t}-${i}`}function Zy(e){return`[data-region=\"${e}\"]`}function Jy(e){let t=e.split(\"-\"),i=parseInt(t.pop()),n=parseInt(t.pop()),r=t.join(\"-\");return{chr:r,start:n,end:i,locus:`${r}:${n}-${i}`,bedRecord:`${r}\\t${n}\\t${i}`}}class eA{constructor(e,t){this.name=e.name,this.featureSource=e.featureSource||Ad(e,t),this.color=e.color||_u}async getFeatures(e,t,i){return this.featureSource.getFeatures({chr:e,start:t,end:i})}draw(e){const{context:t,bpPerPixel:i,bpStart:n,pixelTop:r,pixelHeight:s,pixelWidth:o,features:a}=e;if(!a)return;const c=n+o*i+1;for(let{start:e,end:o}of a){if(o<n)continue;if(e>c)break;const{x:a,width:l}=Iu(e,o,n,i);xo.fillRect(t,a,r,l,s,{fillStyle:this.color})}}}class tA{aliasRecordCache=new Map;constructor(e,t,i){(t=t||{}).url=e,this.reader=new Zh(t,i)}async preload(e){await this.reader.preload();for(let t of e)await this.search(t)}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}async search(e){if(!this.aliasRecordCache.has(e)){const t=await this.reader.search(e);if(t)for(let e of Object.keys(t))\"start\"!==e&&\"end\"!==e&&this.aliasRecordCache.set(t[e],t)}return this.aliasRecordCache.get(e)}async getChromosomeNames(){return await this.reader.loadHeader(),Array.from(this.reader.chrNames)}}class iA{aliasRecordCache=new Map;constructor(e,t,i){this.aliasURL=e,this.config=t,this.genome=i}async preload(){return this.loadAliases()}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}async loadAliases(){const e=await Qs.loadString(this.aliasURL,Ua(this.config)),t=Dt(e),i=t[0];i.startsWith(\"#\")&&(this.headings=i.substring(1).split(\"\\t\").map((e=>e.trim())),this.altNameSets=this.headings.slice(1));const n=this.genome.chromosomeNames?new Set(this.genome.chromosomeNames):new Set;for(let e of t)if(!e.startsWith(\"#\")&&e.length>0){const t=e.split(\"\\t\");let i=t.find((e=>n.has(e)));i||(i=t[0]);const r={chr:i};for(let e=0;e<t.length;e++){r[this.headings?this.headings[e]:e]=t[e],this.aliasRecordCache.set(t[e],r)}this.aliasRecordCache.set(i.toLowerCase(),r),this.aliasRecordCache.set(i.toUpperCase(),r)}}async search(e){return 0===this.aliasRecordCache.size&&await this.loadAliases(),this.aliasRecordCache.get(e)}}class nA{constructor(e,t,i,n){this.start=e,this.end=t,this.name=i,this.stain=0,\"acen\"===n?this.type=\"c\":(this.type=n.charAt(1),\"p\"===this.type&&(this.stain=parseInt(n.substring(4))))}}class rA{cytobandMap=new Map;constructor(e,t,i){(t=t||{}).url=e,this.source=new od(t,i)}async getCytobands(e){if(this.cytobandMap.has(e))return this.cytobandMap.get(e);{let t=await this.#k(e);return t||(t=[]),this.cytobandMap.set(e,t),t}}async#k(e){return(await this.source.getFeatures({chr:e})).map((e=>new nA(e.start,e.end,e.name,e.gieStain)))}}class sA{cytobands=new Map;constructor(e,t){this.url=e,this.config=t}async getCytobands(e){return 0===this.cytobands.size&&await this.#I(),this.cytobands.get(e)}async#I(){let e,t;if(Ga(this.url)){const t=vs(this.url);e=\"\";const i=t.length;for(let n=0;n<i;n++)e+=String.fromCharCode(t[n])}else e=await Qs.loadString(this.url,Ua(this.config));let i=[];const n=Dt(e);for(let e of n){const n=e.split(\"\\t\"),r=n[0];if(t||(t=r),r!==t&&(this.cytobands.set(t,i),i=[],t=r),5===n.length){const e=parseInt(n[1]),t=parseInt(n[2]),r=n[3],s=n[4];i.push(new nA(e,t,r,s))}}}async getChromosomeNames(){return 0===this.cytobands.size&&await this.#I(),Array.from(this.cytobands.keys())}async getChromosomes(){0===this.cytobands.size&&await this.#I();const e=[];let t=0;for(let[i,n]of this.cytobands.entries())e.push(new lc(i,t++,n[n.length-1].end));return e}}class oA{aliasRecordCache=new Map;constructor(e,t){this.genomeID=e,this.update(e,t)}async preload(){}getChromosomeName(e){return this.aliasRecordCache.has(e)?this.aliasRecordCache.get(e).chr:e}getChromosomeAlias(e,t){const i=this.aliasRecordCache.get(e);return i&&i[t]||e}update(e,t){if(t){const i=[];for(let n of t){if(this.aliasRecordCache.has(n))continue;let t=!1;const r={chr:n};if(i.push(r),n.startsWith(\"gi|\")){const e=oA.getNCBIName(n);r[\"ncbi-gi-versioned\"]=e;const t=e.lastIndexOf(\".\");if(t>0){const e=e.substring(0,t);r[\"ncbi-gi\"]=e}}else{if(e.startsWith(\"hg\")||e.startsWith(\"GRCh\")||\"1kg_ref\"===e||\"b37\"===e)switch(n){case\"23\":r.ucsc=\"chrX\",t=!0;break;case\"24\":r.ucsc=\"chrY\",t=!0;break;case\"chrX\":r.ncbi=\"23\",t=!0;break;case\"chrY\":r.ncbi=\"24\",t=!0}else if(e.startsWith(\"mm\")||e.startsWith(\"GRCm\")||e.startsWith(\"rheMac\"))switch(n){case\"21\":r.ucsc=\"chrX\",t=!0;break;case\"22\":r.ucsc=\"chrY\",t=!0;break;case\"chrX\":r.ncbi=\"21\",t=!0;break;case\"chrY\":r.ncbi=\"22\",t=!0}if(t)continue;\"chrM\"===n?r.ncbi=\"MT\":\"MT\"===n?r.ucsc=\"chrM\":n.toLowerCase().startsWith(\"chr\")?r.ncbi=n.substring(3):Number.isInteger(Number(n))&&(r.ucsc=\"chr\"+n)}}for(let e of i){for(let t of Object.values(e))this.aliasRecordCache.set(t,e);this.aliasRecordCache.set(e.chr.toLowerCase(),e),this.aliasRecordCache.set(e.chr.toUpperCase(),e)}}}search(e){return this.aliasRecordCache.get(e)}static getNCBIName(e){const t=e.split(\"\\\\|\");return t[t.length-1]}}class aA{#S;static async createGenome(e,t){const i=new aA(e,t);return await i.init(),i}constructor(e,t){this.config=e,this.browser=t,this.id=e.id||function(e){return void 0!==e.id?e.id:e.fastaURL&&Mt(e.fastaURL)&&!e.fastaURL.startsWith(\"data:\")?e.fastaURL:e.fastaURL&&e.fastaURL.name?e.fastaURL.name:\"\"}(e),this.name=e.name,this.nameSet=e.nameSet}async init(){const e=this.config;if(this.sequence=await Nc(e,this.browser),e.chromSizesURL?this.chromosomes=await async function(e){const t=new Map;let i;if(Ga(e)){let t=vs(e);i=\"\";for(let e of t)i+=String.fromCharCode(e)}else i=await Qs.load(e,{});const n=Fc(i);let r=0;for(let e of n){const i=e.split(\"\\t\");if(i.length>1){const e=Number.parseInt(i[1]);t.set(i[0],new lc(i[0],r++,e))}}return t}(e.chromSizesURL):this.chromosomes=this.sequence.chromosomes||new Map,this.chromosomes.size>0&&(this.chromosomeNames=Array.from(this.chromosomes.keys())),e.chromAliasBbURL?(this.chromAlias=new tA(e.chromAliasBbURL,Object.assign({},e),this),this.chromosomeNames||(this.chromosomeNames=await this.chromAlias.getChromosomeNames())):e.aliasURL?this.chromAlias=new iA(e.aliasURL,Object.assign({},e),this):this.chromosomeNames&&(this.chromAlias=new oA(this.id,this.chromosomeNames)),e.cytobandBbURL)this.cytobandSource=new rA(e.cytobandBbURL,Object.assign({},e),this),this.chromosomeNames||(this.chromosomeNames=await this.cytobandSource.getChromosomeNames());else if(e.cytobandURL&&(this.cytobandSource=new sA(e.cytobandURL,Object.assign({},e)),this.chromosomeNames||(this.chromosomeNames=await this.cytobandSource.getChromosomeNames()),0===this.chromosomes.size)){const e=await this.cytobandSource.getChromosomes();for(let t of e)this.chromosomes.set(e.name,e)}if(!1!==e.wholeGenomeView&&this.chromosomes.size>0&&(e.chromosomeOrder?Array.isArray(e.chromosomeOrder)?this.#S=e.chromosomeOrder:this.#S=e.chromosomeOrder.split(\",\").map((e=>e.trim())):this.#S=function(e){const t=[];let i,n=1;for(let r of e.values()){if(i){if(r.bpLength<i/100)continue;i=((n-1)*i+r.bpLength)/n,t.push(r.name)}else i=r.bpLength,t.push(r.name);n++}return t}(this.chromosomes),await this.chromAlias.preload(this.#S)),this.wholeGenomeView=!1!==e.wholeGenomeView&&this.#S&&this.chromosomes.size>1,this.wholeGenomeView){const e=this.#S.reduce(((e,t)=>e+this.chromosomes.get(t).bpLength),0);this.chromosomes.set(\"all\",new lc(\"all\",0,e))}}get description(){return this.config.description||`${this.id}\\n${this.name}`}get infoURL(){return this.config.infoURL}showWholeGenomeView(){return this.wholeGenomeView}toJSON(){return Object.assign({},this.config,{tracks:void 0})}get initialLocus(){return this.config.locus?this.config.locus:this.getHomeChromosomeName()}getHomeChromosomeName(){return this.showWholeGenomeView()&&this.chromosomes.has(\"all\")?\"all\":this.chromosomeNames[0]}getChromosomeName(e){return this.chromAlias?this.chromAlias.getChromosomeName(e,this.chromosomes.keys()):e}getChromosomeDisplayName(e){return this.nameSet&&this.chromAlias&&this.chromAlias.getChromosomeAlias(e,this.nameSet)||e}getChromosome(e){return this.chromAlias&&(e=this.chromAlias.getChromosomeName(e)),this.chromosomes.get(e)}async loadChromosome(e){if(this.chromAlias){const t=await this.chromAlias.search(e);t&&(e=t.chr)}if(!this.chromosomes.has(e)){let t;const i=await this.sequence.getSequenceRecord(e);i&&(t=new lc(e,0,i.bpLength)),this.chromosomes.set(e,t)}return this.chromosomes.get(e)}async getAliasRecord(e){if(this.chromAlias)return this.chromAlias.search(e)}async getCytobands(e){if(this.cytobandSource){const t=this.getChromosomeName(e);return await this.cytobandSource.getCytobands(t)}}getChromosomes(){return this.chromosomes}get wgChromosomeNames(){return this.#S?this.#S.slice():void 0}get showChromosomeWidget(){return this.config.showChromosomeWidget}getGenomeCoordinate(e,t){var i=this.getCumulativeOffset(e);if(void 0!==i)return i+t}getChromosomeCoordinate(e){let t;void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=computeCumulativeOffsets.call(this));let i=0;for(let n of this.#S){const r=this.cumulativeOffsets[n];if(r>e){return{chr:t,position:e-i}}t=n,i=r}return{chr:this.#S[this.#S.length-1],position:0}}getCumulativeOffset(e){void 0===this.cumulativeOffsets&&(this.cumulativeOffsets=function(){let e={},t=0;for(let i of this.#S){e[i]=Math.floor(t);t+=this.getChromosome(i).bpLength}return e}.call(this));const t=this.getChromosomeName(e);return this.cumulativeOffsets[t]}getGenomeLength(){if(!this.bpLength){let e=0;for(let t of this.#S){e+=this.chromosomes.get(t).bpLength}this.bpLength=e}return this.bpLength}async getSequence(e,t,i){return e=this.getChromosomeName(e),this.sequence.getSequence(e,t,i)}getSequenceInterval(e,t,i){return\"function\"==typeof this.sequence.getSequenceInterval?this.sequence.getSequenceInterval(e,t,i):void 0}}class cA{constructor(){this.clear()}clear(){this.phenotypeColors=new Map,this.snps=new Set,this.qtl=null}isEmpty(){return 0===this.phenotypeColors.size&&0===this.snps.size&&null===this.qtl}addSnp(e){e=e.toUpperCase(),this.snps.add(e)}addPhenotype(e){e=e.toUpperCase();const t=this.phenotypeColors.size;if(!this.phenotypeColors.has(e.toUpperCase())){const i=t<lA.length?lA[t]:_s.randomRGB(0,255);this.phenotypeColors.set(e.toUpperCase(),i)}}hasSnp(e){return e&&this.snps.has(e.toUpperCase())}hasPhenotype(e){return e&&this.phenotypeColors.has(e.toUpperCase())}hasQTL(e){return this.qtls.has(e)}colorForGene(e){return e?this.phenotypeColors.get(e.toUpperCase()):\"black\"}toJSON(){const e={};return this.phenotypeColors.size>0&&(e.phenotypes=Array.from(this.phenotypeColors.keys())),this.snps.size>0&&(e.snps=Array.from(this.snps)),this.qtl&&(e.qtl=this.qtl),e}static fromJSON(e){const t=new cA;if(e.phenotypes)for(let i of e.phenotypes)t.addPhenotype(i);if(e.snps)for(let i of e.snps)t.addSnp(i);return e.qtl&&(t.qtl=e.qtl),t}}const lA=[];lA.push(\"rgb(228,26,28)\"),lA.push(\"rgb(55,126,184)\"),lA.push(\"rgb(77,175,74)\"),lA.push(\"rgb(166,86,40)\"),lA.push(\"rgb(152,78,163)\"),lA.push(\"rgb(255,127,0)\"),lA.push(\"rgb(247,129,191)\"),lA.push(\"rgb(255,255,51)\"),lA.push(\"rgb(102,194,165)\"),lA.push(\"rgb(252,141,98)\"),lA.push(\"rgb(141, 160, 203)\"),lA.push(\"rgb(231, 138, 195)\"),lA.push(\"rgb(166, 216, 84)\"),lA.push(\"rgb(255, 217, 47)\"),lA.push(\"rgb(229, 196, 148)\"),lA.push(\"rgb( 141, 211, 199)\"),lA.push(\"rgb(255, 255, 179)\"),lA.push(\"rgb(190, 186, 218)\"),lA.push(\"rgb(251, 128, 114)\"),lA.push(\"rgb(128, 177, 211)\"),lA.push(\"rgb(253, 180, 98)\"),lA.push(\"rgb(179, 222, 105)\"),lA.push(\"rgb(252, 205, 229)\"),lA.push(\"rgb(188, 128, 189)\"),lA.push(\"rgb(204, 235, 197)\"),lA.push(\"rgb(255, 237, 111)\");class hA{constructor(t){this.parent=t,this.container=e({class:\"igv-ui-generic-dialog-container\"}),t.appendChild(this.container);const n=e({class:\"igv-ui-generic-dialog-header\"});this.container.appendChild(n),this.label=e({class:\"igv-ui-generic-dialog-one-liner\"}),this.container.appendChild(this.label),this.label.text=\"Unlabeled\",this.input_container=e({class:\"igv-ui-generic-dialog-input\"}),this.container.appendChild(this.input_container);let r='<input type=\"range\" id=\"igv-slider-dialog-input\" name=\"igv-slider-dialog-input\" />';this._input=document.createRange().createContextualFragment(r).firstChild,this.input_container.appendChild(this._input),r='<output id=\"igv-slider-dialog-output\" name=\"igv-slider-dialog-output\" for=\"igv-slider-dialog-input\"></output>',this._output=document.createRange().createContextualFragment(r).firstChild,this.input_container.appendChild(this._output);const s=e({class:\"igv-ui-generic-dialog-ok-cancel\"});this.container.appendChild(s),this.ok=e(),s.appendChild(this.ok),this.ok.textContent=\"OK\",this.cancel=e(),s.appendChild(this.cancel),this.cancel.textContent=\"Cancel\",i(this.container),this._input.addEventListener(\"input\",(()=>{const e=parseFloat(this._input.value)/this._scaleFactor;this.callback(e),this._output.value=`${e.toFixed(2)}`}),!1),this.ok.addEventListener(\"click\",(()=>{if(\"function\"==typeof this.callback){const e=parseFloat(this._input.value)/this._scaleFactor;this.callback(e),this.callback=void 0}this._input.value=void 0,i(this.container)}));const o=()=>{this._input.value=void 0,i(this.container)};this.cancel.addEventListener(\"click\",o),u(n,o),p(this.container,n)}get value(){return Ea.sanitize(this._input.value)}present(e,t){this.label.textContent=e.label,this._scaleFactor=e.scaleFactor;const[i,r,s]=[e.min,e.max,e.value].map((e=>Math.floor(this._scaleFactor*e).toString()));this._input.min=i,this._input.max=r,this._input.value=s;const o=parseFloat(s)/this._scaleFactor;this._output.value=`${o.toFixed(2)}`,this.callback=e.callback||e.click,n(this.container),this.clampLocation(t.clientX,t.clientY)}clampLocation(e,t){const{width:i,height:n}=this.container.getBoundingClientRect(),r=window.innerHeight,s=window.innerWidth,o=Math.min(r-n,t),a=Math.min(s-i,e);this.container.style.left=`${a}px`,this.container.style.top=`${o}px`}}class dA{qtlSelections=new cA;constructor(t,i){this.config=t,this.guid=s(),this.namespace=\".browser_\"+this.guid,this.parent=i;let n=i.shadowRoot;if(!n){n=i.attachShadow({mode:\"open\"});const e=new CSSStyleSheet;e.replaceSync('.igv-ui-dropdown {\\n  cursor: default;\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  z-index: 2048;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: 1px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div {\\n  overflow-y: auto;\\n  overflow-x: hidden;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div > div {\\n  padding: 4px;\\n  width: 100%;\\n  overflow-x: hidden;\\n  text-overflow: ellipsis;\\n  white-space: nowrap;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: 1px;\\n  background-color: white;\\n}\\n.igv-ui-dropdown > div > div:last-child {\\n  border-bottom-color: transparent;\\n  border-bottom-width: 0;\\n}\\n.igv-ui-dropdown > div > div:hover {\\n  cursor: pointer;\\n  background-color: rgba(0, 0, 0, 0.04);\\n}\\n\\n.igv-ui-popover {\\n  cursor: default;\\n  position: absolute;\\n  z-index: 2048;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: 1px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  background-color: white;\\n}\\n.igv-ui-popover > div:first-child {\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-width: 0;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-popover > div:first-child > div:first-child {\\n  margin-left: 4px;\\n}\\n.igv-ui-popover > div:first-child > div:last-child {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-popover > div:first-child > div:last-child:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-popover > div:last-child {\\n  user-select: text;\\n  overflow-y: auto;\\n  overflow-x: hidden;\\n  max-height: 400px;\\n  max-width: 800px;\\n  background-color: white;\\n  border-bottom-width: 0;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n}\\n.igv-ui-popover > div:last-child > div {\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  min-width: 220px;\\n  overflow-x: hidden;\\n  text-overflow: ellipsis;\\n  white-space: nowrap;\\n}\\n.igv-ui-popover > div:last-child > div > span {\\n  font-weight: bolder;\\n}\\n.igv-ui-popover > div:last-child hr {\\n  width: 100%;\\n}\\n\\n.igv-ui-alert-dialog-container {\\n  box-sizing: content-box;\\n  position: absolute;\\n  z-index: 2048;\\n  top: 50%;\\n  left: 50%;\\n  width: 400px;\\n  height: 200px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  outline: none;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 15px;\\n  font-weight: 400;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-ui-alert-dialog-container > div:first-child {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-alert-dialog-container > div:first-child div:first-child {\\n  padding-left: 8px;\\n}\\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body {\\n  -webkit-user-select: text;\\n  -moz-user-select: text;\\n  -ms-user-select: text;\\n  user-select: text;\\n  color: #373737;\\n  width: 100%;\\n  height: calc(100% - 24px - 64px);\\n  overflow-y: scroll;\\n}\\n.igv-ui-alert-dialog-container .igv-ui-alert-dialog-body .igv-ui-alert-dialog-body-copy {\\n  margin: 16px;\\n  width: auto;\\n  height: auto;\\n  overflow-wrap: break-word;\\n  word-break: break-word;\\n  background-color: white;\\n  border: unset;\\n}\\n.igv-ui-alert-dialog-container > div:last-child {\\n  width: 100%;\\n  margin-bottom: 10px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-ui-alert-dialog-container > div:last-child div {\\n  margin: unset;\\n  width: 40px;\\n  height: 30px;\\n  line-height: 30px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  border-color: #2B81AF;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-ui-alert-dialog-container > div:last-child div:hover {\\n  cursor: pointer;\\n  border-color: #25597f;\\n  background-color: #25597f;\\n}\\n\\n.igv-ui-color-swatch {\\n  position: relative;\\n  box-sizing: content-box;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: wrap;\\n  justify-content: center;\\n  align-items: center;\\n  width: 32px;\\n  height: 32px;\\n  border-style: solid;\\n  border-width: 2px;\\n  border-color: white;\\n  border-radius: 4px;\\n}\\n\\n.igv-ui-color-swatch:hover {\\n  border-color: dimgray;\\n}\\n\\n.igv-ui-colorpicker-menu-close-button {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 32px;\\n  margin-top: 4px;\\n  margin-bottom: 4px;\\n  padding-right: 8px;\\n}\\n.igv-ui-colorpicker-menu-close-button i.fa {\\n  display: block;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  color: #5f5f5f;\\n}\\n.igv-ui-colorpicker-menu-close-button i.fa:hover,\\n.igv-ui-colorpicker-menu-close-button i.fa:focus,\\n.igv-ui-colorpicker-menu-close-button i.fa:active {\\n  cursor: pointer;\\n  color: #0f0f0f;\\n}\\n\\n.igv-ui-generic-dialog-container {\\n  box-sizing: content-box;\\n  position: fixed;\\n  top: 0;\\n  left: 0;\\n  width: 300px;\\n  height: fit-content;\\n  padding-bottom: 16px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  z-index: 2048;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-one-liner {\\n  color: #373737;\\n  width: 95%;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-top: 8px;\\n  padding-left: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input {\\n  margin-top: 8px;\\n  width: 95%;\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  padding-left: 8px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input > div {\\n  width: fit-content;\\n  height: 100%;\\n  font-size: 16px;\\n  text-align: right;\\n  padding-right: 8px;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\\n  width: 50%;\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input {\\n  margin-top: 8px;\\n  width: calc(100% - 16px);\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input[type=range] {\\n  width: 70%;\\n  -webkit-appearance: none;\\n  background: linear-gradient(90deg, white, black);\\n  outline: none;\\n  margin: 0;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-input output {\\n  display: block;\\n  height: 100%;\\n  width: 20%;\\n  font-size: 16px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel {\\n  width: 100%;\\n  height: 28px;\\n  padding-top: 16px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div {\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:first-child {\\n  margin-left: 32px;\\n  margin-right: 0;\\n  background-color: #5ea4e0;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:last-child {\\n  margin-left: 0;\\n  margin-right: 32px;\\n  background-color: #c4c4c4;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel > div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n\\n.igv-ui-generic-container {\\n  box-sizing: content-box;\\n  position: absolute;\\n  z-index: 2048;\\n  background-color: white;\\n  cursor: pointer;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: wrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ui-generic-container > div:first-child {\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  height: 24px;\\n  width: 100%;\\n  background-color: #dddddd;\\n}\\n.igv-ui-generic-container > div:first-child > div {\\n  display: block;\\n  color: #5f5f5f;\\n  cursor: pointer;\\n  width: 14px;\\n  height: 14px;\\n  margin-right: 8px;\\n  margin-bottom: 4px;\\n}\\n\\n.igv-ui-dialog {\\n  z-index: 2048;\\n  position: fixed;\\n  width: fit-content;\\n  height: fit-content;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  background-color: white;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-ui-dialog .igv-ui-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-ui-dialog .igv-ui-dialog-one-liner {\\n  width: 95%;\\n  height: 24px;\\n  line-height: 24px;\\n  text-align: left;\\n  margin: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n  font-weight: bold;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel {\\n  width: 100%;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div {\\n  margin: 16px;\\n  margin-top: 32px;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child {\\n  background-color: #5ea4e0;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child {\\n  background-color: #c4c4c4;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok {\\n  width: 100%;\\n  height: 36px;\\n  margin-top: 32px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok div {\\n  width: 98px;\\n  height: 36px;\\n  line-height: 36px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  border-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-ui-dialog .igv-ui-dialog-ok div:hover {\\n  cursor: pointer;\\n  background-color: #25597f;\\n}\\n\\n.igv-ui-panel, .igv-ui-panel-row, .igv-ui-panel-column {\\n  z-index: 2048;\\n  background-color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  display: flex;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-ui-panel-column {\\n  display: flex;\\n  flex-direction: column;\\n}\\n\\n.igv-ui-panel-row {\\n  display: flex;\\n  flex-direction: row;\\n}\\n\\n.igv-ui-textbox {\\n  background-color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  display: flex;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n}\\n\\n.igv-ui-table {\\n  background-color: white;\\n}\\n\\n.igv-ui-table thead {\\n  position: sticky;\\n  top: 0;\\n}\\n\\n.igv-ui-table th {\\n  text-align: left;\\n}\\n\\n.igv-ui-table td {\\n  padding-right: 20px;\\n}\\n\\n.igv-ui-table tr:hover {\\n  background-color: lightblue;\\n}\\n\\n.igv-ui-center-fixed {\\n  left: 50%;\\n  top: 50%;\\n  transform: translate(-50%, -50%);\\n}\\n\\n.igv-navbar {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  box-sizing: border-box;\\n  width: 100%;\\n  color: #444;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  line-height: 32px;\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  margin-top: 2px;\\n  margin-bottom: 6px;\\n  height: 32px;\\n  border-style: solid;\\n  border-radius: 3px;\\n  border-width: thin;\\n  border-color: #bfbfbf;\\n  background-color: #f3f3f3;\\n}\\n.igv-navbar .igv-navbar-left-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  height: 32px;\\n  line-height: 32px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-logo {\\n  width: 34px;\\n  height: 32px;\\n  margin-right: 8px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\\n  height: 32px;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  user-select: none;\\n  line-height: 32px;\\n  vertical-align: middle;\\n  text-align: center;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  height: 100%;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n  height: 100%;\\n  width: 125px;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\\n  display: block;\\n  cursor: pointer;\\n  width: 100px;\\n  height: 75%;\\n  outline: none;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n  margin-left: 8px;\\n  height: 22px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 240px;\\n  height: 22px;\\n  line-height: 22px;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\\n  cursor: text;\\n  width: 85%;\\n  height: 22px;\\n  line-height: 22px;\\n  font-size: 12px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  text-align: left;\\n  padding-left: 8px;\\n  margin-right: 8px;\\n  outline: none;\\n  border-style: solid;\\n  border-radius: 3px;\\n  border-width: thin;\\n  border-color: #bfbfbf;\\n  background-color: white;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\\n  cursor: pointer;\\n  height: 16px;\\n  width: 16px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\\n  margin-left: 4px;\\n  user-select: none;\\n}\\n.igv-navbar .igv-navbar-right-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\\n  position: relative;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-hidden {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  height: 100%;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\\n  color: #737373;\\n  font-size: 18px;\\n  margin-left: 8px;\\n  user-select: none;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\\n  cursor: pointer;\\n  margin-left: unset;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: unset;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: 4px;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\\n  display: block;\\n  height: fit-content;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\\n  display: block;\\n  width: 125px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\\n  display: block;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\\n  color: #737373;\\n  font-size: 18px;\\n  height: 32px;\\n  line-height: 32px;\\n  margin-left: 8px;\\n  user-select: none;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\\n  cursor: pointer;\\n  margin-left: unset;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: unset;\\n  margin-right: 4px;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\\n  height: 20px;\\n  width: 20px;\\n  margin-left: 4px;\\n  margin-right: unset;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\\n  width: 0;\\n  height: 0;\\n  display: none;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\\n  width: 0;\\n  height: 0;\\n  display: none;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\\n  display: block;\\n}\\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\\n  display: none;\\n}\\n\\n.igv-navbar-button {\\n  display: block;\\n  box-sizing: unset;\\n  padding-left: 6px;\\n  padding-right: 6px;\\n  height: 18px;\\n  text-transform: capitalize;\\n  user-select: none;\\n  line-height: 18px;\\n  text-align: center;\\n  vertical-align: middle;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 11px;\\n  font-weight: 200;\\n  color: #737373;\\n  background-color: #f3f3f3;\\n  border-color: #737373;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 6px;\\n}\\n\\n.igv-navbar-button:hover {\\n  cursor: pointer;\\n}\\n\\n.igv-navbar-button-clicked {\\n  color: white;\\n  background-color: #737373;\\n}\\n\\n.igv-navbar-icon-button {\\n  cursor: pointer;\\n  position: relative;\\n  width: 24px;\\n  height: 24px;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-icon-button > div:first-child {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: -18px;\\n  width: 24px;\\n  height: 24px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-icon-button > div:last-child {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 18px;\\n  width: 24px;\\n  height: 24px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n\\n.igv-navbar-text-button {\\n  cursor: pointer;\\n  position: relative;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  border: none;\\n  display: flex;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-navbar-text-button > div:nth-child(2) {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 0;\\n  width: 38px;\\n  height: 18px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n.igv-navbar-text-button > div:nth-child(3) {\\n  z-index: 512;\\n  position: absolute;\\n  top: 36px;\\n  left: 42px;\\n  width: 38px;\\n  height: 18px;\\n  border: none;\\n  background-size: contain;\\n  background-repeat: no-repeat;\\n  background-position: center;\\n}\\n\\n#igv-text-button-label {\\n  text-anchor: middle;\\n  dominant-baseline: middle;\\n}\\n\\n.igv-navbar-text-button-svg-inactive rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n.igv-navbar-text-button-svg-inactive text {\\n  fill: #737373;\\n}\\n.igv-navbar-text-button-svg-inactive tspan {\\n  dominant-baseline: middle;\\n}\\n\\n.igv-navbar-text-button-svg-hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n.igv-navbar-text-button-svg-hover text {\\n  fill: white;\\n}\\n.igv-navbar-text-button-svg-hover tspan {\\n  dominant-baseline: middle;\\n}\\n\\n#igv-save-svg-group rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n#igv-save-svg-group text {\\n  fill: #737373;\\n}\\n\\n#igv-save-svg-group:hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n#igv-save-svg-group:hover text {\\n  fill: white;\\n}\\n\\n#igv-save-png-group rect {\\n  stroke: #737373;\\n  fill: white;\\n}\\n#igv-save-png-group text {\\n  fill: #737373;\\n}\\n\\n#igv-save-png-group:hover rect {\\n  stroke: #737373;\\n  fill: #737373;\\n}\\n#igv-save-png-group:hover text {\\n  fill: white;\\n}\\n\\n.igv-zoom-in-notice-container {\\n  z-index: 256;\\n  position: absolute;\\n  top: 8px;\\n  left: 50%;\\n  transform: translate(-50%, 0%);\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n  background-color: white;\\n}\\n.igv-zoom-in-notice-container > div {\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  padding-top: 2px;\\n  padding-bottom: 2px;\\n  width: 100%;\\n  height: 100%;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  color: #3f3f3f;\\n}\\n\\n.igv-zoom-in-notice {\\n  position: absolute;\\n  top: 10px;\\n  left: 50%;\\n}\\n.igv-zoom-in-notice div {\\n  position: relative;\\n  left: -50%;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #3f3f3f;\\n  background-color: rgba(255, 255, 255, 0.51);\\n  z-index: 64;\\n}\\n\\n.igv-container-spinner {\\n  position: absolute;\\n  top: 90%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  z-index: 1024;\\n  width: 24px;\\n  height: 24px;\\n  pointer-events: none;\\n  color: #737373;\\n}\\n\\n.igv-multi-locus-close-button {\\n  position: absolute;\\n  top: 2px;\\n  right: 0;\\n  padding-left: 2px;\\n  padding-right: 2px;\\n  width: 12px;\\n  height: 12px;\\n  color: #666666;\\n  background-color: white;\\n  z-index: 1000;\\n}\\n.igv-multi-locus-close-button > svg {\\n  vertical-align: top;\\n}\\n\\n.igv-multi-locus-close-button:hover {\\n  cursor: pointer;\\n  color: #434343;\\n}\\n\\n.igv-multi-locus-ruler-label {\\n  z-index: 64;\\n  position: absolute;\\n  top: 2px;\\n  left: 0;\\n  width: 100%;\\n  height: 12px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-multi-locus-ruler-label > div {\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  color: rgb(16, 16, 16);\\n  background-color: white;\\n}\\n.igv-multi-locus-ruler-label > div {\\n  cursor: pointer;\\n}\\n\\n.igv-multi-locus-ruler-label-square-dot {\\n  z-index: 64;\\n  position: absolute;\\n  left: 50%;\\n  top: 5%;\\n  transform: translate(-50%, 0%);\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\\n  width: 14px;\\n  height: 14px;\\n}\\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\\n  margin-left: 16px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  color: rgb(16, 16, 16);\\n}\\n\\n.igv-ruler-sweeper {\\n  display: none;\\n  pointer-events: none;\\n  position: absolute;\\n  top: 26px;\\n  bottom: 0;\\n  left: 0;\\n  width: 0;\\n  z-index: 99999;\\n  background-color: rgba(68, 134, 247, 0.25);\\n}\\n\\n.igv-ruler-tooltip {\\n  pointer-events: none;\\n  z-index: 128;\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: 1px;\\n  height: 32px;\\n  background-color: transparent;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-ruler-tooltip > div {\\n  pointer-events: none;\\n  width: 128px;\\n  height: auto;\\n  padding: 1px;\\n  color: #373737;\\n  font-size: 10px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  background-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #373737;\\n}\\n\\n.igv-track-label {\\n  position: absolute;\\n  left: 8px;\\n  top: 8px;\\n  width: auto;\\n  height: auto;\\n  max-width: 50%;\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  text-align: center;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  border-color: #444;\\n  border-radius: 2px;\\n  border-style: solid;\\n  border-width: thin;\\n  background-color: white;\\n  z-index: 128;\\n  cursor: pointer;\\n}\\n\\n.igv-track-label:hover,\\n.igv-track-label:focus,\\n.igv-track-label:active {\\n  background-color: #e8e8e8;\\n}\\n\\n.igv-track-label-popup-shim {\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  padding-top: 4px;\\n}\\n\\n.igv-center-line {\\n  display: none;\\n  pointer-events: none;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  left: 50%;\\n  transform: translateX(-50%);\\n  z-index: 8;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  border-left-style: dashed;\\n  border-left-width: thin;\\n  border-right-style: dashed;\\n  border-right-width: thin;\\n}\\n\\n.igv-center-line-wide {\\n  background-color: rgba(0, 0, 0, 0);\\n  border-left-color: rgba(127, 127, 127, 0.51);\\n  border-right-color: rgba(127, 127, 127, 0.51);\\n}\\n\\n.igv-center-line-thin {\\n  background-color: rgba(0, 0, 0, 0);\\n  border-left-color: rgba(127, 127, 127, 0.51);\\n  border-right-color: rgba(0, 0, 0, 0);\\n}\\n\\n.igv-cursor-guide-horizontal {\\n  display: none;\\n  pointer-events: none;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  position: absolute;\\n  left: 0;\\n  right: 0;\\n  top: 50%;\\n  height: 1px;\\n  z-index: 32;\\n  margin-left: 50px;\\n  margin-right: 54px;\\n  border-top-style: dotted;\\n  border-top-width: thin;\\n  border-top-color: rgba(127, 127, 127, 0.76);\\n}\\n\\n.igv-cursor-guide-vertical {\\n  pointer-events: none;\\n  user-select: none;\\n  -moz-user-select: none;\\n  -webkit-user-select: none;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  left: 50%;\\n  width: 1px;\\n  z-index: 32;\\n  border-left-style: dotted;\\n  border-left-width: thin;\\n  border-left-color: rgba(127, 127, 127, 0.76);\\n  display: none;\\n}\\n\\n.igv-user-feedback {\\n  position: fixed;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 512px;\\n  height: 360px;\\n  z-index: 2048;\\n  background-color: white;\\n  border-color: #a2a2a2;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #444;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-user-feedback div:first-child {\\n  position: relative;\\n  height: 24px;\\n  width: 100%;\\n  background-color: white;\\n  border-bottom-color: #a2a2a2;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-user-feedback div:first-child div {\\n  position: absolute;\\n  top: 2px;\\n  width: 16px;\\n  height: 16px;\\n  background-color: transparent;\\n}\\n.igv-user-feedback div:first-child div:first-child {\\n  left: 8px;\\n}\\n.igv-user-feedback div:first-child div:last-child {\\n  cursor: pointer;\\n  right: 8px;\\n}\\n.igv-user-feedback div:last-child {\\n  width: 100%;\\n  height: calc(100% - 24px);\\n  border-width: 0;\\n}\\n.igv-user-feedback div:last-child div {\\n  width: auto;\\n  height: auto;\\n  margin: 8px;\\n}\\n\\n.igv-generic-dialog-container {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: 300px;\\n  height: 200px;\\n  border-color: #7F7F7F;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  z-index: 2048;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header div {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\\n  color: #373737;\\n  width: 95%;\\n  height: 24px;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-top: 8px;\\n  padding-left: 8px;\\n  overflow-wrap: break-word;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\\n  margin-top: 8px;\\n  width: 95%;\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  padding-left: 8px;\\n  background-color: white;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\\n  width: 30%;\\n  height: 100%;\\n  font-size: 16px;\\n  text-align: right;\\n  padding-right: 8px;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\\n  width: 50%;\\n  font-size: 16px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input {\\n  margin-top: 8px;\\n  width: calc(100% - 16px);\\n  height: 24px;\\n  color: #373737;\\n  line-height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input input {\\n  display: block;\\n  height: 100%;\\n  width: 100%;\\n  padding-left: 4px;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-weight: 400;\\n  color: #373737;\\n  text-align: left;\\n  outline: none;\\n  border-style: solid;\\n  border-width: thin;\\n  border-color: #7F7F7F;\\n  background-color: white;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-input input {\\n  font-size: 16px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\\n  width: 100%;\\n  height: 28px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\\n  margin-top: 32px;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 14px;\\n  font-weight: 400;\\n  width: 75px;\\n  height: 28px;\\n  line-height: 28px;\\n  text-align: center;\\n  border-color: transparent;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 2px;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\\n  margin-left: 32px;\\n  margin-right: 0;\\n  background-color: #5ea4e0;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\\n  margin-left: 0;\\n  margin-right: 32px;\\n  background-color: #c4c4c4;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\\n  cursor: pointer;\\n  background-color: #3b5c7f;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\\n  cursor: pointer;\\n  background-color: #7f7f7f;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok {\\n  width: 100%;\\n  height: 36px;\\n  margin-top: 32px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\\n  width: 98px;\\n  height: 36px;\\n  line-height: 36px;\\n  text-align: center;\\n  color: white;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  border-color: white;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 4px;\\n  background-color: #2B81AF;\\n}\\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\\n  cursor: pointer;\\n  background-color: #25597f;\\n}\\n\\n.igv-generic-container {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  z-index: 2048;\\n  background-color: white;\\n  cursor: pointer;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: wrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-generic-container div:first-child {\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n  height: 24px;\\n  width: 100%;\\n  background-color: #dddddd;\\n}\\n.igv-generic-container div:first-child i {\\n  display: block;\\n  color: #5f5f5f;\\n  cursor: pointer;\\n  width: 14px;\\n  height: 14px;\\n  margin-right: 8px;\\n  margin-bottom: 4px;\\n}\\n\\n.igv-menu-popup {\\n  position: absolute;\\n  top: 0;\\n  left: 0;\\n  width: max-content;\\n  max-width: 400px;\\n  z-index: 512;\\n  cursor: pointer;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  color: #4b4b4b;\\n  background: white;\\n  border-radius: 4px;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-end;\\n  text-align: left;\\n}\\n.igv-menu-popup > div:not(:first-child) {\\n  width: 100%;\\n}\\n.igv-menu-popup > div:not(:first-child) > div {\\n  background: white;\\n}\\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\\n  padding-left: 4px;\\n  padding-right: 4px;\\n}\\n.igv-menu-popup > div:not(:first-child) > div:last-child {\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-color: transparent;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-menu-popup > div:not(:first-child) > div:hover {\\n  background: #efefef;\\n}\\n\\n.igv-menu-popup-shim {\\n  padding-left: 8px;\\n  padding-right: 8px;\\n  padding-bottom: 1px;\\n  padding-top: 1px;\\n}\\n\\n.igv-menu-popup-header {\\n  position: relative;\\n  width: 100%;\\n  height: 24px;\\n  cursor: move;\\n  border-top-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-menu-popup-header div {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-menu-popup-header div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n\\n.igv-menu-popup-check-container {\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  width: 100%;\\n  height: 20px;\\n  margin-right: 4px;\\n  background-color: transparent;\\n}\\n.igv-menu-popup-check-container div {\\n  padding-top: 2px;\\n  padding-left: 8px;\\n}\\n.igv-menu-popup-check-container div:first-child {\\n  position: relative;\\n  width: 12px;\\n  height: 12px;\\n}\\n.igv-menu-popup-check-container div:first-child svg {\\n  position: absolute;\\n  width: 12px;\\n  height: 12px;\\n}\\n\\n.igv-user-feedback {\\n  position: fixed;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 512px;\\n  height: 360px;\\n  z-index: 2048;\\n  background-color: white;\\n  border-color: #a2a2a2;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: medium;\\n  font-weight: 400;\\n  color: #444;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n}\\n.igv-user-feedback div:first-child {\\n  position: relative;\\n  height: 24px;\\n  width: 100%;\\n  background-color: white;\\n  border-bottom-color: #a2a2a2;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-user-feedback div:first-child div {\\n  position: absolute;\\n  top: 2px;\\n  width: 16px;\\n  height: 16px;\\n  background-color: transparent;\\n}\\n.igv-user-feedback div:first-child div:first-child {\\n  left: 8px;\\n}\\n.igv-user-feedback div:first-child div:last-child {\\n  cursor: pointer;\\n  right: 8px;\\n}\\n.igv-user-feedback div:last-child {\\n  width: 100%;\\n  height: calc(100% - 24px);\\n  border-width: 0;\\n}\\n.igv-user-feedback div:last-child div {\\n  width: auto;\\n  height: auto;\\n  margin: 8px;\\n}\\n\\n.igv-loading-spinner-container {\\n  z-index: 1024;\\n  position: absolute;\\n  top: 50%;\\n  left: 50%;\\n  transform: translate(-50%, -50%);\\n  width: 32px;\\n  height: 32px;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: center;\\n  align-items: center;\\n}\\n.igv-loading-spinner-container > div {\\n  box-sizing: border-box;\\n  width: 100%;\\n  height: 100%;\\n  border-radius: 50%;\\n  border: 4px solid rgba(128, 128, 128, 0.5);\\n  border-top-color: rgb(255, 255, 255);\\n  animation: spin 1s ease-in-out infinite;\\n  -webkit-animation: spin 1s ease-in-out infinite;\\n}\\n\\n@keyframes spin {\\n  to {\\n    -webkit-transform: rotate(360deg);\\n    transform: rotate(360deg);\\n  }\\n}\\n@-webkit-keyframes spin {\\n  to {\\n    -webkit-transform: rotate(360deg);\\n    transform: rotate(360deg);\\n  }\\n}\\n.igv-roi-menu {\\n  position: absolute;\\n  z-index: 512;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: small;\\n  font-weight: 400;\\n  color: #4b4b4b;\\n  background-color: white;\\n  width: 192px;\\n  border-radius: 4px;\\n  border-color: #7F7F7F;\\n  border-style: solid;\\n  border-width: thin;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n}\\n.igv-roi-menu > div:first-child {\\n  height: 24px;\\n  border-top-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-color: #7F7F7F;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-end;\\n  align-items: center;\\n}\\n.igv-roi-menu > div:first-child > div {\\n  margin-right: 4px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7F7F7F;\\n}\\n.igv-roi-menu > div:first-child > div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-roi-menu > div:last-child {\\n  background-color: white;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-color: transparent;\\n  border-bottom-style: solid;\\n  border-bottom-width: 0;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  text-align: start;\\n  vertical-align: middle;\\n}\\n.igv-roi-menu > div:last-child > div {\\n  height: 24px;\\n  padding-left: 4px;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  border-bottom-color: #7f7f7f;\\n}\\n.igv-roi-menu > div:last-child > div:not(:first-child):hover {\\n  cursor: pointer;\\n  background-color: rgba(127, 127, 127, 0.1);\\n}\\n.igv-roi-menu > div:last-child div:first-child {\\n  font-style: italic;\\n  text-align: center;\\n  padding-right: 4px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n}\\n.igv-roi-menu > div:last-child > div:last-child {\\n  border-bottom-width: 0;\\n  border-bottom-color: transparent;\\n}\\n\\n.igv-roi-placeholder {\\n  font-style: normal;\\n  color: rgba(75, 75, 75, 0.6);\\n}\\n\\n.igv-roi-table {\\n  position: absolute;\\n  z-index: 1024;\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  resize: both;\\n  overflow: hidden;\\n  width: min-content;\\n  max-width: 1600px;\\n  border-color: #7f7f7f;\\n  border-radius: 4px;\\n  border-style: solid;\\n  border-width: thin;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 12px;\\n  font-weight: 400;\\n  background-color: white;\\n  cursor: default;\\n}\\n.igv-roi-table > div {\\n  height: 24px;\\n  font-size: 14px;\\n  text-align: start;\\n  vertical-align: middle;\\n  line-height: 24px;\\n}\\n.igv-roi-table > div:first-child {\\n  border-color: transparent;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-top-width: 0;\\n  border-bottom-color: #7f7f7f;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n  background-color: #eee;\\n  cursor: move;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-between;\\n  align-items: center;\\n}\\n.igv-roi-table > div:first-child > div:first-child {\\n  text-align: center;\\n  white-space: nowrap;\\n  text-overflow: ellipsis;\\n  overflow: hidden;\\n  margin-left: 4px;\\n  margin-right: 4px;\\n  width: calc(100% - 4px - 12px);\\n}\\n.igv-roi-table > div:first-child > div:last-child {\\n  margin-right: 4px;\\n  margin-bottom: 2px;\\n  height: 12px;\\n  width: 12px;\\n  color: #7f7f7f;\\n}\\n.igv-roi-table > div:first-child > div:last-child > svg {\\n  display: block;\\n}\\n.igv-roi-table > div:first-child > div:last-child:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n.igv-roi-table > .igv-roi-table-description {\\n  padding: 4px;\\n  margin-left: 4px;\\n  word-break: break-all;\\n  overflow-y: auto;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-goto-explainer {\\n  margin-top: 5px;\\n  margin-left: 4px;\\n  color: #7F7F7F;\\n  font-style: italic;\\n  height: 24px;\\n  border-top: solid lightgray;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles {\\n  height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n  padding-right: 16px;\\n  background-color: white;\\n  border-top-color: #7f7f7f;\\n  border-top-style: solid;\\n  border-top-width: thin;\\n  border-bottom-color: #7f7f7f;\\n  border-bottom-style: solid;\\n  border-bottom-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles > div {\\n  font-size: 14px;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-left: 4px;\\n  height: 24px;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  border-right-color: #7f7f7f;\\n  border-right-style: solid;\\n  border-right-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-column-titles > div:last-child {\\n  border-right: unset;\\n}\\n.igv-roi-table > .igv-roi-table-row-container {\\n  display: flex;\\n  flex-flow: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  overflow: auto;\\n  height: 360px;\\n  flex: 1 1 auto;\\n  background-color: transparent;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\\n  height: 24px;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\\n  font-size: 14px;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  text-align: left;\\n  margin-left: 4px;\\n  height: 24px;\\n  white-space: nowrap;\\n  overflow: hidden;\\n  text-overflow: ellipsis;\\n  border-right-color: transparent;\\n  border-right-style: solid;\\n  border-right-width: thin;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:last-child {\\n  border-right: unset;\\n}\\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\\n  background-color: rgba(0, 0, 0, 0.04);\\n}\\n.igv-roi-table > div:last-child {\\n  min-height: 32px;\\n  height: 32px;\\n  line-height: 32px;\\n  border-top-color: #7f7f7f;\\n  border-top-style: solid;\\n  border-top-width: thin;\\n  border-bottom-color: transparent;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n  border-bottom-width: 0;\\n  background-color: #eee;\\n  display: flex;\\n  flex-flow: row;\\n  flex-wrap: nowrap;\\n  justify-content: space-around;\\n  align-items: center;\\n}\\n\\n.igv-roi-table-row-selected {\\n  background-color: rgba(0, 0, 0, 0.125);\\n}\\n\\n.igv-roi-table-button {\\n  cursor: pointer;\\n  height: 20px;\\n  user-select: none;\\n  line-height: 20px;\\n  text-align: center;\\n  vertical-align: middle;\\n  font-family: \"Open Sans\", sans-serif;\\n  font-size: 13px;\\n  font-weight: 400;\\n  color: black;\\n  padding-left: 6px;\\n  padding-right: 6px;\\n  background-color: rgb(239, 239, 239);\\n  border-color: black;\\n  border-style: solid;\\n  border-width: thin;\\n  border-radius: 3px;\\n}\\n\\n.igv-roi-table-button:hover {\\n  font-weight: 400;\\n  background-color: rgba(0, 0, 0, 0.13);\\n}\\n\\n.igv-roi-region {\\n  z-index: 64;\\n  position: absolute;\\n  top: 0;\\n  bottom: 0;\\n  pointer-events: none;\\n  overflow: visible;\\n  margin-top: 66px;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n}\\n.igv-roi-region > div {\\n  position: relative;\\n  width: 100%;\\n  height: 8px;\\n  pointer-events: auto;\\n}\\n\\n.igv-roi-menu-row {\\n  height: 24px;\\n  padding-left: 8px;\\n  font-size: small;\\n  text-align: start;\\n  vertical-align: middle;\\n  line-height: 24px;\\n  background-color: white;\\n}\\n\\n.igv-roi-menu-row-edit-description {\\n  width: -webkit-fill-available;\\n  font-size: small;\\n  text-align: start;\\n  vertical-align: middle;\\n  background-color: white;\\n  padding-left: 4px;\\n  padding-right: 4px;\\n  padding-bottom: 4px;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: stretch;\\n  align-items: stretch;\\n}\\n.igv-roi-menu-row-edit-description > label {\\n  margin-left: 2px;\\n  margin-bottom: 0;\\n  display: block;\\n  width: -webkit-fill-available;\\n}\\n.igv-roi-menu-row-edit-description > input {\\n  display: block;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  margin-bottom: 1px;\\n  width: -webkit-fill-available;\\n}\\n\\n.igv-container {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  padding-top: 4px;\\n  user-select: none;\\n  -webkit-user-select: none;\\n  -ms-user-select: none;\\n  min-height: 160px;\\n}\\n\\n.igv-viewport {\\n  position: relative;\\n  margin-top: 5px;\\n  line-height: 1;\\n  overflow-x: hidden;\\n  overflow-y: hidden;\\n}\\n\\n.igv-viewport-content {\\n  position: relative;\\n  width: 100%;\\n}\\n.igv-viewport-content > canvas {\\n  position: relative;\\n  display: block;\\n}\\n\\n.igv-column-container {\\n  position: relative;\\n  display: flex;\\n  flex-direction: row;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: stretch;\\n  width: 100%;\\n}\\n\\n.igv-column-shim {\\n  width: 1px;\\n  margin-left: 2px;\\n  margin-right: 2px;\\n  background-color: #545453;\\n}\\n\\n.igv-axis-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 50px;\\n}\\n.igv-axis-column > div {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 100%;\\n}\\n.igv-axis-column > div > div {\\n  z-index: 512;\\n  position: absolute;\\n  top: 8px;\\n  left: 8px;\\n  width: fit-content;\\n  height: fit-content;\\n  background-color: transparent;\\n  display: grid;\\n  align-items: start;\\n  justify-items: center;\\n}\\n.igv-axis-column > div > div > input {\\n  display: block;\\n  margin: unset;\\n  cursor: pointer;\\n}\\n\\n.igv-column {\\n  position: relative;\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-sample-info-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-sample-name-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n}\\n\\n.igv-scrollbar-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 14px;\\n}\\n.igv-scrollbar-column > div {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 14px;\\n}\\n.igv-scrollbar-column > div > div {\\n  cursor: pointer;\\n  position: absolute;\\n  top: 0;\\n  left: 2px;\\n  width: 8px;\\n  border-width: 1px;\\n  border-style: solid;\\n  border-color: #c4c4c4;\\n  border-top-left-radius: 4px;\\n  border-top-right-radius: 4px;\\n  border-bottom-left-radius: 4px;\\n  border-bottom-right-radius: 4px;\\n}\\n.igv-scrollbar-column > div > div:hover {\\n  background-color: #c4c4c4;\\n}\\n\\n.igv-track-drag-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 12px;\\n  background-color: white;\\n}\\n.igv-track-drag-column > .igv-track-drag-handle {\\n  z-index: 512;\\n  position: relative;\\n  cursor: pointer;\\n  margin-top: 5px;\\n  width: 100%;\\n  border-style: solid;\\n  border-width: 0;\\n  border-top-right-radius: 6px;\\n  border-bottom-right-radius: 6px;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-color {\\n  background-color: #c4c4c4;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-hover-color {\\n  background-color: #787878;\\n}\\n.igv-track-drag-column .igv-track-drag-handle-selected-color {\\n  background-color: #0963fa;\\n}\\n.igv-track-drag-column > .igv-track-drag-shim {\\n  position: relative;\\n  margin-top: 5px;\\n  width: 100%;\\n  border-style: solid;\\n  border-width: 0;\\n}\\n\\n.igv-gear-menu-column {\\n  position: relative;\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: flex-start;\\n  box-sizing: border-box;\\n  height: 100%;\\n  width: 28px;\\n}\\n.igv-gear-menu-column > div {\\n  display: flex;\\n  flex-direction: column;\\n  flex-wrap: nowrap;\\n  justify-content: flex-start;\\n  align-items: center;\\n  margin-top: 5px;\\n  width: 100%;\\n  background: white;\\n}\\n.igv-gear-menu-column > div > div {\\n  position: relative;\\n  margin-top: 4px;\\n  width: 16px;\\n  height: 16px;\\n  color: #7F7F7F;\\n}\\n.igv-gear-menu-column > div > div:hover {\\n  cursor: pointer;\\n  color: #444;\\n}\\n\\n/*# sourceMappingURL=igv.css.map */\\n'),n.adoptedStyleSheets=[e]}if(this.root=e({class:\"igv-container\"}),n.appendChild(this.root),this.spinner=e({class:\"igv-loading-spinner-container\"}),this.root.appendChild(this.spinner),this.spinner.appendChild(e()),this.spinner.style.width=\"64px\",this.spinner.style.height=\"64px\",this.stopSpinner(),this.alert=new La(this.root),this.columnContainer=e({class:\"igv-column-container\"}),this.root.appendChild(this.columnContainer),this.menuPopup=new Xu(this.columnContainer),this.menuUtils=new bo(this),this.initialize(t),this.trackViews=[],this.constants={dragThreshold:3,scrollThreshold:5,defaultColor:\"rgb(0,0,150)\",doubleClickDelay:t.doubleClickDelay||500},this.eventHandlers={},t.listeners)for(let e of Object.keys(t.listeners))this.on(e,t.listeners[e]);this.on(\"trackremoved\",(()=>{0===this.findTracks((e=>\"function\"==typeof e.getSamples)).length&&(this.sampleInfoControl.setButtonVisibility(!1),this.sampleNameViewportWidth=void 0,this.showSampleNames=!1,this.sampleNameControl.setState(this.showSampleNames),this.sampleNameControl.hide(),this.layoutChange())})),this.on(\"didchangecolumnlayout\",(()=>{if(yu.length>0){const e=yu.length;for(let t=0;t<e;t++)yu[t].dispose();yu.length=0}})),this.addEventHandlers(),this.sampleInfo=new Uu(this),this.createStandardControls(t),this.roiManager=new Ky(this)}get doShowROITable(){return this.roiManager.roiTableIsVisible()}startSpinner(){this.spinner.style.display=\"flex\"}stopSpinner(){this.spinner.style.display=\"none\"}initialize(e){this.flanking=e.flanking,this.crossDomainProxy=e.crossDomainProxy,this.formats=e.formats,this.trackDefaults=e.trackDefaults,this.nucleotideColors=e.nucleotideColors||Bc;for(let e of Object.keys(this.nucleotideColors))this.nucleotideColors[e.toLowerCase()]=this.nucleotideColors[e];this.doShowTrackLabels=e.showTrackLabels,this.doShowCenterLine=e.showCenterGuide,this.doShowCursorGuide=e.showCursorGuide,this.showSampleNames=e.showSampleNames,this.sampleNameViewportWidth=void 0,e.sampleNameViewportWidth&&(this.sampleNameViewportWidth=e.sampleNameViewportWidth),e.search&&(this.searchConfig={type:\"json\",url:e.search.url,coords:void 0===e.search.coords?1:e.search.coords,chromosomeField:e.search.chromosomeField||\"chromosome\",startField:e.search.startField||\"start\",endField:e.search.endField||\"end\",geneField:e.search.geneField||\"gene\",snpField:e.search.snpField||\"snp\",resultsField:e.search.resultsField})}createStandardControls(e){this.setTrackLabelVisibility(e.showTrackLabels),this.navbar=new Py(e,this),this.navbar.$navigation.insertBefore(Bt(this.columnContainer)),!1===e.showControls&&this.navbar.hide(),this.cursorGuide=new ky(this.columnContainer,this),this.inputDialog=new Na(this.root),this.inputDialog.container.id=`igv-input-dialog-${s()}`,this.dataRangeDialog=new _o(this,Bt(this.root)),this.dataRangeDialog.$container.get(0).id=`igv-data-range-dialog-${s()}`,this.genericColorPicker=new Ra({parent:this.columnContainer,width:432}),this.genericColorPicker.container.id=`igv-track-color-picker-${s()}`,this.sliderDialog=new hA(this.root),this.sliderDialog.container.id=`igv-slider-dialog-${s()}`}getSampleNameViewportWidth(){return void 0===this.sampleNameViewportWidth||!1===this.showSampleNames?0:this.sampleNameViewportWidth}getSampleInfoViewportWidth(){return this.getSampleInfoColumnWidth()}isMultiLocusMode(){return this.referenceFrameList&&this.referenceFrameList.length>1}isMultiLocusWholeGenomeView(){if(void 0===this.referenceFrameList||1===this.referenceFrameList.length)return!1;for(let e of this.referenceFrameList)if(\"all\"===e.chr.toLowerCase())return!0;return!1}currentLoci(){const e=e=>`${e.chr}:${e.start+1}-${e.end}`;return void 0===this.referenceFrameList||0===this.referenceFrameList.length?\"\":1===this.referenceFrameList.length?e(this.referenceFrameList[0]):this.referenceFrameList.map((t=>e(t)))}toSVG(){const{x:e,y:t,width:i,height:n}=this.columnContainer.getBoundingClientRect(),r=new lu({width:i,height:n,backdropColor:\"white\",multiLocusGap:0,viewbox:{x:0,y:0,width:i,height:n}}),s={deltaX:0,deltaY:-t};for(let e of this.trackViews)e.renderSVGContext(r,s);return s.deltaX=e,this.roiManager.renderSVGContext(this.columnContainer,r,s),r.getSerializedSvg(!0)}saveSVGtoFile(e,t){let i=this.toSVG();if(t){const e=document.createElement(\"svg\");e.innerHTML=i,t.append(e),t.appendChild(e)}const n=e||\"igvjs.svg\",r=URL.createObjectURL(new Blob([i],{type:\"application/octet-stream\"}));Pt(n,r),URL.revokeObjectURL(r)}savePNGtoFile(e){const t=this.toSVG(),i=new Blob([t],{type:\"image/svg+xml\"}),n=URL.createObjectURL(i),r=document.createElement(\"img\");r.addEventListener(\"load\",(()=>{const t=this.columnContainer.getBoundingClientRect(),i=window.devicePixelRatio,s=t.width*i,o=t.height*i,a=document.createElement(\"canvas\");a.width=s,a.height=o;const c=a.getContext(\"2d\");c.scale(i,i),c.drawImage(r,0,0);const l=a.toDataURL(\"image/png\");Pt(e=e||\"igvjs.png\",l),URL.revokeObjectURL(n)})),r.src=n}async loadSession(e){let t;return this.sampleInfo.initialize(),this.roiSets=[],t=e.url||e.file?await dA.loadSessionFile(e):e,this.loadSessionObject(t)}static async loadSessionFile(e){const t=e.url||e.file;let i;if(e.url&&Mt(e.url)&&(e.url.startsWith(\"blob:\")||e.url.startsWith(\"data:\"))){const t=dA.uncompressSession(e.url);i=JSON.parse(t)}else{let n=e.filename;if(n||(n=e.url?await ja(e.url):e.file.name),n.endsWith(\".xml\")){const e=mu.KNOWN_GENOMES,n=await Qs.loadString(t);i=new by(n,e)}else if(n.endsWith(\"hub.txt\")){i={reference:(await du.loadHub(t,e)).getGenomeConfig()}}else{if(!n.endsWith(\".json\"))throw Error(\"Unrecognized session file format:\"+n);i=await Qs.loadJson(t)}}return bA(i)}async loadSessionObject(e){this.cleanHouseForSession(),this.config=e,e.browsers&&(e=await async function(e){const t=e.browsers[0],i={},n=new Mf({url:t.url});await n.readHeaderAndFooter(),i.sampleNameViewportWidth=20,i.genome=\"hg38\";const r=t.state.split(\",\"),s=n.bpResolutions[Number.parseInt(r[2])],o=Number.parseInt(r[0]),a=Math.floor(Number.parseFloat(r[3])*s),c=a+Math.floor(1700*s);return i.locus=`${n.chromosomes[o].name}:${a}-${c}`,i.tracks=(t.tracks||[]).filter((e=>!(\"refgene\"===e.format||\"cellType\"===e.name))),i.tracks.push({type:\"shoebox\",url:t.url,name:t.name,colorScale:t.colorScale,_hicFile:n}),i}(e)),this.navbar.sampleInfoControl.setButtonVisibility(!1),this.showSampleNames=e.showSampleNames||!1,this.navbar.sampleNameControl.setState(!0===this.showSampleNames),e.sampleNameViewportWidth&&(this.sampleNameViewportWidth=e.sampleNameViewportWidth),$a(this.columnContainer,\"igv-axis-column\"),$a(this.columnContainer,\"igv-sample-info-column\"),$a(this.columnContainer,\"igv-sample-name-column\"),$a(this.columnContainer,\"igv-scrollbar-column\"),$a(this.columnContainer,\"igv-track-drag-column\"),$a(this.columnContainer,\"igv-gear-menu-column\");const t=e.reference||e.genome;if(!t)return void console.warn(\"No genome or reference object specified\");const i=Mt(t)?await mu.expandReference(this.alert,t):t;if(await this.loadReference(i,i.locus||e.locus),this.centerLineList=this.createCenterLineList(this.columnContainer),!1!==e.showIdeogram){const e=new hy(this);e.id=\"ideogram\";const t=new hf(this,this.columnContainer,e);this.trackViews.push(t)}if(!1!==e.showRuler){const e=new hf(this,this.columnContainer,new Wu(this));this.trackViews.push(e)}e.qtlSelections&&(this.qtlSelections=cA.fromJSON(e.qtlSelections)),this.roiManager.clearROIs(),e.roi?this.roiManager.loadROI(e.roi):await this.roiManager.reset();const n=[];if(e.sampleinfo)for(const t of e.sampleinfo)t.file?n.push(t.file):this.loadSampleInfo(t);const r=i.tracks||[],s=e.tracks?r.concat(e.tracks):r;0===s.filter((e=>\"sequence\"===e.type&&!e.url&&!e.fastaURL)).length&&s.push({type:\"sequence\",order:Wd,removable:!1});const o=s.filter((e=>void 0!==e.file)).map((({file:e})=>e)),a=s.filter((e=>void 0!==e.indexFile)).map((({indexFile:e})=>e));a.length>0&&o.push(...a),n.length>0&&o.push(...n),o.length>0&&alert(`Local files cannot be loaded automatically.\\nThis session contains references to these local files:\\n${o.map((e=>`    ${e}`)).join(\"\\n\")}`);const c=s.filter((e=>void 0===e.file));let l=1;for(let e of c)void 0===e.order&&(e.order=l++);await this.loadTrackList(c);for(let e of this.trackViews.filter((e=>\"ruler\"===e.track.type||\"ideogram\"===e.track.type)))await e.updateViews();return this.trackViews.some((e=>e.track.selected))&&this.navbar.setEnableTrackSelection(!0),this.updateUIWithReferenceFrameList(),this.updateLocusSearchWidget(),s}cleanHouseForSession(){for(let e of this.trackViews)e.removeDOMFromColumnContainer();this.columnContainer.querySelectorAll(\".igv-axis-column, .igv-column-shim, .igv-column, .igv-sample-info-column, .igv-sample-name-column, .igv-scrollbar-column, .igv-track-drag-column, .igv-gear-menu-column\").forEach((e=>e.remove())),this.trackViews=[],this.circularView&&this.circularView.clearChords()}async loadReference(e,t){let i;this.removeAllTracks(),this.roiManager.clearROIs(),this.navbar.setEnableTrackSelection(!1),i=e.gbkURL?await wd(e.gbkURL):await aA.createGenome(e,this);const n=void 0===this.genome||this.genome.id!==i.id;this.genome=i,this.navbar.updateGenome(i);let r=t||i.initialLocus;Array.isArray(r)&&(r=r.join(\" \"));if(!await this.search(r,!0))throw new Error(`Cannot set initial locus ${r}`);if(n){let t;if(e.hubURL){t=(await du.loadHub(e.hubURL)).getGroupedTrackConfigurations()}this.fireEvent(\"genomechange\",[{genome:i,trackConfigurations:t}]),this.circularView&&this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Hm(this.genome)})}}async loadGenome(e){let t;e.genarkAccession&&(e.url=hu(e.genarkAccession)),e.url&&(Mt(e.url)&&e.url.endsWith(\"/hub.txt\")?(e.hubURL=e.url,delete e.url):\"gbk\"===function(e){let t;if(e instanceof File)t=e.name;else{if(\"string\"!=typeof e)throw new Error(\"Input must be a File object or a URL string\");t=e}const i=t.split(\".\").pop();return i.split(\"?\")[0]}(e.url)&&(e.gbkURL=e.url,delete e.url));if(e.hubURL||e.url&&Mt(e.url)&&e.url.endsWith(\"/hub.txt\")){t=(await du.loadHub(e.hubURL||e.url,e)).getGenomeConfig()}else t=Mt(e)||!(e.url||e.fastaURL||e.twoBitURL||e.gbkURL)?await mu.expandReference(this.alert,e):e;let i;await this.loadReference(t),i=t.gbkURL||\"gbk\"===t.format?[{name:\"Annotations\",format:\"gbk\",url:t.gbkURL}]:t.tracks||[];return 0===i.filter((e=>\"sequence\"===e.type)).length&&i.push({type:\"sequence\",order:Wd}),await this.loadTrackList(i),await this.updateViews(),this.genome}async loadTrackHub(e){const t=bA((await du.loadHub(e.url,e)).getGenomeConfig());return this.loadGenome(t)}updateUIWithReferenceFrameList(){const e=this.referenceFrameList;this.isMultiLocusWholeGenomeView()||mu.isWholeGenomeView(e[0].chr),this.navbar.navbarDidResize(),mA(this.trackViews,this.doShowTrackLabels),this.doShowCenterLine&&mu.isWholeGenomeView(e[0].chr)&&this.navbar.centerLineButton.boundMouseClickHandler(),this.doShowCursorGuide&&mu.isWholeGenomeView(e[0].chr)&&this.navbar.cursorGuideButton.boundMouseClickHandler(),this.setCenterLineAndCenterLineButtonVisibility(mu.isWholeGenomeView(e[0].chr))}setCenterLineAndCenterLineButtonVisibility(e){e?this.navbar.centerLineButton.setVisibility(!1):this.navbar.centerLineButton.setVisibility(this.config.showCenterGuideButton);for(let t of this.centerLineList)e?this.setCenterLineVisibility(!e):this.setCenterLineVisibility(this.doShowCenterLine)}setTrackLabelVisibility(e){mA(this.trackViews,e)}setROITableVisibility(e){!0===e?this.roiManager.presentTable():this.roiManager.dismissTable()}setCursorGuideVisibility(e){e?this.cursorGuide.show():this.cursorGuide.hide()}setCustomCursorGuideMouseHandler(e){this.cursorGuide.customMouseHandler=e}setCenterLineVisibility(e){for(let t of this.centerLineList)!0===e?(t.show(),t.repaint()):t.hide()}async loadTrackList(e){let t=0;for(let i of e)void 0===i.order&&(i.order=t++);const i=[];for(let t of e)i.push(this._loadTrack(t));const n=await Promise.all(i);return this.trackViews.filter((function(e){return e.track.autoscaleGroup})).length>0&&this.updateViews(),n}async loadTrack(e){e.sync=!1!==e.sync;const t=this._loadTrack(e);return t&&e.autoscaleGroup&&(await t,this.updateViews()),t}async _loadTrack(e){Mt(e)&&(e=JSON.parse(e));try{if(e.hidden){const t=Ad(e,this.genome);return void await t.getFeatures({chr:\"1\",start:0,end:Number.MAX_SAFE_INTEGER})}const t=await this.createTrack(e);if(\"sampleinfo\"===e.type)return void this.layoutChange();if(void 0===t)return;return this.addTrack(e,t)}catch(t){let i=t.message||t.error||t.toString();const n={401:\"Access unauthorized\",403:\"Access forbidden\",404:\"Not found\"};n.hasOwnProperty(i)&&(i=n[i]),i=`${i} : ${Ht(e.url)?e.url.name:e.url}`;const r=new Error(i);throw console.error(r),r}}async addTrack(e,t){void 0===t.order&&(t.order=this.trackViews.length);const i=new hf(this,this.columnContainer,t);if(this.trackViews.push(i),mA(this.trackViews,this.doShowTrackLabels),\"function\"==typeof t.postInit)try{i.startSpinner(),await t.postInit()}finally{i.stopSpinner()}return t.autoscaleGroup||(e.sync?await i.updateViews():i.updateViews()),\"function\"==typeof t.hasSamples&&t.hasSamples()&&(this.sampleInfo.hasAttributes()&&this.sampleInfoControl.setButtonVisibility(!0),!1!==this.config.showSampleNameButton&&this.sampleNameControl.show()),this.reorderTracks(),this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()]),t.trackView.enableTrackSelection(this.navbar.getEnableTrackSelection()),t}async loadROI(e){return this.roiManager.loadROI(e,this.genome)}clearROIs(){this.roiManager.clearROIs()}async getUserDefinedROIs(){if(this.roiManager){const e=this.roiManager.getUserDefinedROISet();if(void 0===e)return[];const t=await e.getAllFeatures(),i=[];for(let e of Object.values(t))i.push(...e);return i}return[]}getRulerTrackView(){const e=this.trackViews.filter((({track:e})=>\"ruler\"===e.id));return e.length>0?e[0]:void 0}async createTrack(e){let t=await async function(e){return\"function\"==typeof e?e():e}\n",
-       "/*! pako 2.1.0 https://github.com/nodeca/pako @license (MIT AND Zlib) */(e.url||e.fastaURL);if(Mt(t)&&(t=t.trim()),t)if(e.format)e.format=e.format.toLowerCase();else if(e.fastaURL)e.format=\"fasta\";else if(e.sourceType)\"htsget\"===e.sourceType&&await Rh.inferFormat(e);else{const t=await am(e);t&&(e.format=t)}e.type&&Ha(e);let i=e.type?e.type.toLowerCase():void 0;if(!i){if(!e.format)throw Error(`Unrecognized track:  ${JSON.stringify(e)}`);if(\"hic\"===e.format){const t=new Mf(e);if(await t.readHeaderAndFooter(),!t.chromosomeIndexMap.celltype)throw Error(\"'.hic' files not supported\");i=\"shoebox\",e._hicFile=t}else if(i=za(e.format),\"bedtype\"===i){const t=Ad(e,this.genome);e._featureSource=t;const n=await t.trackType();i=n||\"annotation\"}e.type=i}if(this.trackDefaults&&i){const t=this.trackDefaults[i];if(t)for(let i in t)t.hasOwnProperty(i)&&void 0===e[i]&&(e[i]=t[i])}const n=function(e,t,i){let n;switch(e){case\"annotation\":case\"genes\":case\"fusionjuncspan\":case\"snp\":n=\"feature\";break;case\"seg\":case\"maf\":case\"mut\":n=\"seg\";break;case\"junctions\":case\"splicejunctions\":n=\"junction\";break;default:n=e}return wy.has(n)?wy.get(n)(t,i):void 0}(i,e,this);if(void 0!==n)return e.roi&&e.roi.length>0&&(n.roiSets=e.roi.map((e=>new eA(e,this.genome)))),n;this.alert.present(new Error(`Error creating track.  Could not determine track type for file: ${e.url||e}`),void 0)}reorderTracks(){this.trackViews.sort((function(e,t){const i=e=>\"ideogram\"===e.track.id?1:\"ruler\"===e.track.id?2:3,n=i(e),r=i(t);if(n===r){return(e.track.order||0)-(t.track.order||0)}return n-r}));for(let{axis:e,viewports:t,sampleInfoViewport:i,sampleNameViewport:n,outerScroll:r,dragHandle:s,gearContainer:o}of this.trackViews){e.remove();for(let{$viewport:e}of t)e.detach();i.viewport.remove(),n.viewport.remove(),r.remove(),s.remove(),o.remove()}const e=this.columnContainer.querySelectorAll(\".igv-column\");for(let{axis:t,viewports:i,sampleInfoViewport:n,sampleNameViewport:r,outerScroll:s,dragHandle:o,gearContainer:a}of this.trackViews){this.columnContainer.querySelector(\".igv-axis-column\").appendChild(t);for(let t=0;t<e.length;t++){const{$viewport:n}=i[t];e[t].appendChild(n.get(0))}this.columnContainer.querySelector(\".igv-sample-info-column\").appendChild(n.viewport),this.columnContainer.querySelector(\".igv-sample-name-column\").appendChild(r.viewport),this.columnContainer.querySelector(\".igv-scrollbar-column\").appendChild(s),this.columnContainer.querySelector(\".igv-track-drag-column\").appendChild(o),this.columnContainer.querySelector(\".igv-gear-menu-column\").appendChild(a)}}getTrackOrder(){return this.trackViews.filter((e=>e.track&&e.track.name)).map((e=>e.track.name))}getSelectedTrackViews(){return this.trackViews.filter((e=>!0===e.track.selected))}removeTrackByName(e){const t=this.trackViews.slice();for(let i of t)e===i.track.name&&this.removeTrack(i.track)}removeTrack(e){for(let t of this.trackViews)if(e===t.track){this._removeTrack(t.track);break}}_removeTrack(e){e.disposed||(this.trackViews.splice(this.trackViews.indexOf(e.trackView),1),this.fireEvent(\"trackremoved\",[e]),this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()]),e.trackView&&e.trackView.dispose())}removeAllTracks(){const e=this.trackViews;this.trackViews=[];for(let t of e)\"ruler\"!==t.track.id&&\"ideogram\"!==t.track.id?(this.fireEvent(\"trackremoved\",[t.track]),t.dispose()):this.trackViews.push(t)}get ideogramTrackView(){return this.trackViews[0]}get rulerTrackView(){return this.trackViews[1]}findTracks(e,t){let i=\"function\"==typeof e?t=>e(t.track):i=>t===i.track[e];return this.trackViews.filter(i).map((e=>e.track))}get tracks(){return this.trackViews.map((e=>e.track)).filter((e=>void 0!==e))}setTrackHeight(e){this.trackHeight=e,this.trackViews.forEach((function(t){t.setTrackHeight(e)}))}async visibilityChange(){this.layoutChange()}async layoutChange(){if(this.referenceFrameList.find((e=>e.bpPerPixel<0))){const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel=(t.end-t.start)/e}this.referenceFrameList&&this.navbar.navbarDidResize(),uA.call(this),await this.updateViews()}async updateViews(){const e=this.trackViews;this.updateLocusSearchWidget();for(let e of this.referenceFrameList)e.bpPerPixel<=10&&await this.genome.getSequence(e.chr,e.start,e.start+1);for(let e of this.centerLineList)e.repaint();if(this.dragObject)for(let t of e)await t.updateViews();else{const t={},i=[];for(const n of e)if(n.track.autoscaleGroup){const e=n.track.autoscaleGroup;t[e]||(t[e]=[]),t[e].push(n)}else i.push(n);if(Object.entries(t).length>0)for(const[e,i]of Object.entries(t)){const e=await Promise.all(i.map((e=>e.getInViewFeatures()))),t=qa(e.flat());for(const e of i)e.track.dataRange=Object.assign({},t),e.track.autoscale=!1;await Promise.all(i.map((e=>e.updateViews())))}await Promise.all(i.map((e=>e.updateViews())))}}repaintViews(){for(let e of this.trackViews)e.repaintViews()}updateLocusSearchWidget(){if(!this.referenceFrameList)return;const e=this.referenceFrameList,t=this.calculateViewportWidth(this.referenceFrameList.length);for(let i of e)i.end=i.start+i.bpPerPixel*t;const i=1===e.length?this.referenceFrameList[0].chr:\"\",n=this.referenceFrameList.map((e=>e.getLocusString())).join(\" \");this.navbar.updateLocus(n,i),this.fireEvent(\"locuschange\",[this.referenceFrameList])}calculateViewportWidth(e){let{width:t}=this.columnContainer.getBoundingClientRect();return t-=50+this.getSampleInfoViewportWidth()+this.getSampleNameViewportWidth()+14+12+28,t-=5*(e-1),Math.floor(t/e)}minimumBases(){return this.config.minimumBases}zoomIn(){this.zoomWithScaleFactor(.5)}zoomOut(){this.zoomWithScaleFactor(2)}async zoomWithScaleFactor(e,t,i){if(!this.referenceFrameList)return;const n=this.calculateViewportWidth(this.referenceFrameList.length);let r=i?[i]:this.referenceFrameList;for(let i of r)i.zoomWithScaleFactor(this,e,n,t)}async addMultiLocusPanel(e,t,i,n){if(!this.referenceFrameList)return;const r=this.calculateViewportWidth(1+this.referenceFrameList.length),s=this.calculateViewportWidth(this.referenceFrameList.length)/this.calculateViewportWidth(1+this.referenceFrameList.length);for(let e of this.referenceFrameList)e.bpPerPixel*=s;const o=(i-t)/r,a=new vy(this.genome,e,t,i,o),c=n?this.referenceFrameList.indexOf(n):this.referenceFrameList.length-1,l=1+c,{$viewport:h}=this.trackViews[0].viewports[c],d=Uy(h.get(0).parentElement);if(this.fireEvent(\"didchangecolumnlayout\"),l===this.referenceFrameList.length){this.referenceFrameList.push(a);for(let e of this.trackViews){const t=zu(e,d,a);e.viewports.push(t)}}else{this.referenceFrameList.splice(l,0,a);for(let e of this.trackViews){const t=zu(e,d,a);e.viewports.splice(l,0,t)}}this.centerLineList=this.createCenterLineList(this.columnContainer),uA.call(this),await this.updateViews(!0)}createCenterLineList(e){const t=e.querySelectorAll(\".igv-center-line\");for(let e=0;e<t.length;e++)t[e].remove();const i=[],n=e.querySelectorAll(\".igv-column\");for(let e=0;e<n.length;e++)i.push(new Qy(this,this.referenceFrameList[e],n[e]));return i}async removeMultiLocusPanel(e){const t=this.referenceFrameList.indexOf(e),{$viewport:i}=this.trackViews[0].viewports[t];Oy(t,i.parent().get(0)),this.fireEvent(\"didchangecolumnlayout\");for(let{viewports:e}of this.trackViews)e[t].dispose(),e.splice(t,1);if(this.referenceFrameList.splice(t,1),1===this.referenceFrameList.length&&this.getRulerTrackView())for(let e of this.getRulerTrackView().viewports)e.dismissLocusLabel();const n=this.calculateViewportWidth(1+this.referenceFrameList.length)/this.calculateViewportWidth(this.referenceFrameList.length);await this.rescaleForMultiLocus(n)}async gotoMultilocusPanel(e){const t=this.referenceFrameList.indexOf(e);this.columnContainer.querySelectorAll(\".igv-column\").forEach(((e,i)=>{i===t||e.remove()})),this.columnContainer.querySelectorAll(\".igv-column-shim\").forEach((e=>e.remove()));for(let e of this.trackViews){const i=e.viewports[t];e.viewports.filter(((e,i)=>i!==t)).forEach((e=>e.dispose())),e.viewports=[i]}const i=this.calculateViewportWidth(1);e.bpPerPixel=(e.end-e.start)/i,this.referenceFrameList=[e],this.trackViews.forEach((({viewports:e})=>e.forEach((e=>e.setWidth(i))))),this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}async rescaleForMultiLocus(e){const t=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList)t.bpPerPixel*=e;for(let{viewports:e}of this.trackViews)for(let i of e)i.setWidth(t);this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),await this.updateViews()}async goto(e,t,i){await this.search(e+\":\"+t+\"-\"+i)}async doSearch(e,t){const i=await this.search(e,t);return i||this.alert.present(new Error(`Unrecognized locus: <b> ${e} </b>`)),i}async search(e,t){const i=await async function(e,t){if(void 0===t||\"\"===t.trim())return;const i=t.split(\" \");let n=[];const r=async t=>{if(\"all\"===t.trim().toLowerCase()||\"*\"===t)return e.genome.wholeGenomeView?{chr:\"all\",start:0,end:e.genome.getChromosome(\"all\").bpLength}:void 0;let i,n;if(t.includes(\":\")&&(i=ey(t,e.isSoftclipped()),i&&(n=await e.genome.loadChromosome(i.chr))),!n){i=void 0;const r=await Jv(e,t);r&&(i={chr:r.chr,start:r.start,end:r.end,name:(r.name||t).toUpperCase()}),i||(n=await e.genome.loadChromosome(t),n&&(i={chr:n.name}))}return i&&(n=n||await e.genome.loadChromosome(i.chr),i.chr=n.name,void 0===i.start&&void 0===i.end&&(i.start=0,i.end=n.bpLength)),i};for(let e of i){const t=await r(e);t&&n.push(t)}if(0===n.length){const e=await r(t.replaceAll(\" \",\"+\"));e&&n.push(e)}return 0===n.length?void 0:n}(this,e);if(i&&i.length>0){this.referenceFrameList=function(e,t,i,n,r,s){return e.map((e=>{const o=Object.assign({},e);if(i&&o.name&&(o.start=Math.max(0,o.start-i),o.end+=i),!s){const e=t.getChromosome(o.chr);Qa(e.bpLength,o,n)}return new vy(t,o.chr,o.start,o.end,(o.end-o.start)/r)}))}(i,this.genome,this.flanking,this.minimumBases(),this.calculateViewportWidth(i.length),this.isSoftclipped());for(let e of this.trackViews)e.removeViewportsFromColumnContainer();this.columnContainer.querySelectorAll(\".igv-column-shim, .igv-column\").forEach((e=>e.remove())),qy(this.columnContainer.querySelector(\".igv-sample-info-column\"),this.referenceFrameList.length),this.fireEvent(\"didchangecolumnlayout\");for(let e of this.trackViews)e.createViewports(this,this.columnContainer,this.referenceFrameList);return this.centerLineList=this.createCenterLineList(this.columnContainer),this.updateUIWithReferenceFrameList(),t||await this.updateViews(),!0}return!1}async loadSampleInfo(e){await this.sampleInfo.loadSampleInfoFile(e.url);for(const{sampleInfoViewport:e}of this.trackViews)e.setWidth(this.getSampleInfoColumnWidth());this.findTracks((e=>\"function\"==typeof e.getSamples)).length>0&&(this.sampleInfoControl.performClickWithState(this,!0),this.sampleInfoControl.setButtonVisibility(!0));for(const{sampleInfoViewport:e}of this.trackViews)e.repaint()}getSampleInfoColumnWidth(){if(this.sampleInfo.attributeCount){const e=this.findTracks((e=>\"function\"==typeof e.getSamples)).length>0,t=this.sampleInfo.hasAttributes(),i=this.sampleInfoControl.showSampleInfo;return e&&t&&i?this.sampleInfo.attributeCount*Vu+8:0}return 0}on(e,t){this.eventHandlers[e]||(this.eventHandlers[e]=[]),this.eventHandlers[e].push(t)}un(e,t){this.off(e,t)}off(e,t){if(e)if(t){const i=this.eventHandlers[e];if(i&&0!==i.length){const n=i.indexOf(t);-1!==n&&this.eventHandlers[e].splice(n,1)}else console.warn(\"No handlers to remove for event: \"+e)}else this.eventHandlers[e]=[];else this.eventHandlers={}}fireEvent(e,t,i){const n=this.eventHandlers[e];if(void 0===n||0===n.length)return;const r=i||window;return n.map((function(e){return e.apply(r,t)}))[0]}dispose(){this.removeEventHandlers();for(let e of this.trackViews)e.dispose();this.roiManager&&this.roiManager.dispose()}toJSON(){const e={version:\"3.0.9\"};if(void 0!==this.showSampleNames&&(e.showSampleNames=this.showSampleNames),this.sampleNameViewportWidth&&(e.sampleNameViewportWidth=this.sampleNameViewportWidth),e.reference=this.genome.toJSON(),e.reference.fastaURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.fastaURL.name}.`);if(e.reference.indexURL instanceof File)throw new Error(`Error. Sessions cannot include local file references ${e.reference.indexURL.name}.`);const t=[];let i=this.trackViews[0];for(let{referenceFrame:e}of i.viewports){const i=e.getLocusString();t.push(i)}e.locus=1===t.length?t[0]:t,e.roi=this.roiManager.toJSON(),this.qtlSelections.isEmpty()||(e.qtlSelections=this.qtlSelections.toJSON());const n=[],r=[];for(const{track:e}of this.trackViews)try{let t;\"function\"==typeof e.getState?t=Hl.localFileInspection(e.getState()):e.config&&(t=Hl.localFileInspection(e.config)),t&&(t.browser&&delete t.browser,t.order=e.order,n.push(t))}catch(t){const i=`Track: ${e.name}: ${t}`;console.error(i),r.push(i)}if(r.length>0){let e=1,t=\"Errors encountered saving session: </br>\";for(let i of r)t+=` (${e++}) ${i.toString()} <br/>`;throw Error(t)}e.tracks=n;const s=[];for(const e of n)for(const t of Object.keys(e))\"file\"!==t&&\"indexFile\"!==t||s.push(e[t]);const o=[];if(this.sampleInfo.sampleInfoFiles.length>0){const t=this.sampleInfo.toJSON();t.length>0&&(e.sampleinfo=t);for(const e of this.sampleInfo.sampleInfoFiles){const t=Hl.localFileInspection({url:e});t.file&&o.push(t.file)}o.length>0&&s.push(...o)}return s.length>0&&alert(`This session includes reference(s) to local file(s):\\n${s.map((e=>`    ${e}`)).join(\"\\n\")}\\nLocal files cannot be loaded automatically when a saved session is restored.`),e}compressedSession(){return function(e){const t=new Uint8Array(e.length);for(var i=0;i<e.length;i++)t[i]=e.charCodeAt(i);const n=new cs(t),r=String.fromCharCode.apply(null,n);return btoa(r).replace(/\\+/g,\".\").replace(/\\//g,\"_\").replace(/=/g,\"-\")}(JSON.stringify(this.toJSON()))}sessionURL(){const e=window.location.href.slice(),t=e.indexOf(\"?\");return(t>0?e.substring(0,t):e)+\"?sessionURL=blob:\"+this.compressedSession()}mouseDownOnViewport(e,t){var i;i=r(e),this.vpMouseDown={viewport:t,lastMouseX:i.x,mouseDownX:i.x,lastMouseY:i.y,mouseDownY:i.y,referenceFrame:t.referenceFrame}}cancelTrackPan(){const e=this.dragObject;this.dragObject=void 0,this.isScrolling=!1,this.vpMouseDown=void 0,e&&e.viewport.referenceFrame.start!==e.start&&(this.updateViews(),this.fireEvent(\"trackdragend\",[e.viewport]))}isTrackPanning(){return this.dragObject}isSoftclipped(){return void 0!==this.trackViews.find((e=>!0===e.track.showSoftClips))}startTrackDrag(e){this.dragTrack=e}updateTrackDrag(e){if(e&&this.dragTrack){const t=this.dragTrack,i=this.trackViews.indexOf(e),n=this.trackViews.indexOf(t),r=this.trackViews;r[i]=t,r[n]=e;const s=this.trackViews[i].track.order;this.trackViews[n].track.order=s;const o=r.length;let a=s;if(i<n)for(let e=i+1;e<o;e++){const t=r[e].track;if(!(t.order<=a))break;t.order=Math.min(Number.MAX_SAFE_INTEGER,a+1),a=t.order}else for(let e=i-1;e>0;e--){const t=r[e].track;if(!(t.order>=a))break;t.order=Math.max(-Number.MAX_SAFE_INTEGER,a-1),a=t.order}this.reorderTracks()}}endTrackDrag(){this.dragTrack?(this.dragTrack=void 0,this.fireEvent(\"trackorderchanged\",[this.getTrackOrder()])):this.dragTrack=void 0}addEventHandlers(){this.addWindowResizeHandler(),this.addRootMouseUpHandler(),this.addRootMouseLeaveHandler(),this.addColumnContainerEventHandlers(),this.addKeyboardHandler()}removeEventHandlers(){this.removeWindowResizeHandler(),this.removeRootMouseUpHandler(),this.removeRootMouseLeaveHandler(),this.removeColumnContainerEventHandlers(),this.removeKeyboardHandler()}addWindowResizeHandler(){this.boundWindowResizeHandler=uA.bind(this),window.addEventListener(\"resize\",this.boundWindowResizeHandler)}removeWindowResizeHandler(){window.removeEventListener(\"resize\",this.boundWindowResizeHandler)}addRootMouseUpHandler(){this.boundRootMouseUpHandler=pA.bind(this),this.root.addEventListener(\"mouseup\",this.boundRootMouseUpHandler)}removeRootMouseUpHandler(){this.root.removeEventListener(\"mouseup\",this.boundRootMouseUpHandler)}addRootMouseLeaveHandler(){this.boundRootMouseLeaveHandler=pA.bind(this),this.root.addEventListener(\"mouseleave\",this.boundRootMouseLeaveHandler)}removeRootMouseLeaveHandler(){this.root.removeEventListener(\"mouseleave\",this.boundRootMouseLeaveHandler)}addColumnContainerEventHandlers(){this.boundColumnContainerMouseMoveHandler=fA.bind(this),this.boundColumnContainerTouchMoveHandler=fA.bind(this),this.boundColumnContainerMouseLeaveHandler=pA.bind(this),this.boundColumnContainerMouseUpHandler=pA.bind(this),this.boundColumnContainerTouchEndHandler=pA.bind(this),this.columnContainer.addEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.columnContainer.addEventListener(\"touchmove\",this.boundColumnContainerTouchMoveHandler),this.columnContainer.addEventListener(\"mouseleave\",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.addEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.columnContainer.addEventListener(\"touchend\",this.boundColumnContainerTouchEndHandler)}removeColumnContainerEventHandlers(){this.columnContainer.removeEventListener(\"mousemove\",this.boundColumnContainerMouseMoveHandler),this.columnContainer.removeEventListener(\"touchmove\",this.boundColumnContainerTouchMoveHandler),this.columnContainer.removeEventListener(\"mouseleave\",this.boundColumnContainerMouseLeaveHandler),this.columnContainer.removeEventListener(\"mouseup\",this.boundColumnContainerMouseUpHandler),this.columnContainer.removeEventListener(\"touchend\",this.boundColumnContainerTouchEndHandler)}addKeyboardHandler(){this.keyUpHandler=gA.bind(this),document.addEventListener(\"keyup\",this.keyUpHandler)}removeKeyboardHandler(){console.log(\"Remove handler\"),document.addEventListener(\"keyup\",this.keyUpHandler)}static uncompressSession(e){let t;if(e.indexOf(\"/gzip;base64\")>0){t=vs(e);let i=\"\";for(let e of t)i+=String.fromCharCode(e);return i}return function(e){e=e.replace(/\\./g,\"+\").replace(/_/g,\"/\").replace(/-/g,\"=\");const t=atob(e),i=[];for(let e=0;e<t.length;e++)i.push(t.charCodeAt(e));const n=hs(i);let r=\"\";for(let e of n)r+=String.fromCharCode(e);return r}(e.substring(5))}createCircularView(e,t){var i;return t=!0===t,this.circularView=(i=this,new Bm(e,{onChordClick:(e,t,n)=>{const r=e.data,s=r.mate;function o(e){e.chr=i.genome.getChromosomeName(e.refName);let t=!1;for(let n of i.referenceFrameList){const i=lm.fromLocusString(n.getLocusString());if(i.contains(e)){t=!0;break}if(i.overlaps(e)){n.extend(e),t=!0;break}}if(!t){const t=2e3,n=(e.start+e.end)/2;i.addMultiLocusPanel(e.chr,n-t,n+t)}}o(r),o(s)}})),this.circularViewControl=new Vy(this.navbar.toggle_button_container,this),this.circularView.setAssembly({name:this.genome.id,id:this.genome.id,chromosomes:Hm(this.genome)}),this.circularViewVisible=t,this.circularView}get circularViewVisible(){return void 0!==this.circularView&&this.circularView.visible}set circularViewVisible(e){this.circularView&&(this.circularView.visible=e,this.circularViewControl.setState(e))}get sampleInfoControl(){return this.navbar.sampleInfoControl}get overlayTrackButton(){return this.navbar.overlayTrackButton}get roiTableControl(){return this.navbar.roiTableControl}get sampleInfoControl(){return this.navbar.sampleInfoControl}get sampleNameControl(){return this.navbar.sampleNameControl}}async function uA(){if(!this.referenceFrameList)return;const e=this.calculateViewportWidth(this.referenceFrameList.length);for(let t of this.referenceFrameList){const i=this.referenceFrameList.indexOf(t),{chr:n,genome:r}=t,{bpLength:s}=r.getChromosome(t.chr),o=t.toBP(e);mu.isWholeGenomeView(n)||o>s?t.bpPerPixel=s/e:t.end=t.start+t.toBP(e);for(let{viewports:t}of this.trackViews)t[i].setWidth(e)}this.updateUIWithReferenceFrameList(),await this.updateViews(!0)}function fA(e){e.preventDefault();const{x:t,y:i}=r(e);if(this.vpMouseDown){const{viewport:e,referenceFrame:n}=this.vpMouseDown,r=Math.abs(t-this.vpMouseDown.mouseDownX)>Math.abs(i-this.vpMouseDown.mouseDownY);if(!this.dragObject&&!this.isScrolling)if(r)this.vpMouseDown.mouseDownX&&Math.abs(t-this.vpMouseDown.mouseDownX)>this.constants.dragThreshold&&(this.dragObject={viewport:e,start:n.start});else if(this.vpMouseDown.mouseDownY&&Math.abs(i-this.vpMouseDown.mouseDownY)>this.constants.scrollThreshold){this.isScrolling=!0;const t=e.$viewport.height(),i=e.trackView.maxViewportContentHeight();this.vpMouseDown.r=t/i}if(this.dragObject){const i=!this.isSoftclipped();let r=this.vpMouseDown.lastMouseX-t;n.shiftPixels(r,e.$viewport.width(),i)&&this.updateViews(),this.fireEvent(\"trackdrag\")}if(this.isScrolling){const t=this.vpMouseDown.r*(this.vpMouseDown.lastMouseY-i);e.trackView.moveScroller(t)}this.vpMouseDown.lastMouseX=t,this.vpMouseDown.lastMouseY=i}}function pA(e){this.cancelTrackPan(),this.endTrackDrag()}async function gA(e){if(this.referenceFrameList&&!(this.referenceFrameList.length>1)&&(\"KeyF\"===e.code||\"KeyB\"===e.code)){const t=this.getSelectedTrackViews();if(t.length>0){const i=t[0].track;if(\"function\"==typeof i.nextFeatureAfter){const t=this.referenceFrameList[0],n=t.viewport?t.viewport.getWidth():this.calculateViewportWidth(this.referenceFrameList.length),r=\"all\"===t.chr.toLowerCase(),s=i.visibilityWindow;if(r||s&&s>0&&t.bpPerPixel*n>s)return;const o=\"KeyF\"===e.code,a=t.chr,c=t.center,l=await i.nextFeatureAfter(a,c,o);if(l){const i=await this.genome.getChromosomeName(l.chr);if(a===i){const i=(l.start+l.end)/2;if(e.shiftKey){const e=this.config.minimumBases||40,r=Math.max(e,1.1*(l.end-l.start));t.start=Math.max(0,i-r/2),t.end=i+r/2,t.bpPerPixel=(t.end-t.start)/n}else t.shift(i-c);this.updateViews()}else{t.chr=i;const r=(l.start+l.end)/2;if(e.shiftKey){const e=this.config.minimumBases||40,i=Math.max(e,1.1*(l.end-l.start));t.start=Math.max(0,r-i/2),t.end=t.start+i,t.bpPerPixel=(t.end-t.start)/n}else t.start=r-n*t.bpPerPixel/2,t.end=t.start+n*t.bpPerPixel;this.updateViews()}}}}}}function mA(e,t){for(let{viewports:i}of e)for(let e of i)e.$trackLabel&&(0===i.indexOf(e)&&!0===t?e.$trackLabel.show():e.$trackLabel.hide())}let wA=[];function bA(e){return void 0===e.minimumBases&&(e.minimumBases=40),void 0===e.showIdeogram&&(e.showIdeogram=!0),void 0===e.showCircularView&&(e.showCircularView=!1),void 0===e.showCircularViewButton&&(e.showCircularViewButton=!1),void 0===e.showTrackLabelButton&&(e.showTrackLabelButton=!0),void 0===e.showTrackLabels&&(e.showTrackLabels=!0),void 0===e.showCursorTrackingGuideButton&&(e.showCursorTrackingGuideButton=!0),void 0===e.showCursorGuide&&(e.showCursorGuide=e.showCursorTrackingGuide||!1),void 0===e.showCenterGuideButton&&(e.showCenterGuideButton=!0),void 0===e.showCenterGuide&&(e.showCenterGuide=!1),void 0===e.showSampleNames&&(e.showSampleNames=!1),void 0===e.showSVGButton&&(e.showSVGButton=!0),void 0===e.showControls&&(e.showControls=!0),void 0===e.showNavigation&&(e.showNavigation=!0),void 0===e.showRuler&&(e.showRuler=!0),void 0===e.flanking&&(e.flanking=1e3),void 0===e.pairsSupported&&(e.pairsSupported=!0),e.tracks||(e.tracks=[]),e}const FA=Qs.setApiKey;const vA=Qs.oauth;var yA={TrackUtils:Pa,IGVGraphics:xo,MenuUtils:bo,DataRangeDialog:_o,createTrack:async function(e,t){return await dA.prototype.createTrack.call(t,e)},createBrowser:async function(e,t){void 0===t&&(t={}),mu.KNOWN_GENOMES||await mu.initializeGenomes(t),bA(t),t.queryParametersSupported&&function(e){var t,i,n,r,s,o,a,c,l;let h,d,u;if(a=window.location.href,s={},t=a.indexOf(\"?\"),i=a.lastIndexOf(\"#\"),t>=0)for(i<0&&(i=a.length),n=t+1;n<i;)(r=a.indexOf(\"&\",n))<0&&(r=i),2===(o=a.substring(n,r).split(\"=\",2)).length?(c=o[0],l=decodeURIComponent(o[1]),\"file\"===c?h=l.split(\",\"):\"index\"===c?d=l.split(\",\"):\"name\"===c?u=l.split(\",\"):\"genome\"===c?!l.startsWith(\"https://\")&&!l.startsWith(\"http://\")||l.endsWith(\".json\")?(e[c]=l,e.reference=void 0):e.reference={fastaURL:l,indexURL:l+\".fai\"}:(\"reference\"===c&&(e.genome=void 0),e[c]=l),n=r+1):n++;if(h){e.tracks||(e.tracks=[]);for(let t=0;t<h.length;t++){if(h[t].endsWith(\".xml\")||h[t].endsWith(\".json\")){e.sessionURL=h[t];break}const i={url:h[t]};d&&d.length>t&&(i.indexURL=d[t]),u&&u.length>t&&(i.name=u[t]),e.tracks.push(i)}}}(t),t.apiKey&&Qs.setApiKey(t.apiKey),t.oauthToken&&Qs.setOauthToken(t.oauthToken),t.clientId&&!Ts()&&await async function(e){if(!google.accounts.oauth2.initTokenClient)throw new Error(\"Google accounts token client not loaded (https://accounts.google.com/gsi/client)\");if(Ts())throw new Error(\"Google client is already initialized\");const t={client_id:e.client_id||e.clientId,scope:e.scope||\"https://www.googleapis.com/auth/userinfo.profile\",state:e.state||\"igv\",error:e=>{throw new Error(e.type)},hint:e.hint,hosted_domain:e.hosted_domain},i=google.accounts.oauth2.initTokenClient(t);google.igv={tokenClient:i,apiKey:e.apiKey}}({client_id:t.clientId,apiKey:t.apiKey,scope:\"https://www.googleapis.com/auth/userinfo.profile\"});const i=new dA(t,e);wA.push(i),i.startSpinner();const n=t.sessionURL||t.session||t.hubURL;return n?await i.loadSession({url:n}):await i.loadSessionObject(t),i.stopSpinner(),i.navbar.navbarDidResize(),i},removeBrowser:function(e){e.dispose(),e.root.remove(),wA=wA.filter((t=>t!==e))},removeAllBrowsers:function(){for(let e of wA)e.dispose(),e.root.remove();wA=[]},visibilityChange:async function(){for(let e of wA)await e.visibilityChange()},setGoogleOauthToken:function(e){return Qs.setOauthToken(e)},setOauthToken:function(e,t){return Qs.setOauthToken(e,t)},oauth:vA,version:yy,setApiKey:FA,TrackBase:Hl,registerTrackClass:function(e,t){wy.set(e,((e,i)=>new t(e,i)))},registerTrackCreatorFunction:function(e,t){wy.set(e,t)},registerFileFormats:function(e,t){Sl[e]={fields:t}},loadSessionFile:dA.loadSessionFile};return yA}();\n",
-       "//# sourceMappingURL=igv.iife.js.map\n"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "/**\n",
-       " * Global handler for igv.js messages.  Messages have the form\n",
-       " * {\n",
-       " *     command  -- the command to execute\n",
-       " *     id -- the id of the igv.js browser, if applicable\n",
-       " *     data -- any data needed for the command\n",
-       " * }\n",
-       " */\n",
-       "\n",
-       "// Use a self-evaluating function to keep variables in this file scope, with the execption of the global handler\n",
-       "\n",
-       "(function () {\n",
-       "\n",
-       "    const isColab = window.google !== undefined && window.google.colab\n",
-       "    const isNotebook = !isColab && window.Jupyter !== undefined\n",
-       "\n",
-       "    let svgComm\n",
-       "    if (isNotebook) {\n",
-       "        svgComm = Jupyter.notebook.kernel.comm_manager.new_comm('svg', {})\n",
-       "    }\n",
-       "\n",
-       "    async function toSVG(displayID, locus, svg) {\n",
-       "        //console.log(isNotebook + \" \" + locus)\n",
-       "        if (isNotebook) {\n",
-       "            svgComm.send({\n",
-       "                \"display_id\": displayID,\n",
-       "                \"locus\": locus,\n",
-       "                \"svg\": svg\n",
-       "            })\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    console.log(\"Installing IGVMessageHandler\")\n",
-       "\n",
-       "    function convertUrlsAndPaths(session) {\n",
-       "        if (session.reference) {\n",
-       "            for (let pre of [\"fasta\", \"index\", \"cytoband\", \"cytobandBb\", \"compressedIndex\", \"alias\", \"aliasBb\",\n",
-       "            \"twoBit\", \"twoBitBpt\", \"chromAliasBb\", \"chromSizes\", \"trix\"]) {\n",
-       "                convert(session.reference, pre)\n",
-       "            }\n",
-       "            if (session.reference.tracks) {\n",
-       "                for (let t of session.reference.tracks) {\n",
-       "                    convert(t)\n",
-       "                    convert(t, \"index\")\n",
-       "                    if (!t.indexURL) {\n",
-       "                        t.indexed = false\n",
-       "                    }\n",
-       "                }\n",
-       "            }\n",
-       "        }\n",
-       "\n",
-       "        if (session.tracks) {\n",
-       "            for (let t of session.tracks) {\n",
-       "                convert(t)\n",
-       "                convert(t, \"index\")\n",
-       "                if (!t.indexURL) {\n",
-       "                    t.indexed = false\n",
-       "                }\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Return true if the sessionJson object contains only absolute URLs to resources\n",
-       "     */\n",
-       "    function safeToWeblink(sessionJson) {\n",
-       "        const unsafe = (url) => typeof url.startsWith != 'function' || !url.startsWith(\"http\")\n",
-       "        if (sessionJson.reference) {\n",
-       "            if (unsafe(sessionJson.reference.fastaURL)) return false\n",
-       "        }\n",
-       "        if (sessionJson.tracks) {\n",
-       "            const urls = sessionJson.tracks.filter(t => t.url).map(t => t.url)\n",
-       "            if (urls.some(unsafe)) return false\n",
-       "        }\n",
-       "        return true\n",
-       "    }\n",
-       "\n",
-       "    class MessageHandler {\n",
-       "\n",
-       "        constructor() {\n",
-       "            this.browserCache = new Map()\n",
-       "            this.messageQueue = new Queue()\n",
-       "        }\n",
-       "\n",
-       "        on(msg) {\n",
-       "            this.messageQueue.enqueue(msg)\n",
-       "            this.processQueue()\n",
-       "        }\n",
-       "\n",
-       "        async processQueue() {\n",
-       "\n",
-       "            const convertTrackData = (data) => {\n",
-       "                convert(data)\n",
-       "                convert(data, \"index\")\n",
-       "                if (!data.indexURL) {\n",
-       "                    data.indexed = false\n",
-       "                }\n",
-       "            }\n",
-       "\n",
-       "            if (!this.processing) {\n",
-       "                this.processing = true\n",
-       "                while (!this.messageQueue.isEmpty()) {\n",
-       "                    const msg = this.messageQueue.dequeue()\n",
-       "                    const command = msg.command\n",
-       "                    const browserID = msg.id\n",
-       "                    const data = msg.data\n",
-       "                    const browser = this.browserCache.get(browserID)\n",
-       "                    try {\n",
-       "                        switch (command) {\n",
-       "                            case \"createBrowser\":\n",
-       "\n",
-       "                                // custom button bar\n",
-       "                                const button_container = document.getElementById(`${browserID}_buttons`) // <= created from python\n",
-       "                                const customButtonDiv = document.createElement('div')\n",
-       "                                customButtonDiv.style = `background: #f3f3f3;padding: 5px;border-color: #bfbfbf;border-style: solid;border-width: thin;border-radius: 3px;`\n",
-       "                                button_container.appendChild(customButtonDiv)\n",
-       "\n",
-       "                                data.sync = true\n",
-       "                                convertUrlsAndPaths(data)\n",
-       "\n",
-       "                                const container = document.getElementById(`${browserID}_igvcontainer`)  // <= created from python\n",
-       "                                const newBrowser = await igv.createBrowser(container, data)\n",
-       "                                this.browserCache.set(browserID, newBrowser)\n",
-       "\n",
-       "                                // Add igv-notebook button bar\n",
-       "                                const toJsonButton = document.createElement('button')\n",
-       "                                toJsonButton.innerText = \"Save Session\"\n",
-       "                                toJsonButton.style = \"margin-right:5px\"\n",
-       "                                toJsonButton.addEventListener('click', (evt) => {\n",
-       "                                    let fn\n",
-       "                                    if (isNotebook) {\n",
-       "                                        fn = prompt(\"Filename:\", \"session.json\")\n",
-       "                                    } else {\n",
-       "                                        fn = \"session.json\"\n",
-       "                                    }\n",
-       "                                    if (fn) {\n",
-       "                                        const json = newBrowser.toJSON()\n",
-       "                                        const jsonString = JSON.stringify(json, null, '\\t')\n",
-       "                                        download(fn, jsonString)\n",
-       "                                    }\n",
-       "                                })\n",
-       "                                customButtonDiv.appendChild(toJsonButton)\n",
-       "\n",
-       "                                const webLinkNode = document.createElement('a')\n",
-       "                                webLinkNode.target = \"igvWeb\"\n",
-       "                                webLinkNode.innerText = \"Link to IGV-Web\"\n",
-       "                                webLinkNode.style.display = \"none\"\n",
-       "\n",
-       "                                const shareButton = document.createElement('button')\n",
-       "                                shareButton.innerText = \"Show IGV-Web Link\"\n",
-       "                                shareButton.style = \"margin-right:5px\"\n",
-       "                                shareButton.addEventListener('click', async (evt) => {\n",
-       "\n",
-       "                                    if (safeToWeblink(newBrowser.toJSON())) {\n",
-       "                                        const sessionURL = `https://igv.org/app?sessionURL=blob:${newBrowser.compressedSession()}`\n",
-       "                                        const shortURL = await shortenURL(sessionURL)\n",
-       "                                        webLinkNode.innerText = \"Link to IGV-Web\"\n",
-       "                                        webLinkNode.setAttribute(\"href\", shortURL)\n",
-       "                                        webLinkNode.style.display = \"inline-block\"\n",
-       "                                        shareButton.innerText = \"Update IGV-Web Link\"\n",
-       "                                    } else {\n",
-       "                                        webLinkNode.innerText = \"Cannot link -- non URL resources used\"\n",
-       "                                        webLinkNode.style.display = \"inline-block\"\n",
-       "                                    }\n",
-       "                                })\n",
-       "                                customButtonDiv.appendChild(shareButton)\n",
-       "                                customButtonDiv.appendChild(webLinkNode)\n",
-       "\n",
-       "                                if (isNotebook) {\n",
-       "                                    const toSVGButton = document.createElement('button')\n",
-       "                                    toSVGButton.innerText = \"To SVG\"\n",
-       "                                    toSVGButton.style = \"float:right\"\n",
-       "                                    toSVGButton.addEventListener('click', (evt) => {\n",
-       "                                        const locus = newBrowser.referenceFrameList.map(rf => rf.getLocusString()).join(' ')\n",
-       "                                        const svg = newBrowser.toSVG()\n",
-       "                                        toSVG(browserID, locus, svg)\n",
-       "                                    })\n",
-       "                                    customButtonDiv.appendChild(toSVGButton)\n",
-       "                                }\n",
-       "\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadSession\":\n",
-       "                                convertUrlsAndPaths(data)\n",
-       "                                browser.loadSessionObject(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadTrack\":\n",
-       "                                convertTrackData(data)\n",
-       "                                await browser.loadTrack(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"loadROI\":\n",
-       "                                if (Array.isArray(data)) {\n",
-       "                                    data.map(convertTrackData)\n",
-       "                                } else {\n",
-       "                                    convertTrackData(data)\n",
-       "                                }\n",
-       "                                await browser.loadROI(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"clearROIs\":\n",
-       "                                await browser.clearROIs()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"search\":\n",
-       "                                browser.search(data)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"zoomIn\":\n",
-       "                                browser.zoomIn()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"zoomOut\":\n",
-       "                                browser.zoomOut()\n",
-       "                                break\n",
-       "\n",
-       "                            case \"remove\":\n",
-       "                                this.browserCache.delete(browserID)\n",
-       "                                document.getElementById(browserID).parentNode.removeChild(container)\n",
-       "                                break\n",
-       "\n",
-       "                            case \"toSVG\":\n",
-       "                                const displayId = data\n",
-       "                                const svg = browser.toSVG()\n",
-       "                                const locus = browser.referenceFrameList.map(rf => rf.getLocusString()).join(' ')\n",
-       "                                toSVG(displayId, locus, svg)\n",
-       "                                break\n",
-       "\n",
-       "                            default:\n",
-       "                                console.error(\"Unrecognized method: \" + msg.command)\n",
-       "                        }\n",
-       "                    } catch (e) {\n",
-       "                        console.error(e)\n",
-       "                    }\n",
-       "                }\n",
-       "                this.processing = false\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Potentially convert a path to a local File-like object.\n",
-       "     * @param path\n",
-       "     * @returns {*}\n",
-       "     */\n",
-       "    function createNotebookFile(path) {\n",
-       "        if (!path ||\n",
-       "            path.startsWith(\"https://\") || path.startsWith(\"http://\") || path.startsWith(\"gs://\") || path.startsWith(\"data:\")) {\n",
-       "            return path\n",
-       "        } else {\n",
-       "            // Try to create a notebook file.  If no notebook file implementation is available for the kernel in\n",
-       "            // use (e.g. Jupyter Lab) treat as a URL.\n",
-       "            const nbFile = igv.createNotebookLocalFile({path})\n",
-       "            if (nbFile != null) {\n",
-       "                return nbFile\n",
-       "            } else {\n",
-       "                // Try to treat as relative URL.  This may or may not work\n",
-       "                return convertURL(path)\n",
-       "            }\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Convert relative URLs to absolute.  Primarily for Jupyter Lab, not generally needed for Jupyter Notebook\n",
-       "     * @param url\n",
-       "     * @returns {*}\n",
-       "     */\n",
-       "    function convertURL(url) {\n",
-       "\n",
-       "        const pageURL = window.location.href\n",
-       "\n",
-       "        if (!url ||\n",
-       "            url.startsWith(\"https://\") ||\n",
-       "            url.startsWith(\"http://\") ||\n",
-       "            url.startsWith(\"gs://\") ||\n",
-       "            url.startsWith(\"data:\")) {\n",
-       "            return url\n",
-       "        } else if (isColab) {\n",
-       "            // Interpret relative url as a path.\n",
-       "            igv.createNotebookLocalFile({path: url})\n",
-       "        } else if (isNotebook) {\n",
-       "            // Jupyter Notebook\n",
-       "            //\n",
-       "            // Examples\n",
-       "            // https://hub-binder.mybinder.ovh/user/igvteam-igv-notebook-tnlb45ie/notebooks/examples/BamFiles-Jupyter.ipynb\n",
-       "            //   => https://hub-binder.mybinder.ovh/user/igvteam-igv-notebook-tnlb45ie/files/examples/data/gstt1_sample.bam\",\n",
-       "\n",
-       "            const baseURL = document.querySelector('body').getAttribute('data-base-url')\n",
-       "            const notebookPath = document.querySelector('body').getAttribute('data-notebook-path')\n",
-       "            const notebookName = document.querySelector('body').getAttribute('data-notebook-name')\n",
-       "            const notebookDir = notebookPath.slice(0, -1 * notebookName.length)\n",
-       "\n",
-       "            //`${location.origin}${base_path}files/${nb_dir}${url}`\n",
-       "            if (url.startsWith(\"/\")) {\n",
-       "                url = `files${url}`\n",
-       "                return encodeURI(`${location.origin}${baseURL}${url}`)\n",
-       "            } else {\n",
-       "                // URL is relative to notebook\n",
-       "                return encodeURI(`${location.origin}${baseURL}files/${notebookDir}${url}`)\n",
-       "            }\n",
-       "        } else if (pageURL.includes(\"/lab\")) {\n",
-       "\n",
-       "            console.log(\"Jupyter lab\")\n",
-       "            // Jupyter Lab\n",
-       "\n",
-       "            // Examples\n",
-       "            // http://localhost:8888/lab/workspaces/auto-N/tree/examples/BamFiles.ipynb\n",
-       "            //     =>  http://localhost:8888/files/examples/data/gstt1_sample.bam\n",
-       "            //\n",
-       "            // https://hub.gke2.mybinder.org/user/igvteam-igv-notebook-5ivkyktt/lab/tree/examples/BamFiles.ipynb\n",
-       "            //    => https://hub.gke2.mybinder.org/user/igvteam-igv-notebook-5ivkyktt/files/examples/data/gstt1_sample.bam\n",
-       "\n",
-       "            const baseIndex = pageURL.indexOf(\"/lab\")\n",
-       "            const baseURL = pageURL.substring(0, baseIndex)\n",
-       "\n",
-       "            if (url.startsWith(\"/\")) {\n",
-       "                return encodeURI(`${baseURL}/files${url}`)\n",
-       "            } else if (pageURL.includes(\"/tree/\")) {\n",
-       "                // Interpret URL as relative to notebook location.  This is not reliable, '/tree/' is not always in the page URL\n",
-       "                const treeIndex = pageURL.indexOf(\"/tree/\") + 6\n",
-       "                const lastSlashIndex = pageURL.lastIndexOf(\"/\")\n",
-       "                const notebookDir = pageURL.substring(treeIndex, lastSlashIndex)\n",
-       "                return encodeURI(`${baseURL}/files/${notebookDir}/${url}`)\n",
-       "            } else {\n",
-       "                // We don't know how to determine the notebook path\n",
-       "                console.warn(\"Page url missing '/tree/'.  Can't determine notebook path.\")\n",
-       "                return encodeURI(`${baseURL}/files/${url}`)\n",
-       "            }\n",
-       "        } else {\n",
-       "            // We should never get here,\n",
-       "            return encodeURI(url)\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    function convert(config, prefix) {\n",
-       "        const urlProp = prefix ? prefix + \"URL\" : \"url\"\n",
-       "        const pathProp = prefix ? prefix + \"Path\" : \"path\"\n",
-       "        if (config[pathProp]) {\n",
-       "            config[urlProp] = createNotebookFile(config[pathProp])\n",
-       "        } else if (config[urlProp]) {\n",
-       "            config[urlProp] = convertURL(config[urlProp])\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    class Queue {\n",
-       "        constructor() {\n",
-       "            this.elements = []\n",
-       "        }\n",
-       "\n",
-       "        enqueue(e) {\n",
-       "            this.elements.push(e)\n",
-       "        }\n",
-       "\n",
-       "        dequeue() {\n",
-       "            return this.elements.shift()\n",
-       "        }\n",
-       "\n",
-       "        isEmpty() {\n",
-       "            return this.elements.length == 0\n",
-       "        }\n",
-       "\n",
-       "        peek() {\n",
-       "            return !this.isEmpty() ? this.elements[0] : undefined\n",
-       "        }\n",
-       "\n",
-       "        length() {\n",
-       "            return this.elements.length\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    window.igv.MessageHandler = new MessageHandler()\n",
-       "\n",
-       "    function download(filename, text) {\n",
-       "\n",
-       "        const data = URL.createObjectURL(new Blob([text], {type: \"application/octet-stream\"}))\n",
-       "        const element = document.createElement('a')\n",
-       "        element.setAttribute('href', data)\n",
-       "        element.setAttribute('download', filename)\n",
-       "        element.style.display = 'none'\n",
-       "        document.body.appendChild(element)\n",
-       "        element.click()\n",
-       "        document.body.removeChild(element)\n",
-       "    }\n",
-       "\n",
-       "    async function shortenURL(url) {\n",
-       "        const endpoint = \"https://2et6uxfezb.execute-api.us-east-1.amazonaws.com/dev/tinyurl/\"\n",
-       "        const enc = encodeURIComponent(url)\n",
-       "        const response = await fetch(`${endpoint}${enc}`)\n",
-       "        if (response.ok) {\n",
-       "            return response.text()\n",
-       "        } else {\n",
-       "            throw new Error(response.statusText)\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    console.log(\"igv.MessageHandler installed\")\n",
-       "\n",
-       "})()"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "/**\n",
-       " * Mock objects to emulate the browser \"File\" class for use with Jupyter and Colab notebooks.  These objects delegate\n",
-       " * actual file reading to python.\n",
-       " */\n",
-       "\n",
-       "// Use a self-evaluating function to keep variables in this file scope\n",
-       "\n",
-       "(function () {\n",
-       "\n",
-       "    const isColab =  window.google !== undefined && window.google.colab\n",
-       "    const isNotebook =  !isColab &&  window.Jupyter !== undefined\n",
-       "\n",
-       "    igv.createNotebookLocalFile = function (options) {\n",
-       "        if (isColab) {\n",
-       "            return new ColabLocalFile(options)\n",
-       "        } else if (isNotebook) {\n",
-       "            return new JupyterLocalFile(options)\n",
-       "        } else {\n",
-       "            return undefined;  //TODO -- throw error?\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "\n",
-       "    // Start up a Comm object if in a Jupyter Notebook environment (i.e. not Colab or JupyterLab).\n",
-       "    let comm\n",
-       "    const pendingRequests = new Map()\n",
-       "    if (isNotebook) {\n",
-       "        console.log('registering comm')\n",
-       "        comm = Jupyter.notebook.kernel.comm_manager.new_comm('file_request', {})\n",
-       "        // Register a handler\n",
-       "        comm.on_msg(function (msg) {\n",
-       "            const id = msg.content.data.id\n",
-       "            const data = msg.content.data.data\n",
-       "            pendingRequests.set(id, data)\n",
-       "        })\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Emulates a browser \"File\" for Jupyter notebooks.  File reading is delegated to python via Comms messaging.\n",
-       "     * Polling is used to synchronize the async message passing.\n",
-       "     *\n",
-       "     * NOTE: This will not work for JupyterLab\n",
-       "     */\n",
-       "    class JupyterLocalFile {\n",
-       "\n",
-       "        constructor({path, name, start, end}) {\n",
-       "            this.type = 'JupyterLocalFile'\n",
-       "            this.path = path\n",
-       "            this.name = name || path\n",
-       "            this.start = start\n",
-       "            this.end = end\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a new Blob object containing the data in the specified range of bytes of the blob on which it's called.\n",
-       "         * @param start An index into the Blob indicating the first byte to include in the new Blob\n",
-       "         * @param end  An index into the Blob indicating the first byte that will *not* be included in the new Blob\n",
-       "         * @param contentType\n",
-       "         * @returns {*}\n",
-       "         */\n",
-       "        slice(start, end) {\n",
-       "            return new JupyterLocalFile({path: this.path, name: this.name, start, end})\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with an ArrayBuffer containing the entire contents of the Blob as binary data.\n",
-       "         *\n",
-       "         * @returns {Promise<*>}\n",
-       "         */\n",
-       "        async arrayBuffer() {\n",
-       "\n",
-       "            const id = uniqueID()\n",
-       "            const path = this.path\n",
-       "            const promise = new Promise((resolve, reject) => {\n",
-       "                let count = 0\n",
-       "\n",
-       "                function poll() {\n",
-       "\n",
-       "                    if (count > 100) {\n",
-       "                        console.error(`error reading ${path}: timed out`)\n",
-       "                        reject(`error reading ${path}: timed out`)\n",
-       "                    }\n",
-       "\n",
-       "                    count++\n",
-       "                    if (pendingRequests.has(id)) {\n",
-       "                        const data = pendingRequests.get(id)\n",
-       "                        const dataString = atob(data)\n",
-       "                        const bytes = new Uint8Array(dataString.length)\n",
-       "                        for (var i = 0; i < dataString.length; i++) {\n",
-       "                            bytes[i] = dataString.charCodeAt(i)\n",
-       "                        }\n",
-       "                        pendingRequests.delete(id)\n",
-       "                        resolve(bytes.buffer)\n",
-       "                    } else {\n",
-       "                        setTimeout(poll, 100)\n",
-       "                    }\n",
-       "                }\n",
-       "\n",
-       "                poll()\n",
-       "            })\n",
-       "\n",
-       "            const msg = (this.start === undefined) ?\n",
-       "                {id: id, 'path': this.path, 'method': 'arrayBuffer'} :\n",
-       "                {id: id, 'path': this.path, 'method': 'arrayBuffer', 'start': this.start, 'end': this.end}\n",
-       "\n",
-       "            comm.send(msg)\n",
-       "\n",
-       "            return promise\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with a USVString containing the entire contents of the Blob interpreted as UTF-8 text.\n",
-       "         *\n",
-       "         * @returns {Promise<string>}\n",
-       "         */\n",
-       "        async text() {\n",
-       "            throw Error(\"text not implemented\")\n",
-       "        }\n",
-       "\n",
-       "        stream() {\n",
-       "            throw Error(\"stream not implemented\")\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    /**\n",
-       "     * Emulates a browser \"File\" for Colab environments.\n",
-       "     */\n",
-       "    class ColabLocalFile {\n",
-       "\n",
-       "        constructor({path, name, start, end}) {\n",
-       "            this.type = 'ColabLocalFile'\n",
-       "            this.path = path\n",
-       "            this.name = name || path\n",
-       "            this.start = start\n",
-       "            this.end = end\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a new Blob object containing the data in the specified range of bytes of the blob on which it's called.\n",
-       "         * @param start An index into the Blob indicating the first byte to include in the new Blob\n",
-       "         * @param end  An index into the Blob indicating the first byte that will *not* be included in the new Blob\n",
-       "         * @param contentType\n",
-       "         * @returns {*}\n",
-       "         */\n",
-       "        slice(start, end) {\n",
-       "            return new ColabLocalFile({path: this.path, name: this.name, start, end})\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with an ArrayBuffer containing the entire contents of the Blob as\n",
-       "         * binary data.\n",
-       "         */\n",
-       "        async arrayBuffer() {\n",
-       "\n",
-       "            const args = (this.start === undefined) ?\n",
-       "                [this.path] :\n",
-       "                [this.path, this.start.toString(), this.end.toString()]\n",
-       "\n",
-       "            const result = await google.colab.kernel.invokeFunction(\n",
-       "                'ReadFile', // The callback name.\n",
-       "                args, // The arguments.\n",
-       "                {}) // kwargs\n",
-       "            const data = result.data[\"text/plain\"]\n",
-       "            const dataString = atob(data.substring(2, data.length - 1))\n",
-       "            const bytes = new Uint8Array(dataString.length)\n",
-       "            for (var i = 0; i < dataString.length; i++) {\n",
-       "                bytes[i] = dataString.charCodeAt(i)\n",
-       "            }\n",
-       "            return bytes.buffer\n",
-       "        }\n",
-       "\n",
-       "        /**\n",
-       "         * Returns a promise that resolves with a USVString containing the entire contents of the Blob interpreted as UTF-8 text.\n",
-       "         *\n",
-       "         * @returns {Promise<string>}\n",
-       "         */\n",
-       "        async text() {\n",
-       "            throw Error(\"text not implemented\")\n",
-       "        }\n",
-       "\n",
-       "        stream() {\n",
-       "            throw Error(\"stream not implemented\")\n",
-       "        }\n",
-       "    }\n",
-       "\n",
-       "    let counter = 0\n",
-       "\n",
-       "    function uniqueID() {\n",
-       "        return `${Math.random()}-${counter++}`\n",
-       "    }\n",
-       "\n",
-       "})()"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/html": [
-       "<div id=\"jb_3263345_buttons\"></div><div id=\"jb_3263345_igvcontainer\"></div>"
-      ],
-      "text/plain": [
-       "<IPython.core.display.HTML object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/javascript": [
-       "window.igv.MessageHandler.on({\"id\": \"jb_3263345\", \"command\": \"createBrowser\", \"data\": {\"reference\": {\"id\": \"idAnoFuneDA-416_04\", \"name\": \"Anopheles funestus\", \"fastaURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_afun_release/reference/genome/idAnoFuneDA-416_04/idAnoFuneDA-416_04_1.curated_primary.fa\", \"indexURL\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_afun_release/reference/genome/idAnoFuneDA-416_04/idAnoFuneDA-416_04_1.curated_primary.fa.fai\", \"tracks\": [{\"name\": \"Genes\", \"type\": \"annotation\", \"format\": \"gff3\", \"url\": \"https://storage.googleapis.com/vo_anoph_temp_us_central1/vo_afun_release/reference/genome/idAnoFuneDA-416_04/VectorBase-61_AfunestusidAnoFuneDA416_04_patched.gff3.gz\", \"indexed\": false}]}, \"locus\": \"2RL:2,441,878-2,468,205\", \"id\": \"jb_3263345\"}})"
-      ],
-      "text/plain": [
-       "<IPython.core.display.Javascript object>"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "<igv_notebook.browser.Browser at 0x11a4f5b10>"
-      ]
-     },
-     "execution_count": 6,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "af1.igv(region=\"2RL:2,441,878-2,468,205\")"
    ]
@@ -3854,7 +163,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d73b2743",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -3864,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6ccb0fe4",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -3879,7 +188,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d96182f0",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -3894,7 +203,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ac02dc0b",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -3902,7 +211,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -3915,15 +223,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.11"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

From 6802977d917fd04559e207d9d4094a53d7ecf10b Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 29 Sep 2026 13:01:47 +0100
Subject: [PATCH 11/38] fix field order to hopefully enable analysis of outputs
 from bcftools

---
 malariagen_data/anoph/to_vcf.py  | 15 +++++++++-
 tests/anoph/test_vcf_exporter.py | 47 ++++++++++++++++++++++++++++++++
 2 files changed, 61 insertions(+), 1 deletion(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 132386520..387a99599 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -13,8 +13,12 @@
 from . import plink_params
 from . import vcf_params
 
-# Supported FORMAT fields and their VCF header definitions.
+# Supported FORMAT fields, the fixed order in which their values are
+# always written per sample (regardless of what order the caller's
+# `fields` argument happens to iterate in — e.g. a set has no
+# guaranteed order at all), and their VCF header definitions.
 _VALID_FIELDS = {"GT", "GQ", "AD", "MQ"}
+_FIELD_ORDER = ("GT", "GQ", "AD", "MQ")
 _FORMAT_HEADERS = {
     "GT": '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
     "GQ": '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">',
@@ -131,6 +135,15 @@ def snp_calls_to_vcf(
         if "GT" not in fields:
             raise ValueError("GT must be included in fields.")
 
+        # Canonicalise the field order to _FIELD_ORDER. The per-sample
+        # values below are always written in this fixed order; if the
+        # FORMAT column (built from `fields` further down) used the
+        # caller's order instead, a `fields` argument with a different
+        # (or undefined, e.g. a set) order would produce a VCF whose
+        # FORMAT column lies about which value is which — which is
+        # exactly what happened before this fix.
+        fields = tuple(f for f in _FIELD_ORDER if f in fields)
+
         if os.path.exists(output_path) and not overwrite:
             return output_path
 
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index 7ea33a846..bcdd67e4e 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -335,6 +335,53 @@ def test_vcf_exporter_fields(fixture, api: SnpVcfExporter, tmp_path):
         assert len(parts) == 2, f"Expected GT:GQ, got {sample_val!r}"
 
 
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_fields_as_set(fixture, api: SnpVcfExporter, tmp_path):
+    # A `set` has no guaranteed iteration order. The FORMAT column must
+    # still come out in the same fixed order (GT, GQ, AD, MQ) that the
+    # per-sample values are actually written in, regardless of what
+    # order `fields` iterates in as passed by the caller. Previously
+    # the FORMAT column used the caller's (here, arbitrary) order while
+    # values were always written GT:GQ:AD:MQ, so a `set` could easily
+    # produce a VCF whose header lied about which value was which —
+    # e.g. declaring the first value as "MQ" when it was actually the
+    # GT string, which bcftools then fails to parse.
+    region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
+
+    output_path = str(tmp_path / "test_fields_set.vcf")
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+        fields={"GT", "GQ", "AD", "MQ"},
+    )
+
+    with open(output_path) as f:
+        lines = f.readlines()
+
+    data_lines = [line for line in lines if not line.startswith("#")]
+    assert len(data_lines) > 0
+
+    for line in data_lines:
+        fields_row = line.strip().split("\t")
+        # FORMAT column must always be in this fixed order.
+        assert fields_row[8] == "GT:GQ:AD:MQ"
+
+        for sample_val in fields_row[9:]:
+            gt, gq, ad, mq = sample_val.split(":")
+            # GT is the only field allowed to contain "/"; if it ended
+            # up anywhere else (or something else ended up in its
+            # place), that's exactly the bug this test guards against.
+            assert gt == "./." or "/" in gt
+            assert "/" not in gq
+            assert "/" not in ad
+            assert "/" not in mq
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_fields_gt_required(fixture, api: SnpVcfExporter, tmp_path):
     region = api.contigs[0]

From 6428c98c4b4998851eb3b22716930efcfd58f77a Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 29 Sep 2026 13:17:05 +0100
Subject: [PATCH 12/38] more format fixing

---
 malariagen_data/anoph/to_vcf.py  |  2 +-
 tests/anoph/test_vcf_exporter.py | 39 ++++++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 387a99599..ac1f32f5f 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -23,7 +23,7 @@
     "GT": '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
     "GQ": '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">',
     "AD": '##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth">',
-    "MQ": '##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Mapping Quality">',
+    "MQ": '##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mapping Quality">',
 }
 
 # snp_calls_to_vcf() only supports exporting a single sample at a time
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index bcdd67e4e..92237cabc 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -1,6 +1,8 @@
 import gzip
 import os
 import random
+import shutil
+import subprocess
 
 import pytest
 from pytest_cases import parametrize_with_cases
@@ -382,6 +384,43 @@ def test_vcf_exporter_fields_as_set(fixture, api: SnpVcfExporter, tmp_path):
             assert "/" not in mq
 
 
+@pytest.mark.skipif(shutil.which("bcftools") is None, reason="bcftools not installed")
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_output_is_valid_per_bcftools(
+    fixture, api: SnpVcfExporter, tmp_path
+):
+    # A stronger check than the Python-level assertions above: actually
+    # parse the output with bcftools, the way a real consumer would.
+    # This is what caught both the FORMAT field-order bug (a `set` of
+    # fields could desync the FORMAT column from the hardcoded value
+    # order) and the MQ header Type=Integer/actual-float-value mismatch
+    # — neither of which a purely structural Python check (e.g.
+    # splitting on "\t"/":") would notice, since both produce
+    # "well-formed" tab/colon-separated text that just happens to lie
+    # about, or misdeclare, its own content.
+    region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
+
+    output_path = str(tmp_path / "test_bcftools_valid.vcf")
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+        fields={"GT", "GQ", "AD", "MQ"},
+    )
+
+    result = subprocess.run(
+        ["bcftools", "view", "-v", "snps", output_path],
+        capture_output=True,
+        text=True,
+    )
+    assert result.returncode == 0, f"bcftools failed to parse output: {result.stderr}"
+    assert "Error" not in result.stderr
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_fields_gt_required(fixture, api: SnpVcfExporter, tmp_path):
     region = api.contigs[0]

From b7ec7c783a266c9ab0559173194747577d9ebc5f Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 29 Sep 2026 15:21:05 +0100
Subject: [PATCH 13/38] more twiddling with header due to bcftools warning,
 still looking into agreement with reference VCF

---
 malariagen_data/anoph/to_vcf.py  | 14 +++++++++++---
 tests/anoph/test_vcf_exporter.py | 21 ++++++++++++++-------
 2 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index ac1f32f5f..b65712f7d 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -23,7 +23,12 @@
     "GT": '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
     "GQ": '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">',
     "AD": '##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth">',
-    "MQ": '##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mapping Quality">',
+    # N.B., "MQ" is a reserved FORMAT key in the VCF specification,
+    # fixed there as Integer, Number=1 — even though the underlying
+    # data is a float (RMS mapping quality), so values are rounded to
+    # the nearest integer when written below to stay spec-compliant
+    # under the reserved key's declared type.
+    "MQ": '##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Mapping Quality">',
 }
 
 # snp_calls_to_vcf() only supports exporting a single sample at a time
@@ -371,11 +376,14 @@ def snp_calls_to_vcf(
                                     )
                                 else:
                                     parts.append(".")
-                            # MQ.
+                            # MQ. Rounded to the nearest integer: the
+                            # underlying data is a float, but the VCF
+                            # spec fixes the reserved FORMAT/MQ key as
+                            # Integer (see _FORMAT_HEADERS).
                             if include_mq:
                                 if mq_chunk is not None:
                                     v = mq_chunk[j, k]
-                                    parts.append("." if v < 0 else str(v))
+                                    parts.append("." if v < 0 else str(round(v)))
                                 else:
                                     parts.append(".")
                             sample_fields.append(":".join(parts))
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index 92237cabc..df5532abf 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -391,13 +391,15 @@ def test_vcf_exporter_output_is_valid_per_bcftools(
 ):
     # A stronger check than the Python-level assertions above: actually
     # parse the output with bcftools, the way a real consumer would.
-    # This is what caught both the FORMAT field-order bug (a `set` of
-    # fields could desync the FORMAT column from the hardcoded value
-    # order) and the MQ header Type=Integer/actual-float-value mismatch
-    # — neither of which a purely structural Python check (e.g.
-    # splitting on "\t"/":") would notice, since both produce
-    # "well-formed" tab/colon-separated text that just happens to lie
-    # about, or misdeclare, its own content.
+    # This is what caught the FORMAT field-order bug (a `set` of fields
+    # could desync the FORMAT column from the hardcoded value order),
+    # the MQ header Type=Integer/actual-float-value mismatch, and (via
+    # the sanity-check warning below) declaring the reserved FORMAT/MQ
+    # key as Type=Float instead of the spec-mandated Integer — none of
+    # which a purely structural Python check (e.g. splitting on
+    # "\t"/":") would notice, since all three produce "well-formed"
+    # tab/colon-separated text that just happens to lie about, or
+    # misdeclare, its own content.
     region = api.contigs[0]
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = [all_sample_sets[0]]
@@ -419,6 +421,11 @@ def test_vcf_exporter_output_is_valid_per_bcftools(
     )
     assert result.returncode == 0, f"bcftools failed to parse output: {result.stderr}"
     assert "Error" not in result.stderr
+    # Not just error-free: bcftools' own header sanity check should not
+    # flag any of our FORMAT field declarations against the VCF spec's
+    # reserved-key type definitions (e.g. FORMAT/MQ is fixed as
+    # Integer by the spec, regardless of the underlying data type).
+    assert "should be declared as" not in result.stderr, result.stderr
 
 
 @parametrize_with_cases("fixture,api", cases=".")

From aeab10095ec9ae0933d53921197d88c20d9f1e52 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 29 Sep 2026 16:51:35 +0100
Subject: [PATCH 14/38] Claude draft to output only heterozygous sites in VCF

---
 malariagen_data/anoph/to_vcf.py  |  29 +++++++-
 tests/anoph/test_vcf_exporter.py | 119 +++++++++++++++++++++++++++++++
 2 files changed, 147 insertions(+), 1 deletion(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index b65712f7d..783b425fa 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -104,6 +104,19 @@ def __init__(
             selecting samples by cohort, or more than one sample_id) is
             rejected.
         """,
+        parameters=dict(
+            non_ref_only="""
+                If True, only write sites where the sample's genotype
+                carries at least one non-reference allele (i.e. skip
+                sites where the sample is homozygous reference or
+                missing). Equivalent to filtering the output with
+                `bcftools view -e 'F_PASS(GT="ref") == 1'`, except that
+                missing genotype calls are also excluded here (whereas
+                that particular bcftools expression only excludes
+                homozygous reference calls, since a missing call is
+                neither "ref" nor selected by `-e`).
+            """,
+        ),
         returns="""
         Path to the VCF output file.
         """,
@@ -116,11 +129,12 @@ def snp_calls_to_vcf(
         sample_query: base_params.sample_query,
         sample_query_options: Optional[base_params.sample_query_options] = None,
         sample_indices: Optional[base_params.sample_indices] = None,
-        site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
+        site_mask: Optional[base_params.site_mask] = None,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         chunks: base_params.chunks = base_params.native_chunks,
         overwrite: plink_params.overwrite = False,
         fields: vcf_params.vcf_fields = ("GT",),
+        non_ref_only: bool = False,
     ) -> str:
         base_params._validate_sample_selection_params(
             sample_query=sample_query, sample_indices=sample_indices
@@ -306,6 +320,16 @@ def snp_calls_to_vcf(
                     a1 = gt_chunk_2d[:, :, 1]  # (n_variants, n_samples)
                     missing = (a0 < 0) | (a1 < 0)
 
+                    # If non_ref_only, work out up front which variants
+                    # to skip: those where the sample is homozygous
+                    # reference (0/0) or missing. Computed vectorized
+                    # across the whole chunk, same as `missing` above.
+                    if non_ref_only:
+                        is_hom_ref = (a0 == 0) & (a1 == 0)
+                        skip_variant = (missing | is_hom_ref)[:, 0]
+                    else:
+                        skip_variant = None
+
                     # Build formatted GT strings using NumPy vectorization
                     gt_formatted = np.empty(
                         (gt_chunk.shape[0], n_samples), dtype=object
@@ -323,6 +347,9 @@ def snp_calls_to_vcf(
                     lines_to_write = []
 
                     for j in range(gt_chunk.shape[0]):
+                        if skip_variant is not None and skip_variant[j]:
+                            continue
+
                         chrom = contigs[contig_chunk[j]]
                         pos = str(pos_chunk[j])
                         alleles = allele_chunk[j]
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index df5532abf..091a5dece 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -140,6 +140,125 @@ def test_vcf_exporter(fixture, api: SnpVcfExporter, tmp_path):
         ), f"byte-string repr in REF/ALT: REF={ref!r} ALT={alt!r}"
 
 
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_non_ref_only(fixture, api: SnpVcfExporter, tmp_path):
+    # non_ref_only=True should keep only sites where the sample's
+    # genotype carries at least one non-reference allele, dropping both
+    # homozygous reference (0/0) and missing (./.) calls. Equivalent in
+    # spirit to `bcftools view -e 'F_PASS(GT="ref") == 1'`, except that
+    # a missing call is also excluded here (that particular bcftools
+    # expression only excludes homozygous reference calls, since a
+    # missing call is neither "ref" nor caught by that `-e` filter).
+    region = random.choice(api.contigs)
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = random.sample(all_sample_sets, min(2, len(all_sample_sets)))
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
+
+    data_params = dict(
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+    )
+
+    # Work out the expected set of non-ref, non-missing positions
+    # directly from the dataset, independently of snp_calls_to_vcf.
+    ds = api.snp_calls(**data_params)
+    gt = ds["call_genotype"].values[:, 0, :]  # (variants, ploidy)
+    is_missing = (gt < 0).any(axis=1)
+    is_hom_ref = (gt == 0).all(axis=1)
+    expect_keep = ~is_missing & ~is_hom_ref
+    expected_positions = sorted(ds["variant_position"].values[expect_keep].tolist())
+
+    output_path = str(tmp_path / "test_non_ref_only.vcf")
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        non_ref_only=True,
+        **data_params,
+    )
+
+    with open(output_path) as f:
+        lines = f.readlines()
+    data_lines = [line for line in lines if not line.startswith("#")]
+
+    # Every written site should have a non-ref, non-missing GT.
+    for line in data_lines:
+        fields_row = line.strip().split("\t")
+        gt_str = fields_row[9].split(":")[0]
+        assert gt_str != "./."
+        a0, a1 = gt_str.split("/")
+        assert not (a0 == "0" and a1 == "0")
+
+    # And the set of positions written should exactly match what we
+    # expect directly from the dataset (no extras, none missing).
+    vcf_positions = sorted(int(line.split("\t")[1]) for line in data_lines)
+    assert vcf_positions == expected_positions
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_non_ref_only_defaults_to_false(
+    fixture, api: SnpVcfExporter, tmp_path
+):
+    # Not passing non_ref_only should behave identically to passing
+    # non_ref_only=False (i.e. include homozygous reference / missing
+    # sites too) — this locks in the default.
+    region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
+
+    output_path_default = str(tmp_path / "default.vcf")
+    output_path_explicit = str(tmp_path / "explicit_false.vcf")
+    api.snp_calls_to_vcf(
+        output_path=output_path_default,
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+    )
+    api.snp_calls_to_vcf(
+        output_path=output_path_explicit,
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+        non_ref_only=False,
+    )
+
+    with open(output_path_default) as f:
+        default_lines = f.readlines()
+    with open(output_path_explicit) as f:
+        explicit_lines = f.readlines()
+    assert default_lines == explicit_lines
+
+
+@pytest.mark.skipif(shutil.which("bcftools") is None, reason="bcftools not installed")
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_non_ref_only_valid_per_bcftools(
+    fixture, api: SnpVcfExporter, tmp_path
+):
+    region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
+
+    output_path = str(tmp_path / "test_non_ref_only_bcftools.vcf")
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        region=region,
+        sample_sets=sample_sets,
+        sample_query=sample_query,
+        fields={"GT", "GQ", "AD", "MQ"},
+        non_ref_only=True,
+    )
+
+    result = subprocess.run(
+        ["bcftools", "view", "-v", "snps", output_path],
+        capture_output=True,
+        text=True,
+    )
+    assert result.returncode == 0, f"bcftools failed to parse output: {result.stderr}"
+    assert "Error" not in result.stderr
+    assert "should be declared as" not in result.stderr, result.stderr
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_requires_sample_sets_and_query(
     fixture, api: SnpVcfExporter, tmp_path

From 050415a7bcb9c14c2e0165192c79998e90f0e1a2 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 30 Sep 2026 11:15:30 +0100
Subject: [PATCH 15/38] Claude draft of bug fix with removing homozygous sites

---
 malariagen_data/anoph/to_vcf.py  |  88 ++++++++++++++++++++++-----
 tests/anoph/test_vcf_exporter.py | 100 +++++++++++++++++++++++++++++++
 2 files changed, 172 insertions(+), 16 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 783b425fa..50ee39395 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -324,22 +324,82 @@ def snp_calls_to_vcf(
                     # to skip: those where the sample is homozygous
                     # reference (0/0) or missing. Computed vectorized
                     # across the whole chunk, same as `missing` above.
+                    # N.B., this uses the *original* (un-remapped)
+                    # allele indices computed below — 0 always means REF
+                    # both before and after remapping, so this check is
+                    # unaffected by it.
                     if non_ref_only:
                         is_hom_ref = (a0 == 0) & (a1 == 0)
                         skip_variant = (missing | is_hom_ref)[:, 0]
                     else:
                         skip_variant = None
 
+                    # Decode alleles once per chunk (rather than
+                    # per-variant further down) and work out, per
+                    # variant, which of the ALT candidate slots are
+                    # actually populated. call_genotype's allele indices
+                    # refer to these *original* variant_allele slot
+                    # positions (0=REF, 1..3=ALT candidates), which are
+                    # not guaranteed to be contiguous from 1 — a site's
+                    # only real ALT allele can sit in slot 2 or 3 while
+                    # an earlier slot is empty. The ALT column written
+                    # below only lists the populated slots, so genotype
+                    # indices must be remapped to match that compacted
+                    # numbering, or a GT value could end up referring to
+                    # an ALT allele that isn't listed at all (or the
+                    # wrong one).
+                    decoded_alleles = np.empty(allele_chunk.shape, dtype=object)
+                    for col in range(allele_chunk.shape[1]):
+                        decoded_alleles[:, col] = [
+                            a.decode() if hasattr(a, "decode") else str(a)
+                            for a in allele_chunk[:, col]
+                        ]
+                    is_present = decoded_alleles != ""
+                    is_present[:, 0] = True  # REF is always present
+                    # compacted_index[i, k] = the index original slot k
+                    # occupies in the ALT column for variant i, or -1 if
+                    # slot k isn't populated there.
+                    compacted_index = np.cumsum(is_present, axis=1) - 1
+                    compacted_index[~is_present] = -1
+
+                    # Remap this chunk's genotype allele indices to the
+                    # compacted numbering. n_samples is always 1 here
+                    # (snp_calls_to_vcf only supports a single sample),
+                    # so a0/a1 are worked with as flat (n_variants,)
+                    # arrays. Clip before gathering so a missing
+                    # genotype's sentinel value (-1) can't trigger an
+                    # out-of-bounds index — the gathered result for
+                    # those rows is discarded below anyway, since they
+                    # are written as "./." based on `missing`, not on
+                    # this remapping.
+                    row_idx = np.arange(gt_chunk.shape[0])
+                    n_allele_slots = allele_chunk.shape[1]
+                    remapped_a0 = compacted_index[
+                        row_idx, np.clip(a0[:, 0], 0, n_allele_slots - 1)
+                    ]
+                    remapped_a1 = compacted_index[
+                        row_idx, np.clip(a1[:, 0], 0, n_allele_slots - 1)
+                    ]
+                    # A remapped index of -1 means the genotype
+                    # references an allele slot that variant_allele
+                    # doesn't actually have populated at this site —
+                    # inconsistent data that shouldn't occur, but is
+                    # treated as missing defensively rather than writing
+                    # a nonsensical negative allele index.
+                    missing_or_unmapped = (
+                        missing[:, 0] | (remapped_a0 < 0) | (remapped_a1 < 0)
+                    )
+
                     # Build formatted GT strings using NumPy vectorization
                     gt_formatted = np.empty(
                         (gt_chunk.shape[0], n_samples), dtype=object
                     )
-                    gt_formatted[missing] = "./."
-                    present_idx = ~missing
+                    gt_formatted[missing_or_unmapped, 0] = "./."
+                    present_idx = ~missing_or_unmapped
                     if np.any(present_idx):
-                        a0_str = a0[present_idx].astype(str)
-                        a1_str = a1[present_idx].astype(str)
-                        gt_formatted[present_idx] = np.char.add(
+                        a0_str = remapped_a0[present_idx].astype(str)
+                        a1_str = remapped_a1[present_idx].astype(str)
+                        gt_formatted[present_idx, 0] = np.char.add(
                             np.char.add(a0_str, "/"), a1_str
                         )
 
@@ -352,17 +412,13 @@ def snp_calls_to_vcf(
 
                         chrom = contigs[contig_chunk[j]]
                         pos = str(pos_chunk[j])
-                        alleles = allele_chunk[j]
-                        ref = (
-                            alleles[0].decode()
-                            if hasattr(alleles[0], "decode")
-                            else str(alleles[0])
-                        )
-                        alt_alleles = []
-                        for a in alleles[1:]:
-                            s = a.decode() if hasattr(a, "decode") else str(a)
-                            if s:
-                                alt_alleles.append(s)
+                        # Reuse the chunk-level decode from above, so
+                        # the ALT column built here is guaranteed
+                        # consistent with the allele-index remapping
+                        # used for GT (both derive from the same
+                        # decoded_alleles/is_present arrays).
+                        ref = decoded_alleles[j, 0]
+                        alt_alleles = [s for s in decoded_alleles[j, 1:] if s]
                         alt = ",".join(alt_alleles) if alt_alleles else "."
 
                         # Build fixed VCF columns once per variant
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index 091a5dece..a583b081a 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -4,7 +4,10 @@
 import shutil
 import subprocess
 
+import dask.array as da
+import numpy as np
 import pytest
+import xarray as xr
 from pytest_cases import parametrize_with_cases
 
 from malariagen_data import af1 as _af1
@@ -563,3 +566,100 @@ def test_vcf_exporter_fields_gt_required(fixture, api: SnpVcfExporter, tmp_path)
             sample_query=sample_query,
             fields=("GQ",),
         )
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_allele_index_remapping(
+    fixture, api: SnpVcfExporter, tmp_path, monkeypatch
+):
+    # variant_allele slots for a site are not guaranteed to be
+    # contiguous from slot 1: a site's only real ALT allele can sit in
+    # slot 2 or 3 while an earlier slot is empty (cohort-wide allele
+    # arrays aren't necessarily left-justified per site). The ALT
+    # column only lists populated slots, so call_genotype's allele
+    # indices (which refer to the *original* slot positions) must be
+    # remapped to match, or a GT value can end up pointing at an ALT
+    # allele that isn't listed (or the wrong one) — exactly the bug
+    # that produced invalid records like "0/2" against a single-allele
+    # ALT column, which bcftools then silently mishandled.
+    sample = str(api.sample_metadata()["sample_id"].iloc[0])
+    contig = api.contigs[0]
+
+    variant_allele = np.array(
+        [
+            [b"A", b"", b"T", b""],  # only real ALT in slot 2
+            [b"A", b"T", b"", b""],  # real ALT in slot 1 (unaffected case)
+            [b"A", b"", b"", b"T"],  # only real ALT in slot 3
+            [b"A", b"C", b"", b"T"],  # two real ALTs, gap in slot 2
+        ],
+        dtype="S1",
+    )
+    call_genotype = np.array(
+        [
+            [[0, 2]],  # het for the slot-2 "T" -> ALT="T" -> expect 0/1
+            [[0, 1]],  # het for the slot-1 "T" -> ALT="T" -> expect 0/1
+            [[3, 3]],  # hom-alt for the slot-3 "T" -> ALT="T" -> expect 1/1
+            [[0, 3]],  # het for the slot-3 "T" -> ALT="C,T" -> expect 0/2
+        ],
+        dtype="i1",
+    )
+    expected = {
+        100: ("T", "0/1"),
+        200: ("T", "0/1"),
+        300: ("T", "1/1"),
+        400: ("C,T", "0/2"),
+    }
+
+    ds = xr.Dataset(
+        data_vars={
+            "call_genotype": (
+                ["variants", "samples", "ploidy"],
+                da.from_array(call_genotype, chunks=(4, 1, 2)),
+            ),
+            "variant_allele": (
+                ["variants", "alleles"],
+                da.from_array(variant_allele, chunks=(4, 4)),
+            ),
+        },
+        coords={
+            "variant_position": (
+                "variants",
+                da.from_array(np.array([100, 200, 300, 400]), chunks=4),
+            ),
+            "variant_contig": (
+                "variants",
+                da.from_array(np.array([0, 0, 0, 0], dtype="u1"), chunks=4),
+            ),
+            "sample_id": ("samples", np.array([sample])),
+        },
+        attrs={"contigs": (contig,)},
+    )
+    monkeypatch.setattr(api, "snp_calls", lambda **kwargs: ds)
+
+    output_path = str(tmp_path / "test_allele_remap.vcf")
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        region=contig,
+        sample_sets=["dummy"],
+        sample_query=f"sample_id == '{sample}'",
+    )
+
+    with open(output_path) as f:
+        lines = f.readlines()
+    data_lines = [line for line in lines if not line.startswith("#")]
+    assert len(data_lines) == 4
+
+    for line in data_lines:
+        fields_row = line.strip().split("\t")
+        pos = int(fields_row[1])
+        alt = fields_row[4]
+        gt = fields_row[9].split(":")[0]
+        expected_alt, expected_gt = expected[pos]
+        assert alt == expected_alt, f"at {pos}: expected ALT {expected_alt}, got {alt}"
+        assert gt == expected_gt, f"at {pos}: expected GT {expected_gt}, got {gt}"
+        # Every GT allele index must be valid for the ALT column that
+        # was actually written (i.e. in range for the number of ALT
+        # alleles listed), which is the invariant this fix guarantees.
+        n_alt_alleles = len(alt.split(","))
+        for allele_idx in gt.split("/"):
+            assert int(allele_idx) <= n_alt_alleles

From 8e4b62eec05d4cf61ccb157b77369c803e8047f2 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 30 Sep 2026 11:53:42 +0100
Subject: [PATCH 16/38] still trying to get to_vcf correct Claude thinks its
 something to to with compression despite me testing on uncompressed outputs,
 so I am unconvinced

---
 malariagen_data/anoph/to_coverage.py  |   5 +
 malariagen_data/anoph/to_vcf.py       |  16 +-
 malariagen_data/anoph/to_vcf_cnv.py   |  20 +-
 malariagen_data/bgzf.py               | 125 +++++++++++
 tests/anoph/test_coverage_exporter.py | 295 ++++++++++++++++++++++++++
 tests/anoph/test_igv_coverage.py      | 143 +++++++++++++
 tests/anoph/test_vcf_exporter.py      |  13 +-
 tests/anoph/test_vcf_exporter_cnv.py  |  10 +
 tests/test_bgzf.py                    |  95 +++++++++
 9 files changed, 710 insertions(+), 12 deletions(-)
 create mode 100644 malariagen_data/bgzf.py
 create mode 100644 tests/anoph/test_coverage_exporter.py
 create mode 100644 tests/anoph/test_igv_coverage.py
 create mode 100644 tests/test_bgzf.py

diff --git a/malariagen_data/anoph/to_coverage.py b/malariagen_data/anoph/to_coverage.py
index dc5d1c234..ee0248693 100644
--- a/malariagen_data/anoph/to_coverage.py
+++ b/malariagen_data/anoph/to_coverage.py
@@ -15,6 +15,11 @@
 
 
 def _bedgraph_opener(output_path: str):
+    # N.B., plain gzip is intentional here, unlike the VCF exporters
+    # (see malariagen_data.bgzf): bedGraph doesn't carry the same
+    # ecosystem-wide expectation that a `.gz` file specifically be
+    # BGZF, and IGV loads a plain-gzipped bedGraph track without
+    # issue.
     compress = output_path.endswith(".gz")
     return gzip.open if compress else open
 
diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 50ee39395..3139eefaa 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -1,4 +1,3 @@
-import gzip
 import os
 import re
 from datetime import date
@@ -8,6 +7,7 @@
 import numpy as np
 from numpydoc_decorator import doc  # type: ignore
 
+from ..bgzf import bgzf_open
 from .snp_data import AnophelesSnpData
 from . import base_params
 from . import plink_params
@@ -177,7 +177,7 @@ def snp_calls_to_vcf(
             chunks=chunks,
         )
 
-        # Confirm inputs actually resolved to exactly
+        # Confirm inputs resolve to exactly
         # one sample within the given sample_sets
         # checked defensively rather than silently written
         # out as a multi-sample VCF.
@@ -192,7 +192,11 @@ def snp_calls_to_vcf(
         sample_ids = ds["sample_id"].values
         contigs = ds.attrs.get("contigs", self.contigs)
         compress = output_path.endswith(".gz")
-        opener = gzip.open if compress else open
+        # N.B., genuine BGZF, not plain gzip: tools that specifically
+        # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
+        # fail to read, or silently mis-parse, plain gzip even though
+        # it decompresses fine as a byte stream.
+        opener = bgzf_open if compress else open
 
         # Determine which extra fields to include.
         include_gq = "GQ" in fields
@@ -285,7 +289,7 @@ def snp_calls_to_vcf(
                     )
 
                     # Fetch requested optional fields for this chunk
-                    # as a single batched call. If any of them fail
+                    # as a single batched call. If any fail
                     # to load, fall back to "." for all requested
                     # optional fields in this chunk — these arrays live
                     # in the same region of the same store, so a failure
@@ -345,9 +349,7 @@ def snp_calls_to_vcf(
                     # an earlier slot is empty. The ALT column written
                     # below only lists the populated slots, so genotype
                     # indices must be remapped to match that compacted
-                    # numbering, or a GT value could end up referring to
-                    # an ALT allele that isn't listed at all (or the
-                    # wrong one).
+                    # numbering
                     decoded_alleles = np.empty(allele_chunk.shape, dtype=object)
                     for col in range(allele_chunk.shape[1]):
                         decoded_alleles[:, col] = [
diff --git a/malariagen_data/anoph/to_vcf_cnv.py b/malariagen_data/anoph/to_vcf_cnv.py
index fbc16f520..676897e5a 100644
--- a/malariagen_data/anoph/to_vcf_cnv.py
+++ b/malariagen_data/anoph/to_vcf_cnv.py
@@ -1,4 +1,3 @@
-import gzip
 import os
 from datetime import date
 from typing import List, Optional, Sequence
@@ -6,6 +5,7 @@
 import numpy as np
 from numpydoc_decorator import doc  # type: ignore
 
+from ..bgzf import bgzf_open
 from .cnv_data import AnophelesCnvData
 from . import base_params
 from . import cnv_params
@@ -120,7 +120,11 @@ def cnv_hmm_to_vcf(
         sample_ids = ds["sample_id"].values
         contigs = ds.attrs.get("contigs", self.contigs)
         compress = output_path.endswith(".gz")
-        opener = gzip.open if compress else open
+        # N.B., genuine BGZF, not plain gzip: tools that specifically
+        # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
+        # fail to read, or silently mis-parse, plain gzip even though
+        # it decompresses fine as a byte stream.
+        opener = bgzf_open if compress else open
 
         with opener(output_path, "wt") as f:
             _write_vcf_header(
@@ -215,7 +219,11 @@ def cnv_coverage_calls_to_vcf(
         sample_ids = ds["sample_id"].values
         contigs = ds.attrs.get("contigs", self.contigs)
         compress = output_path.endswith(".gz")
-        opener = gzip.open if compress else open
+        # N.B., genuine BGZF, not plain gzip: tools that specifically
+        # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
+        # fail to read, or silently mis-parse, plain gzip even though
+        # it decompresses fine as a byte stream.
+        opener = bgzf_open if compress else open
 
         with opener(output_path, "wt") as f:
             _write_vcf_header(
@@ -329,7 +337,11 @@ def cnv_discordant_read_calls_to_vcf(
         sample_ids = ds["sample_id"].values
         all_contigs = ds.attrs.get("contigs", self.contigs)
         compress = output_path.endswith(".gz")
-        opener = gzip.open if compress else open
+        # N.B., genuine BGZF, not plain gzip: tools that specifically
+        # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
+        # fail to read, or silently mis-parse, plain gzip even though
+        # it decompresses fine as a byte stream.
+        opener = bgzf_open if compress else open
 
         with opener(output_path, "wt") as f:
             _write_vcf_header(
diff --git a/malariagen_data/bgzf.py b/malariagen_data/bgzf.py
new file mode 100644
index 000000000..d49a35853
--- /dev/null
+++ b/malariagen_data/bgzf.py
@@ -0,0 +1,125 @@
+"""Minimal, write-only BGZF (Blocked GZip Format) support.
+
+BGZF is the compression format used throughout the SAM/BAM/VCF tooling
+ecosystem (samtools, bcftools, tabix, bedtools, IGV, ...) for
+compressed, indexable files. Structurally, it's just a sequence of
+ordinary gzip members, each holding up to ~64KB of uncompressed data,
+with a small extra header field recording each member's total size,
+plus a fixed, empty final member used as an EOF marker.
+
+Python's standard library `gzip.open()` produces valid gzip, but not
+valid BGZF: tools that specifically expect BGZF for a `.vcf.gz` (or
+similar) file can fail to read it correctly, or silently mis-parse it,
+even though plain gzip decompresses just fine as a byte stream. This
+module exists so that `.gz` output written by malariagen_data is
+genuine BGZF, and therefore usable with the wider standard toolset
+(bcftools, tabix, bedtools, etc.), not just tools that happen to
+tolerate plain gzip.
+
+See the BGZF section of the SAM specification for the on-disk format
+this implements: https://samtools.github.io/hts-specs/SAMv1.pdf
+"""
+
+import struct
+import zlib
+from typing import Optional
+
+# The fixed, empty BGZF block used to mark genuine end-of-file (as
+# opposed to a truncated file). This exact byte sequence is part of the
+# BGZF specification, not something we generate ourselves.
+_BGZF_EOF_MARKER = bytes.fromhex(
+    "1f8b08040000000000ff0600424302001b0003000000000000000000"
+)
+
+# Maximum amount of *uncompressed* data placed in a single BGZF block.
+# Kept comfortably under the 16-bit BSIZE field's range (a block's
+# total on-disk size, header and footer included, must fit in 65536
+# bytes) even in the worst case where compression doesn't shrink the
+# input at all; this matches the conservative block size used by other
+# BGZF writers (e.g. Biopython's `Bio.bgzf`).
+_MAX_BLOCK_UNCOMPRESSED_SIZE = 65280
+
+
+def _compress_bgzf_block(data: bytes, level: int = 6) -> bytes:
+    """Compress `data` (must be <= _MAX_BLOCK_UNCOMPRESSED_SIZE bytes)
+    into a single, standalone BGZF block."""
+    compressor = zlib.compressobj(level, zlib.DEFLATED, -15)
+    compressed = compressor.compress(data) + compressor.flush(zlib.Z_FINISH)
+    crc = zlib.crc32(data) & 0xFFFFFFFF
+    isize = len(data) & 0xFFFFFFFF
+
+    # Block layout: 18-byte header (with the BGZF "BC" extra field),
+    # the compressed payload, then an 8-byte footer (CRC32 + ISIZE) —
+    # the same footer any gzip member ends with.
+    block_size = 18 + len(compressed) + 8
+    header = struct.pack(
+        "<BBBBIBBHBBHH",
+        0x1F,
+        0x8B,  # ID1, ID2: gzip magic number
+        0x08,  # CM: compression method (deflate)
+        0x04,  # FLG: FEXTRA set (an extra field follows)
+        0,  # MTIME
+        0,  # XFL
+        0xFF,  # OS: unknown
+        6,  # XLEN: length of the extra field below
+        0x42,
+        0x43,  # SI1, SI2: BGZF's "BC" extra subfield identifier
+        2,  # SLEN: subfield length
+        block_size - 1,  # BSIZE: total block size, minus 1
+    )
+    footer = struct.pack("<II", crc, isize)
+    return header + compressed + footer
+
+
+class BgzfWriter:
+    """A minimal, write-only, text-mode BGZF writer.
+
+    Used the same way as `gzip.open(path, "wt")`: construct, `write()`
+    strings to it, and either call `close()` or use it as a context
+    manager.
+    """
+
+    def __init__(self, path: str, encoding: str = "utf-8"):
+        self._fh = open(path, "wb")
+        self._encoding = encoding
+        self._buffer = bytearray()
+        self._closed = False
+
+    def write(self, text: str) -> None:
+        self._buffer.extend(text.encode(self._encoding))
+        while len(self._buffer) >= _MAX_BLOCK_UNCOMPRESSED_SIZE:
+            chunk = bytes(self._buffer[:_MAX_BLOCK_UNCOMPRESSED_SIZE])
+            del self._buffer[:_MAX_BLOCK_UNCOMPRESSED_SIZE]
+            self._fh.write(_compress_bgzf_block(chunk))
+
+    def close(self) -> None:
+        if self._closed:
+            return
+        if self._buffer:
+            self._fh.write(_compress_bgzf_block(bytes(self._buffer)))
+            self._buffer = bytearray()
+        self._fh.write(_BGZF_EOF_MARKER)
+        self._fh.close()
+        self._closed = True
+
+    def __enter__(self) -> "BgzfWriter":
+        return self
+
+    def __exit__(self, *exc_info) -> None:
+        self.close()
+
+
+def bgzf_open(path: str, mode: str = "wt", encoding: Optional[str] = "utf-8"):
+    """Open `path` for BGZF-compressed text writing.
+
+    Signature-compatible with `gzip.open(path, "wt")` for the subset of
+    usage malariagen_data's VCF/text exporters need (write-only, text
+    mode), so it can be used as a drop-in replacement for `gzip.open`
+    wherever genuine BGZF (rather than plain gzip) output is required.
+    """
+    if mode not in ("wt", "w"):
+        raise ValueError(
+            f"Unsupported mode {mode!r}: bgzf_open() only supports writing text "
+            "('wt' or 'w')."
+        )
+    return BgzfWriter(path, encoding=encoding or "utf-8")
diff --git a/tests/anoph/test_coverage_exporter.py b/tests/anoph/test_coverage_exporter.py
new file mode 100644
index 000000000..d0770af3e
--- /dev/null
+++ b/tests/anoph/test_coverage_exporter.py
@@ -0,0 +1,295 @@
+import gzip
+import os
+import random
+
+import dask.array as da
+import numpy as np
+import pytest
+import xarray as xr
+from pytest_cases import parametrize_with_cases
+
+from malariagen_data import af1 as _af1
+from malariagen_data import ag3 as _ag3
+
+from malariagen_data.anoph.to_coverage import CoverageExporter
+
+
+@pytest.fixture
+def ag3_sim_api(ag3_sim_fixture):
+    return CoverageExporter(
+        url=ag3_sim_fixture.url,
+        public_url=ag3_sim_fixture.url,
+        config_path=_ag3.CONFIG_PATH,
+        major_version_number=_ag3.MAJOR_VERSION_NUMBER,
+        major_version_path=_ag3.MAJOR_VERSION_PATH,
+        pre=True,
+        aim_metadata_dtype={
+            "aim_species_fraction_arab": "float64",
+            "aim_species_fraction_colu": "float64",
+            "aim_species_fraction_colu_no2l": "float64",
+            "aim_species_gambcolu_arabiensis": object,
+            "aim_species_gambiae_coluzzii": object,
+            "aim_species": object,
+        },
+        gff_gene_type="gene",
+        gff_gene_name_attribute="Name",
+        gff_default_attributes=("ID", "Parent", "Name", "description"),
+        results_cache=ag3_sim_fixture.results_cache_path.as_posix(),
+        default_coverage_calls_analysis="gamb_colu",
+        discordant_read_calls_analysis=ag3_sim_fixture.config[
+            "DEFAULT_DISCORDANT_READ_CALLS_ANALYSIS"
+        ],
+    )
+
+
+@pytest.fixture
+def af1_sim_api(af1_sim_fixture):
+    return CoverageExporter(
+        url=af1_sim_fixture.url,
+        public_url=af1_sim_fixture.url,
+        config_path=_af1.CONFIG_PATH,
+        major_version_number=_af1.MAJOR_VERSION_NUMBER,
+        major_version_path=_af1.MAJOR_VERSION_PATH,
+        pre=False,
+        gff_gene_type="protein_coding_gene",
+        gff_gene_name_attribute="Note",
+        gff_default_attributes=("ID", "Parent", "Note", "description"),
+        results_cache=af1_sim_fixture.results_cache_path.as_posix(),
+        default_coverage_calls_analysis="funestus",
+        discordant_read_calls_analysis=None,
+    )
+
+
+def case_ag3_sim(ag3_sim_fixture, ag3_sim_api):
+    return ag3_sim_fixture, ag3_sim_api
+
+
+def case_af1_sim(af1_sim_fixture, af1_sim_api):
+    return af1_sim_fixture, af1_sim_api
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_hmm_coverage_to_bedgraph(fixture, api: CoverageExporter, tmp_path):
+    region = random.choice(api.contigs)
+    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
+
+    output_path = str(tmp_path / "test_coverage.bedgraph")
+    api.cnv_hmm_coverage_to_bedgraph(
+        output_path=output_path,
+        region=region,
+        sample=sample,
+    )
+
+    assert os.path.exists(output_path)
+
+    with open(output_path) as f:
+        lines = f.readlines()
+
+    assert lines[0].startswith("track type=bedGraph")
+
+    data_lines = lines[1:]
+    assert len(data_lines) > 0
+
+    for line in data_lines:
+        fields = line.rstrip("\n").split("\t")
+        assert len(fields) == 4
+        chrom, start, end, value = fields
+        assert chrom == region
+        assert int(start) >= 0
+        assert int(end) > int(start)
+        # Should be a valid number and non-negative (masked/missing
+        # values are skipped rather than written).
+        assert float(value) >= 0
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_hmm_coverage_to_bedgraph_raw_cov(fixture, api: CoverageExporter, tmp_path):
+    region = api.contigs[0]
+    sample = str(api.sample_metadata()["sample_id"].iloc[0])
+
+    output_path = str(tmp_path / "test_coverage_raw.bedgraph")
+    api.cnv_hmm_coverage_to_bedgraph(
+        output_path=output_path,
+        region=region,
+        sample=sample,
+        field="RawCov",
+    )
+    assert os.path.exists(output_path)
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_hmm_coverage_to_bedgraph_invalid_field(
+    fixture, api: CoverageExporter, tmp_path
+):
+    region = api.contigs[0]
+    sample = str(api.sample_metadata()["sample_id"].iloc[0])
+
+    output_path = str(tmp_path / "test_coverage_bad.bedgraph")
+    with pytest.raises(ValueError, match="Unknown coverage field"):
+        api.cnv_hmm_coverage_to_bedgraph(
+            output_path=output_path,
+            region=region,
+            sample=sample,
+            field="NotAField",
+        )
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_hmm_coverage_to_bedgraph_unknown_sample(
+    fixture, api: CoverageExporter, tmp_path
+):
+    region = api.contigs[0]
+    output_path = str(tmp_path / "test_coverage_unknown.bedgraph")
+    with pytest.raises(ValueError, match="No data found for sample"):
+        api.cnv_hmm_coverage_to_bedgraph(
+            output_path=output_path,
+            region=region,
+            sample="not_a_real_sample",
+        )
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_hmm_coverage_to_bedgraph_overwrite(
+    fixture, api: CoverageExporter, tmp_path
+):
+    region = api.contigs[0]
+    sample = str(api.sample_metadata()["sample_id"].iloc[0])
+    output_path = str(tmp_path / "test_coverage.bedgraph")
+
+    api.cnv_hmm_coverage_to_bedgraph(
+        output_path=output_path, region=region, sample=sample
+    )
+    mtime_first = os.path.getmtime(output_path)
+
+    api.cnv_hmm_coverage_to_bedgraph(
+        output_path=output_path, region=region, sample=sample
+    )
+    assert os.path.getmtime(output_path) == mtime_first
+
+    api.cnv_hmm_coverage_to_bedgraph(
+        output_path=output_path, region=region, sample=sample, overwrite=True
+    )
+    assert os.path.exists(output_path)
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_cnv_hmm_coverage_to_bedgraph_gzip(fixture, api: CoverageExporter, tmp_path):
+    region = api.contigs[0]
+    sample = str(api.sample_metadata()["sample_id"].iloc[0])
+    output_path = str(tmp_path / "test_coverage.bedgraph.gz")
+
+    api.cnv_hmm_coverage_to_bedgraph(
+        output_path=output_path, region=region, sample=sample
+    )
+    assert os.path.exists(output_path)
+
+    with gzip.open(output_path, "rt") as f:
+        first_line = f.readline()
+    assert first_line.startswith("track type=bedGraph")
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_snp_calls_coverage_to_bedgraph(fixture, api: CoverageExporter, tmp_path):
+    region = random.choice(api.contigs)
+    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
+
+    output_path = str(tmp_path / "test_snp_coverage.bedgraph")
+    api.snp_calls_coverage_to_bedgraph(
+        output_path=output_path,
+        region=region,
+        sample=sample,
+    )
+
+    assert os.path.exists(output_path)
+
+    with open(output_path) as f:
+        lines = f.readlines()
+
+    assert lines[0].startswith("track type=bedGraph")
+
+    # N.B., the simulated AD data is filled with a missing-value
+    # sentinel (-1) for every site, so no data lines are expected here;
+    # this exercises that missing values are skipped rather than
+    # written as misleading zero-depth entries. The arithmetic for
+    # sites that do have depth is checked separately below, using a
+    # synthetic dataset.
+    for line in lines[1:]:
+        fields = line.rstrip("\n").split("\t")
+        assert len(fields) == 4
+        chrom, start, end, value = fields
+        assert chrom == region
+        assert int(end) == int(start) + 1
+        assert int(value) >= 0
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_snp_calls_coverage_to_bedgraph_depth_values(
+    fixture, api: CoverageExporter, tmp_path, monkeypatch
+):
+    # Exercise the depth arithmetic directly against a small synthetic
+    # dataset, since the simulated fixture data fills call_AD with a
+    # missing-value sentinel throughout (see test above).
+    contig = api.contigs[0]
+    sample = str(api.sample_metadata()["sample_id"].iloc[0])
+
+    ds = xr.Dataset(
+        data_vars={
+            "call_AD": (
+                ["variants", "samples", "alleles"],
+                da.from_array(
+                    np.array(
+                        [
+                            [[10, 2, 0, 0]],  # total depth 12
+                            [[-1, -1, -1, -1]],  # missing, should be skipped
+                            [[5, -1, 0, 0]],  # negative components clipped to 0
+                        ],
+                        dtype="i2",
+                    ),
+                    chunks=(2, 1, 4),
+                ),
+            ),
+        },
+        coords={
+            "variant_position": (
+                "variants",
+                da.from_array(np.array([100, 200, 300]), chunks=2),
+            ),
+            "variant_contig": (
+                "variants",
+                da.from_array(np.array([0, 0, 0], dtype="u1"), chunks=2),
+            ),
+            "sample_id": ("samples", np.array([sample])),
+        },
+        attrs={"contigs": (contig,)},
+    )
+    monkeypatch.setattr(api, "snp_calls", lambda **kwargs: ds)
+
+    output_path = str(tmp_path / "test_snp_coverage_values.bedgraph")
+    api.snp_calls_coverage_to_bedgraph(
+        output_path=output_path,
+        region=contig,
+        sample=sample,
+    )
+
+    with open(output_path) as f:
+        lines = f.readlines()
+
+    data_lines = [line.rstrip("\n").split("\t") for line in lines[1:]]
+    assert data_lines == [
+        [contig, "99", "100", "12"],
+        [contig, "299", "300", "5"],
+    ]
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_snp_calls_coverage_to_bedgraph_unknown_sample(
+    fixture, api: CoverageExporter, tmp_path
+):
+    region = api.contigs[0]
+    output_path = str(tmp_path / "test_snp_coverage_unknown.bedgraph")
+    with pytest.raises(ValueError, match="No data found for sample"):
+        api.snp_calls_coverage_to_bedgraph(
+            output_path=output_path,
+            region=region,
+            sample="not_a_real_sample",
+        )
diff --git a/tests/anoph/test_igv_coverage.py b/tests/anoph/test_igv_coverage.py
new file mode 100644
index 000000000..a39a0154c
--- /dev/null
+++ b/tests/anoph/test_igv_coverage.py
@@ -0,0 +1,143 @@
+import numpy as np
+import pytest
+from pytest_cases import parametrize_with_cases
+
+from malariagen_data import af1 as _af1
+from malariagen_data import ag3 as _ag3
+from malariagen_data.anoph.igv import AnophelesIgv
+from malariagen_data.anoph.to_coverage import CoverageExporter
+
+
+class _IgvWithCoverage(CoverageExporter, AnophelesIgv):
+    """Combines AnophelesIgv with CoverageExporter, the way the
+    top-level Ag3/Af1 data resource classes do, so that the local
+    coverage fallback functionality can be exercised in isolation."""
+
+
+@pytest.fixture
+def ag3_sim_api(ag3_sim_fixture):
+    return AnophelesIgv(
+        url=ag3_sim_fixture.url,
+        public_url=ag3_sim_fixture.url,
+        config_path=_ag3.CONFIG_PATH,
+        major_version_number=_ag3.MAJOR_VERSION_NUMBER,
+        major_version_path=_ag3.MAJOR_VERSION_PATH,
+        pre=True,
+        aim_metadata_dtype={
+            "aim_species_fraction_arab": "float64",
+            "aim_species_fraction_colu": "float64",
+            "aim_species_fraction_colu_no2l": "float64",
+            "aim_species_gambcolu_arabiensis": object,
+            "aim_species_gambiae_coluzzii": object,
+            "aim_species": object,
+        },
+        gff_gene_type="gene",
+        gff_gene_name_attribute="Name",
+        gff_default_attributes=("ID", "Parent", "Name", "description"),
+        default_site_mask="gamb_colu_arab",
+        results_cache=ag3_sim_fixture.results_cache_path.as_posix(),
+    )
+
+
+@pytest.fixture
+def ag3_sim_api_with_coverage(ag3_sim_fixture):
+    return _IgvWithCoverage(
+        url=ag3_sim_fixture.url,
+        public_url=ag3_sim_fixture.url,
+        config_path=_ag3.CONFIG_PATH,
+        major_version_number=_ag3.MAJOR_VERSION_NUMBER,
+        major_version_path=_ag3.MAJOR_VERSION_PATH,
+        pre=True,
+        aim_metadata_dtype={
+            "aim_species_fraction_arab": "float64",
+            "aim_species_fraction_colu": "float64",
+            "aim_species_fraction_colu_no2l": "float64",
+            "aim_species_gambcolu_arabiensis": object,
+            "aim_species_gambiae_coluzzii": object,
+            "aim_species": object,
+        },
+        gff_gene_type="gene",
+        gff_gene_name_attribute="Name",
+        gff_default_attributes=("ID", "Parent", "Name", "description"),
+        default_site_mask="gamb_colu_arab",
+        results_cache=ag3_sim_fixture.results_cache_path.as_posix(),
+        default_coverage_calls_analysis="gamb_colu",
+        discordant_read_calls_analysis=ag3_sim_fixture.config[
+            "DEFAULT_DISCORDANT_READ_CALLS_ANALYSIS"
+        ],
+    )
+
+
+@pytest.fixture
+def af1_sim_api_with_coverage(af1_sim_fixture):
+    return _IgvWithCoverage(
+        url=af1_sim_fixture.url,
+        public_url=af1_sim_fixture.url,
+        config_path=_af1.CONFIG_PATH,
+        major_version_number=_af1.MAJOR_VERSION_NUMBER,
+        major_version_path=_af1.MAJOR_VERSION_PATH,
+        pre=False,
+        gff_gene_type="protein_coding_gene",
+        gff_gene_name_attribute="Note",
+        gff_default_attributes=("ID", "Parent", "Note", "description"),
+        default_site_mask="funestus",
+        results_cache=af1_sim_fixture.results_cache_path.as_posix(),
+        default_coverage_calls_analysis="funestus",
+        discordant_read_calls_analysis=None,
+    )
+
+
+def case_ag3_sim(ag3_sim_fixture, ag3_sim_api_with_coverage):
+    return ag3_sim_fixture, ag3_sim_api_with_coverage
+
+
+def case_af1_sim(af1_sim_fixture, af1_sim_api_with_coverage):
+    return af1_sim_fixture, af1_sim_api_with_coverage
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_view_coverage(fixture, api: _IgvWithCoverage):
+    region = api.contigs[0]
+    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
+    ret = api.view_coverage(region=region, sample=sample, init=False)
+    # No return value to avoid cluttering notebook output.
+    assert ret is None
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_view_alignments_with_local_coverage_fallback(fixture, api: _IgvWithCoverage):
+    region = api.contigs[0]
+    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
+    ret = api.view_alignments(
+        region=region,
+        sample=sample,
+        init=False,
+        local_coverage_fallback=True,
+    )
+    assert ret is None
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_view_coverage_writes_bedgraph(fixture, api: _IgvWithCoverage, tmp_path):
+    region = api.contigs[0]
+    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
+    output_path = str(tmp_path / "coverage.bedgraph")
+    api.view_coverage(region=region, sample=sample, init=False, output_path=output_path)
+    with open(output_path) as f:
+        first_line = f.readline()
+    assert first_line.startswith("track type=bedGraph")
+
+
+def test_local_coverage_fallback_requires_cnv_mixin(ag3_sim_fixture, ag3_sim_api):
+    # Plain AnophelesIgv, without CoverageExporter mixed in, should
+    # raise a clear error rather than an AttributeError if asked for a
+    # local coverage track.
+    region = ag3_sim_api.contigs[0]
+    sample = str(np.random.choice(ag3_sim_api.sample_metadata()["sample_id"]))
+    with pytest.raises(NotImplementedError):
+        ag3_sim_api.view_alignments(
+            region=region,
+            sample=sample,
+            init=False,
+            local_coverage_fallback=True,
+        )
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index a583b081a..b320a947d 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -415,11 +415,22 @@ def test_vcf_exporter_gzip(fixture, api: SnpVcfExporter, tmp_path):
     )
     assert os.path.exists(output_path)
 
-    # Verify it's valid gzip.
+    # Verify it's valid gzip (BGZF is valid gzip, so this works either
+    # way; the stronger, BGZF-specific check follows below).
     with gzip.open(output_path, "rt") as f:
         first_line = f.readline()
     assert first_line.strip() == "##fileformat=VCFv4.3"
 
+    # Verify it's specifically valid BGZF, not just plain gzip: this is
+    # what tools like tabix/bedtools require for .vcf.gz files, and
+    # what distinguishes genuine BGZF from a plain gzip stream that
+    # happens to decompress fine but isn't block-structured.
+    if shutil.which("bgzip") is not None:
+        result = subprocess.run(
+            ["bgzip", "-t", output_path], capture_output=True, text=True
+        )
+        assert result.returncode == 0, f"not valid BGZF: {result.stderr}"
+
 
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_fields(fixture, api: SnpVcfExporter, tmp_path):
diff --git a/tests/anoph/test_vcf_exporter_cnv.py b/tests/anoph/test_vcf_exporter_cnv.py
index e111ce70b..8081cef1c 100644
--- a/tests/anoph/test_vcf_exporter_cnv.py
+++ b/tests/anoph/test_vcf_exporter_cnv.py
@@ -1,6 +1,8 @@
 import gzip
 import os
 import random
+import shutil
+import subprocess
 
 import pytest
 from pytest_cases import parametrize_with_cases
@@ -232,3 +234,11 @@ def test_cnv_hmm_to_vcf_gzip(fixture, api: CnvVcfExporter, tmp_path):
     with gzip.open(output_path, "rt") as f:
         first_line = f.readline()
     assert first_line.strip() == "##fileformat=VCFv4.3"
+
+    # Verify it's specifically valid BGZF, not just plain gzip — what
+    # tools like tabix/bedtools require for .vcf.gz files.
+    if shutil.which("bgzip") is not None:
+        result = subprocess.run(
+            ["bgzip", "-t", output_path], capture_output=True, text=True
+        )
+        assert result.returncode == 0, f"not valid BGZF: {result.stderr}"
diff --git a/tests/test_bgzf.py b/tests/test_bgzf.py
new file mode 100644
index 000000000..38e8e5d61
--- /dev/null
+++ b/tests/test_bgzf.py
@@ -0,0 +1,95 @@
+import gzip
+import shutil
+import subprocess
+
+import pytest
+
+from malariagen_data.bgzf import _MAX_BLOCK_UNCOMPRESSED_SIZE, bgzf_open
+
+
+def test_bgzf_round_trip(tmp_path):
+    output_path = str(tmp_path / "test.txt.gz")
+    lines = [f"line {i}\n" for i in range(100)]
+
+    with bgzf_open(output_path, "wt") as f:
+        for line in lines:
+            f.write(line)
+
+    # BGZF is valid gzip, so a plain gzip reader must be able to read
+    # the exact content back.
+    with gzip.open(output_path, "rt") as f:
+        content = f.read()
+    assert content == "".join(lines)
+
+
+def test_bgzf_multi_block_round_trip(tmp_path):
+    # Write enough data to force multiple BGZF blocks, and include
+    # content that lands exactly on, just under, and just over a block
+    # boundary, to exercise the block-splitting logic.
+    output_path = str(tmp_path / "test_multiblock.txt.gz")
+    line = "the quick brown fox jumps over the lazy dog 0123456789\n"
+    n_lines = (_MAX_BLOCK_UNCOMPRESSED_SIZE // len(line)) * 3 + 7
+    expected = "".join(f"{i}:{line}" for i in range(n_lines))
+
+    with bgzf_open(output_path, "wt") as f:
+        for i in range(n_lines):
+            f.write(f"{i}:{line}")
+
+    with gzip.open(output_path, "rt") as f:
+        content = f.read()
+    assert content == expected
+
+
+def test_bgzf_empty_file(tmp_path):
+    # Writing nothing should still produce a valid (if empty) BGZF
+    # file, i.e. just the EOF marker.
+    output_path = str(tmp_path / "test_empty.txt.gz")
+    with bgzf_open(output_path, "wt"):
+        pass
+
+    with gzip.open(output_path, "rt") as f:
+        content = f.read()
+    assert content == ""
+
+
+def test_bgzf_rejects_binary_mode(tmp_path):
+    output_path = str(tmp_path / "test.txt.gz")
+    with pytest.raises(ValueError):
+        bgzf_open(output_path, "wb")
+
+
+@pytest.mark.skipif(shutil.which("bgzip") is None, reason="bgzip not installed")
+def test_bgzf_valid_per_bgzip(tmp_path):
+    # The definitive check: the reference BGZF implementation itself
+    # must accept this as valid BGZF, not just "some gzip stream that
+    # happens to decompress correctly."
+    output_path = str(tmp_path / "test.txt.gz")
+    with bgzf_open(output_path, "wt") as f:
+        for i in range(10_000):
+            f.write(f"line {i}\n")
+
+    result = subprocess.run(
+        ["bgzip", "-t", output_path], capture_output=True, text=True
+    )
+    assert result.returncode == 0, f"not valid BGZF: {result.stderr}"
+
+
+@pytest.mark.skipif(shutil.which("tabix") is None, reason="tabix not installed")
+def test_bgzf_tabix_indexable(tmp_path):
+    # tabix specifically requires genuine BGZF block structure to
+    # build an index at all; plain gzip fails here even though it
+    # decompresses fine. This is the property that made bedtools (and
+    # other BGZF-aware tools) unable to read plain-gzip VCF output
+    # correctly, even though bcftools tolerated it.
+    output_path = str(tmp_path / "test.vcf.gz")
+    with bgzf_open(output_path, "wt") as f:
+        f.write("##fileformat=VCFv4.3\n")
+        f.write("##contig=<ID=2R>\n")
+        f.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
+        for pos in (100, 200, 300):
+            f.write(f"2R\t{pos}\t.\tA\tT\t.\t.\t.\n")
+
+    result = subprocess.run(
+        ["tabix", "-p", "vcf", output_path], capture_output=True, text=True
+    )
+    assert result.returncode == 0, f"tabix failed to index: {result.stderr}"

From 417ddb703d4ef1705013ca0ce865e211e3945700 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 30 Sep 2026 13:09:57 +0100
Subject: [PATCH 17/38] removing Claudes allele remapping to see if that
 improves results

---
 malariagen_data/anoph/to_vcf.py | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 3139eefaa..af866b7e4 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -414,15 +414,18 @@ def snp_calls_to_vcf(
 
                         chrom = contigs[contig_chunk[j]]
                         pos = str(pos_chunk[j])
-                        # Reuse the chunk-level decode from above, so
-                        # the ALT column built here is guaranteed
-                        # consistent with the allele-index remapping
-                        # used for GT (both derive from the same
-                        # decoded_alleles/is_present arrays).
-                        ref = decoded_alleles[j, 0]
-                        alt_alleles = [s for s in decoded_alleles[j, 1:] if s]
+                        alleles = allele_chunk[j]
+                        ref = (
+                            alleles[0].decode()
+                            if hasattr(alleles[0], "decode")
+                            else str(alleles[0])
+                        )
+                        alt_alleles = []
+                        for a in alleles[1:]:
+                            s = a.decode() if hasattr(a, "decode") else str(a)
+                            if s:
+                                alt_alleles.append(s)
                         alt = ",".join(alt_alleles) if alt_alleles else "."
-
                         # Build fixed VCF columns once per variant
                         fixed_cols = (
                             f"{chrom}\t{pos}\t.\t{ref}\t{alt}\t.\t.\t.\t{format_str}\t"

From b4876a6b3619f3d5013d0cb2861101ead50b2d58 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 30 Sep 2026 14:36:34 +0100
Subject: [PATCH 18/38] claudes last attempt, problems persisted, going to
 revert to a better version and figure out removing homozygous sites

---
 malariagen_data/anoph/to_vcf.py  | 78 ++++++++++++++++++++------------
 tests/anoph/test_vcf_exporter.py | 73 ++++++++++++++++++++++--------
 2 files changed, 101 insertions(+), 50 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index af866b7e4..00a243dfe 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -340,27 +340,50 @@ def snp_calls_to_vcf(
 
                     # Decode alleles once per chunk (rather than
                     # per-variant further down) and work out, per
-                    # variant, which of the ALT candidate slots are
-                    # actually populated. call_genotype's allele indices
-                    # refer to these *original* variant_allele slot
-                    # positions (0=REF, 1..3=ALT candidates), which are
-                    # not guaranteed to be contiguous from 1 — a site's
-                    # only real ALT allele can sit in slot 2 or 3 while
-                    # an earlier slot is empty. The ALT column written
-                    # below only lists the populated slots, so genotype
-                    # indices must be remapped to match that compacted
-                    # numbering
+                    # variant, which of the (REF + 3 ALT candidate)
+                    # variant_allele slots to actually write to the ALT
+                    # column. variant_allele lists a fixed, canonical
+                    # set of alternate bases per site regardless of
+                    # whether they're relevant to *this* sample — e.g.
+                    # for a REF=C site it lists "A,T,G" as ALT
+                    # candidates even if this sample is only ever
+                    # heterozygous for T, with zero read support for A
+                    # or G. Writing all of them to ALT produces a
+                    # non-standard single-sample VCF (real single-sample
+                    # VCFs only list alleles the sample's own genotype
+                    # actually uses) and breaks REF/ALT-based comparison
+                    # against any VCF that follows that convention,
+                    # since two VCFs listing the "same" call at the same
+                    # position end up with different ALT strings. So
+                    # only a slot that is both non-empty *and* actually
+                    # referenced by this sample's genotype is kept; the
+                    # remaining slots are dropped from ALT, and
+                    # genotype indices remapped to match, exactly as for
+                    # a genuinely empty slot.
                     decoded_alleles = np.empty(allele_chunk.shape, dtype=object)
                     for col in range(allele_chunk.shape[1]):
                         decoded_alleles[:, col] = [
                             a.decode() if hasattr(a, "decode") else str(a)
                             for a in allele_chunk[:, col]
                         ]
+                    n_allele_slots = allele_chunk.shape[1]
                     is_present = decoded_alleles != ""
+
+                    slot_referenced = np.zeros_like(is_present)
+                    slot_referenced[:, 0] = True  # REF is always kept
+                    valid = ~missing[:, 0]
+                    row_idx = np.arange(gt_chunk.shape[0])
+                    safe_a0 = np.clip(a0[:, 0], 0, n_allele_slots - 1)
+                    safe_a1 = np.clip(a1[:, 0], 0, n_allele_slots - 1)
+                    slot_referenced[row_idx[valid], safe_a0[valid]] = True
+                    slot_referenced[row_idx[valid], safe_a1[valid]] = True
+
+                    is_present = is_present & slot_referenced
                     is_present[:, 0] = True  # REF is always present
+
                     # compacted_index[i, k] = the index original slot k
                     # occupies in the ALT column for variant i, or -1 if
-                    # slot k isn't populated there.
+                    # slot k isn't kept there.
                     compacted_index = np.cumsum(is_present, axis=1) - 1
                     compacted_index[~is_present] = -1
 
@@ -374,14 +397,8 @@ def snp_calls_to_vcf(
                     # those rows is discarded below anyway, since they
                     # are written as "./." based on `missing`, not on
                     # this remapping.
-                    row_idx = np.arange(gt_chunk.shape[0])
-                    n_allele_slots = allele_chunk.shape[1]
-                    remapped_a0 = compacted_index[
-                        row_idx, np.clip(a0[:, 0], 0, n_allele_slots - 1)
-                    ]
-                    remapped_a1 = compacted_index[
-                        row_idx, np.clip(a1[:, 0], 0, n_allele_slots - 1)
-                    ]
+                    remapped_a0 = compacted_index[row_idx, safe_a0]
+                    remapped_a1 = compacted_index[row_idx, safe_a1]
                     # A remapped index of -1 means the genotype
                     # references an allele slot that variant_allele
                     # doesn't actually have populated at this site —
@@ -414,18 +431,19 @@ def snp_calls_to_vcf(
 
                         chrom = contigs[contig_chunk[j]]
                         pos = str(pos_chunk[j])
-                        alleles = allele_chunk[j]
-                        ref = (
-                            alleles[0].decode()
-                            if hasattr(alleles[0], "decode")
-                            else str(alleles[0])
-                        )
-                        alt_alleles = []
-                        for a in alleles[1:]:
-                            s = a.decode() if hasattr(a, "decode") else str(a)
-                            if s:
-                                alt_alleles.append(s)
+                        # Reuse the chunk-level decode from above, so
+                        # the ALT column built here is guaranteed
+                        # consistent with the allele-index remapping
+                        # used for GT (both derive from the same
+                        # decoded_alleles/is_present arrays).
+                        ref = decoded_alleles[j, 0]
+                        alt_alleles = [
+                            decoded_alleles[j, k]
+                            for k in range(1, n_allele_slots)
+                            if is_present[j, k]
+                        ]
                         alt = ",".join(alt_alleles) if alt_alleles else "."
+
                         # Build fixed VCF columns once per variant
                         fixed_cols = (
                             f"{chrom}\t{pos}\t.\t{ref}\t{alt}\t.\t.\t.\t{format_str}\t"
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index b320a947d..2edc02c27 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -583,25 +583,42 @@ def test_vcf_exporter_fields_gt_required(fixture, api: SnpVcfExporter, tmp_path)
 def test_vcf_exporter_allele_index_remapping(
     fixture, api: SnpVcfExporter, tmp_path, monkeypatch
 ):
-    # variant_allele slots for a site are not guaranteed to be
-    # contiguous from slot 1: a site's only real ALT allele can sit in
-    # slot 2 or 3 while an earlier slot is empty (cohort-wide allele
-    # arrays aren't necessarily left-justified per site). The ALT
-    # column only lists populated slots, so call_genotype's allele
-    # indices (which refer to the *original* slot positions) must be
-    # remapped to match, or a GT value can end up pointing at an ALT
-    # allele that isn't listed (or the wrong one) — exactly the bug
-    # that produced invalid records like "0/2" against a single-allele
-    # ALT column, which bcftools then silently mishandled.
+    # ALT should only ever list alleles that are both (a) genuinely
+    # populated in variant_allele and (b) actually referenced by this
+    # sample's own genotype. variant_allele lists a fixed, canonical
+    # set of alternate bases per site (e.g. for REF=A it can list
+    # "C,T,G" regardless of what's actually segregating, let alone
+    # relevant to one particular sample), and call_genotype's allele
+    # indices refer to those *original* slot positions, which are not
+    # guaranteed to be contiguous from 1 either (a site's only real ALT
+    # allele can sit in slot 2 or 3 while an earlier slot is empty).
+    # Writing every populated-but-irrelevant slot to ALT (a) produces
+    # invalid records when combined with un-remapped genotype indices
+    # (e.g. "0/2" against a single-allele ALT column, which bcftools
+    # then silently mishandled), and (b) even once indices are
+    # correctly remapped, produces a non-standard single-sample VCF
+    # (real single-sample VCFs only list alleles that sample's
+    # genotype actually uses) that fails REF/ALT-based comparison
+    # against any VCF following that convention — two VCFs recording
+    # the "same" call at the same position end up with different ALT
+    # strings purely because of unrelated candidate alleles.
     sample = str(api.sample_metadata()["sample_id"].iloc[0])
     contig = api.contigs[0]
 
     variant_allele = np.array(
         [
             [b"A", b"", b"T", b""],  # only real ALT in slot 2
-            [b"A", b"T", b"", b""],  # real ALT in slot 1 (unaffected case)
+            [b"A", b"T", b"", b""],  # real ALT in slot 1 (baseline case)
             [b"A", b"", b"", b"T"],  # only real ALT in slot 3
-            [b"A", b"C", b"", b"T"],  # two real ALTs, gap in slot 2
+            [b"A", b"C", b"", b"T"],  # two real ALTs, only one used
+            [b"A", b"C", b"T", b"G"],  # all 3 canonical ALTs populated,
+            #                            only one used (the real-world
+            #                            pattern: REF=A ALT="C,T,G"
+            #                            regardless of relevance)
+            [b"A", b"C", b"T", b"G"],  # all 3 populated, compound het
+            #                            using two of them
+            [b"A", b"C", b"T", b"G"],  # all 3 populated, hom-ref
+            [b"A", b"C", b"T", b"G"],  # all 3 populated, missing
         ],
         dtype="S1",
     )
@@ -610,36 +627,50 @@ def test_vcf_exporter_allele_index_remapping(
             [[0, 2]],  # het for the slot-2 "T" -> ALT="T" -> expect 0/1
             [[0, 1]],  # het for the slot-1 "T" -> ALT="T" -> expect 0/1
             [[3, 3]],  # hom-alt for the slot-3 "T" -> ALT="T" -> expect 1/1
-            [[0, 3]],  # het for the slot-3 "T" -> ALT="C,T" -> expect 0/2
+            [[0, 3]],  # het for slot-3 "T"; slot-1 "C" unused -> expect ALT="T", GT=0/1
+            [
+                [0, 2]
+            ],  # het for slot-2 "T"; "C" and "G" unused -> expect ALT="T", GT=0/1
+            [
+                [1, 3]
+            ],  # het for slot-1 "C" and slot-3 "G"; "T" unused -> expect ALT="C,G", GT=1/2
+            [[0, 0]],  # hom-ref -> expect ALT=".", GT=0/0
+            [[-1, -1]],  # missing -> expect ALT=".", GT=./.
         ],
         dtype="i1",
     )
+    positions = [100, 200, 300, 400, 500, 600, 700, 800]
     expected = {
         100: ("T", "0/1"),
         200: ("T", "0/1"),
         300: ("T", "1/1"),
-        400: ("C,T", "0/2"),
+        400: ("T", "0/1"),
+        500: ("T", "0/1"),
+        600: ("C,G", "1/2"),
+        700: (".", "0/0"),
+        800: (".", "./."),
     }
 
+    n_variants = len(positions)
     ds = xr.Dataset(
         data_vars={
             "call_genotype": (
                 ["variants", "samples", "ploidy"],
-                da.from_array(call_genotype, chunks=(4, 1, 2)),
+                da.from_array(call_genotype, chunks=(n_variants, 1, 2)),
             ),
             "variant_allele": (
                 ["variants", "alleles"],
-                da.from_array(variant_allele, chunks=(4, 4)),
+                da.from_array(variant_allele, chunks=(n_variants, 4)),
             ),
         },
         coords={
             "variant_position": (
                 "variants",
-                da.from_array(np.array([100, 200, 300, 400]), chunks=4),
+                da.from_array(np.array(positions), chunks=n_variants),
             ),
             "variant_contig": (
                 "variants",
-                da.from_array(np.array([0, 0, 0, 0], dtype="u1"), chunks=4),
+                da.from_array(np.zeros(n_variants, dtype="u1"), chunks=n_variants),
             ),
             "sample_id": ("samples", np.array([sample])),
         },
@@ -658,7 +689,7 @@ def test_vcf_exporter_allele_index_remapping(
     with open(output_path) as f:
         lines = f.readlines()
     data_lines = [line for line in lines if not line.startswith("#")]
-    assert len(data_lines) == 4
+    assert len(data_lines) == n_variants
 
     for line in data_lines:
         fields_row = line.strip().split("\t")
@@ -671,6 +702,8 @@ def test_vcf_exporter_allele_index_remapping(
         # Every GT allele index must be valid for the ALT column that
         # was actually written (i.e. in range for the number of ALT
         # alleles listed), which is the invariant this fix guarantees.
-        n_alt_alleles = len(alt.split(","))
+        if gt == "./.":
+            continue
+        n_alt_alleles = 0 if alt == "." else len(alt.split(","))
         for allele_idx in gt.split("/"):
             assert int(allele_idx) <= n_alt_alleles

From 67f4ed65996fb3015bb911b09776ae1871f2e80f Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 30 Sep 2026 16:14:51 +0100
Subject: [PATCH 19/38] removed leftover bits from to_vcf_cnv

---
 malariagen_data/anoph/to_vcf.py     | 363 ++++++++++++----------------
 malariagen_data/anoph/to_vcf_cnv.py |   8 +-
 malariagen_data/bgzf.py             | 125 ----------
 3 files changed, 158 insertions(+), 338 deletions(-)
 delete mode 100644 malariagen_data/bgzf.py

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 00a243dfe..ae68408d1 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -1,18 +1,34 @@
+import gzip
 import os
 import re
 from datetime import date
 from typing import Optional
-
 import dask
+from dask.array.core import Array
+from xarray.core.dataset import Dataset
 import numpy as np
 from numpydoc_decorator import doc  # type: ignore
+from dataclasses import dataclass
+from collections import OrderedDict
+import math
 
-from ..bgzf import bgzf_open
 from .snp_data import AnophelesSnpData
 from . import base_params
 from . import plink_params
 from . import vcf_params
 
+
+@dataclass
+class VariantChunkData:
+    gq_chunk: Array
+    ad_chunk: Array
+    mq_chunk: Array
+    gt_chunk: Array
+    pos_chunk: Array
+    contig_chunk: Array
+    allele_chunk: Array
+
+
 # Supported FORMAT fields, the fixed order in which their values are
 # always written per sample (regardless of what order the caller's
 # `fields` argument happens to iterate in — e.g. a set has no
@@ -104,19 +120,6 @@ def __init__(
             selecting samples by cohort, or more than one sample_id) is
             rejected.
         """,
-        parameters=dict(
-            non_ref_only="""
-                If True, only write sites where the sample's genotype
-                carries at least one non-reference allele (i.e. skip
-                sites where the sample is homozygous reference or
-                missing). Equivalent to filtering the output with
-                `bcftools view -e 'F_PASS(GT="ref") == 1'`, except that
-                missing genotype calls are also excluded here (whereas
-                that particular bcftools expression only excludes
-                homozygous reference calls, since a missing call is
-                neither "ref" nor selected by `-e`).
-            """,
-        ),
         returns="""
         Path to the VCF output file.
         """,
@@ -129,12 +132,11 @@ def snp_calls_to_vcf(
         sample_query: base_params.sample_query,
         sample_query_options: Optional[base_params.sample_query_options] = None,
         sample_indices: Optional[base_params.sample_indices] = None,
-        site_mask: Optional[base_params.site_mask] = None,
+        site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         chunks: base_params.chunks = base_params.native_chunks,
         overwrite: plink_params.overwrite = False,
         fields: vcf_params.vcf_fields = ("GT",),
-        non_ref_only: bool = False,
     ) -> str:
         base_params._validate_sample_selection_params(
             sample_query=sample_query, sample_indices=sample_indices
@@ -177,7 +179,7 @@ def snp_calls_to_vcf(
             chunks=chunks,
         )
 
-        # Confirm inputs resolve to exactly
+        # Confirm inputs actually resolved to exactly
         # one sample within the given sample_sets
         # checked defensively rather than silently written
         # out as a multi-sample VCF.
@@ -192,11 +194,7 @@ def snp_calls_to_vcf(
         sample_ids = ds["sample_id"].values
         contigs = ds.attrs.get("contigs", self.contigs)
         compress = output_path.endswith(".gz")
-        # N.B., genuine BGZF, not plain gzip: tools that specifically
-        # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
-        # fail to read, or silently mis-parse, plain gzip even though
-        # it decompresses fine as a byte stream.
-        opener = bgzf_open if compress else open
+        opener = gzip.open if compress else open
 
         # Determine which extra fields to include.
         include_gq = "GQ" in fields
@@ -232,84 +230,27 @@ def snp_calls_to_vcf(
             contig_data = ds["variant_contig"].data
             allele_data = ds["variant_allele"].data
 
-            # Optional field arrays — may not exist in all datasets.
-            gq_data = None
-            ad_data = None
-            mq_data = None
-            if include_gq:
-                try:
-                    gq_data = ds["call_GQ"].data
-                except KeyError:
-                    pass
-            if include_ad:
-                try:
-                    ad_data = ds["call_AD"].data
-                except KeyError:
-                    pass
-            if include_mq:
-                try:
-                    mq_data = ds["call_MQ"].data
-                except KeyError:
-                    pass
+            optional_arrays = self._get_optional_data(
+                include_gq, include_ad, include_mq, ds
+            )
 
             chunk_sizes = gt_data.chunks[0]
             offsets = np.cumsum((0,) + chunk_sizes)
 
-            # Which optional fields were requested, so we know what to
-            # fetch (and where to put the results) for each chunk below.
-            optional_names = []
-            optional_arrays = []
-            if gq_data is not None:
-                optional_names.append("GQ")
-                optional_arrays.append(gq_data)
-            if ad_data is not None:
-                optional_names.append("AD")
-                optional_arrays.append(ad_data)
-            if mq_data is not None:
-                optional_names.append("MQ")
-                optional_arrays.append(mq_data)
-
             # Write records in chunks.
             with self._spinner(f"Write VCF ({ds.sizes['variants']} variants)"):
                 for ci in range(len(chunk_sizes)):
-                    start = offsets[ci]
-                    stop = offsets[ci + 1]
-
-                    # Fetch the required arrays for this chunk in a
-                    # single batched call, rather than one .compute()
-                    # call per array. Each separate .compute() call is
-                    # its own blocking round trip to the underlying
-                    # store (e.g. GCS); batching lets dask fetch all of
-                    # them concurrently instead of one at a time
-                    gt_chunk, pos_chunk, contig_chunk, allele_chunk = dask.compute(
-                        gt_data[start:stop],
-                        pos_data[start:stop],
-                        contig_data[start:stop],
-                        allele_data[start:stop],
+                    variant_chunk_data = self._get_chunks(
+                        ci,
+                        offsets,
+                        gt_data,
+                        pos_data,
+                        contig_data,
+                        allele_data,
+                        optional_arrays,
                     )
 
-                    # Fetch requested optional fields for this chunk
-                    # as a single batched call. If any fail
-                    # to load, fall back to "." for all requested
-                    # optional fields in this chunk — these arrays live
-                    # in the same region of the same store, so a failure
-                    # affecting one is likely to affect the others too,
-                    gq_chunk = None
-                    ad_chunk = None
-                    mq_chunk = None
-                    if optional_arrays:
-                        try:
-                            computed = dask.compute(
-                                *(arr[start:stop] for arr in optional_arrays)
-                            )
-                            optional_chunks = dict(zip(optional_names, computed))
-                            gq_chunk = optional_chunks.get("GQ")
-                            ad_chunk = optional_chunks.get("AD")
-                            mq_chunk = optional_chunks.get("MQ")
-                        except (FileNotFoundError, KeyError):
-                            pass
-
-                    n_samples = gt_chunk.shape[1]
+                    n_samples = variant_chunk_data.gt_chunk.shape[1]
 
                     # OPTIMIZATION: Vectorize GT field formatting across entire chunk.
                     # Instead of formatting each sample's GT field in a nested Python loop
@@ -317,131 +258,45 @@ def snp_calls_to_vcf(
                     # use NumPy's vectorized string operations on the entire chunk at once.
                     # This provides ~3x speedup while maintaining exact output compatibility.
                     # See issue #1280 for performance analysis.
-                    gt_chunk_2d = gt_chunk.reshape(
-                        gt_chunk.shape[0], gt_chunk.shape[1], 2
+                    gt_chunk_2d = variant_chunk_data.gt_chunk.reshape(
+                        variant_chunk_data.gt_chunk.shape[0],
+                        variant_chunk_data.gt_chunk.shape[1],
+                        2,
                     )
                     a0 = gt_chunk_2d[:, :, 0]  # (n_variants, n_samples)
                     a1 = gt_chunk_2d[:, :, 1]  # (n_variants, n_samples)
                     missing = (a0 < 0) | (a1 < 0)
 
-                    # If non_ref_only, work out up front which variants
-                    # to skip: those where the sample is homozygous
-                    # reference (0/0) or missing. Computed vectorized
-                    # across the whole chunk, same as `missing` above.
-                    # N.B., this uses the *original* (un-remapped)
-                    # allele indices computed below — 0 always means REF
-                    # both before and after remapping, so this check is
-                    # unaffected by it.
-                    if non_ref_only:
-                        is_hom_ref = (a0 == 0) & (a1 == 0)
-                        skip_variant = (missing | is_hom_ref)[:, 0]
-                    else:
-                        skip_variant = None
-
-                    # Decode alleles once per chunk (rather than
-                    # per-variant further down) and work out, per
-                    # variant, which of the (REF + 3 ALT candidate)
-                    # variant_allele slots to actually write to the ALT
-                    # column. variant_allele lists a fixed, canonical
-                    # set of alternate bases per site regardless of
-                    # whether they're relevant to *this* sample — e.g.
-                    # for a REF=C site it lists "A,T,G" as ALT
-                    # candidates even if this sample is only ever
-                    # heterozygous for T, with zero read support for A
-                    # or G. Writing all of them to ALT produces a
-                    # non-standard single-sample VCF (real single-sample
-                    # VCFs only list alleles the sample's own genotype
-                    # actually uses) and breaks REF/ALT-based comparison
-                    # against any VCF that follows that convention,
-                    # since two VCFs listing the "same" call at the same
-                    # position end up with different ALT strings. So
-                    # only a slot that is both non-empty *and* actually
-                    # referenced by this sample's genotype is kept; the
-                    # remaining slots are dropped from ALT, and
-                    # genotype indices remapped to match, exactly as for
-                    # a genuinely empty slot.
-                    decoded_alleles = np.empty(allele_chunk.shape, dtype=object)
-                    for col in range(allele_chunk.shape[1]):
-                        decoded_alleles[:, col] = [
-                            a.decode() if hasattr(a, "decode") else str(a)
-                            for a in allele_chunk[:, col]
-                        ]
-                    n_allele_slots = allele_chunk.shape[1]
-                    is_present = decoded_alleles != ""
-
-                    slot_referenced = np.zeros_like(is_present)
-                    slot_referenced[:, 0] = True  # REF is always kept
-                    valid = ~missing[:, 0]
-                    row_idx = np.arange(gt_chunk.shape[0])
-                    safe_a0 = np.clip(a0[:, 0], 0, n_allele_slots - 1)
-                    safe_a1 = np.clip(a1[:, 0], 0, n_allele_slots - 1)
-                    slot_referenced[row_idx[valid], safe_a0[valid]] = True
-                    slot_referenced[row_idx[valid], safe_a1[valid]] = True
-
-                    is_present = is_present & slot_referenced
-                    is_present[:, 0] = True  # REF is always present
-
-                    # compacted_index[i, k] = the index original slot k
-                    # occupies in the ALT column for variant i, or -1 if
-                    # slot k isn't kept there.
-                    compacted_index = np.cumsum(is_present, axis=1) - 1
-                    compacted_index[~is_present] = -1
-
-                    # Remap this chunk's genotype allele indices to the
-                    # compacted numbering. n_samples is always 1 here
-                    # (snp_calls_to_vcf only supports a single sample),
-                    # so a0/a1 are worked with as flat (n_variants,)
-                    # arrays. Clip before gathering so a missing
-                    # genotype's sentinel value (-1) can't trigger an
-                    # out-of-bounds index — the gathered result for
-                    # those rows is discarded below anyway, since they
-                    # are written as "./." based on `missing`, not on
-                    # this remapping.
-                    remapped_a0 = compacted_index[row_idx, safe_a0]
-                    remapped_a1 = compacted_index[row_idx, safe_a1]
-                    # A remapped index of -1 means the genotype
-                    # references an allele slot that variant_allele
-                    # doesn't actually have populated at this site —
-                    # inconsistent data that shouldn't occur, but is
-                    # treated as missing defensively rather than writing
-                    # a nonsensical negative allele index.
-                    missing_or_unmapped = (
-                        missing[:, 0] | (remapped_a0 < 0) | (remapped_a1 < 0)
-                    )
-
                     # Build formatted GT strings using NumPy vectorization
                     gt_formatted = np.empty(
-                        (gt_chunk.shape[0], n_samples), dtype=object
+                        (variant_chunk_data.gt_chunk.shape[0], n_samples), dtype=object
                     )
-                    gt_formatted[missing_or_unmapped, 0] = "./."
-                    present_idx = ~missing_or_unmapped
+                    gt_formatted[missing] = "./."
+                    present_idx = ~missing
                     if np.any(present_idx):
-                        a0_str = remapped_a0[present_idx].astype(str)
-                        a1_str = remapped_a1[present_idx].astype(str)
-                        gt_formatted[present_idx, 0] = np.char.add(
+                        a0_str = a0[present_idx].astype(str)
+                        a1_str = a1[present_idx].astype(str)
+                        gt_formatted[present_idx] = np.char.add(
                             np.char.add(a0_str, "/"), a1_str
                         )
 
                     # Pre-allocate line buffer for better I/O
                     lines_to_write = []
 
-                    for j in range(gt_chunk.shape[0]):
-                        if skip_variant is not None and skip_variant[j]:
-                            continue
-
-                        chrom = contigs[contig_chunk[j]]
-                        pos = str(pos_chunk[j])
-                        # Reuse the chunk-level decode from above, so
-                        # the ALT column built here is guaranteed
-                        # consistent with the allele-index remapping
-                        # used for GT (both derive from the same
-                        # decoded_alleles/is_present arrays).
-                        ref = decoded_alleles[j, 0]
-                        alt_alleles = [
-                            decoded_alleles[j, k]
-                            for k in range(1, n_allele_slots)
-                            if is_present[j, k]
-                        ]
+                    for j in range(variant_chunk_data.gt_chunk.shape[0]):
+                        chrom = contigs[variant_chunk_data.contig_chunk[j]]
+                        pos = str(variant_chunk_data.pos_chunk[j])
+                        alleles = variant_chunk_data.allele_chunk[j]
+                        ref = (
+                            alleles[0].decode()
+                            if hasattr(alleles[0], "decode")
+                            else str(alleles[0])
+                        )
+                        alt_alleles = []
+                        for a in alleles[1:]:
+                            s = a.decode() if hasattr(a, "decode") else str(a)
+                            if s:
+                                alt_alleles.append(s)
                         alt = ",".join(alt_alleles) if alt_alleles else "."
 
                         # Build fixed VCF columns once per variant
@@ -466,15 +321,15 @@ def snp_calls_to_vcf(
 
                             # GQ.
                             if include_gq:
-                                if gq_chunk is not None:
-                                    v = gq_chunk[j, k]
+                                if variant_chunk_data.gq_chunk is not None:
+                                    v = variant_chunk_data.gq_chunk[j, k]
                                     parts.append("." if v < 0 else str(v))
                                 else:
                                     parts.append(".")
                             # AD.
                             if include_ad:
-                                if ad_chunk is not None:
-                                    ad_vals = ad_chunk[j, k]
+                                if variant_chunk_data.ad_chunk is not None:
+                                    ad_vals = variant_chunk_data.ad_chunk[j, k]
                                     parts.append(
                                         ",".join(
                                             "." if x < 0 else str(x) for x in ad_vals
@@ -487,9 +342,10 @@ def snp_calls_to_vcf(
                             # spec fixes the reserved FORMAT/MQ key as
                             # Integer (see _FORMAT_HEADERS).
                             if include_mq:
-                                if mq_chunk is not None:
-                                    v = mq_chunk[j, k]
-                                    parts.append("." if v < 0 else str(round(v)))
+                                if variant_chunk_data.mq_chunk is not None:
+                                    v = variant_chunk_data.mq_chunk[j, k]
+                                    if not math.isnan(v):
+                                        parts.append("." if v < 0 else str(round(v)))
                                 else:
                                     parts.append(".")
                             sample_fields.append(":".join(parts))
@@ -502,3 +358,92 @@ def snp_calls_to_vcf(
                     f.write("".join(lines_to_write))
 
         return output_path
+
+    def _get_chunks(
+        self,
+        ci: int,
+        offsets: np.array,
+        gt_data: Array,
+        pos_data: Array,
+        contig_data: Array,
+        allele_data: Array,
+        optional_arrays: OrderedDict,
+    ) -> tuple:
+        start = offsets[ci]
+        stop = offsets[ci + 1]
+
+        # Fetch the required arrays for this chunk in a
+        # single batched call, rather than one .compute()
+        # call per array. Each separate .compute() call is
+        # its own blocking round trip to the underlying
+        # store (e.g. GCS); batching lets dask fetch all of
+        # them concurrently instead of one at a time
+        gt_chunk, pos_chunk, contig_chunk, allele_chunk = dask.compute(
+            gt_data[start:stop],
+            pos_data[start:stop],
+            contig_data[start:stop],
+            allele_data[start:stop],
+        )
+        # Fetch requested optional fields for this chunk
+        # as a single batched call. If any of them fail
+        # to load, fall back to "." for all requested
+        # optional fields in this chunk — these arrays live
+        # in the same region of the same store, so a failure
+        # affecting one is likely to affect the others too,
+        gq_chunk = None
+        ad_chunk = None
+        mq_chunk = None
+        if optional_arrays:
+            try:
+                computed = dask.compute(
+                    *(arr[start:stop] for arr in optional_arrays.values())
+                )
+                optional_chunks = dict(zip(optional_arrays.keys(), computed))
+                gq_chunk = optional_chunks.get("GQ")
+                ad_chunk = optional_chunks.get("AD")
+                mq_chunk = optional_chunks.get("MQ")
+            except (FileNotFoundError, KeyError):
+                pass
+        chunk_output = VariantChunkData(
+            gt_chunk=gt_chunk,
+            pos_chunk=pos_chunk,
+            contig_chunk=contig_chunk,
+            allele_chunk=allele_chunk,
+            gq_chunk=gq_chunk,
+            ad_chunk=ad_chunk,
+            mq_chunk=mq_chunk,
+        )
+        return chunk_output
+
+    def _get_optional_data(
+        self, include_gq: bool, include_ad: bool, include_mq: bool, ds: Dataset
+    ) -> OrderedDict:
+        # Optional field arrays — may not exist in all datasets.
+        gq_data = None
+        ad_data = None
+        mq_data = None
+        if include_gq:
+            try:
+                gq_data = ds["call_GQ"].data
+            except KeyError:
+                pass
+        if include_ad:
+            try:
+                ad_data = ds["call_AD"].data
+            except KeyError:
+                pass
+        if include_mq:
+            try:
+                mq_data = ds["call_MQ"].data
+            except KeyError:
+                pass
+        # Which optional fields were requested, so we know what to
+        # fetch (and where to put the results) for each chunk below.
+        optional_arrays = OrderedDict()  # check needed
+        if gq_data is not None:
+            optional_arrays["GQ"] = gq_data
+        if ad_data is not None:
+            optional_arrays["AD"] = ad_data
+        if mq_data is not None:
+            optional_arrays["MQ"] = mq_data
+        return optional_arrays
diff --git a/malariagen_data/anoph/to_vcf_cnv.py b/malariagen_data/anoph/to_vcf_cnv.py
index 676897e5a..b42d63832 100644
--- a/malariagen_data/anoph/to_vcf_cnv.py
+++ b/malariagen_data/anoph/to_vcf_cnv.py
@@ -1,11 +1,11 @@
 import os
 from datetime import date
 from typing import List, Optional, Sequence
+import gzip
 
 import numpy as np
 from numpydoc_decorator import doc  # type: ignore
 
-from ..bgzf import bgzf_open
 from .cnv_data import AnophelesCnvData
 from . import base_params
 from . import cnv_params
@@ -124,7 +124,7 @@ def cnv_hmm_to_vcf(
         # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
         # fail to read, or silently mis-parse, plain gzip even though
         # it decompresses fine as a byte stream.
-        opener = bgzf_open if compress else open
+        opener = gzip.open if compress else open
 
         with opener(output_path, "wt") as f:
             _write_vcf_header(
@@ -223,7 +223,7 @@ def cnv_coverage_calls_to_vcf(
         # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
         # fail to read, or silently mis-parse, plain gzip even though
         # it decompresses fine as a byte stream.
-        opener = bgzf_open if compress else open
+        opener = gzip.open if compress else open
 
         with opener(output_path, "wt") as f:
             _write_vcf_header(
@@ -341,7 +341,7 @@ def cnv_discordant_read_calls_to_vcf(
         # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
         # fail to read, or silently mis-parse, plain gzip even though
         # it decompresses fine as a byte stream.
-        opener = bgzf_open if compress else open
+        opener = gzip.open if compress else open
 
         with opener(output_path, "wt") as f:
             _write_vcf_header(
diff --git a/malariagen_data/bgzf.py b/malariagen_data/bgzf.py
deleted file mode 100644
index d49a35853..000000000
--- a/malariagen_data/bgzf.py
+++ /dev/null
@@ -1,125 +0,0 @@
-"""Minimal, write-only BGZF (Blocked GZip Format) support.
-
-BGZF is the compression format used throughout the SAM/BAM/VCF tooling
-ecosystem (samtools, bcftools, tabix, bedtools, IGV, ...) for
-compressed, indexable files. Structurally, it's just a sequence of
-ordinary gzip members, each holding up to ~64KB of uncompressed data,
-with a small extra header field recording each member's total size,
-plus a fixed, empty final member used as an EOF marker.
-
-Python's standard library `gzip.open()` produces valid gzip, but not
-valid BGZF: tools that specifically expect BGZF for a `.vcf.gz` (or
-similar) file can fail to read it correctly, or silently mis-parse it,
-even though plain gzip decompresses just fine as a byte stream. This
-module exists so that `.gz` output written by malariagen_data is
-genuine BGZF, and therefore usable with the wider standard toolset
-(bcftools, tabix, bedtools, etc.), not just tools that happen to
-tolerate plain gzip.
-
-See the BGZF section of the SAM specification for the on-disk format
-this implements: https://samtools.github.io/hts-specs/SAMv1.pdf
-"""
-
-import struct
-import zlib
-from typing import Optional
-
-# The fixed, empty BGZF block used to mark genuine end-of-file (as
-# opposed to a truncated file). This exact byte sequence is part of the
-# BGZF specification, not something we generate ourselves.
-_BGZF_EOF_MARKER = bytes.fromhex(
-    "1f8b08040000000000ff0600424302001b0003000000000000000000"
-)
-
-# Maximum amount of *uncompressed* data placed in a single BGZF block.
-# Kept comfortably under the 16-bit BSIZE field's range (a block's
-# total on-disk size, header and footer included, must fit in 65536
-# bytes) even in the worst case where compression doesn't shrink the
-# input at all; this matches the conservative block size used by other
-# BGZF writers (e.g. Biopython's `Bio.bgzf`).
-_MAX_BLOCK_UNCOMPRESSED_SIZE = 65280
-
-
-def _compress_bgzf_block(data: bytes, level: int = 6) -> bytes:
-    """Compress `data` (must be <= _MAX_BLOCK_UNCOMPRESSED_SIZE bytes)
-    into a single, standalone BGZF block."""
-    compressor = zlib.compressobj(level, zlib.DEFLATED, -15)
-    compressed = compressor.compress(data) + compressor.flush(zlib.Z_FINISH)
-    crc = zlib.crc32(data) & 0xFFFFFFFF
-    isize = len(data) & 0xFFFFFFFF
-
-    # Block layout: 18-byte header (with the BGZF "BC" extra field),
-    # the compressed payload, then an 8-byte footer (CRC32 + ISIZE) —
-    # the same footer any gzip member ends with.
-    block_size = 18 + len(compressed) + 8
-    header = struct.pack(
-        "<BBBBIBBHBBHH",
-        0x1F,
-        0x8B,  # ID1, ID2: gzip magic number
-        0x08,  # CM: compression method (deflate)
-        0x04,  # FLG: FEXTRA set (an extra field follows)
-        0,  # MTIME
-        0,  # XFL
-        0xFF,  # OS: unknown
-        6,  # XLEN: length of the extra field below
-        0x42,
-        0x43,  # SI1, SI2: BGZF's "BC" extra subfield identifier
-        2,  # SLEN: subfield length
-        block_size - 1,  # BSIZE: total block size, minus 1
-    )
-    footer = struct.pack("<II", crc, isize)
-    return header + compressed + footer
-
-
-class BgzfWriter:
-    """A minimal, write-only, text-mode BGZF writer.
-
-    Used the same way as `gzip.open(path, "wt")`: construct, `write()`
-    strings to it, and either call `close()` or use it as a context
-    manager.
-    """
-
-    def __init__(self, path: str, encoding: str = "utf-8"):
-        self._fh = open(path, "wb")
-        self._encoding = encoding
-        self._buffer = bytearray()
-        self._closed = False
-
-    def write(self, text: str) -> None:
-        self._buffer.extend(text.encode(self._encoding))
-        while len(self._buffer) >= _MAX_BLOCK_UNCOMPRESSED_SIZE:
-            chunk = bytes(self._buffer[:_MAX_BLOCK_UNCOMPRESSED_SIZE])
-            del self._buffer[:_MAX_BLOCK_UNCOMPRESSED_SIZE]
-            self._fh.write(_compress_bgzf_block(chunk))
-
-    def close(self) -> None:
-        if self._closed:
-            return
-        if self._buffer:
-            self._fh.write(_compress_bgzf_block(bytes(self._buffer)))
-            self._buffer = bytearray()
-        self._fh.write(_BGZF_EOF_MARKER)
-        self._fh.close()
-        self._closed = True
-
-    def __enter__(self) -> "BgzfWriter":
-        return self
-
-    def __exit__(self, *exc_info) -> None:
-        self.close()
-
-
-def bgzf_open(path: str, mode: str = "wt", encoding: Optional[str] = "utf-8"):
-    """Open `path` for BGZF-compressed text writing.
-
-    Signature-compatible with `gzip.open(path, "wt")` for the subset of
-    usage malariagen_data's VCF/text exporters need (write-only, text
-    mode), so it can be used as a drop-in replacement for `gzip.open`
-    wherever genuine BGZF (rather than plain gzip) output is required.
-    """
-    if mode not in ("wt", "w"):
-        raise ValueError(
-            f"Unsupported mode {mode!r}: bgzf_open() only supports writing text "
-            "('wt' or 'w')."
-        )
-    return BgzfWriter(path, encoding=encoding or "utf-8")

From 5aabdfd519ba81fa525f03327fecb02f2a747db9 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 30 Sep 2026 17:05:41 +0100
Subject: [PATCH 20/38] try simple if statement to exclude homozygous sites

---
 malariagen_data/anoph/to_vcf.py | 73 +++++++++++++++++----------------
 1 file changed, 38 insertions(+), 35 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index ae68408d1..ff1414ad8 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -265,7 +265,7 @@ def snp_calls_to_vcf(
                     )
                     a0 = gt_chunk_2d[:, :, 0]  # (n_variants, n_samples)
                     a1 = gt_chunk_2d[:, :, 1]  # (n_variants, n_samples)
-                    missing = (a0 < 0) | (a1 < 0)
+                    missing = (a0 < 0) | (a1 < 0)  # array of loci not present
 
                     # Build formatted GT strings using NumPy vectorization
                     gt_formatted = np.empty(
@@ -318,41 +318,44 @@ def snp_calls_to_vcf(
                         # Use pre-formatted GT strings and add other fields
                         for k in range(n_samples):
                             parts = [gt_formatted[j, k]]
-
-                            # GQ.
-                            if include_gq:
-                                if variant_chunk_data.gq_chunk is not None:
-                                    v = variant_chunk_data.gq_chunk[j, k]
-                                    parts.append("." if v < 0 else str(v))
-                                else:
-                                    parts.append(".")
-                            # AD.
-                            if include_ad:
-                                if variant_chunk_data.ad_chunk is not None:
-                                    ad_vals = variant_chunk_data.ad_chunk[j, k]
-                                    parts.append(
-                                        ",".join(
-                                            "." if x < 0 else str(x) for x in ad_vals
+                            if parts != "0/0":  # homozygous genotype
+                                # GQ.
+                                if include_gq:
+                                    if variant_chunk_data.gq_chunk is not None:
+                                        v = variant_chunk_data.gq_chunk[j, k]
+                                        parts.append("." if v < 0 else str(v))
+                                    else:
+                                        parts.append(".")
+                                # AD.
+                                if include_ad:
+                                    if variant_chunk_data.ad_chunk is not None:
+                                        ad_vals = variant_chunk_data.ad_chunk[j, k]
+                                        parts.append(
+                                            ",".join(
+                                                "." if x < 0 else str(x)
+                                                for x in ad_vals
+                                            )
                                         )
-                                    )
-                                else:
-                                    parts.append(".")
-                            # MQ. Rounded to the nearest integer: the
-                            # underlying data is a float, but the VCF
-                            # spec fixes the reserved FORMAT/MQ key as
-                            # Integer (see _FORMAT_HEADERS).
-                            if include_mq:
-                                if variant_chunk_data.mq_chunk is not None:
-                                    v = variant_chunk_data.mq_chunk[j, k]
-                                    if not math.isnan(v):
-                                        parts.append("." if v < 0 else str(round(v)))
-                                else:
-                                    parts.append(".")
-                            sample_fields.append(":".join(parts))
-
-                        # Build and buffer the line
-                        line = fixed_cols + "\t".join(sample_fields) + "\n"
-                        lines_to_write.append(line)
+                                    else:
+                                        parts.append(".")
+                                # MQ. Rounded to the nearest integer: the
+                                # underlying data is a float, but the VCF
+                                # spec fixes the reserved FORMAT/MQ key as
+                                # Integer (see _FORMAT_HEADERS).
+                                if include_mq:
+                                    if variant_chunk_data.mq_chunk is not None:
+                                        v = variant_chunk_data.mq_chunk[j, k]
+                                        if not math.isnan(v):
+                                            parts.append(
+                                                "." if v < 0 else str(round(v))
+                                            )
+                                    else:
+                                        parts.append(".")
+                                sample_fields.append(":".join(parts))
+
+                            # Build and buffer the line
+                            line = fixed_cols + "\t".join(sample_fields) + "\n"
+                            lines_to_write.append(line)
 
                     # Write buffered lines in one go per chunk
                     f.write("".join(lines_to_write))

From b23e4b6f39105b6be806669f938465f688b0ce85 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 30 Sep 2026 17:21:52 +0100
Subject: [PATCH 21/38] fixed indentation to only output heterozygous sites

---
 malariagen_data/anoph/to_vcf.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index ff1414ad8..beb72275b 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -318,7 +318,7 @@ def snp_calls_to_vcf(
                         # Use pre-formatted GT strings and add other fields
                         for k in range(n_samples):
                             parts = [gt_formatted[j, k]]
-                            if parts != "0/0":  # homozygous genotype
+                            if parts != ["0/0"]:  # homozygous genotype
                                 # GQ.
                                 if include_gq:
                                     if variant_chunk_data.gq_chunk is not None:
@@ -353,9 +353,9 @@ def snp_calls_to_vcf(
                                         parts.append(".")
                                 sample_fields.append(":".join(parts))
 
-                            # Build and buffer the line
-                            line = fixed_cols + "\t".join(sample_fields) + "\n"
-                            lines_to_write.append(line)
+                                # Build and buffer the line
+                                line = fixed_cols + "\t".join(sample_fields) + "\n"
+                                lines_to_write.append(line)
 
                     # Write buffered lines in one go per chunk
                     f.write("".join(lines_to_write))

From 4203d04e1d52f8e6588692e491f2de579c1eb30b Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Thu, 1 Oct 2026 13:34:51 +0100
Subject: [PATCH 22/38] reverted igv to original version and removed
 to_coverage as bam urls will be fine

---
 malariagen_data/anoph/igv.py         | 212 +------------------
 malariagen_data/anoph/to_coverage.py | 298 ---------------------------
 malariagen_data/anoph/to_vcf.py      | 107 ++++------
 3 files changed, 45 insertions(+), 572 deletions(-)
 delete mode 100644 malariagen_data/anoph/to_coverage.py

diff --git a/malariagen_data/anoph/igv.py b/malariagen_data/anoph/igv.py
index 19c59ca48..59680640b 100644
--- a/malariagen_data/anoph/igv.py
+++ b/malariagen_data/anoph/igv.py
@@ -1,4 +1,3 @@
-import os
 from typing import List, Optional
 
 import igv_notebook  # type: ignore
@@ -78,97 +77,11 @@ def _igv_site_filters_tracks(
             tracks.append(track_config)
         return tracks
 
-    def _igv_local_coverage_track(
-        self,
-        *,
-        region: Region,
-        sample: str,
-        visibility_window: int,
-        source: str = "cnv_hmm",
-        field: str = "NormCov",
-        output_path: Optional[str] = None,
-    ):
-        # Build a coverage track computed locally from the Zarr arrays
-        # rather than loaded from an externally-hosted file. This is not
-        # a substitute for an alignments track (there are no individual
-        # reads), but gives a fallback source of coverage information
-        # for a sample when the BAM file is not available. Two sources
-        # are supported: "cnv_hmm" gives windowed coverage genome-wide;
-        # "snp_calls" gives per-base read depth, but only at called SNP
-        # sites.
-        #
-        # N.B., this method is only usable when this class is combined
-        # (via cooperative multiple inheritance) with CoverageExporter,
-        # as is the case for the top-level Ag3/Af1 data resource classes.
-        # Methods are accessed via getattr rather than a direct import to
-        # avoid adding CoverageExporter as a base class of AnophelesIgv,
-        # which would conflict with the method resolution order of the
-        # combined data resource classes.
-        extra_kwargs: dict
-        if source == "cnv_hmm":
-            to_bedgraph = getattr(self, "cnv_hmm_coverage_to_bedgraph", None)
-            extra_kwargs = dict(field=field)
-            track_name = f"Coverage ({field}, local) - {sample}"
-            path_suffix = field
-        elif source == "snp_calls":
-            to_bedgraph = getattr(self, "snp_calls_coverage_to_bedgraph", None)
-            extra_kwargs = dict()
-            track_name = f"SNP read depth (local) - {sample}"
-            path_suffix = "AD"
-        else:
-            raise ValueError(
-                f"Unknown coverage source: {source!r}. "
-                "Valid sources are 'cnv_hmm', 'snp_calls'."
-            )
-
-        if to_bedgraph is None:
-            raise NotImplementedError(
-                "Local coverage tracks require this API object to also "
-                "provide CNV and SNP data (see CoverageExporter)."
-            )
-
-        if output_path is None:
-            if self._results_cache is None:
-                raise ValueError(
-                    "Cannot create a local coverage track without knowing "
-                    "where to write it. Either pass `coverage_track_path`, "
-                    "or configure `results_cache` when creating this API "
-                    "object."
-                )
-            safe_region = (
-                str(region).replace(":", "_").replace(",", "").replace("-", "_")
-            )
-            cache_dir = self._results_cache / "igv_coverage"
-            os.makedirs(cache_dir, exist_ok=True)
-            output_path = str(
-                cache_dir / f"{sample}_{safe_region}_{source}_{path_suffix}.bedgraph"
-            )
-
-        to_bedgraph(
-            output_path=output_path,
-            region=region,
-            sample=sample,
-            **extra_kwargs,
-        )
-
-        return {
-            "name": track_name,
-            "url": output_path,
-            "format": "bedgraph",
-            "type": "wig",
-            "visibilityWindow": visibility_window,  # bp
-            "height": 50,
-            "color": "#5e3c99",
-        }
-
     def _igv_view_alignments_tracks(
         self,
         region: Region,
         sample: str,
         visibility_window: int = 20_000,
-        local_coverage_fallback: bool = False,
-        coverage_source: str = "cnv_hmm",
-        coverage_track_path: Optional[str] = None,
     ):
         # Look up sample set for sample.
         try:
@@ -208,10 +121,7 @@ def _igv_view_alignments_tracks(
             }
         )
 
-        # Add alignments track. N.B., this depends on the BAM file being
-        # hosted at `bam_url` and remaining reachable; if that URL stops
-        # working (e.g. following migration of raw data to ENA/EVA) this
-        # track will fail to load in the browser.
+        # Add alignments track.
         tracks.append(
             {
                 "name": "Alignments",
@@ -224,21 +134,6 @@ def _igv_view_alignments_tracks(
             }
         )
 
-        # Optionally also add a coverage track computed locally from CNV
-        # HMM or SNP calls data, as a fallback source of coverage
-        # information that does not depend on the alignments BAM file
-        # remaining available.
-        if local_coverage_fallback:
-            tracks.append(
-                self._igv_local_coverage_track(
-                    region=region,
-                    sample=sample,
-                    visibility_window=visibility_window,
-                    source=coverage_source,
-                    output_path=coverage_track_path,
-                )
-            )
-
         return tracks
 
     @_check_types
@@ -288,28 +183,6 @@ def igv(
                 visible.
             """,
             init="If True, call igv_notebook.init().",
-            local_coverage_fallback="""
-                If True, also add a coverage track computed locally from
-                CNV HMM or SNP calls data. Unlike the alignments track,
-                this does not depend on the BAM file remaining available
-                at its hosted URL, so it provides a fallback source of
-                coverage information if that URL stops working. It is
-                not a substitute for the alignments track, since it
-                contains only summarised coverage values, not individual
-                reads.
-            """,
-            coverage_source="""
-                Which data to compute the local coverage track from, if
-                `local_coverage_fallback` is True. "cnv_hmm" gives
-                windowed coverage genome-wide; "snp_calls" gives
-                per-base read depth, but only at called SNP sites.
-            """,
-            coverage_track_path="""
-                Path to write the local coverage track file to, if
-                `local_coverage_fallback` is True. If not provided,
-                defaults to a location under `results_cache` (which must
-                therefore be configured).
-            """,
         ),
     )
     def view_alignments(
@@ -318,9 +191,6 @@ def view_alignments(
         sample: str,
         visibility_window: int = 20_000,
         init: bool = True,
-        local_coverage_fallback: bool = False,
-        coverage_source: str = "cnv_hmm",
-        coverage_track_path: Optional[str] = None,
     ):
         # Parse region.
         region_prepped: Region = _parse_single_region(self, region)
@@ -331,86 +201,6 @@ def view_alignments(
             region=region_prepped,
             sample=sample,
             visibility_window=visibility_window,
-            local_coverage_fallback=local_coverage_fallback,
-            coverage_source=coverage_source,
-            coverage_track_path=coverage_track_path,
-        )
-
-        # Create IGV browser.
-        self.igv(region=region_prepped, tracks=tracks, init=init)
-
-    @_check_types
-    @doc(
-        summary="""
-            Launch IGV and view sequence read coverage from the given
-            sample, computed locally from CNV HMM or SNP calls data.
-        """,
-        extended_summary="""
-            Unlike `view_alignments()`, this does not depend on an
-            externally-hosted BAM file, or on the WGS data catalog:
-            coverage is derived directly from data already available in
-            the Zarr arrays. It shows only summarised coverage depth,
-            not individual aligned reads, so it is a fallback source of
-            information about read coverage rather than a substitute for
-            viewing alignments.
-        """,
-        parameters=dict(
-            sample="Sample identifier.",
-            source="""
-                Which data to compute the coverage track from.
-                "cnv_hmm" gives windowed coverage genome-wide;
-                "snp_calls" gives per-base read depth, but only at
-                called SNP sites.
-            """,
-            field="""
-                Which coverage field to display, if `source` is
-                "cnv_hmm". "NormCov" is coverage normalised against a set
-                of reference windows; "RawCov" is unnormalised read
-                counts per window. Ignored if `source` is "snp_calls".
-            """,
-            visibility_window="""
-                Zoom level in base pairs at which SNP data will become
-                visible.
-            """,
-            init="If True, call igv_notebook.init().",
-            output_path="""
-                Path to write the local coverage track file to. If not
-                provided, defaults to a location under `results_cache`
-                (which must therefore be configured).
-            """,
-        ),
-    )
-    def view_coverage(
-        self,
-        region: base_params.region,
-        sample: str,
-        source: str = "cnv_hmm",
-        field: str = "NormCov",
-        visibility_window: int = 20_000,
-        init: bool = True,
-        output_path: Optional[str] = None,
-    ):
-        # Parse region.
-        region_prepped: Region = _parse_single_region(self, region)
-        del region
-
-        # Set up site filters tracks, consistent with view_alignments().
-        tracks = self._igv_site_filters_tracks(
-            contig=region_prepped.contig,
-            visibility_window=visibility_window,
-        )
-
-        # Add the locally-computed coverage track. N.B., this does not
-        # touch the WGS data catalog or any externally-hosted files.
-        tracks.append(
-            self._igv_local_coverage_track(
-                region=region_prepped,
-                sample=sample,
-                visibility_window=visibility_window,
-                source=source,
-                field=field,
-                output_path=output_path,
-            )
         )
 
         # Create IGV browser.
diff --git a/malariagen_data/anoph/to_coverage.py b/malariagen_data/anoph/to_coverage.py
deleted file mode 100644
index ee0248693..000000000
--- a/malariagen_data/anoph/to_coverage.py
+++ /dev/null
@@ -1,298 +0,0 @@
-import gzip
-import os
-from typing import List, Optional
-
-import numpy as np
-from numpydoc_decorator import doc  # type: ignore
-
-from .cnv_data import AnophelesCnvData
-from .snp_data import AnophelesSnpData
-from . import base_params
-from . import cnv_params
-from . import plink_params
-
-_VALID_CNV_COVERAGE_FIELDS = {"NormCov", "RawCov"}
-
-
-def _bedgraph_opener(output_path: str):
-    # N.B., plain gzip is intentional here, unlike the VCF exporters
-    # (see malariagen_data.bgzf): bedGraph doesn't carry the same
-    # ecosystem-wide expectation that a `.gz` file specifically be
-    # BGZF, and IGV loads a plain-gzipped bedGraph track without
-    # issue.
-    compress = output_path.endswith(".gz")
-    return gzip.open if compress else open
-
-
-class CoverageExporter(
-    AnophelesCnvData,
-    AnophelesSnpData,
-):
-    """
-    Export per-sample read coverage to bedGraph, derived either from
-    CNV HMM data (windowed coverage, genome-wide) or from SNP calls
-    (per-site read depth, only at called SNP positions).
-
-    N.B., this does not reconstruct read alignments. It cannot
-    substitute for a BAM file, because the underlying Zarr arrays only
-    ever store windowed or per-site summary values (and copy number
-    calls derived from them) rather than individual reads. What this
-    class provides is a coverage-depth track that can be loaded into
-    IGV alongside (or instead of) an alignments track, as a fallback
-    for when the raw BAM file for a sample is not available, e.g.
-    because it is hosted externally and that host has become
-    unreachable.
-    """
-
-    def __init__(
-        self,
-        **kwargs,
-    ):
-        # N.B., this class is designed to work cooperatively, and
-        # so it's important that any remaining parameters are passed
-        # to the superclass constructor.
-        super().__init__(**kwargs)
-
-    def _lookup_sample_set(self, sample: str) -> str:
-        try:
-            sample_rec = self.sample_metadata().set_index("sample_id").loc[sample]
-        except KeyError as e:
-            raise ValueError(
-                f"No data found for sample {sample!r}. This sample might be "
-                "unavailable or irrelevant with respect to settings."
-            ) from e
-        return sample_rec["sample_set"]
-
-    @doc(
-        summary="""
-            Export per-sample CNV HMM coverage to bedGraph format.
-        """,
-        extended_summary="""
-            This function writes windowed read coverage for a single
-            sample, derived from CNV HMM data, to a bedGraph file. This
-            is not a substitute for a BAM file of aligned reads: it
-            contains only per-window summary coverage values (as stored
-            in the Zarr arrays), not individual reads. It is intended as
-            a fallback coverage track for IGV, for use when the aligned
-            reads (BAM) for a sample are not available, e.g. because the
-            file is hosted externally and unreachable. Coverage is
-            available genome-wide (in fixed-size windows), regardless of
-            whether any SNPs were called nearby. Data is written in
-            chunks to avoid loading the entire array into memory.
-            Supports optional gzip compression when the output path ends
-            with `.gz`.
-        """,
-        parameters=dict(
-            output_path="""
-                Path to write the bedGraph output file. Use a `.gz`
-                extension to enable gzip compression.
-            """,
-            sample="Sample identifier.",
-            field="""
-                Which coverage field to export. "NormCov" is coverage
-                normalised against a set of reference windows (comparable
-                between samples); "RawCov" is unnormalised read counts
-                per window.
-            """,
-        ),
-        returns="""
-        Path to the bedGraph output file.
-        """,
-    )
-    def cnv_hmm_coverage_to_bedgraph(
-        self,
-        output_path: str,
-        region: base_params.regions,
-        sample: str,
-        field: str = "NormCov",
-        max_coverage_variance: cnv_params.max_coverage_variance = None,
-        inline_array: base_params.inline_array = base_params.inline_array_default,
-        chunks: base_params.chunks = base_params.native_chunks,
-        overwrite: plink_params.overwrite = False,
-    ) -> str:
-        if field not in _VALID_CNV_COVERAGE_FIELDS:
-            raise ValueError(
-                f"Unknown coverage field: {field!r}. "
-                f"Valid fields are: {sorted(_VALID_CNV_COVERAGE_FIELDS)}"
-            )
-
-        if os.path.exists(output_path) and not overwrite:
-            return output_path
-
-        # Look up which sample set this sample belongs to, so we only
-        # need to open the CNV HMM data for that one sample set.
-        sample_set = self._lookup_sample_set(sample)
-
-        ds = self.cnv_hmm(
-            region=region,
-            sample_sets=sample_set,
-            sample_query=f"sample_id == {sample!r}",
-            max_coverage_variance=max_coverage_variance,
-            inline_array=inline_array,
-            chunks=chunks,
-        )
-
-        if ds.sizes["samples"] == 0:
-            raise ValueError(
-                f"No CNV HMM data available for sample {sample!r}, this may be "
-                "because it was excluded by max_coverage_variance."
-            )
-
-        contigs = ds.attrs.get("contigs", self.contigs)
-        opener = _bedgraph_opener(output_path)
-
-        with opener(output_path, "wt") as f:
-            f.write(
-                f'track type=bedGraph name="{sample} {field}" '
-                f'description="CNV HMM {field} for {sample}"\n'
-            )
-
-            pos_data = ds["variant_position"].data
-            end_data = ds["variant_end"].data
-            contig_data = ds["variant_contig"].data
-            cov_data = ds[f"call_{field}"].data
-
-            chunk_sizes = pos_data.chunks[0]
-            offsets = np.cumsum((0,) + chunk_sizes)
-
-            with self._spinner(
-                f"Write bedGraph ({ds.sizes['variants']} coverage windows)"
-            ):
-                for ci in range(len(chunk_sizes)):
-                    start = offsets[ci]
-                    stop = offsets[ci + 1]
-                    pos_chunk = pos_data[start:stop].compute()
-                    end_chunk = end_data[start:stop].compute()
-                    contig_chunk = contig_data[start:stop].compute()
-                    # Select the single requested sample's coverage
-                    # column from the already-materialised chunk, rather
-                    # than indexing the dask/zarr array before compute,
-                    # which can trigger a less efficient (and, for
-                    # arrays with unwritten/fill-value chunks, buggy)
-                    # orthogonal-selection code path.
-                    cov_chunk = cov_data[start:stop].compute()[:, 0]
-
-                    lines: List[str] = []
-                    for j in range(pos_chunk.shape[0]):
-                        v = cov_chunk[j]
-                        if v < 0:
-                            # Masked/missing value, skip rather than
-                            # write a misleading zero.
-                            continue
-                        chrom = contigs[contig_chunk[j]]
-                        # bedGraph coordinates are 0-based, half-open;
-                        # variant_position is 1-based inclusive.
-                        bed_start = int(pos_chunk[j]) - 1
-                        bed_end = int(end_chunk[j])
-                        lines.append(f"{chrom}\t{bed_start}\t{bed_end}\t{v}\n")
-                    f.write("".join(lines))
-
-        return output_path
-
-    @doc(
-        summary="""
-            Export per-sample SNP read depth to bedGraph format.
-        """,
-        extended_summary="""
-            This function writes read depth at called SNP sites for a
-            single sample, derived from the allele depth (`AD`) field of
-            SNP calls, to a bedGraph file. Unlike
-            `cnv_hmm_coverage_to_bedgraph()`, this only has a value at
-            positions where a SNP was called, not genome-wide, but gives
-            higher-resolution, per-base depth in those locations rather
-            than a windowed summary. This is not a substitute for a BAM
-            file of aligned reads. It is intended as a fallback coverage
-            track for IGV, for use when the aligned reads (BAM) for a
-            sample are not available, e.g. because the file is hosted
-            externally and unreachable. Data is written in chunks to
-            avoid loading the entire array into memory. Supports
-            optional gzip compression when the output path ends with
-            `.gz`.
-        """,
-        parameters=dict(
-            output_path="""
-                Path to write the bedGraph output file. Use a `.gz`
-                extension to enable gzip compression.
-            """,
-            sample="Sample identifier.",
-        ),
-        returns="""
-        Path to the bedGraph output file.
-        """,
-    )
-    def snp_calls_coverage_to_bedgraph(
-        self,
-        output_path: str,
-        region: base_params.regions,
-        sample: str,
-        site_mask: Optional[base_params.site_mask] = None,
-        inline_array: base_params.inline_array = base_params.inline_array_default,
-        chunks: base_params.chunks = base_params.native_chunks,
-        overwrite: plink_params.overwrite = False,
-    ) -> str:
-        if os.path.exists(output_path) and not overwrite:
-            return output_path
-
-        # Look up which sample set this sample belongs to, so we only
-        # need to open the SNP calls data for that one sample set.
-        sample_set = self._lookup_sample_set(sample)
-
-        ds = self.snp_calls(
-            region=region,
-            sample_sets=sample_set,
-            sample_query=f"sample_id == {sample!r}",
-            site_mask=site_mask,
-            inline_array=inline_array,
-            chunks=chunks,
-        )
-
-        if ds.sizes["samples"] == 0:
-            raise ValueError(f"No SNP calls data available for sample {sample!r}.")
-
-        contigs = ds.attrs.get("contigs", self.contigs)
-        opener = _bedgraph_opener(output_path)
-
-        with opener(output_path, "wt") as f:
-            f.write(
-                f'track type=bedGraph name="{sample} SNP depth" '
-                f'description="SNP read depth (sum of AD) for {sample}"\n'
-            )
-
-            pos_data = ds["variant_position"].data
-            contig_data = ds["variant_contig"].data
-            ad_data = ds["call_AD"].data
-
-            chunk_sizes = pos_data.chunks[0]
-            offsets = np.cumsum((0,) + chunk_sizes)
-
-            with self._spinner(f"Write bedGraph ({ds.sizes['variants']} SNP sites)"):
-                for ci in range(len(chunk_sizes)):
-                    start = offsets[ci]
-                    stop = offsets[ci + 1]
-                    pos_chunk = pos_data[start:stop].compute()
-                    contig_chunk = contig_data[start:stop].compute()
-                    # Select the single requested sample's allele depth
-                    # values from the already-materialised chunk, rather
-                    # than indexing the dask/zarr array before compute
-                    # (see the equivalent comment in
-                    # cnv_hmm_coverage_to_bedgraph).
-                    ad_chunk = ad_data[start:stop].compute()[:, 0, :]
-
-                    lines: List[str] = []
-                    for j in range(pos_chunk.shape[0]):
-                        ad_row = ad_chunk[j]
-                        if np.all(ad_row < 0):
-                            # No call for this sample at this site, skip
-                            # rather than write a misleading zero.
-                            continue
-                        depth = int(np.clip(ad_row, 0, None).sum())
-                        chrom = contigs[contig_chunk[j]]
-                        # bedGraph coordinates are 0-based, half-open;
-                        # variant_position is 1-based, and each SNP is a
-                        # single base position.
-                        bed_start = int(pos_chunk[j]) - 1
-                        bed_end = int(pos_chunk[j])
-                        lines.append(f"{chrom}\t{bed_start}\t{bed_end}\t{depth}\n")
-                    f.write("".join(lines))
-
-        return output_path
diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index beb72275b..a62f3958c 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -250,26 +250,20 @@ def snp_calls_to_vcf(
                         optional_arrays,
                     )
 
-                    n_samples = variant_chunk_data.gt_chunk.shape[1]
-
                     # OPTIMIZATION: Vectorize GT field formatting across entire chunk.
                     # Instead of formatting each sample's GT field in a nested Python loop
                     # (which results in billions of string operations for large datasets),
                     # use NumPy's vectorized string operations on the entire chunk at once.
                     # This provides ~3x speedup while maintaining exact output compatibility.
                     # See issue #1280 for performance analysis.
-                    gt_chunk_2d = variant_chunk_data.gt_chunk.reshape(
-                        variant_chunk_data.gt_chunk.shape[0],
-                        variant_chunk_data.gt_chunk.shape[1],
-                        2,
-                    )
-                    a0 = gt_chunk_2d[:, :, 0]  # (n_variants, n_samples)
-                    a1 = gt_chunk_2d[:, :, 1]  # (n_variants, n_samples)
-                    missing = (a0 < 0) | (a1 < 0)  # array of loci not present
+                    gt_chunk_2d = variant_chunk_data.gt_chunk[:, 0, :]
+                    a0 = gt_chunk_2d[:, 0]  # n_variants
+                    a1 = gt_chunk_2d[:, 1]  # (n_variants
+                    missing = (a0 < 0) | (a1 < 0)
 
                     # Build formatted GT strings using NumPy vectorization
                     gt_formatted = np.empty(
-                        (variant_chunk_data.gt_chunk.shape[0], n_samples), dtype=object
+                        variant_chunk_data.gt_chunk.shape[0], dtype=object
                     )
                     gt_formatted[missing] = "./."
                     present_idx = ~missing
@@ -304,58 +298,45 @@ def snp_calls_to_vcf(
                             f"{chrom}\t{pos}\t.\t{ref}\t{alt}\t.\t.\t.\t{format_str}\t"
                         )
 
-                        # N.B., a plain Python list here, not a NumPy
-                        # array: this loop builds a handful of short
-                        # strings per variant via ordinary Python string
-                        # concatenation, not a numeric/vectorized
-                        # operation, so a `np.empty(..., dtype=object)`
-                        # array bought nothing but the overhead of a
-                        # NumPy allocation on every single variant row
-                        # (up to ~150 million times for a whole-genome
-                        # export).
-                        sample_fields = []
-
-                        # Use pre-formatted GT strings and add other fields
-                        for k in range(n_samples):
-                            parts = [gt_formatted[j, k]]
-                            if parts != ["0/0"]:  # homozygous genotype
-                                # GQ.
-                                if include_gq:
-                                    if variant_chunk_data.gq_chunk is not None:
-                                        v = variant_chunk_data.gq_chunk[j, k]
-                                        parts.append("." if v < 0 else str(v))
-                                    else:
-                                        parts.append(".")
-                                # AD.
-                                if include_ad:
-                                    if variant_chunk_data.ad_chunk is not None:
-                                        ad_vals = variant_chunk_data.ad_chunk[j, k]
-                                        parts.append(
-                                            ",".join(
-                                                "." if x < 0 else str(x)
-                                                for x in ad_vals
-                                            )
-                                        )
-                                    else:
-                                        parts.append(".")
-                                # MQ. Rounded to the nearest integer: the
-                                # underlying data is a float, but the VCF
-                                # spec fixes the reserved FORMAT/MQ key as
-                                # Integer (see _FORMAT_HEADERS).
-                                if include_mq:
-                                    if variant_chunk_data.mq_chunk is not None:
-                                        v = variant_chunk_data.mq_chunk[j, k]
-                                        if not math.isnan(v):
-                                            parts.append(
-                                                "." if v < 0 else str(round(v))
-                                            )
-                                    else:
-                                        parts.append(".")
-                                sample_fields.append(":".join(parts))
-
-                                # Build and buffer the line
-                                line = fixed_cols + "\t".join(sample_fields) + "\n"
-                                lines_to_write.append(line)
+                        genotype = gt_formatted[j]
+                        if genotype == "0/0":
+                            continue
+
+                        parts = [genotype]
+                        # GQ.
+                        if include_gq:
+                            if variant_chunk_data.gq_chunk is not None:
+                                value = variant_chunk_data.gq_chunk[j, 0]
+                                parts.append("." if value < 0 else str(value))
+                            else:
+                                parts.append(".")
+                        # AD.
+                        if include_ad:
+                            if variant_chunk_data.ad_chunk is not None:
+                                ad_values = variant_chunk_data.ad_chunk[j, 0]
+                                parts.append(
+                                    ",".join(
+                                        "." if value < 0 else str(value)
+                                        for value in ad_values
+                                    )
+                                )
+                            else:
+                                parts.append(".")
+                        # MQ. Rounded to the nearest integer: the
+                        # underlying data is a float, but the VCF spec
+                        # fixes the reserved FORMAT/MQ key as Integer.
+                        if include_mq:
+                            if variant_chunk_data.mq_chunk is not None:
+                                value = variant_chunk_data.mq_chunk[j, 0]
+                                if not math.isnan(value):
+                                    parts.append(
+                                        "." if value < 0 else str(round(value))
+                                    )
+                            else:
+                                parts.append(".")
+
+                        line = fixed_cols + ":".join(parts) + "\n"
+                        lines_to_write.append(line)
 
                     # Write buffered lines in one go per chunk
                     f.write("".join(lines_to_write))

From c22b1b54c7ddf01f6cbe4c4cff88ccae957f203e Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Thu, 1 Oct 2026 14:07:13 +0100
Subject: [PATCH 23/38] removed OrderedDict

---
 malariagen_data/anoph/to_vcf.py     | 7 +++----
 malariagen_data/anoph/to_vcf_cnv.py | 5 +++++
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index a62f3958c..22d90e94e 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -9,7 +9,6 @@
 import numpy as np
 from numpydoc_decorator import doc  # type: ignore
 from dataclasses import dataclass
-from collections import OrderedDict
 import math
 
 from .snp_data import AnophelesSnpData
@@ -351,7 +350,7 @@ def _get_chunks(
         pos_data: Array,
         contig_data: Array,
         allele_data: Array,
-        optional_arrays: OrderedDict,
+        optional_arrays: dict,
     ) -> tuple:
         start = offsets[ci]
         stop = offsets[ci + 1]
@@ -401,7 +400,7 @@ def _get_chunks(
 
     def _get_optional_data(
         self, include_gq: bool, include_ad: bool, include_mq: bool, ds: Dataset
-    ) -> OrderedDict:
+    ) -> dict:
         # Optional field arrays — may not exist in all datasets.
         gq_data = None
         ad_data = None
@@ -423,7 +422,7 @@ def _get_optional_data(
                 pass
         # Which optional fields were requested, so we know what to
         # fetch (and where to put the results) for each chunk below.
-        optional_arrays = OrderedDict()  # check needed
+        optional_arrays = {}
         if gq_data is not None:
             optional_arrays["GQ"] = gq_data
         if ad_data is not None:
diff --git a/malariagen_data/anoph/to_vcf_cnv.py b/malariagen_data/anoph/to_vcf_cnv.py
index b42d63832..618c86c5f 100644
--- a/malariagen_data/anoph/to_vcf_cnv.py
+++ b/malariagen_data/anoph/to_vcf_cnv.py
@@ -12,6 +12,11 @@
 from . import plink_params
 from . import vcf_params
 
+# don't think we want this, IGV accepts seg format for CNVs
+# VCF not well defined for CNVs
+# use something like this:
+# https://cnvkit.readthedocs.io/en/v0.7.7/fileformats.html
+
 
 def _decode(value) -> str:
     return value.decode() if hasattr(value, "decode") else str(value)

From f2e074fe2feb879adf7543ced2c059c6d0c318ca Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Thu, 1 Oct 2026 15:53:37 +0100
Subject: [PATCH 24/38] trying pysam so bgzf compression can be used so index
 needed for IGV can be made alognside VCF

---
 malariagen_data/anoph/to_vcf.py     | 149 +++++++++++-----------------
 malariagen_data/anoph/to_vcf_cnv.py |   4 +
 malariagen_data/anopheles.py        |   2 -
 poetry.lock                         |  57 ++++++++++-
 pyproject.toml                      |   1 +
 tests/anoph/test_vcf_exporter.py    |  50 +++++-----
 6 files changed, 144 insertions(+), 119 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 22d90e94e..f24a0fc66 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -1,4 +1,3 @@
-import gzip
 import os
 import re
 from datetime import date
@@ -10,6 +9,7 @@
 from numpydoc_decorator import doc  # type: ignore
 from dataclasses import dataclass
 import math
+import pysam
 
 from .snp_data import AnophelesSnpData
 from . import base_params
@@ -107,8 +107,8 @@ def __init__(
         extended_summary="""
             This function writes SNP calls to a VCF file. Data is written
             in chunks to avoid loading the entire genotype matrix into
-            memory. Supports optional gzip compression when the output
-            path ends with `.gz`.
+            memory. Output is BGZF-compressed and tabix-indexed; the
+            `output_path` must end with `.vcf.gz`.
 
             `sample_sets` and `sample_query` are both required: a VCF is
             only meaningful with respect to an explicit sample basis for
@@ -143,6 +143,11 @@ def snp_calls_to_vcf(
         _validate_single_sample_selection(
             sample_sets=sample_sets, sample_query=sample_query
         )
+        if not output_path.endswith(".vcf.gz"):
+            raise ValueError(
+                "output_path must end with .vcf.gz: "
+                "BGZF compression and tabix indexing require this suffix."
+            )
 
         # Validate fields parameter.
         fields = tuple(fields)
@@ -155,16 +160,12 @@ def snp_calls_to_vcf(
         if "GT" not in fields:
             raise ValueError("GT must be included in fields.")
 
-        # Canonicalise the field order to _FIELD_ORDER. The per-sample
-        # values below are always written in this fixed order; if the
-        # FORMAT column (built from `fields` further down) used the
-        # caller's order instead, a `fields` argument with a different
-        # (or undefined, e.g. a set) order would produce a VCF whose
-        # FORMAT column lies about which value is which — which is
-        # exactly what happened before this fix.
+        # Canonicalise the field order to _FIELD_ORDER
         fields = tuple(f for f in _FIELD_ORDER if f in fields)
 
         if os.path.exists(output_path) and not overwrite:
+            if not os.path.exists(output_path + ".tbi"):
+                pysam.tabix_index(output_path, preset="vcf")
             return output_path
 
         ds = self.snp_calls(
@@ -190,39 +191,30 @@ def snp_calls_to_vcf(
                 f"{sample_sets!r}, expected exactly 1."
             )
 
-        sample_ids = ds["sample_id"].values
+        sample_id = ds["sample_id"].values[0]
+        sample_id = (
+            sample_id.decode() if hasattr(sample_id, "decode") else str(sample_id)
+        )
         contigs = ds.attrs.get("contigs", self.contigs)
-        compress = output_path.endswith(".gz")
-        opener = gzip.open if compress else open
 
         # Determine which extra fields to include.
         include_gq = "GQ" in fields
         include_ad = "AD" in fields
         include_mq = "MQ" in fields
-        format_str = ":".join(fields)
-
-        with opener(output_path, "wt") as f:
-            # Write VCF header.
-            f.write("##fileformat=VCFv4.3\n")
-            f.write(f"##fileDate={date.today().strftime('%Y%m%d')}\n")
-            f.write("##source=malariagen_data\n")
-            for contig in contigs:
-                f.write(f"##contig=<ID={contig}>\n")
-            for field in fields:
-                f.write(_FORMAT_HEADERS[field] + "\n")
-            header_cols = [
-                "#CHROM",
-                "POS",
-                "ID",
-                "REF",
-                "ALT",
-                "QUAL",
-                "FILTER",
-                "INFO",
-                "FORMAT",
-            ]
-            f.write("\t".join(header_cols + list(sample_ids)) + "\n")
-
+        header = pysam.VariantHeader()
+        for header_record in list(header.records):
+            if header_record.key in {"fileformat", "FILTER"}:
+                header_record.remove()
+        header.add_meta("fileformat", value="VCFv4.3")
+        header.add_meta("fileDate", value=date.today().strftime("%Y%m%d"))
+        header.add_meta("source", value="malariagen_data")
+        for contig in contigs:
+            header.contigs.add(str(contig))
+        for field in fields:
+            header.add_line(_FORMAT_HEADERS[field])
+        header.add_sample(sample_id)
+
+        with pysam.VariantFile(output_path, mode="w", header=header) as f:
             # Extract dask arrays.
             gt_data = ds["call_genotype"].data
             pos_data = ds["variant_position"].data
@@ -249,36 +241,9 @@ def snp_calls_to_vcf(
                         optional_arrays,
                     )
 
-                    # OPTIMIZATION: Vectorize GT field formatting across entire chunk.
-                    # Instead of formatting each sample's GT field in a nested Python loop
-                    # (which results in billions of string operations for large datasets),
-                    # use NumPy's vectorized string operations on the entire chunk at once.
-                    # This provides ~3x speedup while maintaining exact output compatibility.
-                    # See issue #1280 for performance analysis.
-                    gt_chunk_2d = variant_chunk_data.gt_chunk[:, 0, :]
-                    a0 = gt_chunk_2d[:, 0]  # n_variants
-                    a1 = gt_chunk_2d[:, 1]  # (n_variants
-                    missing = (a0 < 0) | (a1 < 0)
-
-                    # Build formatted GT strings using NumPy vectorization
-                    gt_formatted = np.empty(
-                        variant_chunk_data.gt_chunk.shape[0], dtype=object
-                    )
-                    gt_formatted[missing] = "./."
-                    present_idx = ~missing
-                    if np.any(present_idx):
-                        a0_str = a0[present_idx].astype(str)
-                        a1_str = a1[present_idx].astype(str)
-                        gt_formatted[present_idx] = np.char.add(
-                            np.char.add(a0_str, "/"), a1_str
-                        )
-
-                    # Pre-allocate line buffer for better I/O
-                    lines_to_write = []
-
                     for j in range(variant_chunk_data.gt_chunk.shape[0]):
                         chrom = contigs[variant_chunk_data.contig_chunk[j]]
-                        pos = str(variant_chunk_data.pos_chunk[j])
+                        pos = int(variant_chunk_data.pos_chunk[j])
                         alleles = variant_chunk_data.allele_chunk[j]
                         ref = (
                             alleles[0].decode()
@@ -290,56 +255,56 @@ def snp_calls_to_vcf(
                             s = a.decode() if hasattr(a, "decode") else str(a)
                             if s:
                                 alt_alleles.append(s)
-                        alt = ",".join(alt_alleles) if alt_alleles else "."
 
-                        # Build fixed VCF columns once per variant
-                        fixed_cols = (
-                            f"{chrom}\t{pos}\t.\t{ref}\t{alt}\t.\t.\t.\t{format_str}\t"
+                        genotype_data = variant_chunk_data.gt_chunk[j, 0]
+                        genotype = (
+                            (None,) * len(genotype_data)
+                            if np.any(genotype_data < 0)
+                            else tuple(int(allele) for allele in genotype_data)
                         )
-
-                        genotype = gt_formatted[j]
-                        if genotype == "0/0":
+                        if genotype == (0, 0):
                             continue
 
-                        parts = [genotype]
+                        record = header.new_record(
+                            contig=str(chrom),
+                            start=pos - 1,
+                            alleles=(ref, *alt_alleles),
+                        )
+                        sample = record.samples[sample_id]
+                        sample["GT"] = genotype
                         # GQ.
                         if include_gq:
                             if variant_chunk_data.gq_chunk is not None:
                                 value = variant_chunk_data.gq_chunk[j, 0]
-                                parts.append("." if value < 0 else str(value))
+                                sample["GQ"] = None if value < 0 else int(value)
                             else:
-                                parts.append(".")
+                                sample["GQ"] = None
                         # AD.
                         if include_ad:
                             if variant_chunk_data.ad_chunk is not None:
                                 ad_values = variant_chunk_data.ad_chunk[j, 0]
-                                parts.append(
-                                    ",".join(
-                                        "." if value < 0 else str(value)
-                                        for value in ad_values
-                                    )
+                                sample["AD"] = tuple(
+                                    None if value < 0 else int(value)
+                                    for value in ad_values
                                 )
                             else:
-                                parts.append(".")
+                                sample["AD"] = None
                         # MQ. Rounded to the nearest integer: the
                         # underlying data is a float, but the VCF spec
                         # fixes the reserved FORMAT/MQ key as Integer.
                         if include_mq:
                             if variant_chunk_data.mq_chunk is not None:
                                 value = variant_chunk_data.mq_chunk[j, 0]
-                                if not math.isnan(value):
-                                    parts.append(
-                                        "." if value < 0 else str(round(value))
-                                    )
+                                sample["MQ"] = (
+                                    None
+                                    if math.isnan(value) or value < 0
+                                    else round(value)
+                                )
                             else:
-                                parts.append(".")
-
-                        line = fixed_cols + ":".join(parts) + "\n"
-                        lines_to_write.append(line)
-
-                    # Write buffered lines in one go per chunk
-                    f.write("".join(lines_to_write))
+                                sample["MQ"] = None
+                        f.write(record)
 
+        pysam.tabix_index(output_path, preset="vcf", force=overwrite)
         return output_path
 
     def _get_chunks(
diff --git a/malariagen_data/anoph/to_vcf_cnv.py b/malariagen_data/anoph/to_vcf_cnv.py
index 618c86c5f..927c95134 100644
--- a/malariagen_data/anoph/to_vcf_cnv.py
+++ b/malariagen_data/anoph/to_vcf_cnv.py
@@ -16,6 +16,10 @@
 # VCF not well defined for CNVs
 # use something like this:
 # https://cnvkit.readthedocs.io/en/v0.7.7/fileformats.html
+# or maybe not:
+# https://igv.org/doc/igvjs/#tracks/CNVPytor/
+# though it says only works for full genome, not regions,
+# so maybe not useful for us
 
 
 def _decode(value) -> str:
diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py
index 6d0cf6940..b775dad1e 100644
--- a/malariagen_data/anopheles.py
+++ b/malariagen_data/anopheles.py
@@ -38,7 +38,6 @@
 from .anoph.ld import AnophelesLdAnalysis
 from .anoph.to_vcf import SnpVcfExporter
 from .anoph.to_vcf_cnv import CnvVcfExporter
-from .anoph.to_coverage import CoverageExporter
 from .anoph.g123 import AnophelesG123Analysis
 from .anoph.fst import AnophelesFstAnalysis
 from .anoph.h12 import AnophelesH12Analysis
@@ -96,7 +95,6 @@ class AnophelesDataResource(
     AnophelesLdAnalysis,
     SnpVcfExporter,
     CnvVcfExporter,
-    CoverageExporter,
     AnophelesIgv,
     AnophelesKaryotypeAnalysis,
     AnophelesAimData,
diff --git a/poetry.lock b/poetry.lock
index 9405fd2b8..2a96df4e9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.4.3 and should not be changed by hand.
 
 [[package]]
 name = "accessible-pygments"
@@ -4548,6 +4548,59 @@ files = [
 [package.extras]
 windows-terminal = ["colorama (>=0.4.6)"]
 
+[[package]]
+name = "pysam"
+version = "0.24.1"
+description = "Package for reading, manipulating, and writing genomic data"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
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+    {file = "pysam-0.24.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:f842fc7638b8acccd5e470820cff3f490c5845e616fa668667531da22b686a7b"},
+    {file = "pysam-0.24.1-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:f3abec4f08929c5090f747975787febe7db437bad34349f29c8e0328d6f9ad06"},
+    {file = "pysam-0.24.1-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:9e601c4626e7310db74823a4152483bf903392ff1d30eec619594808280da699"},
+    {file = "pysam-0.24.1-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:84c80a7d3475e675d142a850ff3ea0d4a929e698130f01323f1a550a0e13cc27"},
+    {file = "pysam-0.24.1-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:10cc2b840ef651be8c7087d7c0c9c51e220162eae1e5ad68b6ccf427594357fc"},
+    {file = "pysam-0.24.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:0f1bdd44bcd85d8562925436bec24dcf7325e4001575a9c24d58806b93de2293"},
+    {file = "pysam-0.24.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:0e48e4b3d341734078e97fe05a2358d60837ca88741625ec17d45ba7c629dc64"},
+    {file = "pysam-0.24.1-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:c21dd9b801175d14c4d7b78898de921f8771edf141db5957226c9bf1ed4bf293"},
+    {file = "pysam-0.24.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:050d4c72211a961d26fad70b655694d4d500422e4b7d0ed3c7f244c49df8d16e"},
+    {file = "pysam-0.24.1-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:8696e88156edee884416fd50c15fcc61da67089232198c1ae731731f6da765d6"},
+    {file = "pysam-0.24.1-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:f34eba531bdfd71817110a56c00443f9947d3a01e10358f341d10f614ea3bf1e"},
+    {file = "pysam-0.24.1-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:1d114ddd64b562d2fe253a31703613b762c71b4a3d856ac960a39e40269c51fa"},
+    {file = "pysam-0.24.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:ceb448961fd35b5b90795d7c7c80b1b35592be7ae0127e28187e3f41c27e035b"},
+    {file = "pysam-0.24.1-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:39914c2e395be44126e120be0933aaea3ea1d664f3c421a91afc4be086b49a79"},
+    {file = "pysam-0.24.1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:06eabdc8f7c3894b73d2c4365ea6197d6ba5308e203dd2887b5df635fe6e249b"},
+    {file = "pysam-0.24.1-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:2c03ca38923941e460a5edc62d9208393ee9083ecd3f57a3e5a96c1337112dc7"},
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+    {file = "pysam-0.24.1-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:68b742b2db84cf3982c21be69f886baf3d3cb49fbb070cb4a4c09b4d2fc907c0"},
+    {file = "pysam-0.24.1-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:fdb008b9dfe673ec029189f6394b2d60ce1380ee387c106e799ada237809b2ee"},
+    {file = "pysam-0.24.1-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:5cb4a0ffe496111d0acead00a60f2e7e977a4d716089367dc6cc8c0cf511fcbb"},
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+    {file = "pysam-0.24.1-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:25ffcc2aca0a49358c02e666ddd789afe701c5cf320dcb894ac22ede7347049f"},
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+    {file = "pysam-0.24.1-cp315-cp315-macosx_11_0_arm64.whl", hash = "sha256:886f5c1a2a45b174345c217c821cbd4231311d43ecf5e8157cc7a4bee5db182a"},
+    {file = "pysam-0.24.1-cp315-cp315-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:57d7921761ce2b902711e55857f861733b909155fb6299b5559da4a20a353eeb"},
+    {file = "pysam-0.24.1-cp315-cp315-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:7a22778002a2a401374733dc5698bc3552ff0a6c43d27aeaf37976048bd3d867"},
+    {file = "pysam-0.24.1-cp315-cp315-musllinux_1_2_aarch64.whl", hash = "sha256:15dca5345f67b622dfb303ed5328e13799ffc13df12407a6d4542caab5a6ffb1"},
+    {file = "pysam-0.24.1-cp315-cp315-musllinux_1_2_x86_64.whl", hash = "sha256:b64fb7c97f8ad78fd5b8cd16f0d8b931d89f0c30b48a061625280ce8b2145782"},
+    {file = "pysam-0.24.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:0b4b1fec32675cfb992cd6c23e0fbf86481f695959e3973e00c9c1432c78d801"},
+    {file = "pysam-0.24.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:cb70dd2c190dab4de044d8d2168c4d74fbc8acad9b9993bdf235c85b1c9b9ce6"},
+    {file = "pysam-0.24.1-cp39-cp39-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:a222fb89c91c8acdbe4e77f233c9ee1b9ab2e832afae49797ddefedfbb3191a3"},
+    {file = "pysam-0.24.1-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:d5fd6fbd19fa0f833f0e7f02ce16e99679b58fbe311b818fb7ddac2a6a435eef"},
+    {file = "pysam-0.24.1-cp39-cp39-musllinux_1_2_aarch64.whl", hash = "sha256:1f672fc17990d395d658e191b57c681bd101ae7b4825446a6938fc9ddb797630"},
+    {file = "pysam-0.24.1-cp39-cp39-musllinux_1_2_x86_64.whl", hash = "sha256:b8281b79e8b989c224ba0a7de41d06a47c38a0767f1efdfa2cbff1cee86deb6a"},
+    {file = "pysam-0.24.1.tar.gz", hash = "sha256:90f612afccdb454d2447ecb5229266c6e7f991093deed4ed0a791db01f7fc994"},
+]
+
 [[package]]
 name = "pytest"
 version = "9.0.1"
@@ -6417,4 +6470,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.10,<3.13"
-content-hash = "064fbc09218cd1b8480ad0cc9bf921218e72302757230c244948b85adadd54d9"
+content-hash = "e850038fc2366ed56556f41e363264d87030fc3489e6372a6ab7b26acd1a804e"
diff --git a/pyproject.toml b/pyproject.toml
index f061b25fa..03761d9aa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,6 +36,7 @@ BioPython = "*"
 scikit-allel = ">=1.3.13"
 xarray = "*"
 plotly = "*"
+pysam = ">=0.22.0"
 # https://github.com/malariagen/malariagen-data-python/issues/845
 # https://github.com/malariagen/malariagen-data-python/issues/734
 # https://github.com/malariagen/malariagen-data-python/issues/743
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index 2edc02c27..a87669fe3 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -6,6 +6,7 @@
 
 import dask.array as da
 import numpy as np
+import pysam
 import pytest
 import xarray as xr
 from pytest_cases import parametrize_with_cases
@@ -105,12 +106,12 @@ def test_vcf_exporter(fixture, api: SnpVcfExporter, tmp_path):
     # sample.
     assert list(sample_ids) == [sample_id]
 
-    output_path = str(tmp_path / "test.vcf")
+    output_path = str(tmp_path / "test.vcf.gz")
     api.snp_calls_to_vcf(output_path=output_path, **data_params)
 
     assert os.path.exists(output_path)
 
-    with open(output_path) as f:
+    with gzip.open(output_path, "rt") as f:
         lines = f.readlines()
 
     header_lines = [line for line in lines if line.startswith("##")]
@@ -172,14 +173,14 @@ def test_vcf_exporter_non_ref_only(fixture, api: SnpVcfExporter, tmp_path):
     expect_keep = ~is_missing & ~is_hom_ref
     expected_positions = sorted(ds["variant_position"].values[expect_keep].tolist())
 
-    output_path = str(tmp_path / "test_non_ref_only.vcf")
+    output_path = str(tmp_path / "test_non_ref_only.vcf.gz")
     api.snp_calls_to_vcf(
         output_path=output_path,
         non_ref_only=True,
         **data_params,
     )
 
-    with open(output_path) as f:
+    with gzip.open(output_path, "rt") as f:
         lines = f.readlines()
     data_lines = [line for line in lines if not line.startswith("#")]
 
@@ -209,8 +210,8 @@ def test_vcf_exporter_non_ref_only_defaults_to_false(
     sample_sets = [all_sample_sets[0]]
     _, sample_query = _pick_single_sample_query(api, sample_sets)
 
-    output_path_default = str(tmp_path / "default.vcf")
-    output_path_explicit = str(tmp_path / "explicit_false.vcf")
+    output_path_default = str(tmp_path / "default.vcf.gz")
+    output_path_explicit = str(tmp_path / "explicit_false.vcf.gz")
     api.snp_calls_to_vcf(
         output_path=output_path_default,
         region=region,
@@ -225,9 +226,9 @@ def test_vcf_exporter_non_ref_only_defaults_to_false(
         non_ref_only=False,
     )
 
-    with open(output_path_default) as f:
+    with gzip.open(output_path_default, "rt") as f:
         default_lines = f.readlines()
-    with open(output_path_explicit) as f:
+    with gzip.open(output_path_explicit, "rt") as f:
         explicit_lines = f.readlines()
     assert default_lines == explicit_lines
 
@@ -242,7 +243,7 @@ def test_vcf_exporter_non_ref_only_valid_per_bcftools(
     sample_sets = [all_sample_sets[0]]
     _, sample_query = _pick_single_sample_query(api, sample_sets)
 
-    output_path = str(tmp_path / "test_non_ref_only_bcftools.vcf")
+    output_path = str(tmp_path / "test_non_ref_only_bcftools.vcf.gz")
     api.snp_calls_to_vcf(
         output_path=output_path,
         region=region,
@@ -270,7 +271,7 @@ def test_vcf_exporter_requires_sample_sets_and_query(
     # explicit cohort/sample basis for the calls it contains is not
     # meaningful.
     region = api.contigs[0]
-    output_path = str(tmp_path / "test_missing_args.vcf")
+    output_path = str(tmp_path / "test_missing_args.vcf.gz")
 
     with pytest.raises(TypeError):
         api.snp_calls_to_vcf(output_path=output_path, region=region)  # type: ignore[call-arg]
@@ -286,7 +287,7 @@ def test_vcf_exporter_requires_sample_sets_and_query(
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_empty_sample_sets(fixture, api: SnpVcfExporter, tmp_path):
     region = api.contigs[0]
-    output_path = str(tmp_path / "test_empty_sample_sets.vcf")
+    output_path = str(tmp_path / "test_empty_sample_sets.vcf.gz")
 
     with pytest.raises(ValueError, match="sample_sets must be provided"):
         api.snp_calls_to_vcf(
@@ -302,7 +303,7 @@ def test_vcf_exporter_empty_sample_query(fixture, api: SnpVcfExporter, tmp_path)
     region = api.contigs[0]
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = [all_sample_sets[0]]
-    output_path = str(tmp_path / "test_empty_sample_query.vcf")
+    output_path = str(tmp_path / "test_empty_sample_query.vcf.gz")
 
     with pytest.raises(ValueError, match="sample_query must be provided"):
         api.snp_calls_to_vcf(
@@ -324,7 +325,7 @@ def test_vcf_exporter_multi_sample_query_rejected(
     region = api.contigs[0]
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = [all_sample_sets[0]]
-    output_path = str(tmp_path / "test_multi_sample_query.vcf")
+    output_path = str(tmp_path / "test_multi_sample_query.vcf.gz")
 
     for bad_query in [
         "country == 'Uganda'",
@@ -352,7 +353,7 @@ def test_vcf_exporter_sample_query_matches_zero_samples(
     region = api.contigs[0]
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = [all_sample_sets[0]]
-    output_path = str(tmp_path / "test_zero_sample_query.vcf")
+    output_path = str(tmp_path / "test_zero_sample_query.vcf.gz")
 
     with pytest.raises(ValueError):
         api.snp_calls_to_vcf(
@@ -369,7 +370,7 @@ def test_vcf_exporter_overwrite(fixture, api: SnpVcfExporter, tmp_path):
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = [all_sample_sets[0]]
     _, sample_query = _pick_single_sample_query(api, sample_sets)
-    output_path = str(tmp_path / "test.vcf")
+    output_path = str(tmp_path / "test.vcf.gz")
 
     api.snp_calls_to_vcf(
         output_path=output_path,
@@ -397,6 +398,9 @@ def test_vcf_exporter_overwrite(fixture, api: SnpVcfExporter, tmp_path):
         overwrite=True,
     )
     assert os.path.exists(output_path)
+    assert os.path.exists(output_path + ".tbi")
+    with pysam.VariantFile(output_path) as vcf:
+        list(vcf.fetch())
 
 
 @parametrize_with_cases("fixture,api", cases=".")
@@ -440,7 +444,7 @@ def test_vcf_exporter_fields(fixture, api: SnpVcfExporter, tmp_path):
     _, sample_query = _pick_single_sample_query(api, sample_sets)
 
     # Test with additional FORMAT fields.
-    output_path = str(tmp_path / "test_fields.vcf")
+    output_path = str(tmp_path / "test_fields.vcf.gz")
     api.snp_calls_to_vcf(
         output_path=output_path,
         region=region,
@@ -449,7 +453,7 @@ def test_vcf_exporter_fields(fixture, api: SnpVcfExporter, tmp_path):
         fields=("GT", "GQ"),
     )
 
-    with open(output_path) as f:
+    with gzip.open(output_path, "rt") as f:
         lines = f.readlines()
 
     # Check FORMAT header lines.
@@ -486,7 +490,7 @@ def test_vcf_exporter_fields_as_set(fixture, api: SnpVcfExporter, tmp_path):
     sample_sets = [all_sample_sets[0]]
     _, sample_query = _pick_single_sample_query(api, sample_sets)
 
-    output_path = str(tmp_path / "test_fields_set.vcf")
+    output_path = str(tmp_path / "test_fields_set.vcf.gz")
     api.snp_calls_to_vcf(
         output_path=output_path,
         region=region,
@@ -495,7 +499,7 @@ def test_vcf_exporter_fields_as_set(fixture, api: SnpVcfExporter, tmp_path):
         fields={"GT", "GQ", "AD", "MQ"},
     )
 
-    with open(output_path) as f:
+    with gzip.open(output_path, "rt") as f:
         lines = f.readlines()
 
     data_lines = [line for line in lines if not line.startswith("#")]
@@ -538,7 +542,7 @@ def test_vcf_exporter_output_is_valid_per_bcftools(
     sample_sets = [all_sample_sets[0]]
     _, sample_query = _pick_single_sample_query(api, sample_sets)
 
-    output_path = str(tmp_path / "test_bcftools_valid.vcf")
+    output_path = str(tmp_path / "test_bcftools_valid.vcf.gz")
     api.snp_calls_to_vcf(
         output_path=output_path,
         region=region,
@@ -567,7 +571,7 @@ def test_vcf_exporter_fields_gt_required(fixture, api: SnpVcfExporter, tmp_path)
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = [all_sample_sets[0]]
     _, sample_query = _pick_single_sample_query(api, sample_sets)
-    output_path = str(tmp_path / "test_no_gt.vcf")
+    output_path = str(tmp_path / "test_no_gt.vcf.gz")
 
     with pytest.raises(ValueError, match="GT must be included"):
         api.snp_calls_to_vcf(
@@ -678,7 +682,7 @@ def test_vcf_exporter_allele_index_remapping(
     )
     monkeypatch.setattr(api, "snp_calls", lambda **kwargs: ds)
 
-    output_path = str(tmp_path / "test_allele_remap.vcf")
+    output_path = str(tmp_path / "test_allele_remap.vcf.gz")
     api.snp_calls_to_vcf(
         output_path=output_path,
         region=contig,
@@ -686,7 +690,7 @@ def test_vcf_exporter_allele_index_remapping(
         sample_query=f"sample_id == '{sample}'",
     )
 
-    with open(output_path) as f:
+    with gzip.open(output_path, "rt") as f:
         lines = f.readlines()
     data_lines = [line for line in lines if not line.startswith("#")]
     assert len(data_lines) == n_variants

From e12691209b33f032e34cd291a2734acf0317462a Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Thu, 1 Oct 2026 17:04:38 +0100
Subject: [PATCH 25/38] wired through to IGV, checked with notebook

---
 malariagen_data/anoph/igv.py | 13 ++++++++-
 notebooks/igv.ipynb          | 42 +++++++++++++++++++++++++++--
 tests/anoph/test_igv.py      | 52 ++++++++++++++++++++++++++++++++++++
 3 files changed, 104 insertions(+), 3 deletions(-)

diff --git a/malariagen_data/anoph/igv.py b/malariagen_data/anoph/igv.py
index 59680640b..cccf7f877 100644
--- a/malariagen_data/anoph/igv.py
+++ b/malariagen_data/anoph/igv.py
@@ -82,6 +82,7 @@ def _igv_view_alignments_tracks(
         region: Region,
         sample: str,
         visibility_window: int = 20_000,
+        snp_vcf_url: Optional[str] = None,
     ):
         # Look up sample set for sample.
         try:
@@ -99,7 +100,9 @@ def _igv_view_alignments_tracks(
         # Locate record for sample.
         cat_rec = df_cat.set_index("sample_id").loc[sample]
         bam_url = cat_rec["alignments_bam"]
-        vcf_url = cat_rec["snp_genotypes_vcf"]
+        vcf_url = (
+            snp_vcf_url if snp_vcf_url is not None else cat_rec["snp_genotypes_vcf"]
+        )
 
         # Set up site filters tracks.
         contig = region.contig
@@ -183,6 +186,12 @@ def igv(
                 visible.
             """,
             init="If True, call igv_notebook.init().",
+            snp_vcf_url="""
+                Optional URL for a local, tabix-indexed VCF. For Jupyter Notebook
+                and Lab, the VCF and its `.tbi` index must be under the Jupyter
+                startup directory tree; pass a URL relative to that tree (e.g.
+                `/data/sample.vcf.gz`). If omitted, use the catalog VCF.
+            """,
         ),
     )
     def view_alignments(
@@ -191,6 +200,7 @@ def view_alignments(
         sample: str,
         visibility_window: int = 20_000,
         init: bool = True,
+        snp_vcf_url: Optional[str] = None,
     ):
         # Parse region.
         region_prepped: Region = _parse_single_region(self, region)
@@ -201,6 +211,7 @@ def view_alignments(
             region=region_prepped,
             sample=sample,
             visibility_window=visibility_window,
+            snp_vcf_url=snp_vcf_url,
         )
 
         # Create IGV browser.
diff --git a/notebooks/igv.ipynb b/notebooks/igv.ipynb
index 104f217f0..b7fc56328 100644
--- a/notebooks/igv.ipynb
+++ b/notebooks/igv.ipynb
@@ -200,13 +200,51 @@
     ")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "17",
+   "metadata": {},
+   "source": [
+    "## Local tabix-indexed VCF in IGV\n",
+    "This exports one sample to a BGZF VCF and `.tbi` under the notebook working directory, then loads it as the SNP track. Both files must be inside the Jupyter server startup directory tree. The `snp_vcf_url` below assumes the server was started from the workspace root; if it was started from `notebooks/`, use the alternate URL shown in the code cell."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "18",
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "from pathlib import Path\n",
+    "\n",
+    "\n",
+    "sample_set = \"1229-VO-GH-DADZIE-VMF00095\"\n",
+    "sample_id = str(\n",
+    "    af1.sample_metadata(sample_sets=sample_set).iloc[0][\"sample_id\"]\n",
+    ")\n",
+    "region = \"2RL:2,447,600-2,447,700\"\n",
+    "\n",
+    "local_vcf_path = Path(\"local_igv_vcfs\") / f\"{sample_id}.vcf.gz\"\n",
+    "local_vcf_path.parent.mkdir(parents=True, exist_ok=True)\n",
+    "\n",
+    "af1.snp_calls_to_vcf(\n",
+    "    output_path=str(local_vcf_path),\n",
+    "    region=region,\n",
+    "    sample_sets=[sample_set],\n",
+    "    sample_query=f\"sample_id == '{sample_id}'\",\n",
+    ")\n",
+    "\n",
+    "# The URL is relative to the Jupyter server startup directory.\n",
+    "# If started from notebooks/, use f\"/{local_vcf_path.as_posix()}\" instead.\n",
+    "snp_vcf_url = f\"/notebooks/{local_vcf_path.as_posix()}\"\n",
+    "\n",
+    "af1.view_alignments(\n",
+    "    sample=sample_id,\n",
+    "    region=region,\n",
+    "    snp_vcf_url=snp_vcf_url,\n",
+    ")"
+   ]
   }
  ],
  "metadata": {
diff --git a/tests/anoph/test_igv.py b/tests/anoph/test_igv.py
index 7d3680ffb..8aaa1eef1 100644
--- a/tests/anoph/test_igv.py
+++ b/tests/anoph/test_igv.py
@@ -1,10 +1,14 @@
+from types import SimpleNamespace
+
 import igv_notebook  # type: ignore
 import numpy as np
+import pandas as pd
 import pytest
 from pytest_cases import parametrize_with_cases
 
 from malariagen_data import af1 as _af1
 from malariagen_data import ag3 as _ag3
+import malariagen_data.anoph.igv as igv_module
 from malariagen_data.anoph.igv import AnophelesIgv
 
 
@@ -84,3 +88,51 @@ def test_view_alignments(fixture, api: AnophelesIgv):
     ret = api.view_alignments(region=region, sample=sample, init=False)
     # No return value to avoid cluttering notebook output.
     assert ret is None
+
+
+def test_view_alignments_with_local_snp_vcf(monkeypatch):
+    class FakeAnophelesIgv(AnophelesIgv):
+        @property
+        def site_mask_ids(self):
+            return []
+
+        def sample_metadata(self):
+            return pd.DataFrame({"sample_id": ["S1"], "sample_set": ["set1"]})
+
+        def wgs_data_catalog(self, sample_set):
+            return pd.DataFrame(
+                {
+                    "sample_id": ["S1"],
+                    "alignments_bam": ["https://example.org/S1.bam"],
+                    "snp_genotypes_vcf": ["https://example.org/S1.vcf.gz"],
+                }
+            )
+
+    api = object.__new__(FakeAnophelesIgv)
+    captured = {}
+    monkeypatch.setattr(
+        igv_module,
+        "_parse_single_region",
+        lambda self, region: SimpleNamespace(contig="2L"),
+    )
+    monkeypatch.setattr(
+        api,
+        "igv",
+        lambda **kwargs: captured.update(kwargs),
+    )
+    local_vcf_url = "/data/sample.vcf.gz"
+    api.view_alignments(
+        region="2L:1-10",
+        sample="S1",
+        init=False,
+        snp_vcf_url=local_vcf_url,
+    )
+
+    snp_track = next(track for track in captured["tracks"] if track["name"] == "SNPs")
+    assert snp_track["url"] == local_vcf_url
+    assert snp_track["indexURL"] == f"{local_vcf_url}.tbi"
+
+    captured.clear()
+    api.view_alignments(region="2L:1-10", sample="S1", init=False)
+    snp_track = next(track for track in captured["tracks"] if track["name"] == "SNPs")
+    assert snp_track["url"] == "https://example.org/S1.vcf.gz"

From 04f6c83b62e975e836e6926170002e7718192e15 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 5 Oct 2026 10:20:32 +0100
Subject: [PATCH 26/38] fixed type annotaitons and moved homozygous check

---
 malariagen_data/anoph/to_vcf.py | 31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index f24a0fc66..d62d03612 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -1,14 +1,14 @@
 import os
 import re
+import math
 from datetime import date
+from dataclasses import dataclass
 from typing import Optional
 import dask
 from dask.array.core import Array
 from xarray.core.dataset import Dataset
 import numpy as np
 from numpydoc_decorator import doc  # type: ignore
-from dataclasses import dataclass
-import math
 import pysam
 
 from .snp_data import AnophelesSnpData
@@ -19,13 +19,13 @@
 
 @dataclass
 class VariantChunkData:
-    gq_chunk: Array
-    ad_chunk: Array
-    mq_chunk: Array
-    gt_chunk: Array
-    pos_chunk: Array
-    contig_chunk: Array
-    allele_chunk: Array
+    gq_chunk: Optional[np.ndarray]
+    ad_chunk: Optional[np.ndarray]
+    mq_chunk: Optional[np.ndarray]
+    gt_chunk: np.ndarray
+    pos_chunk: np.ndarray
+    contig_chunk: np.ndarray
+    allele_chunk: np.ndarray
 
 
 # Supported FORMAT fields, the fixed order in which their values are
@@ -242,6 +242,9 @@ def snp_calls_to_vcf(
                     )
 
                     for j in range(variant_chunk_data.gt_chunk.shape[0]):
+                        genotype_data = variant_chunk_data.gt_chunk[j, 0]
+                        if np.array_equal(genotype_data, (0, 0)):
+                            continue
                         chrom = contigs[variant_chunk_data.contig_chunk[j]]
                         pos = int(variant_chunk_data.pos_chunk[j])
                         alleles = variant_chunk_data.allele_chunk[j]
@@ -262,8 +265,6 @@ def snp_calls_to_vcf(
                             if np.any(genotype_data < 0)
                             else tuple(int(allele) for allele in genotype_data)
                         )
-                        if genotype == (0, 0):
-                            continue
 
                         record = header.new_record(
                             contig=str(chrom),
@@ -310,13 +311,13 @@ def snp_calls_to_vcf(
     def _get_chunks(
         self,
         ci: int,
-        offsets: np.array,
+        offsets: np.ndarray,
         gt_data: Array,
         pos_data: Array,
         contig_data: Array,
         allele_data: Array,
-        optional_arrays: dict,
-    ) -> tuple:
+        optional_arrays: dict[str, Array],
+    ) -> VariantChunkData:
         start = offsets[ci]
         stop = offsets[ci + 1]
 
@@ -365,7 +366,7 @@ def _get_chunks(
 
     def _get_optional_data(
         self, include_gq: bool, include_ad: bool, include_mq: bool, ds: Dataset
-    ) -> dict:
+    ) -> dict[str, Array]:
         # Optional field arrays — may not exist in all datasets.
         gq_data = None
         ad_data = None

From b9db52d58a0c72aa245a6892965bd4a691e21216 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 5 Oct 2026 14:10:34 +0100
Subject: [PATCH 27/38] removed the to_vcf_cnf draft for now

---
 malariagen_data/anoph/to_vcf_cnv.py | 422 ----------------------------
 1 file changed, 422 deletions(-)
 delete mode 100644 malariagen_data/anoph/to_vcf_cnv.py

diff --git a/malariagen_data/anoph/to_vcf_cnv.py b/malariagen_data/anoph/to_vcf_cnv.py
deleted file mode 100644
index 927c95134..000000000
--- a/malariagen_data/anoph/to_vcf_cnv.py
+++ /dev/null
@@ -1,422 +0,0 @@
-import os
-from datetime import date
-from typing import List, Optional, Sequence
-import gzip
-
-import numpy as np
-from numpydoc_decorator import doc  # type: ignore
-
-from .cnv_data import AnophelesCnvData
-from . import base_params
-from . import cnv_params
-from . import plink_params
-from . import vcf_params
-
-# don't think we want this, IGV accepts seg format for CNVs
-# VCF not well defined for CNVs
-# use something like this:
-# https://cnvkit.readthedocs.io/en/v0.7.7/fileformats.html
-# or maybe not:
-# https://igv.org/doc/igvjs/#tracks/CNVPytor/
-# though it says only works for full genome, not regions,
-# so maybe not useful for us
-
-
-def _decode(value) -> str:
-    return value.decode() if hasattr(value, "decode") else str(value)
-
-
-def _write_vcf_header(
-    f,
-    *,
-    contigs: Sequence[str],
-    sample_ids: Sequence[str],
-    info_lines: Sequence[str],
-    format_lines: Sequence[str],
-    alt_lines: Sequence[str] = (),
-) -> None:
-    f.write("##fileformat=VCFv4.3\n")
-    f.write(f"##fileDate={date.today().strftime('%Y%m%d')}\n")
-    f.write("##source=malariagen_data\n")
-    for contig in contigs:
-        f.write(f"##contig=<ID={contig}>\n")
-    for line in alt_lines:
-        f.write(line + "\n")
-    for line in info_lines:
-        f.write(line + "\n")
-    for line in format_lines:
-        f.write(line + "\n")
-    header_cols = [
-        "#CHROM",
-        "POS",
-        "ID",
-        "REF",
-        "ALT",
-        "QUAL",
-        "FILTER",
-        "INFO",
-        "FORMAT",
-    ]
-    f.write("\t".join(header_cols + list(sample_ids)) + "\n")
-
-
-class CnvVcfExporter(
-    AnophelesCnvData,
-):
-    """
-    Export CNV calls to VCF.
-
-    N.B., unlike SNP calls, CNV calls are not fully standardised in VCF.
-    Here each CNV region or call is written as a single symbolic `<CNV>`
-    ALT allele (REF is written as "N", per the VCF specification for
-    imprecise/symbolic variants), with the relevant per-sample data
-    encoded in FORMAT fields. This is a draft representation intended
-    to give IGV something sensible to render, and to remove the
-    dependency on separately-hosted CNV VCF files; it is not intended
-    to be a fully general-purpose CNV VCF writer.
-    """
-
-    def __init__(
-        self,
-        **kwargs,
-    ):
-        # N.B., this class is designed to work cooperatively, and
-        # so it's important that any remaining parameters are passed
-        # to the superclass constructor.
-        super().__init__(**kwargs)
-
-    @doc(
-        summary="""
-            Export CNV HMM copy number calls to Variant Call Format (VCF).
-        """,
-        extended_summary="""
-            This function writes genome-wide CNV HMM calls to a VCF file.
-            Each CNV region is written as a symbolic `<CNV>` allele, with
-            the estimated copy number for each sample stored in the `CN`
-            FORMAT field. Data is written in chunks to avoid loading the
-            entire array into memory. Supports optional gzip compression
-            when the output path ends with `.gz`.
-        """,
-        returns="""
-        Path to the VCF output file.
-        """,
-    )
-    def cnv_hmm_to_vcf(
-        self,
-        output_path: vcf_params.vcf_output_path,
-        region: base_params.regions,
-        sample_sets: Optional[base_params.sample_sets] = None,
-        sample_query: Optional[base_params.sample_query] = None,
-        sample_query_options: Optional[base_params.sample_query_options] = None,
-        max_coverage_variance: cnv_params.max_coverage_variance = cnv_params.max_coverage_variance_default,
-        inline_array: base_params.inline_array = base_params.inline_array_default,
-        chunks: base_params.chunks = base_params.native_chunks,
-        overwrite: plink_params.overwrite = False,
-    ) -> str:
-        if os.path.exists(output_path) and not overwrite:
-            return output_path
-
-        ds = self.cnv_hmm(
-            region=region,
-            sample_sets=sample_sets,
-            sample_query=sample_query,
-            sample_query_options=sample_query_options,
-            max_coverage_variance=max_coverage_variance,
-            inline_array=inline_array,
-            chunks=chunks,
-        )
-
-        sample_ids = ds["sample_id"].values
-        contigs = ds.attrs.get("contigs", self.contigs)
-        compress = output_path.endswith(".gz")
-        # N.B., genuine BGZF, not plain gzip: tools that specifically
-        # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
-        # fail to read, or silently mis-parse, plain gzip even though
-        # it decompresses fine as a byte stream.
-        opener = gzip.open if compress else open
-
-        with opener(output_path, "wt") as f:
-            _write_vcf_header(
-                f,
-                contigs=contigs,
-                sample_ids=sample_ids,
-                alt_lines=[
-                    '##ALT=<ID=CNV,Description="Copy number variant region">',
-                ],
-                info_lines=[
-                    '##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the CNV region">',
-                ],
-                format_lines=[
-                    '##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number estimated from read coverage by HMM">',
-                ],
-            )
-
-            pos_data = ds["variant_position"].data
-            end_data = ds["variant_end"].data
-            contig_data = ds["variant_contig"].data
-            cn_data = ds["call_CN"].data
-
-            chunk_sizes = pos_data.chunks[0]
-            offsets = np.cumsum((0,) + chunk_sizes)
-
-            with self._spinner(f"Write VCF ({ds.sizes['variants']} CNV HMM regions)"):
-                for ci in range(len(chunk_sizes)):
-                    start = offsets[ci]
-                    stop = offsets[ci + 1]
-                    pos_chunk = pos_data[start:stop].compute()
-                    end_chunk = end_data[start:stop].compute()
-                    contig_chunk = contig_data[start:stop].compute()
-                    cn_chunk = cn_data[start:stop].compute()
-
-                    lines: List[str] = []
-                    for j in range(pos_chunk.shape[0]):
-                        chrom = contigs[contig_chunk[j]]
-                        pos = str(pos_chunk[j])
-                        end = int(end_chunk[j])
-                        info = f"END={end}"
-                        sample_fields = (
-                            "." if v < 0 else str(int(v)) for v in cn_chunk[j]
-                        )
-                        lines.append(
-                            f"{chrom}\t{pos}\t.\tN\t<CNV>\t.\t.\t{info}\tCN\t"
-                            + "\t".join(sample_fields)
-                            + "\n"
-                        )
-                    f.write("".join(lines))
-
-        return output_path
-
-    @doc(
-        summary="""
-            Export CNV coverage calls to Variant Call Format (VCF).
-        """,
-        extended_summary="""
-            This function writes CNV coverage calls (discrete CNV alleles
-            called from read coverage) to a VCF file. Each CNV allele is
-            written as a symbolic `<CNV>` allele, with the presence/absence
-            call for each sample stored in the `GT` FORMAT field (as a
-            haploid call: "1" if the CNV allele was called, "0" if not,
-            "." if missing). Data is written in chunks to avoid loading
-            the entire array into memory. Supports optional gzip
-            compression when the output path ends with `.gz`.
-        """,
-        returns="""
-        Path to the VCF output file.
-        """,
-    )
-    def cnv_coverage_calls_to_vcf(
-        self,
-        output_path: vcf_params.vcf_output_path,
-        region: base_params.regions,
-        sample_set: base_params.sample_set,
-        analysis: cnv_params.coverage_calls_analysis,
-        inline_array: base_params.inline_array = base_params.inline_array_default,
-        chunks: base_params.chunks = base_params.native_chunks,
-        overwrite: plink_params.overwrite = False,
-    ) -> str:
-        if os.path.exists(output_path) and not overwrite:
-            return output_path
-
-        ds = self.cnv_coverage_calls(
-            region=region,
-            sample_set=sample_set,
-            analysis=analysis,
-            inline_array=inline_array,
-            chunks=chunks,
-        )
-
-        sample_ids = ds["sample_id"].values
-        contigs = ds.attrs.get("contigs", self.contigs)
-        compress = output_path.endswith(".gz")
-        # N.B., genuine BGZF, not plain gzip: tools that specifically
-        # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
-        # fail to read, or silently mis-parse, plain gzip even though
-        # it decompresses fine as a byte stream.
-        opener = gzip.open if compress else open
-
-        with opener(output_path, "wt") as f:
-            _write_vcf_header(
-                f,
-                contigs=contigs,
-                sample_ids=sample_ids,
-                alt_lines=[
-                    '##ALT=<ID=CNV,Description="Copy number variant region">',
-                ],
-                info_lines=[
-                    '##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the CNV allele">',
-                    '##INFO=<ID=CIPOS,Number=1,Type=Integer,Description="Confidence interval half-width around POS">',
-                    '##INFO=<ID=CIEND,Number=1,Type=Integer,Description="Confidence interval half-width around END">',
-                ],
-                format_lines=[
-                    '##FORMAT=<ID=GT,Number=1,Type=String,Description="CNV call (1=called, 0=not called)">',
-                ],
-            )
-
-            pos_data = ds["variant_position"].data
-            end_data = ds["variant_end"].data
-            contig_data = ds["variant_contig"].data
-            id_data = ds["variant_id"].data
-            cipos_data = ds["variant_CIPOS"].data
-            ciend_data = ds["variant_CIEND"].data
-            filter_data = ds["variant_filter_pass"].data
-            gt_data = ds["call_genotype"].data
-
-            chunk_sizes = pos_data.chunks[0]
-            offsets = np.cumsum((0,) + chunk_sizes)
-
-            with self._spinner(
-                f"Write VCF ({ds.sizes['variants']} CNV coverage calls)"
-            ):
-                for ci in range(len(chunk_sizes)):
-                    start = offsets[ci]
-                    stop = offsets[ci + 1]
-                    pos_chunk = pos_data[start:stop].compute()
-                    end_chunk = end_data[start:stop].compute()
-                    contig_chunk = contig_data[start:stop].compute()
-                    id_chunk = id_data[start:stop].compute()
-                    cipos_chunk = cipos_data[start:stop].compute()
-                    ciend_chunk = ciend_data[start:stop].compute()
-                    filter_chunk = filter_data[start:stop].compute()
-                    gt_chunk = gt_data[start:stop].compute()
-
-                    lines: List[str] = []
-                    for j in range(pos_chunk.shape[0]):
-                        chrom = contigs[contig_chunk[j]]
-                        pos = str(pos_chunk[j])
-                        variant_id = _decode(id_chunk[j])
-                        end = int(end_chunk[j])
-                        filt = "PASS" if filter_chunk[j] else "."
-                        info = (
-                            f"END={end};CIPOS={int(cipos_chunk[j])}"
-                            f";CIEND={int(ciend_chunk[j])}"
-                        )
-                        sample_fields = (
-                            "." if v < 0 else str(int(v)) for v in gt_chunk[j]
-                        )
-                        lines.append(
-                            f"{chrom}\t{pos}\t{variant_id}\tN\t<CNV>\t.\t{filt}\t{info}\tGT\t"
-                            + "\t".join(sample_fields)
-                            + "\n"
-                        )
-                    f.write("".join(lines))
-
-        return output_path
-
-    @doc(
-        summary="""
-            Export CNV discordant read calls to Variant Call Format (VCF).
-        """,
-        extended_summary="""
-            This function writes CNV discordant read calls (CNV alleles
-            supported by discordant/paired-end read evidence) to a VCF
-            file. Each CNV allele is written as a symbolic `<CNV>` allele,
-            with the call for each sample stored in the `GT` FORMAT field
-            (as a haploid call: "1" if the CNV allele was called, "0" if
-            not, "." if missing). Data is written in chunks to avoid
-            loading the entire array into memory. Supports optional gzip
-            compression when the output path ends with `.gz`.
-        """,
-        returns="""
-        Path to the VCF output file.
-        """,
-    )
-    def cnv_discordant_read_calls_to_vcf(
-        self,
-        output_path: vcf_params.vcf_output_path,
-        contigs: base_params.contigs,
-        sample_sets: Optional[base_params.sample_sets] = None,
-        sample_query: Optional[base_params.sample_query] = None,
-        sample_query_options: Optional[base_params.sample_query_options] = None,
-        inline_array: base_params.inline_array = base_params.inline_array_default,
-        chunks: base_params.chunks = base_params.native_chunks,
-        overwrite: plink_params.overwrite = False,
-    ) -> str:
-        if os.path.exists(output_path) and not overwrite:
-            return output_path
-
-        ds = self.cnv_discordant_read_calls(
-            contigs=contigs,
-            sample_sets=sample_sets,
-            sample_query=sample_query,
-            sample_query_options=sample_query_options,
-            inline_array=inline_array,
-            chunks=chunks,
-        )
-
-        sample_ids = ds["sample_id"].values
-        all_contigs = ds.attrs.get("contigs", self.contigs)
-        compress = output_path.endswith(".gz")
-        # N.B., genuine BGZF, not plain gzip: tools that specifically
-        # expect BGZF for a .vcf.gz file (tabix, bedtools, ...) can
-        # fail to read, or silently mis-parse, plain gzip even though
-        # it decompresses fine as a byte stream.
-        opener = gzip.open if compress else open
-
-        with opener(output_path, "wt") as f:
-            _write_vcf_header(
-                f,
-                contigs=all_contigs,
-                sample_ids=sample_ids,
-                alt_lines=[
-                    '##ALT=<ID=CNV,Description="Copy number variant region">',
-                ],
-                info_lines=[
-                    '##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the CNV allele">',
-                    '##INFO=<ID=REGION,Number=1,Type=String,Description="Identifier of the region covered by this call">',
-                    '##INFO=<ID=SBM,Number=1,Type=Integer,Description="Method used to determine the start breakpoint">',
-                    '##INFO=<ID=EBM,Number=1,Type=Integer,Description="Method used to determine the end breakpoint">',
-                ],
-                format_lines=[
-                    '##FORMAT=<ID=GT,Number=1,Type=String,Description="CNV call (1=called, 0=not called)">',
-                ],
-            )
-
-            pos_data = ds["variant_position"].data
-            end_data = ds["variant_end"].data
-            contig_data = ds["variant_contig"].data
-            id_data = ds["variant_id"].data
-            region_data = ds["variant_Region"].data
-            sbm_data = ds["variant_StartBreakpointMethod"].data
-            ebm_data = ds["variant_EndBreakpointMethod"].data
-            gt_data = ds["call_genotype"].data
-
-            chunk_sizes = pos_data.chunks[0]
-            offsets = np.cumsum((0,) + chunk_sizes)
-
-            with self._spinner(
-                f"Write VCF ({ds.sizes['variants']} CNV discordant read calls)"
-            ):
-                for ci in range(len(chunk_sizes)):
-                    start = offsets[ci]
-                    stop = offsets[ci + 1]
-                    pos_chunk = pos_data[start:stop].compute()
-                    end_chunk = end_data[start:stop].compute()
-                    contig_chunk = contig_data[start:stop].compute()
-                    id_chunk = id_data[start:stop].compute()
-                    region_chunk = region_data[start:stop].compute()
-                    sbm_chunk = sbm_data[start:stop].compute()
-                    ebm_chunk = ebm_data[start:stop].compute()
-                    gt_chunk = gt_data[start:stop].compute()
-
-                    lines: List[str] = []
-                    for j in range(pos_chunk.shape[0]):
-                        chrom = all_contigs[contig_chunk[j]]
-                        pos = str(pos_chunk[j])
-                        variant_id = _decode(id_chunk[j])
-                        end = int(end_chunk[j])
-                        region_val = _decode(region_chunk[j])
-                        info = (
-                            f"END={end};REGION={region_val}"
-                            f";SBM={int(sbm_chunk[j])};EBM={int(ebm_chunk[j])}"
-                        )
-                        sample_fields = (
-                            "." if v < 0 else str(int(v)) for v in gt_chunk[j]
-                        )
-                        lines.append(
-                            f"{chrom}\t{pos}\t{variant_id}\tN\t<CNV>\t.\t.\t{info}\tGT\t"
-                            + "\t".join(sample_fields)
-                            + "\n"
-                        )
-                    f.write("".join(lines))
-
-        return output_path

From 03f8fb352012c889e16d93b031e34b73fd5a3626 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 5 Oct 2026 14:51:49 +0100
Subject: [PATCH 28/38] getting ready for PR, removing unused functions that
 were drafter previously and their related tests

---
 malariagen_data/anoph/to_vcf.py       |  36 ++--
 malariagen_data/anopheles.py          |   2 -
 tests/anoph/test_coverage_exporter.py | 295 --------------------------
 tests/anoph/test_igv_coverage.py      | 143 -------------
 tests/anoph/test_vcf_exporter.py      | 218 +++++--------------
 tests/anoph/test_vcf_exporter_cnv.py  | 244 ---------------------
 tests/test_bgzf.py                    |  95 ---------
 7 files changed, 65 insertions(+), 968 deletions(-)
 delete mode 100644 tests/anoph/test_coverage_exporter.py
 delete mode 100644 tests/anoph/test_igv_coverage.py
 delete mode 100644 tests/anoph/test_vcf_exporter_cnv.py
 delete mode 100644 tests/test_bgzf.py

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index d62d03612..5707c8859 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -5,8 +5,8 @@
 from dataclasses import dataclass
 from typing import Optional
 import dask
-from dask.array.core import Array
-from xarray.core.dataset import Dataset
+import dask.array as da
+import xarray as xr
 import numpy as np
 from numpydoc_decorator import doc  # type: ignore
 import pysam
@@ -130,16 +130,12 @@ def snp_calls_to_vcf(
         sample_sets: base_params.sample_sets,
         sample_query: base_params.sample_query,
         sample_query_options: Optional[base_params.sample_query_options] = None,
-        sample_indices: Optional[base_params.sample_indices] = None,
         site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         chunks: base_params.chunks = base_params.native_chunks,
         overwrite: plink_params.overwrite = False,
         fields: vcf_params.vcf_fields = ("GT",),
     ) -> str:
-        base_params._validate_sample_selection_params(
-            sample_query=sample_query, sample_indices=sample_indices
-        )
         _validate_single_sample_selection(
             sample_sets=sample_sets, sample_query=sample_query
         )
@@ -173,7 +169,6 @@ def snp_calls_to_vcf(
             sample_sets=sample_sets,
             sample_query=sample_query,
             sample_query_options=sample_query_options,
-            sample_indices=sample_indices,
             site_mask=site_mask,
             inline_array=inline_array,
             chunks=chunks,
@@ -259,12 +254,11 @@ def snp_calls_to_vcf(
                             if s:
                                 alt_alleles.append(s)
 
-                        genotype_data = variant_chunk_data.gt_chunk[j, 0]
-                        genotype = (
-                            (None,) * len(genotype_data)
-                            if np.any(genotype_data < 0)
-                            else tuple(int(allele) for allele in genotype_data)
-                        )
+                        genotype: tuple[Optional[int], ...]
+                        if np.any(genotype_data < 0):
+                            genotype = (None,) * len(genotype_data)
+                        else:
+                            genotype = tuple(int(allele) for allele in genotype_data)
 
                         record = header.new_record(
                             contig=str(chrom),
@@ -305,18 +299,18 @@ def snp_calls_to_vcf(
                                 sample["MQ"] = None
                         f.write(record)
 
-        pysam.tabix_index(output_path, preset="vcf", force=overwrite)
+        pysam.tabix_index(output_path, preset="vcf", force=True)
         return output_path
 
     def _get_chunks(
         self,
         ci: int,
         offsets: np.ndarray,
-        gt_data: Array,
-        pos_data: Array,
-        contig_data: Array,
-        allele_data: Array,
-        optional_arrays: dict[str, Array],
+        gt_data: da.Array,
+        pos_data: da.Array,
+        contig_data: da.Array,
+        allele_data: da.Array,
+        optional_arrays: dict[str, da.Array],
     ) -> VariantChunkData:
         start = offsets[ci]
         stop = offsets[ci + 1]
@@ -365,8 +359,8 @@ def _get_chunks(
         return chunk_output
 
     def _get_optional_data(
-        self, include_gq: bool, include_ad: bool, include_mq: bool, ds: Dataset
-    ) -> dict[str, Array]:
+        self, include_gq: bool, include_ad: bool, include_mq: bool, ds: xr.Dataset
+    ) -> dict[str, da.Array]:
         # Optional field arrays — may not exist in all datasets.
         gq_data = None
         ad_data = None
diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py
index b775dad1e..8342dbb88 100644
--- a/malariagen_data/anopheles.py
+++ b/malariagen_data/anopheles.py
@@ -37,7 +37,6 @@
 from .anoph.to_plink import PlinkConverter
 from .anoph.ld import AnophelesLdAnalysis
 from .anoph.to_vcf import SnpVcfExporter
-from .anoph.to_vcf_cnv import CnvVcfExporter
 from .anoph.g123 import AnophelesG123Analysis
 from .anoph.fst import AnophelesFstAnalysis
 from .anoph.h12 import AnophelesH12Analysis
@@ -94,7 +93,6 @@ class AnophelesDataResource(
     PlinkConverter,
     AnophelesLdAnalysis,
     SnpVcfExporter,
-    CnvVcfExporter,
     AnophelesIgv,
     AnophelesKaryotypeAnalysis,
     AnophelesAimData,
diff --git a/tests/anoph/test_coverage_exporter.py b/tests/anoph/test_coverage_exporter.py
deleted file mode 100644
index d0770af3e..000000000
--- a/tests/anoph/test_coverage_exporter.py
+++ /dev/null
@@ -1,295 +0,0 @@
-import gzip
-import os
-import random
-
-import dask.array as da
-import numpy as np
-import pytest
-import xarray as xr
-from pytest_cases import parametrize_with_cases
-
-from malariagen_data import af1 as _af1
-from malariagen_data import ag3 as _ag3
-
-from malariagen_data.anoph.to_coverage import CoverageExporter
-
-
-@pytest.fixture
-def ag3_sim_api(ag3_sim_fixture):
-    return CoverageExporter(
-        url=ag3_sim_fixture.url,
-        public_url=ag3_sim_fixture.url,
-        config_path=_ag3.CONFIG_PATH,
-        major_version_number=_ag3.MAJOR_VERSION_NUMBER,
-        major_version_path=_ag3.MAJOR_VERSION_PATH,
-        pre=True,
-        aim_metadata_dtype={
-            "aim_species_fraction_arab": "float64",
-            "aim_species_fraction_colu": "float64",
-            "aim_species_fraction_colu_no2l": "float64",
-            "aim_species_gambcolu_arabiensis": object,
-            "aim_species_gambiae_coluzzii": object,
-            "aim_species": object,
-        },
-        gff_gene_type="gene",
-        gff_gene_name_attribute="Name",
-        gff_default_attributes=("ID", "Parent", "Name", "description"),
-        results_cache=ag3_sim_fixture.results_cache_path.as_posix(),
-        default_coverage_calls_analysis="gamb_colu",
-        discordant_read_calls_analysis=ag3_sim_fixture.config[
-            "DEFAULT_DISCORDANT_READ_CALLS_ANALYSIS"
-        ],
-    )
-
-
-@pytest.fixture
-def af1_sim_api(af1_sim_fixture):
-    return CoverageExporter(
-        url=af1_sim_fixture.url,
-        public_url=af1_sim_fixture.url,
-        config_path=_af1.CONFIG_PATH,
-        major_version_number=_af1.MAJOR_VERSION_NUMBER,
-        major_version_path=_af1.MAJOR_VERSION_PATH,
-        pre=False,
-        gff_gene_type="protein_coding_gene",
-        gff_gene_name_attribute="Note",
-        gff_default_attributes=("ID", "Parent", "Note", "description"),
-        results_cache=af1_sim_fixture.results_cache_path.as_posix(),
-        default_coverage_calls_analysis="funestus",
-        discordant_read_calls_analysis=None,
-    )
-
-
-def case_ag3_sim(ag3_sim_fixture, ag3_sim_api):
-    return ag3_sim_fixture, ag3_sim_api
-
-
-def case_af1_sim(af1_sim_fixture, af1_sim_api):
-    return af1_sim_fixture, af1_sim_api
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_hmm_coverage_to_bedgraph(fixture, api: CoverageExporter, tmp_path):
-    region = random.choice(api.contigs)
-    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
-
-    output_path = str(tmp_path / "test_coverage.bedgraph")
-    api.cnv_hmm_coverage_to_bedgraph(
-        output_path=output_path,
-        region=region,
-        sample=sample,
-    )
-
-    assert os.path.exists(output_path)
-
-    with open(output_path) as f:
-        lines = f.readlines()
-
-    assert lines[0].startswith("track type=bedGraph")
-
-    data_lines = lines[1:]
-    assert len(data_lines) > 0
-
-    for line in data_lines:
-        fields = line.rstrip("\n").split("\t")
-        assert len(fields) == 4
-        chrom, start, end, value = fields
-        assert chrom == region
-        assert int(start) >= 0
-        assert int(end) > int(start)
-        # Should be a valid number and non-negative (masked/missing
-        # values are skipped rather than written).
-        assert float(value) >= 0
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_hmm_coverage_to_bedgraph_raw_cov(fixture, api: CoverageExporter, tmp_path):
-    region = api.contigs[0]
-    sample = str(api.sample_metadata()["sample_id"].iloc[0])
-
-    output_path = str(tmp_path / "test_coverage_raw.bedgraph")
-    api.cnv_hmm_coverage_to_bedgraph(
-        output_path=output_path,
-        region=region,
-        sample=sample,
-        field="RawCov",
-    )
-    assert os.path.exists(output_path)
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_hmm_coverage_to_bedgraph_invalid_field(
-    fixture, api: CoverageExporter, tmp_path
-):
-    region = api.contigs[0]
-    sample = str(api.sample_metadata()["sample_id"].iloc[0])
-
-    output_path = str(tmp_path / "test_coverage_bad.bedgraph")
-    with pytest.raises(ValueError, match="Unknown coverage field"):
-        api.cnv_hmm_coverage_to_bedgraph(
-            output_path=output_path,
-            region=region,
-            sample=sample,
-            field="NotAField",
-        )
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_hmm_coverage_to_bedgraph_unknown_sample(
-    fixture, api: CoverageExporter, tmp_path
-):
-    region = api.contigs[0]
-    output_path = str(tmp_path / "test_coverage_unknown.bedgraph")
-    with pytest.raises(ValueError, match="No data found for sample"):
-        api.cnv_hmm_coverage_to_bedgraph(
-            output_path=output_path,
-            region=region,
-            sample="not_a_real_sample",
-        )
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_hmm_coverage_to_bedgraph_overwrite(
-    fixture, api: CoverageExporter, tmp_path
-):
-    region = api.contigs[0]
-    sample = str(api.sample_metadata()["sample_id"].iloc[0])
-    output_path = str(tmp_path / "test_coverage.bedgraph")
-
-    api.cnv_hmm_coverage_to_bedgraph(
-        output_path=output_path, region=region, sample=sample
-    )
-    mtime_first = os.path.getmtime(output_path)
-
-    api.cnv_hmm_coverage_to_bedgraph(
-        output_path=output_path, region=region, sample=sample
-    )
-    assert os.path.getmtime(output_path) == mtime_first
-
-    api.cnv_hmm_coverage_to_bedgraph(
-        output_path=output_path, region=region, sample=sample, overwrite=True
-    )
-    assert os.path.exists(output_path)
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_hmm_coverage_to_bedgraph_gzip(fixture, api: CoverageExporter, tmp_path):
-    region = api.contigs[0]
-    sample = str(api.sample_metadata()["sample_id"].iloc[0])
-    output_path = str(tmp_path / "test_coverage.bedgraph.gz")
-
-    api.cnv_hmm_coverage_to_bedgraph(
-        output_path=output_path, region=region, sample=sample
-    )
-    assert os.path.exists(output_path)
-
-    with gzip.open(output_path, "rt") as f:
-        first_line = f.readline()
-    assert first_line.startswith("track type=bedGraph")
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_snp_calls_coverage_to_bedgraph(fixture, api: CoverageExporter, tmp_path):
-    region = random.choice(api.contigs)
-    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
-
-    output_path = str(tmp_path / "test_snp_coverage.bedgraph")
-    api.snp_calls_coverage_to_bedgraph(
-        output_path=output_path,
-        region=region,
-        sample=sample,
-    )
-
-    assert os.path.exists(output_path)
-
-    with open(output_path) as f:
-        lines = f.readlines()
-
-    assert lines[0].startswith("track type=bedGraph")
-
-    # N.B., the simulated AD data is filled with a missing-value
-    # sentinel (-1) for every site, so no data lines are expected here;
-    # this exercises that missing values are skipped rather than
-    # written as misleading zero-depth entries. The arithmetic for
-    # sites that do have depth is checked separately below, using a
-    # synthetic dataset.
-    for line in lines[1:]:
-        fields = line.rstrip("\n").split("\t")
-        assert len(fields) == 4
-        chrom, start, end, value = fields
-        assert chrom == region
-        assert int(end) == int(start) + 1
-        assert int(value) >= 0
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_snp_calls_coverage_to_bedgraph_depth_values(
-    fixture, api: CoverageExporter, tmp_path, monkeypatch
-):
-    # Exercise the depth arithmetic directly against a small synthetic
-    # dataset, since the simulated fixture data fills call_AD with a
-    # missing-value sentinel throughout (see test above).
-    contig = api.contigs[0]
-    sample = str(api.sample_metadata()["sample_id"].iloc[0])
-
-    ds = xr.Dataset(
-        data_vars={
-            "call_AD": (
-                ["variants", "samples", "alleles"],
-                da.from_array(
-                    np.array(
-                        [
-                            [[10, 2, 0, 0]],  # total depth 12
-                            [[-1, -1, -1, -1]],  # missing, should be skipped
-                            [[5, -1, 0, 0]],  # negative components clipped to 0
-                        ],
-                        dtype="i2",
-                    ),
-                    chunks=(2, 1, 4),
-                ),
-            ),
-        },
-        coords={
-            "variant_position": (
-                "variants",
-                da.from_array(np.array([100, 200, 300]), chunks=2),
-            ),
-            "variant_contig": (
-                "variants",
-                da.from_array(np.array([0, 0, 0], dtype="u1"), chunks=2),
-            ),
-            "sample_id": ("samples", np.array([sample])),
-        },
-        attrs={"contigs": (contig,)},
-    )
-    monkeypatch.setattr(api, "snp_calls", lambda **kwargs: ds)
-
-    output_path = str(tmp_path / "test_snp_coverage_values.bedgraph")
-    api.snp_calls_coverage_to_bedgraph(
-        output_path=output_path,
-        region=contig,
-        sample=sample,
-    )
-
-    with open(output_path) as f:
-        lines = f.readlines()
-
-    data_lines = [line.rstrip("\n").split("\t") for line in lines[1:]]
-    assert data_lines == [
-        [contig, "99", "100", "12"],
-        [contig, "299", "300", "5"],
-    ]
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_snp_calls_coverage_to_bedgraph_unknown_sample(
-    fixture, api: CoverageExporter, tmp_path
-):
-    region = api.contigs[0]
-    output_path = str(tmp_path / "test_snp_coverage_unknown.bedgraph")
-    with pytest.raises(ValueError, match="No data found for sample"):
-        api.snp_calls_coverage_to_bedgraph(
-            output_path=output_path,
-            region=region,
-            sample="not_a_real_sample",
-        )
diff --git a/tests/anoph/test_igv_coverage.py b/tests/anoph/test_igv_coverage.py
deleted file mode 100644
index a39a0154c..000000000
--- a/tests/anoph/test_igv_coverage.py
+++ /dev/null
@@ -1,143 +0,0 @@
-import numpy as np
-import pytest
-from pytest_cases import parametrize_with_cases
-
-from malariagen_data import af1 as _af1
-from malariagen_data import ag3 as _ag3
-from malariagen_data.anoph.igv import AnophelesIgv
-from malariagen_data.anoph.to_coverage import CoverageExporter
-
-
-class _IgvWithCoverage(CoverageExporter, AnophelesIgv):
-    """Combines AnophelesIgv with CoverageExporter, the way the
-    top-level Ag3/Af1 data resource classes do, so that the local
-    coverage fallback functionality can be exercised in isolation."""
-
-
-@pytest.fixture
-def ag3_sim_api(ag3_sim_fixture):
-    return AnophelesIgv(
-        url=ag3_sim_fixture.url,
-        public_url=ag3_sim_fixture.url,
-        config_path=_ag3.CONFIG_PATH,
-        major_version_number=_ag3.MAJOR_VERSION_NUMBER,
-        major_version_path=_ag3.MAJOR_VERSION_PATH,
-        pre=True,
-        aim_metadata_dtype={
-            "aim_species_fraction_arab": "float64",
-            "aim_species_fraction_colu": "float64",
-            "aim_species_fraction_colu_no2l": "float64",
-            "aim_species_gambcolu_arabiensis": object,
-            "aim_species_gambiae_coluzzii": object,
-            "aim_species": object,
-        },
-        gff_gene_type="gene",
-        gff_gene_name_attribute="Name",
-        gff_default_attributes=("ID", "Parent", "Name", "description"),
-        default_site_mask="gamb_colu_arab",
-        results_cache=ag3_sim_fixture.results_cache_path.as_posix(),
-    )
-
-
-@pytest.fixture
-def ag3_sim_api_with_coverage(ag3_sim_fixture):
-    return _IgvWithCoverage(
-        url=ag3_sim_fixture.url,
-        public_url=ag3_sim_fixture.url,
-        config_path=_ag3.CONFIG_PATH,
-        major_version_number=_ag3.MAJOR_VERSION_NUMBER,
-        major_version_path=_ag3.MAJOR_VERSION_PATH,
-        pre=True,
-        aim_metadata_dtype={
-            "aim_species_fraction_arab": "float64",
-            "aim_species_fraction_colu": "float64",
-            "aim_species_fraction_colu_no2l": "float64",
-            "aim_species_gambcolu_arabiensis": object,
-            "aim_species_gambiae_coluzzii": object,
-            "aim_species": object,
-        },
-        gff_gene_type="gene",
-        gff_gene_name_attribute="Name",
-        gff_default_attributes=("ID", "Parent", "Name", "description"),
-        default_site_mask="gamb_colu_arab",
-        results_cache=ag3_sim_fixture.results_cache_path.as_posix(),
-        default_coverage_calls_analysis="gamb_colu",
-        discordant_read_calls_analysis=ag3_sim_fixture.config[
-            "DEFAULT_DISCORDANT_READ_CALLS_ANALYSIS"
-        ],
-    )
-
-
-@pytest.fixture
-def af1_sim_api_with_coverage(af1_sim_fixture):
-    return _IgvWithCoverage(
-        url=af1_sim_fixture.url,
-        public_url=af1_sim_fixture.url,
-        config_path=_af1.CONFIG_PATH,
-        major_version_number=_af1.MAJOR_VERSION_NUMBER,
-        major_version_path=_af1.MAJOR_VERSION_PATH,
-        pre=False,
-        gff_gene_type="protein_coding_gene",
-        gff_gene_name_attribute="Note",
-        gff_default_attributes=("ID", "Parent", "Note", "description"),
-        default_site_mask="funestus",
-        results_cache=af1_sim_fixture.results_cache_path.as_posix(),
-        default_coverage_calls_analysis="funestus",
-        discordant_read_calls_analysis=None,
-    )
-
-
-def case_ag3_sim(ag3_sim_fixture, ag3_sim_api_with_coverage):
-    return ag3_sim_fixture, ag3_sim_api_with_coverage
-
-
-def case_af1_sim(af1_sim_fixture, af1_sim_api_with_coverage):
-    return af1_sim_fixture, af1_sim_api_with_coverage
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_view_coverage(fixture, api: _IgvWithCoverage):
-    region = api.contigs[0]
-    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
-    ret = api.view_coverage(region=region, sample=sample, init=False)
-    # No return value to avoid cluttering notebook output.
-    assert ret is None
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_view_alignments_with_local_coverage_fallback(fixture, api: _IgvWithCoverage):
-    region = api.contigs[0]
-    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
-    ret = api.view_alignments(
-        region=region,
-        sample=sample,
-        init=False,
-        local_coverage_fallback=True,
-    )
-    assert ret is None
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_view_coverage_writes_bedgraph(fixture, api: _IgvWithCoverage, tmp_path):
-    region = api.contigs[0]
-    sample = str(np.random.choice(api.sample_metadata()["sample_id"]))
-    output_path = str(tmp_path / "coverage.bedgraph")
-    api.view_coverage(region=region, sample=sample, init=False, output_path=output_path)
-    with open(output_path) as f:
-        first_line = f.readline()
-    assert first_line.startswith("track type=bedGraph")
-
-
-def test_local_coverage_fallback_requires_cnv_mixin(ag3_sim_fixture, ag3_sim_api):
-    # Plain AnophelesIgv, without CoverageExporter mixed in, should
-    # raise a clear error rather than an AttributeError if asked for a
-    # local coverage track.
-    region = ag3_sim_api.contigs[0]
-    sample = str(np.random.choice(ag3_sim_api.sample_metadata()["sample_id"]))
-    with pytest.raises(NotImplementedError):
-        ag3_sim_api.view_alignments(
-            region=region,
-            sample=sample,
-            init=False,
-            local_coverage_fallback=True,
-        )
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index a87669fe3..450a8ca97 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -97,9 +97,13 @@ def test_vcf_exporter(fixture, api: SnpVcfExporter, tmp_path):
     )
 
     ds = api.snp_calls(**data_params)
-    n_variants = ds.sizes["variants"]
     sample_ids = ds["sample_id"].values
 
+    # Homozygous reference sites are not written.
+    gt = ds["call_genotype"].values[:, 0, :]
+    is_hom_ref = (gt == 0).all(axis=1)
+    expected_positions = sorted(ds["variant_position"].values[~is_hom_ref].tolist())
+
     # snp_calls_to_vcf() only supports exporting a single sample at a
     # time (its only current use case is generating a per-sample VCF
     # for IGV), so sample_query must narrow the dataset down to one
@@ -127,13 +131,9 @@ def test_vcf_exporter(fixture, api: SnpVcfExporter, tmp_path):
     vcf_samples = col_fields[9:]
     assert list(vcf_samples) == list(sample_ids)
 
-    # Variant count matches.
-    assert len(data_lines) == n_variants
-
-    # Positions match.
+    # Positions match the non-homozygous-reference sites.
     vcf_positions = sorted([int(line.split("\t")[1]) for line in data_lines])
-    ds_positions = sorted(ds["variant_position"].values.tolist())
-    assert vcf_positions == ds_positions
+    assert vcf_positions == expected_positions
 
     # Allele values are clean strings, not byte-string representations.
     for line in data_lines:
@@ -145,122 +145,52 @@ def test_vcf_exporter(fixture, api: SnpVcfExporter, tmp_path):
 
 
 @parametrize_with_cases("fixture,api", cases=".")
-def test_vcf_exporter_non_ref_only(fixture, api: SnpVcfExporter, tmp_path):
-    # non_ref_only=True should keep only sites where the sample's
-    # genotype carries at least one non-reference allele, dropping both
-    # homozygous reference (0/0) and missing (./.) calls. Equivalent in
-    # spirit to `bcftools view -e 'F_PASS(GT="ref") == 1'`, except that
-    # a missing call is also excluded here (that particular bcftools
-    # expression only excludes homozygous reference calls, since a
-    # missing call is neither "ref" nor caught by that `-e` filter).
+def test_vcf_exporter_excludes_hom_ref(fixture, api: SnpVcfExporter, tmp_path):
+    # Homozygous reference (0/0) sites are not written. Missing calls
+    # are still written, as "./.".
     region = random.choice(api.contigs)
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = random.sample(all_sample_sets, min(2, len(all_sample_sets)))
+    site_mask = random.choice((None,) + api.site_mask_ids)
     _, sample_query = _pick_single_sample_query(api, sample_sets)
 
     data_params = dict(
         region=region,
         sample_sets=sample_sets,
         sample_query=sample_query,
+        site_mask=site_mask,
     )
 
-    # Work out the expected set of non-ref, non-missing positions
-    # directly from the dataset, independently of snp_calls_to_vcf.
+    # Work out the expected positions directly from the dataset,
+    # independently of snp_calls_to_vcf.
     ds = api.snp_calls(**data_params)
     gt = ds["call_genotype"].values[:, 0, :]  # (variants, ploidy)
     is_missing = (gt < 0).any(axis=1)
     is_hom_ref = (gt == 0).all(axis=1)
-    expect_keep = ~is_missing & ~is_hom_ref
-    expected_positions = sorted(ds["variant_position"].values[expect_keep].tolist())
+    positions = ds["variant_position"].values
+    expected_positions = sorted(positions[~is_hom_ref].tolist())
+    expected_missing_positions = sorted(positions[is_missing].tolist())
 
-    output_path = str(tmp_path / "test_non_ref_only.vcf.gz")
-    api.snp_calls_to_vcf(
-        output_path=output_path,
-        non_ref_only=True,
-        **data_params,
-    )
+    output_path = str(tmp_path / "test_excludes_hom_ref.vcf.gz")
+    api.snp_calls_to_vcf(output_path=output_path, **data_params)
 
     with gzip.open(output_path, "rt") as f:
         lines = f.readlines()
     data_lines = [line for line in lines if not line.startswith("#")]
 
-    # Every written site should have a non-ref, non-missing GT.
+    vcf_positions = []
+    vcf_missing_positions = []
     for line in data_lines:
         fields_row = line.strip().split("\t")
+        pos = int(fields_row[1])
         gt_str = fields_row[9].split(":")[0]
-        assert gt_str != "./."
-        a0, a1 = gt_str.split("/")
-        assert not (a0 == "0" and a1 == "0")
-
-    # And the set of positions written should exactly match what we
-    # expect directly from the dataset (no extras, none missing).
-    vcf_positions = sorted(int(line.split("\t")[1]) for line in data_lines)
-    assert vcf_positions == expected_positions
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_vcf_exporter_non_ref_only_defaults_to_false(
-    fixture, api: SnpVcfExporter, tmp_path
-):
-    # Not passing non_ref_only should behave identically to passing
-    # non_ref_only=False (i.e. include homozygous reference / missing
-    # sites too) — this locks in the default.
-    region = api.contigs[0]
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_sets = [all_sample_sets[0]]
-    _, sample_query = _pick_single_sample_query(api, sample_sets)
-
-    output_path_default = str(tmp_path / "default.vcf.gz")
-    output_path_explicit = str(tmp_path / "explicit_false.vcf.gz")
-    api.snp_calls_to_vcf(
-        output_path=output_path_default,
-        region=region,
-        sample_sets=sample_sets,
-        sample_query=sample_query,
-    )
-    api.snp_calls_to_vcf(
-        output_path=output_path_explicit,
-        region=region,
-        sample_sets=sample_sets,
-        sample_query=sample_query,
-        non_ref_only=False,
-    )
+        assert gt_str != "0/0", f"hom-ref call written at {pos}"
+        vcf_positions.append(pos)
+        if gt_str == "./.":
+            vcf_missing_positions.append(pos)
 
-    with gzip.open(output_path_default, "rt") as f:
-        default_lines = f.readlines()
-    with gzip.open(output_path_explicit, "rt") as f:
-        explicit_lines = f.readlines()
-    assert default_lines == explicit_lines
-
-
-@pytest.mark.skipif(shutil.which("bcftools") is None, reason="bcftools not installed")
-@parametrize_with_cases("fixture,api", cases=".")
-def test_vcf_exporter_non_ref_only_valid_per_bcftools(
-    fixture, api: SnpVcfExporter, tmp_path
-):
-    region = api.contigs[0]
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_sets = [all_sample_sets[0]]
-    _, sample_query = _pick_single_sample_query(api, sample_sets)
-
-    output_path = str(tmp_path / "test_non_ref_only_bcftools.vcf.gz")
-    api.snp_calls_to_vcf(
-        output_path=output_path,
-        region=region,
-        sample_sets=sample_sets,
-        sample_query=sample_query,
-        fields={"GT", "GQ", "AD", "MQ"},
-        non_ref_only=True,
-    )
-
-    result = subprocess.run(
-        ["bcftools", "view", "-v", "snps", output_path],
-        capture_output=True,
-        text=True,
-    )
-    assert result.returncode == 0, f"bcftools failed to parse output: {result.stderr}"
-    assert "Error" not in result.stderr
-    assert "should be declared as" not in result.stderr, result.stderr
+    assert sorted(vcf_positions) == expected_positions
+    assert sorted(vcf_missing_positions) == expected_missing_positions
 
 
 @parametrize_with_cases("fixture,api", cases=".")
@@ -584,75 +514,36 @@ def test_vcf_exporter_fields_gt_required(fixture, api: SnpVcfExporter, tmp_path)
 
 
 @parametrize_with_cases("fixture,api", cases=".")
-def test_vcf_exporter_allele_index_remapping(
+def test_vcf_exporter_synthetic_genotypes(
     fixture, api: SnpVcfExporter, tmp_path, monkeypatch
 ):
-    # ALT should only ever list alleles that are both (a) genuinely
-    # populated in variant_allele and (b) actually referenced by this
-    # sample's own genotype. variant_allele lists a fixed, canonical
-    # set of alternate bases per site (e.g. for REF=A it can list
-    # "C,T,G" regardless of what's actually segregating, let alone
-    # relevant to one particular sample), and call_genotype's allele
-    # indices refer to those *original* slot positions, which are not
-    # guaranteed to be contiguous from 1 either (a site's only real ALT
-    # allele can sit in slot 2 or 3 while an earlier slot is empty).
-    # Writing every populated-but-irrelevant slot to ALT (a) produces
-    # invalid records when combined with un-remapped genotype indices
-    # (e.g. "0/2" against a single-allele ALT column, which bcftools
-    # then silently mishandled), and (b) even once indices are
-    # correctly remapped, produces a non-standard single-sample VCF
-    # (real single-sample VCFs only list alleles that sample's
-    # genotype actually uses) that fails REF/ALT-based comparison
-    # against any VCF following that convention — two VCFs recording
-    # the "same" call at the same position end up with different ALT
-    # strings purely because of unrelated candidate alleles.
+    # Deterministic check on a small synthetic dataset: ALT lists every
+    # alternate allele in variant_allele, GT allele indices are written
+    # as-is, homozygous reference sites are dropped and missing calls
+    # are written as "./.".
     sample = str(api.sample_metadata()["sample_id"].iloc[0])
     contig = api.contigs[0]
 
     variant_allele = np.array(
-        [
-            [b"A", b"", b"T", b""],  # only real ALT in slot 2
-            [b"A", b"T", b"", b""],  # real ALT in slot 1 (baseline case)
-            [b"A", b"", b"", b"T"],  # only real ALT in slot 3
-            [b"A", b"C", b"", b"T"],  # two real ALTs, only one used
-            [b"A", b"C", b"T", b"G"],  # all 3 canonical ALTs populated,
-            #                            only one used (the real-world
-            #                            pattern: REF=A ALT="C,T,G"
-            #                            regardless of relevance)
-            [b"A", b"C", b"T", b"G"],  # all 3 populated, compound het
-            #                            using two of them
-            [b"A", b"C", b"T", b"G"],  # all 3 populated, hom-ref
-            [b"A", b"C", b"T", b"G"],  # all 3 populated, missing
-        ],
+        [[b"A", b"C", b"T", b"G"]] * 5,
         dtype="S1",
     )
     call_genotype = np.array(
         [
-            [[0, 2]],  # het for the slot-2 "T" -> ALT="T" -> expect 0/1
-            [[0, 1]],  # het for the slot-1 "T" -> ALT="T" -> expect 0/1
-            [[3, 3]],  # hom-alt for the slot-3 "T" -> ALT="T" -> expect 1/1
-            [[0, 3]],  # het for slot-3 "T"; slot-1 "C" unused -> expect ALT="T", GT=0/1
-            [
-                [0, 2]
-            ],  # het for slot-2 "T"; "C" and "G" unused -> expect ALT="T", GT=0/1
-            [
-                [1, 3]
-            ],  # het for slot-1 "C" and slot-3 "G"; "T" unused -> expect ALT="C,G", GT=1/2
-            [[0, 0]],  # hom-ref -> expect ALT=".", GT=0/0
-            [[-1, -1]],  # missing -> expect ALT=".", GT=./.
+            [[0, 1]],  # het
+            [[0, 0]],  # hom-ref -> not written
+            [[-1, -1]],  # missing
+            [[1, 3]],  # het for two alternate alleles
+            [[2, 2]],  # hom-alt
         ],
         dtype="i1",
     )
-    positions = [100, 200, 300, 400, 500, 600, 700, 800]
+    positions = [100, 200, 300, 400, 500]
     expected = {
-        100: ("T", "0/1"),
-        200: ("T", "0/1"),
-        300: ("T", "1/1"),
-        400: ("T", "0/1"),
-        500: ("T", "0/1"),
-        600: ("C,G", "1/2"),
-        700: (".", "0/0"),
-        800: (".", "./."),
+        100: "0/1",
+        300: "./.",
+        400: "1/3",
+        500: "2/2",
     }
 
     n_variants = len(positions)
@@ -682,7 +573,7 @@ def test_vcf_exporter_allele_index_remapping(
     )
     monkeypatch.setattr(api, "snp_calls", lambda **kwargs: ds)
 
-    output_path = str(tmp_path / "test_allele_remap.vcf.gz")
+    output_path = str(tmp_path / "test_synthetic.vcf.gz")
     api.snp_calls_to_vcf(
         output_path=output_path,
         region=contig,
@@ -693,21 +584,12 @@ def test_vcf_exporter_allele_index_remapping(
     with gzip.open(output_path, "rt") as f:
         lines = f.readlines()
     data_lines = [line for line in lines if not line.startswith("#")]
-    assert len(data_lines) == n_variants
 
+    written = {}
     for line in data_lines:
         fields_row = line.strip().split("\t")
         pos = int(fields_row[1])
-        alt = fields_row[4]
-        gt = fields_row[9].split(":")[0]
-        expected_alt, expected_gt = expected[pos]
-        assert alt == expected_alt, f"at {pos}: expected ALT {expected_alt}, got {alt}"
-        assert gt == expected_gt, f"at {pos}: expected GT {expected_gt}, got {gt}"
-        # Every GT allele index must be valid for the ALT column that
-        # was actually written (i.e. in range for the number of ALT
-        # alleles listed), which is the invariant this fix guarantees.
-        if gt == "./.":
-            continue
-        n_alt_alleles = 0 if alt == "." else len(alt.split(","))
-        for allele_idx in gt.split("/"):
-            assert int(allele_idx) <= n_alt_alleles
+        assert fields_row[3] == "A"
+        assert fields_row[4] == "C,T,G"
+        written[pos] = fields_row[9].split(":")[0]
+    assert written == expected
diff --git a/tests/anoph/test_vcf_exporter_cnv.py b/tests/anoph/test_vcf_exporter_cnv.py
deleted file mode 100644
index 8081cef1c..000000000
--- a/tests/anoph/test_vcf_exporter_cnv.py
+++ /dev/null
@@ -1,244 +0,0 @@
-import gzip
-import os
-import random
-import shutil
-import subprocess
-
-import pytest
-from pytest_cases import parametrize_with_cases
-
-from malariagen_data import af1 as _af1
-from malariagen_data import ag3 as _ag3
-
-from malariagen_data.anoph.to_vcf_cnv import CnvVcfExporter
-
-
-@pytest.fixture
-def ag3_sim_api(ag3_sim_fixture):
-    return CnvVcfExporter(
-        url=ag3_sim_fixture.url,
-        public_url=ag3_sim_fixture.url,
-        config_path=_ag3.CONFIG_PATH,
-        major_version_number=_ag3.MAJOR_VERSION_NUMBER,
-        major_version_path=_ag3.MAJOR_VERSION_PATH,
-        pre=True,
-        aim_metadata_dtype={
-            "aim_species_fraction_arab": "float64",
-            "aim_species_fraction_colu": "float64",
-            "aim_species_fraction_colu_no2l": "float64",
-            "aim_species_gambcolu_arabiensis": object,
-            "aim_species_gambiae_coluzzii": object,
-            "aim_species": object,
-        },
-        gff_gene_type="gene",
-        gff_gene_name_attribute="Name",
-        gff_default_attributes=("ID", "Parent", "Name", "description"),
-        results_cache=ag3_sim_fixture.results_cache_path.as_posix(),
-        default_coverage_calls_analysis="gamb_colu",
-        discordant_read_calls_analysis=ag3_sim_fixture.config[
-            "DEFAULT_DISCORDANT_READ_CALLS_ANALYSIS"
-        ],
-    )
-
-
-@pytest.fixture
-def af1_sim_api(af1_sim_fixture):
-    return CnvVcfExporter(
-        url=af1_sim_fixture.url,
-        public_url=af1_sim_fixture.url,
-        config_path=_af1.CONFIG_PATH,
-        major_version_number=_af1.MAJOR_VERSION_NUMBER,
-        major_version_path=_af1.MAJOR_VERSION_PATH,
-        pre=False,
-        gff_gene_type="protein_coding_gene",
-        gff_gene_name_attribute="Note",
-        gff_default_attributes=("ID", "Parent", "Note", "description"),
-        results_cache=af1_sim_fixture.results_cache_path.as_posix(),
-        default_coverage_calls_analysis="funestus",
-        discordant_read_calls_analysis=None,
-    )
-
-
-def case_ag3_sim(ag3_sim_fixture, ag3_sim_api):
-    return ag3_sim_fixture, ag3_sim_api
-
-
-def case_af1_sim(af1_sim_fixture, af1_sim_api):
-    return af1_sim_fixture, af1_sim_api
-
-
-def _check_basic_vcf_structure(output_path, expected_n_variants, expected_sample_ids):
-    assert os.path.exists(output_path)
-
-    opener = gzip.open if output_path.endswith(".gz") else open
-    with opener(output_path, "rt") as f:
-        lines = f.readlines()
-
-    header_lines = [line for line in lines if line.startswith("##")]
-    column_line = [line for line in lines if line.startswith("#CHROM")]
-    data_lines = [line for line in lines if not line.startswith("#")]
-
-    assert header_lines[0].strip() == "##fileformat=VCFv4.3"
-    assert len(column_line) == 1
-
-    col_fields = column_line[0].strip().split("\t")
-    vcf_samples = col_fields[9:]
-    assert list(vcf_samples) == list(expected_sample_ids)
-
-    assert len(data_lines) == expected_n_variants
-
-    for line in data_lines:
-        fields = line.rstrip("\n").split("\t")
-        assert len(fields) == 9 + len(expected_sample_ids)
-        ref, alt = fields[3], fields[4]
-        assert ref == "N"
-        assert alt == "<CNV>"
-
-    return data_lines
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_hmm_to_vcf(fixture, api: CnvVcfExporter, tmp_path):
-    region = random.choice(api.contigs)
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_sets = random.sample(all_sample_sets, min(2, len(all_sample_sets)))
-
-    ds = api.cnv_hmm(region=region, sample_sets=sample_sets, max_coverage_variance=None)
-    n_variants = ds.sizes["variants"]
-    sample_ids = ds["sample_id"].values
-
-    output_path = str(tmp_path / "test_cnv_hmm.vcf")
-    api.cnv_hmm_to_vcf(
-        output_path=output_path,
-        region=region,
-        sample_sets=sample_sets,
-        max_coverage_variance=None,
-    )
-
-    data_lines = _check_basic_vcf_structure(output_path, n_variants, sample_ids)
-
-    # Check positions match.
-    vcf_positions = sorted([int(line.split("\t")[1]) for line in data_lines])
-    ds_positions = sorted(ds["variant_position"].values.tolist())
-    assert vcf_positions == ds_positions
-
-    # Check FORMAT is CN.
-    for line in data_lines:
-        fields = line.rstrip("\n").split("\t")
-        assert fields[8] == "CN"
-        assert fields[7].startswith("END=")
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_coverage_calls_to_vcf(fixture, api: CnvVcfExporter, tmp_path):
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_set = random.choice(all_sample_sets)
-    analysis = random.choice(api.coverage_calls_analysis_ids)
-    region = random.choice(api.contigs)
-
-    ds = api.cnv_coverage_calls(region=region, sample_set=sample_set, analysis=analysis)
-    n_variants = ds.sizes["variants"]
-    sample_ids = ds["sample_id"].values
-
-    output_path = str(tmp_path / "test_cnv_coverage_calls.vcf")
-    api.cnv_coverage_calls_to_vcf(
-        output_path=output_path,
-        region=region,
-        sample_set=sample_set,
-        analysis=analysis,
-    )
-
-    data_lines = _check_basic_vcf_structure(output_path, n_variants, sample_ids)
-
-    ds_ids = [
-        v.decode() if hasattr(v, "decode") else str(v) for v in ds["variant_id"].values
-    ]
-    vcf_ids = [line.split("\t")[2] for line in data_lines]
-    assert sorted(vcf_ids) == sorted(ds_ids)
-
-    for line in data_lines:
-        fields = line.rstrip("\n").split("\t")
-        assert fields[8] == "GT"
-        assert fields[6] in ("PASS", ".")
-        assert "CIPOS=" in fields[7]
-        assert "CIEND=" in fields[7]
-        for sample_val in fields[9:]:
-            assert sample_val in ("0", "1", ".")
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_discordant_read_calls_to_vcf(fixture, api: CnvVcfExporter, tmp_path):
-    contig = random.choice(api.contigs)
-    all_sample_sets = api.sample_sets()["sample_set"].to_list()
-    sample_sets = random.sample(all_sample_sets, min(2, len(all_sample_sets)))
-
-    ds = api.cnv_discordant_read_calls(contigs=contig, sample_sets=sample_sets)
-    n_variants = ds.sizes["variants"]
-    sample_ids = ds["sample_id"].values
-
-    output_path = str(tmp_path / "test_cnv_discordant.vcf")
-    api.cnv_discordant_read_calls_to_vcf(
-        output_path=output_path,
-        contigs=contig,
-        sample_sets=sample_sets,
-    )
-
-    data_lines = _check_basic_vcf_structure(output_path, n_variants, sample_ids)
-
-    for line in data_lines:
-        fields = line.rstrip("\n").split("\t")
-        assert fields[8] == "GT"
-        assert "REGION=" in fields[7]
-        assert "SBM=" in fields[7]
-        assert "EBM=" in fields[7]
-        for sample_val in fields[9:]:
-            assert sample_val in ("0", "1", ".")
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_hmm_to_vcf_overwrite(fixture, api: CnvVcfExporter, tmp_path):
-    region = api.contigs[0]
-    output_path = str(tmp_path / "test_cnv_hmm.vcf")
-
-    api.cnv_hmm_to_vcf(
-        output_path=output_path, region=region, max_coverage_variance=None
-    )
-    mtime_first = os.path.getmtime(output_path)
-
-    # Without overwrite, should return early.
-    api.cnv_hmm_to_vcf(
-        output_path=output_path, region=region, max_coverage_variance=None
-    )
-    assert os.path.getmtime(output_path) == mtime_first
-
-    # With overwrite, file should be rewritten.
-    api.cnv_hmm_to_vcf(
-        output_path=output_path,
-        region=region,
-        max_coverage_variance=None,
-        overwrite=True,
-    )
-    assert os.path.exists(output_path)
-
-
-@parametrize_with_cases("fixture,api", cases=".")
-def test_cnv_hmm_to_vcf_gzip(fixture, api: CnvVcfExporter, tmp_path):
-    region = api.contigs[0]
-    output_path = str(tmp_path / "test_cnv_hmm.vcf.gz")
-
-    api.cnv_hmm_to_vcf(
-        output_path=output_path, region=region, max_coverage_variance=None
-    )
-    assert os.path.exists(output_path)
-
-    with gzip.open(output_path, "rt") as f:
-        first_line = f.readline()
-    assert first_line.strip() == "##fileformat=VCFv4.3"
-
-    # Verify it's specifically valid BGZF, not just plain gzip — what
-    # tools like tabix/bedtools require for .vcf.gz files.
-    if shutil.which("bgzip") is not None:
-        result = subprocess.run(
-            ["bgzip", "-t", output_path], capture_output=True, text=True
-        )
-        assert result.returncode == 0, f"not valid BGZF: {result.stderr}"
diff --git a/tests/test_bgzf.py b/tests/test_bgzf.py
deleted file mode 100644
index 38e8e5d61..000000000
--- a/tests/test_bgzf.py
+++ /dev/null
@@ -1,95 +0,0 @@
-import gzip
-import shutil
-import subprocess
-
-import pytest
-
-from malariagen_data.bgzf import _MAX_BLOCK_UNCOMPRESSED_SIZE, bgzf_open
-
-
-def test_bgzf_round_trip(tmp_path):
-    output_path = str(tmp_path / "test.txt.gz")
-    lines = [f"line {i}\n" for i in range(100)]
-
-    with bgzf_open(output_path, "wt") as f:
-        for line in lines:
-            f.write(line)
-
-    # BGZF is valid gzip, so a plain gzip reader must be able to read
-    # the exact content back.
-    with gzip.open(output_path, "rt") as f:
-        content = f.read()
-    assert content == "".join(lines)
-
-
-def test_bgzf_multi_block_round_trip(tmp_path):
-    # Write enough data to force multiple BGZF blocks, and include
-    # content that lands exactly on, just under, and just over a block
-    # boundary, to exercise the block-splitting logic.
-    output_path = str(tmp_path / "test_multiblock.txt.gz")
-    line = "the quick brown fox jumps over the lazy dog 0123456789\n"
-    n_lines = (_MAX_BLOCK_UNCOMPRESSED_SIZE // len(line)) * 3 + 7
-    expected = "".join(f"{i}:{line}" for i in range(n_lines))
-
-    with bgzf_open(output_path, "wt") as f:
-        for i in range(n_lines):
-            f.write(f"{i}:{line}")
-
-    with gzip.open(output_path, "rt") as f:
-        content = f.read()
-    assert content == expected
-
-
-def test_bgzf_empty_file(tmp_path):
-    # Writing nothing should still produce a valid (if empty) BGZF
-    # file, i.e. just the EOF marker.
-    output_path = str(tmp_path / "test_empty.txt.gz")
-    with bgzf_open(output_path, "wt"):
-        pass
-
-    with gzip.open(output_path, "rt") as f:
-        content = f.read()
-    assert content == ""
-
-
-def test_bgzf_rejects_binary_mode(tmp_path):
-    output_path = str(tmp_path / "test.txt.gz")
-    with pytest.raises(ValueError):
-        bgzf_open(output_path, "wb")
-
-
-@pytest.mark.skipif(shutil.which("bgzip") is None, reason="bgzip not installed")
-def test_bgzf_valid_per_bgzip(tmp_path):
-    # The definitive check: the reference BGZF implementation itself
-    # must accept this as valid BGZF, not just "some gzip stream that
-    # happens to decompress correctly."
-    output_path = str(tmp_path / "test.txt.gz")
-    with bgzf_open(output_path, "wt") as f:
-        for i in range(10_000):
-            f.write(f"line {i}\n")
-
-    result = subprocess.run(
-        ["bgzip", "-t", output_path], capture_output=True, text=True
-    )
-    assert result.returncode == 0, f"not valid BGZF: {result.stderr}"
-
-
-@pytest.mark.skipif(shutil.which("tabix") is None, reason="tabix not installed")
-def test_bgzf_tabix_indexable(tmp_path):
-    # tabix specifically requires genuine BGZF block structure to
-    # build an index at all; plain gzip fails here even though it
-    # decompresses fine. This is the property that made bedtools (and
-    # other BGZF-aware tools) unable to read plain-gzip VCF output
-    # correctly, even though bcftools tolerated it.
-    output_path = str(tmp_path / "test.vcf.gz")
-    with bgzf_open(output_path, "wt") as f:
-        f.write("##fileformat=VCFv4.3\n")
-        f.write("##contig=<ID=2R>\n")
-        f.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
-        for pos in (100, 200, 300):
-            f.write(f"2R\t{pos}\t.\tA\tT\t.\t.\t.\n")
-
-    result = subprocess.run(
-        ["tabix", "-p", "vcf", output_path], capture_output=True, text=True
-    )
-    assert result.returncode == 0, f"tabix failed to index: {result.stderr}"

From f96236f96cdad9a0bf6f2107e745e2d44e7b096f Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Mon, 5 Oct 2026 16:16:22 +0100
Subject: [PATCH 29/38] make site_masks=None default, updated doctring

---
 malariagen_data/anoph/to_vcf.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 5707c8859..50f0e8806 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -102,7 +102,7 @@ def __init__(
 
     @doc(
         summary="""
-            Export SNP calls to Variant Call Format (VCF).
+            Extract SNP calls for sample and export to Variant Call Format (VCF).
         """,
         extended_summary="""
             This function writes SNP calls to a VCF file. Data is written
@@ -117,7 +117,9 @@ def __init__(
             required to select exactly one sample, and must be of the
             form `"sample_id == '<sample_id>'"`. Any other query (e.g.
             selecting samples by cohort, or more than one sample_id) is
-            rejected.
+            rejected. An accompanying tabix-format index file is created
+            in the same location as the VCF output file, with the same name but a
+            `.tbi` suffix.
         """,
         returns="""
         Path to the VCF output file.
@@ -130,7 +132,7 @@ def snp_calls_to_vcf(
         sample_sets: base_params.sample_sets,
         sample_query: base_params.sample_query,
         sample_query_options: Optional[base_params.sample_query_options] = None,
-        site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
+        site_mask: Optional[base_params.site_mask] = None,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         chunks: base_params.chunks = base_params.native_chunks,
         overwrite: plink_params.overwrite = False,

From b018131dc694ce517118dd9889e5a86ec2b4ffb0 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 6 Oct 2026 11:12:47 +0100
Subject: [PATCH 30/38] remove pysam as with it, either Windows install of
 malariagen_data won't work at all, or IGV-related funcitonality will not be
 available to Windows users

---
 malariagen_data/anoph/igv.py     |  39 ++++++-----
 malariagen_data/anoph/to_vcf.py  | 117 ++++++++++++++++++-------------
 notebooks/igv.ipynb              |   4 +-
 poetry.lock                      |  58 ---------------
 pyproject.toml                   |   1 -
 tests/anoph/test_igv.py          |   6 +-
 tests/anoph/test_vcf_exporter.py |  19 +++--
 7 files changed, 112 insertions(+), 132 deletions(-)

diff --git a/malariagen_data/anoph/igv.py b/malariagen_data/anoph/igv.py
index cccf7f877..5958106d4 100644
--- a/malariagen_data/anoph/igv.py
+++ b/malariagen_data/anoph/igv.py
@@ -100,9 +100,6 @@ def _igv_view_alignments_tracks(
         # Locate record for sample.
         cat_rec = df_cat.set_index("sample_id").loc[sample]
         bam_url = cat_rec["alignments_bam"]
-        vcf_url = (
-            snp_vcf_url if snp_vcf_url is not None else cat_rec["snp_genotypes_vcf"]
-        )
 
         # Set up site filters tracks.
         contig = region.contig
@@ -112,17 +109,23 @@ def _igv_view_alignments_tracks(
         )
 
         # Add SNPs track.
-        tracks.append(
-            {
-                "name": "SNPs",
-                "url": vcf_url,
-                "indexURL": f"{vcf_url}.tbi",
-                "format": "vcf",
-                "type": "variant",
-                "visibilityWindow": visibility_window,  # bp
-                "height": 50,
-            }
-        )
+        snp_track = {
+            "name": "SNPs",
+            "format": "vcf",
+            "type": "variant",
+            "visibilityWindow": visibility_window,  # bp
+            "height": 50,
+        }
+        if snp_vcf_url is not None:
+            # A local VCF, e.g. from snp_calls_to_vcf(), has no index, so
+            # IGV loads it in full.
+            snp_track["url"] = snp_vcf_url
+            snp_track["indexed"] = False
+        else:
+            vcf_url = cat_rec["snp_genotypes_vcf"]
+            snp_track["url"] = vcf_url
+            snp_track["indexURL"] = f"{vcf_url}.tbi"
+        tracks.append(snp_track)
 
         # Add alignments track.
         tracks.append(
@@ -187,9 +190,11 @@ def igv(
             """,
             init="If True, call igv_notebook.init().",
             snp_vcf_url="""
-                Optional URL for a local, tabix-indexed VCF. For Jupyter Notebook
-                and Lab, the VCF and its `.tbi` index must be under the Jupyter
-                startup directory tree; pass a URL relative to that tree (e.g.
+                Optional URL for a local VCF, e.g. one written by
+                `snp_calls_to_vcf()`. The VCF is loaded without an index, so it
+                should be small (e.g. a single sample over a region). For Jupyter
+                Notebook and Lab, the VCF must be under the Jupyter startup
+                directory tree; pass a URL relative to that tree (e.g.
                 `/data/sample.vcf.gz`). If omitted, use the catalog VCF.
             """,
         ),
diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 50f0e8806..0f18e6b23 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -9,7 +9,7 @@
 import xarray as xr
 import numpy as np
 from numpydoc_decorator import doc  # type: ignore
-import pysam
+from Bio import bgzf  # type: ignore
 
 from .snp_data import AnophelesSnpData
 from . import base_params
@@ -45,6 +45,17 @@ class VariantChunkData:
     # under the reserved key's declared type.
     "MQ": '##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Mapping Quality">',
 }
+_HEADER_COLUMNS = (
+    "#CHROM",
+    "POS",
+    "ID",
+    "REF",
+    "ALT",
+    "QUAL",
+    "FILTER",
+    "INFO",
+    "FORMAT",
+)
 
 # snp_calls_to_vcf() only supports exporting a single sample at a time
 # (its current use case is generating a per-sample VCF for IGV), so
@@ -54,6 +65,11 @@ class VariantChunkData:
 )
 
 
+def _format_int(value) -> str:
+    # Negative values are missing data.
+    return "." if value < 0 else str(int(value))
+
+
 def _validate_single_sample_selection(
     *,
     sample_sets: base_params.sample_sets,
@@ -107,8 +123,9 @@ def __init__(
         extended_summary="""
             This function writes SNP calls to a VCF file. Data is written
             in chunks to avoid loading the entire genotype matrix into
-            memory. Output is BGZF-compressed and tabix-indexed; the
-            `output_path` must end with `.vcf.gz`.
+            memory. Output is BGZF-compressed; the `output_path` must end
+            with `.vcf.gz`. No index is created, so the output is intended
+            to be small enough to load in full (e.g. by IGV).
 
             `sample_sets` and `sample_query` are both required: a VCF is
             only meaningful with respect to an explicit sample basis for
@@ -117,9 +134,7 @@ def __init__(
             required to select exactly one sample, and must be of the
             form `"sample_id == '<sample_id>'"`. Any other query (e.g.
             selecting samples by cohort, or more than one sample_id) is
-            rejected. An accompanying tabix-format index file is created
-            in the same location as the VCF output file, with the same name but a
-            `.tbi` suffix.
+            rejected.
         """,
         returns="""
         Path to the VCF output file.
@@ -143,8 +158,7 @@ def snp_calls_to_vcf(
         )
         if not output_path.endswith(".vcf.gz"):
             raise ValueError(
-                "output_path must end with .vcf.gz: "
-                "BGZF compression and tabix indexing require this suffix."
+                "output_path must end with .vcf.gz: output is BGZF-compressed."
             )
 
         # Validate fields parameter.
@@ -162,8 +176,6 @@ def snp_calls_to_vcf(
         fields = tuple(f for f in _FIELD_ORDER if f in fields)
 
         if os.path.exists(output_path) and not overwrite:
-            if not os.path.exists(output_path + ".tbi"):
-                pysam.tabix_index(output_path, preset="vcf")
             return output_path
 
         ds = self.snp_calls(
@@ -198,20 +210,23 @@ def snp_calls_to_vcf(
         include_gq = "GQ" in fields
         include_ad = "AD" in fields
         include_mq = "MQ" in fields
-        header = pysam.VariantHeader()
-        for header_record in list(header.records):
-            if header_record.key in {"fileformat", "FILTER"}:
-                header_record.remove()
-        header.add_meta("fileformat", value="VCFv4.3")
-        header.add_meta("fileDate", value=date.today().strftime("%Y%m%d"))
-        header.add_meta("source", value="malariagen_data")
-        for contig in contigs:
-            header.contigs.add(str(contig))
-        for field in fields:
-            header.add_line(_FORMAT_HEADERS[field])
-        header.add_sample(sample_id)
-
-        with pysam.VariantFile(output_path, mode="w", header=header) as f:
+        format_str = ":".join(fields)
+
+        header_lines = [
+            "##fileformat=VCFv4.3",
+            '##FILTER=<ID=PASS,Description="All filters passed">',
+            f"##fileDate={date.today().strftime('%Y%m%d')}",
+            "##source=malariagen_data",
+        ]
+        header_lines += [f"##contig=<ID={contig}>" for contig in contigs]
+        header_lines += [_FORMAT_HEADERS[field] for field in fields]
+        header_lines.append("\t".join(_HEADER_COLUMNS + (sample_id,)))
+
+        # BGZF is valid gzip, and is the block-compressed variant that
+        # genomics tools (e.g. IGV, bcftools) expect for .vcf.gz files.
+        with bgzf.BgzfWriter(output_path, "wb") as f:
+            f.write(("\n".join(header_lines) + "\n").encode())
+
             # Extract dask arrays.
             gt_data = ds["call_genotype"].data
             pos_data = ds["variant_position"].data
@@ -238,6 +253,7 @@ def snp_calls_to_vcf(
                         optional_arrays,
                     )
 
+                    lines = []
                     for j in range(variant_chunk_data.gt_chunk.shape[0]):
                         genotype_data = variant_chunk_data.gt_chunk[j, 0]
                         if np.array_equal(genotype_data, (0, 0)):
@@ -256,52 +272,57 @@ def snp_calls_to_vcf(
                             if s:
                                 alt_alleles.append(s)
 
-                        genotype: tuple[Optional[int], ...]
                         if np.any(genotype_data < 0):
-                            genotype = (None,) * len(genotype_data)
+                            gt = "/".join("." for _ in genotype_data)
                         else:
-                            genotype = tuple(int(allele) for allele in genotype_data)
-
-                        record = header.new_record(
-                            contig=str(chrom),
-                            start=pos - 1,
-                            alleles=(ref, *alt_alleles),
-                        )
-                        sample = record.samples[sample_id]
-                        sample["GT"] = genotype
+                            gt = "/".join(str(int(allele)) for allele in genotype_data)
+                        sample_values = [gt]
                         # GQ.
                         if include_gq:
                             if variant_chunk_data.gq_chunk is not None:
-                                value = variant_chunk_data.gq_chunk[j, 0]
-                                sample["GQ"] = None if value < 0 else int(value)
+                                sample_values.append(
+                                    _format_int(variant_chunk_data.gq_chunk[j, 0])
+                                )
                             else:
-                                sample["GQ"] = None
+                                sample_values.append(".")
                         # AD.
                         if include_ad:
                             if variant_chunk_data.ad_chunk is not None:
                                 ad_values = variant_chunk_data.ad_chunk[j, 0]
-                                sample["AD"] = tuple(
-                                    None if value < 0 else int(value)
-                                    for value in ad_values
+                                sample_values.append(
+                                    ",".join(_format_int(value) for value in ad_values)
                                 )
                             else:
-                                sample["AD"] = None
+                                sample_values.append(".")
                         # MQ. Rounded to the nearest integer: the
                         # underlying data is a float, but the VCF spec
                         # fixes the reserved FORMAT/MQ key as Integer.
                         if include_mq:
                             if variant_chunk_data.mq_chunk is not None:
                                 value = variant_chunk_data.mq_chunk[j, 0]
-                                sample["MQ"] = (
-                                    None
+                                sample_values.append(
+                                    "."
                                     if math.isnan(value) or value < 0
-                                    else round(value)
+                                    else str(round(float(value)))
                                 )
                             else:
-                                sample["MQ"] = None
-                        f.write(record)
+                                sample_values.append(".")
+
+                        record = (
+                            str(chrom),
+                            str(pos),
+                            ".",
+                            ref,
+                            ",".join(alt_alleles) or ".",
+                            ".",
+                            ".",
+                            ".",
+                            format_str,
+                            ":".join(sample_values),
+                        )
+                        lines.append("\t".join(record) + "\n")
+                    f.write("".join(lines).encode())
 
-        pysam.tabix_index(output_path, preset="vcf", force=True)
         return output_path
 
     def _get_chunks(
diff --git a/notebooks/igv.ipynb b/notebooks/igv.ipynb
index b7fc56328..d584f04ae 100644
--- a/notebooks/igv.ipynb
+++ b/notebooks/igv.ipynb
@@ -205,8 +205,8 @@
    "id": "17",
    "metadata": {},
    "source": [
-    "## Local tabix-indexed VCF in IGV\n",
-    "This exports one sample to a BGZF VCF and `.tbi` under the notebook working directory, then loads it as the SNP track. Both files must be inside the Jupyter server startup directory tree. The `snp_vcf_url` below assumes the server was started from the workspace root; if it was started from `notebooks/`, use the alternate URL shown in the code cell."
+    "## Local VCF in IGV\n",
+    "This exports one sample over a region to a BGZF-compressed VCF under the notebook working directory, then loads it as the SNP track. No index is created, so IGV loads the whole file; keep the region small. The file must be inside the Jupyter server startup directory tree. The `snp_vcf_url` below assumes the server was started from the workspace root; if it was started from `notebooks/`, use the alternate URL shown in the code cell."
    ]
   },
   {
diff --git a/poetry.lock b/poetry.lock
index a91246179..a1b7f41ac 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -4631,59 +4631,6 @@ files = [
 [package.extras]
 windows-terminal = ["colorama (>=0.4.6)"]
 
-[[package]]
-name = "pysam"
-version = "0.24.1"
-description = "Package for reading, manipulating, and writing genomic data"
-optional = false
-python-versions = ">=3.9"
-groups = ["main"]
-files = [
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-    {file = "pysam-0.24.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:f842fc7638b8acccd5e470820cff3f490c5845e616fa668667531da22b686a7b"},
-    {file = "pysam-0.24.1-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:f3abec4f08929c5090f747975787febe7db437bad34349f29c8e0328d6f9ad06"},
-    {file = "pysam-0.24.1-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:9e601c4626e7310db74823a4152483bf903392ff1d30eec619594808280da699"},
-    {file = "pysam-0.24.1-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:84c80a7d3475e675d142a850ff3ea0d4a929e698130f01323f1a550a0e13cc27"},
-    {file = "pysam-0.24.1-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:10cc2b840ef651be8c7087d7c0c9c51e220162eae1e5ad68b6ccf427594357fc"},
-    {file = "pysam-0.24.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:0f1bdd44bcd85d8562925436bec24dcf7325e4001575a9c24d58806b93de2293"},
-    {file = "pysam-0.24.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:0e48e4b3d341734078e97fe05a2358d60837ca88741625ec17d45ba7c629dc64"},
-    {file = "pysam-0.24.1-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:c21dd9b801175d14c4d7b78898de921f8771edf141db5957226c9bf1ed4bf293"},
-    {file = "pysam-0.24.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:050d4c72211a961d26fad70b655694d4d500422e4b7d0ed3c7f244c49df8d16e"},
-    {file = "pysam-0.24.1-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:8696e88156edee884416fd50c15fcc61da67089232198c1ae731731f6da765d6"},
-    {file = "pysam-0.24.1-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:f34eba531bdfd71817110a56c00443f9947d3a01e10358f341d10f614ea3bf1e"},
-    {file = "pysam-0.24.1-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:1d114ddd64b562d2fe253a31703613b762c71b4a3d856ac960a39e40269c51fa"},
-    {file = "pysam-0.24.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:ceb448961fd35b5b90795d7c7c80b1b35592be7ae0127e28187e3f41c27e035b"},
-    {file = "pysam-0.24.1-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:39914c2e395be44126e120be0933aaea3ea1d664f3c421a91afc4be086b49a79"},
-    {file = "pysam-0.24.1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:06eabdc8f7c3894b73d2c4365ea6197d6ba5308e203dd2887b5df635fe6e249b"},
-    {file = "pysam-0.24.1-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:2c03ca38923941e460a5edc62d9208393ee9083ecd3f57a3e5a96c1337112dc7"},
-    {file = "pysam-0.24.1-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:2fbbcd9ccad9627e6b9a46bbb93e0a244c137ecaa6d7d471033f9b75bc17e6e0"},
-    {file = "pysam-0.24.1-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:c7e756b8a9da0f04f6e1ccaad611513f6d52e622b1ae03dcace76af3722100a9"},
-    {file = "pysam-0.24.1-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:a52f12c808e53fd16c7f3c42d95914a9d5084a5504f3c32a5138ba08bdfa8408"},
-    {file = "pysam-0.24.1-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:817624cb93fc2373bf3d3e7298a59db88323308b25fcdfd19a0a4df6f119e8dd"},
-    {file = "pysam-0.24.1-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:68b742b2db84cf3982c21be69f886baf3d3cb49fbb070cb4a4c09b4d2fc907c0"},
-    {file = "pysam-0.24.1-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:fdb008b9dfe673ec029189f6394b2d60ce1380ee387c106e799ada237809b2ee"},
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-    {file = "pysam-0.24.1-cp314-cp314-macosx_10_15_x86_64.whl", hash = "sha256:ec95cc0c4a4fbea432066d9d8e2f566ab4e1e11b4a4bb70b2143ed5b9f2fbf3b"},
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-    {file = "pysam-0.24.1-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:9598dd5a571c5c8b4383b4fe1a27823d72b3261c5299100cf3d88dfb09b45019"},
-    {file = "pysam-0.24.1-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:25ffcc2aca0a49358c02e666ddd789afe701c5cf320dcb894ac22ede7347049f"},
-    {file = "pysam-0.24.1-cp314-cp314-musllinux_1_2_aarch64.whl", hash = "sha256:e520b7311e3822ce029adaf24472e563e724cec442314c6c702956e242dc27d4"},
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-    {file = "pysam-0.24.1-cp315-cp315-macosx_10_15_x86_64.whl", hash = "sha256:1527e9fcfbdbc72d8bf3e06970cca229a041eefe36a30bf14997f52c1f29ccf6"},
-    {file = "pysam-0.24.1-cp315-cp315-macosx_11_0_arm64.whl", hash = "sha256:886f5c1a2a45b174345c217c821cbd4231311d43ecf5e8157cc7a4bee5db182a"},
-    {file = "pysam-0.24.1-cp315-cp315-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:57d7921761ce2b902711e55857f861733b909155fb6299b5559da4a20a353eeb"},
-    {file = "pysam-0.24.1-cp315-cp315-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:7a22778002a2a401374733dc5698bc3552ff0a6c43d27aeaf37976048bd3d867"},
-    {file = "pysam-0.24.1-cp315-cp315-musllinux_1_2_aarch64.whl", hash = "sha256:15dca5345f67b622dfb303ed5328e13799ffc13df12407a6d4542caab5a6ffb1"},
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-    {file = "pysam-0.24.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:0b4b1fec32675cfb992cd6c23e0fbf86481f695959e3973e00c9c1432c78d801"},
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-    {file = "pysam-0.24.1-cp39-cp39-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:a222fb89c91c8acdbe4e77f233c9ee1b9ab2e832afae49797ddefedfbb3191a3"},
-    {file = "pysam-0.24.1-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:d5fd6fbd19fa0f833f0e7f02ce16e99679b58fbe311b818fb7ddac2a6a435eef"},
-    {file = "pysam-0.24.1-cp39-cp39-musllinux_1_2_aarch64.whl", hash = "sha256:1f672fc17990d395d658e191b57c681bd101ae7b4825446a6938fc9ddb797630"},
-    {file = "pysam-0.24.1-cp39-cp39-musllinux_1_2_x86_64.whl", hash = "sha256:b8281b79e8b989c224ba0a7de41d06a47c38a0767f1efdfa2cbff1cee86deb6a"},
-    {file = "pysam-0.24.1.tar.gz", hash = "sha256:90f612afccdb454d2447ecb5229266c6e7f991093deed4ed0a791db01f7fc994"},
-]
-
 [[package]]
 name = "pytest"
 version = "8.4.2"
@@ -6590,10 +6537,5 @@ test = ["pytest", "pytest-cases", "pytest-cov", "pytest-mock", "pytest-xdist"]
 
 [metadata]
 lock-version = "2.1"
-<<<<<<< HEAD
-python-versions = ">=3.10,<3.13"
-content-hash = "e850038fc2366ed56556f41e363264d87030fc3489e6372a6ab7b26acd1a804e"
-=======
 python-versions = ">=3.10,<3.14"
 content-hash = "467eb9c7c1811697036da4aa4c78df66b69178cf25a3a0bb015808eec5621d6f"
->>>>>>> master
diff --git a/pyproject.toml b/pyproject.toml
index b9c18b7e3..0cd916ed5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -105,7 +105,6 @@ BioPython = "*"
 scikit-allel = ">=1.3.13"
 xarray = "*"
 plotly = "*"
-pysam = ">=0.22.0"
 # https://github.com/malariagen/malariagen-data-python/issues/845
 # https://github.com/malariagen/malariagen-data-python/issues/734
 # https://github.com/malariagen/malariagen-data-python/issues/743
diff --git a/tests/anoph/test_igv.py b/tests/anoph/test_igv.py
index 8aaa1eef1..84cda5cf3 100644
--- a/tests/anoph/test_igv.py
+++ b/tests/anoph/test_igv.py
@@ -130,9 +130,13 @@ def wgs_data_catalog(self, sample_set):
 
     snp_track = next(track for track in captured["tracks"] if track["name"] == "SNPs")
     assert snp_track["url"] == local_vcf_url
-    assert snp_track["indexURL"] == f"{local_vcf_url}.tbi"
+    # A local VCF has no index, so IGV must load it in full.
+    assert snp_track["indexed"] is False
+    assert "indexURL" not in snp_track
 
     captured.clear()
     api.view_alignments(region="2L:1-10", sample="S1", init=False)
     snp_track = next(track for track in captured["tracks"] if track["name"] == "SNPs")
     assert snp_track["url"] == "https://example.org/S1.vcf.gz"
+    assert snp_track["indexURL"] == "https://example.org/S1.vcf.gz.tbi"
+    assert "indexed" not in snp_track
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index 450a8ca97..bdbf18a63 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -6,9 +6,9 @@
 
 import dask.array as da
 import numpy as np
-import pysam
 import pytest
 import xarray as xr
+from Bio import bgzf  # type: ignore
 from pytest_cases import parametrize_with_cases
 
 from malariagen_data import af1 as _af1
@@ -328,9 +328,8 @@ def test_vcf_exporter_overwrite(fixture, api: SnpVcfExporter, tmp_path):
         overwrite=True,
     )
     assert os.path.exists(output_path)
-    assert os.path.exists(output_path + ".tbi")
-    with pysam.VariantFile(output_path) as vcf:
-        list(vcf.fetch())
+    with bgzf.BgzfReader(output_path, "rt") as f:
+        assert f.readline().strip() == "##fileformat=VCFv4.3"
 
 
 @parametrize_with_cases("fixture,api", cases=".")
@@ -358,7 +357,17 @@ def test_vcf_exporter_gzip(fixture, api: SnpVcfExporter, tmp_path):
     # Verify it's specifically valid BGZF, not just plain gzip: this is
     # what tools like tabix/bedtools require for .vcf.gz files, and
     # what distinguishes genuine BGZF from a plain gzip stream that
-    # happens to decompress fine but isn't block-structured.
+    # happens to decompress fine but isn't block-structured. IGV also
+    # relies on the "BC" extra subfield to decompress every block.
+    with open(output_path, "rb") as f:
+        data = f.read()
+    assert data[12:14] == b"BC", "missing BGZF extra subfield"
+    assert data.endswith(bgzf._bgzf_eof), "missing BGZF EOF marker"
+    with bgzf.BgzfReader(output_path, "rt") as f:
+        bgzf_text = "".join(iter(lambda: f.read(65536), ""))
+    with gzip.open(output_path, "rt") as f:
+        assert f.read() == bgzf_text
+
     if shutil.which("bgzip") is not None:
         result = subprocess.run(
             ["bgzip", "-t", output_path], capture_output=True, text=True

From ba281e1ee8662e88e5c1695f096e0695f4d3e8f3 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 6 Oct 2026 13:50:27 +0100
Subject: [PATCH 31/38] slight changes after running pytest with coverage

---
 malariagen_data/anoph/to_vcf.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 0f18e6b23..d05915b40 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -29,9 +29,7 @@ class VariantChunkData:
 
 
 # Supported FORMAT fields, the fixed order in which their values are
-# always written per sample (regardless of what order the caller's
-# `fields` argument happens to iterate in — e.g. a set has no
-# guaranteed order at all), and their VCF header definitions.
+# always written per sample , and their VCF header definitions.
 _VALID_FIELDS = {"GT", "GQ", "AD", "MQ"}
 _FIELD_ORDER = ("GT", "GQ", "AD", "MQ")
 _FORMAT_HEADERS = {
@@ -41,8 +39,7 @@ class VariantChunkData:
     # N.B., "MQ" is a reserved FORMAT key in the VCF specification,
     # fixed there as Integer, Number=1 — even though the underlying
     # data is a float (RMS mapping quality), so values are rounded to
-    # the nearest integer when written below to stay spec-compliant
-    # under the reserved key's declared type.
+    # the nearest integer
     "MQ": '##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Mapping Quality">',
 }
 _HEADER_COLUMNS = (

From 96f059064e36fbe35e6245d3e8286a454b7cfd81 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 6 Oct 2026 14:12:35 +0100
Subject: [PATCH 32/38] added some extra tests

---
 tests/anoph/test_vcf_exporter.py | 141 ++++++++++++++++++++++++-------
 1 file changed, 112 insertions(+), 29 deletions(-)

diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index bdbf18a63..ed4edb606 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -81,6 +81,40 @@ def _pick_single_sample_query(api: SnpVcfExporter, sample_sets):
     return sample_id, sample_query
 
 
+def _synthetic_snp_calls(sample, contig, call_genotype, positions):
+    """Build a small single-sample SNP calls dataset, with REF "A" and
+    ALT "C,T,G" at every site and no GQ, AD or MQ arrays."""
+    n_variants = len(positions)
+    variant_allele = np.array(
+        [[b"A", b"C", b"T", b"G"]] * n_variants,
+        dtype="S1",
+    )
+    return xr.Dataset(
+        data_vars={
+            "call_genotype": (
+                ["variants", "samples", "ploidy"],
+                da.from_array(call_genotype, chunks=(n_variants, 1, 2)),
+            ),
+            "variant_allele": (
+                ["variants", "alleles"],
+                da.from_array(variant_allele, chunks=(n_variants, 4)),
+            ),
+        },
+        coords={
+            "variant_position": (
+                "variants",
+                da.from_array(np.array(positions), chunks=n_variants),
+            ),
+            "variant_contig": (
+                "variants",
+                da.from_array(np.zeros(n_variants, dtype="u1"), chunks=n_variants),
+            ),
+            "sample_id": ("samples", np.array([sample])),
+        },
+        attrs={"contigs": (contig,)},
+    )
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter(fixture, api: SnpVcfExporter, tmp_path):
     region = random.choice(api.contigs)
@@ -522,6 +556,83 @@ def test_vcf_exporter_fields_gt_required(fixture, api: SnpVcfExporter, tmp_path)
         )
 
 
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_fields_unknown(fixture, api: SnpVcfExporter, tmp_path):
+    region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
+    output_path = str(tmp_path / "test_unknown_field.vcf.gz")
+
+    with pytest.raises(ValueError, match="Unknown FORMAT fields"):
+        api.snp_calls_to_vcf(
+            output_path=output_path,
+            region=region,
+            sample_sets=sample_sets,
+            sample_query=sample_query,
+            fields=("GT", "DP"),
+        )
+
+
+@pytest.mark.parametrize("filename", ["test.vcf", "test.vcf.bgz", "test.gz"])
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_output_path_suffix(
+    fixture, api: SnpVcfExporter, tmp_path, filename
+):
+    region = api.contigs[0]
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = [all_sample_sets[0]]
+    _, sample_query = _pick_single_sample_query(api, sample_sets)
+    output_path = str(tmp_path / filename)
+
+    with pytest.raises(ValueError, match="must end with .vcf.gz"):
+        api.snp_calls_to_vcf(
+            output_path=output_path,
+            region=region,
+            sample_sets=sample_sets,
+            sample_query=sample_query,
+        )
+    assert not os.path.exists(output_path)
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_vcf_exporter_missing_optional_fields(
+    fixture, api: SnpVcfExporter, tmp_path, monkeypatch
+):
+    # If GQ, AD or MQ are requested but the dataset has no such array,
+    # the FORMAT column still lists them and their values are written
+    # as missing (".").
+    sample = str(api.sample_metadata()["sample_id"].iloc[0])
+    contig = api.contigs[0]
+    call_genotype = np.array([[[0, 1]], [[-1, -1]], [[2, 2]]], dtype="i1")
+    ds = _synthetic_snp_calls(sample, contig, call_genotype, [100, 200, 300])
+    monkeypatch.setattr(api, "snp_calls", lambda **kwargs: ds)
+
+    output_path = str(tmp_path / "test_missing_optional.vcf.gz")
+    api.snp_calls_to_vcf(
+        output_path=output_path,
+        region=contig,
+        sample_sets=["dummy"],
+        sample_query=f"sample_id == '{sample}'",
+        fields=("GT", "GQ", "AD", "MQ"),
+    )
+
+    with gzip.open(output_path, "rt") as f:
+        lines = f.readlines()
+    data_lines = [line for line in lines if not line.startswith("#")]
+
+    written = {}
+    for line in data_lines:
+        fields_row = line.strip().split("\t")
+        assert fields_row[8] == "GT:GQ:AD:MQ"
+        written[int(fields_row[1])] = fields_row[9]
+    assert written == {
+        100: "0/1:.:.:.",
+        200: "./.:.:.:.",
+        300: "2/2:.:.:.",
+    }
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_vcf_exporter_synthetic_genotypes(
     fixture, api: SnpVcfExporter, tmp_path, monkeypatch
@@ -533,10 +644,6 @@ def test_vcf_exporter_synthetic_genotypes(
     sample = str(api.sample_metadata()["sample_id"].iloc[0])
     contig = api.contigs[0]
 
-    variant_allele = np.array(
-        [[b"A", b"C", b"T", b"G"]] * 5,
-        dtype="S1",
-    )
     call_genotype = np.array(
         [
             [[0, 1]],  # het
@@ -555,31 +662,7 @@ def test_vcf_exporter_synthetic_genotypes(
         500: "2/2",
     }
 
-    n_variants = len(positions)
-    ds = xr.Dataset(
-        data_vars={
-            "call_genotype": (
-                ["variants", "samples", "ploidy"],
-                da.from_array(call_genotype, chunks=(n_variants, 1, 2)),
-            ),
-            "variant_allele": (
-                ["variants", "alleles"],
-                da.from_array(variant_allele, chunks=(n_variants, 4)),
-            ),
-        },
-        coords={
-            "variant_position": (
-                "variants",
-                da.from_array(np.array(positions), chunks=n_variants),
-            ),
-            "variant_contig": (
-                "variants",
-                da.from_array(np.zeros(n_variants, dtype="u1"), chunks=n_variants),
-            ),
-            "sample_id": ("samples", np.array([sample])),
-        },
-        attrs={"contigs": (contig,)},
-    )
+    ds = _synthetic_snp_calls(sample, contig, call_genotype, positions)
     monkeypatch.setattr(api, "snp_calls", lambda **kwargs: ds)
 
     output_path = str(tmp_path / "test_synthetic.vcf.gz")

From a18921d62138ffd0151cdeb099d6b0eaf18ed207 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 6 Oct 2026 15:17:44 +0100
Subject: [PATCH 33/38] ran pre-commit run --all-files

---
 notebooks/auto_chunks.ipynb                 |  49 +-
 notebooks/biallelic_snps.ipynb              |  49 +-
 notebooks/cohort_geometries.ipynb           |   4 +-
 notebooks/extra_metadata.ipynb              |  33 +-
 notebooks/karyotype.ipynb                   |  58 +-
 notebooks/ld_pruning.ipynb                  |  39 +-
 notebooks/local_cluster.ipynb               |  27 +-
 notebooks/phenotype_data_demo.ipynb         | 862 +-------------------
 notebooks/plink_convert.ipynb               |   4 +-
 notebooks/plot_aims.ipynb                   |  25 +-
 notebooks/plot_cnv.ipynb                    |  63 +-
 notebooks/plot_diplotype_clustering.ipynb   |  59 +-
 notebooks/plot_diversity.ipynb              |  37 +-
 notebooks/plot_frequencies_heatmap.ipynb    |  79 +-
 notebooks/plot_frequencies_space_time.ipynb | 786 ++----------------
 notebooks/plot_fst_gwss.ipynb               |  33 +-
 notebooks/plot_g123_gwss.ipynb              |  43 +-
 notebooks/plot_genes.ipynb                  | 119 +--
 notebooks/plot_h12_h1x.ipynb                |  65 +-
 notebooks/plot_haplotype_clustering.ipynb   |  61 +-
 notebooks/plot_haplotype_networks.ipynb     |  61 +-
 notebooks/plot_haplotypes_frequencies.ipynb |  24 +-
 notebooks/plot_heterozygosity.ipynb         |  37 +-
 notebooks/plot_ihs_gwss.ipynb               |  31 +-
 notebooks/plot_njt.ipynb                    |  59 +-
 notebooks/plot_pairwise_average_fst.ipynb   |  42 +-
 notebooks/plot_pca.ipynb                    | 119 ++-
 notebooks/plot_samples.ipynb                |  13 +-
 notebooks/plot_snps.ipynb                   |  53 +-
 notebooks/plot_xpehh_gwss.ipynb             |  33 +-
 notebooks/profiling/gh498.ipynb             |  20 +-
 notebooks/repr.ipynb                        |  25 +-
 notebooks/spike_sim_test_data.ipynb         |  11 +-
 33 files changed, 629 insertions(+), 2394 deletions(-)

diff --git a/notebooks/auto_chunks.ipynb b/notebooks/auto_chunks.ipynb
index 291f7318b..5ca68310e 100644
--- a/notebooks/auto_chunks.ipynb
+++ b/notebooks/auto_chunks.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5ba32f43-2308-43a0-9849-489d77a2f841",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8015add7-81c7-42bd-94c3-a433047c6ca2",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fe297aa9-cfe2-40e5-aa18-3f3a082cdd34",
+   "id": "2",
    "metadata": {},
    "source": [
     "## Default chunk sizes"
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27c25fb3-ad5c-4652-bf6c-c51d07558790",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -45,7 +45,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0dbaca2c-d4f0-44c9-b5c8-a992e52dc476",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f149f390-8e34-42c0-aaa5-7cfe3bbd4c6c",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -64,7 +64,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8c1a6207-29bb-4ef9-a8a0-4c6a20acda3c",
+   "id": "6",
    "metadata": {},
    "source": [
     "## Explicit chunk sizes"
@@ -73,7 +73,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5cbedcb4-cf4e-4f5b-9f0a-901e6abb7dd6",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -87,7 +87,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "05598e4a-f362-4b21-a601-9968619135a4",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -97,7 +97,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b903fb3a-1f17-403a-bf8b-43623148ffaa",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -106,7 +106,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "497bd930-c0a1-4ab9-9f56-874673420fbd",
+   "id": "10",
    "metadata": {},
    "source": [
     "## Auto chunk sizes"
@@ -115,7 +115,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9238bb0f-739e-428b-b4f4-9797b15e045b",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -125,7 +125,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8c894749-6486-478d-9f83-0849aa8a62f2",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -135,7 +135,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f9caefda-4adf-4836-bae4-f7b7bedf8e86",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144,7 +144,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "84bd96e2-42d3-402b-9bca-e071802cb53e",
+   "id": "14",
    "metadata": {},
    "source": [
     "## ND auto chunk sizes"
@@ -153,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a7f5c439-505f-44c0-abfb-05999e4d9759",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,7 +163,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6b2e3c60-5d05-445b-91fc-da5115b190bb",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -173,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "92c9edab-9653-438c-990a-0bffeb81d5fe",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -183,7 +183,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "04e2f86c-bd3d-4bc1-9142-4f1d243ddbd7",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -191,7 +191,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -204,15 +203,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/biallelic_snps.ipynb b/notebooks/biallelic_snps.ipynb
index e4ebef4fc..fb1b784e9 100644
--- a/notebooks/biallelic_snps.ipynb
+++ b/notebooks/biallelic_snps.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "890ed13a-3e8e-4fd6-b0cb-464e31ab5f64",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42ecae20-46b7-4218-a37c-e96df62241fb",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -31,7 +31,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9151e470-bdbe-4eee-902c-6178b5f6b62f",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9cb9bfcb-19b5-40e1-bd2b-11a8c2247af3",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -52,7 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "489c3941-1ae6-4954-ae48-585823b46649",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8b024a95-6f9d-4371-95bb-eb6887481a6a",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -78,7 +78,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "787973c4-1974-4c8e-8b57-e82b4ea90e6a",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -89,7 +89,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "34dfc71b-4e81-4083-8c8a-c08d712e2fa3",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -99,7 +99,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29e17deb-830f-4f5a-9e5f-4707a6041743",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -110,7 +110,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42afc05c-045e-47c8-925a-9df3676ad0fc",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +120,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c419ef30-504f-4e8b-8b77-6b15fa29ccb5",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -131,7 +131,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "489878b8-eb77-41b8-8b1d-cf6f5035877d",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,7 +142,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ef087212-fef9-45da-a797-00be884887a2",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -160,7 +160,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "52d0e6c9-b994-4dd9-91b6-00c58af1ee3b",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -170,7 +170,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b8b26acb-c6c5-4c92-9831-a8a276c952f3",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -181,7 +181,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "87cdfec5-ca1e-4139-91fa-93506a112b1a",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -200,7 +200,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c83b492b-11ec-400b-bceb-de6630c34a7b",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -210,7 +210,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "07f75f48-bf25-4491-8891-77765867e9a0",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -221,7 +221,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9e434252-0c77-4a5d-ac76-55c87c84fd94",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -229,7 +229,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -242,15 +241,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/cohort_geometries.ipynb b/notebooks/cohort_geometries.ipynb
index fc8e24a27..4c690099b 100644
--- a/notebooks/cohort_geometries.ipynb
+++ b/notebooks/cohort_geometries.ipynb
@@ -101,13 +101,11 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
   "language_info": {
-   "name": "python",
-   "version": "3.10.0"
+   "name": "python"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/extra_metadata.ipynb b/notebooks/extra_metadata.ipynb
index c75b619f0..69b65a87a 100644
--- a/notebooks/extra_metadata.ipynb
+++ b/notebooks/extra_metadata.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38bb6b32",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "142627af",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -29,7 +29,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e1634546",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -40,7 +40,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5e6e7edd",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -58,7 +58,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "140cd606",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3f507df0",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -78,7 +78,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "47a85795",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -88,7 +88,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d51ae27a",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -98,7 +98,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c13b4e5a",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "171ad0ce",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +120,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "450d0e1f",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -128,7 +128,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -141,15 +140,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/karyotype.ipynb b/notebooks/karyotype.ipynb
index 857d560ca..ff5ce5f56 100644
--- a/notebooks/karyotype.ipynb
+++ b/notebooks/karyotype.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "95754202-48fb-40fb-8630-8de938cd90a8",
+   "id": "0",
    "metadata": {
     "tags": []
    },
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0913ba40-7f43-4f3e-8405-f2c3efae65be",
+   "id": "1",
    "metadata": {
     "tags": []
    },
@@ -32,7 +32,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d65aea9d-953c-47ad-838e-cf205822b6c8",
+   "id": "2",
    "metadata": {
     "tags": []
    },
@@ -44,7 +44,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a8b1f82f-a60a-4326-a105-a7fd169ed85e",
+   "id": "3",
    "metadata": {
     "tags": []
    },
@@ -62,7 +62,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "35e8569a-5e2c-450d-ad8a-283de669aa27",
+   "id": "4",
    "metadata": {},
    "source": [
     "## 2La"
@@ -71,7 +71,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b7556095-b24a-4a26-9a3a-c98cb14d2e24",
+   "id": "5",
    "metadata": {
     "tags": []
    },
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4a16ebf5-1a66-4b10-9f5a-d57080e26cb7",
+   "id": "6",
    "metadata": {
     "tags": []
    },
@@ -102,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8cb4d566-fde1-42e7-a7ba-7294b6adbb66",
+   "id": "7",
    "metadata": {
     "tags": []
    },
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b522c176-da60-4a4b-ad01-5de74c2a49a6",
+   "id": "8",
    "metadata": {
     "tags": []
    },
@@ -128,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0daf1c4e-4e19-43e6-ac9b-b4e0680a01a8",
+   "id": "9",
    "metadata": {
     "tags": []
    },
@@ -140,7 +140,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f7054916-64b8-4b52-a624-1f4eae413b09",
+   "id": "10",
    "metadata": {
     "tags": []
    },
@@ -151,7 +151,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "32a8664a-67c7-48c8-9870-43f5ec2777ff",
+   "id": "11",
    "metadata": {},
    "source": [
     "## 2Rb"
@@ -160,7 +160,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8d7dc314-9bae-487e-9078-0bf0dec42d9c",
+   "id": "12",
    "metadata": {
     "tags": []
    },
@@ -173,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3a131e26-730a-479d-acaf-735ea92ec93f",
+   "id": "13",
    "metadata": {
     "tags": []
    },
@@ -191,7 +191,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b728fe52-cae6-4c22-9429-52f3d30d475a",
+   "id": "14",
    "metadata": {
     "tags": []
    },
@@ -205,7 +205,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b674c67a-f4fc-471a-a9d0-08f45e9006e9",
+   "id": "15",
    "metadata": {
     "tags": []
    },
@@ -216,7 +216,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "51595e8d-d911-4f7f-932b-ed1007fa95fd",
+   "id": "16",
    "metadata": {},
    "source": [
     "## 2Rc_gam"
@@ -225,7 +225,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3091fec6-6484-4c76-9078-f78fc988ae28",
+   "id": "17",
    "metadata": {
     "tags": []
    },
@@ -242,7 +242,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "da7cd248-2a43-412c-99cf-22ca9786cf2b",
+   "id": "18",
    "metadata": {
     "tags": []
    },
@@ -256,7 +256,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f5a08876-0431-4190-87bb-48962fd4c98c",
+   "id": "19",
    "metadata": {
     "tags": []
    },
@@ -275,7 +275,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fa62428f-09c8-4dc5-b45b-e4761041b966",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -287,7 +287,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2287b6e9-50b7-4ce4-9ef5-a4dd0e5463af",
+   "id": "21",
    "metadata": {
     "tags": []
    },
@@ -300,7 +300,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8fc6d2af-3d22-42e3-8ca8-756c4e72b141",
+   "id": "22",
    "metadata": {},
    "source": [
     "## 2Rc_col"
@@ -309,7 +309,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "483722dc-86ba-4766-826b-c7d3d2d00cf5",
+   "id": "23",
    "metadata": {
     "tags": []
    },
@@ -326,7 +326,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8ec9135f-4abc-432b-9707-14db25e650ea",
+   "id": "24",
    "metadata": {
     "tags": []
    },
@@ -340,7 +340,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1bcb2209-a5db-4cc2-8fac-d51dae1f214c",
+   "id": "25",
    "metadata": {
     "tags": []
    },
@@ -359,7 +359,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ecee39ab-b8f5-4a79-a31b-2badfafc329b",
+   "id": "26",
    "metadata": {
     "tags": []
    },
@@ -379,7 +379,6 @@
    "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m124"
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -392,8 +391,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/ld_pruning.ipynb b/notebooks/ld_pruning.ipynb
index 292649aeb..f2637cc44 100644
--- a/notebooks/ld_pruning.ipynb
+++ b/notebooks/ld_pruning.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "a1b2c3d4-e5f6-7890-abcd-ef1234567890",
+   "id": "0",
    "metadata": {},
    "source": [
     "# LD-pruned biallelic SNP calls\n",
@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b2c3d4e5-f6a7-8901-bcde-f12345678901",
+   "id": "1",
    "metadata": {},
    "source": [
     "## Setup"
@@ -23,7 +23,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c3d4e5f6-a7b8-9012-cdef-123456789012",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -33,7 +33,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d4e5f6a7-b8c9-0123-defa-234567890123",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -47,7 +47,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e5f6a7b8-c9d0-1234-efab-345678901234",
+   "id": "4",
    "metadata": {},
    "source": [
     "## Basic usage"
@@ -56,7 +56,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f6a7b8c9-d0e1-2345-fabc-456789012345",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +71,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a7b8c9d0-e1f2-3456-abcd-567890123456",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -83,7 +83,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b8c9d0e1-f2a3-4567-bcde-678901234567",
+   "id": "7",
    "metadata": {},
    "source": [
     "## Effect of LD parameters"
@@ -92,7 +92,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c9d0e1f2-a3b4-5678-cdef-789012345678",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -118,7 +118,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d0e1f2a3-b4c5-6789-defa-890123456789",
+   "id": "9",
    "metadata": {},
    "source": [
     "## Before vs after pruning"
@@ -127,7 +127,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e1f2a3b4-c5d6-7890-efab-901234567890",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -145,7 +145,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f2a3b4c5-d6e7-8901-fabc-012345678901",
+   "id": "11",
    "metadata": {},
    "source": [
     "## Downstream compatibility\n",
@@ -156,7 +156,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a3b4c5d6-e7f8-9012-abcd-123456789abc",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -179,7 +179,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b4c5d6e7-f8a9-0123-bcde-234567890bcd",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -187,7 +187,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -200,15 +199,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/local_cluster.ipynb b/notebooks/local_cluster.ipynb
index 91d56dc41..66da8100b 100644
--- a/notebooks/local_cluster.ipynb
+++ b/notebooks/local_cluster.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5ba32f43-2308-43a0-9849-489d77a2f841",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8015add7-81c7-42bd-94c3-a433047c6ca2",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +27,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27c25fb3-ad5c-4652-bf6c-c51d07558790",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -39,7 +39,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "176f77d9-6376-41ce-b3bf-d8025b5a7174",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -52,7 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d9657559-8fc9-4a70-97da-12208b9502ea",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -63,7 +63,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "37bbdfb4-b27d-49d0-9888-042f33d17d32",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -75,7 +75,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "87aad9d0-75e6-4d9c-b6a2-814b8fe2ccea",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -85,7 +85,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a6508f51-6915-4da5-b3ce-f3baa4f69937",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -93,7 +93,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -106,15 +105,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/phenotype_data_demo.ipynb b/notebooks/phenotype_data_demo.ipynb
index ac1e224f8..dccab55ee 100644
--- a/notebooks/phenotype_data_demo.ipynb
+++ b/notebooks/phenotype_data_demo.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "cef10418-08a1-4cc4-a3b0-b8b516cc64fd",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Demonstrating New Phenotype Data Access and Filtering\n",
@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "29554ea2-5e37-40b6-90c1-08088bf9793a",
+   "id": "1",
    "metadata": {},
    "source": [
     "## 1. Setup and Imports\n",
@@ -23,351 +23,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "id": "f1280de7-129f-4875-bf12-eb68b8d88573",
+   "execution_count": null,
+   "id": "2",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/javascript": [
-       "'use strict';\n",
-       "(function(root) {\n",
-       "  function now() {\n",
-       "    return new Date();\n",
-       "  }\n",
-       "\n",
-       "  const force = true;\n",
-       "\n",
-       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
-       "    root._bokeh_onload_callbacks = [];\n",
-       "    root._bokeh_is_loading = undefined;\n",
-       "  }\n",
-       "\n",
-       "const JS_MIME_TYPE = 'application/javascript';\n",
-       "  const HTML_MIME_TYPE = 'text/html';\n",
-       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
-       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
-       "\n",
-       "  /**\n",
-       "   * Render data to the DOM node\n",
-       "   */\n",
-       "  function render(props, node) {\n",
-       "    const script = document.createElement(\"script\");\n",
-       "    node.appendChild(script);\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when an output is cleared or removed\n",
-       "   */\n",
-       "  function handleClearOutput(event, handle) {\n",
-       "    function drop(id) {\n",
-       "      const view = Bokeh.index.get_by_id(id)\n",
-       "      if (view != null) {\n",
-       "        view.model.document.clear()\n",
-       "        Bokeh.index.delete(view)\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    const cell = handle.cell;\n",
-       "\n",
-       "    const id = cell.output_area._bokeh_element_id;\n",
-       "    const server_id = cell.output_area._bokeh_server_id;\n",
-       "\n",
-       "    // Clean up Bokeh references\n",
-       "    if (id != null) {\n",
-       "      drop(id)\n",
-       "    }\n",
-       "\n",
-       "    if (server_id !== undefined) {\n",
-       "      // Clean up Bokeh references\n",
-       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
-       "      cell.notebook.kernel.execute(cmd_clean, {\n",
-       "        iopub: {\n",
-       "          output: function(msg) {\n",
-       "            const id = msg.content.text.trim()\n",
-       "            drop(id)\n",
-       "          }\n",
-       "        }\n",
-       "      });\n",
-       "      // Destroy server and session\n",
-       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
-       "      cell.notebook.kernel.execute(cmd_destroy);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  /**\n",
-       "   * Handle when a new output is added\n",
-       "   */\n",
-       "  function handleAddOutput(event, handle) {\n",
-       "    const output_area = handle.output_area;\n",
-       "    const output = handle.output;\n",
-       "\n",
-       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
-       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
-       "      return\n",
-       "    }\n",
-       "\n",
-       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
-       "\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
-       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
-       "      // store reference to embed id on output_area\n",
-       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
-       "    }\n",
-       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
-       "      const bk_div = document.createElement(\"div\");\n",
-       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
-       "      const script_attrs = bk_div.children[0].attributes;\n",
-       "      for (let i = 0; i < script_attrs.length; i++) {\n",
-       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
-       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
-       "      }\n",
-       "      // store reference to server id on output_area\n",
-       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function register_renderer(events, OutputArea) {\n",
-       "\n",
-       "    function append_mime(data, metadata, element) {\n",
-       "      // create a DOM node to render to\n",
-       "      const toinsert = this.create_output_subarea(\n",
-       "        metadata,\n",
-       "        CLASS_NAME,\n",
-       "        EXEC_MIME_TYPE\n",
-       "      );\n",
-       "      this.keyboard_manager.register_events(toinsert);\n",
-       "      // Render to node\n",
-       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
-       "      render(props, toinsert[toinsert.length - 1]);\n",
-       "      element.append(toinsert);\n",
-       "      return toinsert\n",
-       "    }\n",
-       "\n",
-       "    /* Handle when an output is cleared or removed */\n",
-       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
-       "    events.on('delete.Cell', handleClearOutput);\n",
-       "\n",
-       "    /* Handle when a new output is added */\n",
-       "    events.on('output_added.OutputArea', handleAddOutput);\n",
-       "\n",
-       "    /**\n",
-       "     * Register the mime type and append_mime function with output_area\n",
-       "     */\n",
-       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
-       "      /* Is output safe? */\n",
-       "      safe: true,\n",
-       "      /* Index of renderer in `output_area.display_order` */\n",
-       "      index: 0\n",
-       "    });\n",
-       "  }\n",
-       "\n",
-       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
-       "  if (root.Jupyter !== undefined) {\n",
-       "    const events = require('base/js/events');\n",
-       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
-       "\n",
-       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
-       "      register_renderer(events, OutputArea);\n",
-       "    }\n",
-       "  }\n",
-       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
-       "    root._bokeh_timeout = Date.now() + 5000;\n",
-       "    root._bokeh_failed_load = false;\n",
-       "  }\n",
-       "\n",
-       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
-       "     \"<div style='background-color: #fdd'>\\n\"+\n",
-       "     \"<p>\\n\"+\n",
-       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
-       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
-       "     \"</p>\\n\"+\n",
-       "     \"<ul>\\n\"+\n",
-       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
-       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
-       "     \"</ul>\\n\"+\n",
-       "     \"<code>\\n\"+\n",
-       "     \"from bokeh.resources import INLINE\\n\"+\n",
-       "     \"output_notebook(resources=INLINE)\\n\"+\n",
-       "     \"</code>\\n\"+\n",
-       "     \"</div>\"}};\n",
-       "\n",
-       "  function display_loaded(error = null) {\n",
-       "    const el = document.getElementById(null);\n",
-       "    if (el != null) {\n",
-       "      const html = (() => {\n",
-       "        if (typeof root.Bokeh === \"undefined\") {\n",
-       "          if (error == null) {\n",
-       "            return \"BokehJS is loading ...\";\n",
-       "          } else {\n",
-       "            return \"BokehJS failed to load.\";\n",
-       "          }\n",
-       "        } else {\n",
-       "          const prefix = `BokehJS ${root.Bokeh.version}`;\n",
-       "          if (error == null) {\n",
-       "            return `${prefix} successfully loaded.`;\n",
-       "          } else {\n",
-       "            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n",
-       "          }\n",
-       "        }\n",
-       "      })();\n",
-       "      el.innerHTML = html;\n",
-       "\n",
-       "      if (error != null) {\n",
-       "        const wrapper = document.createElement(\"div\");\n",
-       "        wrapper.style.overflow = \"auto\";\n",
-       "        wrapper.style.height = \"5em\";\n",
-       "        wrapper.style.resize = \"vertical\";\n",
-       "        const content = document.createElement(\"div\");\n",
-       "        content.style.fontFamily = \"monospace\";\n",
-       "        content.style.whiteSpace = \"pre-wrap\";\n",
-       "        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n",
-       "        content.textContent = error.stack ?? error.toString();\n",
-       "        wrapper.append(content);\n",
-       "        el.append(wrapper);\n",
-       "      }\n",
-       "    } else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(() => display_loaded(error), 100);\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  function run_callbacks() {\n",
-       "    try {\n",
-       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
-       "        if (callback != null)\n",
-       "          callback();\n",
-       "      });\n",
-       "    } finally {\n",
-       "      delete root._bokeh_onload_callbacks\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
-       "  }\n",
-       "\n",
-       "  function load_libs(css_urls, js_urls, callback) {\n",
-       "    if (css_urls == null) css_urls = [];\n",
-       "    if (js_urls == null) js_urls = [];\n",
-       "\n",
-       "    root._bokeh_onload_callbacks.push(callback);\n",
-       "    if (root._bokeh_is_loading > 0) {\n",
-       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
-       "      return null;\n",
-       "    }\n",
-       "    if (js_urls == null || js_urls.length === 0) {\n",
-       "      run_callbacks();\n",
-       "      return null;\n",
-       "    }\n",
-       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
-       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
-       "\n",
-       "    function on_load() {\n",
-       "      root._bokeh_is_loading--;\n",
-       "      if (root._bokeh_is_loading === 0) {\n",
-       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
-       "        run_callbacks()\n",
-       "      }\n",
-       "    }\n",
-       "\n",
-       "    function on_error(url) {\n",
-       "      console.error(\"failed to load \" + url);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < css_urls.length; i++) {\n",
-       "      const url = css_urls[i];\n",
-       "      const element = document.createElement(\"link\");\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.rel = \"stylesheet\";\n",
-       "      element.type = \"text/css\";\n",
-       "      element.href = url;\n",
-       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
-       "      document.body.appendChild(element);\n",
-       "    }\n",
-       "\n",
-       "    for (let i = 0; i < js_urls.length; i++) {\n",
-       "      const url = js_urls[i];\n",
-       "      const element = document.createElement('script');\n",
-       "      element.onload = on_load;\n",
-       "      element.onerror = on_error.bind(null, url);\n",
-       "      element.async = false;\n",
-       "      element.src = url;\n",
-       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
-       "      document.head.appendChild(element);\n",
-       "    }\n",
-       "  };\n",
-       "\n",
-       "  function inject_raw_css(css) {\n",
-       "    const element = document.createElement(\"style\");\n",
-       "    element.appendChild(document.createTextNode(css));\n",
-       "    document.body.appendChild(element);\n",
-       "  }\n",
-       "\n",
-       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.3.min.js\"];\n",
-       "  const css_urls = [];\n",
-       "\n",
-       "  const inline_js = [    function(Bokeh) {\n",
-       "      Bokeh.set_log_level(\"info\");\n",
-       "    },\n",
-       "function(Bokeh) {\n",
-       "    }\n",
-       "  ];\n",
-       "\n",
-       "  function run_inline_js() {\n",
-       "    if (root.Bokeh !== undefined || force === true) {\n",
-       "      try {\n",
-       "            for (let i = 0; i < inline_js.length; i++) {\n",
-       "      inline_js[i].call(root, root.Bokeh);\n",
-       "    }\n",
-       "\n",
-       "      } catch (error) {throw error;\n",
-       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
-       "      setTimeout(run_inline_js, 100);\n",
-       "    } else if (!root._bokeh_failed_load) {\n",
-       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
-       "      root._bokeh_failed_load = true;\n",
-       "    } else if (force !== true) {\n",
-       "      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
-       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
-       "    }\n",
-       "  }\n",
-       "\n",
-       "  if (root._bokeh_is_loading === 0) {\n",
-       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
-       "    run_inline_js();\n",
-       "  } else {\n",
-       "    load_libs(css_urls, js_urls, function() {\n",
-       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
-       "      run_inline_js();\n",
-       "    });\n",
-       "  }\n",
-       "}(window));"
-      ],
-      "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded(error = null) {\n    const el = document.getElementById(null);\n    if (el != null) {\n      const html = (() => {\n        if (typeof root.Bokeh === \"undefined\") {\n          if (error == null) {\n            return \"BokehJS is loading ...\";\n          } else {\n            return \"BokehJS failed to load.\";\n          }\n        } else {\n          const prefix = `BokehJS ${root.Bokeh.version}`;\n          if (error == null) {\n            return `${prefix} successfully loaded.`;\n          } else {\n            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n          }\n        }\n      })();\n      el.innerHTML = html;\n\n      if (error != null) {\n        const wrapper = document.createElement(\"div\");\n        wrapper.style.overflow = \"auto\";\n        wrapper.style.height = \"5em\";\n        wrapper.style.resize = \"vertical\";\n        const content = document.createElement(\"div\");\n        content.style.fontFamily = \"monospace\";\n        content.style.whiteSpace = \"pre-wrap\";\n        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n        content.textContent = error.stack ?? error.toString();\n        wrapper.append(content);\n        el.append(wrapper);\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(() => display_loaded(error), 100);\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.3.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n      try {\n            for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n\n      } catch (error) {throw error;\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "MalariaGEN Ag3 API client initialized.\n",
-      "<MalariaGEN Ag3 API client>\n",
-      "Storage URL             : gs://vo_agam_release_master_us_central1/\n",
-      "Data releases available : 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 3.10, 3.11, 3.12, 3.13, 3.14, 3.15\n",
-      "Results cache           : None\n",
-      "Cohorts analysis        : 20250502\n",
-      "AIM analysis            : 20220528\n",
-      "Site filters analysis   : dt_20200416\n",
-      "Software version        : malariagen_data 15.2.2.post22+48d1097a\n",
-      "Client location         : Tanger-Tetouan-Al Hoceima, Morocco\n",
-      "---\n",
-      "Please note that data are subject to terms of use,\n",
-      "for more information see https://www.malariagen.net/data\n",
-      "or contact support@malariagen.net. For API documentation see \n",
-      "https://malariagen.github.io/malariagen-data-python/v15.2.2.post22+48d1097a/Ag3.html\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import pandas as pd\n",
     "import xarray as xr\n",
@@ -387,7 +46,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5b1975f3-ad03-450d-b387-6d2ffd5c0143",
+   "id": "3",
    "metadata": {},
    "source": [
     "## 2. Listing Available Phenotype Sample Sets\n",
@@ -396,20 +55,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
-   "id": "7dd3ebc4-64f7-4d0b-ad01-fbc1e08b0636",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Available phenotype sample sets: ['1237-VO-BJ-DJOGBENOU-VMF00050', '1244-VO-GH-YAWSON-VMF00051', '1245-VO-CI-CONSTANT-VMF00054', '1253-VO-TG-DJOGBENOU-VMF00052']\n",
-      "\n",
-      "Using sample set for demonstration: 1237-VO-BJ-DJOGBENOU-VMF00050\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "phenotype_sample_sets = ag3.phenotype_sample_sets()\n",
     "print(f\"Available phenotype sample sets: {phenotype_sample_sets}\")\n",
@@ -428,7 +77,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1319b97a-bd6f-4246-b653-a394aee97930",
+   "id": "5",
    "metadata": {},
    "source": [
     "## 3. Loading Phenotype Data with sample_query\n",
@@ -437,7 +86,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6f6d5023-17b1-4988-8683-22b3f71096ff",
+   "id": "6",
    "metadata": {},
    "source": [
     "### Example 1: Filter by a specific insecticide"
@@ -445,93 +94,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "id": "c0b9d0ae-6a79-458a-ad9f-9281a1c6112e",
+   "execution_count": null,
+   "id": "7",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "--- Loading phenotype data for '1237-VO-BJ-DJOGBENOU-VMF00050' filtered by Deltamethrin ---\n",
-      "Shape of DataFrame: (88, 60)         \n",
-      "\n",
-      "First 5 rows of the filtered DataFrame:\n",
-      "\n",
-      "Unique insecticides in filtered data: ['Deltamethrin']\n",
-      "\n",
-      "DataFrame Info:\n",
-      "<class 'pandas.core.frame.DataFrame'>\n",
-      "Index: 88 entries, 0 to 87\n",
-      "Data columns (total 60 columns):\n",
-      " #   Column                           Non-Null Count  Dtype  \n",
-      "---  ------                           --------------  -----  \n",
-      " 0   sample_id                        88 non-null     object \n",
-      " 1   country                          88 non-null     object \n",
-      " 2   location                         88 non-null     object \n",
-      " 3   insecticide                      88 non-null     object \n",
-      " 4   dose                             88 non-null     float64\n",
-      " 5   phenotype                        88 non-null     object \n",
-      " 6   sample_set                       88 non-null     object \n",
-      " 7   partner_sample_id                88 non-null     object \n",
-      " 8   contributor                      88 non-null     object \n",
-      " 9   year                             88 non-null     int64  \n",
-      " 10  month                            88 non-null     int64  \n",
-      " 11  latitude                         88 non-null     float64\n",
-      " 12  longitude                        88 non-null     float64\n",
-      " 13  sex_call                         88 non-null     object \n",
-      " 14  release                          88 non-null     object \n",
-      " 15  quarter                          88 non-null     int64  \n",
-      " 16  study_id                         88 non-null     object \n",
-      " 17  study_url                        88 non-null     object \n",
-      " 18  terms_of_use_expiry_date         88 non-null     object \n",
-      " 19  terms_of_use_url                 88 non-null     object \n",
-      " 20  unrestricted_use                 88 non-null     bool   \n",
-      " 21  mean_cov                         88 non-null     Float64\n",
-      " 22  median_cov                       88 non-null     Int64  \n",
-      " 23  modal_cov                        88 non-null     Int64  \n",
-      " 24  mean_cov_2L                      88 non-null     Float64\n",
-      " 25  median_cov_2L                    88 non-null     Int64  \n",
-      " 26  mode_cov_2L                      88 non-null     Int64  \n",
-      " 27  mean_cov_2R                      88 non-null     Float64\n",
-      " 28  median_cov_2R                    88 non-null     Int64  \n",
-      " 29  mode_cov_2R                      88 non-null     Int64  \n",
-      " 30  mean_cov_3L                      88 non-null     Float64\n",
-      " 31  median_cov_3L                    88 non-null     Int64  \n",
-      " 32  mode_cov_3L                      88 non-null     Int64  \n",
-      " 33  mean_cov_3R                      88 non-null     Float64\n",
-      " 34  median_cov_3R                    88 non-null     Int64  \n",
-      " 35  mode_cov_3R                      88 non-null     Int64  \n",
-      " 36  mean_cov_X                       88 non-null     Float64\n",
-      " 37  median_cov_X                     88 non-null     Int64  \n",
-      " 38  mode_cov_X                       88 non-null     Int64  \n",
-      " 39  frac_gen_cov                     88 non-null     Float64\n",
-      " 40  divergence                       88 non-null     Float64\n",
-      " 41  contam_pct                       88 non-null     Float64\n",
-      " 42  contam_LLR                       88 non-null     Float64\n",
-      " 43  aim_species_fraction_arab        88 non-null     float64\n",
-      " 44  aim_species_fraction_colu        88 non-null     float64\n",
-      " 45  aim_species_fraction_colu_no2l   88 non-null     float64\n",
-      " 46  aim_species_gambcolu_arabiensis  88 non-null     object \n",
-      " 47  aim_species_gambiae_coluzzii     88 non-null     object \n",
-      " 48  aim_species                      88 non-null     object \n",
-      " 49  country_iso                      88 non-null     object \n",
-      " 50  admin1_name                      88 non-null     object \n",
-      " 51  admin1_iso                       88 non-null     object \n",
-      " 52  admin2_name                      88 non-null     object \n",
-      " 53  taxon                            88 non-null     object \n",
-      " 54  cohort_admin1_year               88 non-null     object \n",
-      " 55  cohort_admin1_month              88 non-null     object \n",
-      " 56  cohort_admin1_quarter            88 non-null     object \n",
-      " 57  cohort_admin2_year               88 non-null     object \n",
-      " 58  cohort_admin2_month              88 non-null     object \n",
-      " 59  cohort_admin2_quarter            88 non-null     object \n",
-      "dtypes: Float64(10), Int64(12), bool(1), float64(6), int64(3), object(28)\n",
-      "memory usage: 43.2+ KB\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(\n",
     "    f\"\\n--- Loading phenotype data for '{demo_sample_set}' filtered by Deltamethrin ---\"\n",
@@ -552,7 +118,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "daede4ca-01cc-450a-8185-294033af85ad",
+   "id": "8",
    "metadata": {},
    "source": [
     "### Example 2: Filter by multiple conditions (insecticide and dose)"
@@ -560,94 +126,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "id": "eab7d81c-d80c-4279-9263-a0d7b425ff85",
+   "execution_count": null,
+   "id": "9",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "--- Loading phenotype data filtered by Deltamethrin and dose >= 1.0 ---\n",
-      "Shape of DataFrame: (48, 60)\n",
-      "\n",
-      "First 5 rows of the multi-filtered DataFrame:\n",
-      "\n",
-      "Unique insecticides: ['Deltamethrin']\n",
-      "Unique doses: [2.]\n",
-      "\n",
-      "DataFrame Info:\n",
-      "<class 'pandas.core.frame.DataFrame'>\n",
-      "Index: 48 entries, 40 to 87\n",
-      "Data columns (total 60 columns):\n",
-      " #   Column                           Non-Null Count  Dtype  \n",
-      "---  ------                           --------------  -----  \n",
-      " 0   sample_id                        48 non-null     object \n",
-      " 1   country                          48 non-null     object \n",
-      " 2   location                         48 non-null     object \n",
-      " 3   insecticide                      48 non-null     object \n",
-      " 4   dose                             48 non-null     float64\n",
-      " 5   phenotype                        48 non-null     object \n",
-      " 6   sample_set                       48 non-null     object \n",
-      " 7   partner_sample_id                48 non-null     object \n",
-      " 8   contributor                      48 non-null     object \n",
-      " 9   year                             48 non-null     int64  \n",
-      " 10  month                            48 non-null     int64  \n",
-      " 11  latitude                         48 non-null     float64\n",
-      " 12  longitude                        48 non-null     float64\n",
-      " 13  sex_call                         48 non-null     object \n",
-      " 14  release                          48 non-null     object \n",
-      " 15  quarter                          48 non-null     int64  \n",
-      " 16  study_id                         48 non-null     object \n",
-      " 17  study_url                        48 non-null     object \n",
-      " 18  terms_of_use_expiry_date         48 non-null     object \n",
-      " 19  terms_of_use_url                 48 non-null     object \n",
-      " 20  unrestricted_use                 48 non-null     bool   \n",
-      " 21  mean_cov                         48 non-null     Float64\n",
-      " 22  median_cov                       48 non-null     Int64  \n",
-      " 23  modal_cov                        48 non-null     Int64  \n",
-      " 24  mean_cov_2L                      48 non-null     Float64\n",
-      " 25  median_cov_2L                    48 non-null     Int64  \n",
-      " 26  mode_cov_2L                      48 non-null     Int64  \n",
-      " 27  mean_cov_2R                      48 non-null     Float64\n",
-      " 28  median_cov_2R                    48 non-null     Int64  \n",
-      " 29  mode_cov_2R                      48 non-null     Int64  \n",
-      " 30  mean_cov_3L                      48 non-null     Float64\n",
-      " 31  median_cov_3L                    48 non-null     Int64  \n",
-      " 32  mode_cov_3L                      48 non-null     Int64  \n",
-      " 33  mean_cov_3R                      48 non-null     Float64\n",
-      " 34  median_cov_3R                    48 non-null     Int64  \n",
-      " 35  mode_cov_3R                      48 non-null     Int64  \n",
-      " 36  mean_cov_X                       48 non-null     Float64\n",
-      " 37  median_cov_X                     48 non-null     Int64  \n",
-      " 38  mode_cov_X                       48 non-null     Int64  \n",
-      " 39  frac_gen_cov                     48 non-null     Float64\n",
-      " 40  divergence                       48 non-null     Float64\n",
-      " 41  contam_pct                       48 non-null     Float64\n",
-      " 42  contam_LLR                       48 non-null     Float64\n",
-      " 43  aim_species_fraction_arab        48 non-null     float64\n",
-      " 44  aim_species_fraction_colu        48 non-null     float64\n",
-      " 45  aim_species_fraction_colu_no2l   48 non-null     float64\n",
-      " 46  aim_species_gambcolu_arabiensis  48 non-null     object \n",
-      " 47  aim_species_gambiae_coluzzii     48 non-null     object \n",
-      " 48  aim_species                      48 non-null     object \n",
-      " 49  country_iso                      48 non-null     object \n",
-      " 50  admin1_name                      48 non-null     object \n",
-      " 51  admin1_iso                       48 non-null     object \n",
-      " 52  admin2_name                      48 non-null     object \n",
-      " 53  taxon                            48 non-null     object \n",
-      " 54  cohort_admin1_year               48 non-null     object \n",
-      " 55  cohort_admin1_month              48 non-null     object \n",
-      " 56  cohort_admin1_quarter            48 non-null     object \n",
-      " 57  cohort_admin2_year               48 non-null     object \n",
-      " 58  cohort_admin2_month              48 non-null     object \n",
-      " 59  cohort_admin2_quarter            48 non-null     object \n",
-      "dtypes: Float64(10), Int64(12), bool(1), float64(6), int64(3), object(28)\n",
-      "memory usage: 23.6+ KB\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(f\"\\n--- Loading phenotype data filtered by Deltamethrin and dose >= 1.0 ---\")\n",
     "df_filtered_multi = ag3.phenotype_data(\n",
@@ -667,7 +149,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fc1cc12c-b24b-41f3-b147-9e4d817ab588",
+   "id": "10",
    "metadata": {},
    "source": [
     "### Example 3: Applying cohort size filtering\n",
@@ -676,91 +158,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
-   "id": "de8cd777-a4b2-44dd-a0bf-64a6ef419da7",
+   "execution_count": null,
+   "id": "11",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "--- Loading phenotype data with min_cohort_size=10 ---\n",
-      "Shape of DataFrame: (88, 60)\n",
-      "\n",
-      "First 5 rows of the cohort-filtered DataFrame:\n",
-      "\n",
-      "DataFrame Info:\n",
-      "<class 'pandas.core.frame.DataFrame'>\n",
-      "RangeIndex: 88 entries, 0 to 87\n",
-      "Data columns (total 60 columns):\n",
-      " #   Column                           Non-Null Count  Dtype  \n",
-      "---  ------                           --------------  -----  \n",
-      " 0   sample_id                        88 non-null     object \n",
-      " 1   country                          88 non-null     object \n",
-      " 2   location                         88 non-null     object \n",
-      " 3   insecticide                      88 non-null     object \n",
-      " 4   dose                             88 non-null     float64\n",
-      " 5   phenotype                        88 non-null     object \n",
-      " 6   sample_set                       88 non-null     object \n",
-      " 7   partner_sample_id                88 non-null     object \n",
-      " 8   contributor                      88 non-null     object \n",
-      " 9   year                             88 non-null     int64  \n",
-      " 10  month                            88 non-null     int64  \n",
-      " 11  latitude                         88 non-null     float64\n",
-      " 12  longitude                        88 non-null     float64\n",
-      " 13  sex_call                         88 non-null     object \n",
-      " 14  release                          88 non-null     object \n",
-      " 15  quarter                          88 non-null     int64  \n",
-      " 16  study_id                         88 non-null     object \n",
-      " 17  study_url                        88 non-null     object \n",
-      " 18  terms_of_use_expiry_date         88 non-null     object \n",
-      " 19  terms_of_use_url                 88 non-null     object \n",
-      " 20  unrestricted_use                 88 non-null     bool   \n",
-      " 21  mean_cov                         88 non-null     Float64\n",
-      " 22  median_cov                       88 non-null     Int64  \n",
-      " 23  modal_cov                        88 non-null     Int64  \n",
-      " 24  mean_cov_2L                      88 non-null     Float64\n",
-      " 25  median_cov_2L                    88 non-null     Int64  \n",
-      " 26  mode_cov_2L                      88 non-null     Int64  \n",
-      " 27  mean_cov_2R                      88 non-null     Float64\n",
-      " 28  median_cov_2R                    88 non-null     Int64  \n",
-      " 29  mode_cov_2R                      88 non-null     Int64  \n",
-      " 30  mean_cov_3L                      88 non-null     Float64\n",
-      " 31  median_cov_3L                    88 non-null     Int64  \n",
-      " 32  mode_cov_3L                      88 non-null     Int64  \n",
-      " 33  mean_cov_3R                      88 non-null     Float64\n",
-      " 34  median_cov_3R                    88 non-null     Int64  \n",
-      " 35  mode_cov_3R                      88 non-null     Int64  \n",
-      " 36  mean_cov_X                       88 non-null     Float64\n",
-      " 37  median_cov_X                     88 non-null     Int64  \n",
-      " 38  mode_cov_X                       88 non-null     Int64  \n",
-      " 39  frac_gen_cov                     88 non-null     Float64\n",
-      " 40  divergence                       88 non-null     Float64\n",
-      " 41  contam_pct                       88 non-null     Float64\n",
-      " 42  contam_LLR                       88 non-null     Float64\n",
-      " 43  aim_species_fraction_arab        88 non-null     float64\n",
-      " 44  aim_species_fraction_colu        88 non-null     float64\n",
-      " 45  aim_species_fraction_colu_no2l   88 non-null     float64\n",
-      " 46  aim_species_gambcolu_arabiensis  88 non-null     object \n",
-      " 47  aim_species_gambiae_coluzzii     88 non-null     object \n",
-      " 48  aim_species                      88 non-null     object \n",
-      " 49  country_iso                      88 non-null     object \n",
-      " 50  admin1_name                      88 non-null     object \n",
-      " 51  admin1_iso                       88 non-null     object \n",
-      " 52  admin2_name                      88 non-null     object \n",
-      " 53  taxon                            88 non-null     object \n",
-      " 54  cohort_admin1_year               88 non-null     object \n",
-      " 55  cohort_admin1_month              88 non-null     object \n",
-      " 56  cohort_admin1_quarter            88 non-null     object \n",
-      " 57  cohort_admin2_year               88 non-null     object \n",
-      " 58  cohort_admin2_month              88 non-null     object \n",
-      " 59  cohort_admin2_quarter            88 non-null     object \n",
-      "dtypes: Float64(10), Int64(12), bool(1), float64(6), int64(3), object(28)\n",
-      "memory usage: 42.7+ KB\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(f\"\\n--- Loading phenotype data with min_cohort_size=10 ---\")\n",
     "df_cohort_filtered = ag3.phenotype_data(\n",
@@ -787,51 +188,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
-   "id": "9a1f4cc9-528f-40bf-9efe-71aee41c21c3",
+   "execution_count": null,
+   "id": "12",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "--- Getting binary phenotype outcomes for '1237-VO-BJ-DJOGBENOU-VMF00050' ---\n",
-      "Shape of binary series: (88,)\n",
-      "First 5 entries:\n",
-      "sample_id\n",
-      "VBS18949-5562STDY7801785    0.0\n",
-      "VBS18950-5562STDY7801786    0.0\n",
-      "VBS18951-5562STDY7801787    0.0\n",
-      "VBS18952-5562STDY7801788    0.0\n",
-      "VBS18953-5562STDY7801789    0.0\n",
-      "Name: phenotype_binary, dtype: float64\n",
-      "Unique values in series: [0. 1.]\n",
-      "\n",
-      "Shape of binary series (alive Deltamethrin): (48,)\n",
-      "First 5 entries:\n",
-      "sample_id\n",
-      "VBS18995-5562STDY7801828    1.0\n",
-      "VBS18996-5562STDY7801829    1.0\n",
-      "VBS18998-5562STDY7801830    1.0\n",
-      "VBS18999-5562STDY7801831    1.0\n",
-      "VBS19000-5562STDY7801832    1.0\n",
-      "Name: phenotype_binary, dtype: float64\n",
-      "Unique values in series: [1.]\n",
-      "\n",
-      "Shape of binary series (dose 0.5): (40,)\n",
-      "First 5 entries:\n",
-      "sample_id\n",
-      "VBS18949-5562STDY7801785    0.0\n",
-      "VBS18950-5562STDY7801786    0.0\n",
-      "VBS18951-5562STDY7801787    0.0\n",
-      "VBS18952-5562STDY7801788    0.0\n",
-      "VBS18953-5562STDY7801789    0.0\n",
-      "Name: phenotype_binary, dtype: float64\n",
-      "Unique values in series: [0.]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(f\"\\n--- Getting binary phenotype outcomes for '{demo_sample_set}' ---\")\n",
     "\n",
@@ -872,7 +232,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a92e430e-7f40-48a8-8c98-2405d27aabfb",
+   "id": "13",
    "metadata": {},
    "source": [
     "## 4. Getting Binary Phenotype Outcomes with phenotype_binary\n",
@@ -882,51 +242,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
-   "id": "fda88368",
+   "execution_count": null,
+   "id": "14",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "--- Getting binary phenotype outcomes for '1237-VO-BJ-DJOGBENOU-VMF00050' ---\n",
-      "Shape of binary series: (88,)\n",
-      "First 5 entries:\n",
-      "sample_id\n",
-      "VBS18949-5562STDY7801785    0.0\n",
-      "VBS18950-5562STDY7801786    0.0\n",
-      "VBS18951-5562STDY7801787    0.0\n",
-      "VBS18952-5562STDY7801788    0.0\n",
-      "VBS18953-5562STDY7801789    0.0\n",
-      "Name: phenotype_binary, dtype: float64\n",
-      "Unique values in series: [0. 1.]\n",
-      "\n",
-      "Shape of binary series (alive Deltamethrin): (48,)\n",
-      "First 5 entries:\n",
-      "sample_id\n",
-      "VBS18995-5562STDY7801828    1.0\n",
-      "VBS18996-5562STDY7801829    1.0\n",
-      "VBS18998-5562STDY7801830    1.0\n",
-      "VBS18999-5562STDY7801831    1.0\n",
-      "VBS19000-5562STDY7801832    1.0\n",
-      "Name: phenotype_binary, dtype: float64\n",
-      "Unique values in series: [1.]\n",
-      "\n",
-      "Shape of binary series (dose 0.5): (40,)\n",
-      "First 5 entries:\n",
-      "sample_id\n",
-      "VBS18949-5562STDY7801785    0.0\n",
-      "VBS18950-5562STDY7801786    0.0\n",
-      "VBS18951-5562STDY7801787    0.0\n",
-      "VBS18952-5562STDY7801788    0.0\n",
-      "VBS18953-5562STDY7801789    0.0\n",
-      "Name: phenotype_binary, dtype: float64\n",
-      "Unique values in series: [0.]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(f\"\\n--- Getting binary phenotype outcomes for '{demo_sample_set}' ---\")\n",
     "\n",
@@ -967,7 +286,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "62e84ea0",
+   "id": "15",
    "metadata": {},
    "source": [
     "## 5. Loading Phenotype Data Merged with SNP Calls\n",
@@ -976,64 +295,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
-   "id": "726ab8a3-6573-49d5-9b29-479176e5dee6",
+   "execution_count": null,
+   "id": "16",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "--- Loading phenotype data merged with SNP calls ---\n",
-      "Dataset dimensions: FrozenMappingWarningOnValuesAccess({'samples': 48, 'variants': 10001, 'alleles': 4, 'ploidy': 2})\n",
-      "\n",
-      "Dataset structure (rich display):\n",
-      "\n",
-      "First 5 samples and their phenotype_binary values:\n",
-      "[1. 1. 1. 1. 1.]\n",
-      "\n",
-      "First 5 samples and their insecticide values:\n",
-      "['Deltamethrin' 'Deltamethrin' 'Deltamethrin' 'Deltamethrin'\n",
-      " 'Deltamethrin']\n",
-      "\n",
-      "First 5 variant positions:\n",
-      "[2420000 2420001 2420002 2420003 2420004]\n",
-      "\n",
-      "Dataset Info:\n",
-      "xarray.Dataset {\n",
-      "dimensions:\n",
-      "\tsamples = 48 ;\n",
-      "\tvariants = 10001 ;\n",
-      "\talleles = 4 ;\n",
-      "\tploidy = 2 ;\n",
-      "\n",
-      "variables:\n",
-      "\tfloat64 phenotype_binary(samples) ;\n",
-      "\tobject insecticide(samples) ;\n",
-      "\tfloat64 dose(samples) ;\n",
-      "\tobject phenotype(samples) ;\n",
-      "\tobject location(samples) ;\n",
-      "\tobject country(samples) ;\n",
-      "\tobject sample_set(samples) ;\n",
-      "\tobject samples(samples) ;\n",
-      "\t|S1 variant_allele(variants, alleles) ;\n",
-      "\tbool variant_filter_pass_gamb_colu_arab(variants) ;\n",
-      "\tbool variant_filter_pass_gamb_colu(variants) ;\n",
-      "\tbool variant_filter_pass_arab(variants) ;\n",
-      "\tint32 variant_position(variants) ;\n",
-      "\tuint8 variant_contig(variants) ;\n",
-      "\tint8 call_genotype(variants, samples, ploidy) ;\n",
-      "\tint16 call_GQ(variants, samples) ;\n",
-      "\tfloat32 call_MQ(variants, samples) ;\n",
-      "\tint16 call_AD(variants, samples, alleles) ;\n",
-      "\tbool call_genotype_mask(variants, samples, ploidy) ;\n",
-      "\n",
-      "// global attributes:\n",
-      "}"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(f\"\\n--- Loading phenotype data merged with SNP calls ---\")\n",
     "\n",
@@ -1062,7 +327,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "99e7b505-4ea4-43dc-91ae-14ac8f12076e",
+   "id": "17",
    "metadata": {},
    "source": [
     "## 6. Loading Phenotype Data Merged with Haplotypes\n",
@@ -1071,57 +336,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
-   "id": "403f3a26-71eb-4781-975d-d94b7a021d97",
+   "execution_count": null,
+   "id": "18",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "--- Loading phenotype data merged with Haplotypes ---\n",
-      "Dataset dimensions: FrozenMappingWarningOnValuesAccess({'samples': 40, 'variants': 2153, 'alleles': 2, 'ploidy': 2})\n",
-      "\n",
-      "Dataset structure (rich display):\n",
-      "\n",
-      "First 5 samples and their phenotype_binary values:\n",
-      "[0. 0. 0. 0. 0.]\n",
-      "\n",
-      "First 5 samples and their insecticide values:\n",
-      "['Deltamethrin' 'Deltamethrin' 'Deltamethrin' 'Deltamethrin'\n",
-      " 'Deltamethrin']\n",
-      "\n",
-      "First 5 variant positions:\n",
-      "[2420351 2420359 2420370 2420371 2420375]\n",
-      "\n",
-      "Dataset Info:\n",
-      "xarray.Dataset {\n",
-      "dimensions:\n",
-      "\tsamples = 40 ;\n",
-      "\tvariants = 2153 ;\n",
-      "\talleles = 2 ;\n",
-      "\tploidy = 2 ;\n",
-      "\n",
-      "variables:\n",
-      "\tfloat64 phenotype_binary(samples) ;\n",
-      "\tobject insecticide(samples) ;\n",
-      "\tfloat64 dose(samples) ;\n",
-      "\tobject phenotype(samples) ;\n",
-      "\tobject location(samples) ;\n",
-      "\tobject country(samples) ;\n",
-      "\tobject sample_set(samples) ;\n",
-      "\tobject samples(samples) ;\n",
-      "\tint32 variant_position(variants) ;\n",
-      "\tuint8 variant_contig(variants) ;\n",
-      "\t|S1 variant_allele(variants, alleles) ;\n",
-      "\tint8 call_genotype(variants, samples, ploidy) ;\n",
-      "\n",
-      "// global attributes:\n",
-      "}"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(f\"\\n--- Loading phenotype data merged with Haplotypes ---\")\n",
     "\n",
@@ -1150,7 +368,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e2ca345f-33e9-481d-8cf6-0ec08253121c",
+   "id": "19",
    "metadata": {},
    "source": [
     "## Conclusion\n",
@@ -1160,7 +378,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1173,8 +390,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.4"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plink_convert.ipynb b/notebooks/plink_convert.ipynb
index a82710ef2..192a0ee1f 100644
--- a/notebooks/plink_convert.ipynb
+++ b/notebooks/plink_convert.ipynb
@@ -29,7 +29,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "malariagen_plink",
    "language": "python",
    "name": "python3"
   },
@@ -42,8 +41,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.5"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_aims.ipynb b/notebooks/plot_aims.ipynb
index 580a64a39..0e045d92d 100644
--- a/notebooks/plot_aims.ipynb
+++ b/notebooks/plot_aims.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17ea65d6",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8e5fa0a3",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15a6c908",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a2bfe151",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "446a82fb",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2c181775",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "98686752",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -84,7 +84,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -97,15 +96,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_cnv.ipynb b/notebooks/plot_cnv.ipynb
index 87def583b..666648045 100644
--- a/notebooks/plot_cnv.ipynb
+++ b/notebooks/plot_cnv.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a6b71675",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,7 +14,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4526413e",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5ef6e539",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "74c46a04",
+   "id": "3",
    "metadata": {},
    "source": [
     "## CNV HMM coverage"
@@ -49,7 +49,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4ccf170b",
+   "id": "4",
    "metadata": {},
    "source": [
     "### Ag3"
@@ -58,7 +58,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d6bb2a01",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "acd1653f",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -86,7 +86,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f6bbcce7",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +100,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "300c961c",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fc1acd04",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -128,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e995780b",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +141,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1de6d11f",
+   "id": "11",
    "metadata": {},
    "source": [
     "### Af1"
@@ -150,7 +150,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3a94daf7",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,7 +163,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a302d86c",
+   "id": "13",
    "metadata": {},
    "source": [
     "## CNV HMM heatmap"
@@ -171,7 +171,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1e5b281f",
+   "id": "14",
    "metadata": {},
    "source": [
     "### Ag3"
@@ -180,7 +180,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17a8a79d",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -193,7 +193,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "649a9194",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -206,7 +206,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "81b8ece4",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -219,7 +219,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c8d588ae",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -233,7 +233,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "54fc714b",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -247,7 +247,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1d240bb8",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -260,7 +260,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ddc76e07",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -274,7 +274,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cac3c68b",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -287,7 +287,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c566c8ac",
+   "id": "23",
    "metadata": {},
    "source": [
     "### Af1"
@@ -296,7 +296,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5c4dcf97",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -310,7 +310,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "abdffd76",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -318,7 +318,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -331,15 +330,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_diplotype_clustering.ipynb b/notebooks/plot_diplotype_clustering.ipynb
index 83a7df3ea..0f32ce3e8 100644
--- a/notebooks/plot_diplotype_clustering.ipynb
+++ b/notebooks/plot_diplotype_clustering.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d3f73666",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -12,7 +12,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0b889fd3",
+   "id": "1",
    "metadata": {},
    "source": [
     "## Ag3"
@@ -21,7 +21,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ae9caa20-bdce-4b69-81f9-32d560caa5a2",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -36,7 +36,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15d0bf3e-bbbe-4b67-a39d-c7ed5622cc3b",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -60,7 +60,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "92a9bdfd-d808-4c07-8bdd-f2eb3d1e5614",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -82,7 +82,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b6976257-a5be-489f-940f-9e6c717394b1",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -104,7 +104,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ccb2366f",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -125,7 +125,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c0420334-124d-4bab-9ef7-bb9ceb99d6f0",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -145,7 +145,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e957de19-af70-412a-8c75-2e6835ffb2cd",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -167,7 +167,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "857145af",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -189,7 +189,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f41b7e63",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -208,7 +208,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b93d6d94-1add-4ba4-8618-87a11c843e6e",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -227,7 +227,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5773cf5a-6040-4ed9-8bdd-01d7f16408a7",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -247,7 +247,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "52c159c8-1751-4be7-92d9-52bd17751259",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -264,7 +264,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7bd7b04c-5401-4c1e-92eb-cae5b3d87851",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -284,7 +284,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9f6415e6-8d0d-4446-9adb-58c5b236dbcc",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -303,7 +303,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31df6632-8025-4f55-9d5d-9d04978b1690",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -322,7 +322,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6016ee62",
+   "id": "17",
    "metadata": {},
    "source": [
     "## Af1"
@@ -331,7 +331,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "87f36d07",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -347,7 +347,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e1f68c6c",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -368,7 +368,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5bc93110",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -388,7 +388,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "45bdce7c",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -406,7 +406,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5979cca3",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -426,7 +426,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5318dd95-0621-47c1-a3d7-ccfe1950e73f",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -434,7 +434,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -447,20 +446,12 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "pygments_lexer": "ipython3"
   },
   "vscode": {
    "interpreter": {
     "hash": "3b9ddb1005cd06989fd869b9e3d566470f1be01faa610bb17d64e58e32302e8b"
    }
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_diversity.ipynb b/notebooks/plot_diversity.ipynb
index d6d3cd17a..4215cdcdd 100644
--- a/notebooks/plot_diversity.ipynb
+++ b/notebooks/plot_diversity.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a383fb19-cc62-4433-9f05-ba2709dd446b",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "56ea182c-2446-45ba-921a-a0b5cc1d413e",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "75759d4b-d0f8-4489-bda2-5d7d1d9adf17",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "531a2131-c2e1-42fc-85b6-09561b67c820",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -56,7 +56,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e86a9ebd-5fba-4d6e-8ffb-6338d6a59e11",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +74,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "da8bcab8-897f-4f5b-9058-137fb3ee1064",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b3f385ed-d0f8-45da-9ae1-e8ef4f2360c3",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -94,7 +94,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7b0b6f96-f292-446b-a231-6a82fb4fb808",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -104,7 +104,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "63e55e75-ff85-46e1-b20f-4edd2a02ab92",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "149cab79-3f22-4a20-8a13-63f9319d466c",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -124,7 +124,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1928463b-2461-4025-898f-dc05dc0cb214",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -134,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fa7cad0a-e9cb-4d06-bece-298642fa79b3",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144,7 +144,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "431f1274-fc55-4baa-8c67-f8f3d16d5874",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -152,7 +152,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -165,15 +164,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_frequencies_heatmap.ipynb b/notebooks/plot_frequencies_heatmap.ipynb
index daab3576e..1aa68d198 100644
--- a/notebooks/plot_frequencies_heatmap.ipynb
+++ b/notebooks/plot_frequencies_heatmap.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "820bd2a0-eb8c-42e7-ba56-bef15ae7358a",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "702a2213",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -37,7 +37,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "7607169c",
+   "id": "2",
    "metadata": {},
    "source": [
     "## SNP allele frequencies"
@@ -46,7 +46,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ab3ddd98",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +62,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "204d0b93",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cc92d92f-31ed-4d1b-ac22-0282692db8c1",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ea2ee8e2",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -96,7 +96,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "60f9e53f",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "055a88cb",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -118,7 +118,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b41a1026",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -128,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "69ee0608",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -138,7 +138,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7bcfc20a",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -153,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "86ee6d8a",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -164,7 +164,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "65c5093e",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -174,7 +174,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "2a682de7",
+   "id": "14",
    "metadata": {},
    "source": [
     "## Amino acid frequencies"
@@ -183,7 +183,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c24c45f6",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -198,7 +198,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "64066236",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -208,7 +208,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3a83a404",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -218,7 +218,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d5a68fe6",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -230,7 +230,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1fca6e11",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -246,7 +246,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9d55aa57",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -256,7 +256,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "63f02680",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -271,7 +271,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a8895338",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -286,7 +286,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "220945ee",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -296,7 +296,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "7a9b4bc6",
+   "id": "24",
    "metadata": {},
    "source": [
     "## Gene CNV frequencies"
@@ -305,7 +305,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8c914a1b",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -315,7 +315,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "edd39fc3",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -330,7 +330,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fa51bcc3-90fc-4879-8366-b2ad80bc833b",
+   "id": "27",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -340,7 +340,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "763ed786",
+   "id": "28",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -352,7 +352,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f5099554",
+   "id": "29",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -364,7 +364,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f3c20291",
+   "id": "30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -378,7 +378,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "86c5c594",
+   "id": "31",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -402,7 +402,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6d7ad130-30c2-4cd3-8906-a7ada3ccc75f",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -416,7 +416,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "83aab417-632e-4fd2-8da4-3ffdd6e233f6",
+   "id": "33",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -424,7 +424,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -437,15 +436,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_frequencies_space_time.ipynb b/notebooks/plot_frequencies_space_time.ipynb
index 231d86aaa..bb3977e0f 100644
--- a/notebooks/plot_frequencies_space_time.ipynb
+++ b/notebooks/plot_frequencies_space_time.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "47f669f3",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f820bc66-2fb2-4ca2-9b54-824e50d61a0a",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +27,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22b94b9c",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "865f02ea-0673-4d35-ad9e-33088e2d0e58",
+   "id": "3",
    "metadata": {},
    "source": [
     "## Gene CNV frequencies"
@@ -50,7 +50,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1c612c69-27ee-4f50-b467-786bd998de58",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7b38fb26-9562-4f52-9381-ced0687b5a40",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -78,7 +78,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "790c99e8",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -88,7 +88,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1bfc7298",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +100,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fb104e66-7ba0-42ec-9ed0-625a43b69d5b",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ccf5279d-fc5a-4efe-972e-60c7b9515558",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -127,7 +127,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "8d39da45-6875-42e1-9b84-2f0a64189ff4",
+   "id": "10",
    "metadata": {},
    "source": [
     "## Amino acid change frequencies"
@@ -136,7 +136,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bf75e5b1-f2ca-41f4-a0fd-08a03c979fa4",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -155,7 +155,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2c6ffd89-7edc-4f90-bd23-b03e15ce9714",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -165,7 +165,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c058a196-2f78-49a0-8a18-cb2420c3278a",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -183,7 +183,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e733c877-a1f1-4dc6-b8a3-a9652430ff39",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -193,7 +193,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "82927720",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -203,7 +203,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5f9257e0",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -213,7 +213,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "94ccc5bf",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -231,7 +231,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10d0004b",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -241,7 +241,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "9b189c4f-fbf6-45cf-96ef-04817084b5ec",
+   "id": "19",
    "metadata": {},
    "source": [
     "## SNP allele frequencies"
@@ -250,7 +250,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c3738721-8d16-40dd-8a4d-4b588af36b15",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -273,7 +273,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5c743429",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -283,7 +283,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e16ab3fe",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -293,7 +293,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26af27a1",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -303,7 +303,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9f6a7920",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -322,7 +322,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "03cfc0e7",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -332,7 +332,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28922f73-f38d-424a-a9c5-1e839c86567b",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -350,7 +350,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2a8ea4a0-6bf7-41a3-b734-06535e7dbbc8",
+   "id": "27",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -360,7 +360,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5ce2800c-dfa5-49c3-bde4-3b67423f7807",
+   "id": "28",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -378,7 +378,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b0f6bda5",
+   "id": "29",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -387,7 +387,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a94d6521",
+   "id": "30",
    "metadata": {},
    "source": [
     "### SNP allele frequencies using `taxon_by`"
@@ -396,7 +396,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0cf222ee",
+   "id": "31",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -420,7 +420,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2b7e9acc",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -430,14 +430,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2c3227e4",
+   "id": "33",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "markdown",
-   "id": "eb89088f",
+   "id": "34",
    "metadata": {},
    "source": [
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+   "pygments_lexer": "ipython3"
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diff --git a/notebooks/plot_fst_gwss.ipynb b/notebooks/plot_fst_gwss.ipynb
index a627356d6..4b89cca28 100644
--- a/notebooks/plot_fst_gwss.ipynb
+++ b/notebooks/plot_fst_gwss.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a31720f1",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -21,7 +21,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ece45863",
+   "id": "1",
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    "source": [
@@ -39,7 +39,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30c285b1-533c-409c-ad40-86ffed0a9e41",
+   "id": "2",
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    "source": [
@@ -49,7 +49,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "effd3060",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -67,7 +67,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8e747d9a",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -87,7 +87,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b63d02fe",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -105,7 +105,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f77bbae1",
+   "id": "6",
    "metadata": {},
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    "source": [
@@ -123,7 +123,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1b87b2f2",
+   "id": "7",
    "metadata": {},
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    "source": [
@@ -140,7 +140,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9e3fc1c8",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -157,7 +157,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9875e22f",
+   "id": "9",
    "metadata": {},
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    "source": []
@@ -165,7 +165,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "950fe2b8",
+   "id": "10",
    "metadata": {},
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@@ -173,7 +173,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -186,15 +185,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
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-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_g123_gwss.ipynb b/notebooks/plot_g123_gwss.ipynb
index f2f31a42f..79fd65732 100644
--- a/notebooks/plot_g123_gwss.ipynb
+++ b/notebooks/plot_g123_gwss.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a31720f1",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -21,7 +21,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ece45863",
+   "id": "1",
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    "source": [
@@ -39,7 +39,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9ada4f50-bfc0-4524-96de-8903896c7c68",
+   "id": "2",
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@@ -49,7 +49,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "44ff6b91-cc69-4683-b408-45f199816d9a",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +62,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "db33f6d9",
+   "id": "4",
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    "source": [
@@ -79,7 +79,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a585cbba-ea63-4fd9-97ca-d97a3a4f163a",
+   "id": "5",
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    "source": [
@@ -96,7 +96,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "effd3060",
+   "id": "6",
    "metadata": {},
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    "source": [
@@ -115,7 +115,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "efe89451-f05b-4e55-83ef-0f85204f4b04",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -134,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8e747d9a",
+   "id": "8",
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    "source": [
@@ -155,7 +155,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b63d02fe",
+   "id": "9",
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@@ -175,7 +175,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e6d69754-951c-48be-9eaf-c3ff2ead80b4",
+   "id": "10",
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@@ -194,7 +194,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f4c9c960-0f72-497d-9938-4dc9516498c8",
+   "id": "11",
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    "source": [
@@ -204,7 +204,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cd3c2a2d",
+   "id": "12",
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    "source": [
@@ -216,7 +216,7 @@
   {
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    "execution_count": null,
-   "id": "1b87b2f2",
+   "id": "13",
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@@ -234,7 +234,7 @@
   {
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    "execution_count": null,
-   "id": "9e3fc1c8",
+   "id": "14",
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    "source": [
@@ -252,7 +252,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6ef172dc-e697-4a6c-b63d-d8841aca3b97",
+   "id": "15",
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    "outputs": [],
    "source": []
@@ -260,7 +260,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -273,15 +272,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
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+   "pygments_lexer": "ipython3"
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  "nbformat": 4,
diff --git a/notebooks/plot_genes.ipynb b/notebooks/plot_genes.ipynb
index 8e7e9ff02..d72d7e8a2 100644
--- a/notebooks/plot_genes.ipynb
+++ b/notebooks/plot_genes.ipynb
@@ -3,15 +3,8 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "381912bf",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2022-03-09T18:09:27.950846Z",
-     "iopub.status.busy": "2022-03-09T18:09:27.950618Z",
-     "iopub.status.idle": "2022-03-09T18:09:29.094180Z",
-     "shell.execute_reply": "2022-03-09T18:09:29.093711Z"
-    }
-   },
+   "id": "0",
+   "metadata": {},
    "outputs": [],
    "source": [
     "import malariagen_data\n",
@@ -22,15 +15,8 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d1f1824b",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2022-03-09T18:09:29.096307Z",
-     "iopub.status.busy": "2022-03-09T18:09:29.096169Z",
-     "iopub.status.idle": "2022-03-09T18:09:29.271174Z",
-     "shell.execute_reply": "2022-03-09T18:09:29.270693Z"
-    }
-   },
+   "id": "1",
+   "metadata": {},
    "outputs": [],
    "source": [
     "ag3 = malariagen_data.Ag3(\n",
@@ -43,15 +29,8 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f54b8381",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2022-03-09T18:09:29.273487Z",
-     "iopub.status.busy": "2022-03-09T18:09:29.273298Z",
-     "iopub.status.idle": "2022-03-09T18:09:31.492555Z",
-     "shell.execute_reply": "2022-03-09T18:09:31.492104Z"
-    }
-   },
+   "id": "2",
+   "metadata": {},
    "outputs": [],
    "source": [
     "ag3.plot_genes(\"2R\")"
@@ -60,15 +39,8 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6c6865ac",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2022-03-09T18:09:31.499205Z",
-     "iopub.status.busy": "2022-03-09T18:09:31.499024Z",
-     "iopub.status.idle": "2022-03-09T18:09:31.551337Z",
-     "shell.execute_reply": "2022-03-09T18:09:31.550930Z"
-    }
-   },
+   "id": "3",
+   "metadata": {},
    "outputs": [],
    "source": [
     "ag3.plot_genes(\"2R:28,000,000-29,000,000\")"
@@ -77,15 +49,8 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "40b63386",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2022-03-09T18:09:31.553318Z",
-     "iopub.status.busy": "2022-03-09T18:09:31.553187Z",
-     "iopub.status.idle": "2022-03-09T18:09:31.702387Z",
-     "shell.execute_reply": "2022-03-09T18:09:31.701939Z"
-    }
-   },
+   "id": "4",
+   "metadata": {},
    "outputs": [],
    "source": [
     "fig = bklay.column(\n",
@@ -101,7 +66,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4df200c7",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -111,15 +76,8 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "066fb262",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2022-03-09T18:09:31.712754Z",
-     "iopub.status.busy": "2022-03-09T18:09:31.712597Z",
-     "iopub.status.idle": "2022-03-09T18:09:33.866554Z",
-     "shell.execute_reply": "2022-03-09T18:09:33.865947Z"
-    }
-   },
+   "id": "6",
+   "metadata": {},
    "outputs": [],
    "source": [
     "ag3.plot_transcript(\"AGAP004707-RD\")"
@@ -128,7 +86,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8694654d",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -138,15 +96,8 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ce93e47e",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2022-03-09T18:09:33.868626Z",
-     "iopub.status.busy": "2022-03-09T18:09:33.868483Z",
-     "iopub.status.idle": "2022-03-09T18:09:34.121104Z",
-     "shell.execute_reply": "2022-03-09T18:09:34.120683Z"
-    }
-   },
+   "id": "8",
+   "metadata": {},
    "outputs": [],
    "source": [
     "ag3.plot_transcript(\"AGAP004050-RA\")"
@@ -155,15 +106,8 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "86178607",
-   "metadata": {
-    "execution": {
-     "iopub.execute_input": "2022-03-09T18:09:34.123309Z",
-     "iopub.status.busy": "2022-03-09T18:09:34.123167Z",
-     "iopub.status.idle": "2022-03-09T18:09:35.690698Z",
-     "shell.execute_reply": "2022-03-09T18:09:35.690292Z"
-    }
-   },
+   "id": "9",
+   "metadata": {},
    "outputs": [],
    "source": [
     "fig1 = ag3.plot_transcript(f\"AGAP004707-RA\", show=False)\n",
@@ -184,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "be70a93a",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -198,7 +142,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "48814614",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -208,7 +152,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0c3399fa",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -218,7 +162,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0ed22cf1",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -228,7 +172,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0589ed21",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -238,7 +182,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c27741d9",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -258,7 +202,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "523197c3",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -294,7 +238,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e2a3a927",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -302,7 +246,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mgen_data_py3.11",
    "language": "python",
    "name": "python3"
   },
@@ -315,15 +258,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.5"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_h12_h1x.ipynb b/notebooks/plot_h12_h1x.ipynb
index 2f751b5c8..f253a5b40 100644
--- a/notebooks/plot_h12_h1x.ipynb
+++ b/notebooks/plot_h12_h1x.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ced974cd",
+   "id": "0",
    "metadata": {
     "tags": []
    },
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9d17216f",
+   "id": "1",
    "metadata": {
     "tags": []
    },
@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a67ec21b",
+   "id": "2",
    "metadata": {},
    "source": [
     "## Ag3"
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "65b7ff2f",
+   "id": "3",
    "metadata": {
     "tags": []
    },
@@ -53,7 +53,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ac276861-43fb-4f09-b004-57487d75aa41",
+   "id": "4",
    "metadata": {
     "tags": []
    },
@@ -65,7 +65,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a7c10446",
+   "id": "5",
    "metadata": {
     "tags": []
    },
@@ -82,7 +82,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b0d308fe-4e8a-412f-9487-7f1c29d3323a",
+   "id": "6",
    "metadata": {
     "tags": []
    },
@@ -99,7 +99,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "63cb17ff",
+   "id": "7",
    "metadata": {
     "tags": []
    },
@@ -118,7 +118,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4470d24c-8cf1-4d22-b774-0121b4560e27",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -135,7 +135,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cd125828",
+   "id": "9",
    "metadata": {
     "tags": []
    },
@@ -155,7 +155,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5716e777",
+   "id": "10",
    "metadata": {
     "tags": []
    },
@@ -174,7 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fe11bb35",
+   "id": "11",
    "metadata": {
     "tags": []
    },
@@ -194,7 +194,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b4b7a8d2-95d0-48dc-a32f-3bc96aacfb9f",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -213,7 +213,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "73e0e746-add1-4774-bced-461c9742bd95",
+   "id": "13",
    "metadata": {
     "tags": []
    },
@@ -225,7 +225,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "67f48075-6b79-4722-82f7-278bd0868410",
+   "id": "14",
    "metadata": {
     "tags": []
    },
@@ -244,7 +244,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c3e4622b-31e9-444a-8a09-1590862709fe",
+   "id": "15",
    "metadata": {
     "tags": []
    },
@@ -262,7 +262,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2801861c",
+   "id": "16",
    "metadata": {},
    "source": [
     "## Af1"
@@ -271,7 +271,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9144452f",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -287,7 +287,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c5d835e1",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -301,7 +301,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1aaa0573-723c-43b1-baea-750172c4dabc",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -309,7 +309,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ffc7dc06-6bdb-42d2-a1fb-878612d10dd1",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -317,7 +317,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "89b1cd80",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -333,7 +333,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "82cefa93",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -349,7 +349,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "981ba052-1960-4f2e-ba91-72ac442ca178",
+   "id": "23",
    "metadata": {
     "tags": []
    },
@@ -368,7 +368,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e3296b4c-cd72-436f-b21a-d210c7520c39",
+   "id": "24",
    "metadata": {
     "tags": []
    },
@@ -386,7 +386,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1a60cc83-cf30-4152-9eb0-dae7c00ac41b",
+   "id": "25",
    "metadata": {
     "tags": []
    },
@@ -404,7 +404,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a3b1c22e",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -427,7 +427,6 @@
    "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m125"
   },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -440,20 +439,12 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "pygments_lexer": "ipython3"
   },
   "vscode": {
    "interpreter": {
     "hash": "3b9ddb1005cd06989fd869b9e3d566470f1be01faa610bb17d64e58e32302e8b"
    }
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_haplotype_clustering.ipynb b/notebooks/plot_haplotype_clustering.ipynb
index f035681b9..8c1e37492 100644
--- a/notebooks/plot_haplotype_clustering.ipynb
+++ b/notebooks/plot_haplotype_clustering.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d3f73666",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "0b889fd3",
+   "id": "1",
    "metadata": {},
    "source": [
     "## Ag3"
@@ -22,7 +22,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38abbb28",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "60bd6d1f-e8bd-499e-8c78-e64d2d7e9210",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +62,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "04e74ac9-51db-4bae-875c-1ee50e02d024",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -81,7 +81,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "637ae668-c3b8-4914-a0c2-1587cc252c0c",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +95,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9bca4ab4-89b4-4238-9f82-d7920e107583",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -111,7 +111,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ccb2366f",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -132,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c0420334-124d-4bab-9ef7-bb9ceb99d6f0",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -154,7 +154,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e957de19-af70-412a-8c75-2e6835ffb2cd",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -176,7 +176,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "857145af",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -197,7 +197,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f41b7e63",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -216,7 +216,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b93d6d94-1add-4ba4-8618-87a11c843e6e",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -235,7 +235,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5773cf5a-6040-4ed9-8bdd-01d7f16408a7",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -255,7 +255,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "52c159c8-1751-4be7-92d9-52bd17751259",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -272,7 +272,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7bd7b04c-5401-4c1e-92eb-cae5b3d87851",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -291,7 +291,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9f6415e6-8d0d-4446-9adb-58c5b236dbcc",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -310,7 +310,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31df6632-8025-4f55-9d5d-9d04978b1690",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -331,7 +331,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "51846e18",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -354,7 +354,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "6016ee62",
+   "id": "19",
    "metadata": {},
    "source": [
     "## Af1"
@@ -363,7 +363,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "87f36d07",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -379,7 +379,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e1f68c6c",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -399,7 +399,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5bc93110",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -419,7 +419,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "45bdce7c",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -437,7 +437,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5979cca3",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -445,7 +445,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -458,15 +457,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.8"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_haplotype_networks.ipynb b/notebooks/plot_haplotype_networks.ipynb
index 0ecc0d121..7088b6725 100644
--- a/notebooks/plot_haplotype_networks.ipynb
+++ b/notebooks/plot_haplotype_networks.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "f6b86889",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Haplotype Network Plotting Examples\n",
@@ -12,7 +12,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1cadfacf",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -22,7 +22,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "dcfe9fab",
+   "id": "2",
    "metadata": {},
    "source": [
     "## Ag3"
@@ -31,7 +31,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0ebfe96b",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -47,7 +47,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "e3ffe116",
+   "id": "4",
    "metadata": {},
    "source": [
     "N.B., manually specifying the server_port parameter doesn't seem to be necessary on colab, but is needed when running locally via Jupyter notebook, otherwise get \"Address already in use\" error and cannot run multiple plots in same notebook."
@@ -55,7 +55,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e5687f24",
+   "id": "5",
    "metadata": {},
    "source": [
     "## Example 1: Direct Column Name (String)\n",
@@ -65,7 +65,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "81ceebb1-2316-4a0f-bf85-55cc561ab00c",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -82,7 +82,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2798b459",
+   "id": "7",
    "metadata": {},
    "source": [
     "## Example 2: Cohorts Prefix (String)\n",
@@ -92,7 +92,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3206fc04-1074-4f6c-8130-81dadff05c72",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "44c6a40b",
+   "id": "9",
    "metadata": {},
    "source": [
     "This example uses a dictionary to define custom color groups based on conditions applied to the `\"country\"` column."
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8236cd99",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -134,7 +134,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bd1962ba",
+   "id": "11",
    "metadata": {},
    "source": [
     "Setting `color=None` applies the default coloring scheme, typically uniform across all nodes."
@@ -143,7 +143,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "eab4c6fb",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -159,7 +159,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "20b54aa0",
+   "id": "13",
    "metadata": {},
    "source": [
     "This replicates Example 1 but uses `server_mode=\"external\"`, useful for rendering plots in certain environments."
@@ -168,7 +168,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "698ab518",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,7 +186,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "bc416bb4",
+   "id": "15",
    "metadata": {},
    "source": [
     "## Af1"
@@ -195,7 +195,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5e601014",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -210,7 +210,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d8aeab21",
+   "id": "17",
    "metadata": {},
    "source": [
     "Here, nodes are colored based on the `\"sample_set\"` column."
@@ -219,7 +219,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6b6f149e",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -236,7 +236,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b1cde074",
+   "id": "19",
    "metadata": {},
    "source": [
     "Using `\"year\"` implies the function looks for `\"cohorts_year\"` in the metadata."
@@ -245,7 +245,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6d7fc155",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -260,7 +260,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e6e60160",
+   "id": "21",
    "metadata": {},
    "source": [
     "A dictionary defines custom groups based on the `\"year\"` column (assuming year data is available)."
@@ -269,7 +269,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "882e6b8f",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -285,7 +285,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "485becad",
+   "id": "23",
    "metadata": {},
    "source": [
     "With `color=None`, the default coloring is applied."
@@ -294,7 +294,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bd013c5c",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -310,7 +310,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -323,15 +322,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.0"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_haplotypes_frequencies.ipynb b/notebooks/plot_haplotypes_frequencies.ipynb
index 9ad777363..d88f3c20b 100644
--- a/notebooks/plot_haplotypes_frequencies.ipynb
+++ b/notebooks/plot_haplotypes_frequencies.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "74a45bfa-2af5-4a9d-9285-84f34a82d986",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Ag3"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a46f23bf-2635-4249-b115-aa8cfd35d33f",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8130522f-98de-463f-83fd-a1c1c460e00e",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2cefad62-e558-4797-9d1a-4b501ad364b0",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -53,7 +53,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6bac8aca-8835-43b7-84c0-f6eb62594d91",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2770b59a-6b6d-4458-99cf-cdf08e47ddac",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a771fda2-ae68-46bc-b38e-2f4ba6b41b71",
+   "id": "6",
    "metadata": {},
    "source": [
     "# Af1"
@@ -86,7 +86,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "415cc454-ffdd-4bff-8881-95180bcf66f6",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +100,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5d8fb2b5-5b49-4856-8e1c-895174e32f04",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ef2cb769-4a8d-49fe-8e28-c9dc1af0159d",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -125,7 +125,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -138,8 +137,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_heterozygosity.ipynb b/notebooks/plot_heterozygosity.ipynb
index 136836b47..89a75efd8 100644
--- a/notebooks/plot_heterozygosity.ipynb
+++ b/notebooks/plot_heterozygosity.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29e2e4a7",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -19,7 +19,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a751077f",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4b2bb835",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -50,7 +50,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ac466ddf",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -65,7 +65,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "522b2a30",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -80,7 +80,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10aff683",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +95,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0c66bd85",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -105,7 +105,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a8fc0887",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -118,7 +118,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e564c19b",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -133,7 +133,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c0202112",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -143,7 +143,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3ebba22a",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -156,7 +156,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "df452208",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -171,7 +171,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "af3bf25f",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -179,7 +179,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -192,15 +191,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_ihs_gwss.ipynb b/notebooks/plot_ihs_gwss.ipynb
index 4a8fa53c7..3fd872e69 100644
--- a/notebooks/plot_ihs_gwss.ipynb
+++ b/notebooks/plot_ihs_gwss.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a31720f1",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ece45863",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -37,7 +37,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "effd3060",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8e747d9a",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b63d02fe",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -94,7 +94,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f77bbae1",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -112,7 +112,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cd3c2a2d",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -122,7 +122,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1b87b2f2",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -138,7 +138,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9e3fc1c8",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -154,7 +154,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "110b81e5",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -162,7 +162,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -175,15 +174,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_njt.ipynb b/notebooks/plot_njt.ipynb
index 7ece0d852..94e210973 100644
--- a/notebooks/plot_njt.ipynb
+++ b/notebooks/plot_njt.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3139f0e8-e82f-4d3d-a031-bc9c2d92edd8",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3112b35f-d951-441e-a850-59615aa1f9ec",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1e83d8ad-e20e-449b-8601-150540e6dd82",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2964c092-65de-4d2a-9dd9-970418b13bd8",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -53,7 +53,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5f86a798-51c8-4c79-ac60-e7520ab9a503",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "392e6c4c-512f-4a80-bbe9-932280a4efdb",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4437435f-d3b3-4ad6-9e62-6e5f6f01edea",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -102,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "664a9d48-001e-40ed-8901-08bccb2184ba",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -119,7 +119,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "76405cc3-6cdd-4067-a2cb-71095d2c28b3",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -137,7 +137,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "972f4787-7c2b-47e2-859c-cd1cc800d92e",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -153,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "95d20897-6100-4b11-a3e6-38155feb98c2",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -168,7 +168,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5bf936d6-5dc0-409c-828d-7af326102d41",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,7 +186,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8ea0532c-58f4-4bdf-bd56-0bdfb245e060",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -204,7 +204,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2335937a-eec7-4d9e-b4ca-b737ff481cd6",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -220,7 +220,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "68fb01ae-2567-4c13-b0a3-5890b38165d5",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -236,7 +236,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2f1139fe-9c06-420f-855f-e3900186768a",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -252,7 +252,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3f8f8976-0080-4f44-b665-1534980f0da1",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -269,7 +269,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18fde26a-339a-44a1-a91f-425f22ed96d1",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -286,7 +286,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "72155de8-c657-4530-af38-82e0248b85a8",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -301,7 +301,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "69aec527-1351-44ba-b394-681fd3d424dd",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -316,7 +316,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38a2817d-933e-46f8-af0a-fedeb7370a38",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -333,7 +333,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9c1dc76a-1fea-49ee-9341-a7542b2a74f0",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -346,7 +346,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bc7b2566-ac5d-4ca0-bc91-0208fe9d2cb0",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -363,7 +363,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9f5cd515-4933-4f08-82cc-c0fa57e77fb3",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -371,7 +371,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -384,15 +383,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_pairwise_average_fst.ipynb b/notebooks/plot_pairwise_average_fst.ipynb
index 0b41014a6..b519e3776 100644
--- a/notebooks/plot_pairwise_average_fst.ipynb
+++ b/notebooks/plot_pairwise_average_fst.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d0f3796b-cc12-4370-bdb2-ad4f4bd50a3e",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -17,7 +17,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0e719256-3561-4362-a169-c38c9fe96972",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -33,7 +33,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6af54463-584b-443b-9538-cd141578fde4",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "be539d92-3bd5-40b5-b67f-7ae6569db62f",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a7c0815f-7ca9-4ed0-9982-16409f2bc675",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -73,7 +73,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "53a6b0e2-959d-4af1-92ed-bdb748be51c1",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -91,7 +91,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35959f42-732e-40fa-86ad-16d95fb6e740",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -101,7 +101,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35d304bd-3f39-4dc7-9f7d-905068d5cd0d",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -111,7 +111,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ec418b8f-1451-415e-96e5-bcc5e98428bb",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -121,7 +121,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c16035d2-b5d3-4441-87d9-eda953079161",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -131,7 +131,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13afd6ed-7962-4935-b1f1-ed12f5e2ceed",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -143,7 +143,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "48a52211-2ef9-47da-b715-d0d74a69a4ad",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -162,7 +162,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "09cc1824-e6f4-4799-a8f4-cf61e472eaf8",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -172,7 +172,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "95f112d2-fe76-4091-b73b-d7a17a61cc18",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -182,7 +182,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "908b08c8-290f-49d1-b3d3-cb8f9e7d2d21",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -192,7 +192,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "818fdac7-dcb4-4da2-8a52-f16ce51a2c0d",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -215,7 +215,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "65c1bdd5-f1d2-4814-93e5-ddb1d9c42258",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -225,7 +225,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5ec8cfe3-336c-4362-9361-78d40ffa0a8e",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -233,7 +233,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2d3236a2-842d-4c13-92ec-9a4338750aca",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -241,7 +241,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -254,8 +253,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_pca.ipynb b/notebooks/plot_pca.ipynb
index 74421ccc3..a32a6000a 100644
--- a/notebooks/plot_pca.ipynb
+++ b/notebooks/plot_pca.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "7d93e741-bddf-4a29-aea2-7bc6be697cb7",
+   "id": "0",
    "metadata": {},
    "source": [
     "# PCA plotting"
@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2f274c61-c660-47b0-92b9-83ab701eb9eb",
+   "id": "1",
    "metadata": {},
    "source": [
     "### Setup"
@@ -19,7 +19,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36039d6f",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -29,7 +29,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d8bf7a3a",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -44,7 +44,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bfd56044",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -59,7 +59,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4e5e1c70",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b3760474-2ab2-4291-b5ee-48feccd091f4",
+   "id": "6",
    "metadata": {},
    "source": [
     "## Mayotte"
@@ -77,7 +77,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e5743579",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -92,7 +92,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ede14f05-a45d-4e12-9e02-3f4980d867cd",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -102,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5578c99a-37b1-4011-b34f-267aad0b2763",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a027022f-f700-49c1-8f2d-a43100956155",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -127,7 +127,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b73b8a6f",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +141,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c0b018e3",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -151,7 +151,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32e505db",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,7 +163,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "467dbd69-8ba2-41a2-8d01-d9fa78d42326",
+   "id": "14",
    "metadata": {},
    "source": [
     "## Burkina Faso"
@@ -172,7 +172,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6a2ce979-1553-4459-b3c1-f3dea40bc1a1",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -187,7 +187,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4cb47917-0d8c-47c8-a68d-34d193e2f61a",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -201,7 +201,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "241cae4e-3305-4c2a-845f-8871a1a114d4",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -214,7 +214,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a2b46eb9-832d-417c-a082-9fc365b0fc62",
+   "id": "18",
    "metadata": {},
    "source": [
     "## Ag3.0"
@@ -223,7 +223,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8ac26ed8",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -238,7 +238,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6e02f847",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -253,7 +253,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4b957863",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -263,7 +263,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17baa8d0",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -277,7 +277,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "114fb016",
+   "id": "23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -293,7 +293,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "92795fa4",
+   "id": "24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -307,7 +307,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e0c10b0d-3244-4862-acb7-cf60b9a6a9f2",
+   "id": "25",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -324,7 +324,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "727402e7-43a1-4c7d-b21e-a051cd881f01",
+   "id": "26",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -337,7 +337,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cccf1386-c578-4af3-97ec-dc7704840102",
+   "id": "27",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -351,7 +351,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1b1a399a-762d-42db-9e40-776575d9ef5a",
+   "id": "28",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -364,7 +364,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "14d04103-2f6f-4f53-8d35-f286de5980d2",
+   "id": "29",
    "metadata": {},
    "source": [
     "## Af1.0"
@@ -373,7 +373,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6c3fc8d5",
+   "id": "30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -388,7 +388,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fbe1f54f",
+   "id": "31",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -398,7 +398,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5c055c99",
+   "id": "32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -411,7 +411,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ea74cb43",
+   "id": "33",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -425,7 +425,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fdfbcd5a-5ef4-4cbc-b430-c0b541925142",
+   "id": "34",
    "metadata": {},
    "source": [
     "## Excluding samples"
@@ -434,7 +434,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6c3251e2-a95c-4d4a-bff1-8e632be0eaf5",
+   "id": "35",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -449,7 +449,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1f0b88a7-d9f6-44a8-9778-4cbaad397765",
+   "id": "36",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -459,7 +459,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4e370936-925a-4e97-86cb-b22f72b39e64",
+   "id": "37",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -469,7 +469,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9ea24435-d752-4269-a391-b057e1650d44",
+   "id": "38",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -482,7 +482,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0f114dd9-965d-4579-8cce-76f45fde6a37",
+   "id": "39",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -500,7 +500,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a5392844-a828-48f3-8222-bfc1817c3493",
+   "id": "40",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -510,7 +510,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6d87eeb5-8dc6-4a31-a8a3-e936d4d05215",
+   "id": "41",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -520,7 +520,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "770b01ee-642e-4903-93fa-eef084924234",
+   "id": "42",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -530,7 +530,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9438fd91-b463-4d28-8279-5eaa728a8f2e",
+   "id": "43",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -542,7 +542,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "58e7b2c1-b4c1-4c93-823c-8531693636e4",
+   "id": "44",
    "metadata": {},
    "source": [
     "## Excluding samples during fit"
@@ -551,7 +551,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1014a17c-12bb-46c3-9a7b-f2449d205ce3",
+   "id": "45",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -569,7 +569,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e48d46dd-5c7f-4573-a5f5-c15a389d2e1e",
+   "id": "46",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -579,7 +579,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1fb5192e-f63f-443d-91a9-e82b2de14c69",
+   "id": "47",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -589,7 +589,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "873c53f5-8690-4690-85f0-8ce1845e2862",
+   "id": "48",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -599,7 +599,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0bb86ba2-e428-4ae0-9e0c-703345c89324",
+   "id": "49",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -612,7 +612,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7b28c4c8-9382-4889-8651-77ef0be929f6",
+   "id": "50",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -624,7 +624,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f1e8c954",
+   "id": "51",
    "metadata": {},
    "source": [
     "## PCA with cohort downsampling"
@@ -633,7 +633,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e4a484f3",
+   "id": "52",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -653,7 +653,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "abb2ee83",
+   "id": "53",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -661,7 +661,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -674,15 +673,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_samples.ipynb b/notebooks/plot_samples.ipynb
index 2f7f31c8a..ec7be4fe3 100644
--- a/notebooks/plot_samples.ipynb
+++ b/notebooks/plot_samples.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -256,7 +256,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "mgen_data_py3.11",
    "language": "python",
    "name": "python3"
   },
@@ -269,15 +268,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.5"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_snps.ipynb b/notebooks/plot_snps.ipynb
index 5daa69c4e..502545139 100644
--- a/notebooks/plot_snps.ipynb
+++ b/notebooks/plot_snps.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14640993",
+   "id": "0",
    "metadata": {
     "tags": []
    },
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5d740cac",
+   "id": "1",
    "metadata": {
     "tags": []
    },
@@ -31,7 +31,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bd576b75",
+   "id": "2",
    "metadata": {
     "tags": []
    },
@@ -43,7 +43,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7de3ba82",
+   "id": "3",
    "metadata": {
     "tags": []
    },
@@ -56,7 +56,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3a3de267-affa-46e6-92b9-d07553cad816",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -66,7 +66,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2c66985f-592b-4fb5-a560-5cdedb472bee",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "82096dc0",
+   "id": "6",
    "metadata": {
     "tags": []
    },
@@ -88,7 +88,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10c340aa",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -98,7 +98,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e8e463dd",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7fb757a7",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -118,7 +118,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0e3a8961",
+   "id": "10",
    "metadata": {
     "tags": []
    },
@@ -132,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "63aca10c",
+   "id": "11",
    "metadata": {
     "tags": []
    },
@@ -144,7 +144,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6fb5216e",
+   "id": "12",
    "metadata": {
     "tags": []
    },
@@ -158,7 +158,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0d88ceb5",
+   "id": "13",
    "metadata": {
     "tags": []
    },
@@ -174,7 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0c98cabe",
+   "id": "14",
    "metadata": {
     "tags": []
    },
@@ -186,7 +186,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8a7c297d",
+   "id": "15",
    "metadata": {
     "tags": []
    },
@@ -198,7 +198,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d0552711",
+   "id": "16",
    "metadata": {
     "tags": []
    },
@@ -210,7 +210,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d269e02e",
+   "id": "17",
    "metadata": {
     "tags": []
    },
@@ -224,7 +224,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "872c56ab",
+   "id": "18",
    "metadata": {
     "tags": []
    },
@@ -238,7 +238,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c24a21ab",
+   "id": "19",
    "metadata": {
     "tags": []
    },
@@ -254,7 +254,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "60280e52",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -262,7 +262,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -275,15 +274,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_xpehh_gwss.ipynb b/notebooks/plot_xpehh_gwss.ipynb
index cd9e67583..ba03632a5 100644
--- a/notebooks/plot_xpehh_gwss.ipynb
+++ b/notebooks/plot_xpehh_gwss.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32067e1d",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "966049ec",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "838eddc4",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -54,7 +54,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e780aa23",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -75,7 +75,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b26a9654",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -93,7 +93,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "181227f6",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -111,7 +111,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "89cf50ac",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -130,7 +130,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "78b452f5",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -140,7 +140,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "079a3308",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -157,7 +157,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d6290896",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -174,7 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a5aed96d",
+   "id": "10",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -182,7 +182,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -195,15 +194,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/profiling/gh498.ipynb b/notebooks/profiling/gh498.ipynb
index 06012f43e..21818ea9b 100644
--- a/notebooks/profiling/gh498.ipynb
+++ b/notebooks/profiling/gh498.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a790fb90-492e-480a-9403-d1d242c48389",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a00d7b52-ac2e-44ef-9e08-a9d33ee90276",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0fdd5aea-803c-477e-9b35-8edc61a31b7e",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -45,7 +45,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ff092693-dd1e-44ff-bd09-7cfb57b9134f",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9a75f64f-fe2c-44d9-abae-18ff8453d154",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0c433078-8c78-4a2a-93d3-d9330762bbbd",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -96,7 +96,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8f945545-7a73-4c9a-8867-e2cae9e1aece",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1fcae9c4-9c1c-402f-a6c9-70a7f6f939a7",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -125,7 +125,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -138,8 +137,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.18"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/repr.ipynb b/notebooks/repr.ipynb
index 3b8c2a289..7aa1dbb88 100644
--- a/notebooks/repr.ipynb
+++ b/notebooks/repr.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "aa5bad7b",
+   "id": "0",
    "metadata": {
     "tags": []
    },
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24cdd3a1",
+   "id": "1",
    "metadata": {
     "tags": []
    },
@@ -27,7 +27,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "362dedbf",
+   "id": "2",
    "metadata": {
     "tags": []
    },
@@ -39,7 +39,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "294fc8b7",
+   "id": "3",
    "metadata": {
     "tags": []
    },
@@ -51,7 +51,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9ca832ac",
+   "id": "4",
    "metadata": {
     "tags": []
    },
@@ -64,7 +64,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "73e79af6",
+   "id": "5",
    "metadata": {
     "tags": []
    },
@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4781d110",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -84,7 +84,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -97,15 +96,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/spike_sim_test_data.ipynb b/notebooks/spike_sim_test_data.ipynb
index ba87ef806..ae7709062 100644
--- a/notebooks/spike_sim_test_data.ipynb
+++ b/notebooks/spike_sim_test_data.ipynb
@@ -1197,7 +1197,6 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1210,15 +1209,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
-  },
-  "widgets": {
-   "application/vnd.jupyter.widget-state+json": {
-    "state": {},
-    "version_major": 2,
-    "version_minor": 0
-   }
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

From a0cf6b8543a35c59e529eb8f12857a253600161a Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 6 Oct 2026 15:47:36 +0100
Subject: [PATCH 34/38] think i fixed tests failing under CI

---
 tests/anoph/test_igv.py          |  5 ++---
 tests/anoph/test_vcf_exporter.py | 25 ++++++++++++-------------
 2 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/tests/anoph/test_igv.py b/tests/anoph/test_igv.py
index 84cda5cf3..61faa0645 100644
--- a/tests/anoph/test_igv.py
+++ b/tests/anoph/test_igv.py
@@ -1,5 +1,3 @@
-from types import SimpleNamespace
-
 import igv_notebook  # type: ignore
 import numpy as np
 import pandas as pd
@@ -10,6 +8,7 @@
 from malariagen_data import ag3 as _ag3
 import malariagen_data.anoph.igv as igv_module
 from malariagen_data.anoph.igv import AnophelesIgv
+from malariagen_data.util import Region
 
 
 @pytest.fixture
@@ -113,7 +112,7 @@ def wgs_data_catalog(self, sample_set):
     monkeypatch.setattr(
         igv_module,
         "_parse_single_region",
-        lambda self, region: SimpleNamespace(contig="2L"),
+        lambda self, region: Region("2L", 1, 10),
     )
     monkeypatch.setattr(
         api,
diff --git a/tests/anoph/test_vcf_exporter.py b/tests/anoph/test_vcf_exporter.py
index ed4edb606..f4eead2d7 100644
--- a/tests/anoph/test_vcf_exporter.py
+++ b/tests/anoph/test_vcf_exporter.py
@@ -448,28 +448,27 @@ def test_vcf_exporter_fields(fixture, api: SnpVcfExporter, tmp_path):
 
 
 @parametrize_with_cases("fixture,api", cases=".")
-def test_vcf_exporter_fields_as_set(fixture, api: SnpVcfExporter, tmp_path):
-    # A `set` has no guaranteed iteration order. The FORMAT column must
-    # still come out in the same fixed order (GT, GQ, AD, MQ) that the
-    # per-sample values are actually written in, regardless of what
-    # order `fields` iterates in as passed by the caller. Previously
-    # the FORMAT column used the caller's (here, arbitrary) order while
-    # values were always written GT:GQ:AD:MQ, so a `set` could easily
-    # produce a VCF whose header lied about which value was which —
-    # e.g. declaring the first value as "MQ" when it was actually the
-    # GT string, which bcftools then fails to parse.
+def test_vcf_exporter_fields_order(fixture, api: SnpVcfExporter, tmp_path):
+    # The FORMAT column must come out in the same fixed order (GT, GQ,
+    # AD, MQ) that the per-sample values are actually written in,
+    # regardless of the order of `fields` as passed by the caller.
+    # Previously the FORMAT column used the caller's order while values
+    # were always written GT:GQ:AD:MQ, producing a VCF whose header lied
+    # about which value was which — e.g. declaring the first value as
+    # "MQ" when it was actually the GT string, which bcftools then
+    # fails to parse.
     region = api.contigs[0]
     all_sample_sets = api.sample_sets()["sample_set"].to_list()
     sample_sets = [all_sample_sets[0]]
     _, sample_query = _pick_single_sample_query(api, sample_sets)
 
-    output_path = str(tmp_path / "test_fields_set.vcf.gz")
+    output_path = str(tmp_path / "test_fields_order.vcf.gz")
     api.snp_calls_to_vcf(
         output_path=output_path,
         region=region,
         sample_sets=sample_sets,
         sample_query=sample_query,
-        fields={"GT", "GQ", "AD", "MQ"},
+        fields=("MQ", "AD", "GT", "GQ"),
     )
 
     with gzip.open(output_path, "rt") as f:
@@ -521,7 +520,7 @@ def test_vcf_exporter_output_is_valid_per_bcftools(
         region=region,
         sample_sets=sample_sets,
         sample_query=sample_query,
-        fields={"GT", "GQ", "AD", "MQ"},
+        fields=("MQ", "AD", "GT", "GQ"),
     )
 
     result = subprocess.run(

From 4e20404bc055b5c2be42e7f36a2052ae84064067 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 7 Oct 2026 11:22:11 +0100
Subject: [PATCH 35/38] limit region size to ensure it will load in IGV

---
 malariagen_data/anoph/to_vcf.py | 14 ++++++++++++++
 notebooks/igv.ipynb             |  8 ++++++++
 2 files changed, 22 insertions(+)

diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index d05915b40..6dc6b018d 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -15,6 +15,7 @@
 from . import base_params
 from . import plink_params
 from . import vcf_params
+from ..util import _parse_multi_region
 
 
 @dataclass
@@ -145,6 +146,7 @@ def snp_calls_to_vcf(
         sample_query: base_params.sample_query,
         sample_query_options: Optional[base_params.sample_query_options] = None,
         site_mask: Optional[base_params.site_mask] = None,
+        max_region_size: Optional[int] = 1_000_000,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         chunks: base_params.chunks = base_params.native_chunks,
         overwrite: plink_params.overwrite = False,
@@ -168,6 +170,18 @@ def snp_calls_to_vcf(
             )
         if "GT" not in fields:
             raise ValueError("GT must be included in fields.")
+        # IGV loads the whole (unindexed) VCF into the browser, so cap the
+        # total region size.
+        region_size = sum(
+            self.genome_sequence(region=r).shape[0]
+            for r in _parse_multi_region(self, region)
+        )
+        if max_region_size is not None and region_size > max_region_size:
+            raise ValueError(
+                f"region {region!r} spans {region_size:,} bp, more than "
+                f"max_region_size ({max_region_size:,} bp). Use a smaller region, "
+                'e.g. "2R:2,400,000-2,500,000", or set max_region_size=None.'
+            )
 
         # Canonicalise the field order to _FIELD_ORDER
         fields = tuple(f for f in _FIELD_ORDER if f in fields)
diff --git a/notebooks/igv.ipynb b/notebooks/igv.ipynb
index d584f04ae..9626a7d09 100644
--- a/notebooks/igv.ipynb
+++ b/notebooks/igv.ipynb
@@ -245,6 +245,14 @@
     "    snp_vcf_url=snp_vcf_url,\n",
     ")"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "19",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

From 98ad89aa41ac1cef9ae3fabaa2aca36cee272cc9 Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 7 Oct 2026 13:53:39 +0100
Subject: [PATCH 36/38] fixed vcf paths for jupyter lab

---
 malariagen_data/anoph/igv.py        | 42 ++++++++++++++++---------
 malariagen_data/anoph/to_vcf.py     |  2 +-
 malariagen_data/anoph/vcf_params.py | 11 ++++++-
 notebooks/igv.ipynb                 | 26 +++++++++++-----
 tests/anoph/test_igv.py             | 48 ++++++++++++++++++++---------
 5 files changed, 90 insertions(+), 39 deletions(-)

diff --git a/malariagen_data/anoph/igv.py b/malariagen_data/anoph/igv.py
index 5958106d4..964f8dddc 100644
--- a/malariagen_data/anoph/igv.py
+++ b/malariagen_data/anoph/igv.py
@@ -1,4 +1,6 @@
-from typing import List, Optional
+import base64
+import os
+from typing import List, Optional, Union
 
 import igv_notebook  # type: ignore
 from numpydoc_decorator import doc  # type: ignore
@@ -8,6 +10,15 @@
 from .snp_data import AnophelesSnpData
 
 
+def _vcf_data_uri(path: Union[str, os.PathLike]) -> str:
+    """Read a local VCF file and return it as a data URI."""
+    with open(path, "rb") as f:
+        data = f.read()
+    is_gzip = data[:2] == b"\x1f\x8b"
+    media_type = "application/gzip" if is_gzip else "text/plain"
+    return f"data:{media_type};base64,{base64.b64encode(data).decode()}"
+
+
 class AnophelesIgv(
     AnophelesSnpData,
 ):
@@ -82,7 +93,7 @@ def _igv_view_alignments_tracks(
         region: Region,
         sample: str,
         visibility_window: int = 20_000,
-        snp_vcf_url: Optional[str] = None,
+        snp_vcf_path: Optional[Union[str, os.PathLike]] = None,
     ):
         # Look up sample set for sample.
         try:
@@ -116,10 +127,12 @@ def _igv_view_alignments_tracks(
             "visibilityWindow": visibility_window,  # bp
             "height": 50,
         }
-        if snp_vcf_url is not None:
-            # A local VCF, e.g. from snp_calls_to_vcf(), has no index, so
-            # IGV loads it in full.
-            snp_track["url"] = snp_vcf_url
+        if snp_vcf_path is not None:
+            # Embed the local VCF, e.g. from snp_calls_to_vcf(), in the track
+            # as a data URI, so it doesn't need to be served over HTTP (which
+            # isn't possible in all notebook environments, e.g. VS Code). It
+            # has no index, so IGV loads it in full.
+            snp_track["url"] = _vcf_data_uri(snp_vcf_path)
             snp_track["indexed"] = False
         else:
             vcf_url = cat_rec["snp_genotypes_vcf"]
@@ -189,13 +202,12 @@ def igv(
                 visible.
             """,
             init="If True, call igv_notebook.init().",
-            snp_vcf_url="""
-                Optional URL for a local VCF, e.g. one written by
-                `snp_calls_to_vcf()`. The VCF is loaded without an index, so it
-                should be small (e.g. a single sample over a region). For Jupyter
-                Notebook and Lab, the VCF must be under the Jupyter startup
-                directory tree; pass a URL relative to that tree (e.g.
-                `/data/sample.vcf.gz`). If omitted, use the catalog VCF.
+            snp_vcf_path="""
+                Optional path to a local VCF file (`.vcf` or `.vcf.gz`), e.g. one
+                written by `snp_calls_to_vcf()`, to show as the SNPs track. The
+                file is embedded in the notebook and loaded in full, so it should
+                be small (e.g. a single sample over a region). If omitted, use
+                the catalog VCF.
             """,
         ),
     )
@@ -205,7 +217,7 @@ def view_alignments(
         sample: str,
         visibility_window: int = 20_000,
         init: bool = True,
-        snp_vcf_url: Optional[str] = None,
+        snp_vcf_path: Optional[Union[str, os.PathLike]] = None,
     ):
         # Parse region.
         region_prepped: Region = _parse_single_region(self, region)
@@ -216,7 +228,7 @@ def view_alignments(
             region=region_prepped,
             sample=sample,
             visibility_window=visibility_window,
-            snp_vcf_url=snp_vcf_url,
+            snp_vcf_path=snp_vcf_path,
         )
 
         # Create IGV browser.
diff --git a/malariagen_data/anoph/to_vcf.py b/malariagen_data/anoph/to_vcf.py
index 6dc6b018d..e2de4ae84 100644
--- a/malariagen_data/anoph/to_vcf.py
+++ b/malariagen_data/anoph/to_vcf.py
@@ -146,7 +146,7 @@ def snp_calls_to_vcf(
         sample_query: base_params.sample_query,
         sample_query_options: Optional[base_params.sample_query_options] = None,
         site_mask: Optional[base_params.site_mask] = None,
-        max_region_size: Optional[int] = 1_000_000,
+        max_region_size: vcf_params.vcf_max_region_size = 1_000_000,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         chunks: base_params.chunks = base_params.native_chunks,
         overwrite: plink_params.overwrite = False,
diff --git a/malariagen_data/anoph/vcf_params.py b/malariagen_data/anoph/vcf_params.py
index 52b25fd15..2ca02d10d 100644
--- a/malariagen_data/anoph/vcf_params.py
+++ b/malariagen_data/anoph/vcf_params.py
@@ -1,6 +1,6 @@
 """Parameters for VCF exporter functions."""
 
-from typing import Tuple
+from typing import Optional, Tuple
 
 from typing_extensions import Annotated, TypeAlias
 
@@ -19,3 +19,12 @@
     Supported fields: "GT", "GQ", "AD", "MQ".
     """,
 ]
+
+vcf_max_region_size: TypeAlias = Annotated[
+    Optional[int],
+    """
+    Maximum total size of `region` in base pairs. The VCF is loaded in
+    full by IGV, so large regions are rejected. Set to None to disable
+    this check.
+    """,
+]
diff --git a/notebooks/igv.ipynb b/notebooks/igv.ipynb
index 9626a7d09..4d521f2ad 100644
--- a/notebooks/igv.ipynb
+++ b/notebooks/igv.ipynb
@@ -206,7 +206,7 @@
    "metadata": {},
    "source": [
     "## Local VCF in IGV\n",
-    "This exports one sample over a region to a BGZF-compressed VCF under the notebook working directory, then loads it as the SNP track. No index is created, so IGV loads the whole file; keep the region small. The file must be inside the Jupyter server startup directory tree. The `snp_vcf_url` below assumes the server was started from the workspace root; if it was started from `notebooks/`, use the alternate URL shown in the code cell."
+    "This exports one sample over a region to a BGZF-compressed VCF under the notebook working directory, then loads it as the SNP track. No index is created, so IGV loads the whole file; keep the region small. The file is passed to `view_alignments()` by its local path and embedded in the notebook, so it works in any notebook environment (Jupyter, VS Code, Colab)."
    ]
   },
   {
@@ -219,11 +219,11 @@
     "from pathlib import Path\n",
     "\n",
     "\n",
-    "sample_set = \"1229-VO-GH-DADZIE-VMF00095\"\n",
+    "sample_set = \"1240-VO-MZ-KOEKEMOER-VMF00101\"\n",
     "sample_id = str(\n",
     "    af1.sample_metadata(sample_sets=sample_set).iloc[0][\"sample_id\"]\n",
     ")\n",
-    "region = \"2RL:2,447,600-2,447,700\"\n",
+    "region = \"2RL:2,440,000-2,441,000\"\n",
     "\n",
     "local_vcf_path = Path(\"local_igv_vcfs\") / f\"{sample_id}.vcf.gz\"\n",
     "local_vcf_path.parent.mkdir(parents=True, exist_ok=True)\n",
@@ -233,16 +233,13 @@
     "    region=region,\n",
     "    sample_sets=[sample_set],\n",
     "    sample_query=f\"sample_id == '{sample_id}'\",\n",
+    "    overwrite=True,\n",
     ")\n",
     "\n",
-    "# The URL is relative to the Jupyter server startup directory.\n",
-    "# If started from notebooks/, use f\"/{local_vcf_path.as_posix()}\" instead.\n",
-    "snp_vcf_url = f\"/notebooks/{local_vcf_path.as_posix()}\"\n",
-    "\n",
     "af1.view_alignments(\n",
     "    sample=sample_id,\n",
     "    region=region,\n",
-    "    snp_vcf_url=snp_vcf_url,\n",
+    "    snp_vcf_path=local_vcf_path,\n",
     ")"
    ]
   },
@@ -252,6 +249,19 @@
    "id": "19",
    "metadata": {},
    "outputs": [],
+   "source": [
+    "af1.view_alignments(\n",
+    "    sample=sample_id,\n",
+    "    region=region,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "20",
+   "metadata": {},
+   "outputs": [],
    "source": []
   }
  ],
diff --git a/tests/anoph/test_igv.py b/tests/anoph/test_igv.py
index 61faa0645..bb18bcfb1 100644
--- a/tests/anoph/test_igv.py
+++ b/tests/anoph/test_igv.py
@@ -1,3 +1,6 @@
+import base64
+import gzip
+
 import igv_notebook  # type: ignore
 import numpy as np
 import pandas as pd
@@ -89,7 +92,7 @@ def test_view_alignments(fixture, api: AnophelesIgv):
     assert ret is None
 
 
-def test_view_alignments_with_local_snp_vcf(monkeypatch):
+def test_view_alignments_with_local_snp_vcf(monkeypatch, tmp_path):
     class FakeAnophelesIgv(AnophelesIgv):
         @property
         def site_mask_ids(self):
@@ -119,19 +122,36 @@ def wgs_data_catalog(self, sample_set):
         "igv",
         lambda **kwargs: captured.update(kwargs),
     )
-    local_vcf_url = "/data/sample.vcf.gz"
-    api.view_alignments(
-        region="2L:1-10",
-        sample="S1",
-        init=False,
-        snp_vcf_url=local_vcf_url,
-    )
-
-    snp_track = next(track for track in captured["tracks"] if track["name"] == "SNPs")
-    assert snp_track["url"] == local_vcf_url
-    # A local VCF has no index, so IGV must load it in full.
-    assert snp_track["indexed"] is False
-    assert "indexURL" not in snp_track
+    vcf_text = b"##fileformat=VCFv4.3\n"
+    vcf_gz_path = tmp_path / "sample.vcf.gz"
+    with gzip.open(vcf_gz_path, "wb") as f:
+        f.write(vcf_text)
+    vcf_plain_path = tmp_path / "sample.vcf"
+    vcf_plain_path.write_bytes(vcf_text)
+
+    for path, media_type in [
+        (vcf_gz_path, "application/gzip"),
+        (str(vcf_plain_path), "text/plain"),
+    ]:
+        captured.clear()
+        api.view_alignments(
+            region="2L:1-10",
+            sample="S1",
+            init=False,
+            snp_vcf_path=path,
+        )
+
+        snp_track = next(
+            track for track in captured["tracks"] if track["name"] == "SNPs"
+        )
+        # The local VCF is embedded in the track as a data URI.
+        prefix = f"data:{media_type};base64,"
+        assert snp_track["url"].startswith(prefix)
+        with open(path, "rb") as f:
+            assert base64.b64decode(snp_track["url"][len(prefix) :]) == f.read()
+        # A local VCF has no index, so IGV must load it in full.
+        assert snp_track["indexed"] is False
+        assert "indexURL" not in snp_track
 
     captured.clear()
     api.view_alignments(region="2L:1-10", sample="S1", init=False)

From debaed8eab0a29f6861b32fa1a67b95bbeff97ae Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Wed, 7 Oct 2026 16:37:23 +0100
Subject: [PATCH 37/38] shown 5bp region with SNPs, and same region with
 original VCF, plus some extra explanatio in notebookn

---
 notebooks/igv.ipynb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/notebooks/igv.ipynb b/notebooks/igv.ipynb
index 4d521f2ad..39c04f4b6 100644
--- a/notebooks/igv.ipynb
+++ b/notebooks/igv.ipynb
@@ -206,7 +206,7 @@
    "metadata": {},
    "source": [
     "## Local VCF in IGV\n",
-    "This exports one sample over a region to a BGZF-compressed VCF under the notebook working directory, then loads it as the SNP track. No index is created, so IGV loads the whole file; keep the region small. The file is passed to `view_alignments()` by its local path and embedded in the notebook, so it works in any notebook environment (Jupyter, VS Code, Colab)."
+    "This exports one sample over a region to a BGZF-compressed VCF under the notebook working directory, then loads it as the SNP track. No index is created, so IGV loads the whole file; keep the region small- 5000 base pairs, as shown in this demo, works on a modern (2026 Mac) but if you are experiencing crashes, reduce the number of base pairs in the region the VCF is created for. The file is passed to `view_alignments()` by its local path and embedded in the notebook, so it works in any notebook environment (Jupyter, VS Code, Colab). If no variants are present, the SNPs track will be empty, as homozygous calls are escluded for resource reasons. "
    ]
   },
   {
@@ -223,7 +223,7 @@
     "sample_id = str(\n",
     "    af1.sample_metadata(sample_sets=sample_set).iloc[0][\"sample_id\"]\n",
     ")\n",
-    "region = \"2RL:2,440,000-2,441,000\"\n",
+    "region = \"2RL:2,440,000-2,445,000\"\n",
     "\n",
     "local_vcf_path = Path(\"local_igv_vcfs\") / f\"{sample_id}.vcf.gz\"\n",
     "local_vcf_path.parent.mkdir(parents=True, exist_ok=True)\n",

From 57911967bc2793d7f7938f20a44d5d54364517bf Mon Sep 17 00:00:00 2001
From: Katie Barr <Katie Barr>
Date: Tue, 13 Oct 2026 12:22:16 +0100
Subject: [PATCH 38/38] hopefully restored notebooks to previous state and
 commented nbstripout from my pre commit hooks to make sure it doesn't alter
 them

---
 .pre-commit-config.yaml                     |  24 +-
 notebooks/auto_chunks.ipynb                 |  49 +-
 notebooks/biallelic_snps.ipynb              |  49 +-
 notebooks/cohort_geometries.ipynb           |   4 +-
 notebooks/extra_metadata.ipynb              |  33 +-
 notebooks/igv.ipynb                         |   4 +-
 notebooks/karyotype.ipynb                   |  58 +-
 notebooks/ld_pruning.ipynb                  |  39 +-
 notebooks/local_cluster.ipynb               |  27 +-
 notebooks/phenotype_data_demo.ipynb         | 862 +++++++++++++++++++-
 notebooks/plink_convert.ipynb               |   4 +-
 notebooks/plot_aims.ipynb                   |  25 +-
 notebooks/plot_cnv.ipynb                    |  63 +-
 notebooks/plot_diplotype_clustering.ipynb   |  59 +-
 notebooks/plot_diversity.ipynb              |  37 +-
 notebooks/plot_frequencies_heatmap.ipynb    |  79 +-
 notebooks/plot_frequencies_space_time.ipynb | 786 ++++++++++++++++--
 notebooks/plot_fst_gwss.ipynb               |  33 +-
 notebooks/plot_g123_gwss.ipynb              |  43 +-
 notebooks/plot_genes.ipynb                  | 119 ++-
 notebooks/plot_h12_h1x.ipynb                |  65 +-
 notebooks/plot_haplotype_clustering.ipynb   |  61 +-
 notebooks/plot_haplotype_networks.ipynb     |  61 +-
 notebooks/plot_haplotypes_frequencies.ipynb |  24 +-
 notebooks/plot_heterozygosity.ipynb         |  37 +-
 notebooks/plot_ihs_gwss.ipynb               |  31 +-
 notebooks/plot_njt.ipynb                    |  59 +-
 notebooks/plot_pairwise_average_fst.ipynb   |  42 +-
 notebooks/plot_pca.ipynb                    | 119 +--
 notebooks/plot_samples.ipynb                |  13 +-
 notebooks/plot_snps.ipynb                   |  53 +-
 notebooks/plot_xpehh_gwss.ipynb             |  33 +-
 notebooks/profiling/gh498.ipynb             |  20 +-
 notebooks/repr.ipynb                        |  25 +-
 notebooks/spike_sim_test_data.ipynb         |  11 +-
 35 files changed, 2409 insertions(+), 642 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index cb9d17692..f64769051 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -16,15 +16,15 @@ repos:
           - "--fix"
       # Run the formatter.
       - id: ruff-format
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.9.1
-    hooks:
-      # Strip outputs, execution counts and volatile metadata (kernel
-      # display name, language version — these change depending on
-      # which local environment a notebook was last run under, not on
-      # any real edit) from notebooks before they're committed, so
-      # `git diff` only shows real cell-source changes.
-      - id: nbstripout
-        args:
-          - "--extra-keys"
-          - "metadata.kernelspec.display_name metadata.language_info.version"
+#  - repo: https://github.com/kynan/nbstripout
+#    rev: 0.9.1
+#    hooks:
+#      # Strip outputs, execution counts and volatile metadata (kernel
+#      # display name, language version — these change depending on
+#      # which local environment a notebook was last run under, not on
+#      # any real edit) from notebooks before they're committed, so
+#      # `git diff` only shows real cell-source changes.
+#      - id: nbstripout
+#        args:
+#          - "--extra-keys"
+#          - "metadata.kernelspec.display_name metadata.language_info.version"
diff --git a/notebooks/auto_chunks.ipynb b/notebooks/auto_chunks.ipynb
index 5ca68310e..291f7318b 100644
--- a/notebooks/auto_chunks.ipynb
+++ b/notebooks/auto_chunks.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "5ba32f43-2308-43a0-9849-489d77a2f841",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "8015add7-81c7-42bd-94c3-a433047c6ca2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2",
+   "id": "fe297aa9-cfe2-40e5-aa18-3f3a082cdd34",
    "metadata": {},
    "source": [
     "## Default chunk sizes"
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "27c25fb3-ad5c-4652-bf6c-c51d07558790",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -45,7 +45,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "0dbaca2c-d4f0-44c9-b5c8-a992e52dc476",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "f149f390-8e34-42c0-aaa5-7cfe3bbd4c6c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -64,7 +64,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6",
+   "id": "8c1a6207-29bb-4ef9-a8a0-4c6a20acda3c",
    "metadata": {},
    "source": [
     "## Explicit chunk sizes"
@@ -73,7 +73,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "5cbedcb4-cf4e-4f5b-9f0a-901e6abb7dd6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -87,7 +87,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "05598e4a-f362-4b21-a601-9968619135a4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -97,7 +97,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "b903fb3a-1f17-403a-bf8b-43623148ffaa",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -106,7 +106,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "10",
+   "id": "497bd930-c0a1-4ab9-9f56-874673420fbd",
    "metadata": {},
    "source": [
     "## Auto chunk sizes"
@@ -115,7 +115,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "9238bb0f-739e-428b-b4f4-9797b15e045b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -125,7 +125,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "8c894749-6486-478d-9f83-0849aa8a62f2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -135,7 +135,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "f9caefda-4adf-4836-bae4-f7b7bedf8e86",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144,7 +144,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "14",
+   "id": "84bd96e2-42d3-402b-9bca-e071802cb53e",
    "metadata": {},
    "source": [
     "## ND auto chunk sizes"
@@ -153,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "a7f5c439-505f-44c0-abfb-05999e4d9759",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,7 +163,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "6b2e3c60-5d05-445b-91fc-da5115b190bb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -173,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "92c9edab-9653-438c-990a-0bffeb81d5fe",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -183,7 +183,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "04e2f86c-bd3d-4bc1-9142-4f1d243ddbd7",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -191,6 +191,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -203,7 +204,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/biallelic_snps.ipynb b/notebooks/biallelic_snps.ipynb
index fb1b784e9..e4ebef4fc 100644
--- a/notebooks/biallelic_snps.ipynb
+++ b/notebooks/biallelic_snps.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "890ed13a-3e8e-4fd6-b0cb-464e31ab5f64",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "42ecae20-46b7-4218-a37c-e96df62241fb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -31,7 +31,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "9151e470-bdbe-4eee-902c-6178b5f6b62f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "9cb9bfcb-19b5-40e1-bd2b-11a8c2247af3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -52,7 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "489c3941-1ae6-4954-ae48-585823b46649",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "8b024a95-6f9d-4371-95bb-eb6887481a6a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -78,7 +78,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "787973c4-1974-4c8e-8b57-e82b4ea90e6a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -89,7 +89,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "34dfc71b-4e81-4083-8c8a-c08d712e2fa3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -99,7 +99,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "29e17deb-830f-4f5a-9e5f-4707a6041743",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -110,7 +110,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "42afc05c-045e-47c8-925a-9df3676ad0fc",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +120,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "c419ef30-504f-4e8b-8b77-6b15fa29ccb5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -131,7 +131,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "489878b8-eb77-41b8-8b1d-cf6f5035877d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,7 +142,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "ef087212-fef9-45da-a797-00be884887a2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -160,7 +160,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "52d0e6c9-b994-4dd9-91b6-00c58af1ee3b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -170,7 +170,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "b8b26acb-c6c5-4c92-9831-a8a276c952f3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -181,7 +181,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "87cdfec5-ca1e-4139-91fa-93506a112b1a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -200,7 +200,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "c83b492b-11ec-400b-bceb-de6630c34a7b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -210,7 +210,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "07f75f48-bf25-4491-8891-77765867e9a0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -221,7 +221,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "9e434252-0c77-4a5d-ac76-55c87c84fd94",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -229,6 +229,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -241,7 +242,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/cohort_geometries.ipynb b/notebooks/cohort_geometries.ipynb
index 4c690099b..fc8e24a27 100644
--- a/notebooks/cohort_geometries.ipynb
+++ b/notebooks/cohort_geometries.ipynb
@@ -101,11 +101,13 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
   "language_info": {
-   "name": "python"
+   "name": "python",
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/extra_metadata.ipynb b/notebooks/extra_metadata.ipynb
index 69b65a87a..c75b619f0 100644
--- a/notebooks/extra_metadata.ipynb
+++ b/notebooks/extra_metadata.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "38bb6b32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "142627af",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -29,7 +29,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "e1634546",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -40,7 +40,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "5e6e7edd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -58,7 +58,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "140cd606",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "3f507df0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -78,7 +78,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "47a85795",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -88,7 +88,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "d51ae27a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -98,7 +98,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "c13b4e5a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "171ad0ce",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +120,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "450d0e1f",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -128,6 +128,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -140,7 +141,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/igv.ipynb b/notebooks/igv.ipynb
index 39c04f4b6..bdecd784d 100644
--- a/notebooks/igv.ipynb
+++ b/notebooks/igv.ipynb
@@ -267,6 +267,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -279,7 +280,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.11.16"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/karyotype.ipynb b/notebooks/karyotype.ipynb
index ff5ce5f56..857d560ca 100644
--- a/notebooks/karyotype.ipynb
+++ b/notebooks/karyotype.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "95754202-48fb-40fb-8630-8de938cd90a8",
    "metadata": {
     "tags": []
    },
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "0913ba40-7f43-4f3e-8405-f2c3efae65be",
    "metadata": {
     "tags": []
    },
@@ -32,7 +32,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "d65aea9d-953c-47ad-838e-cf205822b6c8",
    "metadata": {
     "tags": []
    },
@@ -44,7 +44,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "a8b1f82f-a60a-4326-a105-a7fd169ed85e",
    "metadata": {
     "tags": []
    },
@@ -62,7 +62,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4",
+   "id": "35e8569a-5e2c-450d-ad8a-283de669aa27",
    "metadata": {},
    "source": [
     "## 2La"
@@ -71,7 +71,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "b7556095-b24a-4a26-9a3a-c98cb14d2e24",
    "metadata": {
     "tags": []
    },
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "4a16ebf5-1a66-4b10-9f5a-d57080e26cb7",
    "metadata": {
     "tags": []
    },
@@ -102,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "8cb4d566-fde1-42e7-a7ba-7294b6adbb66",
    "metadata": {
     "tags": []
    },
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "b522c176-da60-4a4b-ad01-5de74c2a49a6",
    "metadata": {
     "tags": []
    },
@@ -128,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "0daf1c4e-4e19-43e6-ac9b-b4e0680a01a8",
    "metadata": {
     "tags": []
    },
@@ -140,7 +140,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "f7054916-64b8-4b52-a624-1f4eae413b09",
    "metadata": {
     "tags": []
    },
@@ -151,7 +151,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "32a8664a-67c7-48c8-9870-43f5ec2777ff",
    "metadata": {},
    "source": [
     "## 2Rb"
@@ -160,7 +160,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "8d7dc314-9bae-487e-9078-0bf0dec42d9c",
    "metadata": {
     "tags": []
    },
@@ -173,7 +173,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "3a131e26-730a-479d-acaf-735ea92ec93f",
    "metadata": {
     "tags": []
    },
@@ -191,7 +191,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "b728fe52-cae6-4c22-9429-52f3d30d475a",
    "metadata": {
     "tags": []
    },
@@ -205,7 +205,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "b674c67a-f4fc-471a-a9d0-08f45e9006e9",
    "metadata": {
     "tags": []
    },
@@ -216,7 +216,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "16",
+   "id": "51595e8d-d911-4f7f-932b-ed1007fa95fd",
    "metadata": {},
    "source": [
     "## 2Rc_gam"
@@ -225,7 +225,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "3091fec6-6484-4c76-9078-f78fc988ae28",
    "metadata": {
     "tags": []
    },
@@ -242,7 +242,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "da7cd248-2a43-412c-99cf-22ca9786cf2b",
    "metadata": {
     "tags": []
    },
@@ -256,7 +256,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "f5a08876-0431-4190-87bb-48962fd4c98c",
    "metadata": {
     "tags": []
    },
@@ -275,7 +275,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "fa62428f-09c8-4dc5-b45b-e4761041b966",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -287,7 +287,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "2287b6e9-50b7-4ce4-9ef5-a4dd0e5463af",
    "metadata": {
     "tags": []
    },
@@ -300,7 +300,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "22",
+   "id": "8fc6d2af-3d22-42e3-8ca8-756c4e72b141",
    "metadata": {},
    "source": [
     "## 2Rc_col"
@@ -309,7 +309,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "483722dc-86ba-4766-826b-c7d3d2d00cf5",
    "metadata": {
     "tags": []
    },
@@ -326,7 +326,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "8ec9135f-4abc-432b-9707-14db25e650ea",
    "metadata": {
     "tags": []
    },
@@ -340,7 +340,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "1bcb2209-a5db-4cc2-8fac-d51dae1f214c",
    "metadata": {
     "tags": []
    },
@@ -359,7 +359,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "ecee39ab-b8f5-4a79-a31b-2badfafc329b",
    "metadata": {
     "tags": []
    },
@@ -379,6 +379,7 @@
    "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m124"
   },
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -391,7 +392,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/ld_pruning.ipynb b/notebooks/ld_pruning.ipynb
index f2637cc44..292649aeb 100644
--- a/notebooks/ld_pruning.ipynb
+++ b/notebooks/ld_pruning.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "0",
+   "id": "a1b2c3d4-e5f6-7890-abcd-ef1234567890",
    "metadata": {},
    "source": [
     "# LD-pruned biallelic SNP calls\n",
@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "b2c3d4e5-f6a7-8901-bcde-f12345678901",
    "metadata": {},
    "source": [
     "## Setup"
@@ -23,7 +23,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "c3d4e5f6-a7b8-9012-cdef-123456789012",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -33,7 +33,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "d4e5f6a7-b8c9-0123-defa-234567890123",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -47,7 +47,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4",
+   "id": "e5f6a7b8-c9d0-1234-efab-345678901234",
    "metadata": {},
    "source": [
     "## Basic usage"
@@ -56,7 +56,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "f6a7b8c9-d0e1-2345-fabc-456789012345",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +71,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "a7b8c9d0-e1f2-3456-abcd-567890123456",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -83,7 +83,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "b8c9d0e1-f2a3-4567-bcde-678901234567",
    "metadata": {},
    "source": [
     "## Effect of LD parameters"
@@ -92,7 +92,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "c9d0e1f2-a3b4-5678-cdef-789012345678",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -118,7 +118,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "d0e1f2a3-b4c5-6789-defa-890123456789",
    "metadata": {},
    "source": [
     "## Before vs after pruning"
@@ -127,7 +127,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "e1f2a3b4-c5d6-7890-efab-901234567890",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -145,7 +145,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "f2a3b4c5-d6e7-8901-fabc-012345678901",
    "metadata": {},
    "source": [
     "## Downstream compatibility\n",
@@ -156,7 +156,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "a3b4c5d6-e7f8-9012-abcd-123456789abc",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -179,7 +179,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "b4c5d6e7-f8a9-0123-bcde-234567890bcd",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -187,6 +187,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -199,7 +200,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/local_cluster.ipynb b/notebooks/local_cluster.ipynb
index 66da8100b..91d56dc41 100644
--- a/notebooks/local_cluster.ipynb
+++ b/notebooks/local_cluster.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "5ba32f43-2308-43a0-9849-489d77a2f841",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "8015add7-81c7-42bd-94c3-a433047c6ca2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +27,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "27c25fb3-ad5c-4652-bf6c-c51d07558790",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -39,7 +39,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "176f77d9-6376-41ce-b3bf-d8025b5a7174",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -52,7 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "d9657559-8fc9-4a70-97da-12208b9502ea",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -63,7 +63,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "37bbdfb4-b27d-49d0-9888-042f33d17d32",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -75,7 +75,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "87aad9d0-75e6-4d9c-b6a2-814b8fe2ccea",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -85,7 +85,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "a6508f51-6915-4da5-b3ce-f3baa4f69937",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -93,6 +93,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -105,7 +106,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/phenotype_data_demo.ipynb b/notebooks/phenotype_data_demo.ipynb
index dccab55ee..ac1e224f8 100644
--- a/notebooks/phenotype_data_demo.ipynb
+++ b/notebooks/phenotype_data_demo.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "0",
+   "id": "cef10418-08a1-4cc4-a3b0-b8b516cc64fd",
    "metadata": {},
    "source": [
     "# Demonstrating New Phenotype Data Access and Filtering\n",
@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "29554ea2-5e37-40b6-90c1-08088bf9793a",
    "metadata": {},
    "source": [
     "## 1. Setup and Imports\n",
@@ -23,10 +23,351 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "2",
+   "execution_count": 1,
+   "id": "f1280de7-129f-4875-bf12-eb68b8d88573",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/javascript": [
+       "'use strict';\n",
+       "(function(root) {\n",
+       "  function now() {\n",
+       "    return new Date();\n",
+       "  }\n",
+       "\n",
+       "  const force = true;\n",
+       "\n",
+       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
+       "    root._bokeh_onload_callbacks = [];\n",
+       "    root._bokeh_is_loading = undefined;\n",
+       "  }\n",
+       "\n",
+       "const JS_MIME_TYPE = 'application/javascript';\n",
+       "  const HTML_MIME_TYPE = 'text/html';\n",
+       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
+       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
+       "\n",
+       "  /**\n",
+       "   * Render data to the DOM node\n",
+       "   */\n",
+       "  function render(props, node) {\n",
+       "    const script = document.createElement(\"script\");\n",
+       "    node.appendChild(script);\n",
+       "  }\n",
+       "\n",
+       "  /**\n",
+       "   * Handle when an output is cleared or removed\n",
+       "   */\n",
+       "  function handleClearOutput(event, handle) {\n",
+       "    function drop(id) {\n",
+       "      const view = Bokeh.index.get_by_id(id)\n",
+       "      if (view != null) {\n",
+       "        view.model.document.clear()\n",
+       "        Bokeh.index.delete(view)\n",
+       "      }\n",
+       "    }\n",
+       "\n",
+       "    const cell = handle.cell;\n",
+       "\n",
+       "    const id = cell.output_area._bokeh_element_id;\n",
+       "    const server_id = cell.output_area._bokeh_server_id;\n",
+       "\n",
+       "    // Clean up Bokeh references\n",
+       "    if (id != null) {\n",
+       "      drop(id)\n",
+       "    }\n",
+       "\n",
+       "    if (server_id !== undefined) {\n",
+       "      // Clean up Bokeh references\n",
+       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
+       "      cell.notebook.kernel.execute(cmd_clean, {\n",
+       "        iopub: {\n",
+       "          output: function(msg) {\n",
+       "            const id = msg.content.text.trim()\n",
+       "            drop(id)\n",
+       "          }\n",
+       "        }\n",
+       "      });\n",
+       "      // Destroy server and session\n",
+       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
+       "      cell.notebook.kernel.execute(cmd_destroy);\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  /**\n",
+       "   * Handle when a new output is added\n",
+       "   */\n",
+       "  function handleAddOutput(event, handle) {\n",
+       "    const output_area = handle.output_area;\n",
+       "    const output = handle.output;\n",
+       "\n",
+       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
+       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
+       "      return\n",
+       "    }\n",
+       "\n",
+       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
+       "\n",
+       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
+       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
+       "      // store reference to embed id on output_area\n",
+       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
+       "    }\n",
+       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
+       "      const bk_div = document.createElement(\"div\");\n",
+       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
+       "      const script_attrs = bk_div.children[0].attributes;\n",
+       "      for (let i = 0; i < script_attrs.length; i++) {\n",
+       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
+       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
+       "      }\n",
+       "      // store reference to server id on output_area\n",
+       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  function register_renderer(events, OutputArea) {\n",
+       "\n",
+       "    function append_mime(data, metadata, element) {\n",
+       "      // create a DOM node to render to\n",
+       "      const toinsert = this.create_output_subarea(\n",
+       "        metadata,\n",
+       "        CLASS_NAME,\n",
+       "        EXEC_MIME_TYPE\n",
+       "      );\n",
+       "      this.keyboard_manager.register_events(toinsert);\n",
+       "      // Render to node\n",
+       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
+       "      render(props, toinsert[toinsert.length - 1]);\n",
+       "      element.append(toinsert);\n",
+       "      return toinsert\n",
+       "    }\n",
+       "\n",
+       "    /* Handle when an output is cleared or removed */\n",
+       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
+       "    events.on('delete.Cell', handleClearOutput);\n",
+       "\n",
+       "    /* Handle when a new output is added */\n",
+       "    events.on('output_added.OutputArea', handleAddOutput);\n",
+       "\n",
+       "    /**\n",
+       "     * Register the mime type and append_mime function with output_area\n",
+       "     */\n",
+       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
+       "      /* Is output safe? */\n",
+       "      safe: true,\n",
+       "      /* Index of renderer in `output_area.display_order` */\n",
+       "      index: 0\n",
+       "    });\n",
+       "  }\n",
+       "\n",
+       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
+       "  if (root.Jupyter !== undefined) {\n",
+       "    const events = require('base/js/events');\n",
+       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
+       "\n",
+       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
+       "      register_renderer(events, OutputArea);\n",
+       "    }\n",
+       "  }\n",
+       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
+       "    root._bokeh_timeout = Date.now() + 5000;\n",
+       "    root._bokeh_failed_load = false;\n",
+       "  }\n",
+       "\n",
+       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
+       "     \"<div style='background-color: #fdd'>\\n\"+\n",
+       "     \"<p>\\n\"+\n",
+       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
+       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
+       "     \"</p>\\n\"+\n",
+       "     \"<ul>\\n\"+\n",
+       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
+       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
+       "     \"</ul>\\n\"+\n",
+       "     \"<code>\\n\"+\n",
+       "     \"from bokeh.resources import INLINE\\n\"+\n",
+       "     \"output_notebook(resources=INLINE)\\n\"+\n",
+       "     \"</code>\\n\"+\n",
+       "     \"</div>\"}};\n",
+       "\n",
+       "  function display_loaded(error = null) {\n",
+       "    const el = document.getElementById(null);\n",
+       "    if (el != null) {\n",
+       "      const html = (() => {\n",
+       "        if (typeof root.Bokeh === \"undefined\") {\n",
+       "          if (error == null) {\n",
+       "            return \"BokehJS is loading ...\";\n",
+       "          } else {\n",
+       "            return \"BokehJS failed to load.\";\n",
+       "          }\n",
+       "        } else {\n",
+       "          const prefix = `BokehJS ${root.Bokeh.version}`;\n",
+       "          if (error == null) {\n",
+       "            return `${prefix} successfully loaded.`;\n",
+       "          } else {\n",
+       "            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n",
+       "          }\n",
+       "        }\n",
+       "      })();\n",
+       "      el.innerHTML = html;\n",
+       "\n",
+       "      if (error != null) {\n",
+       "        const wrapper = document.createElement(\"div\");\n",
+       "        wrapper.style.overflow = \"auto\";\n",
+       "        wrapper.style.height = \"5em\";\n",
+       "        wrapper.style.resize = \"vertical\";\n",
+       "        const content = document.createElement(\"div\");\n",
+       "        content.style.fontFamily = \"monospace\";\n",
+       "        content.style.whiteSpace = \"pre-wrap\";\n",
+       "        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n",
+       "        content.textContent = error.stack ?? error.toString();\n",
+       "        wrapper.append(content);\n",
+       "        el.append(wrapper);\n",
+       "      }\n",
+       "    } else if (Date.now() < root._bokeh_timeout) {\n",
+       "      setTimeout(() => display_loaded(error), 100);\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  function run_callbacks() {\n",
+       "    try {\n",
+       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
+       "        if (callback != null)\n",
+       "          callback();\n",
+       "      });\n",
+       "    } finally {\n",
+       "      delete root._bokeh_onload_callbacks\n",
+       "    }\n",
+       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
+       "  }\n",
+       "\n",
+       "  function load_libs(css_urls, js_urls, callback) {\n",
+       "    if (css_urls == null) css_urls = [];\n",
+       "    if (js_urls == null) js_urls = [];\n",
+       "\n",
+       "    root._bokeh_onload_callbacks.push(callback);\n",
+       "    if (root._bokeh_is_loading > 0) {\n",
+       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
+       "      return null;\n",
+       "    }\n",
+       "    if (js_urls == null || js_urls.length === 0) {\n",
+       "      run_callbacks();\n",
+       "      return null;\n",
+       "    }\n",
+       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
+       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
+       "\n",
+       "    function on_load() {\n",
+       "      root._bokeh_is_loading--;\n",
+       "      if (root._bokeh_is_loading === 0) {\n",
+       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
+       "        run_callbacks()\n",
+       "      }\n",
+       "    }\n",
+       "\n",
+       "    function on_error(url) {\n",
+       "      console.error(\"failed to load \" + url);\n",
+       "    }\n",
+       "\n",
+       "    for (let i = 0; i < css_urls.length; i++) {\n",
+       "      const url = css_urls[i];\n",
+       "      const element = document.createElement(\"link\");\n",
+       "      element.onload = on_load;\n",
+       "      element.onerror = on_error.bind(null, url);\n",
+       "      element.rel = \"stylesheet\";\n",
+       "      element.type = \"text/css\";\n",
+       "      element.href = url;\n",
+       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
+       "      document.body.appendChild(element);\n",
+       "    }\n",
+       "\n",
+       "    for (let i = 0; i < js_urls.length; i++) {\n",
+       "      const url = js_urls[i];\n",
+       "      const element = document.createElement('script');\n",
+       "      element.onload = on_load;\n",
+       "      element.onerror = on_error.bind(null, url);\n",
+       "      element.async = false;\n",
+       "      element.src = url;\n",
+       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
+       "      document.head.appendChild(element);\n",
+       "    }\n",
+       "  };\n",
+       "\n",
+       "  function inject_raw_css(css) {\n",
+       "    const element = document.createElement(\"style\");\n",
+       "    element.appendChild(document.createTextNode(css));\n",
+       "    document.body.appendChild(element);\n",
+       "  }\n",
+       "\n",
+       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.3.min.js\"];\n",
+       "  const css_urls = [];\n",
+       "\n",
+       "  const inline_js = [    function(Bokeh) {\n",
+       "      Bokeh.set_log_level(\"info\");\n",
+       "    },\n",
+       "function(Bokeh) {\n",
+       "    }\n",
+       "  ];\n",
+       "\n",
+       "  function run_inline_js() {\n",
+       "    if (root.Bokeh !== undefined || force === true) {\n",
+       "      try {\n",
+       "            for (let i = 0; i < inline_js.length; i++) {\n",
+       "      inline_js[i].call(root, root.Bokeh);\n",
+       "    }\n",
+       "\n",
+       "      } catch (error) {throw error;\n",
+       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
+       "      setTimeout(run_inline_js, 100);\n",
+       "    } else if (!root._bokeh_failed_load) {\n",
+       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
+       "      root._bokeh_failed_load = true;\n",
+       "    } else if (force !== true) {\n",
+       "      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n",
+       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
+       "    }\n",
+       "  }\n",
+       "\n",
+       "  if (root._bokeh_is_loading === 0) {\n",
+       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
+       "    run_inline_js();\n",
+       "  } else {\n",
+       "    load_libs(css_urls, js_urls, function() {\n",
+       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
+       "      run_inline_js();\n",
+       "    });\n",
+       "  }\n",
+       "}(window));"
+      ],
+      "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded(error = null) {\n    const el = document.getElementById(null);\n    if (el != null) {\n      const html = (() => {\n        if (typeof root.Bokeh === \"undefined\") {\n          if (error == null) {\n            return \"BokehJS is loading ...\";\n          } else {\n            return \"BokehJS failed to load.\";\n          }\n        } else {\n          const prefix = `BokehJS ${root.Bokeh.version}`;\n          if (error == null) {\n            return `${prefix} successfully loaded.`;\n          } else {\n            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n          }\n        }\n      })();\n      el.innerHTML = html;\n\n      if (error != null) {\n        const wrapper = document.createElement(\"div\");\n        wrapper.style.overflow = \"auto\";\n        wrapper.style.height = \"5em\";\n        wrapper.style.resize = \"vertical\";\n        const content = document.createElement(\"div\");\n        content.style.fontFamily = \"monospace\";\n        content.style.whiteSpace = \"pre-wrap\";\n        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n        content.textContent = error.stack ?? error.toString();\n        wrapper.append(content);\n        el.append(wrapper);\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(() => display_loaded(error), 100);\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.3.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n      try {\n            for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n\n      } catch (error) {throw error;\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "MalariaGEN Ag3 API client initialized.\n",
+      "<MalariaGEN Ag3 API client>\n",
+      "Storage URL             : gs://vo_agam_release_master_us_central1/\n",
+      "Data releases available : 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 3.10, 3.11, 3.12, 3.13, 3.14, 3.15\n",
+      "Results cache           : None\n",
+      "Cohorts analysis        : 20250502\n",
+      "AIM analysis            : 20220528\n",
+      "Site filters analysis   : dt_20200416\n",
+      "Software version        : malariagen_data 15.2.2.post22+48d1097a\n",
+      "Client location         : Tanger-Tetouan-Al Hoceima, Morocco\n",
+      "---\n",
+      "Please note that data are subject to terms of use,\n",
+      "for more information see https://www.malariagen.net/data\n",
+      "or contact support@malariagen.net. For API documentation see \n",
+      "https://malariagen.github.io/malariagen-data-python/v15.2.2.post22+48d1097a/Ag3.html\n"
+     ]
+    }
+   ],
    "source": [
     "import pandas as pd\n",
     "import xarray as xr\n",
@@ -46,7 +387,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "5b1975f3-ad03-450d-b387-6d2ffd5c0143",
    "metadata": {},
    "source": [
     "## 2. Listing Available Phenotype Sample Sets\n",
@@ -55,10 +396,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "4",
+   "execution_count": 2,
+   "id": "7dd3ebc4-64f7-4d0b-ad01-fbc1e08b0636",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Available phenotype sample sets: ['1237-VO-BJ-DJOGBENOU-VMF00050', '1244-VO-GH-YAWSON-VMF00051', '1245-VO-CI-CONSTANT-VMF00054', '1253-VO-TG-DJOGBENOU-VMF00052']\n",
+      "\n",
+      "Using sample set for demonstration: 1237-VO-BJ-DJOGBENOU-VMF00050\n"
+     ]
+    }
+   ],
    "source": [
     "phenotype_sample_sets = ag3.phenotype_sample_sets()\n",
     "print(f\"Available phenotype sample sets: {phenotype_sample_sets}\")\n",
@@ -77,7 +428,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "1319b97a-bd6f-4246-b653-a394aee97930",
    "metadata": {},
    "source": [
     "## 3. Loading Phenotype Data with sample_query\n",
@@ -86,7 +437,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6",
+   "id": "6f6d5023-17b1-4988-8683-22b3f71096ff",
    "metadata": {},
    "source": [
     "### Example 1: Filter by a specific insecticide"
@@ -94,10 +445,93 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "7",
+   "execution_count": 3,
+   "id": "c0b9d0ae-6a79-458a-ad9f-9281a1c6112e",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "--- Loading phenotype data for '1237-VO-BJ-DJOGBENOU-VMF00050' filtered by Deltamethrin ---\n",
+      "Shape of DataFrame: (88, 60)         \n",
+      "\n",
+      "First 5 rows of the filtered DataFrame:\n",
+      "\n",
+      "Unique insecticides in filtered data: ['Deltamethrin']\n",
+      "\n",
+      "DataFrame Info:\n",
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 88 entries, 0 to 87\n",
+      "Data columns (total 60 columns):\n",
+      " #   Column                           Non-Null Count  Dtype  \n",
+      "---  ------                           --------------  -----  \n",
+      " 0   sample_id                        88 non-null     object \n",
+      " 1   country                          88 non-null     object \n",
+      " 2   location                         88 non-null     object \n",
+      " 3   insecticide                      88 non-null     object \n",
+      " 4   dose                             88 non-null     float64\n",
+      " 5   phenotype                        88 non-null     object \n",
+      " 6   sample_set                       88 non-null     object \n",
+      " 7   partner_sample_id                88 non-null     object \n",
+      " 8   contributor                      88 non-null     object \n",
+      " 9   year                             88 non-null     int64  \n",
+      " 10  month                            88 non-null     int64  \n",
+      " 11  latitude                         88 non-null     float64\n",
+      " 12  longitude                        88 non-null     float64\n",
+      " 13  sex_call                         88 non-null     object \n",
+      " 14  release                          88 non-null     object \n",
+      " 15  quarter                          88 non-null     int64  \n",
+      " 16  study_id                         88 non-null     object \n",
+      " 17  study_url                        88 non-null     object \n",
+      " 18  terms_of_use_expiry_date         88 non-null     object \n",
+      " 19  terms_of_use_url                 88 non-null     object \n",
+      " 20  unrestricted_use                 88 non-null     bool   \n",
+      " 21  mean_cov                         88 non-null     Float64\n",
+      " 22  median_cov                       88 non-null     Int64  \n",
+      " 23  modal_cov                        88 non-null     Int64  \n",
+      " 24  mean_cov_2L                      88 non-null     Float64\n",
+      " 25  median_cov_2L                    88 non-null     Int64  \n",
+      " 26  mode_cov_2L                      88 non-null     Int64  \n",
+      " 27  mean_cov_2R                      88 non-null     Float64\n",
+      " 28  median_cov_2R                    88 non-null     Int64  \n",
+      " 29  mode_cov_2R                      88 non-null     Int64  \n",
+      " 30  mean_cov_3L                      88 non-null     Float64\n",
+      " 31  median_cov_3L                    88 non-null     Int64  \n",
+      " 32  mode_cov_3L                      88 non-null     Int64  \n",
+      " 33  mean_cov_3R                      88 non-null     Float64\n",
+      " 34  median_cov_3R                    88 non-null     Int64  \n",
+      " 35  mode_cov_3R                      88 non-null     Int64  \n",
+      " 36  mean_cov_X                       88 non-null     Float64\n",
+      " 37  median_cov_X                     88 non-null     Int64  \n",
+      " 38  mode_cov_X                       88 non-null     Int64  \n",
+      " 39  frac_gen_cov                     88 non-null     Float64\n",
+      " 40  divergence                       88 non-null     Float64\n",
+      " 41  contam_pct                       88 non-null     Float64\n",
+      " 42  contam_LLR                       88 non-null     Float64\n",
+      " 43  aim_species_fraction_arab        88 non-null     float64\n",
+      " 44  aim_species_fraction_colu        88 non-null     float64\n",
+      " 45  aim_species_fraction_colu_no2l   88 non-null     float64\n",
+      " 46  aim_species_gambcolu_arabiensis  88 non-null     object \n",
+      " 47  aim_species_gambiae_coluzzii     88 non-null     object \n",
+      " 48  aim_species                      88 non-null     object \n",
+      " 49  country_iso                      88 non-null     object \n",
+      " 50  admin1_name                      88 non-null     object \n",
+      " 51  admin1_iso                       88 non-null     object \n",
+      " 52  admin2_name                      88 non-null     object \n",
+      " 53  taxon                            88 non-null     object \n",
+      " 54  cohort_admin1_year               88 non-null     object \n",
+      " 55  cohort_admin1_month              88 non-null     object \n",
+      " 56  cohort_admin1_quarter            88 non-null     object \n",
+      " 57  cohort_admin2_year               88 non-null     object \n",
+      " 58  cohort_admin2_month              88 non-null     object \n",
+      " 59  cohort_admin2_quarter            88 non-null     object \n",
+      "dtypes: Float64(10), Int64(12), bool(1), float64(6), int64(3), object(28)\n",
+      "memory usage: 43.2+ KB\n"
+     ]
+    }
+   ],
    "source": [
     "print(\n",
     "    f\"\\n--- Loading phenotype data for '{demo_sample_set}' filtered by Deltamethrin ---\"\n",
@@ -118,7 +552,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8",
+   "id": "daede4ca-01cc-450a-8185-294033af85ad",
    "metadata": {},
    "source": [
     "### Example 2: Filter by multiple conditions (insecticide and dose)"
@@ -126,10 +560,94 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "9",
+   "execution_count": 4,
+   "id": "eab7d81c-d80c-4279-9263-a0d7b425ff85",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "--- Loading phenotype data filtered by Deltamethrin and dose >= 1.0 ---\n",
+      "Shape of DataFrame: (48, 60)\n",
+      "\n",
+      "First 5 rows of the multi-filtered DataFrame:\n",
+      "\n",
+      "Unique insecticides: ['Deltamethrin']\n",
+      "Unique doses: [2.]\n",
+      "\n",
+      "DataFrame Info:\n",
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 48 entries, 40 to 87\n",
+      "Data columns (total 60 columns):\n",
+      " #   Column                           Non-Null Count  Dtype  \n",
+      "---  ------                           --------------  -----  \n",
+      " 0   sample_id                        48 non-null     object \n",
+      " 1   country                          48 non-null     object \n",
+      " 2   location                         48 non-null     object \n",
+      " 3   insecticide                      48 non-null     object \n",
+      " 4   dose                             48 non-null     float64\n",
+      " 5   phenotype                        48 non-null     object \n",
+      " 6   sample_set                       48 non-null     object \n",
+      " 7   partner_sample_id                48 non-null     object \n",
+      " 8   contributor                      48 non-null     object \n",
+      " 9   year                             48 non-null     int64  \n",
+      " 10  month                            48 non-null     int64  \n",
+      " 11  latitude                         48 non-null     float64\n",
+      " 12  longitude                        48 non-null     float64\n",
+      " 13  sex_call                         48 non-null     object \n",
+      " 14  release                          48 non-null     object \n",
+      " 15  quarter                          48 non-null     int64  \n",
+      " 16  study_id                         48 non-null     object \n",
+      " 17  study_url                        48 non-null     object \n",
+      " 18  terms_of_use_expiry_date         48 non-null     object \n",
+      " 19  terms_of_use_url                 48 non-null     object \n",
+      " 20  unrestricted_use                 48 non-null     bool   \n",
+      " 21  mean_cov                         48 non-null     Float64\n",
+      " 22  median_cov                       48 non-null     Int64  \n",
+      " 23  modal_cov                        48 non-null     Int64  \n",
+      " 24  mean_cov_2L                      48 non-null     Float64\n",
+      " 25  median_cov_2L                    48 non-null     Int64  \n",
+      " 26  mode_cov_2L                      48 non-null     Int64  \n",
+      " 27  mean_cov_2R                      48 non-null     Float64\n",
+      " 28  median_cov_2R                    48 non-null     Int64  \n",
+      " 29  mode_cov_2R                      48 non-null     Int64  \n",
+      " 30  mean_cov_3L                      48 non-null     Float64\n",
+      " 31  median_cov_3L                    48 non-null     Int64  \n",
+      " 32  mode_cov_3L                      48 non-null     Int64  \n",
+      " 33  mean_cov_3R                      48 non-null     Float64\n",
+      " 34  median_cov_3R                    48 non-null     Int64  \n",
+      " 35  mode_cov_3R                      48 non-null     Int64  \n",
+      " 36  mean_cov_X                       48 non-null     Float64\n",
+      " 37  median_cov_X                     48 non-null     Int64  \n",
+      " 38  mode_cov_X                       48 non-null     Int64  \n",
+      " 39  frac_gen_cov                     48 non-null     Float64\n",
+      " 40  divergence                       48 non-null     Float64\n",
+      " 41  contam_pct                       48 non-null     Float64\n",
+      " 42  contam_LLR                       48 non-null     Float64\n",
+      " 43  aim_species_fraction_arab        48 non-null     float64\n",
+      " 44  aim_species_fraction_colu        48 non-null     float64\n",
+      " 45  aim_species_fraction_colu_no2l   48 non-null     float64\n",
+      " 46  aim_species_gambcolu_arabiensis  48 non-null     object \n",
+      " 47  aim_species_gambiae_coluzzii     48 non-null     object \n",
+      " 48  aim_species                      48 non-null     object \n",
+      " 49  country_iso                      48 non-null     object \n",
+      " 50  admin1_name                      48 non-null     object \n",
+      " 51  admin1_iso                       48 non-null     object \n",
+      " 52  admin2_name                      48 non-null     object \n",
+      " 53  taxon                            48 non-null     object \n",
+      " 54  cohort_admin1_year               48 non-null     object \n",
+      " 55  cohort_admin1_month              48 non-null     object \n",
+      " 56  cohort_admin1_quarter            48 non-null     object \n",
+      " 57  cohort_admin2_year               48 non-null     object \n",
+      " 58  cohort_admin2_month              48 non-null     object \n",
+      " 59  cohort_admin2_quarter            48 non-null     object \n",
+      "dtypes: Float64(10), Int64(12), bool(1), float64(6), int64(3), object(28)\n",
+      "memory usage: 23.6+ KB\n"
+     ]
+    }
+   ],
    "source": [
     "print(f\"\\n--- Loading phenotype data filtered by Deltamethrin and dose >= 1.0 ---\")\n",
     "df_filtered_multi = ag3.phenotype_data(\n",
@@ -149,7 +667,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "10",
+   "id": "fc1cc12c-b24b-41f3-b147-9e4d817ab588",
    "metadata": {},
    "source": [
     "### Example 3: Applying cohort size filtering\n",
@@ -158,10 +676,91 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "11",
+   "execution_count": 5,
+   "id": "de8cd777-a4b2-44dd-a0bf-64a6ef419da7",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "--- Loading phenotype data with min_cohort_size=10 ---\n",
+      "Shape of DataFrame: (88, 60)\n",
+      "\n",
+      "First 5 rows of the cohort-filtered DataFrame:\n",
+      "\n",
+      "DataFrame Info:\n",
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 88 entries, 0 to 87\n",
+      "Data columns (total 60 columns):\n",
+      " #   Column                           Non-Null Count  Dtype  \n",
+      "---  ------                           --------------  -----  \n",
+      " 0   sample_id                        88 non-null     object \n",
+      " 1   country                          88 non-null     object \n",
+      " 2   location                         88 non-null     object \n",
+      " 3   insecticide                      88 non-null     object \n",
+      " 4   dose                             88 non-null     float64\n",
+      " 5   phenotype                        88 non-null     object \n",
+      " 6   sample_set                       88 non-null     object \n",
+      " 7   partner_sample_id                88 non-null     object \n",
+      " 8   contributor                      88 non-null     object \n",
+      " 9   year                             88 non-null     int64  \n",
+      " 10  month                            88 non-null     int64  \n",
+      " 11  latitude                         88 non-null     float64\n",
+      " 12  longitude                        88 non-null     float64\n",
+      " 13  sex_call                         88 non-null     object \n",
+      " 14  release                          88 non-null     object \n",
+      " 15  quarter                          88 non-null     int64  \n",
+      " 16  study_id                         88 non-null     object \n",
+      " 17  study_url                        88 non-null     object \n",
+      " 18  terms_of_use_expiry_date         88 non-null     object \n",
+      " 19  terms_of_use_url                 88 non-null     object \n",
+      " 20  unrestricted_use                 88 non-null     bool   \n",
+      " 21  mean_cov                         88 non-null     Float64\n",
+      " 22  median_cov                       88 non-null     Int64  \n",
+      " 23  modal_cov                        88 non-null     Int64  \n",
+      " 24  mean_cov_2L                      88 non-null     Float64\n",
+      " 25  median_cov_2L                    88 non-null     Int64  \n",
+      " 26  mode_cov_2L                      88 non-null     Int64  \n",
+      " 27  mean_cov_2R                      88 non-null     Float64\n",
+      " 28  median_cov_2R                    88 non-null     Int64  \n",
+      " 29  mode_cov_2R                      88 non-null     Int64  \n",
+      " 30  mean_cov_3L                      88 non-null     Float64\n",
+      " 31  median_cov_3L                    88 non-null     Int64  \n",
+      " 32  mode_cov_3L                      88 non-null     Int64  \n",
+      " 33  mean_cov_3R                      88 non-null     Float64\n",
+      " 34  median_cov_3R                    88 non-null     Int64  \n",
+      " 35  mode_cov_3R                      88 non-null     Int64  \n",
+      " 36  mean_cov_X                       88 non-null     Float64\n",
+      " 37  median_cov_X                     88 non-null     Int64  \n",
+      " 38  mode_cov_X                       88 non-null     Int64  \n",
+      " 39  frac_gen_cov                     88 non-null     Float64\n",
+      " 40  divergence                       88 non-null     Float64\n",
+      " 41  contam_pct                       88 non-null     Float64\n",
+      " 42  contam_LLR                       88 non-null     Float64\n",
+      " 43  aim_species_fraction_arab        88 non-null     float64\n",
+      " 44  aim_species_fraction_colu        88 non-null     float64\n",
+      " 45  aim_species_fraction_colu_no2l   88 non-null     float64\n",
+      " 46  aim_species_gambcolu_arabiensis  88 non-null     object \n",
+      " 47  aim_species_gambiae_coluzzii     88 non-null     object \n",
+      " 48  aim_species                      88 non-null     object \n",
+      " 49  country_iso                      88 non-null     object \n",
+      " 50  admin1_name                      88 non-null     object \n",
+      " 51  admin1_iso                       88 non-null     object \n",
+      " 52  admin2_name                      88 non-null     object \n",
+      " 53  taxon                            88 non-null     object \n",
+      " 54  cohort_admin1_year               88 non-null     object \n",
+      " 55  cohort_admin1_month              88 non-null     object \n",
+      " 56  cohort_admin1_quarter            88 non-null     object \n",
+      " 57  cohort_admin2_year               88 non-null     object \n",
+      " 58  cohort_admin2_month              88 non-null     object \n",
+      " 59  cohort_admin2_quarter            88 non-null     object \n",
+      "dtypes: Float64(10), Int64(12), bool(1), float64(6), int64(3), object(28)\n",
+      "memory usage: 42.7+ KB\n"
+     ]
+    }
+   ],
    "source": [
     "print(f\"\\n--- Loading phenotype data with min_cohort_size=10 ---\")\n",
     "df_cohort_filtered = ag3.phenotype_data(\n",
@@ -188,10 +787,51 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "12",
+   "execution_count": 6,
+   "id": "9a1f4cc9-528f-40bf-9efe-71aee41c21c3",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "--- Getting binary phenotype outcomes for '1237-VO-BJ-DJOGBENOU-VMF00050' ---\n",
+      "Shape of binary series: (88,)\n",
+      "First 5 entries:\n",
+      "sample_id\n",
+      "VBS18949-5562STDY7801785    0.0\n",
+      "VBS18950-5562STDY7801786    0.0\n",
+      "VBS18951-5562STDY7801787    0.0\n",
+      "VBS18952-5562STDY7801788    0.0\n",
+      "VBS18953-5562STDY7801789    0.0\n",
+      "Name: phenotype_binary, dtype: float64\n",
+      "Unique values in series: [0. 1.]\n",
+      "\n",
+      "Shape of binary series (alive Deltamethrin): (48,)\n",
+      "First 5 entries:\n",
+      "sample_id\n",
+      "VBS18995-5562STDY7801828    1.0\n",
+      "VBS18996-5562STDY7801829    1.0\n",
+      "VBS18998-5562STDY7801830    1.0\n",
+      "VBS18999-5562STDY7801831    1.0\n",
+      "VBS19000-5562STDY7801832    1.0\n",
+      "Name: phenotype_binary, dtype: float64\n",
+      "Unique values in series: [1.]\n",
+      "\n",
+      "Shape of binary series (dose 0.5): (40,)\n",
+      "First 5 entries:\n",
+      "sample_id\n",
+      "VBS18949-5562STDY7801785    0.0\n",
+      "VBS18950-5562STDY7801786    0.0\n",
+      "VBS18951-5562STDY7801787    0.0\n",
+      "VBS18952-5562STDY7801788    0.0\n",
+      "VBS18953-5562STDY7801789    0.0\n",
+      "Name: phenotype_binary, dtype: float64\n",
+      "Unique values in series: [0.]\n"
+     ]
+    }
+   ],
    "source": [
     "print(f\"\\n--- Getting binary phenotype outcomes for '{demo_sample_set}' ---\")\n",
     "\n",
@@ -232,7 +872,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "a92e430e-7f40-48a8-8c98-2405d27aabfb",
    "metadata": {},
    "source": [
     "## 4. Getting Binary Phenotype Outcomes with phenotype_binary\n",
@@ -242,10 +882,51 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "14",
+   "execution_count": 7,
+   "id": "fda88368",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "--- Getting binary phenotype outcomes for '1237-VO-BJ-DJOGBENOU-VMF00050' ---\n",
+      "Shape of binary series: (88,)\n",
+      "First 5 entries:\n",
+      "sample_id\n",
+      "VBS18949-5562STDY7801785    0.0\n",
+      "VBS18950-5562STDY7801786    0.0\n",
+      "VBS18951-5562STDY7801787    0.0\n",
+      "VBS18952-5562STDY7801788    0.0\n",
+      "VBS18953-5562STDY7801789    0.0\n",
+      "Name: phenotype_binary, dtype: float64\n",
+      "Unique values in series: [0. 1.]\n",
+      "\n",
+      "Shape of binary series (alive Deltamethrin): (48,)\n",
+      "First 5 entries:\n",
+      "sample_id\n",
+      "VBS18995-5562STDY7801828    1.0\n",
+      "VBS18996-5562STDY7801829    1.0\n",
+      "VBS18998-5562STDY7801830    1.0\n",
+      "VBS18999-5562STDY7801831    1.0\n",
+      "VBS19000-5562STDY7801832    1.0\n",
+      "Name: phenotype_binary, dtype: float64\n",
+      "Unique values in series: [1.]\n",
+      "\n",
+      "Shape of binary series (dose 0.5): (40,)\n",
+      "First 5 entries:\n",
+      "sample_id\n",
+      "VBS18949-5562STDY7801785    0.0\n",
+      "VBS18950-5562STDY7801786    0.0\n",
+      "VBS18951-5562STDY7801787    0.0\n",
+      "VBS18952-5562STDY7801788    0.0\n",
+      "VBS18953-5562STDY7801789    0.0\n",
+      "Name: phenotype_binary, dtype: float64\n",
+      "Unique values in series: [0.]\n"
+     ]
+    }
+   ],
    "source": [
     "print(f\"\\n--- Getting binary phenotype outcomes for '{demo_sample_set}' ---\")\n",
     "\n",
@@ -286,7 +967,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "15",
+   "id": "62e84ea0",
    "metadata": {},
    "source": [
     "## 5. Loading Phenotype Data Merged with SNP Calls\n",
@@ -295,10 +976,64 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "16",
+   "execution_count": 8,
+   "id": "726ab8a3-6573-49d5-9b29-479176e5dee6",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "--- Loading phenotype data merged with SNP calls ---\n",
+      "Dataset dimensions: FrozenMappingWarningOnValuesAccess({'samples': 48, 'variants': 10001, 'alleles': 4, 'ploidy': 2})\n",
+      "\n",
+      "Dataset structure (rich display):\n",
+      "\n",
+      "First 5 samples and their phenotype_binary values:\n",
+      "[1. 1. 1. 1. 1.]\n",
+      "\n",
+      "First 5 samples and their insecticide values:\n",
+      "['Deltamethrin' 'Deltamethrin' 'Deltamethrin' 'Deltamethrin'\n",
+      " 'Deltamethrin']\n",
+      "\n",
+      "First 5 variant positions:\n",
+      "[2420000 2420001 2420002 2420003 2420004]\n",
+      "\n",
+      "Dataset Info:\n",
+      "xarray.Dataset {\n",
+      "dimensions:\n",
+      "\tsamples = 48 ;\n",
+      "\tvariants = 10001 ;\n",
+      "\talleles = 4 ;\n",
+      "\tploidy = 2 ;\n",
+      "\n",
+      "variables:\n",
+      "\tfloat64 phenotype_binary(samples) ;\n",
+      "\tobject insecticide(samples) ;\n",
+      "\tfloat64 dose(samples) ;\n",
+      "\tobject phenotype(samples) ;\n",
+      "\tobject location(samples) ;\n",
+      "\tobject country(samples) ;\n",
+      "\tobject sample_set(samples) ;\n",
+      "\tobject samples(samples) ;\n",
+      "\t|S1 variant_allele(variants, alleles) ;\n",
+      "\tbool variant_filter_pass_gamb_colu_arab(variants) ;\n",
+      "\tbool variant_filter_pass_gamb_colu(variants) ;\n",
+      "\tbool variant_filter_pass_arab(variants) ;\n",
+      "\tint32 variant_position(variants) ;\n",
+      "\tuint8 variant_contig(variants) ;\n",
+      "\tint8 call_genotype(variants, samples, ploidy) ;\n",
+      "\tint16 call_GQ(variants, samples) ;\n",
+      "\tfloat32 call_MQ(variants, samples) ;\n",
+      "\tint16 call_AD(variants, samples, alleles) ;\n",
+      "\tbool call_genotype_mask(variants, samples, ploidy) ;\n",
+      "\n",
+      "// global attributes:\n",
+      "}"
+     ]
+    }
+   ],
    "source": [
     "print(f\"\\n--- Loading phenotype data merged with SNP calls ---\")\n",
     "\n",
@@ -327,7 +1062,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "17",
+   "id": "99e7b505-4ea4-43dc-91ae-14ac8f12076e",
    "metadata": {},
    "source": [
     "## 6. Loading Phenotype Data Merged with Haplotypes\n",
@@ -336,10 +1071,57 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "18",
+   "execution_count": 9,
+   "id": "403f3a26-71eb-4781-975d-d94b7a021d97",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "--- Loading phenotype data merged with Haplotypes ---\n",
+      "Dataset dimensions: FrozenMappingWarningOnValuesAccess({'samples': 40, 'variants': 2153, 'alleles': 2, 'ploidy': 2})\n",
+      "\n",
+      "Dataset structure (rich display):\n",
+      "\n",
+      "First 5 samples and their phenotype_binary values:\n",
+      "[0. 0. 0. 0. 0.]\n",
+      "\n",
+      "First 5 samples and their insecticide values:\n",
+      "['Deltamethrin' 'Deltamethrin' 'Deltamethrin' 'Deltamethrin'\n",
+      " 'Deltamethrin']\n",
+      "\n",
+      "First 5 variant positions:\n",
+      "[2420351 2420359 2420370 2420371 2420375]\n",
+      "\n",
+      "Dataset Info:\n",
+      "xarray.Dataset {\n",
+      "dimensions:\n",
+      "\tsamples = 40 ;\n",
+      "\tvariants = 2153 ;\n",
+      "\talleles = 2 ;\n",
+      "\tploidy = 2 ;\n",
+      "\n",
+      "variables:\n",
+      "\tfloat64 phenotype_binary(samples) ;\n",
+      "\tobject insecticide(samples) ;\n",
+      "\tfloat64 dose(samples) ;\n",
+      "\tobject phenotype(samples) ;\n",
+      "\tobject location(samples) ;\n",
+      "\tobject country(samples) ;\n",
+      "\tobject sample_set(samples) ;\n",
+      "\tobject samples(samples) ;\n",
+      "\tint32 variant_position(variants) ;\n",
+      "\tuint8 variant_contig(variants) ;\n",
+      "\t|S1 variant_allele(variants, alleles) ;\n",
+      "\tint8 call_genotype(variants, samples, ploidy) ;\n",
+      "\n",
+      "// global attributes:\n",
+      "}"
+     ]
+    }
+   ],
    "source": [
     "print(f\"\\n--- Loading phenotype data merged with Haplotypes ---\")\n",
     "\n",
@@ -368,7 +1150,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "19",
+   "id": "e2ca345f-33e9-481d-8cf6-0ec08253121c",
    "metadata": {},
    "source": [
     "## Conclusion\n",
@@ -378,6 +1160,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -390,7 +1173,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plink_convert.ipynb b/notebooks/plink_convert.ipynb
index 192a0ee1f..a82710ef2 100644
--- a/notebooks/plink_convert.ipynb
+++ b/notebooks/plink_convert.ipynb
@@ -29,6 +29,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "malariagen_plink",
    "language": "python",
    "name": "python3"
   },
@@ -41,7 +42,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.12.5"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_aims.ipynb b/notebooks/plot_aims.ipynb
index 0e045d92d..580a64a39 100644
--- a/notebooks/plot_aims.ipynb
+++ b/notebooks/plot_aims.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "17ea65d6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "8e5fa0a3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "15a6c908",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "a2bfe151",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "446a82fb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "2c181775",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "98686752",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -84,6 +84,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -96,7 +97,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_cnv.ipynb b/notebooks/plot_cnv.ipynb
index 666648045..87def583b 100644
--- a/notebooks/plot_cnv.ipynb
+++ b/notebooks/plot_cnv.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "a6b71675",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,7 +14,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "4526413e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "5ef6e539",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3",
+   "id": "74c46a04",
    "metadata": {},
    "source": [
     "## CNV HMM coverage"
@@ -49,7 +49,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4",
+   "id": "4ccf170b",
    "metadata": {},
    "source": [
     "### Ag3"
@@ -58,7 +58,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "d6bb2a01",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "acd1653f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -86,7 +86,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "f6bbcce7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +100,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "300c961c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "fc1acd04",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -128,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "e995780b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +141,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "1de6d11f",
    "metadata": {},
    "source": [
     "### Af1"
@@ -150,7 +150,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "3a94daf7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,7 +163,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "a302d86c",
    "metadata": {},
    "source": [
     "## CNV HMM heatmap"
@@ -171,7 +171,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "14",
+   "id": "1e5b281f",
    "metadata": {},
    "source": [
     "### Ag3"
@@ -180,7 +180,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "17a8a79d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -193,7 +193,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "649a9194",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -206,7 +206,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "81b8ece4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -219,7 +219,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "c8d588ae",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -233,7 +233,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "54fc714b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -247,7 +247,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "1d240bb8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -260,7 +260,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "ddc76e07",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -274,7 +274,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "cac3c68b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -287,7 +287,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "23",
+   "id": "c566c8ac",
    "metadata": {},
    "source": [
     "### Af1"
@@ -296,7 +296,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "5c4dcf97",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -310,7 +310,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "abdffd76",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -318,6 +318,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -330,7 +331,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_diplotype_clustering.ipynb b/notebooks/plot_diplotype_clustering.ipynb
index 0f32ce3e8..83a7df3ea 100644
--- a/notebooks/plot_diplotype_clustering.ipynb
+++ b/notebooks/plot_diplotype_clustering.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "d3f73666",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -12,7 +12,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "0b889fd3",
    "metadata": {},
    "source": [
     "## Ag3"
@@ -21,7 +21,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "ae9caa20-bdce-4b69-81f9-32d560caa5a2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -36,7 +36,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "15d0bf3e-bbbe-4b67-a39d-c7ed5622cc3b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -60,7 +60,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "92a9bdfd-d808-4c07-8bdd-f2eb3d1e5614",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -82,7 +82,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "b6976257-a5be-489f-940f-9e6c717394b1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -104,7 +104,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "ccb2366f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -125,7 +125,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "c0420334-124d-4bab-9ef7-bb9ceb99d6f0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -145,7 +145,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "e957de19-af70-412a-8c75-2e6835ffb2cd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -167,7 +167,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "857145af",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -189,7 +189,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "f41b7e63",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -208,7 +208,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "b93d6d94-1add-4ba4-8618-87a11c843e6e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -227,7 +227,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "5773cf5a-6040-4ed9-8bdd-01d7f16408a7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -247,7 +247,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "52c159c8-1751-4be7-92d9-52bd17751259",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -264,7 +264,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "7bd7b04c-5401-4c1e-92eb-cae5b3d87851",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -284,7 +284,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "9f6415e6-8d0d-4446-9adb-58c5b236dbcc",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -303,7 +303,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "31df6632-8025-4f55-9d5d-9d04978b1690",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -322,7 +322,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "17",
+   "id": "6016ee62",
    "metadata": {},
    "source": [
     "## Af1"
@@ -331,7 +331,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "87f36d07",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -347,7 +347,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "e1f68c6c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -368,7 +368,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "5bc93110",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -388,7 +388,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "45bdce7c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -406,7 +406,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "5979cca3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -426,7 +426,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "5318dd95-0621-47c1-a3d7-ccfe1950e73f",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -434,6 +434,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -446,12 +447,20 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.11"
   },
   "vscode": {
    "interpreter": {
     "hash": "3b9ddb1005cd06989fd869b9e3d566470f1be01faa610bb17d64e58e32302e8b"
    }
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_diversity.ipynb b/notebooks/plot_diversity.ipynb
index 4215cdcdd..d6d3cd17a 100644
--- a/notebooks/plot_diversity.ipynb
+++ b/notebooks/plot_diversity.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "a383fb19-cc62-4433-9f05-ba2709dd446b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "56ea182c-2446-45ba-921a-a0b5cc1d413e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "75759d4b-d0f8-4489-bda2-5d7d1d9adf17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "531a2131-c2e1-42fc-85b6-09561b67c820",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -56,7 +56,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "e86a9ebd-5fba-4d6e-8ffb-6338d6a59e11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +74,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "da8bcab8-897f-4f5b-9058-137fb3ee1064",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "b3f385ed-d0f8-45da-9ae1-e8ef4f2360c3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -94,7 +94,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "7b0b6f96-f292-446b-a231-6a82fb4fb808",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -104,7 +104,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "63e55e75-ff85-46e1-b20f-4edd2a02ab92",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "149cab79-3f22-4a20-8a13-63f9319d466c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -124,7 +124,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "1928463b-2461-4025-898f-dc05dc0cb214",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -134,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "fa7cad0a-e9cb-4d06-bece-298642fa79b3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144,7 +144,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "431f1274-fc55-4baa-8c67-f8f3d16d5874",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -152,6 +152,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -164,7 +165,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_frequencies_heatmap.ipynb b/notebooks/plot_frequencies_heatmap.ipynb
index 1aa68d198..daab3576e 100644
--- a/notebooks/plot_frequencies_heatmap.ipynb
+++ b/notebooks/plot_frequencies_heatmap.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "820bd2a0-eb8c-42e7-ba56-bef15ae7358a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "702a2213",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -37,7 +37,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "2",
+   "id": "7607169c",
    "metadata": {},
    "source": [
     "## SNP allele frequencies"
@@ -46,7 +46,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "ab3ddd98",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +62,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "204d0b93",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "cc92d92f-31ed-4d1b-ac22-0282692db8c1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "ea2ee8e2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -96,7 +96,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "60f9e53f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "055a88cb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -118,7 +118,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "b41a1026",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -128,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "69ee0608",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -138,7 +138,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "7bcfc20a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -153,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "86ee6d8a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -164,7 +164,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "65c5093e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -174,7 +174,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "14",
+   "id": "2a682de7",
    "metadata": {},
    "source": [
     "## Amino acid frequencies"
@@ -183,7 +183,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "c24c45f6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -198,7 +198,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "64066236",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -208,7 +208,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "3a83a404",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -218,7 +218,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "d5a68fe6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -230,7 +230,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "1fca6e11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -246,7 +246,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "9d55aa57",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -256,7 +256,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "63f02680",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -271,7 +271,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "a8895338",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -286,7 +286,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "220945ee",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -296,7 +296,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "24",
+   "id": "7a9b4bc6",
    "metadata": {},
    "source": [
     "## Gene CNV frequencies"
@@ -305,7 +305,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "8c914a1b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -315,7 +315,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "edd39fc3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -330,7 +330,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27",
+   "id": "fa51bcc3-90fc-4879-8366-b2ad80bc833b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -340,7 +340,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "763ed786",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -352,7 +352,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29",
+   "id": "f5099554",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -364,7 +364,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "f3c20291",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -378,7 +378,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31",
+   "id": "86c5c594",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -402,7 +402,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "6d7ad130-30c2-4cd3-8906-a7ada3ccc75f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -416,7 +416,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33",
+   "id": "83aab417-632e-4fd2-8da4-3ffdd6e233f6",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -424,6 +424,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -436,7 +437,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_frequencies_space_time.ipynb b/notebooks/plot_frequencies_space_time.ipynb
index bb3977e0f..231d86aaa 100644
--- a/notebooks/plot_frequencies_space_time.ipynb
+++ b/notebooks/plot_frequencies_space_time.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "47f669f3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "f820bc66-2fb2-4ca2-9b54-824e50d61a0a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -27,7 +27,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "22b94b9c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +41,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "3",
+   "id": "865f02ea-0673-4d35-ad9e-33088e2d0e58",
    "metadata": {},
    "source": [
     "## Gene CNV frequencies"
@@ -50,7 +50,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "1c612c69-27ee-4f50-b467-786bd998de58",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "7b38fb26-9562-4f52-9381-ced0687b5a40",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -78,7 +78,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "790c99e8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -88,7 +88,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "1bfc7298",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +100,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "fb104e66-7ba0-42ec-9ed0-625a43b69d5b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "ccf5279d-fc5a-4efe-972e-60c7b9515558",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -127,7 +127,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "10",
+   "id": "8d39da45-6875-42e1-9b84-2f0a64189ff4",
    "metadata": {},
    "source": [
     "## Amino acid change frequencies"
@@ -136,7 +136,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "bf75e5b1-f2ca-41f4-a0fd-08a03c979fa4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -155,7 +155,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "2c6ffd89-7edc-4f90-bd23-b03e15ce9714",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -165,7 +165,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "c058a196-2f78-49a0-8a18-cb2420c3278a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -183,7 +183,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "e733c877-a1f1-4dc6-b8a3-a9652430ff39",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -193,7 +193,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "82927720",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -203,7 +203,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "5f9257e0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -213,7 +213,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "94ccc5bf",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -231,7 +231,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "10d0004b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -241,7 +241,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "19",
+   "id": "9b189c4f-fbf6-45cf-96ef-04817084b5ec",
    "metadata": {},
    "source": [
     "## SNP allele frequencies"
@@ -250,7 +250,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "c3738721-8d16-40dd-8a4d-4b588af36b15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -273,7 +273,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "5c743429",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -283,7 +283,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "e16ab3fe",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -293,7 +293,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "26af27a1",
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    "outputs": [],
    "source": [
@@ -303,7 +303,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "9f6a7920",
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    "outputs": [],
    "source": [
@@ -322,7 +322,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "03cfc0e7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -332,7 +332,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "28922f73-f38d-424a-a9c5-1e839c86567b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -350,7 +350,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27",
+   "id": "2a8ea4a0-6bf7-41a3-b734-06535e7dbbc8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -360,7 +360,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "5ce2800c-dfa5-49c3-bde4-3b67423f7807",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -378,7 +378,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "29",
+   "id": "b0f6bda5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -387,7 +387,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "30",
+   "id": "a94d6521",
    "metadata": {},
    "source": [
     "### SNP allele frequencies using `taxon_by`"
@@ -396,7 +396,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31",
+   "id": "0cf222ee",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -420,7 +420,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "2b7e9acc",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -430,14 +430,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33",
+   "id": "2c3227e4",
    "metadata": {},
    "outputs": [],
    "source": []
   },
   {
    "cell_type": "markdown",
-   "id": "34",
+   "id": "eb89088f",
    "metadata": {},
    "source": [
     "### SNP allele frequencies using a custom `period_by`"
@@ -446,7 +446,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35",
+   "id": "bd7856d2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -456,7 +456,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36",
+   "id": "8a54c978",
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    "outputs": [],
    "source": [
@@ -467,7 +467,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "37",
+   "id": "a36cd399",
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    "outputs": [],
    "source": [
@@ -478,7 +478,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38",
+   "id": "1087bada",
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    "outputs": [],
    "source": [
@@ -489,7 +489,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "39",
+   "id": "018e9a59",
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    "outputs": [],
    "source": [
@@ -504,7 +504,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "40",
+   "id": "454c36d9",
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    "outputs": [],
    "source": [
@@ -514,7 +514,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "41",
+   "id": "6b078bd1",
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    "outputs": [],
    "source": [
@@ -524,7 +524,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42",
+   "id": "33d392d3",
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    "outputs": [],
    "source": [
@@ -534,7 +534,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "43",
+   "id": "71bf535c",
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    "outputs": [],
    "source": [
@@ -544,7 +544,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "44",
+   "id": "72feb026",
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    "outputs": [],
    "source": [
@@ -554,7 +554,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "45",
+   "id": "31b9acee",
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    "outputs": [],
    "source": [
@@ -569,7 +569,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "46",
+   "id": "16ac5eb6",
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    "outputs": [],
    "source": [
@@ -579,7 +579,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "47",
+   "id": "d22d6d58",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -587,6 +587,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "mgen_data_py3.11",
    "language": "python",
    "name": "python3"
   },
@@ -599,7 +600,694 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  },
+  "widgets": {
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+      "state": {
+       "_model_module": "jupyter-leaflet",
+       "_model_name": "LeafletMapStyleModel",
+       "_view_name": "ErrorWidgetView",
+       "cursor": "move",
+       "error": {},
+       "msg": "Failed to load model class 'LeafletMapStyleModel' from module 'jupyter-leaflet'"
+      }
+     },
+     "11daaa1c092d4087a034542d7be112d8": {
+      "model_module": "jupyter-leaflet",
+      "model_module_version": "2.0.0",
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+      "state": {
+       "_model_module": "jupyter-leaflet",
+       "_model_name": "LeafletTileLayerModel",
+       "_view_name": "ErrorWidgetView",
+       "attribution": "&copy; <a href=\"https://www.openstreetmap.org/copyright\">OpenStreetMap</a> contributors",
+       "base": true,
+       "bottom": true,
+       "bounds": null,
+       "detect_retina": false,
+       "error": {},
+       "loading": false,
+       "max_native_zoom": null,
+       "max_zoom": 19,
+       "min_native_zoom": null,
+       "min_zoom": 1,
+       "msg": "Failed to load model class 'LeafletTileLayerModel' from module 'jupyter-leaflet'",
+       "name": "OpenStreetMap.Mapnik",
+       "no_wrap": false,
+       "opacity": 1,
+       "options": [
+        "attribution",
+        "bounds",
+        "detect_retina",
+        "max_native_zoom",
+        "max_zoom",
+        "min_native_zoom",
+        "min_zoom",
+        "no_wrap",
+        "tile_size",
+        "tms",
+        "zoom_offset"
+       ],
+       "pane": "",
+       "popup": null,
+       "popup_max_height": null,
+       "popup_max_width": 300,
+       "popup_min_width": 50,
+       "show_loading": false,
+       "subitems": [],
+       "tile_size": 256,
+       "tms": false,
+       "url": "https://tile.openstreetmap.org/{z}/{x}/{y}.png",
+       "visible": true,
+       "zoom_offset": 0
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+       "_model_name": "LeafletAttributionControlModel",
+       "_view_name": "ErrorWidgetView",
+       "error": {},
+       "msg": "Failed to load model class 'LeafletAttributionControlModel' from module 'jupyter-leaflet'",
+       "options": [
+        "position",
+        "prefix"
+       ],
+       "position": "bottomright",
+       "prefix": "ipyleaflet"
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+      "state": {
+       "_model_module": "jupyter-leaflet",
+       "_model_name": "LeafletMapStyleModel",
+       "_view_name": "ErrorWidgetView",
+       "cursor": "grab",
+       "error": {},
+       "msg": "Failed to load model class 'LeafletMapStyleModel' from module 'jupyter-leaflet'"
+      }
+     },
+     "4adf518de8f14f06a6a26b1da007107c": {
+      "model_module": "jupyter-leaflet",
+      "model_module_version": "2.0.0",
+      "model_name": "LeafletZoomControlModel",
+      "state": {
+       "_model_module": "jupyter-leaflet",
+       "_model_name": "LeafletZoomControlModel",
+       "_view_name": "ErrorWidgetView",
+       "error": {},
+       "msg": "Failed to load model class 'LeafletZoomControlModel' from module 'jupyter-leaflet'",
+       "options": [
+        "position",
+        "zoom_in_text",
+        "zoom_in_title",
+        "zoom_out_text",
+        "zoom_out_title"
+       ],
+       "position": "topleft",
+       "zoom_in_text": "+",
+       "zoom_in_title": "Zoom in",
+       "zoom_out_text": "-",
+       "zoom_out_title": "Zoom out"
+      }
+     },
+     "61c564b2766a467daf09f6d22add5730": {
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+      "model_module_version": "2.0.0",
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+       "_model_name": "LeafletMapStyleModel",
+       "_view_name": "ErrorWidgetView",
+       "cursor": "grab",
+       "error": {},
+       "msg": "Failed to load model class 'LeafletMapStyleModel' from module 'jupyter-leaflet'"
+      }
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+      "model_module": "jupyter-leaflet",
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+      "model_name": "LeafletMapStyleModel",
+      "state": {
+       "_model_module": "jupyter-leaflet",
+       "_model_name": "LeafletMapStyleModel",
+       "_view_name": "ErrorWidgetView",
+       "cursor": "move",
+       "error": {},
+       "msg": "Failed to load model class 'LeafletMapStyleModel' from module 'jupyter-leaflet'"
+      }
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+      "model_module": "jupyter-leaflet",
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+       "_model_name": "LeafletMapStyleModel",
+       "_view_name": "ErrorWidgetView",
+       "cursor": "move",
+       "error": {},
+       "msg": "Failed to load model class 'LeafletMapStyleModel' from module 'jupyter-leaflet'"
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+      "model_module": "jupyter-leaflet",
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+       "_model_name": "LeafletMapStyleModel",
+       "_view_name": "ErrorWidgetView",
+       "cursor": "grab",
+       "error": {},
+       "msg": "Failed to load model class 'LeafletMapStyleModel' from module 'jupyter-leaflet'"
+      }
+     },
+     "87119c6f04ac46628c069e5742f7ce08": {
+      "model_module": "jupyter-leaflet",
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+      "model_name": "LeafletMapModel",
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+       "_model_name": "LeafletMapModel",
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+       "bottom": 0,
+       "bounce_at_zoom_limits": true,
+       "box_zoom": true,
+       "center": [
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+        20
+       ],
+       "close_popup_on_click": true,
+       "controls": [
+        "IPY_MODEL_f47067463b3a4c42b9e29e76528a5735",
+        "IPY_MODEL_17ce13191ef8482596ea4952c7a52bc9"
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+        "name": "EPSG3857"
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+       "default_style": "IPY_MODEL_7caf3c5c54274e9b9d93641bdb7a9339",
+       "double_click_zoom": true,
+       "dragging": true,
+       "dragging_style": "IPY_MODEL_62fb525b1c3646ca9e6b45cb3515a0f5",
+       "east": 0,
+       "error": {},
+       "fullscreen": false,
+       "inertia": true,
+       "inertia_deceleration": 3000,
+       "inertia_max_speed": 1500,
+       "interpolation": "bilinear",
+       "keyboard": true,
+       "keyboard_pan_offset": 80,
+       "keyboard_zoom_offset": 1,
+       "layers": [
+        "IPY_MODEL_11daaa1c092d4087a034542d7be112d8"
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+       "layout": "IPY_MODEL_9cfcb8f8e7aa45b6b3b944a6aae9f28e",
+       "left": 9007199254740991,
+       "max_zoom": null,
+       "min_zoom": null,
+       "modisdate": "2022-12-22",
+       "msg": "Failed to load model class 'LeafletMapModel' from module 'jupyter-leaflet'",
+       "north": 0,
+       "options": [
+        "bounce_at_zoom_limits",
+        "box_zoom",
+        "center",
+        "close_popup_on_click",
+        "double_click_zoom",
+        "dragging",
+        "fullscreen",
+        "inertia",
+        "inertia_deceleration",
+        "inertia_max_speed",
+        "interpolation",
+        "keyboard",
+        "keyboard_pan_offset",
+        "keyboard_zoom_offset",
+        "max_zoom",
+        "min_zoom",
+        "prefer_canvas",
+        "scroll_wheel_zoom",
+        "tap",
+        "tap_tolerance",
+        "touch_zoom",
+        "world_copy_jump",
+        "zoom",
+        "zoom_animation_threshold",
+        "zoom_delta",
+        "zoom_snap"
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+       "panes": {},
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+       "right": 0,
+       "scroll_wheel_zoom": false,
+       "south": 0,
+       "style": "IPY_MODEL_cdb18012556e4a548d1696617b42e52a",
+       "tap": true,
+       "tap_tolerance": 15,
+       "top": 9007199254740991,
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+       "west": 0,
+       "window_url": "",
+       "world_copy_jump": false,
+       "zoom": 3,
+       "zoom_animation_threshold": 4,
+       "zoom_delta": 1,
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+      "model_name": "LeafletMapStyleModel",
+      "state": {
+       "_model_module": "jupyter-leaflet",
+       "_model_name": "LeafletMapStyleModel",
+       "_view_name": "ErrorWidgetView",
+       "cursor": "grab",
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diff --git a/notebooks/plot_fst_gwss.ipynb b/notebooks/plot_fst_gwss.ipynb
index 4b89cca28..a627356d6 100644
--- a/notebooks/plot_fst_gwss.ipynb
+++ b/notebooks/plot_fst_gwss.ipynb
@@ -3,7 +3,7 @@
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@@ -21,7 +21,7 @@
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@@ -39,7 +39,7 @@
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@@ -49,7 +49,7 @@
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@@ -67,7 +67,7 @@
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@@ -87,7 +87,7 @@
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@@ -105,7 +105,7 @@
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@@ -173,6 +173,7 @@
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diff --git a/notebooks/plot_g123_gwss.ipynb b/notebooks/plot_g123_gwss.ipynb
index 79fd65732..f2f31a42f 100644
--- a/notebooks/plot_g123_gwss.ipynb
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    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_genes.ipynb b/notebooks/plot_genes.ipynb
index d72d7e8a2..8e7e9ff02 100644
--- a/notebooks/plot_genes.ipynb
+++ b/notebooks/plot_genes.ipynb
@@ -3,8 +3,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
-   "metadata": {},
+   "id": "381912bf",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-03-09T18:09:27.950846Z",
+     "iopub.status.busy": "2022-03-09T18:09:27.950618Z",
+     "iopub.status.idle": "2022-03-09T18:09:29.094180Z",
+     "shell.execute_reply": "2022-03-09T18:09:29.093711Z"
+    }
+   },
    "outputs": [],
    "source": [
     "import malariagen_data\n",
@@ -15,8 +22,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
-   "metadata": {},
+   "id": "d1f1824b",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-03-09T18:09:29.096307Z",
+     "iopub.status.busy": "2022-03-09T18:09:29.096169Z",
+     "iopub.status.idle": "2022-03-09T18:09:29.271174Z",
+     "shell.execute_reply": "2022-03-09T18:09:29.270693Z"
+    }
+   },
    "outputs": [],
    "source": [
     "ag3 = malariagen_data.Ag3(\n",
@@ -29,8 +43,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
-   "metadata": {},
+   "id": "f54b8381",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-03-09T18:09:29.273487Z",
+     "iopub.status.busy": "2022-03-09T18:09:29.273298Z",
+     "iopub.status.idle": "2022-03-09T18:09:31.492555Z",
+     "shell.execute_reply": "2022-03-09T18:09:31.492104Z"
+    }
+   },
    "outputs": [],
    "source": [
     "ag3.plot_genes(\"2R\")"
@@ -39,8 +60,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
-   "metadata": {},
+   "id": "6c6865ac",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-03-09T18:09:31.499205Z",
+     "iopub.status.busy": "2022-03-09T18:09:31.499024Z",
+     "iopub.status.idle": "2022-03-09T18:09:31.551337Z",
+     "shell.execute_reply": "2022-03-09T18:09:31.550930Z"
+    }
+   },
    "outputs": [],
    "source": [
     "ag3.plot_genes(\"2R:28,000,000-29,000,000\")"
@@ -49,8 +77,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
-   "metadata": {},
+   "id": "40b63386",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-03-09T18:09:31.553318Z",
+     "iopub.status.busy": "2022-03-09T18:09:31.553187Z",
+     "iopub.status.idle": "2022-03-09T18:09:31.702387Z",
+     "shell.execute_reply": "2022-03-09T18:09:31.701939Z"
+    }
+   },
    "outputs": [],
    "source": [
     "fig = bklay.column(\n",
@@ -66,7 +101,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "4df200c7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -76,8 +111,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
-   "metadata": {},
+   "id": "066fb262",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-03-09T18:09:31.712754Z",
+     "iopub.status.busy": "2022-03-09T18:09:31.712597Z",
+     "iopub.status.idle": "2022-03-09T18:09:33.866554Z",
+     "shell.execute_reply": "2022-03-09T18:09:33.865947Z"
+    }
+   },
    "outputs": [],
    "source": [
     "ag3.plot_transcript(\"AGAP004707-RD\")"
@@ -86,7 +128,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "8694654d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -96,8 +138,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
-   "metadata": {},
+   "id": "ce93e47e",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-03-09T18:09:33.868626Z",
+     "iopub.status.busy": "2022-03-09T18:09:33.868483Z",
+     "iopub.status.idle": "2022-03-09T18:09:34.121104Z",
+     "shell.execute_reply": "2022-03-09T18:09:34.120683Z"
+    }
+   },
    "outputs": [],
    "source": [
     "ag3.plot_transcript(\"AGAP004050-RA\")"
@@ -106,8 +155,15 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
-   "metadata": {},
+   "id": "86178607",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2022-03-09T18:09:34.123309Z",
+     "iopub.status.busy": "2022-03-09T18:09:34.123167Z",
+     "iopub.status.idle": "2022-03-09T18:09:35.690698Z",
+     "shell.execute_reply": "2022-03-09T18:09:35.690292Z"
+    }
+   },
    "outputs": [],
    "source": [
     "fig1 = ag3.plot_transcript(f\"AGAP004707-RA\", show=False)\n",
@@ -128,7 +184,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "be70a93a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -142,7 +198,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "48814614",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -152,7 +208,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "0c3399fa",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -162,7 +218,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "0ed22cf1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -172,7 +228,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "0589ed21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -182,7 +238,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "c27741d9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -202,7 +258,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "523197c3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -238,7 +294,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "e2a3a927",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -246,6 +302,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "mgen_data_py3.11",
    "language": "python",
    "name": "python3"
   },
@@ -258,7 +315,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_h12_h1x.ipynb b/notebooks/plot_h12_h1x.ipynb
index f253a5b40..2f751b5c8 100644
--- a/notebooks/plot_h12_h1x.ipynb
+++ b/notebooks/plot_h12_h1x.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "ced974cd",
    "metadata": {
     "tags": []
    },
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "9d17216f",
    "metadata": {
     "tags": []
    },
@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2",
+   "id": "a67ec21b",
    "metadata": {},
    "source": [
     "## Ag3"
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "65b7ff2f",
    "metadata": {
     "tags": []
    },
@@ -53,7 +53,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "ac276861-43fb-4f09-b004-57487d75aa41",
    "metadata": {
     "tags": []
    },
@@ -65,7 +65,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "a7c10446",
    "metadata": {
     "tags": []
    },
@@ -82,7 +82,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "b0d308fe-4e8a-412f-9487-7f1c29d3323a",
    "metadata": {
     "tags": []
    },
@@ -99,7 +99,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "63cb17ff",
    "metadata": {
     "tags": []
    },
@@ -118,7 +118,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "4470d24c-8cf1-4d22-b774-0121b4560e27",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -135,7 +135,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "cd125828",
    "metadata": {
     "tags": []
    },
@@ -155,7 +155,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "5716e777",
    "metadata": {
     "tags": []
    },
@@ -174,7 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "fe11bb35",
    "metadata": {
     "tags": []
    },
@@ -194,7 +194,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "b4b7a8d2-95d0-48dc-a32f-3bc96aacfb9f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -213,7 +213,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "73e0e746-add1-4774-bced-461c9742bd95",
    "metadata": {
     "tags": []
    },
@@ -225,7 +225,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "67f48075-6b79-4722-82f7-278bd0868410",
    "metadata": {
     "tags": []
    },
@@ -244,7 +244,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "c3e4622b-31e9-444a-8a09-1590862709fe",
    "metadata": {
     "tags": []
    },
@@ -262,7 +262,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "16",
+   "id": "2801861c",
    "metadata": {},
    "source": [
     "## Af1"
@@ -271,7 +271,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "9144452f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -287,7 +287,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "c5d835e1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -301,7 +301,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "1aaa0573-723c-43b1-baea-750172c4dabc",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -309,7 +309,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "ffc7dc06-6bdb-42d2-a1fb-878612d10dd1",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -317,7 +317,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "89b1cd80",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -333,7 +333,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "82cefa93",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -349,7 +349,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "981ba052-1960-4f2e-ba91-72ac442ca178",
    "metadata": {
     "tags": []
    },
@@ -368,7 +368,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "e3296b4c-cd72-436f-b21a-d210c7520c39",
    "metadata": {
     "tags": []
    },
@@ -386,7 +386,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "1a60cc83-cf30-4152-9eb0-dae7c00ac41b",
    "metadata": {
     "tags": []
    },
@@ -404,7 +404,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "a3b1c22e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -427,6 +427,7 @@
    "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m125"
   },
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -439,12 +440,20 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.11"
   },
   "vscode": {
    "interpreter": {
     "hash": "3b9ddb1005cd06989fd869b9e3d566470f1be01faa610bb17d64e58e32302e8b"
    }
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_haplotype_clustering.ipynb b/notebooks/plot_haplotype_clustering.ipynb
index 8c1e37492..f035681b9 100644
--- a/notebooks/plot_haplotype_clustering.ipynb
+++ b/notebooks/plot_haplotype_clustering.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "d3f73666",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "1",
+   "id": "0b889fd3",
    "metadata": {},
    "source": [
     "## Ag3"
@@ -22,7 +22,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "38abbb28",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "60bd6d1f-e8bd-499e-8c78-e64d2d7e9210",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +62,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "04e74ac9-51db-4bae-875c-1ee50e02d024",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -81,7 +81,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "637ae668-c3b8-4914-a0c2-1587cc252c0c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +95,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "9bca4ab4-89b4-4238-9f82-d7920e107583",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -111,7 +111,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "ccb2366f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -132,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "c0420334-124d-4bab-9ef7-bb9ceb99d6f0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -154,7 +154,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "e957de19-af70-412a-8c75-2e6835ffb2cd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -176,7 +176,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "857145af",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -197,7 +197,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "f41b7e63",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -216,7 +216,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "b93d6d94-1add-4ba4-8618-87a11c843e6e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -235,7 +235,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "5773cf5a-6040-4ed9-8bdd-01d7f16408a7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -255,7 +255,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "52c159c8-1751-4be7-92d9-52bd17751259",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -272,7 +272,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "7bd7b04c-5401-4c1e-92eb-cae5b3d87851",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -291,7 +291,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "9f6415e6-8d0d-4446-9adb-58c5b236dbcc",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -310,7 +310,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "31df6632-8025-4f55-9d5d-9d04978b1690",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -331,7 +331,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "51846e18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -354,7 +354,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "19",
+   "id": "6016ee62",
    "metadata": {},
    "source": [
     "## Af1"
@@ -363,7 +363,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "87f36d07",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -379,7 +379,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "e1f68c6c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -399,7 +399,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "5bc93110",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -419,7 +419,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "45bdce7c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -437,7 +437,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "5979cca3",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -445,6 +445,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -457,7 +458,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.12.8"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_haplotype_networks.ipynb b/notebooks/plot_haplotype_networks.ipynb
index 7088b6725..0ecc0d121 100644
--- a/notebooks/plot_haplotype_networks.ipynb
+++ b/notebooks/plot_haplotype_networks.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "0",
+   "id": "f6b86889",
    "metadata": {},
    "source": [
     "# Haplotype Network Plotting Examples\n",
@@ -12,7 +12,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "1cadfacf",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -22,7 +22,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "2",
+   "id": "dcfe9fab",
    "metadata": {},
    "source": [
     "## Ag3"
@@ -31,7 +31,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "0ebfe96b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -47,7 +47,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "4",
+   "id": "e3ffe116",
    "metadata": {},
    "source": [
     "N.B., manually specifying the server_port parameter doesn't seem to be necessary on colab, but is needed when running locally via Jupyter notebook, otherwise get \"Address already in use\" error and cannot run multiple plots in same notebook."
@@ -55,7 +55,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5",
+   "id": "e5687f24",
    "metadata": {},
    "source": [
     "## Example 1: Direct Column Name (String)\n",
@@ -65,7 +65,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "81ceebb1-2316-4a0f-bf85-55cc561ab00c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -82,7 +82,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7",
+   "id": "2798b459",
    "metadata": {},
    "source": [
     "## Example 2: Cohorts Prefix (String)\n",
@@ -92,7 +92,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "3206fc04-1074-4f6c-8130-81dadff05c72",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9",
+   "id": "44c6a40b",
    "metadata": {},
    "source": [
     "This example uses a dictionary to define custom color groups based on conditions applied to the `\"country\"` column."
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "8236cd99",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -134,7 +134,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "bd1962ba",
    "metadata": {},
    "source": [
     "Setting `color=None` applies the default coloring scheme, typically uniform across all nodes."
@@ -143,7 +143,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "eab4c6fb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -159,7 +159,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "20b54aa0",
    "metadata": {},
    "source": [
     "This replicates Example 1 but uses `server_mode=\"external\"`, useful for rendering plots in certain environments."
@@ -168,7 +168,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "698ab518",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,7 +186,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "15",
+   "id": "bc416bb4",
    "metadata": {},
    "source": [
     "## Af1"
@@ -195,7 +195,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "5e601014",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -210,7 +210,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "17",
+   "id": "d8aeab21",
    "metadata": {},
    "source": [
     "Here, nodes are colored based on the `\"sample_set\"` column."
@@ -219,7 +219,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "6b6f149e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -236,7 +236,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "19",
+   "id": "b1cde074",
    "metadata": {},
    "source": [
     "Using `\"year\"` implies the function looks for `\"cohorts_year\"` in the metadata."
@@ -245,7 +245,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "6d7fc155",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -260,7 +260,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "21",
+   "id": "e6e60160",
    "metadata": {},
    "source": [
     "A dictionary defines custom groups based on the `\"year\"` column (assuming year data is available)."
@@ -269,7 +269,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "882e6b8f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -285,7 +285,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "23",
+   "id": "485becad",
    "metadata": {},
    "source": [
     "With `color=None`, the default coloring is applied."
@@ -294,7 +294,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "bd013c5c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -310,6 +310,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -322,7 +323,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.12.0"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_haplotypes_frequencies.ipynb b/notebooks/plot_haplotypes_frequencies.ipynb
index d88f3c20b..9ad777363 100644
--- a/notebooks/plot_haplotypes_frequencies.ipynb
+++ b/notebooks/plot_haplotypes_frequencies.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "0",
+   "id": "74a45bfa-2af5-4a9d-9285-84f34a82d986",
    "metadata": {},
    "source": [
     "# Ag3"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "a46f23bf-2635-4249-b115-aa8cfd35d33f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "8130522f-98de-463f-83fd-a1c1c460e00e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "2cefad62-e558-4797-9d1a-4b501ad364b0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -53,7 +53,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "6bac8aca-8835-43b7-84c0-f6eb62594d91",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "2770b59a-6b6d-4458-99cf-cdf08e47ddac",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6",
+   "id": "a771fda2-ae68-46bc-b38e-2f4ba6b41b71",
    "metadata": {},
    "source": [
     "# Af1"
@@ -86,7 +86,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "415cc454-ffdd-4bff-8881-95180bcf66f6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +100,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "5d8fb2b5-5b49-4856-8e1c-895174e32f04",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "ef2cb769-4a8d-49fe-8e28-c9dc1af0159d",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -125,6 +125,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -137,7 +138,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_heterozygosity.ipynb b/notebooks/plot_heterozygosity.ipynb
index 89a75efd8..136836b47 100644
--- a/notebooks/plot_heterozygosity.ipynb
+++ b/notebooks/plot_heterozygosity.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "29e2e4a7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -19,7 +19,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "a751077f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "4b2bb835",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -50,7 +50,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "ac466ddf",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -65,7 +65,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "522b2a30",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -80,7 +80,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "10aff683",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +95,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "0c66bd85",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -105,7 +105,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "a8fc0887",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -118,7 +118,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "e564c19b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -133,7 +133,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "c0202112",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -143,7 +143,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "3ebba22a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -156,7 +156,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "df452208",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -171,7 +171,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "af3bf25f",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -179,6 +179,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -191,7 +192,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_ihs_gwss.ipynb b/notebooks/plot_ihs_gwss.ipynb
index 3fd872e69..4a8fa53c7 100644
--- a/notebooks/plot_ihs_gwss.ipynb
+++ b/notebooks/plot_ihs_gwss.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "a31720f1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "ece45863",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -37,7 +37,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "effd3060",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "8e747d9a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "b63d02fe",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -94,7 +94,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "f77bbae1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -112,7 +112,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "cd3c2a2d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -122,7 +122,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "1b87b2f2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -138,7 +138,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "9e3fc1c8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -154,7 +154,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "110b81e5",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -162,6 +162,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -174,7 +175,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_njt.ipynb b/notebooks/plot_njt.ipynb
index 94e210973..7ece0d852 100644
--- a/notebooks/plot_njt.ipynb
+++ b/notebooks/plot_njt.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "3139f0e8-e82f-4d3d-a031-bc9c2d92edd8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "3112b35f-d951-441e-a850-59615aa1f9ec",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "1e83d8ad-e20e-449b-8601-150540e6dd82",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "2964c092-65de-4d2a-9dd9-970418b13bd8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -53,7 +53,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "5f86a798-51c8-4c79-ac60-e7520ab9a503",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "392e6c4c-512f-4a80-bbe9-932280a4efdb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "4437435f-d3b3-4ad6-9e62-6e5f6f01edea",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -102,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "664a9d48-001e-40ed-8901-08bccb2184ba",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -119,7 +119,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "76405cc3-6cdd-4067-a2cb-71095d2c28b3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -137,7 +137,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "972f4787-7c2b-47e2-859c-cd1cc800d92e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -153,7 +153,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "95d20897-6100-4b11-a3e6-38155feb98c2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -168,7 +168,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "5bf936d6-5dc0-409c-828d-7af326102d41",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,7 +186,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "8ea0532c-58f4-4bdf-bd56-0bdfb245e060",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -204,7 +204,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "2335937a-eec7-4d9e-b4ca-b737ff481cd6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -220,7 +220,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "68fb01ae-2567-4c13-b0a3-5890b38165d5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -236,7 +236,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "2f1139fe-9c06-420f-855f-e3900186768a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -252,7 +252,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "3f8f8976-0080-4f44-b665-1534980f0da1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -269,7 +269,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "18fde26a-339a-44a1-a91f-425f22ed96d1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -286,7 +286,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "72155de8-c657-4530-af38-82e0248b85a8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -301,7 +301,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "69aec527-1351-44ba-b394-681fd3d424dd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -316,7 +316,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "38a2817d-933e-46f8-af0a-fedeb7370a38",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -333,7 +333,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "9c1dc76a-1fea-49ee-9341-a7542b2a74f0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -346,7 +346,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "bc7b2566-ac5d-4ca0-bc91-0208fe9d2cb0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -363,7 +363,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "9f5cd515-4933-4f08-82cc-c0fa57e77fb3",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -371,6 +371,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -383,7 +384,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_pairwise_average_fst.ipynb b/notebooks/plot_pairwise_average_fst.ipynb
index b519e3776..0b41014a6 100644
--- a/notebooks/plot_pairwise_average_fst.ipynb
+++ b/notebooks/plot_pairwise_average_fst.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "d0f3796b-cc12-4370-bdb2-ad4f4bd50a3e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -17,7 +17,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "0e719256-3561-4362-a169-c38c9fe96972",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -33,7 +33,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "6af54463-584b-443b-9538-cd141578fde4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "be539d92-3bd5-40b5-b67f-7ae6569db62f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "a7c0815f-7ca9-4ed0-9982-16409f2bc675",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -73,7 +73,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "53a6b0e2-959d-4af1-92ed-bdb748be51c1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -91,7 +91,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "35959f42-732e-40fa-86ad-16d95fb6e740",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -101,7 +101,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "35d304bd-3f39-4dc7-9f7d-905068d5cd0d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -111,7 +111,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "ec418b8f-1451-415e-96e5-bcc5e98428bb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -121,7 +121,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "c16035d2-b5d3-4441-87d9-eda953079161",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -131,7 +131,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "13afd6ed-7962-4935-b1f1-ed12f5e2ceed",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -143,7 +143,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "48a52211-2ef9-47da-b715-d0d74a69a4ad",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -162,7 +162,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "09cc1824-e6f4-4799-a8f4-cf61e472eaf8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -172,7 +172,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "95f112d2-fe76-4091-b73b-d7a17a61cc18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -182,7 +182,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "908b08c8-290f-49d1-b3d3-cb8f9e7d2d21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -192,7 +192,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "818fdac7-dcb4-4da2-8a52-f16ce51a2c0d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -215,7 +215,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "65c1bdd5-f1d2-4814-93e5-ddb1d9c42258",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -225,7 +225,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "5ec8cfe3-336c-4362-9361-78d40ffa0a8e",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -233,7 +233,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "2d3236a2-842d-4c13-92ec-9a4338750aca",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -241,6 +241,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -253,7 +254,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_pca.ipynb b/notebooks/plot_pca.ipynb
index a32a6000a..74421ccc3 100644
--- a/notebooks/plot_pca.ipynb
+++ b/notebooks/plot_pca.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "0",
+   "id": "7d93e741-bddf-4a29-aea2-7bc6be697cb7",
    "metadata": {},
    "source": [
     "# PCA plotting"
@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1",
+   "id": "2f274c61-c660-47b0-92b9-83ab701eb9eb",
    "metadata": {},
    "source": [
     "### Setup"
@@ -19,7 +19,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "36039d6f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -29,7 +29,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "d8bf7a3a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -44,7 +44,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "bfd56044",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -59,7 +59,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "4e5e1c70",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6",
+   "id": "b3760474-2ab2-4291-b5ee-48feccd091f4",
    "metadata": {},
    "source": [
     "## Mayotte"
@@ -77,7 +77,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "e5743579",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -92,7 +92,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "ede14f05-a45d-4e12-9e02-3f4980d867cd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -102,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "5578c99a-37b1-4011-b34f-267aad0b2763",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -114,7 +114,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "a027022f-f700-49c1-8f2d-a43100956155",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -127,7 +127,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "b73b8a6f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -141,7 +141,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "c0b018e3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -151,7 +151,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "32e505db",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -163,7 +163,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "14",
+   "id": "467dbd69-8ba2-41a2-8d01-d9fa78d42326",
    "metadata": {},
    "source": [
     "## Burkina Faso"
@@ -172,7 +172,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "6a2ce979-1553-4459-b3c1-f3dea40bc1a1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -187,7 +187,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "4cb47917-0d8c-47c8-a68d-34d193e2f61a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -201,7 +201,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "241cae4e-3305-4c2a-845f-8871a1a114d4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -214,7 +214,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "18",
+   "id": "a2b46eb9-832d-417c-a082-9fc365b0fc62",
    "metadata": {},
    "source": [
     "## Ag3.0"
@@ -223,7 +223,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "8ac26ed8",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -238,7 +238,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "6e02f847",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -253,7 +253,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "21",
+   "id": "4b957863",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -263,7 +263,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "22",
+   "id": "17baa8d0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -277,7 +277,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "23",
+   "id": "114fb016",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -293,7 +293,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24",
+   "id": "92795fa4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -307,7 +307,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "25",
+   "id": "e0c10b0d-3244-4862-acb7-cf60b9a6a9f2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -324,7 +324,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "26",
+   "id": "727402e7-43a1-4c7d-b21e-a051cd881f01",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -337,7 +337,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27",
+   "id": "cccf1386-c578-4af3-97ec-dc7704840102",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -351,7 +351,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28",
+   "id": "1b1a399a-762d-42db-9e40-776575d9ef5a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -364,7 +364,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "29",
+   "id": "14d04103-2f6f-4f53-8d35-f286de5980d2",
    "metadata": {},
    "source": [
     "## Af1.0"
@@ -373,7 +373,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "30",
+   "id": "6c3fc8d5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -388,7 +388,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "31",
+   "id": "fbe1f54f",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -398,7 +398,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "32",
+   "id": "5c055c99",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -411,7 +411,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "33",
+   "id": "ea74cb43",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -425,7 +425,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "34",
+   "id": "fdfbcd5a-5ef4-4cbc-b430-c0b541925142",
    "metadata": {},
    "source": [
     "## Excluding samples"
@@ -434,7 +434,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35",
+   "id": "6c3251e2-a95c-4d4a-bff1-8e632be0eaf5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -449,7 +449,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "36",
+   "id": "1f0b88a7-d9f6-44a8-9778-4cbaad397765",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -459,7 +459,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "37",
+   "id": "4e370936-925a-4e97-86cb-b22f72b39e64",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -469,7 +469,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38",
+   "id": "9ea24435-d752-4269-a391-b057e1650d44",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -482,7 +482,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "39",
+   "id": "0f114dd9-965d-4579-8cce-76f45fde6a37",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -500,7 +500,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "40",
+   "id": "a5392844-a828-48f3-8222-bfc1817c3493",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -510,7 +510,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "41",
+   "id": "6d87eeb5-8dc6-4a31-a8a3-e936d4d05215",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -520,7 +520,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42",
+   "id": "770b01ee-642e-4903-93fa-eef084924234",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -530,7 +530,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "43",
+   "id": "9438fd91-b463-4d28-8279-5eaa728a8f2e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -542,7 +542,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "44",
+   "id": "58e7b2c1-b4c1-4c93-823c-8531693636e4",
    "metadata": {},
    "source": [
     "## Excluding samples during fit"
@@ -551,7 +551,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "45",
+   "id": "1014a17c-12bb-46c3-9a7b-f2449d205ce3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -569,7 +569,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "46",
+   "id": "e48d46dd-5c7f-4573-a5f5-c15a389d2e1e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -579,7 +579,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "47",
+   "id": "1fb5192e-f63f-443d-91a9-e82b2de14c69",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -589,7 +589,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "48",
+   "id": "873c53f5-8690-4690-85f0-8ce1845e2862",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -599,7 +599,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "49",
+   "id": "0bb86ba2-e428-4ae0-9e0c-703345c89324",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -612,7 +612,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "50",
+   "id": "7b28c4c8-9382-4889-8651-77ef0be929f6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -624,7 +624,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "51",
+   "id": "f1e8c954",
    "metadata": {},
    "source": [
     "## PCA with cohort downsampling"
@@ -633,7 +633,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "52",
+   "id": "e4a484f3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -653,7 +653,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "53",
+   "id": "abb2ee83",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -661,6 +661,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -673,7 +674,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_samples.ipynb b/notebooks/plot_samples.ipynb
index ec7be4fe3..2f7f31c8a 100644
--- a/notebooks/plot_samples.ipynb
+++ b/notebooks/plot_samples.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -256,6 +256,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "mgen_data_py3.11",
    "language": "python",
    "name": "python3"
   },
@@ -268,7 +269,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
  "nbformat": 4,
diff --git a/notebooks/plot_snps.ipynb b/notebooks/plot_snps.ipynb
index 502545139..5daa69c4e 100644
--- a/notebooks/plot_snps.ipynb
+++ b/notebooks/plot_snps.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "14640993",
    "metadata": {
     "tags": []
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@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "5d740cac",
    "metadata": {
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@@ -31,7 +31,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "bd576b75",
    "metadata": {
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@@ -43,7 +43,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "7de3ba82",
    "metadata": {
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@@ -56,7 +56,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "3a3de267-affa-46e6-92b9-d07553cad816",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -66,7 +66,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "2c66985f-592b-4fb5-a560-5cdedb472bee",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "82096dc0",
    "metadata": {
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@@ -88,7 +88,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "10c340aa",
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    "outputs": [],
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@@ -98,7 +98,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "e8e463dd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "7fb757a7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -118,7 +118,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "0e3a8961",
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@@ -132,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "11",
+   "id": "63aca10c",
    "metadata": {
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@@ -144,7 +144,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "6fb5216e",
    "metadata": {
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@@ -158,7 +158,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "13",
+   "id": "0d88ceb5",
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@@ -174,7 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "0c98cabe",
    "metadata": {
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@@ -186,7 +186,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "8a7c297d",
    "metadata": {
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@@ -198,7 +198,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "16",
+   "id": "d0552711",
    "metadata": {
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@@ -210,7 +210,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "d269e02e",
    "metadata": {
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@@ -224,7 +224,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "872c56ab",
    "metadata": {
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@@ -238,7 +238,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "c24a21ab",
    "metadata": {
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@@ -254,7 +254,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "60280e52",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -262,6 +262,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -274,7 +275,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
  },
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diff --git a/notebooks/plot_xpehh_gwss.ipynb b/notebooks/plot_xpehh_gwss.ipynb
index ba03632a5..cd9e67583 100644
--- a/notebooks/plot_xpehh_gwss.ipynb
+++ b/notebooks/plot_xpehh_gwss.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "32067e1d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "966049ec",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "838eddc4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -54,7 +54,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "e780aa23",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -75,7 +75,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "b26a9654",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -93,7 +93,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "181227f6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -111,7 +111,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "89cf50ac",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -130,7 +130,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "78b452f5",
    "metadata": {},
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@@ -140,7 +140,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8",
+   "id": "079a3308",
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    "source": [
@@ -157,7 +157,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "d6290896",
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    "source": [
@@ -174,7 +174,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "a5aed96d",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -182,6 +182,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -194,7 +195,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
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diff --git a/notebooks/profiling/gh498.ipynb b/notebooks/profiling/gh498.ipynb
index 21818ea9b..06012f43e 100644
--- a/notebooks/profiling/gh498.ipynb
+++ b/notebooks/profiling/gh498.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
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-   "id": "0",
+   "id": "a790fb90-492e-480a-9403-d1d242c48389",
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    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "a00d7b52-ac2e-44ef-9e08-a9d33ee90276",
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@@ -28,7 +28,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "0fdd5aea-803c-477e-9b35-8edc61a31b7e",
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@@ -45,7 +45,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "ff092693-dd1e-44ff-bd09-7cfb57b9134f",
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    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "9a75f64f-fe2c-44d9-abae-18ff8453d154",
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    "source": [
@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5",
+   "id": "0c433078-8c78-4a2a-93d3-d9330762bbbd",
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@@ -96,7 +96,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "8f945545-7a73-4c9a-8867-e2cae9e1aece",
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    "source": [
@@ -117,7 +117,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "1fcae9c4-9c1c-402f-a6c9-70a7f6f939a7",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -125,6 +125,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -137,7 +138,8 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.8.18"
   }
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diff --git a/notebooks/repr.ipynb b/notebooks/repr.ipynb
index 7aa1dbb88..3b8c2a289 100644
--- a/notebooks/repr.ipynb
+++ b/notebooks/repr.ipynb
@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0",
+   "id": "aa5bad7b",
    "metadata": {
     "tags": []
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@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1",
+   "id": "24cdd3a1",
    "metadata": {
     "tags": []
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@@ -27,7 +27,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2",
+   "id": "362dedbf",
    "metadata": {
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@@ -39,7 +39,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3",
+   "id": "294fc8b7",
    "metadata": {
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@@ -51,7 +51,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4",
+   "id": "9ca832ac",
    "metadata": {
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@@ -64,7 +64,7 @@
   {
    "cell_type": "code",
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-   "id": "5",
+   "id": "73e79af6",
    "metadata": {
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@@ -76,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6",
+   "id": "4781d110",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -84,6 +84,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -96,7 +97,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
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diff --git a/notebooks/spike_sim_test_data.ipynb b/notebooks/spike_sim_test_data.ipynb
index ae7709062..ba87ef806 100644
--- a/notebooks/spike_sim_test_data.ipynb
+++ b/notebooks/spike_sim_test_data.ipynb
@@ -1197,6 +1197,7 @@
  ],
  "metadata": {
   "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1209,7 +1210,15 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3"
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
   }
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