Issues

Reproducing TelomereHunter's telomere content
AdamaJava/adamajava#367 · opened on Jun 18, 2024
Difficulty Extracting Telomere Length Data from qmotif XML Output
AdamaJava/adamajava#351 · opened on Apr 4, 2024
1
addition of hg38 telomere coordinates for qmotif
AdamaJava/adamajava#346 · opened on Feb 15, 2024
3
multi threading bug in XmlUtils.updateMapWithLimit
AdamaJava/adamajava#333 · opened on May 24, 2023
org.qcmg.picard.SAMFileReaderFactory keeps spawning processes
AdamaJava/adamajava#330 · opened on Mar 20, 2023
7
Default value for build (37) is always used in maf file
AdamaJava/adamajava#324 · opened on Oct 14, 2022
input format issue on qbasepileup indel mode
AdamaJava/adamajava#305 · opened on Feb 28, 2022
input output format issue on qbasepileup coverage mode
AdamaJava/adamajava#304 · opened on Feb 28, 2022
qp2 produces different output with different threading options
AdamaJava/adamajava#289 · opened on Dec 6, 2021
7
QSamToFastq.java exception
AdamaJava/adamajava#281 · opened on Sep 20, 2021
At least some of our VCFs are invalid according to the VCF spec.
AdamaJava/adamajava#265 · opened on Jun 14, 2021
7
qprofiler - Fastq mode can't convert String to Integer
AdamaJava/adamajava#248 · opened on Feb 25, 2021
1
to deprecate qSNP related QSnpGATKRecord and QSnpRecord
AdamaJava/adamajava#231 · opened on Jan 31, 2021
1
documentation for qmotif points to sourceforge for tar location
AdamaJava/adamajava#225 · opened on Jan 19, 2021
Exception control
AdamaJava/adamajava#219 · opened on Dec 7, 2020
Patten.split vs String.split
AdamaJava/adamajava#218 · opened on Dec 7, 2020
tidy up classes loading relationship
AdamaJava/adamajava#217 · opened on Dec 4, 2020
3
Scaled Counts is Negative 1
AdamaJava/adamajava#207 · opened on Nov 3, 2020
xml indentation issue
AdamaJava/adamajava#204 · opened on Oct 31, 2020
Add Details to qMotif Documentation
AdamaJava/adamajava#203 · opened on Oct 29, 2020
encoding issue in qio
AdamaJava/adamajava#198 · opened on Oct 22, 2020
buffered IO vs stream IO
AdamaJava/adamajava#197 · opened on Oct 22, 2020
Combined variants at same position - how to report
AdamaJava/adamajava#155 · opened on Feb 17, 2020
Adjust wdl task runtime attributes (mem, cpu etc) depending on size of input
AdamaJava/adamajava#134 · opened on Oct 24, 2019
3
COV vcf header should contain coverage cutoff values used
AdamaJava/adamajava#85 · opened on Jul 19, 2019 · Vcf header tidy-up