Repository navigation
Add tsinfer 1.0 chr20p matching benchmarks - #6
Merged
Merged
Conversation
Benchmark the tsinfer-hmm and tsls engines on the ancestor and sample matching phases of a tsinfer 1.0 inference of 1000 Genomes chr20p, using tsinfer's paths as ground truth. - tsinfer_groups.py recomputes tsinfer's match groups (run in the tsinfer environment). - tsinfer_data.py makes ancestor workloads for any group, by cutting the ancestors tree sequence before the group, and sample workloads. - run.py uses a workload's model.json and per-query site windows. - tsinfer_summary.py compares the paths with tsinfer's and reports times and memory. - The engines take alleles and weight_by_n options, and share a base class.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Benchmark the tsinfer-hmm and tsls engines on the ancestor and sample matching phases of a tsinfer 1.0 inference of 1000 Genomes chr20p, using tsinfer's paths as ground truth.