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kevlar-dev / kevlar

Reference-free variant discovery in large eukaryotic genomes
https://kevlar.readthedocs.io
MIT License
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Split workflow #314

Closed standage closed 5 years ago

standage commented 5 years ago

Accelerating the assemble/localize/align/call portion of the workflow via Python's threading module has proven unsuccessful, despite its dispatch of the assembly tasks the C extensions. This update modifies the split, localize, call, and simlike modules and the mark I Snakemake workflow to support parallel processing during that portion of the procedure.

codecov[bot] commented 5 years ago

Codecov Report

Merging #314 into master will decrease coverage by 0.26%. The diff coverage is 63.63%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #314      +/-   ##
==========================================
- Coverage   95.95%   95.69%   -0.27%     
==========================================
  Files          44       44              
  Lines        2819     2834      +15     
  Branches      491      496       +5     
==========================================
+ Hits         2705     2712       +7     
- Misses         84       89       +5     
- Partials       30       33       +3
Impacted Files Coverage Δ
kevlar/call.py 87.2% <0%> (-1.42%) :arrow_down:
kevlar/simlike.py 85.79% <100%> (-0.09%) :arrow_down:
kevlar/cli/simlike.py 100% <100%> (ø) :arrow_up:
kevlar/localize.py 98.64% <100%> (ø) :arrow_up:
kevlar/vcf.py 96.69% <100%> (+0.06%) :arrow_up:
kevlar/cli/localize.py 100% <100%> (ø) :arrow_up:
kevlar/split.py 76.92% <45.45%> (-23.08%) :arrow_down:

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