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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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Updates to localize & alac modules #301

Closed standage closed 5 years ago

standage commented 5 years ago

This PR started with the intent to deprecate kevlar localize and the commands that depend on it (kevlar alac and kevlar simplex). However, the brand-spanking-new kevlar cutout intentionally has essentially the same interface as kevlar localize, so the PR turned into a refactoring. The old kevlar localize module has been deleted and the new kevlar cutout module has been renamed kevlar localize. The kevlar alac module has been updated (and simplified!) to support the new streaming conventions.

codecov[bot] commented 5 years ago

Codecov Report

Merging #301 into master will decrease coverage by 0.05%. The diff coverage is 99.2%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #301      +/-   ##
==========================================
- Coverage   96.89%   96.83%   -0.06%     
==========================================
  Files          50       48       -2     
  Lines        2997     2910      -87     
  Branches      515      501      -14     
==========================================
- Hits         2904     2818      -86     
- Misses         59       60       +1     
+ Partials       34       32       -2
Impacted Files Coverage Δ
kevlar/cli/__init__.py 100% <ø> (ø) :arrow_up:
kevlar/__init__.py 93.26% <ø> (-0.07%) :arrow_down:
kevlar/call.py 87.5% <100%> (+0.24%) :arrow_up:
kevlar/alac.py 98% <100%> (-0.8%) :arrow_down:
kevlar/reference.py 97.53% <100%> (+0.12%) :arrow_up:
kevlar/cli/localize.py 100% <100%> (ø) :arrow_up:
kevlar/assemble.py 100% <100%> (ø) :arrow_up:
kevlar/localize.py 98.65% <98.92%> (-1.35%) :arrow_down:

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