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kevlar-dev / kevlar

Reference-free variant discovery in large eukaryotic genomes
https://kevlar.readthedocs.io
MIT License
40 stars 9 forks source link

Drop all handling of mate sequences #353

Closed standage closed 5 years ago

standage commented 5 years ago

This update drops all handling of mate sequences. The ability to parse augmented Fastx files with mate seqs is retained for now, although kevlar will no longer create augfastx files with mate seq annotations. Closes #344.

codecov[bot] commented 5 years ago

Codecov Report

Merging #353 into master will increase coverage by 2.04%. The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #353      +/-   ##
==========================================
+ Coverage   95.09%   97.13%   +2.04%     
==========================================
  Files          48       48              
  Lines        3056     2894     -162     
  Branches      575      532      -43     
==========================================
- Hits         2906     2811      -95     
+ Misses        108       51      -57     
+ Partials       42       32      -10
Impacted Files Coverage Δ
kevlar/simlike.py 98.65% <ø> (+2.17%) :arrow_up:
kevlar/call.py 95.15% <ø> (+6.82%) :arrow_up:
kevlar/seqio.py 100% <ø> (+32.69%) :arrow_up:
kevlar/varmap.py 99.01% <ø> (ø) :arrow_down:
kevlar/__init__.py 90.27% <ø> (-1.07%) :arrow_down:
kevlar/cli/augment.py 100% <ø> (ø) :arrow_up:
kevlar/novel.py 98.64% <100%> (-0.02%) :arrow_down:
kevlar/vcf.py 95.97% <100%> (-0.01%) :arrow_down:
kevlar/augment.py 100% <100%> (ø) :arrow_up:

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