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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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Extend variant-spanning-kmer-mask capability to `kevlar call` #302

Closed standage closed 5 years ago

standage commented 5 years ago

This update extends the ability to create a mask of variant-spanning k-mers to kevlar call via the --gen-mask option, This was previously introduced to kevlar alac only. Both implementations now actually report if the FPR is higher than the user-supplied max FPR.

Closes #295.

codecov[bot] commented 5 years ago

Codecov Report

Merging #302 into master will increase coverage by <.01%. The diff coverage is 96.96%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #302      +/-   ##
==========================================
+ Coverage   96.83%   96.83%   +<.01%     
==========================================
  Files          48       48              
  Lines        2910     2943      +33     
  Branches      501      507       +6     
==========================================
+ Hits         2818     2850      +32     
  Misses         60       60              
- Partials       32       33       +1
Impacted Files Coverage Δ
kevlar/cli/call.py 100% <100%> (ø) :arrow_up:
kevlar/alac.py 98.21% <100%> (+0.21%) :arrow_up:
kevlar/call.py 88.8% <95.23%> (+1.29%) :arrow_up:

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