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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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Discard short alignment blocks prior to variant calling #303

Closed standage closed 5 years ago

standage commented 5 years ago

Short alignment blocks are a cause for suspicion, and in any case can result in variant-spanning windows shorter than ksize, for which likelihood scores cannot be computed. This update discards alignment blocks shorter than ksize in length prior to variant calling. Closes #260.

codecov[bot] commented 5 years ago

Codecov Report

Merging #303 into master will increase coverage by <.01%. The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #303      +/-   ##
==========================================
+ Coverage   96.83%   96.84%   +<.01%     
==========================================
  Files          48       48              
  Lines        2943     2946       +3     
  Branches      507      508       +1     
==========================================
+ Hits         2850     2853       +3     
  Misses         60       60              
  Partials       33       33
Impacted Files Coverage Δ
kevlar/cli/alac.py 100% <ø> (ø) :arrow_up:
kevlar/cli/localize.py 100% <ø> (ø) :arrow_up:
kevlar/varmap.py 100% <100%> (ø) :arrow_up:

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