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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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Handle multinucleotide variants correctly #332

Closed standage closed 5 years ago

standage commented 5 years ago

The first commit in this PR is a regression test for correct handling of multinucleotide variants. It fails at the moment since MNVs are not yet handled correctly. When this bug is fixed, adjacent single-nucleotide substitutions will be merged into a single variant for subsequent processing and analysis. See #331.

codecov[bot] commented 5 years ago

Codecov Report

Merging #332 into master will decrease coverage by 0.15%. The diff coverage is 82.35%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #332      +/-   ##
==========================================
- Coverage   95.22%   95.06%   -0.16%     
==========================================
  Files          47       47              
  Lines        2910     2941      +31     
  Branches      534      544      +10     
==========================================
+ Hits         2771     2796      +25     
- Misses        103      106       +3     
- Partials       36       39       +3
Impacted Files Coverage Δ
kevlar/call.py 88.32% <100%> (+1.12%) :arrow_up:
kevlar/vcf.py 96.57% <68.42%> (-2.2%) :arrow_down:

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