kevlar-dev / kevlar

Reference-free variant discovery in large eukaryotic genomes

https://kevlar.readthedocs.io

MIT License

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Update VCF parser #359

Closed standage closed 5 years ago

standage commented 5 years ago

This update modifies kevlar's VCF parser so that it does not choke on VCF produced by scalpel or DiscoSnp++. In particular, it checks whether VCF FILTER strings matched the pre-defined filters used by kevlar. If not, it prints a warning message rather than throwing an exception. This warning message can be disabled by setting reader.suppress_filter_warnings to True.

Closes #358.

codecov[bot] commented 5 years ago

Codecov Report

Merging #359 into master will decrease coverage by 0.27%. The diff coverage is 38.46%.

@@            Coverage Diff             @@
##           master     #359      +/-   ##
==========================================
- Coverage   97.05%   96.79%   -0.27%     
==========================================
  Files          48       48              
  Lines        2886     2895       +9     
  Branches      533      536       +3     
==========================================
+ Hits         2801     2802       +1     
- Misses         52       58       +6     
- Partials       33       35       +2

Impacted Files	Coverage Δ
kevlar/vcf.py	`93.31% <38.46%> (-2.69%)`	:arrow_down:

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update e55ba25...c9d5dbb. Read the comment docs.

codecov-io commented 5 years ago

Codecov Report

Merging #359 into master will decrease coverage by 0.27%. The diff coverage is 38.46%.

@@            Coverage Diff             @@
##           master     #359      +/-   ##
==========================================
- Coverage   97.05%   96.79%   -0.27%     
==========================================
  Files          48       48              
  Lines        2886     2895       +9     
  Branches      533      536       +3     
==========================================
+ Hits         2801     2802       +1     
- Misses         52       58       +6     
- Partials       33       35       +2

Impacted Files	Coverage Δ
kevlar/vcf.py	`93.31% <38.46%> (-2.69%)`	:arrow_down:

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update c4d4ddd...a17fddf. Read the comment docs.