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Made number of samples to put variant site in M2 pon adjustable #4566

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merged 2 commits into from
Mar 23, 2018

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davidbenjamin
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@takutosato Can you review this?

@sooheelee This closes #4552.

@davidbenjamin davidbenjamin added this to the Popularize Mutect 2 at the Broad milestone Mar 23, 2018
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codecov-io commented Mar 23, 2018

Codecov Report

Merging #4566 into master will increase coverage by 0.005%.
The diff coverage is 100%.

@@              Coverage Diff               @@
##              master    #4566       +/-   ##
==============================================
+ Coverage     79.845%   79.85%   +0.005%     
  Complexity     16964    16964               
==============================================
  Files           1062     1062               
  Lines          61676    61677        +1     
  Branches        9983     9983               
==============================================
+ Hits           49245    49249        +4     
+ Misses          8539     8536        -3     
  Partials        3892     3892
Impacted Files Coverage Δ Complexity Δ
...ls/walkers/mutect/CreateSomaticPanelOfNormals.java 87.5% <100%> (+0.227%) 8 <2> (ø) ⬇️
...e/hellbender/engine/spark/SparkContextFactory.java 73.973% <0%> (+2.74%) 11% <0%> (ø) ⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java 90% <0%> (+10%) 3% <0%> (ø) ⬇️

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One comment. No need for a second review

@@ -114,6 +118,14 @@
doc="VCFs for samples to include. May be specified either one at a time, or as one or more .args file containing multiple VCFs, one per line.", optional = false)
private Set<File> vcfs = new LinkedHashSet<>(0);

/**
* The VCFs can be input as either one or more .args file(s) containing one VCF per line, or VCFs can be
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I think this comment block got copied and pasted from above

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Whoops!

@davidbenjamin davidbenjamin merged commit 3dc6834 into master Mar 23, 2018
@davidbenjamin davidbenjamin deleted the db_m2_pon branch March 27, 2018 19:04
cwhelan pushed a commit to cwhelan/gatk-linked-reads that referenced this pull request May 25, 2018
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Feature request for CreateSomaticPanelOfNormals to allow changing number of coincident samples
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