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fixed a bug where normal p value argument in FilterMutectCalls was static #5982

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merged 1 commit into from
Jun 6, 2019

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@davidbenjamin davidbenjamin commented Jun 4, 2019

@takutosato Silly error on my part. Made the argument parser crash whenever the argument was set to a non-default value.

@Closes #5978.

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codecov bot commented Jun 4, 2019

Codecov Report

Merging #5982 into master will decrease coverage by 0.204%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #5982       +/-   ##
===============================================
- Coverage     86.929%   86.725%   -0.204%     
+ Complexity     32721     32644       -77     
===============================================
  Files           2013      2013               
  Lines         151306    151354       +48     
  Branches       16610     16622       +12     
===============================================
- Hits          131529    131262      -267     
- Misses         13720     14064      +344     
+ Partials        6057      6028       -29
Impacted Files Coverage Δ Complexity Δ
.../mutect/filtering/M2FiltersArgumentCollection.java 94.737% <ø> (+0.142%) 6 <0> (ø) ⬇️
...lkers/mutect/filtering/Mutect2FilteringEngine.java 97.17% <100%> (ø) 45 <0> (ø) ⬇️
...walkers/mutect/filtering/NormalArtifactFilter.java 96% <100%> (+0.348%) 8 <1> (ø) ⬇️
...ils/nio/NioFileCopierWithProgressMeterResults.java 0% <0%> (-94.737%) 0% <0%> (-9%)
...s/spark/ParallelCopyGCSDirectoryIntoHDFSSpark.java 0% <0%> (-74.257%) 0% <0%> (-17%)
...nder/tools/spark/pipelines/PrintVariantsSpark.java 0% <0%> (-66.667%) 0% <0%> (-2%)
...ols/funcotator/FuncotatorDataSourceDownloader.java 0% <0%> (-66.197%) 0% <0%> (-14%)
...nder/utils/nio/NioFileCopierWithProgressMeter.java 17% <0%> (-52.5%) 9% <0%> (-30%)
...oadinstitute/hellbender/utils/gcs/BucketUtils.java 60% <0%> (-18.667%) 32% <0%> (-8%)
...transforms/markduplicates/MarkDuplicatesSpark.java 77.372% <0%> (-13.253%) 50% <0%> (+9%)
... and 9 more

@davidbenjamin davidbenjamin merged commit 353b991 into master Jun 6, 2019
@davidbenjamin davidbenjamin deleted the db_static_arg_whoops branch June 6, 2019 16:23
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FilterMutectCalls doesn't accept this parameter --normal-p-value-threshold
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