added option for ValidateBasicSomaticShortMutations to output a vcf #4999
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davidbenjamin
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Codecov Report
@@ Coverage Diff @@
## master #4999 +/- ##
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- Coverage 86.382% 86.378% -0.004%
- Complexity 28674 28679 +5
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Files 1785 1785
Lines 132713 132742 +29
Branches 14766 14773 +7
===============================================
+ Hits 114640 114660 +20
- Misses 12746 12748 +2
- Partials 5327 5334 +7
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takutosato
approved these changes
Jul 23, 2018
| import java.util.stream.Collectors; | ||
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| import static org.broadinstitute.hellbender.utils.variant.GATKVCFConstants.ALLELE_BALANCE_HET_KEY; |
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There's a bunch of unused imports
| "Validation judgment: validated, unvalidated, or skipped."); | ||
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| public static enum Judgment { |
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IntelliJ says nested enums are implicitly static
| @@ -180,4 +180,49 @@ private void assertValidationResult(final List<AnnotatedInterval> variantValidat | |||
| discoveryAltCoverage, discoveryAltCoverage + discoveryRefCoverage, | |||
| minCount)); | |||
| } | |||
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| //TODO delete this!!!! | |||
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Either delete or make this a real test
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@takutosato This lets
ValidateBasicSomaticShortMutationsoptionally annotate theevalvcf with validationINFOfields in addition to the standard output of a tsv. Having a vcf is more convenient for some things in MC3.