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An option to not actually write out the results of select variants 

-- Useful for performance testing of the SV operations themselves.
This commit is contained in:
Mark DePristo 2012-06-04 19:03:43 -04:00
parent 6f7a01e00d
commit 5b8bd81991
1 changed files with 10 additions and 3 deletions
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13
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -319,6 +319,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
@Argument(fullName="forceGenotypesDecode", doc="If true, the incoming VariantContext will have its genotypes forcibly decoded by computing AC across all genotypes. For efficiency testing only", required=false) @Argument(fullName="forceGenotypesDecode", doc="If true, the incoming VariantContext will have its genotypes forcibly decoded by computing AC across all genotypes. For efficiency testing only", required=false)
private boolean forceGenotypesDecode = false; private boolean forceGenotypesDecode = false;
@Hidden
@Argument(fullName="justRead", doc="If true, we won't actually write the output file. For efficiency testing only", required=false)
private boolean justRead = false;
/* Private class used to store the intermediate variants in the integer random selection process */ /* Private class used to store the intermediate variants in the integer random selection process */
private class RandomVariantStructure { private class RandomVariantStructure {
@ -505,8 +509,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
vc = vc.fullyDecode(vcfRods.get(vc.getSource())); vc = vc.fullyDecode(vcfRods.get(vc.getSource()));
// an option for performance testing only // an option for performance testing only
if ( forceGenotypesDecode ) if ( forceGenotypesDecode ) {
logger.info("forceGenotypesDecode with getCalledChrCount() = " + vc.getCalledChrCount()); final int x = vc.getCalledChrCount();
//logger.info("forceGenotypesDecode with getCalledChrCount() = " + );
}
if ( IDsToKeep != null && ! IDsToKeep.contains(vc.getID()) ) if ( IDsToKeep != null && ! IDsToKeep.contains(vc.getID()) )
continue; continue;
@ -572,7 +578,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
randomlyAddVariant(++variantNumber, sub); randomlyAddVariant(++variantNumber, sub);
} }
else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) { else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
vcfWriter.add(sub); if ( ! justRead )
vcfWriter.add(sub);
} }
} }
} }