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Hidden option to SelectVariants to force the genotypes information to be decoded by computing AC

This commit is contained in:
Mark DePristo 2012-06-04 07:04:14 -04:00
parent 17fbd103d0
commit 37b8d70321
1 changed files with 13 additions and 1 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -315,6 +315,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
@Argument(fullName="fullyDecode", doc="If true, the incoming VariantContext will be fully decoded", required=false)
private boolean fullyDecode = false;
@Hidden
@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 class used to store the intermediate variants in the integer random selection process */
private class RandomVariantStructure {
private VariantContext vc;
@ -495,7 +500,14 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
}
for (VariantContext vc : vcs) {
if ( fullyDecode ) vc = vc.fullyDecode(vcfRods.get(vc.getSource()));
// an option for performance testing only
if ( fullyDecode )
vc = vc.fullyDecode(vcfRods.get(vc.getSource()));
// an option for performance testing only
if ( forceGenotypesDecode )
logger.info("forceGenotypesDecode with getCalledChrCount() = " + vc.getCalledChrCount());
if ( IDsToKeep != null && ! IDsToKeep.contains(vc.getID()) )
continue;