diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 3805e48df..690cc71ac 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -315,6 +315,11 @@ public class SelectVariants extends RodWalker 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 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;