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No longer emits records at filtered sites, in sub-sampling mode 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4883 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-12-20 16:43:50 +00:00
parent 60880b925f
commit b3ac47812c
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -1008,7 +1008,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
}
private void writeVCF(VariantContext vc) {
if ( samplesToPhase == null || vc.isVariant() ) // if we are only operating on specific samples, don't write out all sites, just those where the VC is variant
if ( samplesToPhase == null || (vc.isVariant() && vc.isNotFiltered())) // if we are only operating on specific samples, don't write out all sites, just those where the VC is variant
WriteVCF.writeVCF(vc, writer, logger);
}