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RBP now operates correctly at non-variant sites so we can phase hom-ref genotypes with -sampleToPhase 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4903 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-12-23 13:11:22 +00:00
parent 376bc563d4
commit 8c583ea405
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -201,7 +201,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
if (tracker == null) if (tracker == null)
return null; return null;
// todo -- potential performance problem here with unconditional, frequent writes to debug
mostDownstreamLocusReached = ref.getLocus(); mostDownstreamLocusReached = ref.getLocus();
if ( DEBUG ) logger.debug("map() at: " + mostDownstreamLocusReached); if ( DEBUG ) logger.debug("map() at: " + mostDownstreamLocusReached);
@ -217,7 +216,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
VariantAndReads vr = new VariantAndReads(vc, context); VariantAndReads vr = new VariantAndReads(vc, context);
unphasedSiteQueue.add(vr); unphasedSiteQueue.add(vr);
// todo -- potential performance problem here with unconditional, frequent writes to debug
if ( DEBUG ) logger.debug("Added variant to queue = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),vr.variant)); if ( DEBUG ) logger.debug("Added variant to queue = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),vr.variant));
} }
else { else {
@ -1008,12 +1006,14 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
} }
private void writeVCF(VariantContext vc) { private void writeVCF(VariantContext vc) {
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 if ( vc.isNotFiltered() )
//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); WriteVCF.writeVCF(vc, writer, logger);
} }
public static boolean processVariantInPhasing(VariantContext vc) { public static boolean processVariantInPhasing(VariantContext vc) {
return isUnfilteredBiallelicSNP(vc); return vc.isNotFiltered() && ((vc.isSNP() && vc.isBiallelic()) || ! vc.isVariant()); // we can handle the non-variant case as well
//return isUnfilteredBiallelicSNP(vc);
} }
@ -1887,4 +1887,4 @@ class MultipleBaseCounts {
return sb.toString(); return sb.toString();
} }
} }