From 639ecdc931325819eb9adeda0d80402152cf93ac Mon Sep 17 00:00:00 2001 From: fromer Date: Mon, 1 Nov 2010 19:02:52 +0000 Subject: [PATCH] Noted in comment that using a single sample in MergePhasedSegregatingAlternateAllelesVCFWriter does NOT update any of the INFO fields, though this could be changed in the future... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4604 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/contexts/variantcontext/VariantContextUtils.java | 3 --- .../MergePhasedSegregatingAlternateAllelesVCFWriter.java | 2 +- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java index b8610da56..ba3154977 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java @@ -818,9 +818,6 @@ public class VariantContextUtils { VariantContext mergedVc = new VariantContext(mergedName, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles(), mergedGenotypes, mergedNegLog10PError, mergedFilters, mergedAttribs); - /* Calculate VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY from scratch - [though technically they should already be consistent with each of vc1 and vc2's respective alleles]: - */ mergedAttribs = new HashMap(mergedVc.getAttributes()); VariantContextUtils.calculateChromosomeCounts(mergedVc, mergedAttribs, true); mergedVc = VariantContext.modifyAttributes(mergedVc, mergedAttribs); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java index 32b72c394..c01051b8f 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java @@ -107,7 +107,7 @@ public class MergePhasedSegregatingAlternateAllelesVCFWriter implements VCFWrite public void add(VariantContext vc, byte refBase) { if (useSingleSample != null) { // only want to output context for one sample Genotype sampGt = vc.getGenotype(useSingleSample); - if (sampGt != null) + if (sampGt != null) // TODO: subContextFromGenotypes() does not handle any INFO fields [AB, HaplotypeScore, MQ, etc.]. Note that even SelectVariants.subsetRecord() only handles AC,AN,AF, and DP! vc = vc.subContextFromGenotypes(sampGt); else // asked for a sample that this vc does not contain, so ignore this vc: return;