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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
This commit is contained in:
fromer 2010-11-01 19:02:52 +00:00
parent 8439f0aa61
commit 639ecdc931
2 changed files with 1 additions and 4 deletions
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3
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -818,9 +818,6 @@ public class VariantContextUtils {
VariantContext mergedVc = new VariantContext(mergedName, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles(), mergedGenotypes, mergedNegLog10PError, mergedFilters, mergedAttribs); 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<String, Object>(mergedVc.getAttributes()); mergedAttribs = new HashMap<String, Object>(mergedVc.getAttributes());
VariantContextUtils.calculateChromosomeCounts(mergedVc, mergedAttribs, true); VariantContextUtils.calculateChromosomeCounts(mergedVc, mergedAttribs, true);
mergedVc = VariantContext.modifyAttributes(mergedVc, mergedAttribs); mergedVc = VariantContext.modifyAttributes(mergedVc, mergedAttribs);

2
java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergePhasedSegregatingAlternateAllelesVCFWriter.java
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@ -107,7 +107,7 @@ public class MergePhasedSegregatingAlternateAllelesVCFWriter implements VCFWrite
public void add(VariantContext vc, byte refBase) { public void add(VariantContext vc, byte refBase) {
if (useSingleSample != null) { // only want to output context for one sample if (useSingleSample != null) { // only want to output context for one sample
Genotype sampGt = vc.getGenotype(useSingleSample); 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); vc = vc.subContextFromGenotypes(sampGt);
else // asked for a sample that this vc does not contain, so ignore this vc: else // asked for a sample that this vc does not contain, so ignore this vc:
return; return;