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Bug fixes to hapmap conversion in VariantsToVCF

This commit is contained in:
Eric Banks 2012-10-29 01:45:33 -04:00
parent 43625f652e
commit ac99437eec
2 changed files with 2 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -364,7 +364,7 @@ public class VariantContextAdaptors {
long end = hapmap.getEnd();
if ( deletionLength > 0 )
end += deletionLength;
end += (deletionLength - 1);
VariantContext vc = new VariantContextBuilder(name, hapmap.getChr(), hapmap.getStart(), end, alleles).id(hapmap.getName()).genotypes(genotypes).make();
return vc;
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -160,7 +160,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
alleleMap.put(RawHapMapFeature.DELETION, Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
alleleMap.put(RawHapMapFeature.INSERTION, Allele.create((char)ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
hapmap.setActualAlleles(alleleMap);
// also, use the correct positioning for insertions