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When creating a synthetic VC based on the passed in alleles, set the reference base for indel.

This commit is contained in:
Eric Banks 2012-03-13 10:59:58 -04:00
parent 1675bd4dd7
commit 5200f7f919
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -253,7 +253,7 @@ public class UnifiedGenotyperEngine {
VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles); VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null ) if ( vcInput == null )
return null; return null;
vc = new VariantContextBuilder("UG_call", ref.getLocus().getContig(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()).make(); vc = new VariantContextBuilder("UG_call", ref.getLocus().getContig(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()).referenceBaseForIndel(vcInput.getReferenceBaseForIndel()).make();
} else { } else {
// deal with bad/non-standard reference bases // deal with bad/non-standard reference bases
if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) ) if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) )