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Bug fix based on GATK run report 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5354 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2011-03-02 14:18:12 +00:00
parent 660998065b
commit ae42c0c7da
1 changed files with 2 additions and 0 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -211,6 +211,8 @@ public class UnifiedGenotyperEngine {
VariantContext vc; VariantContext vc;
if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true); final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
if ( vcInput == null )
return null;
vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()); vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles());
} else { } else {
Set<Allele> alleles = new HashSet<Allele>(); Set<Allele> alleles = new HashSet<Allele>();