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re-fixing for a different approach suggested by eric! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5402 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro 2011-03-08 04:54:49 +00:00
parent 5564838087
commit b733cba7c7
1 changed files with 1 additions and 1 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -210,7 +210,7 @@ public class UnifiedGenotyperEngine {
private VariantContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, AlignmentContext rawContext) { private VariantContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, AlignmentContext rawContext) {
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(), false); final VariantContext vcInput = tracker.getVariantContext(ref, "alleles", null, ref.getLocus(), true);
if ( vcInput == null ) if ( vcInput == null )
return 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());