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Minor update 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5778 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-05-08 03:48:37 +00:00
parent 15c7bd82a5
commit bf40351094
1 changed files with 2 additions and 6 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
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@ -95,15 +95,11 @@ public class VariantValidationAssessor extends RodWalker<Pair<VariantContext, By
if ( tracker == null ) if ( tracker == null )
return null; return null;
List<Object> rods = tracker.getReferenceMetaData(INPUT_VARIANT_ROD_BINDING_NAME); VariantContext vc = tracker.getVariantContext(ref, INPUT_VARIANT_ROD_BINDING_NAME, ref.getLocus());
// ignore places where we don't have a variant // ignore places where we don't have a variant
if ( rods.size() == 0 ) if ( vc == null )
return null; return null;
Object rod = rods.get(0);
VariantContext vc = VariantContextAdaptors.toVariantContext(INPUT_VARIANT_ROD_BINDING_NAME, rod, ref);
if ( sampleNames == null ) if ( sampleNames == null )
sampleNames = new TreeSet<String>(vc.getSampleNames()); sampleNames = new TreeSet<String>(vc.getSampleNames());