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VariantAnnotator shouldn't die when multiple records occur at the same position 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4853 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-12-16 04:05:47 +00:00
parent b1f0df0047
commit 9f3e56e487
1 changed files with 7 additions and 4 deletions
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11
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -202,12 +202,13 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
if ( tracker == null )
return 0;
VariantContext vc = tracker.getVariantContext(ref, "variant", null, context.getLocation(), true);
if ( vc == null )
Collection<VariantContext> VCs = tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
if ( VCs.size() == 0 )
return 0;
Collection<VariantContext> annotatedVCs = VCs;
// if the reference base is not ambiguous, we can annotate
Collection<VariantContext> annotatedVCs = Arrays.asList(vc);
Map<String, StratifiedAlignmentContext> stratifiedContexts;
if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
if ( ! context.hasExtendedEventPileup() ) {
@ -216,7 +217,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
stratifiedContexts = StratifiedAlignmentContext.splitContextBySampleName(context.getExtendedEventPileup(), ASSUME_SINGLE_SAMPLE);
}
if ( stratifiedContexts != null ) {
annotatedVCs = engine.annotateContext(tracker, ref, stratifiedContexts, vc);
annotatedVCs = new ArrayList<VariantContext>(VCs.size());
for ( VariantContext vc : VCs )
annotatedVCs.addAll(engine.annotateContext(tracker, ref, stratifiedContexts, vc));
}
}