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Check that we're biallelic before calling isSNP() 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2127 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-23 20:20:48 +00:00
parent 5744a1d968
commit ed4cf3de57
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java
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@ -23,7 +23,7 @@ public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {
public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
Variation snp = (Variation)tracker.lookup("snps", null); Variation snp = (Variation)tracker.lookup("snps", null);
return (snp != null && snp.isSNP()) ? context.getLocation() : null; return (snp != null && snp.isBiallelic() && snp.isSNP()) ? context.getLocation() : null;
} }
public void onTraversalDone(GenomeLoc sum) { public void onTraversalDone(GenomeLoc sum) {