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print out the right variant 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1543 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2009-09-08 01:37:35 +00:00
parent 5791da17ae
commit 4a95f2181d
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java
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@ -102,7 +102,7 @@ public class SNPGenotypeConcordance implements ConcordanceType {
else if ( call1.isSNP() && call2.isReference() && bestVsRef1 >= LOD ) else if ( call1.isSNP() && call2.isReference() && bestVsRef1 >= LOD )
printVariant(refVsVar1Writer, call1); printVariant(refVsVar1Writer, call1);
else if ( call2.isSNP() && call1.isReference() && bestVsRef2 >= LOD ) else if ( call2.isSNP() && call1.isReference() && bestVsRef2 >= LOD )
printVariant(refVsVar2Writer, call1); printVariant(refVsVar2Writer, call2);
} }
private boolean sameVariantAllele(String genotype1, String genotype2, char ref) { private boolean sameVariantAllele(String genotype1, String genotype2, char ref) {