make isReference do the right thing

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1439 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-19 20:32:29 +00:00 · 2009-08-19 20:32:29 +00:00 · ed8c92a12a
parent 21091b9839
commit ed8c92a12a
1 changed files with 1 additions and 1 deletions
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java
@ -119,7 +119,7 @@ public class rodVariants extends BasicReferenceOrderedDatum implements AllelicVa
    }

    public boolean isReference() {
-        return refBase == bestGenotype.charAt(0);
+        return refBase == bestGenotype.charAt(0) && refBase == bestGenotype.charAt(1);
    }

    public boolean isSNP() {