From ed8c92a12a4264cd53ec494caa2019ad11d76afe Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 19 Aug 2009 20:32:29 +0000
Subject: [PATCH] make isReference do the right thing

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1439 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java
index 6ce702957..0710046d1 100755
--- 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() {