From fa75efb6ac9985efbbad36349337aa1eb8cbc1b3 Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 13 May 2011 21:54:54 +0000
Subject: [PATCH] Backing off - need to change pileup interface for rank sum
 tests before indels can be annotated with them

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5804 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/annotator/RankSumTest.java               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index 809c59dec..b1a86ecf0 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -22,7 +22,7 @@ public abstract class RankSumTest implements InfoFieldAnnotation, StandardAnnota
         if ( stratifiedContexts.size() == 0 )
             return null;
          
-        if ( !vc.isBiallelic()  )
+        if ( !vc.isBiallelic() || !vc.isSNP() )
             return null;
         
         final Map<String, Genotype> genotypes = vc.getGenotypes();