From a7ff9caf546685b560f8e8f20f5a0b23f7273ab3 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 3 Aug 2010 05:37:17 +0000
Subject: [PATCH] Added sanity check against bad people and/or crazy big indels
 at edges of ref context

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3918 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 5091cc33f..4a814b1a0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -767,7 +767,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
 
     // create a Consensus from just the indel string that falls on the reference
     private Consensus createAlternateConsensus(final int indexOnRef, final byte[] reference, final byte[] indelStr, final boolean isDeletion) {
-        if ( indexOnRef < 0 )
+        if ( indexOnRef < 0 || indexOnRef >= reference.length )
             return null;
 
         // create the new consensus