From 18271aa1f4b38fefa859412ce2624351cec55485 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 24 Mar 2011 04:17:23 +0000
Subject: [PATCH] It never fails to amaze me that aligners can find so many
 different ways to place indels off the ends of contigs

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5503 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 0f16de587..399e96e1b 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -722,7 +722,7 @@ public class AlignmentUtils {
         byte[] alt = new byte[refSeq.length + (indelLength * (indel.getOperator() == CigarOperator.D ? -1 : 1))];
 
         // add the bases before the indel, making sure it's not aligned off the end of the reference
-        if ( refIndex > alt.length )
+        if ( refIndex > alt.length || refIndex > refSeq.length )
             return null;
         System.arraycopy(refSeq, 0, alt, 0, refIndex);
         int currentPos = refIndex;