From 4c12df372c8563cf597c4d531ef2ea786feb875d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 12 May 2009 19:21:33 +0000
Subject: [PATCH] Dumb, dumb bug.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@672 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/playground/gatk/walkers/IntervalCleanerWalker.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
index 62ecdd154..a256d746d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
@@ -90,7 +90,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
 
         int sum = 0;
         for ( int readIndex = 0 ; readIndex < read.length() ; readIndex++, refIndex++ ) {
-            if ( refIndex > ref.length() )
+            if ( refIndex >= ref.length() )
                 sum += MAX_QUAL;
             else if ( Character.toUpperCase(read.charAt(readIndex)) != Character.toUpperCase(ref.charAt(refIndex)) )
                 sum += (int)quals.charAt(readIndex) - 33;