From c0b4317311fee9029839f5fc3065e5157f66ce8c Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 22 Oct 2010 15:08:25 +0000
Subject: [PATCH] Er, here's the right fix

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4552 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/FilterLiftedVariants.java | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index 22d3cc21f..e82cf5245 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -65,9 +65,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
 
         boolean failed = false;
         byte[] recordRef = vc.getReference().getBases();
-        for (int i = 0; i < recordRef.length; i++) {
-            if ( i > MAX_VARIANT_SIZE )
-                break;
+        for (int i = 0; i < recordRef.length && i < MAX_VARIANT_SIZE; i++) {
             if ( recordRef[i] != ref[i + (vc.isSNP() ? 0 : 1)] ) {
                 failed = true;
                 break;