From 9d56355abe36282fbcd48a0ce7b640efbbdb73fa Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Apr 2009 21:46:27 +0000
Subject: [PATCH] bug fixed when reference name was passed as a string instead
 of actual reference bases

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@416 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/playground/indels/AlignmentUtils.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java b/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
index dad7c907f..9d37dd359 100644
--- a/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
@@ -25,7 +25,7 @@ public class AlignmentUtils {
      * @return
      */
     public static int numMismatches(SAMRecord r, ReferenceSequence ref) {
-        return numMismatches(r, ref.getBases().toString());
+        return numMismatches(r, new String(ref.getBases()));
     }
 
     public static int numMismatches(SAMRecord r, String ref) {