From 6fda78f93fbb3d38203cdd075f70da98bcaa9c32 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 20 Apr 2010 19:17:40 +0000
Subject: [PATCH] Always return deleted bases in upper case

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3218 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/pileup/ReadBackedExtendedEventPileup.java       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
index 42605ec1d..5dc24c71a 100644
--- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
@@ -389,7 +389,7 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
         if ( refBases == null ) {
             return  Integer.toString(length)+"D"; // if we do not have reference bases, we can only report something like "5D"
         } else {
-            return "-"+new String(refBases,1,length);
+            return "-"+new String(refBases,1,length).toUpperCase();
         }
     }