From 7ad87d328dd08152e877e2bf8a60147b315863f0 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 28 Sep 2010 19:05:46 +0000
Subject: [PATCH] Make sure to uppercase ref bases since they aren't coming
 from the engine

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4364 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 03e2c8fb6..f497d8dd1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -1319,6 +1319,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 long padRight = Math.min(loc.getStop()+REFERENCE_PADDING, referenceReader.getSequenceDictionary().getSequence(loc.getContig()).getSequenceLength());
                 loc = GenomeLocParser.createGenomeLoc(loc.getContigIndex(), padLeft, padRight);
                 reference = referenceReader.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
+                StringUtil.toUpperCase(reference);
             }
 
             return reference;