From 9b0bdbbf299e720474eed227707db050d56acac4 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 15 Dec 2009 19:02:23 +0000
Subject: [PATCH] Fix for homopolymer bug: ref was lowercase, alt allele was
 uppercase, so alt != ref.  Yuck. This is a temporary fix - pushed more
 elegant solution over to Matt.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2360 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/annotator/HomopolymerRun.java          | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
index 7f9130c93..6de1bf4f5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
@@ -39,14 +39,14 @@ public class HomopolymerRun extends StandardVariantAnnotation {
 
         int leftRun = 0;
         for ( int i = refBasePos - 1; i >= 0; i--) {
-            if ( bases[i] != altAllele )
+            if ( Character.toUpperCase(bases[i]) != altAllele )
                 break;
             leftRun++;
         }
 
         int rightRun = 0;
         for ( int i = refBasePos + 1; i < bases.length; i++) {
-            if ( bases[i] != altAllele )
+            if ( Character.toUpperCase(bases[i]) != altAllele )
                 break;
             rightRun++;
         }