From 4a7902bb8ea7345b90e33596e44ddd2978e2bdde Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 10 May 2010 14:53:38 +0000
Subject: [PATCH] Bases 'A' and 'a' (etc.) no longer considered different.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3339 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/diagnostics/ComputeConfusionMatrix.java        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java
index e3cbb163b..458537dc7 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/ComputeConfusionMatrix.java
@@ -119,7 +119,7 @@ public class ComputeConfusionMatrix extends LocusWalker<Integer, Integer> {
     }
 
     private void incrementConfusionCounts(String context, String altBase, String refBase) {
-        String key = String.format("%s:%s:%s", context, altBase, refBase);
+        String key = String.format("%s:%s:%s", context, altBase.toUpperCase(), refBase.toUpperCase());
 
         Integer counts = confusionCounts.get(key);
         if (counts == null) { counts = 0; }