From cac125b35cf8837e6883e6b6f692e209c3ea2a1a Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 20 Apr 2010 16:37:28 +0000
Subject: [PATCH] Fixed incorrect symbol printed into the output file (tag had
 'R', should have had 'T')

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3209 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelGenotyperV2Walker.java       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
index d628ba400..711f20139 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
@@ -1069,7 +1069,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
 
         public String makeStatsString(String prefix) {
              StringBuilder message = new StringBuilder();
-             message.append(prefix+"OBS_COUNTS[C/A/R]:"+getConsensusVariantCount()+"/"+getAllVariantCount()+"/"+getCoverage());
+             message.append(prefix+"OBS_COUNTS[C/A/T]:"+getConsensusVariantCount()+"/"+getAllVariantCount()+"/"+getCoverage());
              message.append('\t');
              message.append(prefix+"AV_MM[C/R]:"+String.format("%.2f/%.2f",getAvConsensusMismatches(),
                                  getAvRefMismatches()));