From a27e8b1dc666a811bc2a11069a77398358e66e2f Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 16 May 2011 15:32:58 +0000
Subject: [PATCH] Bug fix - use correct variable to retrieve from map.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5811 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
index 17a1fbe8c..5de01392c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
@@ -433,7 +433,7 @@ public class HaplotypeIndelErrorModel {
             // = sum_j(-10*log10(Pr(R_j | Hi) since reads are assumed to be independent
             int j=0;
             for (Allele a: haplotypesInVC.keySet()) {
-                readLikelihoods[i][j]= computeReadLikelihoodGivenHaplotype(haplotypesInVC.get(j), read);
+                readLikelihoods[i][j]= computeReadLikelihoodGivenHaplotype(haplotypesInVC.get(a), read);
                 if (DEBUG) {
                     System.out.print(read.getReadName()+" ");