From a10cfe213bf360b9f83310b7c2dc1c06c4fa7d20 Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 20 Sep 2010 17:04:39 +0000
Subject: [PATCH] Small bug fix in simple indel genotyper: Likelihood of case
 where best haplotype pair was (REF,REF) was not computed correctly.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4314 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../oneoffprojects/walkers/SimpleIndelGenotyperWalker.java  | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java
index a4ee07319..f6bd5de79 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java
@@ -227,7 +227,7 @@ public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
         }
 
         int bestIndexI =-1, bestIndexJ=-1;
-        double callConfidence = 0.0;
+        double callConfidence = bestLikelihood;
 
 
         if (pileup.getReads().size() > 0) {
@@ -270,8 +270,8 @@ public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
                     if (haplotypeLikehoodMatrix[i][j] < bestLikelihood) {
                         bestIndexI = i;
                         bestIndexJ = j;
-                        if (i > 0 || j > 0)
-                            callConfidence = bestLikelihood - haplotypeLikehoodMatrix[i][j];
+
+                        callConfidence = bestLikelihood - haplotypeLikehoodMatrix[i][j];
                         bestLikelihood = haplotypeLikehoodMatrix[i][j];
                     }
                 }