From ee06c7f29fed10ceaaa334d507b191b669d8f370 Mon Sep 17 00:00:00 2001
From: sjia <sjia@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 3 Sep 2009 19:41:12 +0000
Subject: [PATCH] git-svn-id:
 file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1525
 348d0f76-0448-11de-a6fe-93d51630548a

---
 .../playground/gatk/walkers/HLAcaller/CallHLAWalker.java      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
index 0d4349588..8466597f8 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
@@ -13,7 +13,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
 import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoods;
-import org.broadinstitute.sting.gatk.walkers.genotyper.ThreeStateErrorGenotypeLikelihoods;
+import org.broadinstitute.sting.gatk.walkers.genotyper.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Pair;
@@ -228,7 +228,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
             //Store confidence scores - this is a local hash that we use to get likelihood given a particular genotype
             Scores = new Hashtable();
             for ( DiploidGenotype g : DiploidGenotype.values() ) {
-                Scores.put(g.toString(), gl.getLikelihood(g));
+                Scores.put(g.toString(), G.getLikelihood(g));
             }
 
             //Get likelihood score for homozygous ref: used to normalize likelihoood scores at 0.