From 043c97eedefc9d6fe544dad0086f5ad0a11cbc19 Mon Sep 17 00:00:00 2001
From: sjia <sjia@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 3 Sep 2009 19:34:42 +0000
Subject: [PATCH] git-svn-id:
 file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1524
 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 97c0f20ae..0d4349588 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
@@ -198,7 +198,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
             }
 
             //Calculate posterior probabilities!
-            GenotypeLikelihoods gl = new ThreeStateErrorGenotypeLikelihoods();
+            GenotypeLikelihoods G = new EmpiricalSubstitutionGenotypeLikelihoods();
 
             //I've tried simply adding the entire pileup to g, but quality scores are not checked, and 'N' bases throw an error
             //(GenotypeLikelihoods potentially has bug on line 57)
@@ -217,7 +217,7 @@ public class CallHLAWalker extends LocusWalker<Integer, Pair<Long, Long>>{
                     if (base == 'T'){numTs++;}
                     if (base == 'g'){numGs++;}
                     //consider base in likelihood calculations if it looks good and has high mapping score
-                    gl.add(base, qual, read, offset);
+                    G.add(base, qual, read, offset);
                 }
             }