From dfe4cf13014c27bad575c26ab24eae6e2d85c50f Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 8 Jan 2013 09:24:12 -0500
Subject: [PATCH] When merging the PerReadAlleleLikelihoodMap classes, I forgot
 to initialize the underlying objects.   This was causing the LargeScaleTests
 to fail.

---
 .../sting/utils/genotyper/PerReadAlleleLikelihoodMap.java    | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
index 5dcd5eb6c..2379ccd1d 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
@@ -41,7 +41,10 @@ public class PerReadAlleleLikelihoodMap {
     protected List<Allele> alleles;
     protected Map<GATKSAMRecord, Map<Allele, Double>> likelihoodReadMap;
 
-    public PerReadAlleleLikelihoodMap() {}
+    public PerReadAlleleLikelihoodMap() {
+        likelihoodReadMap = new LinkedHashMap<GATKSAMRecord,Map<Allele,Double>>();
+        alleles = new ArrayList<Allele>();
+    }
 
     public void add(GATKSAMRecord read, Allele a, Double likelihood) {
         Map<Allele,Double> likelihoodMap;