From 6df6c1abd538f5616fb624236e0f9cd36a0871ea Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 6 Sep 2012 13:14:18 -0400
Subject: [PATCH] Fix for PBT to stop NPE when there are no likelihoods present

---
 .../sting/gatk/walkers/phasing/PhaseByTransmission.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
index bbd4bf92f..00acf854a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -541,7 +541,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
     //Get a Map of genotype likelihoods.
     //In case of null, unavailable or no call, all likelihoods are 1/3.
     private EnumMap<GenotypeType,Double> getLikelihoodsAsMapSafeNull(Genotype genotype){
-        if(genotype == null || !genotype.isCalled()){
+        if(genotype == null || !genotype.isCalled() || genotype.getLikelihoods() == null){
             EnumMap<GenotypeType,Double> likelihoods = new EnumMap<GenotypeType, Double>(GenotypeType.class);
             likelihoods.put(GenotypeType.HOM_REF,1.0/3.0);
             likelihoods.put(GenotypeType.HET,1.0/3.0);