From 2830dc70b7c6dde5df797477b671169192eca241 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 Apr 2011 20:11:17 +0000
Subject: [PATCH] UG can still return null in certain nasty cases

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5642 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/UGCalcLikelihoods.java      | 3 ++-
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 5 +++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
index edbb1c2db..f3f48f501 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
@@ -103,7 +103,8 @@ public class UGCalcLikelihoods extends LocusWalker<VariantCallContext, Integer>
             return null;
         }
 
-        return new VariantCallContext(UG_engine.calculateLikelihoods(tracker, refContext, rawContext, vc.getAlternateAllele(0), true), refContext.getBase(), true);
+        VariantContext call = UG_engine.calculateLikelihoods(tracker, refContext, rawContext, vc.getAlternateAllele(0), true);
+        return call == null ? null : new VariantCallContext(call, refContext.getBase(), true);
     }
 
     public Integer reduceInit() { return 0; }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index a89ce0ba0..b3ff6af80 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -175,12 +175,13 @@ public class UnifiedGenotyperEngine {
      */
     public VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext, Allele alternateAlleleToUse, boolean useBAQedPileup) {
         final GenotypeLikelihoodsCalculationModel.Model model = getCurrentGLModel( rawContext );
-        if( model == null ) {
+        if( model == null )
             return null;
-        }
+
         Map<String, AlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
         if ( stratifiedContexts == null )
             return null;
+
         return calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, alternateAlleleToUse, useBAQedPileup, model);
     }