From 54facb2c51ae1869d5daf04b508dc1c2d28b17c5 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 27 Feb 2011 06:08:32 +0000
Subject: [PATCH] Small change for Mauricio so that the correct metrics get
 output when running in GENOTYPE_GIVEN_ALLELES mode.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5327 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 f764aada0..fe22a6d2c 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -159,7 +159,7 @@ public class UnifiedGenotyperEngine {
     public VariantCallContext calculateLikelihoodsAndGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
         Map<String, StratifiedAlignmentContext> stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext);
         VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, StratifiedAlignmentContext.StratifiedContextType.COMPLETE, null);
-        if ( vc == null )
+        if ( vc == null || !vc.hasGenotypes() )
             return null;
 
         VariantCallContext vcc = calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc);
@@ -195,7 +195,7 @@ public class UnifiedGenotyperEngine {
 
         Allele refAllele = glcm.get().getLikelihoods(tracker, refContext, stratifiedContexts, type, genotypePriors, GLs, alternateAlleleToUse);
 
-        if (refAllele != null)
+        if ( refAllele != null )
             return createVariantContextFromLikelihoods(refContext, refAllele, GLs);
         else
             return null;