From 5eaf8002810237e3dfa67cf72a619a39c3cb45fd Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Wed, 9 Nov 2011 11:22:20 -0500
Subject: [PATCH] a

---
 .../sting/gatk/walkers/annotator/MVLikelihoodRatio.java    | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
index 8da64608f..795c430bf 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
@@ -33,8 +33,11 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
         if ( mendelianViolation == null ) {
-            if ( walker instanceof VariantAnnotator && ((VariantAnnotator) walker).familyStr != null) {
-                mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).familyStr, ((VariantAnnotator)walker).minGenotypeQualityP );
+            if ( walker instanceof VariantAnnotator) {
+		if ( ((VariantAnnotator) walker).familyStr != null )
+		    mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).familyStr, ((VariantAnnotator)walker).minGenotypeQualityP );
+		else
+		    return new HashMap<String,Object>();
             }
             else {
                 throw new UserException("Mendelian violation annotation can only be used from the Variant Annotator");