From d3a533b82e29d39d32af2c3a6992ef0a466ff09a Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Wed, 9 Nov 2011 11:22:26 -0500
Subject: [PATCH] Revert "a"

This reverts commit 1175f50ddbf389f5da74d27dc725596582ae15af.
---
 .../sting/gatk/walkers/annotator/MVLikelihoodRatio.java    | 7 ++-----
 1 file changed, 2 insertions(+), 5 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 795c430bf..8da64608f 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
@@ -33,11 +33,8 @@ 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) {
-		if ( ((VariantAnnotator) walker).familyStr != null )
-		    mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).familyStr, ((VariantAnnotator)walker).minGenotypeQualityP );
-		else
-		    return new HashMap<String,Object>();
+            if ( walker instanceof VariantAnnotator && ((VariantAnnotator) walker).familyStr != null) {
+                mendelianViolation = new MendelianViolation(((VariantAnnotator)walker).familyStr, ((VariantAnnotator)walker).minGenotypeQualityP );
             }
             else {
                 throw new UserException("Mendelian violation annotation can only be used from the Variant Annotator");