From cfbf062f298946a127307cf64e1adf181602c411 Mon Sep 17 00:00:00 2001
From: David Benjamin <davidben@broadinstitute.org>
Date: Sun, 3 Apr 2016 21:22:07 -0400
Subject: [PATCH] fixed bug in dbSNP binding in VariantAnnotationEngine

---
 .../gatk/tools/walkers/annotator/VariantAnnotatorEngine.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
index e8394cec4..40360262a 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
@@ -163,7 +163,7 @@ public class VariantAnnotatorEngine {
         final Map<RodBinding<VariantContext>, String> overlapBindings = new LinkedHashMap<>();
         for ( final RodBinding<VariantContext> b : walker.getCompRodBindings())
             if ( b.isBound() ) overlapBindings.put(b, b.getName());
-        if ( dbSNPBinding != null && ! overlapBindings.keySet().contains(VCFConstants.DBSNP_KEY) )
+        if ( dbSNPBinding != null && ! overlapBindings.values().contains(VCFConstants.DBSNP_KEY) )
             overlapBindings.put(dbSNPBinding, VCFConstants.DBSNP_KEY); // add overlap detection with DBSNP by default
 
         variantOverlapAnnotator = new VariantOverlapAnnotator(dbSNPBinding, overlapBindings, engine.getGenomeLocParser());