From f1b09db39e9ccf80b6728c20bdfc453dbd8c7c7c Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 10 Aug 2011 23:08:47 -0400
Subject: [PATCH] Fixes for rod bindings

---
 .../sting/gatk/walkers/annotator/VariantAnnotatorEngine.java    | 2 +-
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index c0bfd254b..a7837813a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -109,7 +109,7 @@ public class VariantAnnotatorEngine {
 
         // check to see whether comp rods were included
         final RodBinding<VariantContext> dbsnp = walker.getDbsnpRodBinding();
-        if ( dbsnp.isBound() )
+        if ( dbsnp != null &&  dbsnp.isBound() )
             dbAnnotations.put(dbsnp, VCFConstants.DBSNP_KEY);
 
         final List<RodBinding<VariantContext>> comps = walker.getCompRodBindings();
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 7733635bd..0f2d73c3a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -69,7 +69,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
       */
     @ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
     public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
-    public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return RodBinding.makeUnbound(SnpEffFeature.class); }
+    public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return null; }
     public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
     public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }