From 480e7a798476ac577d7e059ab592a38d5298f1d2 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Tue, 9 Aug 2011 16:30:08 -0400
Subject: [PATCH] Correctly initialize the optional SnpEff rod binding in
 VariantAnnotator using RodBinding.makeUnbound()

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

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index efa40d9a8..54231e9b4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -58,7 +58,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
     @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
 
     @Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
-    public RodBinding<SnpEffFeature> snpEffFile;
+    public RodBinding<SnpEffFeature> snpEffFile = RodBinding.makeUnbound(SnpEffFeature.class);
 
     /**
       * A dbSNP VCF file from which to annotate.