From 1246b8904908d3e05329032be7263d0408ab76d9 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 15 Aug 2011 16:00:43 -0400
Subject: [PATCH] Forgot to initialize variants on the merge

---
 .../gatk/walkers/fasta/FastaAlternateReferenceWalker.java      | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
index 365d3c2c9..a57fabc39 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
+import java.util.Collections;
 import java.util.List;
 
 
@@ -49,7 +50,7 @@ import java.util.List;
 public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
 
     @Input(fullName = "variant", shortName = "V", doc="variants to model", required=false)
-    public List<RodBinding<VariantContext>> variants;
+    public List<RodBinding<VariantContext>> variants = Collections.emptyList();
 
     @Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
     public RodBinding<VariantContext> snpmask;