From 186a8dd698c6f656de2a290724f1173ba749ff4d Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 27 Oct 2009 21:52:52 +0000
Subject: [PATCH] Trivial protection for null value

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1918 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/fasta/FastaReferenceWalker.java         | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
index 8f377cae3..165f2b423 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java
@@ -33,6 +33,9 @@ public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, Gen
     }
 
 	public GenomeLoc reduce(Pair<GenomeLoc, String> value, GenomeLoc sum) {
+        if ( value == null )
+            return sum;
+
         // if there is no interval to the left, then this is the first one
         if ( sum == null ) {
             sum = value.first;