From 75ad6bbef7f11f5599eb9cc530475e2cee7fd903 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 25 Oct 2009 02:30:36 +0000
Subject: [PATCH] Check that map isn't being called passing in null arguments.
 (This seems wrong; see JIRA entry GSA-211)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1907 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/fasta/CreateSequenomMask.java            | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java
index 251c1fe5e..86effd9be 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java
@@ -15,6 +15,8 @@ public class CreateSequenomMask extends RodWalker<Integer, Integer> {
 
 	public Integer map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
         int result = 0;
+        if ( rodData == null ) // apparently, RodWalkers make funky map calls
+            return 0;
 
         Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
         while (rods.hasNext()) {