From 5b78354efd9be6ab3f718310752f832a65c93625 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 16 Dec 2009 22:37:45 +0000
Subject: [PATCH] Fixed NPE in index check with RefWalkers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2384 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 062c05b31..a86e49edd 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -573,7 +573,7 @@ public class GenomeAnalysisEngine {
                                              ReferenceSequenceFile drivingDataSource,
                                              GenomeLocSortedSet intervals,
                                              Integer maxIterations) {
-        if(!readsDataSource.hasIndex()) {
+        if(readsDataSource != null && !readsDataSource.hasIndex()) {
             if(!getArguments().unsafe || intervals != null)
                 throw new StingException("The GATK cannot currently process unindexed BAM files");