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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
This commit is contained in:
hanna 2009-12-16 22:37:45 +00:00
parent e6127cd6c5
commit 5b78354efd
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -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");