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Damn unit tests have a null Toolkit()... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1654 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-18 17:10:49 +00:00
parent 90626c843d
commit b19fd4d45c
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java
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@ -74,7 +74,8 @@ public class CleanedReadInjector extends ReadWalker<Integer,Integer> {
// If there are intervals specified by the user,record them so we can make sure not
// to emit reads outside the intervals. For now, we'll group them by chromosome to
// make lookup a bit faster.
if ( this.getToolkit().getArguments().intervals != null ) {
if ( this.getToolkit() != null &&
this.getToolkit().getArguments().intervals != null ) {
intervals = new HashMap<String, ArrayList<GenomeLoc>>();
List<GenomeLoc> locs = GenomeAnalysisEngine.parseIntervalRegion(this.getToolkit().getArguments().intervals);
Iterator<GenomeLoc> iter = GenomeLocSortedSet.createSetFromList(locs).iterator();