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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
This commit is contained in:
ebanks 2009-10-25 02:30:36 +00:00
parent b4f55df600
commit 75ad6bbef7
1 changed files with 2 additions and 0 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/fasta/CreateSequenomMask.java
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@ -15,6 +15,8 @@ public class CreateSequenomMask extends RodWalker<Integer, Integer> {
public Integer map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
int result = 0; int result = 0;
if ( rodData == null ) // apparently, RodWalkers make funky map calls
return 0;
Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator(); Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
while (rods.hasNext()) { while (rods.hasNext()) {