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Temporary workaround for samtools index bug: there seems to be an off-by-one error. Will file bug report. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@470 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2009-04-17 23:14:41 +00:00
parent 758db73b98
commit eafb4633ba
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
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@ -118,9 +118,9 @@ public class SAMDataSource implements SimpleDataSource {
// we do different things for locus and read modes // we do different things for locus and read modes
if (locusMode) { if (locusMode) {
iter.queryOverlapping(location.getContig(), (int) location.getStart(), (int) location.getStop()); iter.queryOverlapping(location.getContig(), (int) location.getStart(), (int) location.getStop()+1);
} else { } else {
iter.queryContained(location.getContig(), (int) location.getStart(), (int) location.getStop()); iter.queryContained(location.getContig(), (int) location.getStart(), (int) location.getStop()+1);
} }
// return the iterator // return the iterator