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(Hopefully) temporary hack: load contig information by contig name rather than contig id to avoid 

off-by-one errors.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2078 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-11-18 23:33:27 +00:00
parent 0fbd81766b
commit 85bc9d3e91
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -92,7 +92,7 @@ public class LocusIteratorByState extends LocusIterator {
public int getGenomePosition() { return read.getAlignmentStart() + getGenomeOffset(); }
public GenomeLoc getLocation() {
return GenomeLocParser.createGenomeLoc(read.getReferenceIndex(), getGenomePosition());
return GenomeLocParser.createGenomeLoc(read.getReferenceName(), getGenomePosition());
}
//private CigarElement getCurElement() { return curElement; }