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forgot to take out some test code 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1157 348d0f76-0448-11de-a6fe-93d51630548a
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aaron 2009-07-02 14:18:37 +00:00
parent bc17ff567a
commit 1c83b4d949
1 changed files with 3 additions and 7 deletions
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10
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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@ -77,15 +77,11 @@ public class LocusReferenceView extends ReferenceView {
*/ */
public char[] getReferenceBases( GenomeLoc genomeLoc ) { public char[] getReferenceBases( GenomeLoc genomeLoc ) {
long stop = genomeLoc.getStop(); long stop = genomeLoc.getStop();
long other = reference.getSequence(genomeLoc.getContig()).length(); long seqLength = reference.getSequence(genomeLoc.getContig()).length();
if (other < genomeLoc.getStop()) { if (seqLength < genomeLoc.getStop()) {
stop = other; stop = seqLength;
} }
ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop); ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop);
if (genomeLoc.getStop() - stop < 0) {
int y = 0;
y++;
}
return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray(); return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray();
} }