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A quick change to provide more verbose output. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1197 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-07-08 19:08:19 +00:00
parent 433ad1f060
commit e106cf73d8
1 changed files with 3 additions and 2 deletions
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5
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -522,8 +522,9 @@ public class GenomeLocParser {
if (loc.getContigIndex() < 0 || loc.getContigIndex() >= contigInfo.getSequences().size()) {
throw new StingException("Genome loc passed in to setStart has a contig index outside the range of our current sequence dictionary");
}
if (start > GenomeLocParser.contigInfo.getSequences().get(loc.getContigIndex()).getSequenceLength()) {
throw new StingException("start value of " + start + " is greater than the contig length, and is not -1.");
int length = GenomeLocParser.contigInfo.getSequences().get(loc.getContigIndex()).getSequenceLength();
if (start > length) {
throw new StingException("start value of " + start + " is greater than the contig length, and is not -1. (length = " + length + ").");
}
return verifyGenomeLoc(new GenomeLoc(loc.getContig(), loc.getContigIndex(), start, loc.getStop()));
}