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The tighter interval validation wasn't interacting well with unmapped 

intervals -- altered the validation methods to not throw an error for 
unmapped intervals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5700 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-04-27 20:56:46 +00:00
parent 6d5e45b5c6
commit 6e9e766a71
1 changed files with 8 additions and 0 deletions
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8
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -493,6 +493,10 @@ public class GenomeLocParser {
* *
*/ */
private GenomeLoc exceptionOnInvalidGenomeLoc(GenomeLoc toReturn) { private GenomeLoc exceptionOnInvalidGenomeLoc(GenomeLoc toReturn) {
if ( GenomeLoc.isUnmapped(toReturn) ) {
return toReturn;
}
if (toReturn.getStart() < 0) { if (toReturn.getStart() < 0) {
throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the start position is less than 0 " + throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the start position is less than 0 " +
"in interval: " + toReturn); "in interval: " + toReturn);
@ -526,6 +530,10 @@ public class GenomeLocParser {
* @param locus Locus to verify. * @param locus Locus to verify.
*/ */
private void exceptionOnInvalidGenomeLocBounds(GenomeLoc locus) { private void exceptionOnInvalidGenomeLocBounds(GenomeLoc locus) {
if ( GenomeLoc.isUnmapped(locus) ) {
return;
}
int contigSize = contigInfo.getSequence(locus.getContigIndex()).getSequenceLength(); int contigSize = contigInfo.getSequence(locus.getContigIndex()).getSequenceLength();
if(locus.getStart() > contigSize) if(locus.getStart() > contigSize)
throw new UserException.MalformedGenomeLoc("GenomeLoc is invalid: locus start is after the end of contig",locus); throw new UserException.MalformedGenomeLoc("GenomeLoc is invalid: locus start is after the end of contig",locus);