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Better bounding for the locus window. Don't make the locus window calculation blow up if the GenomeLoc ends 

up being outside the reference.  Force the blowup elsewhere.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2573 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-01-13 17:03:54 +00:00
parent 8ca5bba738
commit 05575e2e56
1 changed files with 6 additions and 4 deletions
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10
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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@ -176,9 +176,6 @@ public class LocusReferenceView extends ReferenceView {
* @param genomeLoc location to verify. * @param genomeLoc location to verify.
*/ */
private void validateLocation( GenomeLoc genomeLoc ) throws InvalidPositionException { private void validateLocation( GenomeLoc genomeLoc ) throws InvalidPositionException {
// if( !genomeLoc.isSingleBP() )
// throw new InvalidPositionException(
// String.format("Requested position larger than one base; start = %d, stop = %d", genomeLoc.getStart(), genomeLoc.getStop()));
if( bounds != null && !bounds.containsP(genomeLoc) ) if( bounds != null && !bounds.containsP(genomeLoc) )
throw new InvalidPositionException( throw new InvalidPositionException(
String.format("Requested position %s not within interval %s", genomeLoc, bounds)); String.format("Requested position %s not within interval %s", genomeLoc, bounds));
@ -190,6 +187,8 @@ public class LocusReferenceView extends ReferenceView {
* @return The expanded window. * @return The expanded window.
*/ */
private long getWindowStart( GenomeLoc locus ) { private long getWindowStart( GenomeLoc locus ) {
// If the locus is not within the bounds of the contig it allegedly maps to, don't expand the locus at all.
if(locus.getStart() < 1) return locus.getStart();
return Math.max( locus.getStart() + windowStart, 1 ); return Math.max( locus.getStart() + windowStart, 1 );
} }
@ -199,6 +198,9 @@ public class LocusReferenceView extends ReferenceView {
* @return The expanded window. * @return The expanded window.
*/ */
private long getWindowStop( GenomeLoc locus ) { private long getWindowStop( GenomeLoc locus ) {
return Math.min( locus.getStop() + windowStop, reference.getSequenceDictionary().getSequence(locus.getContig()).getSequenceLength() ); // If the locus is not within the bounds of the contig it allegedly maps to, don't expand the locus at all.
long sequenceLength = reference.getSequenceDictionary().getSequence(locus.getContig()).getSequenceLength();
if(locus.getStop() > sequenceLength) return locus.getStop();
return Math.min( locus.getStop() + windowStop, sequenceLength );
} }
} }