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Removed sanity check that required GenomeLoc argument to be strictly 1-base long. We need to relax this in order to be able to pass around a reference context containing full-length chunk of deleted reference bases 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2485 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-12-30 20:14:08 +00:00
parent 497ae700c4
commit 8932e67325
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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@ -149,9 +149,9 @@ public class LocusReferenceView extends ReferenceView {
* @param genomeLoc location to verify.
*/
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( !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) )
throw new InvalidPositionException(
String.format("Requested position %s not within interval %s", genomeLoc, bounds));