From 8932e6732519c03b55b3c968aab373bed54cd128 Mon Sep 17 00:00:00 2001 From: asivache Date: Wed, 30 Dec 2009 20:14:08 +0000 Subject: [PATCH] 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 --- .../gatk/datasources/providers/LocusReferenceView.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java index ad9ed191b..b6e0002bf 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java @@ -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));