From 543aefc3d7fa7df61ee6462b6b6b08131d8a9be5 Mon Sep 17 00:00:00 2001 From: asivache Date: Mon, 22 Mar 2010 19:20:34 +0000 Subject: [PATCH] Fixing the bug introduced with the earlier commit. When trimming locus to the current bases, we need to take into account expanded boundaries (for windowed reference traversals) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3059 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/datasources/providers/LocusReferenceView.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 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 cc8d003c0..67ff504a1 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java @@ -158,8 +158,10 @@ public class LocusReferenceView extends ReferenceView { } protected GenomeLoc trimToBounds(GenomeLoc l) { - if ( l.getStart() < bounds.getStart() ) l = GenomeLocParser.setStart(l, bounds.getStart()); - if ( l.getStop() > bounds.getStop() ) l = GenomeLocParser.setStop(l, bounds.getStop()); + long expandedStart = getWindowStart( bounds ); + long expandedStop = getWindowStop( bounds ); + if ( l.getStart() < expandedStart ) l = GenomeLocParser.setStart(l, expandedStart); + if ( l.getStop() > expandedStop ) l = GenomeLocParser.setStop(l, expandedStop); return l; }