From 1c83b4d949d791851bd903be0a90c66d34d8e310 Mon Sep 17 00:00:00 2001 From: aaron Date: Thu, 2 Jul 2009 14:18:37 +0000 Subject: [PATCH] forgot to take out some test code git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1157 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/datasources/providers/LocusReferenceView.java | 10 +++------- 1 file changed, 3 insertions(+), 7 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 ff17403c0..99c72ecfa 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java @@ -77,15 +77,11 @@ public class LocusReferenceView extends ReferenceView { */ public char[] getReferenceBases( GenomeLoc genomeLoc ) { long stop = genomeLoc.getStop(); - long other = reference.getSequence(genomeLoc.getContig()).length(); - if (other < genomeLoc.getStop()) { - stop = other; + long seqLength = reference.getSequence(genomeLoc.getContig()).length(); + if (seqLength < genomeLoc.getStop()) { + stop = seqLength; } ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop); - if (genomeLoc.getStop() - stop < 0) { - int y = 0; - y++; - } return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray(); }