From b24e1134f92f112070b64310b5b6425f3c308ea3 Mon Sep 17 00:00:00 2001 From: aaron Date: Fri, 7 Jan 2011 22:32:50 +0000 Subject: [PATCH] unfortunately samrecord pileup also uses zero length intervals to indicate deletions; this will have to be a BED specific exception. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4964 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/refdata/utils/GATKFeature.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java b/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java index f24df2a4a..9453ec484 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java @@ -75,9 +75,6 @@ public abstract class GATKFeature implements Feature { } public GenomeLoc getLocation() { if (position == null) position = genomeLocParser.createGenomeLoc(feature.getChr(), feature.getStart(), feature.getEnd()); - if (position.getStart() > position.getStop()) { - throw new UserException.BadInput("A feature produced by the reference metadata track named \"" + this.name + "\" at position " + position + " has a start greater than the stop; this is an invalid this is an invalid position"); - } return position; }