From e5e249d4aca87d458b53988a6a5560dabb04d465 Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 5 Jul 2009 03:25:57 +0000 Subject: [PATCH] temporary fix to deal with screwy SOLiD reads git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1168 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/traversals/TraverseReads.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index b74ea7223..c0a887b3c 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -124,6 +124,10 @@ public class TraverseReads extends TraversalEngine { // get the genome loc from the read GenomeLoc site = GenomeLocParser.createGenomeLoc(read); + // this is a temporary fix to deal with unmapped reads which "map" to a given location and have a MAPPED flag set + if ( site.getStop() != -1 && site.getStop() < site.getStart() ) + continue; + // Jump forward in the reference to this locus location locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0));