From 04ecbf10abe1b37f7fae3cf050528d6f55871d72 Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 14 Jun 2011 17:44:11 +0000 Subject: [PATCH] Fixes the constraint-generated error about stop being less than start in GenomeLocParser.createGenomeLoc. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5999 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/indels/IndelGenotyperV2Walker.java | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java index 0e02d4c98..eea12e00a 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java @@ -642,8 +642,10 @@ public class IndelGenotyperV2Walker extends ReadWalker { // if indel is too close to the end of the window but we need to emit anyway (force-shift), adjust right: if ( right > normal_context.getStop() ) right = normal_context.getStop(); - location = getToolkit().getGenomeLocParser().setStart(location,pos); - location = getToolkit().getGenomeLocParser().setStop(location,pos); // retrieve annotation data + // location = getToolkit().getGenomeLocParser().setStart(location,pos); + // location = getToolkit().getGenomeLocParser().setStop(location,pos); // retrieve annotation data + + location = getToolkit().getGenomeLocParser().createGenomeLoc(location.getContig(), pos); boolean haveCall = normalCall.isCall(); // cache the value @@ -816,8 +818,10 @@ public class IndelGenotyperV2Walker extends ReadWalker { if ( right > tumor_context.getStop() ) right = tumor_context.getStop(); // if indel is too close to the end of the window but we need to emit anyway (force-shift), adjust right - location = getToolkit().getGenomeLocParser().setStart(location,pos); - location = getToolkit().getGenomeLocParser().setStop(location,pos); // retrieve annotation data +// location = getToolkit().getGenomeLocParser().setStart(location,pos); +// location = getToolkit().getGenomeLocParser().setStop(location,pos); // retrieve annotation data + + location = getToolkit().getGenomeLocParser().createGenomeLoc(location.getContig(),pos); // retrieve annotation data boolean haveCall = tumorCall.isCall(); // cache the value