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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
This commit is contained in:
asivache 2011-06-14 17:44:11 +00:00
parent 14d7ee073b
commit 04ecbf10ab
1 changed files with 8 additions and 4 deletions
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12
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -642,8 +642,10 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
// if indel is too close to the end of the window but we need to emit anyway (force-shift), adjust right: // 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(); if ( right > normal_context.getStop() ) right = normal_context.getStop();
location = getToolkit().getGenomeLocParser().setStart(location,pos); // location = getToolkit().getGenomeLocParser().setStart(location,pos);
location = getToolkit().getGenomeLocParser().setStop(location,pos); // retrieve annotation data // location = getToolkit().getGenomeLocParser().setStop(location,pos); // retrieve annotation data
location = getToolkit().getGenomeLocParser().createGenomeLoc(location.getContig(), pos);
boolean haveCall = normalCall.isCall(); // cache the value boolean haveCall = normalCall.isCall(); // cache the value
@ -816,8 +818,10 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
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 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().setStart(location,pos);
location = getToolkit().getGenomeLocParser().setStop(location,pos); // retrieve annotation data // 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 boolean haveCall = tumorCall.isCall(); // cache the value