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Inadvertently removed interval file support in new TbLbR. Fixed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@540 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-04-26 18:15:42 +00:00
parent c9e9731495
commit 1e2e78265d
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -333,7 +333,11 @@ public class GenomeAnalysisTK extends CommandLineProgram {
engine.initialize(); engine.initialize();
if( microScheduler != null ) { if( microScheduler != null ) {
List<GenomeLoc> locs = GenomeLoc.parseGenomeLocs( REGION_STR ); List<GenomeLoc> locs = null;
if (INTERVALS_FILE != null)
locs = GenomeLoc.IntervalFileToList(INTERVALS_FILE);
else
locs = GenomeLoc.parseGenomeLocs( REGION_STR );
microScheduler.execute( my_walker, locs ); microScheduler.execute( my_walker, locs );
} }
else else