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* re-enabled setting of sequence dictionary information on GenomeLoc 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@366 348d0f76-0448-11de-a6fe-93d51630548a
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kcibul 2009-04-12 02:44:14 +00:00
parent ce72932a45
commit c7777d46d6
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -273,7 +273,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
// Prepare the sort ordering w.r.t. the sequence dictionary // Prepare the sort ordering w.r.t. the sequence dictionary
if (REF_FILE_ARG != null) { if (REF_FILE_ARG != null) {
final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG); final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG);
//GenomeLoc.setupRefContigOrdering(refFile); GenomeLoc.setupRefContigOrdering(refFile);
} }
// Determine the validation stringency. Default to ValidationStringency.STRICT. // Determine the validation stringency. Default to ValidationStringency.STRICT.