From 0d825ccfc1258877dab97c6ecc70b0bbd30b5aa2 Mon Sep 17 00:00:00 2001 From: hanna Date: Thu, 9 Apr 2009 21:27:57 +0000 Subject: [PATCH] Oops. Fixed duplicate reference to the reference. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@353 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/GenomeAnalysisTK.java | 7 ------- 1 file changed, 7 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java index 953876412..1c9cf35ec 100644 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java @@ -242,13 +242,6 @@ public class GenomeAnalysisTK extends CommandLineProgram { throw new RuntimeException( "Unable to access walker", ex ); } - // Prepare the sort ordering w.r.t. the sequence dictionary - FastaSequenceFile2 refFile = null; - if (REF_FILE_ARG != null) { - refFile = new FastaSequenceFile2(REF_FILE_ARG); - GenomeLoc.setupRefContigOrdering(refFile); - } - MicroManager microManager = null; // Try to get the walker specified