From ee2f022c71e2efabf19ed2b899a052f2fb5fcfa0 Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 24 Apr 2009 19:50:11 +0000 Subject: [PATCH] Make new TraverseByLociByReference the default. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@532 348d0f76-0448-11de-a6fe-93d51630548a --- .../broadinstitute/sting/gatk/GenomeAnalysisTK.java | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java index 26f24c4f3..101440671 100644 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java @@ -15,7 +15,6 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.traversals.*; import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.IntervalWalker; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.GenomeLoc; @@ -28,8 +27,6 @@ import java.io.FileNotFoundException; import java.io.PrintStream; import java.util.ArrayList; import java.util.List; -import java.util.Arrays; -import java.util.Collections; public class GenomeAnalysisTK extends CommandLineProgram { public static GenomeAnalysisTK Instance = null; @@ -60,7 +57,7 @@ public class GenomeAnalysisTK extends CommandLineProgram { private TraversalEngine engine = null; public boolean DEBUGGING = false; public Boolean WALK_ALL_LOCI = false; - public Boolean ENABLE_THREADING = false; + public Boolean DISABLE_THREADING = false; /** * An output file presented to the walker. @@ -130,7 +127,7 @@ public class GenomeAnalysisTK extends CommandLineProgram { m_parser.addOptionalArg("outerr", "oe", "A joint file for 'normal' and error output presented to the walker. Will overwrite contents if file exists.", "outErrFileName"); m_parser.addOptionalArg("numthreads", "nt", "How many threads should be allocated to running this analysis.", "numThreads"); - m_parser.addOptionalFlag("enablethreading", "et", "Enable experimental threading support.", "ENABLE_THREADING"); + m_parser.addOptionalFlag("disablethreading", "dt", "Disable experimental threading support.", "DISABLE_THREADING"); // --rodBind //m_parser.addOptionalArg("rods", "B", "Bind rod with and to ", "ROD_BINDINGS"); @@ -268,12 +265,13 @@ public class GenomeAnalysisTK extends CommandLineProgram { if ( WALK_ALL_LOCI ) { // TODO: Temporary debugging code. Activate the new debugging code only when the MicroManager // is not filtered. - if( ENABLE_THREADING ) { - logger.warn("Preliminary threading support enabled"); + if( !DISABLE_THREADING ) { + logger.warn("Preliminary threading support ENABLED"); microManager = new MicroManager( INPUT_FILES, REF_FILE_ARG, numThreads ); this.engine = microManager.getTraversalEngine(); } else { + logger.warn("Preliminary threading support DISABLED"); this.engine = new TraverseByLociByReference(INPUT_FILES, REF_FILE_ARG, rods); } }