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Make new TraverseByLociByReference the default. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@532 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-04-24 19:50:11 +00:00
parent e50ae97fe1
commit ee2f022c71
1 changed files with 5 additions and 7 deletions
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12
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -15,7 +15,6 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.traversals.*; import org.broadinstitute.sting.gatk.traversals.*;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; 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.IntervalWalker;
import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
@ -28,8 +27,6 @@ import java.io.FileNotFoundException;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Arrays;
import java.util.Collections;
public class GenomeAnalysisTK extends CommandLineProgram { public class GenomeAnalysisTK extends CommandLineProgram {
public static GenomeAnalysisTK Instance = null; public static GenomeAnalysisTK Instance = null;
@ -60,7 +57,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
private TraversalEngine engine = null; private TraversalEngine engine = null;
public boolean DEBUGGING = false; public boolean DEBUGGING = false;
public Boolean WALK_ALL_LOCI = false; public Boolean WALK_ALL_LOCI = false;
public Boolean ENABLE_THREADING = false; public Boolean DISABLE_THREADING = false;
/** /**
* An output file presented to the walker. * 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("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.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 <name> <type> <file> // --rodBind <name> <type> <file>
//m_parser.addOptionalArg("rods", "B", "Bind rod with <name> and <type> to <file>", "ROD_BINDINGS"); //m_parser.addOptionalArg("rods", "B", "Bind rod with <name> and <type> to <file>", "ROD_BINDINGS");
@ -268,12 +265,13 @@ public class GenomeAnalysisTK extends CommandLineProgram {
if ( WALK_ALL_LOCI ) { if ( WALK_ALL_LOCI ) {
// TODO: Temporary debugging code. Activate the new debugging code only when the MicroManager // TODO: Temporary debugging code. Activate the new debugging code only when the MicroManager
// is not filtered. // is not filtered.
if( ENABLE_THREADING ) { if( !DISABLE_THREADING ) {
logger.warn("Preliminary threading support enabled"); logger.warn("Preliminary threading support ENABLED");
microManager = new MicroManager( INPUT_FILES, REF_FILE_ARG, numThreads ); microManager = new MicroManager( INPUT_FILES, REF_FILE_ARG, numThreads );
this.engine = microManager.getTraversalEngine(); this.engine = microManager.getTraversalEngine();
} }
else { else {
logger.warn("Preliminary threading support DISABLED");
this.engine = new TraverseByLociByReference(INPUT_FILES, REF_FILE_ARG, rods); this.engine = new TraverseByLociByReference(INPUT_FILES, REF_FILE_ARG, rods);
} }
} }