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More cleanup. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@539 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-04-26 17:46:52 +00:00
parent 4036f24909
commit c9e9731495
3 changed files with 6 additions and 7 deletions
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6
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -10,8 +10,8 @@ import net.sf.samtools.util.RuntimeIOException;
import org.apache.commons.cli.Option; import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder; import org.apache.commons.cli.OptionBuilder;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.executive.LinearMicroManager;
import org.broadinstitute.sting.gatk.executive.MicroScheduler; import org.broadinstitute.sting.gatk.executive.MicroScheduler;
import org.broadinstitute.sting.gatk.executive.LinearMicroScheduler;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; 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.*;
@ -264,11 +264,11 @@ public class GenomeAnalysisTK extends CommandLineProgram {
Utils.scareUser(String.format("Analysis %s doesn't support SAM/BAM reads, but a read file %s was provided", Analysis_Name, INPUT_FILES)); Utils.scareUser(String.format("Analysis %s doesn't support SAM/BAM reads, but a read file %s was provided", Analysis_Name, INPUT_FILES));
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 MicroScheduler
// is not filtered. // is not filtered.
if( !DISABLE_THREADING ) { if( !DISABLE_THREADING ) {
logger.warn("Preliminary threading support ENABLED"); logger.warn("Preliminary threading support ENABLED");
microScheduler = new LinearMicroManager( INPUT_FILES, REF_FILE_ARG, numThreads ); microScheduler = new LinearMicroScheduler( INPUT_FILES, REF_FILE_ARG, numThreads );
this.engine = microScheduler.getTraversalEngine(); this.engine = microScheduler.getTraversalEngine();
} }
else { else {

5
java/src/org/broadinstitute/sting/gatk/executive/LinearMicroManager.java → java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -12,7 +12,6 @@ import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import java.io.File; import java.io.File;
import java.util.List; import java.util.List;
@ -21,7 +20,7 @@ import java.util.List;
* A micro-scheduling manager for N-way threaded execution of a traversal * A micro-scheduling manager for N-way threaded execution of a traversal
* *
*/ */
public class LinearMicroManager extends MicroScheduler { public class LinearMicroScheduler extends MicroScheduler {
private TraverseLociByReference traversalEngine = null; private TraverseLociByReference traversalEngine = null;
@ -29,7 +28,7 @@ public class LinearMicroManager extends MicroScheduler {
return traversalEngine; return traversalEngine;
} }
public LinearMicroManager( List<File> reads, // the reads file(s) public LinearMicroScheduler( List<File> reads, // the reads file(s)
File refFile, // the reference file driving the traversal File refFile, // the reference file driving the traversal
int nThreadsToUse ) { // maximum number of threads to use to do the work int nThreadsToUse ) { // maximum number of threads to use to do the work
super( reads, refFile ); super( reads, refFile );

2
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -27,7 +27,7 @@ public abstract class MicroScheduler {
private List<File> reads; private List<File> reads;
private static long SHARD_SIZE = 100000L; private static long SHARD_SIZE = 100000L;
protected static Logger logger = Logger.getLogger(LinearMicroManager.class); protected static Logger logger = Logger.getLogger(MicroScheduler.class);
protected IndexedFastaSequenceFile reference; protected IndexedFastaSequenceFile reference;