51 lines
1.6 KiB
Java
51 lines
1.6 KiB
Java
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package org.broadinstitute.sting.gatk.executive;
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import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
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import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.io.File;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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* User: mhanna
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* Date: Apr 26, 2009
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* Time: 5:41:04 PM
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* To change this template use File | Settings | File Templates.
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*/
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/**
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* A microscheduler that schedules shards according to a tree-like structure.
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* Requires a special walker tagged with a 'TreeReducible' interface.
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*/
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public class HierarchicalMicroScheduler extends MicroScheduler {
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/**
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* How many threads should the hierarchical scheduler try to keep busy.
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*/
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private int nThreadsToUse;
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private TraverseLociByReference traversalEngine = null;
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/**
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* Create a new hierarchical microscheduler to process the given reads and reference.
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* @param reads Reads file(s) to process.
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* @param refFile Reference for driving the traversal.
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* @param nThreadsToUse maximum number of threads to use to do the work
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*/
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protected HierarchicalMicroScheduler( List<File> reads, File refFile, int nThreadsToUse ) {
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super( reads, refFile );
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this.nThreadsToUse = nThreadsToUse;
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traversalEngine = new TraverseLociByReference( reads, refFile, new java.util.ArrayList() );
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}
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public TraversalEngine getTraversalEngine() {
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return traversalEngine;
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}
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public void execute( Walker walker, List<GenomeLoc> intervals ) {
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}
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}
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