80 lines
2.9 KiB
Java
Executable File
80 lines
2.9 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.executive;
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import org.broadinstitute.sting.gatk.dataSources.providers.LocusContextProvider;
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import org.broadinstitute.sting.gatk.dataSources.providers.ReferenceProvider;
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import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
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import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
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import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
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import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
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import org.broadinstitute.sting.gatk.OutputTracker;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import java.util.concurrent.Callable;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.util.CloseableIterator;
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/**
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* User: hanna
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* Date: Apr 29, 2009
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* Time: 4:40:38 PM
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* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
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* Software and documentation are copyright 2005 by the Broad Institute.
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* All rights are reserved.
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*
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* Users acknowledge that this software is supplied without any warranty or support.
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* The Broad Institute is not responsible for its use, misuse, or
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* functionality.
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*/
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/**
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* Carries the walker over a given shard, in a callable interface.
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*/
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public class ShardTraverser implements Callable {
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private Walker walker;
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private TraverseLociByReference traversalEngine;
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private Shard shard;
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private IndexedFastaSequenceFile reference;
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private SAMDataSource reads;
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private OutputMerger output;
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public ShardTraverser( TraverseLociByReference traversalEngine,
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Walker walker,
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Shard shard,
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IndexedFastaSequenceFile reference,
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SAMDataSource reads,
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OutputMerger output ) {
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this.walker = walker;
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this.traversalEngine = traversalEngine;
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this.shard = shard;
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this.reference = reference;
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this.reads = reads;
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this.output = output;
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}
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public Object call() {
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Object accumulator = ((LocusWalker<?,?>)walker).reduceInit();
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CloseableIterator<SAMRecord> readShard = null;
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readShard = reads.seek( shard );
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ReferenceProvider referenceProvider = new ReferenceProvider( reference, shard.getGenomeLoc() );
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LocusContextProvider locusProvider = new LocusContextProvider( readShard );
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OutputTracker outputTracker = GenomeAnalysisTK.Instance.getOutputTracker();
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outputTracker.setLocalStreams( output.getOutStream(), output.getErrStream() );
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try {
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accumulator = traversalEngine.traverse( walker, shard, referenceProvider, locusProvider, accumulator );
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}
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finally {
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readShard.close();
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output.complete();
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outputTracker.removeLocalStreams();
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}
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return accumulator;
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}
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}
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