123 lines
4.9 KiB
Java
123 lines
4.9 KiB
Java
package org.broadinstitute.sting.gatk.executive;
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import org.apache.log4j.Logger;
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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.shards.ShardStrategy;
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import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory;
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import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
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import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SimpleDataSourceLoadException;
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import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2;
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import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
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import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
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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.GenomeLoc;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.List;
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/**
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* A micro-scheduling manager for N-way threaded execution of a traversal
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*
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*/
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public class MicroManager {
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private static long SHARD_SIZE = 100000L;
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private List<File> reads;
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private IndexedFastaSequenceFile ref;
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private TraverseLociByReference traversalEngine = null;
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protected static Logger logger = Logger.getLogger(MicroManager.class);
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protected List<GenomeLoc> intervalList = null;
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public TraversalEngine getTraversalEngine() {
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return traversalEngine;
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}
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public MicroManager( List<File> reads, // the reads file(s)
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File refFile, // the reference file driving the traversal
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int nThreadsToUse ) { // maximum number of threads to use to do the work
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this.reads = reads;
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try {
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ref = new IndexedFastaSequenceFile(refFile);
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}
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catch( FileNotFoundException ex ) {
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throw new RuntimeException("File not found opening fasta file; please do this check before MicroManaging", ex);
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}
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GenomeLoc.setupRefContigOrdering(ref);
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traversalEngine = new TraverseLociByReference( reads, refFile, new java.util.ArrayList() );
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}
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public void setIntervalList(List<GenomeLoc> intervalList) {
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this.intervalList = intervalList;
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}
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public void execute( Walker walker, // the analysis technique to use.
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List<GenomeLoc> locations ) { // list of work to do
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ShardStrategy shardStrategy = null;
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if( locations != null )
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shardStrategy = ShardStrategyFactory.shatter( ShardStrategyFactory.SHATTER_STRATEGY.LINEAR,
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ref.getSequenceDictionary(),
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SHARD_SIZE,
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locations );
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else
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shardStrategy = ShardStrategyFactory.shatter( ShardStrategyFactory.SHATTER_STRATEGY.LINEAR,
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ref.getSequenceDictionary(),
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SHARD_SIZE );
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SAMDataSource dataSource = null;
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try {
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dataSource = new SAMDataSource( TraversalEngine.unpackReads(reads) );
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}
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catch( SimpleDataSourceLoadException ex ) {
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throw new RuntimeException( ex );
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}
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catch( FileNotFoundException ex ) {
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throw new RuntimeException( ex );
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}
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boolean walkerInitialized = false;
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Object accumulator = null;
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for(Shard shard: shardStrategy) {
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GenomeLoc span = shard.getGenomeLoc();
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MergingSamRecordIterator2 readShard = null;
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try {
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readShard = dataSource.seek( span );
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}
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catch( SimpleDataSourceLoadException ex ) {
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throw new RuntimeException( ex );
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}
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ReferenceProvider referenceProvider = new ReferenceProvider( ref, span );
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LocusContextProvider locusProvider = new LocusContextProvider( readShard );
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// set the sam header of the traversal engine
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traversalEngine.setSAMHeader(readShard.getMergedHeader());
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if (!walkerInitialized) {
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walker.initialize();
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accumulator = ((LocusWalker<?,?>)walker).reduceInit();
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walkerInitialized = true;
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}
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accumulator = traversalEngine.traverse( walker, shard, referenceProvider, locusProvider, accumulator );
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readShard.close();
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}
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traversalEngine.printOnTraversalDone("loci", accumulator);
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walker.onTraversalDone(accumulator);
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}
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}
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