90 lines
3.9 KiB
Java
90 lines
3.9 KiB
Java
package org.broadinstitute.sting.gatk.executive;
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import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
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import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
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import org.broadinstitute.sting.gatk.datasources.providers.ReadShardDataProvider;
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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.simpleDataSources.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
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import org.broadinstitute.sting.gatk.walkers.Walker;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
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import org.broadinstitute.sting.gatk.io.OutputTracker;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import java.util.Collection;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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/** A micro-scheduling manager for single-threaded execution of a traversal. */
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public class LinearMicroScheduler extends MicroScheduler {
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/**
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* A direct output tracker for directly managing output.
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*/
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private DirectOutputTracker outputTracker = new DirectOutputTracker();
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/**
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* Create a new linear microscheduler to process the given reads and reference.
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*
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* @param walker Walker for the traversal.
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* @param reads Reads file(s) to process.
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* @param reference Reference for driving the traversal.
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* @param rods Reference-ordered data.
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*/
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protected LinearMicroScheduler(GenomeAnalysisEngine engine, Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection<ReferenceOrderedDataSource> rods ) {
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super(engine, walker, reads, reference, rods);
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}
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/**
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* Run this traversal over the specified subsection of the dataset.
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*
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* @param walker Computation to perform over dataset.
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* @param shardStrategy A strategy for sharding the data.
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*/
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public Object execute(Walker walker, ShardStrategy shardStrategy) {
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traversalEngine.startTimers();
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walker.initialize();
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Accumulator accumulator = Accumulator.create(engine,walker);
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for (Shard shard : processingTracker.onlyOwned(shardStrategy, engine.getName())) {
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if ( shard == null ) // we ran out of shards that aren't owned
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break;
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if(shard.getShardType() == Shard.ShardType.LOCUS) {
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LocusWalker lWalker = (LocusWalker)walker;
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WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(), getReadIterator(shard), shard.getGenomeLocs(), lWalker.getDiscards(), engine.getSampleMetadata());
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for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
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ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),engine.getGenomeLocParser(),iterator.getLocus(),iterator,reference,rods);
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Object result = traversalEngine.traverse(walker, dataProvider, accumulator.getReduceInit());
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accumulator.accumulate(dataProvider,result);
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dataProvider.close();
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}
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windowMaker.close();
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}
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else {
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ShardDataProvider dataProvider = new ReadShardDataProvider(shard,engine.getGenomeLocParser(),getReadIterator(shard),reference,rods);
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Object result = traversalEngine.traverse(walker, dataProvider, accumulator.getReduceInit());
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accumulator.accumulate(dataProvider,result);
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dataProvider.close();
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}
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}
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Object result = accumulator.finishTraversal();
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printOnTraversalDone(result,engine.getCumulativeMetrics());
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outputTracker.close();
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cleanup();
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return accumulator;
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}
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/**
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* @{inheritDoc}
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*/
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public OutputTracker getOutputTracker() { return outputTracker; }
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}
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