gatk-3.8/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

package org.broadinstitute.sting.gatk.executive;

import net.sf.picard.reference.ReferenceSequenceFile;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory;
import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.gatk.traversals.TraverseReads;
import org.broadinstitute.sting.gatk.traversals.TraverseLoci;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.Reads;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;

import java.io.File;
import java.io.FileNotFoundException;
import java.util.List;
import java.util.Map;
import java.util.HashMap;
import java.util.ArrayList;

/**
 * Created by IntelliJ IDEA.
 * User: mhanna
 * Date: Apr 26, 2009
 * Time: 12:37:23 PM
 * To change this template use File | Settings | File Templates.
 */

/** Shards and schedules data in manageable chunks. */
public abstract class MicroScheduler {
    private static long SHARD_SIZE = 100000L;

    protected static Logger logger = Logger.getLogger(MicroScheduler.class);

    protected final TraversalEngine traversalEngine;
    protected final IndexedFastaSequenceFile reference;

    private final SAMDataSource reads;
    private final List<ReferenceOrderedDataSource> rods;

    /**
     * MicroScheduler factory function.  Create a microscheduler appropriate for reducing the
     * selected walker.
     * @param walker Which walker to use.
     * @param nThreadsToUse Number of threads to utilize.
     * @return The best-fit microscheduler.
     */
    public static MicroScheduler create(Walker walker, Reads reads, File ref, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods, int nThreadsToUse) {
        if (walker instanceof TreeReducible && nThreadsToUse > 1) {
            logger.info("Creating hierarchical microscheduler");
            return new HierarchicalMicroScheduler(walker, reads, ref, rods, nThreadsToUse);
        } else {
            logger.info("Creating linear microscheduler");
            return new LinearMicroScheduler(walker, reads, ref, rods);
        }
    }

    /**
     * Create a microscheduler given the reads and reference.
     * @param reads The reads.
     * @param refFile File pointer to the reference.
     */
    protected MicroScheduler(Walker walker, Reads reads, File refFile, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
        if (walker instanceof ReadWalker) {
            traversalEngine = new TraverseReads(reads.getReadsFiles(), refFile, rods);
        } else {
            traversalEngine = new TraverseLoci(reads.getReadsFiles(), refFile, rods);
        }

        this.reads = getReadsDataSource(reads);
        this.reference = openReferenceSequenceFile(refFile);
        this.rods = getReferenceOrderedDataSources(rods);
    }

    /**
     * A temporary getter for the traversal engine.  In the future, clients
     * of the microscheduler shouldn't need to know anything about the traversal engine.
     * @return The traversal engine.
     */
    public TraversalEngine getTraversalEngine() {
        return traversalEngine;
    }

    /**
     * Walks a walker over the given list of intervals.
     * @param walker Computation to perform over dataset.
     * @param intervals A list of intervals over which to walk.  Null for whole dataset.
     * @return the return type of the walker
     */
    public abstract Object execute(Walker walker, GenomeLocSortedSet intervals);

    /**
     * Get the sharding strategy given a driving data source.
     * @param walker Walker for which to infer sharding strategy.
     * @param drivingDataSource Data on which to shard.
     * @param intervals Intervals to use when limiting sharding.
     * @return Sharding strategy for this driving data source.
     */
    protected ShardStrategy getShardStrategy(Walker walker, ReferenceSequenceFile drivingDataSource, GenomeLocSortedSet intervals) {
        ShardStrategy shardStrategy = null;
        ShardStrategyFactory.SHATTER_STRATEGY shardType;
        if (walker instanceof LocusWalker) {
            if (intervals != null) {
                shardType = (walker.isReduceByInterval()) ?
                             ShardStrategyFactory.SHATTER_STRATEGY.INTERVAL :
                             ShardStrategyFactory.SHATTER_STRATEGY.LINEAR;

                shardStrategy = ShardStrategyFactory.shatter(shardType,
                                                             drivingDataSource.getSequenceDictionary(),
                                                             SHARD_SIZE,
                                                             intervals);
            } else
                shardStrategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR,
                                                             drivingDataSource.getSequenceDictionary(),
                                                             SHARD_SIZE);

        } else if (walker instanceof ReadWalker) {

            shardType = ShardStrategyFactory.SHATTER_STRATEGY.READS;

            if (intervals != null) {
                shardStrategy = ShardStrategyFactory.shatter(shardType,
                                                             drivingDataSource.getSequenceDictionary(),
                                                             SHARD_SIZE,
                                                             intervals);
            } else {
                shardStrategy = ShardStrategyFactory.shatter(shardType,
                                                             drivingDataSource.getSequenceDictionary(),
                                                             SHARD_SIZE);
            }
        } else
            throw new StingException("Unable to support walker of type" + walker.getClass().getName());

        return shardStrategy;
    }

    /**
     * Gets an window into all the data that can be viewed as a single shard.
     * @param shard The section of data to view.
     * @return An accessor for all the data in this shard.
     */
    protected ShardDataProvider getShardDataProvider(Shard shard) {
        return new ShardDataProvider(shard, reads, reference, rods);
    }

    /**
     * Gets a data source for the given set of reads.
     * @return A data source for the given set of reads.
     */
    private SAMDataSource getReadsDataSource(Reads reads) {
        // By reference traversals are happy with no reads.  Make sure that case is handled.
        if (reads.getReadsFiles().size() == 0)
            return null;

        SAMDataSource dataSource = new SAMDataSource(reads);

        // Side effect: initialize the traversal engine with reads data.
        // TODO: Give users a dedicated way of getting the header so that the MicroScheduler
        //       doesn't have to bend over backward providing legacy getters and setters.
        traversalEngine.setSAMHeader(dataSource.getHeader());

        return dataSource;
    }

    /**
     * Open the reference-ordered data sources.
     * @return A list of reference-ordered data sources.
     */
    private List<ReferenceOrderedDataSource> getReferenceOrderedDataSources(List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
        List<ReferenceOrderedDataSource> dataSources = new ArrayList<ReferenceOrderedDataSource>();
        for (ReferenceOrderedData<? extends ReferenceOrderedDatum> rod : rods)
            dataSources.add(new ReferenceOrderedDataSource(rod));
        return dataSources;
    }

    /**
     * Opens a reference sequence file paired with an index.
     * @param refFile Handle to a reference sequence file.  Non-null.
     * @return A thread-safe file wrapper.
     */
    private IndexedFastaSequenceFile openReferenceSequenceFile(File refFile) {
        IndexedFastaSequenceFile ref = null;
        try {
            ref = new IndexedFastaSequenceFile(refFile);
        }
        catch (FileNotFoundException ex) {
            throw new StingException("I/O error while opening fasta file: " + ex.getMessage(), ex);
        }
        GenomeLoc.setupRefContigOrdering(ref);
        return ref;
    }
}