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

package org.broadinstitute.sting.gatk.executive;

import org.broadinstitute.sting.gatk.dataSources.providers.LocusContextProvider;
import org.broadinstitute.sting.gatk.dataSources.providers.ReferenceProvider;
import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.traversals.TraverseByReads;
import org.broadinstitute.sting.gatk.traversals.TraverseLociByReference;
import org.broadinstitute.sting.gatk.traversals.TraverseReads;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.utils.GenomeLoc;

import java.io.File;
import java.util.List;

/** A micro-scheduling manager for single-threaded execution of a traversal. */
public class LinearMicroScheduler extends MicroScheduler {

    private boolean isAReadWalker = false;

    /**
     * Create a new linear microscheduler to process the given reads and reference.
     *
     * @param reads   Reads file(s) to process.
     * @param refFile Reference for driving the traversal.
     */
    protected LinearMicroScheduler(List<File> reads, File refFile, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods, Walker walker) {
        super(reads, refFile);

        // determine if we're a read walker: they get a slightly different, but not in any way worse execute methodology. I pinky swear...
        isAReadWalker = (walker instanceof ReadWalker) ? true : false;

        if (isAReadWalker) {
            traversalEngine = new TraverseByReads(reads, refFile, rods);
        } else {
            traversalEngine = new TraverseLociByReference(reads, refFile, rods);
        }
    }

    /**
     * Run this traversal over the specified subsection of the dataset.
     *
     * @param walker    Computation to perform over dataset.
     * @param locations Subset of the dataset over which to walk.
     */
    public void execute(Walker walker, List<GenomeLoc> locations) {
        ShardStrategy shardStrategy = getShardStrategy(reference, locations);
        SAMDataSource dataSource = getReadsDataSource();

        walker.initialize();
        Object accumulator = walker.reduceInit();

        for (Shard shard : shardStrategy) {

            StingSAMIterator readShard = dataSource.seek(shard);

            ReferenceProvider referenceProvider = new ReferenceProvider(reference, shard);
            LocusContextProvider locusProvider = new LocusContextProvider(readShard);

            if (!isAReadWalker) {
                accumulator = ((TraverseLociByReference) traversalEngine).traverse(walker, shard, referenceProvider, locusProvider, accumulator);
            } else {
                accumulator = ((TraverseReads) traversalEngine).traverse(walker, shard, readShard, accumulator);
            }

            readShard.close();
        }

        traversalEngine.printOnTraversalDone(accumulator);

        walker.onTraversalDone(accumulator);
    }


}