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.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.shards.Shard;
import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;

import java.util.Collection;

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

    /**
     * Create a new linear microscheduler to process the given reads and reference.
     *
     * @param walker    Walker for the traversal.
     * @param reads     Reads file(s) to process.
     * @param reference Reference for driving the traversal.
     * @param rods      Reference-ordered data.
     */
    protected LinearMicroScheduler( Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection<ReferenceOrderedDataSource> rods ) {
        super(walker, reads, reference, rods);
    }

    /**
     * Run this traversal over the specified subsection of the dataset.
     *
     * @param walker    Computation to perform over dataset.
     * @param shardStrategy A strategy for sharding the data.
     */
    public Object execute(Walker walker, ShardStrategy shardStrategy, int maxIterations) {
        // Having maxiterations in the execute method is a holdover from the old TraversalEngine days.
        // Lets do something else with this.
        traversalEngine.setMaximumIterations(maxIterations);

        walker.initialize();
        Accumulator accumulator = Accumulator.create(walker);

        for (Shard shard : shardStrategy) {
            ShardDataProvider dataProvider = getShardDataProvider( shard );

            Object result = traversalEngine.traverse(walker, shard, dataProvider, accumulator.getReduceInit());
            accumulator.accumulate( shard, result );

            dataProvider.close();
        }

        Object result = accumulator.finishTraversal();

        printOnTraversalDone(result);

        return accumulator;
    }


}