gatk-3.8/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java

package org.broadinstitute.sting.gatk.traversals;

import net.sf.samtools.SAMRecord;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.WalkerManager;
import org.broadinstitute.sting.gatk.datasources.providers.ReadBasedReferenceOrderedView;
import org.broadinstitute.sting.gatk.datasources.providers.ReadReferenceView;
import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLocParser;

/*
 * Copyright (c) 2009 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */

/**
 * @author aaron
 * @version 1.0
 * @date Apr 24, 2009
 * <p/>
 * Class TraverseReads
 * <p/>
 * This class handles traversing by reads in the new shardable style
 */
public class TraverseReads extends TraversalEngine {    
    /** our log, which we want to capture anything from this class */
    protected static Logger logger = Logger.getLogger(TraverseReads.class);

    /** descriptor of the type */
    private static final String READS_STRING = "reads";

    /**
     * Traverse by reads, given the data and the walker
     *
     * @param walker the walker to traverse with
     * @param dataProvider the provider of the reads data
     * @param sum the value of type T, specified by the walker, to feed to the walkers reduce function
     * @param <M> the map type of the walker
     * @param <T> the reduce type of the walker
     * @return the reduce variable of the read walker
     */
    public <M, T> T traverse(Walker<M, T> walker,
                             ShardDataProvider dataProvider,
                             T sum) {

        logger.debug(String.format("TraverseReads.traverse Covered dataset is %s", dataProvider));

        if (!(walker instanceof ReadWalker))
            throw new IllegalArgumentException("Walker isn't a read walker!");

        if( !dataProvider.hasReads() )
            throw new IllegalArgumentException("Unable to traverse reads; no read data is available.");

        ReadWalker<M, T> readWalker = (ReadWalker<M, T>) walker;
        boolean needsReferenceBasesP = WalkerManager.isRequired(walker, DataSource.REFERENCE_BASES);

        ReadView reads = new ReadView(dataProvider);
        ReadReferenceView reference = new ReadReferenceView(dataProvider);

        // get the reference ordered data
        ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);

        // while we still have more reads
        for (SAMRecord read : reads) {
            // an array of characters that represent the reference
            char[] refSeq = null;

            // get the array of characters for the reference sequence, since we're a mapped read
            if (needsReferenceBasesP && !read.getReadUnmappedFlag() && dataProvider.hasReference())
                refSeq = reference.getReferenceBases(read);

            // update the number of reads we've seen
            TraversalStatistics.nRecords++;
            TraversalStatistics.nReads++;

            // if the read is mapped, create a metadata tracker
            ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;

            final boolean keepMeP = readWalker.filter(refSeq, read);
            if (keepMeP) {
                M x = readWalker.map(refSeq, read, tracker); // the tracker can be null
                sum = readWalker.reduce(x, sum);
            }

            printProgress(READS_STRING,
                          (read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) ?
                                  null :
                                  GenomeLocParser.createGenomeLoc(read.getReferenceIndex(),read.getAlignmentStart()));
        }
        return sum;
    }

    /**
     * Temporary override of printOnTraversalDone.
     * TODO: Add some sort of TE.getName() function once all TraversalEngines are ported.
     * @param sum Result of the computation.
     * @param <T> Type of the result.
     */
    public <T> void printOnTraversalDone( T sum ) {
        printOnTraversalDone(READS_STRING, sum );
    }
}