gatk-3.8/java/src/org/broadinstitute/sting/gatk/walkers/PrintRODsWalker.java

/*
 * 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.
 */

package org.broadinstitute.sting.gatk.walkers;

import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.utils.genotype.Variation;

import java.util.Iterator;

/**
 * Prints out all of the RODs in the input data set. Data is rendered using the toString() method
 * of the given ROD.
 */
public class PrintRODsWalker extends RodWalker<Integer, Integer> {

    /**
     * Initialize the number of loci processed to zero.
     *
     * @return 0
     */
    public Integer reduceInit() { return 0; }

    /**
     * For each site of interest, rescore the genotype likelihoods by applying the specified feature set.
     *
     * @param tracker  the meta-data tracker
     * @param ref      the reference base
     * @param context  the context for the given locus
     * @return 1 if the locus was successfully processed, 0 if otherwise
     */
    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        if ( tracker == null )
            return 0;

        Iterator<ReferenceOrderedDatum> rods = tracker.getAllRods().iterator();
        while ( rods.hasNext() ) {
            ReferenceOrderedDatum rod = rods.next();
            if ( rod instanceof Variation )
                out.println(rod.toString());
        }

        return 1;
    }

    /**
     * Increment the number of rods processed.
     *
     * @param value result of the map.
     * @param sum   accumulator for the reduce.
     * @return the new number of rods processed.
     */
    public Integer reduce(Integer value, Integer sum) {
        return sum + value;
    }

    public void onTraversalDone(Integer result) {}    
}