gatk-3.8/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java

package org.broadinstitute.sting.alignment;

import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.alignment.bwa.c.BWACConfiguration;
import net.sf.samtools.SAMRecord;

import java.util.Random;
import java.util.Iterator;

/**
 * Align reads to the reference specified by BWTPrefix.
 *
 * @author mhanna
 * @version 0.1
 */
public class AlignmentWalker extends ReadWalker<Integer,Integer> {
    @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false)
    String prefix = "/Users/mhanna/reference/Ecoli/Escherichia_coli_K12_MG1655.fasta";

    /**
     * The actual aligner.
     */
    private BWACAligner aligner = null;

    /**
     * A random number generator, used to generate alignments.
     */
    private Random random = new Random();

    /**
     * Create an aligner object.  The aligner object will load and hold the BWT until close() is called.
     */    
    @Override
    public void initialize() {
        BWACConfiguration configuration = new BWACConfiguration(prefix);
        aligner = new BWACAligner(configuration);
    }

    /**
     * Aligns a read to the given reference.
     * @param ref Reference over the read.  Read will most likely be unmapped, so ref will be null.
     * @param read Read to align.
     * @return Number of alignments found for this read.
     */
    @Override
    public Integer map(char[] ref, SAMRecord read) {
        Iterator<SAMRecord[]> alignedReads = aligner.align(read);
        if(alignedReads.hasNext()) {
            SAMRecord[] bestAlignments = alignedReads.next();
            SAMRecord selectedRead = bestAlignments[random.nextInt(bestAlignments.length)];
            out.println(selectedRead.format());
            return bestAlignments.length;
        }
        else {
            out.println(read.format());
            return 0;
        }
    }

    /**
     * Initial value for reduce.  In this case, alignments will be counted.
     * @return 0, indicating no alignments yet found.
     */
    @Override
    public Integer reduceInit() { return 0; }

    /**
     * Calculates the number of alignments found.
     * @param value Number of alignments found by this map.
     * @param sum Number of alignments found before this map.
     * @return Number of alignments found up to and including this map.
     */    
    @Override
    public Integer reduce(Integer value, Integer sum) {
        return value + sum;
    }

    /**
     * Cleanup.
     * @param result Number of reads processed.
     */    
    @Override
    public void onTraversalDone(Integer result) {
        aligner.close();
        super.onTraversalDone(result);
    }

}