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.utils.Utils;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.alignment.bwa.c.BWACConfiguration;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;

/**
 * Align reads to the reference specified by BWTPrefix.
 *
 * @author mhanna
 * @version 0.1
 */
@WalkerName("Align")
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";

    @Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false)
    String outputBamFile = null;

    @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false)
    public Integer bamCompression = 5;        

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

    /**
     * Target for reads to output.
     */
    private SAMFileWriter outputBam = null;

    /**
     * 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);

        if ( outputBamFile != null ) {
            SAMFileHeader header = this.getToolkit().getSAMFileHeader();
            outputBam = Utils.createSAMFileWriterWithCompression(header, false, outputBamFile, bamCompression);
        }
    }

    /**
     * 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) {
        SAMRecord alignedRead = aligner.align(read);
        if (outputBam != null) {
            outputBam.addAlignment(alignedRead);
        } else {
            out.println(alignedRead.format());
        }
        return 1;
    }

    /**
     * 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);
    }

}