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

/*
 * Copyright (c) 2010 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
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 * 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,
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 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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package org.broadinstitute.sting.alignment;

import net.sf.picard.reference.ReferenceSequenceFileFactory;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceDictionary;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.BWTFiles;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;

import java.io.File;

/**
 * Aligns reads to a given reference using Heng Li's BWA aligner, presenting the resulting alignments in SAM or BAM format.
 * Mimics the steps 'bwa aln' followed by 'bwa samse' using the BWA/C implementation.
 *
 * @author mhanna
 * @version 0.1
 */
@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
@WalkerName("Align")
public class AlignmentWalker extends ReadWalker<Integer,Integer> {
    @Argument(fullName="target_reference",shortName="target_ref",doc="The reference to which reads in the source file should be aligned.  Alongside this reference should sit index files " +
                                                                     "generated by bwa index -d bwtsw.  If unspecified, will default " +
                                                                     "to the reference specified via the -R argument.",required=false)
    private File targetReferenceFile = null;

    @Output
    private StingSAMFileWriter out = null;

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

    /**
     * New header to use, if desired.
     */
    private SAMFileHeader header;

    /**
     * Create an aligner object.  The aligner object will load and hold the BWT until close() is called.
     */    
    @Override
    public void initialize() {
        if(targetReferenceFile == null)
            targetReferenceFile = getToolkit().getArguments().referenceFile;
        BWTFiles bwtFiles = new BWTFiles(targetReferenceFile.getAbsolutePath());
        BWAConfiguration configuration = new BWAConfiguration();
        aligner = new BWACAligner(bwtFiles,configuration);

        // Take the header of the SAM file, tweak it by adding in the reference dictionary and specifying that the target file is unsorted.
        header = getToolkit().getSAMFileHeader().clone();
        SAMSequenceDictionary referenceDictionary =
                ReferenceSequenceFileFactory.getReferenceSequenceFile(targetReferenceFile).getSequenceDictionary();
        header.setSequenceDictionary(referenceDictionary);
        header.setSortOrder(SAMFileHeader.SortOrder.unsorted);

        out.writeHeader(header);
    }

    /**
     * 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(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
        SAMRecord alignedRead = aligner.align(read,header);
        out.addAlignment(alignedRead);
        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);
    }

}