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

package org.broadinstitute.sting.gatk.walkers;

import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.Utils;

import java.io.PrintStream;
import java.io.FileNotFoundException;
import java.io.File;
import java.util.Random;

/*
 * 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.
 */

/**
 * This walker prints out the reads from the BAM files provided to the traversal engines.
 * It also supports the command line option '-outputBamFile filname', which outputs all the
 * reads to a specified BAM file
 * The walker now also optionally filters reads based on command line options.
 */
@Requires({DataSource.READS, DataSource.REFERENCE})
public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {

    /** an optional argument to dump the reads out to a BAM file */
    @Argument(fullName = "outputBamFile", shortName = "of", doc = "Write output to this BAM filename instead of STDOUT", required = false)
    SAMFileWriter outputBamFile = null;
    @Argument(fullName = "maxReadLength", shortName = "maxRead", doc="Discard reads with length greater than the specified value", required = false)
    Integer maxLength = null;
    @Argument(fullName = "platform", shortName = "platform", doc="Discard reads not generated by the specified platform", required = false)
    String platform = null;
    // E.g. ILLUMINA, 454

    /**
     * The initialize function.
     */
    public void initialize() {
        if  ( platform != null )
            platform = platform.toUpperCase();
    }

    /**
     * The reads filter function.
     * @param ref the reference bases that correspond to our read, if a reference was provided
     * @param read the read itself, as a SAMRecord
     * @return true if the read passes the filter, false if it doesn't
     */
    public boolean filter(char[] ref, SAMRecord read) {
        if ( maxLength != null && read.getReadLength() > maxLength )
            return false;
        if  ( platform != null ) {
            Object readGroupAttr = read.getAttribute("RG");
            if ( readGroupAttr != null ) {
                SAMReadGroupRecord readGroup = getToolkit().getSAMFileHeader().getReadGroup(readGroupAttr.toString());
                if ( readGroup != null ) {
                    Object readPlatformAttr = readGroup.getAttribute("PL");
                    if ( readPlatformAttr != null )
                        return readPlatformAttr.toString().toUpperCase().contains(platform);
                }
            }
        }
        return true;
	}

    /**
     * The reads map function.
     * @param ref the reference bases that correspond to our read, if a reference was provided
     * @param read the read itself, as a SAMRecord
     * @return the read itself
     */
    public SAMRecord map( char[] ref, SAMRecord read ) {
        return read;
    }

    /**
     * reduceInit is called once before any calls to the map function.  We use it here to setup the output
     * bam file, if it was specified on the command line
     * @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
     */
    public SAMFileWriter reduceInit() {
        return outputBamFile;
    }

    /**
     * given a read and a output location, reduce by emitting the read
     * @param read the read itself
     * @param output the output source
     * @return the SAMFileWriter, so that the next reduce can emit to the same source
     */
    public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
        if (output != null) {
            output.addAlignment(read);
        } else {
            out.println(read.format());
        }

        return output;
    }


    /**
     * when we're done traversing, close the reads file
     * @param output the SAMFileWriter we've used in the reduce phase
     */
    public void onTraversalDone( SAMFileWriter output ) {
        if (output != null) {
            output.close();
        }
    }
}