101 lines
3.7 KiB
Java
Executable File
101 lines
3.7 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.walkers;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMFileWriter;
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import net.sf.samtools.SAMFileHeader;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.Utils;
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import java.io.PrintStream;
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import java.io.FileNotFoundException;
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import java.io.File;
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import java.util.Random;
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/*
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* Copyright (c) 2009 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* This walker prints out the reads from the BAM files provided to the traversal engines.
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* It also supports the command line option '-outputBamFile filname', which outputs all the
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* reads to a specified BAM file
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*/
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public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
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/** an optional argument to dump the reads out to a BAM file */
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@Argument(fullName = "outputBamFile", shortName = "of", doc = "Write output to this BAM filename instead of STDOUT", required = false)
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String outputBamFile = null;
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/**
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* The reads map function.
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* @param ref the reference bases that correspond to our read, if a reference was provided
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* @param read the read itself, as a SAMRecord
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* @return the read itself
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*/
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public SAMRecord map( char[] ref, SAMRecord read ) {
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return read;
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}
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/**
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* reduceInit is called once before any calls to the map function. We use it here to setup the output
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* bam file, if it was specified on the command line
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* @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
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*/
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public SAMFileWriter reduceInit() {
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if (outputBamFile != null) {
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SAMFileHeader header = this.getToolkit().getEngine().getSAMHeader();
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return Utils.createSAMFileWriterWithCompression(header, true, outputBamFile, getToolkit().getBAMCompression());
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} else {
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return null;
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}
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}
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/**
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* given a read and a output location, reduce by emitting the read
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* @param read the read itself
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* @param output the output source
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* @return the SAMFileWriter, so that the next reduce can emit to the same source
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*/
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public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
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if (output != null) {
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output.addAlignment(read);
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} else {
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out.println(read.format());
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}
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return output;
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}
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/**
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* when we're done traversing, close the reads file
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* @param output the SAMFileWriter we've used in the reduce phase
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*/
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public void onTraversalDone( SAMFileWriter output ) {
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if (output != null) {
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output.close();
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}
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}
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}
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