118 lines
4.6 KiB
Java
Executable File
118 lines
4.6 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.walkers;
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import net.sf.samtools.SAMFileWriter;
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import net.sf.samtools.SAMReadGroupRecord;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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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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* The walker now also optionally filters reads based on command line options.
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*/
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@Requires({DataSource.READS, DataSource.REFERENCE})
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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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SAMFileWriter outputBamFile = null;
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@Argument(fullName = "maxReadLength", shortName = "maxRead", doc="Discard reads with length greater than the specified value", required = false)
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Integer maxLength = null;
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@Argument(fullName = "platform", shortName = "platform", doc="Discard reads not generated by the specified platform", required = false)
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String platform = null;
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// E.g. ILLUMINA, 454
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/**
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* The initialize function.
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*/
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public void initialize() {
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if ( platform != null )
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platform = platform.toUpperCase();
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}
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/**
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* The reads filter 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 true if the read passes the filter, false if it doesn't
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*/
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public boolean filter(char[] ref, SAMRecord read) {
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if ( maxLength != null && read.getReadLength() > maxLength )
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return false;
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if ( platform != null ) {
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Object readGroupAttr = read.getAttribute("RG");
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if ( readGroupAttr != null ) {
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SAMReadGroupRecord readGroup = getToolkit().getSAMFileHeader().getReadGroup(readGroupAttr.toString());
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if ( readGroup != null ) {
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Object readPlatformAttr = readGroup.getAttribute("PL");
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if ( readPlatformAttr != null )
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return readPlatformAttr.toString().toUpperCase().contains(platform);
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}
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}
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}
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return true;
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}
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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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return outputBamFile;
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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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