/*
* Copyright (c) 2012 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.
*/
package org.broadinstitute.gatk.utils.sam;
import htsjdk.samtools.*;
import htsjdk.samtools.util.ProgressLoggerInterface;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.exceptions.GATKException;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import java.io.File;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
/**
* Created by IntelliJ IDEA.
* User: asivache
* Date: May 31, 2011
* Time: 3:52:49 PM
* To change this template use File | Settings | File Templates.
*/
public class NWaySAMFileWriter implements SAMFileWriter {
private Map<SAMReaderID,SAMFileWriter> writerMap = null;
private boolean presorted ;
GenomeAnalysisEngine toolkit;
boolean KEEP_ALL_PG_RECORDS = false;
public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order,
boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord, boolean keep_records) {
this.presorted = presorted;
this.toolkit = toolkit;
this.KEEP_ALL_PG_RECORDS = keep_records;
writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
setupByReader(toolkit,in2out,order, presorted, indexOnTheFly, generateMD5, pRecord);
}
public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order,
boolean presorted, boolean indexOnTheFly , boolean generateMD5, SAMProgramRecord pRecord, boolean keep_records) {
this.presorted = presorted;
this.toolkit = toolkit;
this.KEEP_ALL_PG_RECORDS = keep_records;
writerMap = new HashMap<SAMReaderID,SAMFileWriter>();
setupByReader(toolkit,ext,order, presorted, indexOnTheFly, generateMD5, pRecord);
}
public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order,
boolean presorted, boolean indexOnTheFly, boolean generateMD5) {
this(toolkit, in2out, order, presorted, indexOnTheFly, generateMD5, null,false);
}
public NWaySAMFileWriter(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order,
boolean presorted, boolean indexOnTheFly , boolean generateMD5) {
this(toolkit, ext, order, presorted, indexOnTheFly, generateMD5, null,false);
}
/**
* Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved
* from <code>toolkit</code>). The <code>in2out</code> map must contain an entry for each input filename and map it
* onto a unique output file name.
* @param toolkit
* @param in2out
*/
public void setupByReader(GenomeAnalysisEngine toolkit, Map<String,String> in2out, SAMFileHeader.SortOrder order,
boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord) {
if ( in2out==null ) throw new GATKException("input-output bam filename map for n-way-out writing is NULL");
for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
String outName;
if ( ! in2out.containsKey(fName) )
throw new UserException.BadInput("Input-output bam filename map does not contain an entry for the input file "+fName);
outName = in2out.get(fName);
if ( writerMap.containsKey( rid ) )
throw new GATKException("nWayOut mode: Reader id for input sam file "+fName+" is already registered; "+
"map file likely contains multiple entries for this input file");
addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5, pRecord);
}
}
/**
* Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK engine (those will be retrieved
* from <code>toolkit</code>). The output file names will be generated automatically by stripping ".sam" or ".bam" off the
* input file name and adding ext instead (e.g. ".cleaned.bam").
* onto a unique output file name.
* @param toolkit
* @param ext
*/
public void setupByReader(GenomeAnalysisEngine toolkit, String ext, SAMFileHeader.SortOrder order,
boolean presorted, boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord pRecord) {
for ( SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs() ) {
String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
String outName;
int pos ;
if ( fName.toUpperCase().endsWith(".BAM") ) pos = fName.toUpperCase().lastIndexOf(".BAM");
else {
if ( fName.toUpperCase().endsWith(".SAM") ) pos = fName.toUpperCase().lastIndexOf(".SAM");
else throw new UserException.BadInput("Input file name "+fName+" does not end with .sam or .bam");
}
String prefix = fName.substring(0,pos);
outName = prefix+ext;
if ( writerMap.containsKey( rid ) )
throw new GATKException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
addWriter(rid,outName, order, presorted, indexOnTheFly, generateMD5, pRecord);
}
}
private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted,
boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord programRecord) {
File f = new File(outName);
SAMFileHeader header = Utils.setupWriter(toolkit.getSAMFileHeader(id), programRecord);
SAMFileWriterFactory factory = new SAMFileWriterFactory();
factory.setCreateIndex(indexOnTheFly);
factory.setCreateMd5File(generateMD5);
SAMFileWriter sw = factory.makeSAMOrBAMWriter(header, presorted, f);
writerMap.put(id,sw);
}
public Collection<SAMFileWriter> getWriters() {
return writerMap.values();
}
public void addAlignment(SAMRecord samRecord) {
final SAMReaderID id = toolkit.getReaderIDForRead(samRecord);
String rg = samRecord.getStringAttribute("RG");
if ( rg != null ) {
String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg);
samRecord.setAttribute("RG",rg_orig);
}
addAlignment(samRecord, id);
}
public void addAlignment(SAMRecord samRecord, SAMReaderID readerID) {
writerMap.get(readerID).addAlignment(samRecord);
}
public SAMFileHeader getFileHeader() {
return toolkit.getSAMFileHeader();
}
public void close() {
for ( SAMFileWriter w : writerMap.values() ) w.close();
}
@Override
public void setProgressLogger(final ProgressLoggerInterface logger) {
for (final SAMFileWriter writer: writerMap.values()) {
writer.setProgressLogger(logger);
}
}
}