/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.splitermergers;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMFileWriterFactory;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SamInputResource;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import java.io.File;
import java.io.IOException;
import java.util.Iterator;
import java.util.Set;
import fr.ens.biologie.genomique.eoulsan.EoulsanException;
import fr.ens.biologie.genomique.eoulsan.EoulsanLogger;
import fr.ens.biologie.genomique.eoulsan.EoulsanRuntime;
import fr.ens.biologie.genomique.eoulsan.core.Parameter;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;
import fr.ens.biologie.genomique.eoulsan.data.DataFormat;
import fr.ens.biologie.genomique.eoulsan.data.DataFormats;
/**
* This class define a merger class for SAM files.
* @author Laurent Jourdren
* @since 2.0
*/
public class BAMMerger implements Merger {
@Override
public DataFormat getFormat() {
return DataFormats.MAPPER_RESULTS_BAM;
}
@Override
public void configure(final Set<Parameter> conf) throws EoulsanException {
// The merge does not need any parameter
for (Parameter p : conf) {
throw new EoulsanException("Unknown parameter for "
+ getFormat().getName() + " merger: " + p.getName());
}
}
@Override
public void merge(final Iterator<DataFile> inFileIterator,
final DataFile outFile) throws IOException {
// Get temporary directory
final File tmpDir = EoulsanRuntime.getRuntime().getTempDirectory();
SAMFileWriter outputSam = null;
while (inFileIterator.hasNext()) {
// Get input file
final DataFile inFile = inFileIterator.next();
EoulsanLogger.getLogger()
.info("Merge " + inFile.getName() + " to " + outFile.getName());
// Get reader
final SamReader inputSam = SamReaderFactory.makeDefault()
.open(SamInputResource.of(inFile.open()));
// Get Writer
if (outputSam == null) {
outputSam = new SAMFileWriterFactory().setTempDirectory(tmpDir)
.makeBAMWriter(inputSam.getFileHeader(), false, outFile.create());
}
// Write all the entries of the input file to the output file
for (SAMRecord samRecord : inputSam) {
outputSam.addAlignment(samRecord);
}
inputSam.close();
}
outputSam.close();
}
}