/*
* 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 java.io.FileNotFoundException;
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.bio.BadBioEntryException;
import fr.ens.biologie.genomique.eoulsan.bio.ReadSequence;
import fr.ens.biologie.genomique.eoulsan.bio.io.FastqReader;
import fr.ens.biologie.genomique.eoulsan.bio.io.FastqWriter;
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 FASTQ files.
* @author Laurent Jourdren
* @since 2.0
*/
public class FastqMerger implements Merger {
@Override
public DataFormat getFormat() {
return DataFormats.READS_FASTQ;
}
@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> inDataFileIterator,
final DataFile outFile) throws FileNotFoundException, IOException {
final FastqWriter writer = new FastqWriter(outFile.create());
while (inDataFileIterator.hasNext()) {
// Get input file
final DataFile inFile = inDataFileIterator.next();
EoulsanLogger.getLogger()
.info("Merge " + inFile.getName() + " to " + outFile.getName());
final FastqReader reader = new FastqReader(inFile.open());
for (final ReadSequence read : reader) {
writer.write(read);
}
reader.close();
try {
reader.throwException();
} catch (BadBioEntryException e) {
throw new IOException(e);
}
}
writer.close();
}
}