/*
* 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.modules.fastqc;
import static com.google.common.base.Preconditions.checkNotNull;
import java.io.File;
import java.io.IOException;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.SamInputResource;
import htsjdk.samtools.SamReader;
import htsjdk.samtools.SamReaderFactory;
import uk.ac.babraham.FastQC.Sequence.Sequence;
import uk.ac.babraham.FastQC.Sequence.SequenceFormatException;
/**
* This class define a SequenceFile for SAM files.
* @author Laurent Jourdren
* @since 2.0
*/
public class SAMSequenceFile implements CounterSequenceFile {
private final DataFile file;
private final SamReader reader;
private final SAMRecordIterator iterator;
private long count;
@Override
public File getFile() {
return new File(this.file.getName());
}
@Override
public int getPercentComplete() {
return 0;
}
@Override
public boolean hasNext() {
final boolean result = this.iterator.hasNext();
if (!result) {
try {
reader.close();
} catch (IOException e) {
}
}
return result;
}
@Override
public boolean isColorspace() {
return false;
}
@Override
public String name() {
return file.getName();
}
@Override
public Sequence next() throws SequenceFormatException {
final SAMRecord record = this.iterator.next();
this.count++;
return new Sequence(this, record.getReadString(),
record.getBaseQualityString(), record.getReadName());
}
@Override
public long getCount() {
return count;
}
//
// Constructor
//
/**
* Public constructor.
* @param inFile SAM input file
* @throws IOException if an error occurs when opening the file
*/
public SAMSequenceFile(final DataFile inFile) throws IOException {
checkNotNull(inFile, "file argument cannot be null");
this.file = inFile;
this.reader =
SamReaderFactory.makeDefault().open(SamInputResource.of(inFile.open()));
this.iterator = reader.iterator();
}
}