/*
* 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.bio.io.hadoop;
import static fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters.ENTRIES_WRITTEN;
import static fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters.INPUT_ENTRIES;
import java.io.DataOutputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.RecordWriter;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
/**
* This class define a RecordWriter for SAM files.
* @author Laurent Jourdren
* @since 2.0
*/
public class SAMRecordWriter extends RecordWriter<Text, Text> {
private static final String COUNTERS_GROUP = "SAM Output Format Counters";
private static final byte[] newline;
static {
newline = "\n".getBytes(StandardCharsets.UTF_8);
}
private final DataOutputStream out;
private final TaskAttemptContext context;
@Override
public synchronized void write(final Text key, final Text value)
throws IOException, InterruptedException {
this.context.getCounter(COUNTERS_GROUP, INPUT_ENTRIES).increment(1);
if (value == null) {
return;
}
this.out.write(value.getBytes(), 0, value.getLength());
this.out.write(newline);
this.context.getCounter(COUNTERS_GROUP, ENTRIES_WRITTEN).increment(1);
}
@Override
public synchronized void close(final TaskAttemptContext context)
throws IOException {
this.out.close();
}
//
// Constructor
//
/**
* Public constructor.
* @param context the context
* @param out data output stream
*/
public SAMRecordWriter(final TaskAttemptContext context,
final DataOutputStream out) {
this.context = context;
this.out = out;
}
}