/*
* 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 java.io.DataOutputStream;
import java.io.IOException;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapreduce.RecordWriter;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.util.ReflectionUtils;
/**
* This class define a FASTQ output format.
* @author Laurent Jourdren
* @since 2.0
*/
public class FastqOutputFormat extends FileOutputFormat<Text, Text> {
@Override
public RecordWriter<Text, Text> getRecordWriter(TaskAttemptContext context)
throws IOException, InterruptedException {
Configuration conf = context.getConfiguration();
boolean isCompressed = getCompressOutput(context);
CompressionCodec codec = null;
String extension = "";
if (isCompressed) {
Class<? extends CompressionCodec> codecClass =
getOutputCompressorClass(context, GzipCodec.class);
codec = ReflectionUtils.newInstance(codecClass, conf);
extension = codec.getDefaultExtension();
}
// Get the output file path
final Path file = getDefaultWorkFile(context, extension);
final FileSystem fs = file.getFileSystem(conf);
if (!isCompressed) {
FSDataOutputStream fileOut = fs.create(file, false);
return new FastqRecordWriter(context, fileOut);
} else {
FSDataOutputStream fileOut = fs.create(file, false);
return new FastqRecordWriter(context,
new DataOutputStream(codec.createOutputStream(fileOut)));
}
}
}