/*
 *                  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 org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.apache.hadoop.io.compress.SplittableCompressionCodec;
import org.apache.hadoop.mapreduce.InputSplit;
import org.apache.hadoop.mapreduce.JobContext;
import org.apache.hadoop.mapreduce.RecordReader;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;

/**
 * This class define an InputFormat for FASTQ files for the Hadoop MapReduce
 * framework.
 * @since 1.0
 * @author Laurent Jourdren
 */
public class FastqInputFormat extends FileInputFormat<Text, Text> {

  @Override
  public RecordReader<Text, Text> createRecordReader(
      final InputSplit inputSplit,
      final TaskAttemptContext taskAttemptContext) {

    return new FastqRecordReader(taskAttemptContext);
  }

  @Override
  protected boolean isSplitable(JobContext context, Path file) {

    final CompressionCodec codec =
        new CompressionCodecFactory(context.getConfiguration()).getCodec(file);

    if (null == codec) {
      return true;
    }

    return codec instanceof SplittableCompressionCodec;
  }

}