/*
* 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.expression.hadoop;
import java.io.IOException;
import java.util.Iterator;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Reducer;
/**
* Reducer for the expression estimation with htseq-count.
* @since 1.2
* @author Claire Wallon
*/
public class HTSeqCountReducer
extends Reducer<Text, LongWritable, Text, LongWritable> {
final LongWritable outValue = new LongWritable();
/**
* This method allow to sum of the values of an Iterable of longs.
* @param values values to sum
* @return the sum of the values
*/
private static long sum(final Iterable<LongWritable> values) {
final Iterator<LongWritable> it = values.iterator();
long result = 0L;
while (it.hasNext()) {
result += it.next().get();
}
return result;
}
/**
* 'key': annotation identifier of the feature (gene, mRNA, exon...).
* 'values': a list of '1', the size of this list is the number of reads found
* on the feature.
*/
@Override
protected void reduce(final Text key, final Iterable<LongWritable> values,
final Context context) throws IOException, InterruptedException {
this.outValue.set(sum(values));
context.write(key, this.outValue);
}
}