Package fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop

Class PreTreatmentExpressionReducer

java.lang.Object

org.apache.hadoop.mapreduce.Reducer<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionReducer

public class PreTreatmentExpressionReducer
extends org.apache.hadoop.mapreduce.Reducer<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

This class define a reducer for the pretreatment of paired-end data before the expression estimation step.

Since:

1.2

Author:

Claire Wallon

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.Reducer

org.apache.hadoop.mapreduce.Reducer.Context

Constructor Summary

Constructors

Constructor	Description
PreTreatmentExpressionReducer()

Method Summary

Modifier and Type	Method	Description
protected void	reduce(org.apache.hadoop.io.Text key, Iterable<org.apache.hadoop.io.Text> values, org.apache.hadoop.mapreduce.Reducer.Context context)	'key': the identifier of the aligned read without the integer indicating the member of the pair.
protected void	setup(org.apache.hadoop.mapreduce.Reducer.Context context)

Methods inherited from class org.apache.hadoop.mapreduce.Reducer

cleanup, run

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PreTreatmentExpressionReducer

public PreTreatmentExpressionReducer()

Method Detail

setup

protected void setup(org.apache.hadoop.mapreduce.Reducer.Context context)
              throws IOException,
                     InterruptedException

Overrides:

setup in class org.apache.hadoop.mapreduce.Reducer<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException

reduce

protected void reduce(org.apache.hadoop.io.Text key,
                      Iterable<org.apache.hadoop.io.Text> values,
                      org.apache.hadoop.mapreduce.Reducer.Context context)
               throws IOException,
                      InterruptedException

'key': the identifier of the aligned read without the integer indicating the member of the pair. 'values': the rest of the paired alignments, i.e the SAM line of the first paired alignment and the SAM line of the second paired alignment.

Overrides:

reduce in class org.apache.hadoop.mapreduce.Reducer<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException