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

Class SAMFilterReducer

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.mapping.hadoop.SAMFilterReducer

public class SAMFilterReducer
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 alignments filtering.

Since:

1.0

Author:

Laurent Jourdren

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
SAMFilterReducer()

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': identifier of the aligned read, without the integer indicating the pair member if data are in paired-end mode.
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

SAMFilterReducer

public SAMFilterReducer()

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': identifier of the aligned read, without the integer indicating the pair member if data are in paired-end mode. 'value': alignments without the identifier part of the SAM line.

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