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

Class ReadsMapperMapper

java.lang.Object

org.apache.hadoop.mapreduce.Mapper<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.ReadsMapperMapper

public class ReadsMapperMapper
extends org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

This class defines a generic mapper for reads mapping.

Since:

1.0

Author:

Laurent Jourdren

Nested Class Summary

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

org.apache.hadoop.mapreduce.Mapper.Context

Constructor Summary

Constructors

Constructor	Description
ReadsMapperMapper()

Method Summary

Modifier and Type	Method	Description
protected void	cleanup(org.apache.hadoop.mapreduce.Mapper.Context context)
protected void	map(org.apache.hadoop.io.Text key, org.apache.hadoop.io.Text value, org.apache.hadoop.mapreduce.Mapper.Context context)	'key': offset of the beginning of the line from the beginning of the TFQ file.
protected void	setup(org.apache.hadoop.mapreduce.Mapper.Context context)

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

run

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadsMapperMapper

public ReadsMapperMapper()

Method Detail

map

protected void map(org.apache.hadoop.io.Text key,
                   org.apache.hadoop.io.Text value,
                   org.apache.hadoop.mapreduce.Mapper.Context context)
            throws IOException,
                   InterruptedException

'key': offset of the beginning of the line from the beginning of the TFQ file. 'value': the TFQ line (3 fields if data are in single-end mode, 6 fields if data are in paired-end mode).

Overrides:

map in class org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException

setup

protected void setup(org.apache.hadoop.mapreduce.Mapper.Context context)
              throws IOException

Overrides:

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

Throws:

IOException

cleanup

protected void cleanup(org.apache.hadoop.mapreduce.Mapper.Context context)
                throws IOException,
                       InterruptedException

Overrides:

cleanup in class org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException