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

Class PreTreatmentMapper

java.lang.Object

org.apache.hadoop.mapreduce.Mapper<org.apache.hadoop.io.LongWritable,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

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

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

This class defines a mapper for the pretreatment of paired-end data before the reads filtering step.

Since:

1.2

Author:

Claire Wallon

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
PreTreatmentMapper()

Method Summary

Modifier and Type	Method	Description
protected void	cleanup(org.apache.hadoop.mapreduce.Mapper.Context context)
protected void	map(org.apache.hadoop.io.LongWritable 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

PreTreatmentMapper

public PreTreatmentMapper()

Method Detail

setup

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

Overrides:

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

Throws:

IOException

InterruptedException

map

protected void map(org.apache.hadoop.io.LongWritable 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 record.

Overrides:

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

Throws:

IOException

InterruptedException

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.LongWritable,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text,org.apache.hadoop.io.Text>

Throws:

IOException

InterruptedException