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

Class ExpressionSAMOutputMapper

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.expression.hadoop.ExpressionSAMOutputMapper

public class ExpressionSAMOutputMapper
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>

Mapper for the expression estimation with a SAM output.

Since:

2.3

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
ExpressionSAMOutputMapper()

Method Summary

Modifier and Type	Method	Description
void	cleanup(org.apache.hadoop.mapreduce.Mapper.Context context)
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 alignment file.
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

ExpressionSAMOutputMapper

public ExpressionSAMOutputMapper()

Method Detail

setup

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

Throws:

IOException

InterruptedException

map

public 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 alignment file. 'value': the SAM record, if data are in paired-end mode, 'value' contains the two paired alignments separated by a '£' (TSAM format).

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

cleanup

public void cleanup(org.apache.hadoop.mapreduce.Mapper.Context context)
             throws IOException

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