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

Class FilterAndMapReadsHadoopModule

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule

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

All Implemented Interfaces:

Module

public class FilterAndMapReadsHadoopModule
extends AbstractFilterAndMapReadsModule

This class define a Step that filter and map read in Hadoop mode.

Since:

1.0

Author:

Laurent Jourdren

Field Summary

Fields inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule

GENOME_DESCRIPTION_PORT_NAME, HADOOP_TIMEOUT, MAPPER_INDEX_PORT_NAME, MODULE_NAME, READS_PORT_NAME

Constructor Summary

Constructors

Constructor	Description
FilterAndMapReadsHadoopModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
InputPorts	getInputPorts()	Get the input data format.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule

getAlignmentsFilterParameters, getCounterGroup, getDescription, getMapper, getMapperArguments, getMapperFlavor, getMapperHadoopMemoryRequired, getMapperHadoopThreads, getMapperName, getMapperVersion, getName, getOutputPorts, getReadFilterParameters, getReducerTaskCount, getVersion, isPairedEnd

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

getChecker, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

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

Constructor Detail

FilterAndMapReadsHadoopModule

public FilterAndMapReadsHadoopModule()

Method Detail

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractFilterAndMapReadsModule

Returns:

a set with DataFormat or null if the module does not any need input format

configure

public void configure(StepConfigurationContext context,
                      Set<Parameter> stepParameters)
               throws EoulsanException

Description copied from interface: Module

Set the parameters of the step to configure the module.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractFilterAndMapReadsModule

Parameters:

context - configuration context. The context can be null for generator steps

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Description copied from interface: Module

Execute a task step.

Parameters:

context - Execution context

status - of the task