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

Class ReadsMapperLocalModule

java.lang.Object

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

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

fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule

All Implemented Interfaces:

Module

public class ReadsMapperLocalModule
extends AbstractReadsMapperModule

This class define a module for reads mapping.

Since:

1.0

Author:

Laurent Jourdren, Maria Bernard

Field Summary

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

COUNTER_GROUP, GENOME_DESCRIPTION_PORT_NAME, HADOOP_THREADS_PARAMETER_NAME, HADOOP_TIMEOUT, LOCAL_THREADS_PARAMETER_NAME, MAPPER_ARGUMENTS_PARAMETER_NAME, MAPPER_DOCKER_IMAGE_PARAMETER_NAME, MAPPER_FLAVOR_PARAMETER_NAME, MAPPER_INDEX_PORT_NAME, MAPPER_NAME_PARAMETER_NAME, MAPPER_VERSION_PARAMETER_NAME, MAX_LOCAL_THREADS_PARAMETER_NAME, MODULE_NAME, READS_PORT_NAME, USE_BUNDLED_BINARIES_PARAMETER_NAME

Constructor Summary

Constructors

Constructor	Description
ReadsMapperLocalModule()

Method Summary

Modifier and Type	Method	Description
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
InputPorts	getInputPorts()	Get the input data format.
OutputPorts	getOutputPorts()	Get the output data format.
ParallelizationMode	getParallelizationMode()	Get the parallelization mode of the module.

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

configure, getDescription, getMapper, getMapperArguments, getMapperDockerImage, getMapperFlavor, getMapperHadoopMemoryRequired, getMapperHadoopThreads, getMapperLocalThreads, getMapperName, getMapperVersion, getName, getReducerTaskCount, getVersion, isUseBundledBinaries

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

getChecker, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadsMapperLocalModule

public ReadsMapperLocalModule()

Method Detail

getParallelizationMode

public ParallelizationMode getParallelizationMode()

Description copied from interface: Module

Get the parallelization mode of the module.

Specified by:

getParallelizationMode in interface Module

Overrides:

getParallelizationMode in class AbstractModule

Returns:

a ParallelizationMode enum

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractModule

Returns:

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

getOutputPorts

public OutputPorts getOutputPorts()

Description copied from interface: Module

Get the output data format.

Specified by:

getOutputPorts in interface Module

Overrides:

getOutputPorts in class AbstractReadsMapperModule

Returns:

an set with DataFormat or null if the module does not produce any output data

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