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

Class ExpressionHadoopModule

java.lang.Object

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

fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule

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

All Implemented Interfaces:

Module

public class ExpressionHadoopModule
extends AbstractExpressionModule

This class is the main class for the expression program of the reads in hadoop mode.

Since:

1.0

Author:

Laurent Jourdren

Field Summary

Fields inherited from class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule

COUNTER_PARAMETER_NAME, FEATURES_FILE_FORMAT_PARAMETER_NAME, MODULE_NAME, OUTPUT_FILE_FORMAT_PARAMETER_NAME

Constructor Summary

Constructors

Constructor	Description
ExpressionHadoopModule()

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.
static boolean	isPairedData(InputStream samIs)	Check if a SAM file contains paired-end data.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule

getDescription, getName, getOutputPorts, getVersion

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

getChecker, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

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

Constructor Details

ExpressionHadoopModule

public ExpressionHadoopModule()

Method Details

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractExpressionModule

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 AbstractExpressionModule

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

Returns:

a TaskResult object

isPairedData

public static boolean isPairedData(InputStream samIs)

Check if a SAM file contains paired-end data.

Parameters:

samIs - the SAM file input stream

Returns:

true if the SAM file contains paired-end data