Package fr.ens.biologie.genomique.eoulsan.modules.chipseq

Class RmDupLocalModule

java.lang.Object

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

fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule

All Implemented Interfaces:

Module

public class RmDupLocalModule
extends AbstractModule

This class removes PCR duplicates from a SAM file. It uses Picard's MarkDuplicates to either mark or remove PCR duplicates.

Author:

Celine Hernandez - CSB lab - ENS - Paris

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	COUNTER_GROUP	Group for hadoop counters.

Constructor Summary

Constructors

Constructor	Description
RmDupLocalModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
String	getDescription()	A short description of the tool and what is done in the step.
InputPorts	getInputPorts()	Define input port.
String	getName()	Name of the Step.
OutputPorts	getOutputPorts()	Define output port.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Version.

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

Field Detail

COUNTER_GROUP

protected static final String COUNTER_GROUP

Group for hadoop counters.

See Also:

Constant Field Values

Constructor Detail

RmDupLocalModule

public RmDupLocalModule()

Method Detail

getName

public String getName()

Name of the Step.

Returns:

the name of the module

getDescription

public String getDescription()

A short description of the tool and what is done in the step.

Specified by:

getDescription in interface Module

Overrides:

getDescription in class AbstractModule

Returns:

the description of the module

getVersion

public fr.ens.biologie.genomique.kenetre.util.Version getVersion()

Version.

Returns:

a Version object with the version of the Module

getInputPorts

public InputPorts getInputPorts()

Define input port.

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()

Define output port.

Specified by:

getOutputPorts in interface Module

Overrides:

getOutputPorts in class AbstractModule

Returns:

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

configure

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

Set the parameters of the step to configure the step.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractModule

Parameters:

stepParameters - parameters of the step

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

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