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

Class CountSplicedReadsModule

java.lang.Object

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

fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule

All Implemented Interfaces:

Module

public class CountSplicedReadsModule
extends AbstractModule

This step computes how many spliced alignments there are in a SAM file. This QC step computes the number of spliced alignments in a SAM file, as well as the total number of mapped reads.

Author:

Celine Hernandez - CSB lab - ENS - Paris

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	COUNTER_GROUP

Constructor Summary

Constructors

Constructor	Description
CountSplicedReadsModule()

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)	Install all the files necessary in the tmp folder, then run idr.
String	getDescription()	A short description of the tool and what is done in the step.
InputPorts	getInputPorts()	Define input ports.
String	getName()	Name of the Step.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Version.

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

getChecker, getOutputPorts, 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

See Also:

Constant Field Values

Constructor Detail

CountSplicedReadsModule

public CountSplicedReadsModule()

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 ports.

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

configure

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

Set the parameters of the step to configure the step. No parameter accepted.

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 provided

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Install all the files necessary in the tmp folder, then run idr.

Parameters:

context - Execution context

status - of the task