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

Class AbstractSAMFilterModule

java.lang.Object

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

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

All Implemented Interfaces:

Module

Direct Known Subclasses:

SAMFilterHadoopModule, SAMFilterLocalModule

public abstract class AbstractSAMFilterModule
extends AbstractModule

This class define an abstract module for alignments filtering.

Since:

1.0

Author:

Laurent Jourdren, Claire Wallon

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	COUNTER_GROUP

Constructor Summary

Constructors

Constructor	Description
AbstractSAMFilterModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
protected fr.ens.biologie.genomique.kenetre.bio.alignmentfilter.MultiReadAlignmentFilter	getAlignmentFilter(fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer incrementer, String counterGroup)	Get the ReadAlignmentsFilter object.
protected Map<String,String>	getAlignmentsFilterParameters()	Get the parameters of the alignments filter.
String	getDescription()	Get the description of the module
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Get the name of the module.
OutputPorts	getOutputPorts()	Get the output data format.
protected int	getReducerTaskCount()	Get the reducer task count.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Get version of the Module.

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

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.core.Module

execute

Field Detail

COUNTER_GROUP

protected static final String COUNTER_GROUP

See Also:

Constant Field Values

Constructor Detail

AbstractSAMFilterModule

public AbstractSAMFilterModule()

Method Detail

getAlignmentsFilterParameters

protected Map<String,String> getAlignmentsFilterParameters()

Get the parameters of the alignments filter.

Returns:

a map with all the parameters of the filter

getReducerTaskCount

protected int getReducerTaskCount()

Get the reducer task count.

Returns:

the reducer task count

getName

public String getName()

Description copied from interface: Module

Get the name of the module.

Returns:

the name of the module

getDescription

public String getDescription()

Description copied from interface: Module

Get the description of the module

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()

Description copied from interface: Module

Get version of the Module.

Returns:

a Version object with the version of the Module

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 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

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 AbstractModule

Parameters:

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

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

getAlignmentFilter

protected fr.ens.biologie.genomique.kenetre.bio.alignmentfilter.MultiReadAlignmentFilter getAlignmentFilter(fr.ens.biologie.genomique.kenetre.log.GenericLogger logger,
                                                                                                            fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer incrementer,
                                                                                                            String counterGroup)
                                                                                                     throws EoulsanException

Get the ReadAlignmentsFilter object.

Parameters:

logger - generic logger

incrementer - incrementer to use

counterGroup - counter group for the incrementer

Returns:

a new ReadAlignmentsFilter object

Throws:

EoulsanException - if an error occurs while initialize one of the filter