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

Class AbstractReadsMapperModule

java.lang.Object

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

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

All Implemented Interfaces:

Module

Direct Known Subclasses:

ReadsMapperHadoopModule, ReadsMapperLocalModule

public abstract class AbstractReadsMapperModule
extends AbstractModule

This class define an abstract module for read mapping.

Since:

1.0

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	COUNTER_GROUP
protected static String	GENOME_DESCRIPTION_PORT_NAME
static String	HADOOP_THREADS_PARAMETER_NAME
static int	HADOOP_TIMEOUT
static String	LOCAL_THREADS_PARAMETER_NAME
static String	MAPPER_ARGUMENTS_PARAMETER_NAME
static String	MAPPER_DOCKER_IMAGE_PARAMETER_NAME
static String	MAPPER_FLAVOR_PARAMETER_NAME
protected static String	MAPPER_INDEX_PORT_NAME
static String	MAPPER_NAME_PARAMETER_NAME
static String	MAPPER_VERSION_PARAMETER_NAME
static String	MAX_LOCAL_THREADS_PARAMETER_NAME
static String	MODULE_NAME
protected static String	READS_PORT_NAME
static String	USE_BUNDLED_BINARIES_PARAMETER_NAME

Constructor Summary

Constructors

Constructor	Description
AbstractReadsMapperModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
String	getDescription()	Get the description of the module
protected fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper	getMapper()	Get the mapper object.
protected String	getMapperArguments()	Get the arguments of the mapper to use.
protected String	getMapperDockerImage()	Get the mapper Docker image to use.
protected String	getMapperFlavor()	Get the flavor of the mapper to use.
protected int	getMapperHadoopMemoryRequired()	Get the amount in MB of memory required to execute the mapper.
protected int	getMapperHadoopThreads()	Get the number of threads to use in local mode.
protected int	getMapperLocalThreads()	Get the number of threads to use in local mode.
protected String	getMapperName()	Get the name of the mapper to use.
protected String	getMapperVersion()	Get the version of the mapper to use.
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.
protected boolean	isUseBundledBinaries()	Test if the bundled binaries must be used to perform the step.

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

getChecker, getInputPorts, 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

MODULE_NAME

public static final String MODULE_NAME

See Also:

Constant Field Values

COUNTER_GROUP

protected static final String COUNTER_GROUP

See Also:

Constant Field Values

READS_PORT_NAME

protected static final String READS_PORT_NAME

See Also:

Constant Field Values

MAPPER_INDEX_PORT_NAME

protected static final String MAPPER_INDEX_PORT_NAME

See Also:

Constant Field Values

GENOME_DESCRIPTION_PORT_NAME

protected static final String GENOME_DESCRIPTION_PORT_NAME

See Also:

Constant Field Values

MAPPER_NAME_PARAMETER_NAME

public static final String MAPPER_NAME_PARAMETER_NAME

See Also:

Constant Field Values

MAPPER_VERSION_PARAMETER_NAME

public static final String MAPPER_VERSION_PARAMETER_NAME

See Also:

Constant Field Values

MAPPER_FLAVOR_PARAMETER_NAME

public static final String MAPPER_FLAVOR_PARAMETER_NAME

See Also:

Constant Field Values

USE_BUNDLED_BINARIES_PARAMETER_NAME

public static final String USE_BUNDLED_BINARIES_PARAMETER_NAME

See Also:

Constant Field Values

MAPPER_DOCKER_IMAGE_PARAMETER_NAME

public static final String MAPPER_DOCKER_IMAGE_PARAMETER_NAME

See Also:

Constant Field Values

MAPPER_ARGUMENTS_PARAMETER_NAME

public static final String MAPPER_ARGUMENTS_PARAMETER_NAME

See Also:

Constant Field Values

HADOOP_THREADS_PARAMETER_NAME

public static final String HADOOP_THREADS_PARAMETER_NAME

See Also:

Constant Field Values

LOCAL_THREADS_PARAMETER_NAME

public static final String LOCAL_THREADS_PARAMETER_NAME

See Also:

Constant Field Values

MAX_LOCAL_THREADS_PARAMETER_NAME

public static final String MAX_LOCAL_THREADS_PARAMETER_NAME

See Also:

Constant Field Values

HADOOP_TIMEOUT

public static final int HADOOP_TIMEOUT

See Also:

Constant Field Values

Constructor Detail

AbstractReadsMapperModule

public AbstractReadsMapperModule()

Method Detail

getMapperName

protected String getMapperName()

Get the name of the mapper to use.

Returns:

Returns the mapperName

getMapperVersion

protected String getMapperVersion()

Get the version of the mapper to use.

Returns:

the version of the mapper to use

getMapperFlavor

protected String getMapperFlavor()

Get the flavor of the mapper to use.

Returns:

the flavor of the mapper to use

isUseBundledBinaries

protected boolean isUseBundledBinaries()

Test if the bundled binaries must be used to perform the step.

Returns:

true if the bundled binaries must be used to perform the step

getMapperDockerImage

protected String getMapperDockerImage()

Get the mapper Docker image to use.

Returns:

the mapper Docker image to use

getMapperArguments

protected String getMapperArguments()

Get the arguments of the mapper to use.

Returns:

Returns the mapperArguments

getMapperLocalThreads

protected int getMapperLocalThreads()

Get the number of threads to use in local mode.

Returns:

Returns the mapperThreads

getMapperHadoopThreads

protected int getMapperHadoopThreads()

Get the number of threads to use in local mode.

Returns:

Returns the mapperThreads

getMapperHadoopMemoryRequired

protected int getMapperHadoopMemoryRequired()

Get the amount in MB of memory required to execute the mapper. This value is required by Hadoop scheduler and if the mapper require more memory than declared the mapper process will be killed.

Returns:

the amount of memory required by the mapper in MB

getMapper

protected fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper getMapper()

Get the mapper object.

Returns:

the mapper object

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

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