Class AbstractReadsMapperModule
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
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- fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
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- 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
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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
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Constructor Summary
Constructors Constructor Description AbstractReadsMapperModule()
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Method Summary
All Methods Instance Methods Concrete Methods 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 moduleprotected 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
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Field Detail
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MODULE_NAME
public static final String MODULE_NAME
- See Also:
- Constant Field Values
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COUNTER_GROUP
protected static final String COUNTER_GROUP
- See Also:
- Constant Field Values
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READS_PORT_NAME
protected static final String READS_PORT_NAME
- See Also:
- Constant Field Values
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MAPPER_INDEX_PORT_NAME
protected static final String MAPPER_INDEX_PORT_NAME
- See Also:
- Constant Field Values
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GENOME_DESCRIPTION_PORT_NAME
protected static final String GENOME_DESCRIPTION_PORT_NAME
- See Also:
- Constant Field Values
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MAPPER_NAME_PARAMETER_NAME
public static final String MAPPER_NAME_PARAMETER_NAME
- See Also:
- Constant Field Values
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MAPPER_VERSION_PARAMETER_NAME
public static final String MAPPER_VERSION_PARAMETER_NAME
- See Also:
- Constant Field Values
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MAPPER_FLAVOR_PARAMETER_NAME
public static final String MAPPER_FLAVOR_PARAMETER_NAME
- See Also:
- Constant Field Values
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USE_BUNDLED_BINARIES_PARAMETER_NAME
public static final String USE_BUNDLED_BINARIES_PARAMETER_NAME
- See Also:
- Constant Field Values
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MAPPER_DOCKER_IMAGE_PARAMETER_NAME
public static final String MAPPER_DOCKER_IMAGE_PARAMETER_NAME
- See Also:
- Constant Field Values
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MAPPER_ARGUMENTS_PARAMETER_NAME
public static final String MAPPER_ARGUMENTS_PARAMETER_NAME
- See Also:
- Constant Field Values
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HADOOP_THREADS_PARAMETER_NAME
public static final String HADOOP_THREADS_PARAMETER_NAME
- See Also:
- Constant Field Values
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LOCAL_THREADS_PARAMETER_NAME
public static final String LOCAL_THREADS_PARAMETER_NAME
- See Also:
- Constant Field Values
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MAX_LOCAL_THREADS_PARAMETER_NAME
public static final String MAX_LOCAL_THREADS_PARAMETER_NAME
- See Also:
- Constant Field Values
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HADOOP_TIMEOUT
public static final int HADOOP_TIMEOUT
- See Also:
- Constant Field Values
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Method Detail
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getMapperName
protected String getMapperName()
Get the name of the mapper to use.- Returns:
- Returns the mapperName
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getMapperVersion
protected String getMapperVersion()
Get the version of the mapper to use.- Returns:
- the version of the mapper to use
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getMapperFlavor
protected String getMapperFlavor()
Get the flavor of the mapper to use.- Returns:
- the flavor of the mapper to use
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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
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getMapperDockerImage
protected String getMapperDockerImage()
Get the mapper Docker image to use.- Returns:
- the mapper Docker image to use
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getMapperArguments
protected String getMapperArguments()
Get the arguments of the mapper to use.- Returns:
- Returns the mapperArguments
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getMapperLocalThreads
protected int getMapperLocalThreads()
Get the number of threads to use in local mode.- Returns:
- Returns the mapperThreads
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getMapperHadoopThreads
protected int getMapperHadoopThreads()
Get the number of threads to use in local mode.- Returns:
- Returns the mapperThreads
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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
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getMapper
protected fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper getMapper()
Get the mapper object.- Returns:
- the mapper object
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getReducerTaskCount
protected int getReducerTaskCount()
Get the reducer task count.- Returns:
- the reducer task count
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getName
public String getName()
Description copied from interface:Module
Get the name of the module.- Returns:
- the name of the module
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getDescription
public String getDescription()
Description copied from interface:Module
Get the description of the module- Specified by:
getDescription
in interfaceModule
- Overrides:
getDescription
in classAbstractModule
- Returns:
- the description of the module
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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
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getOutputPorts
public OutputPorts getOutputPorts()
Description copied from interface:Module
Get the output data format.- Specified by:
getOutputPorts
in interfaceModule
- Overrides:
getOutputPorts
in classAbstractModule
- Returns:
- an set with DataFormat or null if the module does not produce any output data
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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 interfaceModule
- Overrides:
configure
in classAbstractModule
- Parameters:
context
- configuration context. The context can be null for generator stepsstepParameters
- parameters of the step- Throws:
EoulsanException
- if a parameter is invalid
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