Class ReadsMapperLocalModule
java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
- All Implemented Interfaces:
Module
This class define a module for reads mapping.
- Since:
- 1.0
- Author:
- Laurent Jourdren, Maria Bernard
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Field Summary
Fields inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
HADOOP_THREADS_PARAMETER_NAME, HADOOP_TIMEOUT, LOCAL_THREADS_PARAMETER_NAME, MAPPER_ARGUMENTS_PARAMETER_NAME, MAPPER_DOCKER_IMAGE_PARAMETER_NAME, MAPPER_FLAVOR_PARAMETER_NAME, MAPPER_NAME_PARAMETER_NAME, MAPPER_VERSION_PARAMETER_NAME, MAX_LOCAL_THREADS_PARAMETER_NAME, MODULE_NAME, USE_BUNDLED_BINARIES_PARAMETER_NAME -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionexecute(TaskContext context, TaskStatus status) Execute a task step.Get the input data format.Get the output data format.Get the parallelization mode of the module.Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
configure, getDescription, getName, getVersionMethods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker, getRequiredEoulsanVersion, getRequirements
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Constructor Details
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ReadsMapperLocalModule
public ReadsMapperLocalModule()
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Method Details
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getParallelizationMode
Description copied from interface:ModuleGet the parallelization mode of the module.- Specified by:
getParallelizationModein interfaceModule- Overrides:
getParallelizationModein classAbstractModule- Returns:
- a ParallelizationMode enum
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getInputPorts
Description copied from interface:ModuleGet the input data format.- Specified by:
getInputPortsin interfaceModule- Overrides:
getInputPortsin classAbstractModule- Returns:
- a set with DataFormat or null if the module does not any need input format
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getOutputPorts
Description copied from interface:ModuleGet the output data format.- Specified by:
getOutputPortsin interfaceModule- Overrides:
getOutputPortsin classAbstractReadsMapperModule- Returns:
- an set with DataFormat or null if the module does not produce any output data
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execute
Description copied from interface:ModuleExecute a task step.- Parameters:
context- Execution contextstatus- of the task- Returns:
- a TaskResult object
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