Class ReadsMapperLocalModule
- 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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- fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
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- All Implemented Interfaces:
Module
public class ReadsMapperLocalModule extends AbstractReadsMapperModule
This class define a module for reads mapping.- Since:
- 1.0
- Author:
- Laurent Jourdren, Maria Bernard
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Field Summary
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Fields inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
COUNTER_GROUP, GENOME_DESCRIPTION_PORT_NAME, HADOOP_THREADS_PARAMETER_NAME, HADOOP_TIMEOUT, LOCAL_THREADS_PARAMETER_NAME, MAPPER_ARGUMENTS_PARAMETER_NAME, MAPPER_DOCKER_IMAGE_PARAMETER_NAME, MAPPER_FLAVOR_PARAMETER_NAME, MAPPER_INDEX_PORT_NAME, MAPPER_NAME_PARAMETER_NAME, MAPPER_VERSION_PARAMETER_NAME, MAX_LOCAL_THREADS_PARAMETER_NAME, MODULE_NAME, READS_PORT_NAME, USE_BUNDLED_BINARIES_PARAMETER_NAME
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Constructor Summary
Constructors Constructor Description ReadsMapperLocalModule()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description TaskResult
execute(TaskContext context, TaskStatus status)
Execute a task step.InputPorts
getInputPorts()
Get the input data format.OutputPorts
getOutputPorts()
Get the output data format.ParallelizationMode
getParallelizationMode()
Get the parallelization mode of the module.-
Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
configure, getDescription, getMapper, getMapperArguments, getMapperDockerImage, getMapperFlavor, getMapperHadoopMemoryRequired, getMapperHadoopThreads, getMapperLocalThreads, getMapperName, getMapperVersion, getName, getReducerTaskCount, getVersion, isUseBundledBinaries
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Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker, getRequiredEoulsanVersion, getRequirements
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Method Detail
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getParallelizationMode
public ParallelizationMode getParallelizationMode()
Description copied from interface:Module
Get the parallelization mode of the module.- Specified by:
getParallelizationMode
in interfaceModule
- Overrides:
getParallelizationMode
in classAbstractModule
- Returns:
- a ParallelizationMode enum
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getInputPorts
public InputPorts getInputPorts()
Description copied from interface:Module
Get the input data format.- Specified by:
getInputPorts
in interfaceModule
- Overrides:
getInputPorts
in classAbstractModule
- Returns:
- a set with DataFormat or null if the module does not any need input format
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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 classAbstractReadsMapperModule
- Returns:
- an set with DataFormat or null if the module does not produce any output data
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execute
public TaskResult execute(TaskContext context, TaskStatus status)
Description copied from interface:Module
Execute a task step.- Parameters:
context
- Execution contextstatus
- of the task
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