Class FilterAndMapReadsHadoopModule
- 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.AbstractFilterAndMapReadsModule
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- fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
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- All Implemented Interfaces:
Module
public class FilterAndMapReadsHadoopModule extends AbstractFilterAndMapReadsModule
This class define a Step that filter and map read in Hadoop mode.- Since:
- 1.0
- Author:
- Laurent Jourdren
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Field Summary
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Fields inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
GENOME_DESCRIPTION_PORT_NAME, HADOOP_TIMEOUT, MAPPER_INDEX_PORT_NAME, MODULE_NAME, READS_PORT_NAME
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Constructor Summary
Constructors Constructor Description FilterAndMapReadsHadoopModule()
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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.TaskResult
execute(TaskContext context, TaskStatus status)
Execute a task step.InputPorts
getInputPorts()
Get the input data format.-
Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getAlignmentsFilterParameters, getCounterGroup, getDescription, getMapper, getMapperArguments, getMapperFlavor, getMapperHadoopMemoryRequired, getMapperHadoopThreads, getMapperName, getMapperVersion, getName, getOutputPorts, getReadFilterParameters, getReducerTaskCount, getVersion, isPairedEnd
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Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker, getParallelizationMode, getRequiredEoulsanVersion, getRequirements
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Method Detail
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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 classAbstractFilterAndMapReadsModule
- Returns:
- a set with DataFormat or null if the module does not any need input format
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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 classAbstractFilterAndMapReadsModule
- 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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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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