Class ExpressionHadoopModule
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
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- fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
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- fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
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- All Implemented Interfaces:
Module
public class ExpressionHadoopModule extends AbstractExpressionModule
This class is the main class for the expression program of the reads 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.expression.AbstractExpressionModule
COUNTER_GROUP, COUNTER_PARAMETER_NAME, FEATURES_FILE_FORMAT_PARAMETER_NAME, MODULE_NAME, OUTPUT_FILE_FORMAT_PARAMETER_NAME
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Constructor Summary
Constructors Constructor Description ExpressionHadoopModule()
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Method Summary
All Methods Static 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.static boolean
isPairedData(InputStream samIs)
Check if a SAM file contains paired-end data.-
Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getDescription, getExpressionCounter, getName, getOutputPorts, getVersion, isGTFInputFormat, isSAMOutputFormat
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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 classAbstractExpressionModule
- 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 classAbstractExpressionModule
- 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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isPairedData
public static boolean isPairedData(InputStream samIs)
Check if a SAM file contains paired-end data.- Parameters:
samIs
- the SAM file input stream- Returns:
- true if the SAM file contains paired-end data
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