Class MergeInputRepLocalModule
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
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- fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
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- All Implemented Interfaces:
Module
public class MergeInputRepLocalModule extends AbstractModule
This class merges SAM files of input of the same experiment. It uses Picard's MergeSamFiles to merge SAM files from inputs of the same experiment.- Author:
- Celine Hernandez - CSB lab - ENS - Paris
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Constructor Summary
Constructors Constructor Description MergeInputRepLocalModule()
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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 step.TaskResult
execute(TaskContext context, TaskStatus status)
Merge input replicates.String
getDescription()
A short description of the tool and what is done in the step.InputPorts
getInputPorts()
Define input port.String
getName()
Name of the Step.OutputPorts
getOutputPorts()
Define output port.fr.ens.biologie.genomique.kenetre.util.Version
getVersion()
Version.-
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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getName
public String getName()
Name of the Step.- Returns:
- the name of the module
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getDescription
public String getDescription()
A short description of the tool and what is done in the step.- 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()
Version.- Returns:
- a Version object with the version of the Module
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getInputPorts
public InputPorts getInputPorts()
Define input port.- 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()
Define output port.- 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
Set the parameters of the step to configure the step.- Specified by:
configure
in interfaceModule
- Overrides:
configure
in classAbstractModule
- Parameters:
stepParameters
- parameters of the stepcontext
- configuration context. The context can be null for generator steps- Throws:
EoulsanException
- if a parameter is invalid
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execute
public TaskResult execute(TaskContext context, TaskStatus status)
Merge input replicates.- Parameters:
context
- Execution contextstatus
- of the task
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