Class MergePeaksModule
- 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.peakcalling.MergePeaksModule
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- All Implemented Interfaces:
Module
public class MergePeaksModule extends AbstractModule
This class defines the peak merging step. It merges peak files created by a peak caller into one BED file.- Author:
- Pierre-Marie Chiaroni - CSB lab - ENS - Paris, Celine Hernandez - CSB lab - ENS - Paris
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Constructor Summary
Constructors Constructor Description MergePeaksModule()
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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)
Execute a task step.String
getDescription()
Get the description of the moduleInputPorts
getInputPorts()
Get the input data format.String
getName()
Get the name of the module.fr.ens.biologie.genomique.kenetre.util.Version
getVersion()
Get version of the Module.-
Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker, getOutputPorts, getParallelizationMode, getRequiredEoulsanVersion, getRequirements
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Method Detail
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getName
public String getName()
Description copied from interface:Module
Get the name of the module.- Returns:
- the name of the module
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getDescription
public String getDescription()
Description copied from interface:Module
Get the description of the module- 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()
Description copied from interface:Module
Get version of the Module.- Returns:
- a Version object with the version of the Module
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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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configure
public void configure(StepConfigurationContext context, Set<Parameter> stepParameters)
Set the parameters of the step to configure the step. Nothing to configure for such a simple 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
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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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