Package fr.ens.biologie.genomique.eoulsan.modules.chipseq

Class RmDupLocalModule

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
All Implemented Interfaces:
Module
public class RmDupLocalModule extends AbstractModule
This class removes PCR duplicates from a SAM file. It uses Picard's MarkDuplicates to either mark or remove PCR duplicates.
Author:
Celine Hernandez - CSB lab - ENS - Paris

  • Constructor Details

    • RmDupLocalModule

      public RmDupLocalModule()

  • Method Details

    • getName

      public String getName()
      Name of the Step.
      Returns:
      the name of the module

    • getDescription

      public String getDescription()
      A short description of the tool and what is done in the step.
      Specified by:
      getDescription in interface Module
      Overrides:
      getDescription in class AbstractModule
      Returns:
      the description of the module

    • getVersion

      public fr.ens.biologie.genomique.kenetre.util.Version getVersion()
      Version.
      Returns:
      a Version object with the version of the Module

    • getInputPorts

      public InputPorts getInputPorts()
      Define input port.
      Specified by:
      getInputPorts in interface Module
      Overrides:
      getInputPorts in class AbstractModule
      Returns:
      a set with DataFormat or null if the module does not any need input format

    • getOutputPorts

      public OutputPorts getOutputPorts()
      Define output port.
      Specified by:
      getOutputPorts in interface Module
      Overrides:
      getOutputPorts in class AbstractModule
      Returns:
      an set with DataFormat or null if the module does not produce any output data

    • 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 interface Module
      Overrides:
      configure in class AbstractModule
      Parameters:
      stepParameters - parameters of the step
      context - configuration context. The context can be null for generator steps
      Throws:
      EoulsanException - if a parameter is invalid

    • execute

      public TaskResult execute(TaskContext context, TaskStatus status)
      Description copied from interface: Module
      Execute a task step.
      Parameters:
      context - Execution context
      status - of the task
      Returns:
      a TaskResult object