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

Class MergeInputRepLocalModule

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
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

  • Constructor Details

    • MergeInputRepLocalModule

      public MergeInputRepLocalModule()

  • 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)
      Merge input replicates.
      Parameters:
      context - Execution context
      status - of the task
      Returns:
      a TaskResult object