Package fr.ens.biologie.genomique.eoulsan.checkers

Class ReadsChecker

java.lang.Object
fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
All Implemented Interfaces:
Checker
public class ReadsChecker extends Object implements Checker
This class define a checker on FASTQ files.
Since:
1.0
Author:
Laurent Jourdren

  • Field Details

  • Constructor Details

    • ReadsChecker

      public ReadsChecker()

  • Method Details

    • getName

      public String getName()
      Description copied from interface: Checker
      Get the name of the checker.
      Specified by:
      getName in interface Checker
      Returns:
      the name of the checker

    • isDesignChecker

      public boolean isDesignChecker()
      Description copied from interface: Checker
      Test if the Checker is a design checker.
      Specified by:
      isDesignChecker in interface Checker
      Returns:
      true if this a design checker

    • getFormat

      public DataFormat getFormat()
      Description copied from interface: Checker
      Get format related to the checker.
      Specified by:
      getFormat in interface Checker
      Returns:
      a DataFormat object

    • getCheckersRequired

      public Set<DataFormat> getCheckersRequired()
      Description copied from interface: Checker
      Get the list of Checker required to run before this checker.
      Specified by:
      getCheckersRequired in interface Checker
      Returns:
      a list of DataFormat that are checked by the required checkers

    • configure

      public void configure(Set<Parameter> stepParameters) throws EoulsanException
      Description copied from interface: Checker
      Set the parameters of the checker to configure the checker.
      Specified by:
      configure in interface Checker
      Parameters:
      stepParameters - parameters of the step
      Throws:
      EoulsanException - if a parameter is invalid

    • check

      public boolean check(Data data, CheckStore checkInfo) throws EoulsanException
      Description copied from interface: Checker
      Launch the check.
      Specified by:
      check in interface Checker
      Parameters:
      data - data to check
      checkInfo - object that contains data shared between the checkers
      Returns:
      true if check pass
      Throws:
      EoulsanException - if an error occurs while executing step