Class ConvertSequencingArtifactToOxoG


  • @DocumentedFeature
    public class ConvertSequencingArtifactToOxoG
    extends CommandLineProgram
    • Field Detail

      • INPUT_BASE

        @Argument(shortName="I",
                  doc="Basename of the input artifact metrics file (output by CollectSequencingArtifactMetrics). If this is not  specified, you must specify PRE_ADAPTER_IN and BAIT_BIAS_IN",
                  optional=true)
        public File INPUT_BASE
      • PRE_ADAPTER_IN

        @Argument(doc="The pre adapter details input file. Defaults to a filename based on the input basename",
                  optional=true)
        public File PRE_ADAPTER_IN
      • BAIT_BIAS_IN

        @Argument(doc="The bait bias input file. Defaults to a filename based on the input basename",
                  optional=true)
        public File BAIT_BIAS_IN
      • OUTPUT_BASE

        @Argument(shortName="O",
                  doc="Basename for output OxoG metrics. Defaults to same basename as input metrics",
                  optional=true)
        public File OUTPUT_BASE
      • OXOG_OUT

        @Argument(doc="File for the output OxoG metrics. Defaults to a filename based on the output basename",
                  optional=true)
        public File OXOG_OUT
    • Constructor Detail

      • ConvertSequencingArtifactToOxoG

        public ConvertSequencingArtifactToOxoG()
    • Method Detail

      • customCommandLineValidation

        protected String[] customCommandLineValidation()
        Description copied from class: CommandLineProgram
        Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.
        Overrides:
        customCommandLineValidation in class CommandLineProgram
        Returns:
        null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
      • doWork

        protected int doWork()
        Description copied from class: CommandLineProgram
        Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
        Specified by:
        doWork in class CommandLineProgram
        Returns:
        program exit status.