Class CheckDuplicateMarking


  • @DocumentedFeature(enable=false)
    public class CheckDuplicateMarking
    extends CommandLineProgram
    • Field Detail

      • INPUT

        @Argument(doc="Input BAM or SAM file to check.",
                  shortName="I")
        public File INPUT
      • OUTPUT

        @Argument(doc="Output file into which bad querynames will be placed (if not null).",
                  shortName="O",
                  optional=true)
        public File OUTPUT
      • MODE

        @Argument(doc="Which reads of the same name should be checked to have same duplicate marking.")
        public CheckDuplicateMarking.Mode MODE
    • Constructor Detail

      • CheckDuplicateMarking

        public CheckDuplicateMarking()
    • Method Detail

      • 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.