Package picard.sam

Class AddOATag

    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="SAM or BAM input file")
        public String INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="SAM or BAM file to write merged result to")
        public String OUTPUT
      • INTERVAL_LIST

        @Argument(shortName="L",
                  doc="If provided, only records that overlap given interval list will have the OA tag added.",
                  optional=true)
        public File INTERVAL_LIST
    • Constructor Detail

      • AddOATag

        public AddOATag()
    • 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.