Class NonNFastaSize


  • @DocumentedFeature
    public class NonNFastaSize
    extends CommandLineProgram
    A tool to count the number of non-N bases in a fasta file
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="The input FASTA file.")
        public File INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="The output file in which to record the count.")
        public File OUTPUT
      • INTERVALS

        @Argument(shortName="INTERVALS",
                  doc="An interval list file that contains the locations of the positions to assess.  If not provided, the entire reference will be used",
                  optional=true)
        public File INTERVALS
    • Constructor Detail

      • NonNFastaSize

        public NonNFastaSize()
    • Method Detail

      • main

        public static void main​(String[] args)
      • 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.