Class NonNFastaSize

java.lang.Object
picard.cmdline.CommandLineProgram
picard.reference.NonNFastaSize

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

    • 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 Details

    • NonNFastaSize

      public NonNFastaSize()
  • Method Details

    • 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.