Class NormalizeFasta


  • @DocumentedFeature
    public class NormalizeFasta
    extends CommandLineProgram
    Little program to "normalize" a fasta file to ensure that all line of sequence are the same length, and are a reasonable length!
    • Field Detail

      • INPUT

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

        @Argument(shortName="O",
                  doc="The output FASTA file to write.")
        public File OUTPUT
      • LINE_LENGTH

        @Argument(doc="The line length to be used for the output FASTA file.")
        public int LINE_LENGTH
      • TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE

        @Argument(doc="Truncate sequence names at first whitespace.")
        public boolean TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE
    • Constructor Detail

      • NormalizeFasta

        public NormalizeFasta()
    • 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.