Class NormalizeFasta

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

    • 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 Details

    • NormalizeFasta

      public NormalizeFasta()
  • 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.