Class ExtractSequences

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

@DocumentedFeature public class ExtractSequences extends CommandLineProgram
Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.
  • Field Details

    • INTERVAL_LIST

      @Argument(doc="Interval list describing intervals to be extracted from the reference sequence.") public File INTERVAL_LIST
    • OUTPUT

      @Argument(shortName="O", doc="Output FASTA file.") public File OUTPUT
    • LINE_LENGTH

      @Argument(doc="Maximum line length for sequence data.") public int LINE_LENGTH
  • Constructor Details

    • ExtractSequences

      public ExtractSequences()
  • Method Details

    • requiresReference

      protected boolean requiresReference()
      Overrides:
      requiresReference in class CommandLineProgram
    • 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.