Package picard.util

Class BedToIntervalList


@DocumentedFeature public class BedToIntervalList extends CommandLineProgram
  • Field Details

    • INPUT

      @Argument(shortName="I", doc="The input BED file") public File INPUT
    • SEQUENCE_DICTIONARY

      @Argument(shortName="SD", doc="The sequence dictionary, or BAM/VCF/IntervalList from which a dictionary can be extracted.") public File SEQUENCE_DICTIONARY
    • OUTPUT

      @Argument(shortName="O", doc="The output Picard Interval List") public File OUTPUT
    • SORT

      @Argument(doc="If true, sort the output interval list before writing it.") public boolean SORT
    • UNIQUE

      @Argument(doc="If true, unique the output interval list by merging overlapping regions, before writing it (implies sort=true).") public boolean UNIQUE
    • DROP_MISSING_CONTIGS

      @Hidden @Argument(doc="If true, entries that are on contig-names that are missing from the provided dictionary will be dropped.") public boolean DROP_MISSING_CONTIGS
  • Constructor Details

    • BedToIntervalList

      public BedToIntervalList()
  • 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.