Package picard.util

Class BedToIntervalList

    • Field Detail

      • 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
    • Constructor Detail

      • BedToIntervalList

        public BedToIntervalList()
    • 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.