code: def annotate(args):
      
      p = OptionParser(annotate.__doc__.format(", ".join(Overlap_types)))
      p.add_option("--maxhang", default=100, type="int",
                   help="Max hang to call dovetail overlap [default: %default]")
      p.add_option("--all", default=False, action="store_true",
                   help="Output all lines [default: terminal/containment]")
  
      opts, args = p.parse_args(args)
  
      if len(args) != 1:
          sys.exit(not p.print_help())
  
      coordsfile, = args
      fp = open(coordsfile)
  
      for row in fp:
          try:
              c = CoordsLine(row)
          except AssertionError:
              continue
  
          ov = c.overlap(opts.maxhang)
          if not opts.all and ov == 0:
              continue
  
          print("{0}\t{1}".format(row.strip(), Overlap_types[ov]))
docs: %prog annotate coordsfile
  
      Annotate coordsfile to append an additional column, with the following
      overlaps: {0}.