code: def set_pairs(self):
          
          self.set_usage(self.set_pairs.__doc__)
  
          self.add_option("--pairsfile", default=None,
                  help="Write valid pairs to pairsfile [default: %default]")
          self.add_option("--nrows", default=200000, type="int",
                  help="Only use the first n lines [default: %default]")
          self.set_mates()
          self.add_option("--pdf", default=False, action="store_true",
                  help="Print PDF instead ASCII histogram [default: %default]")
          self.add_option("--bins", default=20, type="int",
                  help="Number of bins in the histogram [default: %default]")
          self.add_option("--distmode", default="ss", choices=("ss", "ee"),
                  help="Distance mode between paired reads, ss is outer distance, " \
                       "ee is inner distance [default: %default]")
docs: %prog pairs <blastfile|samfile|bedfile>
  
          Report how many paired ends mapped, avg distance between paired ends, etc.
          Paired reads must have the same prefix, use --rclip to remove trailing
          part, e.g. /1, /2, or .f, .r, default behavior is to truncate until last
          char.