code: def fixpairs(args):
      
      p = OptionParser(fixpairs.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) != 3:
          sys.exit(not p.print_help())
  
      pairsfile, sep, sd = args
      newpairsfile = pairsfile.rsplit(".", 1)[0] + ".new.pairs"
      sep = int(sep)
      sd = int(sd)
  
      p = PairsFile(pairsfile)
      p.fixLibraryStats(sep, sd)
      p.write(newpairsfile)
docs: %prog fixpairs pairsfile sep sd
  
      Fix pairs library stats. This is sometime useful to modify library stats,
      for example, the separation between paired reads after importing the data.