docs: def parseFASTAEditingCommandLineOptions(args, reads):
      """
      Examine parsed FASTA editing command-line options and return information
      about kept sites and sequences.
  
      @param args: An argparse namespace, as returned by the argparse
          C{parse_args} function.
      @param reads: A C{Reads} instance to filter.
      @return: The filtered C{Reads} instance.
      """
      removeGaps = args.removeGaps
      removeDescriptions = args.removeDescriptions
      truncateTitlesAfter = args.truncateTitlesAfter
      keepSites = (
          parseRangeString(args.keepSites, convertToZeroBased=True)
          if args.keepSites else None)
  
      if args.keepSitesFile:
          keepSites = keepSites or set()
          with open(args.keepSitesFile) as fp:
              for lineNumber, line in enumerate(fp):
                  try:
                      keepSites.update(
                          parseRangeString(line, convertToZeroBased=True))
                  except ValueError as e:
                      raise ValueError(
                          'Keep sites file %r line %d could not be parsed: '
                          '%s' % (args.keepSitesFile, lineNumber, e))
  
      removeSites = (
          parseRangeString(args.removeSites, convertToZeroBased=True)
          if args.removeSites else None)
  
      if args.removeSitesFile:
          removeSites = removeSites or set()
          with open(args.removeSitesFile) as fp:
              for lineNumber, line in enumerate(fp):
                  try:
                      removeSites.update(
                          parseRangeString(line, convertToZeroBased=True))
                  except ValueError as e:
                      raise ValueError(
                          'Remove sites file %r line %d parse error: %s'
                          % (args.removeSitesFile, lineNumber, e))
  
      return reads.filter(
          removeGaps=removeGaps,
          truncateTitlesAfter=truncateTitlesAfter,
          removeDescriptions=removeDescriptions,
          idLambda=args.idLambda, readLambda=args.readLambda,
          keepSites=keepSites, removeSites=removeSites,
          reverse=args.reverse, reverseComplement=args.reverseComplement)