docs: def addFASTAEditingCommandLineOptions(parser):
      """
      Add standard FASTA editing command-line options to an argparse parser.
  
      These are options that can be used to alter FASTA records, NOT options
      that simply select or reject those things (for those see
      addFASTAFilteringCommandLineOptions).
  
      @param parser: An C{argparse.ArgumentParser} instance.
      """
      # A mutually exclusive group for --keepSites, --keepSitesFile,
      # --removeSites, and --removeSitesFile.
      group = parser.add_mutually_exclusive_group()
  
      # In the 4 options below, the 'indices' alternate names are kept for
      # backwards compatibility.
      group.add_argument(
          '--keepSites', '--keepIndices',
          help=('Specify 1-based sequence sites to keep. All other sites will '
                'be removed. The sites must be given in the form e.g., '
                '24,100-200,260. Note that the requested sites will be taken '
                'from the input sequences in order, not in the order given by '
                '--keepSites. I.e., --keepSites 5,8-10 will get you the same '
                'result as --keepSites 8-10,5.'))
  
      group.add_argument(
          '--keepSitesFile', '--keepIndicesFile',
          help=('Specify a file containing 1-based sites to keep. All other '
                'sequence sites will be removed. Lines in the file must be '
                'given in the form e.g., 24,100-200,260. See --keepSites for '
                'more detail.'))
  
      group.add_argument(
          '--removeSites', '--removeIndices',
          help=('Specify 1-based sites to remove. All other sequence sites will '
                'be kept. The sites must be given in the form e.g., '
                '24,100-200,260. See --keepSites for more detail.'))
  
      group.add_argument(
          '--removeSitesFile', '--removeIndicesFile',
          help=('Specify a file containing 1-based sites to remove. All other '
                'sequence sites will be kept. Lines in the file must be given '
                'in the form e.g., 24,100-200,260. See --keepSites for more '
                'detail.'))
  
      parser.add_argument(
          '--removeGaps', action='store_true', default=False,
          help="If True, gap ('-') characters in sequences will be removed.")
  
      parser.add_argument(
          '--truncateTitlesAfter',
          help=('A string that sequence titles (ids) will be truncated beyond. '
                'If the truncated version of a title has already been seen, '
                'that title will be skipped.'))
  
      parser.add_argument(
          '--removeDescriptions', action='store_true', default=False,
          help=('Read id descriptions will be removed. The '
                'description is the part of a sequence id after the '
                'first whitespace (if any).'))
  
      parser.add_argument(
          '--idLambda', metavar='LAMBDA-FUNCTION',
          help=('A one-argument function taking and returning a read id. '
                'E.g., --idLambda "lambda id: id.split(\'_\')[0]" or '
                '--idLambda "lambda id: id[:10]". If the function returns None, '
                'the read will be filtered out.'))
  
      parser.add_argument(
          '--readLambda', metavar='LAMBDA-FUNCTION',
          help=('A one-argument function taking and returning a read. '
                'E.g., --readLambda "lambda r: Read(r.id.split(\'_\')[0], '
                'r.sequence.strip(\'-\')". Make sure to also modify the quality '
                'string if you change the length of a FASTQ sequence. If the '
                'function returns None, the read will be filtered out. The '
                'function will be passed to eval with the dark.reads classes '
                'Read, DNARead, AARead, etc. all in scope.'))
  
      parser.add_argument(
          '--reverse', action='store_true', default=False,
          help=('Reverse the sequences. Note that this is NOT reverse '
                'complementing.'))
  
      parser.add_argument(
          '--reverseComplement', action='store_true', default=False,
          help='Reverse complement the sequences.')