message: refactor: adjust grammar and formatting in cli descriptions
diff: @@ -195,21 +195,21 @@ std::tuple<CliParams, NextalignOptions> parseCommandLine(
  (
  "score-gap-open-in-frame",
  - "(optional) As score-gap-open, but for opening gaps at the beginning of a codon. Should be smaller than score-gap-open but bigger than score-gap-open-out-of-frame to avoid gaps in genes but favor gaps that align with codons.",
  + "(optional) As `--score-gap-open`, but for opening gaps at the beginning of a codon. Should be less than `--score-gap-open` but greater than `--score-gap-open-out-of-frame`, to avoid gaps in genes, but favor gaps that align with codons.",
  cxxopts::value<int>()->default_value(std::to_string(getDefaultOptions().alignment.scoreGapOpenInFrame)),
  "SCORE_GAP_OPEN_IN_FRAME"
  )
  (
  "score-gap-open-out-of-frame",
  - "(optional) As score-gap-open, but for opening gaps at the beginning of a codon. Should be smaller than score-gap-out-of-frame to favor gaps that align with codons.",
  + "(optional) As `--score-gap-open`, but for opening gaps at the beginning of a codon. Should be smaller than `--score-gap-out-of-frame` to favor gaps that align with codons.",
  cxxopts::value<int>()->default_value(std::to_string(getDefaultOptions().alignment.scoreGapOpenOutOfFrame)),
  "SCORE_GAP_OPEN_OUT_OF_FRAME"
  )
  (
  "score-mismatch",
  - "(optional) Score for aligned nucleotides or amino acids that differ in state. Should be 0 or negative. Note that this is redundantly parameterized with `score-match`.",
  + "(optional) Score for aligned nucleotides or amino acids that differ in state. Should be 0 or negative. Note that this is redundantly parameterized with `--score-match`.",
  cxxopts::value<int>()->default_value(std::to_string(getDefaultOptions().alignment.scoreMismatch)),
  "SCORE_MISMATCH"
  )
  