message: feat: add `--no-translate-past-stop` flag to Nextalign CLI
diff: @@ -121,6 +121,8 @@ NextalignOptions validateOptions(const cxxopts::ParseResult &cxxOptsParsed) {
  options.seedAa.minSeeds = getParamRequiredDefaulted<int>(cxxOptsParsed, "aa-min-seeds", ensurePositive);
  options.seedAa.seedSpacing = getParamRequiredDefaulted<int>(cxxOptsParsed, "aa-seed-spacing", ensureNonNegative);
  options.seedAa.mismatchesAllowed = getParamRequiredDefaulted<int>(cxxOptsParsed, "aa-mismatches-allowed", ensureNonNegative);
  +
  + options.translatePastStop = !getParamOptional<bool>(cxxOptsParsed, "no-translate-past-stop").value_or(true);
  // clang-format on
  return options;
  @@ -365,6 +367,13 @@ std::tuple<CliParams, cxxopts::Options, NextalignOptions> parseCommandLine(int a
  cxxopts::value<int>()->default_value(std::to_string(getDefaultOptions().seedAa.mismatchesAllowed)),
  "AA_MISMATCHES_ALLOWED"
  )
  +
  + (
  + "no-translate-past-stop",
  + "(optional, boolean) Whether to stop gene translation after first stop codon. It will cut the genes in places cases where mutations resulted in premature stop codons. If this flag is present, the aminoacid sequences wil be truncated at the first stop codon and analysis of aminoacid mutations will not be available for the regions after first stop codon.",
  + cxxopts::value<bool>(),
  + "WRITE_REF"
  + )
  ;
  // clang-format on
  