message: fix: ensure peptide file output
diff: @@ -207,7 +207,7 @@ std::tuple<CliParams, cxxopts::Options, NextalignOptions> parseCommandLine(
  (
  "genes",
  - "(optional, string) List of genes to translate. Requires `--genemap`. If not supplied or empty, sequence will not be translated. If non-empty, should contain a coma-separated list of gene names. Parameters `--genes` and `--genemap` should be either both specified or both omitted.",
  + "(optional, string) List of genes to translate and to take into account during alignment. If not supplied or empty, sequence will not be translated. If non-empty, should contain a coma-separated list of gene names",
  cxxopts::value<std::string>(),
  "GENES"
  )
  @@ -436,6 +436,7 @@ std::tuple<CliParams, cxxopts::Options, NextalignOptions> parseCommandLine(
  cliParams.inputRootSeq = getParamRequired<std::string>(cxxOpts, cxxOptsParsed, "input-root-seq");
  cliParams.inputTree = getParamRequired<std::string>(cxxOpts, cxxOptsParsed, "input-tree");
  cliParams.inputQcConfig = getParamRequired<std::string>(cxxOpts, cxxOptsParsed, "input-qc-config");
  + cliParams.genes = getParamOptional<std::string>(cxxOptsParsed, "genes");
  cliParams.inputGeneMap = getParamRequired<std::string>(cxxOpts, cxxOptsParsed, "input-gene-map");
  cliParams.inputPcrPrimers = getParamRequired<std::string>(cxxOpts, cxxOptsParsed, "input-pcr-primers");
  cliParams.outputJson = getParamOptional<std::string>(cxxOptsParsed, "output-json");
  @@ -868,11 +869,8 @@ int main(int argc, char *argv[]) {
  std::map<std::string, std::ofstream> outputGeneFiles;
  for (const auto &[geneName, outputGenePath] : paths.outputGenes) {
  - const auto result = outputGeneFiles.emplace(
  - std::piecewise_construct, std::forward_as_tuple(geneName), std::forward_as_tuple(outputGenePath));
  -
  + const auto result = outputGeneFiles.emplace(std::make_pair(geneName, outputGenePath));
  const auto &outputGeneFile = result.first->second;
  -
  if (!outputGeneFile.good()) {
  throw ErrorIoUnableToWrite(fmt::format("Error: unable to write \"{:s}\"\n", outputGenePath.string()));
  }
  