message: fix: prevent local variable shadowing
diff: @@ -682,8 +682,8 @@ void run(
  }
  }
  - const auto &ref = output.result.ref;
  - const auto &query = output.result.query;
  + const auto &refAligned = output.result.ref;
  + const auto &queryAligned = output.result.query;
  const auto &alignmentScore = output.result.alignmentScore;
  const auto &insertions = output.result.insertions;
  const auto &queryPeptides = output.result.queryPeptides;
  @@ -698,7 +698,7 @@ void run(
  // TODO: hoist ref sequence transforms - process and write results only once, outside of main loop
  if (!refsHaveBeenWritten) {
  - outputFastaStream << fmt::format(">{:s}\n{:s}\n", refName, ref);
  + outputFastaStream << fmt::format(">{:s}\n{:s}\n", refName, refAligned);
  outputFastaStream.flush();
  for (const auto &peptide : refPeptides) {
  @@ -710,7 +710,7 @@ void run(
  }
  - outputFastaStream << fmt::format(">{:s}\n{:s}\n", seqName, query);
  + outputFastaStream << fmt::format(">{:s}\n{:s}\n", seqName, queryAligned);
  for (const auto &peptide : queryPeptides) {
  outputGeneStreams[peptide.name] << fmt::format(">{:s}\n{:s}\n", seqName, peptide.seq);
  