message: feat: tune params to improve peptide alignment
  This improves calculation of bandwidth and shift for peptide alignment, previously introduced in
  In this version, we ensure that the sequences with large insertions (large number of ref gaps) get a large enough band width.
diff: @@ -62,10 +62,10 @@ GapCounts countGaps(const NucleotideSequence& seq) {
  }
  AlignmentParams calculateAaAlignmentParams(const GapCounts& queryGapCounts, const GapCounts& refGapCounts) {
  - constexpr int BASE_BAND_WIDTH = 3;// An arbitrary magic number to give some additional room for alignment
  + constexpr int BASE_BAND_WIDTH = 5;// An arbitrary magic number to give some additional room for alignment
  - const int bandWidth = std::max(queryGapCounts.internal, refGapCounts.internal) / 3 + BASE_BAND_WIDTH;
  - const int shift = queryGapCounts.leading / 3 + bandWidth / 2;
  + const int bandWidth = (queryGapCounts.internal + refGapCounts.internal) / 3 + BASE_BAND_WIDTH;
  + const int shift = (queryGapCounts.leading - refGapCounts.leading) / 3 + (queryGapCounts.internal - refGapCounts.internal) / 6;
  debug_trace("Deduced alignment params: bandWidth={:}, shift={:}\n", bandWidth, shift);
  