message: fix: limit search of trailing gaps up to the first leading gap
  To avoid double-counting
diff: @@ -36,7 +36,7 @@ GapCounts countGaps(const NucleotideSequence& seq) {
  // Rewind backwards starting from the end, until the first non-gap
  int end = len - 1;
  - while (end >= 0 && isGap(seq[end])) {
  + while (end > begin && isGap(seq[end])) {
  --end;
  }
  