message: fix: off by one errors in alignment
diff: @@ -94,12 +94,12 @@ pub fn backtrace(
  // Add right overhang, i.e. unaligned parts of the query or reference
  if rPos < ref_len - 1 {
  - for i in (rPos..ref_len - 1).rev() {
  + for i in (rPos + 1..ref_len).rev() {
  aln_qry.push(Nuc::GAP);
  aln_ref.push(ref_seq[i as usize]);
  }
  } else if qPos < qry_len - 1 {
  - for i in (qPos..qry_len - 1).rev() {
  + for i in (qPos + 1..qry_len).rev() {
  aln_qry.push(qry_seq[i as usize]);
  aln_ref.push(Nuc::GAP);
  }
  @@ -151,12 +151,12 @@ pub fn backtrace(
  // Add left overhang, i.e. unaligned parts of the query or reference
  if rPos >= 0 {
  - for i in (0..rPos).rev() {
  + for i in (0..=rPos).rev() {
  aln_qry.push(Nuc::GAP);
  aln_ref.push(ref_seq[i as usize]);
  }
  } else if qPos >= 0 {
  - for i in (0..qPos).rev() {
  + for i in (0..=qPos).rev() {
  aln_qry.push(qry_seq[i as usize]);
  aln_ref.push(Nuc::GAP);
  }
  