message: feat: add left-align-gaps CLI flag, default still right-align
diff: @@ -37,6 +37,11 @@ pub fn score_matrix<T: Letter<T>>(
  trace!("Score matrix: allocated alignment band of size={band_size}");
  + // Whether alignment is left or right aligned
  + // If default changes, need to change logic here
  + // Right align is default so ignored at the moment
  + let left_align = if params.left_align_gaps { 1 } else { 0 };
  +
  // fill scores with alignment scores
  // if the colon marks the position in the sequence before rPos,qPos
  // R: ...ACT:X
  @@ -141,7 +146,7 @@ pub fn score_matrix<T: Letter<T>>(
  }
  // could factor out tmp_score, replacing with ref_gaps but maybe less readable
  ref_gaps = tmp_score;
  - if score < tmp_score {
  + if score + left_align < tmp_score {
  score = tmp_score;
  origin = REF_GAP_MATRIX;
  }
  @@ -167,7 +172,7 @@ pub fn score_matrix<T: Letter<T>>(
  tmp_score = q_gap_open;
  }
  qry_gaps[qpos] = tmp_score;
  - if score < tmp_score {
  + if score + left_align < tmp_score {
  score = tmp_score;
  origin = QRY_GAP_MATRIX;
  }
  