message: feat: remove indels from coverage calculation
  I'm not sure how handle Ns and ambiguous characters that appear in indels
  The formula as is assumes `missing` and `non_acgtns` don't count bases
  in indels
diff: @@ -150,7 +150,7 @@ pub fn nextclade_run_one(
  let aa_changes_groups = group_adjacent_aa_subs_and_dels(&aa_substitutions, &aa_deletions);
  let total_aligned_nucs = alignment_end - alignment_start;
  - let total_covered_nucs = total_aligned_nucs - total_missing - total_non_acgtns - total_deletions + total_insertions;
  + let total_covered_nucs = total_aligned_nucs - total_missing - total_non_acgtns;
  let coverage = total_covered_nucs as f64 / ref_seq.len() as f64;
  let qc = qc_run(
  