Terminal Ns not recognized as missing

[ktmeaton]

While investigating https://github.com/cov-lineages/pango-designation/issues/590, I noticed that samples with the BA.2 S2M deletion (29734:29759) were being incorrectly visualized as having reference bases in sc2rf:

Consensus View:

sc2rf View:

I think this could be for a couple of reasons:

1. When --enable-deletions is used, perhaps deletions should not be considered missing data?

   missings_matches = ["N"]
   if not args.enable_deletions:
       missings_matches.append("-")

2. I think there is missing logic when detecting a run of Ns, to catch if that runs proceeds to the end of the genome?

   if s in missings_matches:
       # we've been tracking a run of N's, this base marks the end              
       if start_n == -1:
           start_n = i  # mark the start of possible run of N's
   elif start_n >= 0:
       missings.append((start_n, i-1))  # Python-style (closed, open) interval
       start_n = -1
   
   # Missing logic to catch missing data at the end of the genome?
   if i == len(reference) and s in missings_matches:
       missings.append((start_n, i-1))

With these changes, the sc2rf output more closely matches the consensus sequence/my expectation:

I think this is a bug, but if it's the intended behaviour for deletions, please let me know. Thanks!

[ktmeaton]

Sorry, the code for both of these is:

python3 sc2rf.py pango_designation_590.fasta --ansi --unique 1 --enable-deletions