[BUG]: The fasta sequence does not match the REF allele at OQ234674.1:1946 about nf-flu

[peterk87]

Thanks @Codes1985 for reporting this issue! I was hoping something like this wouldn't crop up with Clair3 and Bcftools!

I've usually gotten around this issue by changing all ambiguous bases in a ref seq to N, but I like your solution better since there's no modification and duplication of data required. I'll work this into the next patch release (3.3.3) that I'm working on in #41 since the changes are fairly minor, but critical!

[Codes1985]

You're most welcome, @peterk87! Very happy to help. We are rapidly approaching flu season, so it's good to iron out as many wrinkles as we can before then. Regarding #41, I agree. I was going to comment there that I found an edge case where subtypes were not being reported for fluA samples because those metadata were not actually included for the sequences identified as the top BLAST match (curses, NCBI!). So, your solution sounds great, and I think it will remedy the situation I came across, as well!

[peterk87]

Fixed in #41 and released in 3.3.3