search

bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
1.06k stars 182 forks source link

DNA letter check logic #756

Open ftegenfe opened 1 year ago

ftegenfe commented 1 year ago

Hello, when I run diamond on AA fasta files, it sometimes fails claiming there are only DNA letters even if that is not true. Looking in the code I see this conforms with the logic. This concerns the function SequenceFile::load_onepass() . I wonder isn't it more logical to fail the check only if ALL sequences in the test range (CHECK_FOR_DNA_COUNT) are DNA? I am aware of the --ignore-warning option but I encountered this in a package which uses diamond internally. It's a suggestion - I fixed this by rearranging the sequences in the fasta file :)

bbuchfink commented 12 months ago

Yes that would probably make sense changing that, I'll look into it.