Closed Percud closed 4 months ago
Yes, you are correct. However, a fix is non-trivial. I will keep this in mind and come back to this problem later. Thanks for the test case.
Actually simpler than I thought. Let me know if you still see this issue.
Hi,
I am using miniprot to identify genes and pseudogenes in primate genomes. It appears that miniprot (0.12-r237) does not penalize (nor acknowledge) an inserted stop codon.
For instance with these example sequences:
The genomic sequence is a pseudogene with a W->* mutation. I can retrieve the correct alignment by lowering the penalty for frameshift/stop (-F):
However, with the default parameter, miniprot prefers to insert a stop codon and open two gaps. This inserted stop codon is not acknowledged in the gff.
Best regards, Riccardo