MOB-cluster not updating reference sequences? #184
Description
Hi, is it by design that mob_cluster in update mode does not add the new sequences to the reference FASTA? My understanding of this section:
https://github.com/phac-nml/mob-suite/blob/3.1.9/mob_suite/mob_cluster.py#L620-L632
is that is basically copies ref_fasta to update_fasta because I don't see any manipulation of tmp_ref_fasta_file but I could be missing something...thanks!
As an add-on, is there any deduplication in MOB-cluster following the logic of #135 (comment), specifically only keeping 1 plasmids per secondary cluster ID? I couldn't find any logic to this effect.