any interest in passing -O *.sto to hmmbuild so we can use the cons seq later for a curation by --hand?

I'd say yes! If you could update the

HMMER_HMMSEARCH

to do that (similarly to the other passed flags with files (-A, --tblout and --domtblout)), and then we can update in #C07URFZF074 and output that by default. Feel free to tag me as reviewer

HMMER_HMMBUILD

? 😄

Oh, the -O flag can go into both 😄 Ofc, in #C07URFZF074 we will have to decide at which point to do that automatically (if additional sequence recruitment is enabled, then we do this at the

hmmsearch

step, otherwise at

hmmbuild

. So I guess we'll have to update both modules in one go 😉

Ah thanks, but I did a test and re-read the manual which states: "-O writes an “annotated, possibly modified” source alignment, and that some residues may be shifted to satisfy Plan7 constraints, specifically because Plan7 does not allow insert→delete transitions" so for my use-case the coords don't match the seed alignment. I'm gonna leave it as is 😄