I've got a bead on the popgen summary stats, think i can code it up this weekend. Where do you think is the best place to put it? Slap it on at the end of step 7? Or have it be more of a standalone thing like svd4tet?
The argument for just tacking it on to step 7 is that if we just always do it no matter what there doesn't have to be a special paramsdict or cli flag. Also the time to calculate and the way i'm doing it is v fast, takes <5 minutes on real data.
I'm not married to either strategy, but figure i'd check if you had a preference.
Yeah, it'll be fun when it works. My inclination is to put it in the 'analysis' dir, but looks like svd is using main. Unless you have a better idea i guess i'll make a new directory ipyrad/sumstats? Better ideas?
the name main isn't really special, other than we tell setup.py to use that file to build the cli for that thing. But yeah, feel free to rearrange things into subdirectories inside analysis if that makes more sense.
maybe things don't need to be grouped into analysis, was just an early idea.