Large emhaplofreq

[alexlancaster]

@rsingle still needed or not?

meanwhile I'll resync with main

[alexlancaster]

Looks like the .dat file could be turned into a .pop for unit tests and moved to tests/data/ (or data/samples if they are just to be kept around). could they be repurposed for haplo-stats unit tests, since eventually we'll be moving to that?

[rsingle]

@rsingle still needed or not?

meanwhile I'll resync with main

I'd like to keep this branch around for a bit.

[rsingle]

Looks like the .dat file could be turned into a .pop for unit tests and moved to tests/data/ (or data/samples if they are just to be kept around). could they be repurposed for haplo-stats unit tests, since eventually we'll be moving to that?

Yes, that sounds like a good idea. I don't think it is worth spending a lot of time on the emhaplofreq-related questions for large size (but I still want to keep it around for a bit).

[alexlancaster]

Looks like the .dat file could be turned into a .pop for unit tests and moved to tests/data/ (or data/samples if they are just to be kept around). could they be repurposed for haplo-stats unit tests, since eventually we'll be moving to that?

Yes, that sounds like a good idea. I don't think it is worth spending a lot of time on the emhaplofreq-related questions for large size (but I still want to keep it around for a bit).

My general philosophy with branches is that most should be relatively short-lived, i.e. create them when working on a feature, then merge and delete when done. Otherwise they go stale quickly. That said, I'm happy to keep longer running branches going, so long as they are kept up to date with main.

So in that spirit, I propose that since the data files don't affect anything in the code - they should just be merged into main (they can be reworked into unit tests later). That just leaves the modifications to the emhaplofreq.h (which I think I made when I was playing around with runs - I don't know if there's anything critical there to keep). We can continue to keep this branch as a sandbox, but push any changes upstream as long as they don't break anything.

What about the separate changes the haplo-stats branch (#111)? That's a similar case, except that there's an additional emhaplofreqLDfix.c file