Closed scharch closed 6 years ago
Yes. This was the idea with having --rearrange-from-scratch and --mutate-from-scratch separate. I think I added that ^ exception because at some later date I changed some things about how the options worked, and I wanted to go back through and make sure that specifying them separately still worked as intended. OK, will go do that now...
OK I've separated --rearrange-from-scratch and --mutate-from-scratch, and hopefully clarified them and the related options. lmk if it doesn't behave as expected.
switched interface a bit (to clarify what's coming from where) so using --shm-parameter-dir and --reco-parameter-dir instead of --parameter-dir when simulation from scratch.
https://github.com/psathyrella/partis/commit/b0c45c4e1ad884ab2b61ebc2dc52ba43dd60458f
Seems like there should be a way to override SHM, while still keeping the derived recombination parameters (or vice versa).