Jerome Kelleher
Jerome Kelleher
We should provide simple methods for reading/writing RateMaps in binary and text formats. These should use numpy methods only, we don't need anything like zarr here. This is separate to...
It would be useful to have a method that would combine two or more RateMaps and return an iterator over the distinct intervals at the rates. So, in usage, it...
Currently a WIP, but the idea is to support all-nodes matching a-la tsinfer in the LS HMM. It turns out that this is significantly different to the "samples-only" approach that...
After #2786 we don't actually use tsk_diff_iter_t at all in the library. As it's not part of the public API (and it causes some annoying problems internally, e.g. [here](https://github.com/tskit-dev/tskit/blob/f7ba5489ae9fa7bede54ad856f181c85f8759f6e/c/tskit/trees.c#L447)) I...
We should be able to substantially simplify the stats API algorithms by using the tsk_tree_position_t class. This should be done before we generalise to windows that are not [0, L)...
Once #2782 is implemented we can easily support threading along the genome by following the approach for divergence matrix in #2736.
I think we can rephrase at least ``genetic_relatedness`` (aka eGRM) in terms of ``divergence_matrix``, which should substantially improve performance (although waiting for #2779 which is needed for decent site-mode performance)....
Currently the stats API requires that we cover the entire genome with windows, which is restrictive. In particular, it prevents us from parallelising along the genome in a simple way....
Following up on #2736, we need to document the function. Note that I left the old partially implemented version of divergence matrix as a commented out block here as it...