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Population-scale genomics
I'm a bit confused about what the ``tsk_bit_array_`` struct really is. I thought it was a straightforward bit-set implementation, but there's the idea of ``rows`` which I'm confused by. Is...
The bit_array methods currently have pointer chasing like ``self->data`` within loops, which might reduce performance. It's worth declaring restrict pointers for these to help the compiler out. ```c void tsk_bit_array_add(tsk_bit_array_t...
As mentioned [here](https://github.com/tskit-dev/tskit/pull/2805#issuecomment-1646665089) by @petrelharp during the review of #2805, we'd like a better treatment of missing data. As implemented, we compute $w_{AB}$, $w_{Ab}$, $w_{aB}$, but use the total number...
We'd like to implement two-population versions of the statistics we've implemented thus far: $D$, $D^{\prime}$, $D^{2}$, $D_{z}$, $\pi_{2}$, $r$, $r^{2}$ This means that we'll strictly require two sample sets, comparing...
Over at #2805, @lkirk has implemented various two-locus stats, e.g. r^2, D, etcetera. The strategy for computing these is to sum something over all pairs of alleles (one allele from...
The ``trees.c`` file is pretty big, and there's a lot of code involved in the general stats. Also, there will be stats we want to compute which use the variant...
At the moment, much of the detail is described in https://tskit.dev/msprime/docs/stable/pedigrees.html#pedigree-encoding. I think some of this is general to `tskit` rather than `msprime`, and so a short description of pedigree...
When packaging tskit for nixpkgs ([see here](https://github.com/NixOS/nixpkgs/blob/master/pkgs/development/python-modules/tskit/default.nix)) I noticed that the python API tests folder was not included in the archive. This is not the case for msprime for example,...
In e.g. forward simulations, it is common to way to adjust the times in a TableCollection so as to put the current generation at time 0. It is easy to...
While thinking with metadata for the `tskit` poster, I remembered this on the queue. As discussed with @benjeffery - this is mostly a documentation PR, but it also changes behaviour...