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tskit-dev
Population-scale genomics
I've been using this `CMakeLists.txt` using the following code in my code for a while now: ``` add_subdirectory("extern/tskit/c" "extern/tskit") target_link_libraries(${MY_TARGET} INTERFACE tskit) # ${MY_TARGET} is header-only, thus INTERFACE ```
I spotted a typo in one of the tskit documentation pages and wanted to quickly fix it using the "Edit on GitHub" link, as advised in "Development". However, it appears...
I came across a discrepancy between the `tskit` classification of tree topologies and the Kingman coalescent. If genealogies are rooted, bifurcating trees with nodes ordered in time, then there are...
For simplicity, code to check for consistency of the chromosome name was removed from the new [`msprime.read_hapmap()` code](https://github.com/tskit-dev/msprime/pull/1346). However, it seems a good idea to check, by default, that if...
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...
I would expect the `Tree.count_topologies()` method to return the Counter objects only for the valid sample sets, but iterating over a `tskit.TopologyCounter` seems never to end: ``` c = tskit.Tree.generate_star(3).count_topologies([[0],[1],[2]])...
I came across a minor issue with the plotting code: the `draw_svg` warning for mutations above unplotted nodes uses the `logging` module instead of the `warnings` module, that we'd usually...
