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tskit-dev
Population-scale genomics
It has popped up in a few places that our laxity in not checking the correctness of mutation parents at TreeSequence initialisation was a mistake, and we really should be...
Introduces the ability to subset the branch LD matrix with genomic positions. This is a little trickier than subsetting the LD matrix with sites because positions can map to duplicate...
Here @tforest and I are starting in on adding time windows to statistics. We're starting with what was sketched out in #683, and will explain things in more detail here...
Hello! While trying to compile some code, which included elements of tskit, in the Linux environment of the University of Arizona HPC unit, I noticed that some errors were thrown...
New extension (pun intended) to the `extend_edges` algorithm now called `extend_paths` (subject to change). We noticed that certain examples within unary regions would not be extended simply with extend edges....
Having converted the output of Relate to a tree sequence using relate_lib (https://github.com/leospeidel/relate_lib), I was trying to obtain a subsection of the full ts. I got the following error, suggesting...
@hyanwong, Gil and I have recently discussed details of a "windowed" GNN, which would use either span- or time-based windows to calculate the nearest neighbours of a set of focal...
I've recently fixed the codecov path issues, but we're still seeing some upload problems from forks. See https://github.com/tskit-dev/tskit/actions/runs/8722766656/job/23929376280?pr=2915 This seems to be because forks of public repos don't get the...
