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Population-scale genomics
It would be nice to have a function to calculate the selection test described in the Relate paper (p.16 of supplement) for mutations in a given tree. Or perhaps this...
When having a quick look at a Tree, it's often good to know some basic node summaries. I'd like to add mean internal node arity to the list.
Our current newick parsing relies on the `newick` python library, which for trees we've tested is ~120x slower than parsing with a common (C extension) `R` library. My initial rough...
Summary with click to expand for details.
Once we have a citation for tskit we should add some small unobtrusive hint to cite tskit to the notebook representations.
There are often times when we'd like to get the genotypes for a given site as the actual alleles rather than the indexes into the alleles list. (This is what...
Let `G` be the "extended genotype matrix", whose rows are indexed by mutations (not sites) and samples, with `G[i,j] = 1` if the sample has inherited that mutation and `0`...
@DomNelson and I were just discussing the possibility of adding support for multiple chromosomes to tskit. One possibility which seems like it might be a reasonably smooth path forward is...
See https://github.com/tskit-dev/tsinfer/discussions/629 for a use-case and https://github.com/tskit-dev/tsinfer/discussions/629#discussioncomment-2155840 for some code that I think does the trick, modulo top-level metadata. There might be difficulty if there is stuff in a schema...
A good number of times I have made tables that aren't valid tree sequences. When trying to convert them, I get errors such as ``` _tskit.LibraryError: time[parent] must be greater...