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Population-scale genomics
## Description Continuing from #2874, we want to finish moving over the tree-positioning code to use `tree_pos` efficiently. At the moment, `tsk.tree_seek` will either call `tsk_tree_seek_from_null` or `tsk_tree_seek_linear` depending on...
Currently, the emission probability for calculating the forward, backward, and Viterbi matrices is defined as follows: ``` p_e = mu; if (is_match) { p_e = 1 - (num_alleles - 1)...
I failed to pip install the development version of tskit on my computer, and I guess it is because I'm using a Windows computer, as I was able to install...
I'm thinking that the `CoalescenceTimeDistribution` class would be best moved to a separate package (where it can be numba-fied), and that instead we'll want to put an efficient algorithm for...
Implement a python interface to the 2-locus statistics so that we may begin more rigorous testing.
It would be handy to have a ``mid`` property on the Interval class, much like we have ``span`` at the moment. This would be ``self.left + (self.right - self.left) /...
hey team- working with @mufernando on some stdpopsim coding we stumbled upon a bug with `write_vcf`. using the default `position_transform` value, `write_vcf` can return position `0` which isn't allowed under...
Fixes #2838 Note that this is a fairly breaking change that we should think about, given that the default is for msprime output to require the new flag to `write_vcf`.
Just a quick thought: would it be helpful to cache the number of variable sites in a tree sequence, as well as the number of actual sites? I am starting...
At the moment, the `write_vcf()` function simply outputs the 0th allele from variant.alleles (i.e. the ancestral state) as the REF. If we have defined a [reference sequence](https://tskit.dev/tskit/docs/stable/data-model.html#reference-sequence), then presumably we...