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Population-scale genomics
As discussed in https://github.com/tskit-dev/tskit/discussions/2089 and with some code providing a workaround in https://github.com/tskit-dev/what-is-an-arg-paper/issues/80. Also note that issue https://github.com/tskit-dev/tskit/issues/1120 discusses how we might avoid a large increase in the number of...
I wonder if it would be more user friendly to have the width of a tree in an SVG plot to be proportional to the number of samples, so that...
In `test_highlevel.py`, is there supposed to be `self.verify_provenances_format()` in `test_output_format()`? `provenances_file` is being passed to `ts.dump_text()`, but the output provenance file is not being verified subsequently, like the other output...
I was just after getting the oldest node(s) in the tree sequence, which I did by `node_times = ts.tables.nodes.time; oldest = np.flatnonzero(node_times == np.max(node_times))` but beginners might not know how...
This is going to be necessary for stdpopsim. We can do it easily in python at first as I [did here](https://github.com/petrelharp/treestats_ms/blob/c706c88a882646fa5d4a627a970101cdaf961646/figures/plot_1kg_diversity.py#L88).
this would be simple, as watterson's theta is ```ts.segregating_sites()/sum([1/i for i in range(1, ts.num_samples])```
We can at times end up with a large number of fixed mutations. It would be nice to have a way to remove these. I think we discussed having `simplify()`...
At the moment the genome positions in both text and SVG plots are listed in standard coordinates (interpreted as "base pairs"), but often the sequences run to thousands or millions...
This PR is for adding the `path` function which outputs the path between nodes u and v. It is needed for the B2 index https://github.com/tskit-dev/tskit/pull/2327 (issue https://github.com/tskit-dev/tskit/pull/2252). By the way,...
In #2334 we simplified the semantics of the ``population`` argument in split_edges and decapitate to default to -1 rather than inherit from the child node. It will probably be useful...
