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Population-scale genomics
Mutation mode is described in https://github.com/tskit-dev/tskit/issues/3299 and related work is in https://github.com/tskit-dev/tskit/pull/3266 and https://github.com/tskit-dev/tskit/pull/3271. The current docs say `site: How many mutations differentiate these two genomes?` https://github.com/tskit-dev/tskit/blob/e4ca46969bb32f3de612c5653ba280446f4b9f5e/docs/stats.md?plain=1#L212. This should be...
Currently we have [three modes](https://tskit.dev/tskit/docs/latest/stats.html#sec-stats-mode) for statistics. Quoting from there: > These three examples can all be answered in the same way with the tree sequence: first, draw all the...
We should implement the `TreeSequence.allele_frequencies(sample_sets)` function, which returns a numpy array of (non-ancestral allele frequencies) x (sample_sets). Here's an implementation: ``` def allele_frequencies(ts, sample_sets=None): if sample_sets is None: sample_sets =...
Following up on #3314. Not entirely sure what this entails as there's various choices about how the work was split up I think.
In discussion with @benjeffery we decided that TreeIndexes is a better name for the low-level structure used to keep track of how we iterate over trees than TreePosition. In an...
A common thing we'd like to do is to visualize *shared* structure in the trees across a region of the genome. It occurs to me that one way to do...
I started to have a look at https://github.com/tskit-dev/tskit/issues/1896 where one of the possible solutions is decoding haplotypes in C. (The current methods all do this by iterating over sites then...
This is a WIP; for now I'm just moving the python implementation in `tests/test_tree_stats.py` over here from #3266.
For the purposes of assessing how the two-locus framework performs relative to the LD Calculator, I've performed a series of benchmarks. In our initial benchmarks, the two-locus framework was rather...
I frequently use `msprime.RateMap` and often need to write these out to hapmap format, e.g. for input to a standalone tool. I noticed that tskit-dev/msprime#1338 discusses adding `RateMap.write_hapmap`, but afaik...
