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Population-scale genomics
Following up on #1596, we'd like to build out some basic functionality to help us work with cross coalescence statistics. The simplest thing we can do to start with (as...
## Description Fixes #1294. Should probably add some tests for attributes of the graph like `branch_length`, `left`, and `right`. # PR Checklist: - [x] Tests that fully cover new/changed functionality....
As shown in https://github.com/tskit-dev/msprime/discussions/1901 metadata validation is proving to be quite expensive for msprime simulations. One option would be to change our code to use https://github.com/horejsek/python-fastjsonschema It has [conda-forge](https://anaconda.org/conda-forge/python-fastjsonschema) and...
This script: ``` import tskit t = tskit.TableCollection(sequence_length=1) t.nodes.add_row(flags=1, time=0) t.nodes.add_row(flags=1, time=0) ts = t.tree_sequence() tr = ts.first() print("MRCA", tr.mrca(0, 1)) print("TMRCA", tr.tmrca(0, 1)) ``` produces ``` MRCA -1 Traceback...
Reasoning: #2047. See also #464. Presumably we also want a `get_individuals_associated with_sample_nodes()` function.
After a brief chat with @petrelharp we thought it might be time to revisit the general structure of https://tskit.dev/tskit/docs/stable/stats.html, because (for instance) it doesn't mention the LDcalc stuff, or have...
It would be good to add an example of using at least some of the statistics on the Statistics page. It's a bit of a wall of text at the...
An error that I have seen quite a few people make already is that they pass in a list of individual ids to `samples=`, instead of their constituent nodes. It's...
The possibility of missing data is being added in #272; the stats need to be modified to take this into account. At least two issues: 1. Site stats: isolated samples...
Following up on #1937, it would be generally useful to make the node based caching in the general stat framework optional in the C code. Then propagate the option back...