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Population-scale genomics
Getting the state that a mutation inherited is fiddly right now, and has been annoying me quite bit recently. We should add a method to the Python object at least...
WIP This additional check causes 658 test failures in python and 6 in C, I think all of which would be solved by computing mutation parents. Will do a perf...
Noted by @petrelharp (in #3179) the immediate next steps for moving the LD methods forward are: - write docs explaining output dimensions - explicitly test output dimensions (the current test...
When I recently tried to follow the instructions on the dev docs to set up the environment to build docs locally, I ran into some problems. @benjeffery helped me get...
@tforest points out that right now, ``` >>> ts.allele_frequency_spectrum([[0, 1, 2]], mode='branch').shape (4,) ``` but ``` >>> ts.allele_frequency_spectrum([0, 1, 2], mode='branch').shape Traceback (most recent call last): File "", line 1,...
Diploid Ne is given by `1/(2*pair_coalescence_rate)`. Although the `pair_coalescence_rate` implementation is consistent with msprime.DemographyDebugger, it's different from things like PSMC or MSMC that encourage users to interpret things in terms...
I've created this PR on the `tskit` repo for visibility - eventually this will live at https://github.com/tskit-dev/administrative. Following the meeting and discussion yesterday, I've written up what I consider to...
We've talked about having a numba support for tskit in various places, so let's add a new optional module "tskit.jit" which provides basic utilities for numba. This would be an...
Following up on #3212, we should perform the check on mutation parent integrity at the same time as doing the tree integrity. It'll be easy enough to do. We can...
#3091 introduced returning a numpy structured array from a compatible metadata buffer. The `StructCodec` allows the specification of string encoding in the schema, however numpy only supports `bytes` and `utf-32`...