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Population-scale genomics
## Description Adding ```centre=False``` option to ```genetic_relatedness``` statistic, so that it can calculate, for example, the non-mean-centred shared times between samples. So far I've just added the option to the...
In #1320 we [bemoaned the introduction](https://github.com/tskit-dev/tskit/pull/1320#issuecomment-823238645) of new `Tree.parent_array[u]`, `Tree.left_sib_array[u]`, etc. notation, which are the array-based (direct memory access) equivalent of `Tree.parent(u)`, `Tree.left_sib(u)`, etc. Nevertheless, this made it into [tskit...
When messing with metadata in tables where the schema allows null entries, it is helpful to be able to clear the table. I'm currently doing: ``` tables.nodes.packset_metadata([b''] * tables.nodes.num_rows) ```...
## Description This PR adds a collection of tests to check haploid and diploid Li and Stephens for forwards, backwards, and viterbi by testing a set of implementations against each...
I have spent some time recently with the new IBD segment functionality in the recent 4.1 version. The tutorial is here: https://tskit.dev/tskit/docs/stable/ibd.html. I find that the current IBD segment definition...
Here's a first pass at removing cacheing to reduce memory consumption in the general_stat framework. I've only tweaked the branch C function, and the python tests are passing. Without caching,...
Over in stdpopsim we're wanting to compute frequency spectra for only a certain set of mutations (the non-neutral ones, for instance). These are mixed right in with neutral ones (consider...
``` >>> print(ts.tables.nodes.metadata_schema) OrderedDict([('codec', 'json')]) >>> ts.tables.nodes.metadata_schema["codec"] TypeError: 'MetadataSchema' object is not subscriptable >>> ts.tables.nodes.metadata_schema.asdict()["codec"] 'json' ``` Having to use `.asdict()` to get the schema values, when the printed version...