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Population-scale genomics
It'd be nice to do e.g. ``` ts.samples("popA") ``` where `"popA"` is the *name* of a population, rather than the index. Currently we end up doing things like this: ```...
Something like `ts.node(metadata=('key', 'subkey', 'value')` would be a handy convenience to have. It would mean things like `ts.node(metadata=('name', 'es423'))` would work well or `ts.individual(metadata=('accession','id','BOB'))`. We considered hardcoding for example `ts.node(name="es423")`...
WIP related to #1315. Edited 14 Feb 22 into something resembling a usable API. @petrelharp @gregorgorjanc This mock-up consists of a class in `test_stats.py` that: (a) walks over nodes in...
A new test file ``test_table_transforms.py`` was added in #2240. This is intended to be used for things like ``trim``, etc, that do transformations on the tables. Move the appropriate tests...
3.11 betas are coming out, with this version having some breakage in the C API.
I want a function that will remove the topology after (forwards in time) a specific time, and mark each extant lineage with as a sample. The intuition is that we're...
We need to explain what it means and how to use it.
Might as well document ``tsk_table_collection_ibd_segments`` and associated structs while our heads are in it. Probably worth doing the ``tsk_table_collection_find_ibd`` which takes a function pointer (#1663) at the same time so...
We want to implement functions in the Variant class to calculate various metrics to evaluate genotype imputation performance (discussed #2193). The simplest metric is the **_overall concordance_**, which is the...
Another metric is the squared correlation, which is simply the square of the Pearson correlation coefficient between the allele dosage of the true genotypes and the allele dosage of the...