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Population-scale genomics
Right now it's very hard to find the documentation for how to read and write data using the tables API. There's a whole bunch of different ways of doing things,...
We need some examples to help illustrate how to use ``keep_rows`` and the ``id_map`` well. Here's one example (taken from the tests in #2707) See also #2529 ``` def test_delete_unreferenced_nodes(self):...
It'd been pointed out that other tools like - ADMIXTOOLS (or, the frontend admixr) - treemix report statistics (eg f3) calculated from only polymorphic sites instead of the whole genome...
#1868 merged a change in which we only run ``test_tables.py`` and ``test_lowlevel.py`` when calculating the low-level module test coverage. This resulted in a small drop in coverage. We should go...
At the moment the docstring of the functions `tskit.all_tree_shapes` and `tskit.all_tree_labellings` claims the `:rtype:` is a `tskit.Tree`, but it's actually an iterator over trees (or more specifically a generator of...
The documentation in #392 looks great. If folks are using that part of the API, then they probably want to know about accessing the number of samples below a node...
Now #1199 does this for individuals (yay!) but we still don't have a method, besides `canonicalise`, that will do this. Seems like it should be a standard part of `sort`....
Adding ```python tables1.tree_sequence() tables2.tree_sequence() ``` at https://github.com/tskit-dev/tskit/blob/main/python/tests/test_tables.py#L1409 causes: `_tskit.LibraryError: Parent mutation ID must be < current ID`
When `tsk_individual_table_topological_sort` is called, it may rearrange an individual table that is already in a topologically sorted order. For example, if we have two parents and their child in a...
The top-level [tskit.write_ms()](https://github.com/tskit-dev/tskit/blob/ed3742d09452477ca8a690de9c41612e9b66c4df/python/tskit/trees.py#L7221) method, added in #854, does not appear in the online documentation anywhere, although it is documented (eg `help(tskit.write_ms)` works). I think this should go in a subsection...