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Population-scale genomics
It's useful for algorithm development to be able to "flip" the coordinates of a tree sequence around so that we read the trees and sites in the opposite order. I...
This is also used to look for selection. See also #1314 - maybe this is related, as each coalescence is the end of a linage.
It would be good to make the [Tree.sites](https://github.com/tskit-dev/tskit/blob/d421b4396a46472f74d8667a37413c188d1bddaf/python/tskit/trees.py#L1972) method reversable so that we can get at the sites backwards when running through the trees in reverse. You can always just...
There doesn't seem to be much validation of the schema itself when we set a metadata schema. E.g., if we do: ```python import tskit tables = tskit.TableCollection(1) tables.nodes.metadata_schema = tskit.MetadataSchema(...
We currently have no HTML representation of a TableCollection, although ``__str__`` is defined. Showing the same data as ``__str__`` seems like a good approach.
At the moment, I'm pretty sure that operations which change the coordinate system, primarily `trim`, `rtrim`, and `ltrim`, don't touch the reference sequence at all. I guess eventually they should...
As discussed in #1899 30% of the time required to load a 1G tree sequence is spent checking its integrity. We could bypass this by recording when check integrity has...
Assuming that we agree on filtering candidate segments based on the ``among`` and ``between`` segments within the IBD finding algorithm as proposed in #1662, the interface between the IBD finding...
Currently, if you want to query whether a schema is set you need to write: ```python if table.metadata_schema == tskit.MetadataSchema(schema=None): # do something ``` and to set to a null...
