Jerome Kelleher

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...

Method to 'prune back' a tree sequence

18

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...

Document IBD structures in C

1

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...

When having a quick look at a Tree, it's often good to know some basic node summaries. I'd like to add mean internal node arity to the list.

Variant method to get all alleles as a string

6

There are often times when we'd like to get the genotypes for a given site as the actual alleles rather than the indexes into the alleles list. (This is what...

Multiple chromosomes

32

@DomNelson and I were just discussing the possibility of adding support for multiple chromosomes to tskit. One possibility which seems like it might be a reasonably smooth path forward is...

Makes stats cache optional

3

Alternative approach for #1937

Method to "reverse" a tree sequence

3

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...

Tree.sites iterator isn't reversable

2

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...

MetadataSchema doesn't validate the schema

3

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(...