Jerome Kelleher

A pull request would be very welcome if you'd like to contribute @atongsa! If you're interested, we'd be happy to provide some concrete pointers on where to start. (The [development...

As it's a "derived" statistic, I would imagine the implementation would look something like that of [Fst](https://github.com/tskit-dev/tskit/blob/c12f384c6c7820f783a59537b6a31ba3e6a141fb/python/tskit/trees.py#L8297). However, it may be that it's not as complicated as that. Perhaps you...

Also, if you *do* have VCF data then you'd probably be better off using something like [sgkit](https://pystatgen.github.io/sgkit/latest/index.html) which has an implementation of [PBS](https://pystatgen.github.io/sgkit/latest/generated/sgkit.pbs.html#sgkit-pbs)

Riiight. Maybe the topological sort algorithm that @benjeffery developed for pedigrees could be used for this?

I think the first iteration of this would be to just call ``compute_mutation_parents`` (or the underlying algorithm used) after the existing checks have passed, and then check that the results...

Probably adding the lowest-level compute_mutation_times bits in C would reduce that - I'd imagine tables.compute_mutation_times is already doing some of the checking

Adding this to 1.0 for now, but can probably bump if we don't decide to fix the mutation ordering for that.

Are you sure it's memory allocations here and not overhead associated with seeking along the sequence? I'd be surprised if malloc overhead was significant here

Is there an off-by-one misunderstanding along the line here somewhere? I.e., should we interpret the contig length in the VCZ as being one-based, inclusive?

This is partially done, with #2296 creating the lineage_t struct, and #2297 moving the label, population and hull attributes to this struct in the minimal working way. Follow ups will...