Jerome Kelleher

Yes, it's a bug really that we don't fully validate the mutation parents on tree sequence creation.

Note this is straightforwardly added once #3228 as a numpy array ``mutations_inherited_state``, computed like this: ```python def compute_inherited_state(ts): derived_state = ts.mutations_derived_state ancestral_state = ts.sites_ancestral_state inherited_state = ancestral_state[ts.mutations_site] mutations_with_parent = ts.mutations_parent...

Yep - and their inherited state is the site's ancestral state. This is really for complicated stuff like SARS-CoV-2 where we get up to 30K mutations per site.

Yes - but let's get some other projects shipped first

No hurry with it - probably good for me to do so I have some idea how GitHub actions work!

We wouldn't bother in msprime because the overhead could be significant when we run large numbers of replicates of small simulations (a reasonably common case). If you're running hundreds of...

Do we want this for 0.2.0 @petrelharp, or can we push it down the road to 0.2.1? I'd like to ship a reasonably complete set of statistics as soon as...

Thanks @castedo, that sounds ideal. The benchmarks we did in the paper you mentioned will give a good idea of the sort of scenarios we're imagining, we'd be applying individual...

I don't think we can cover every possible corner case here @castedo - nature is pretty creative with coming up with weird stuff. "Does what you'd want in most cases"...

Sounds good @petrelharp. Maybe worth knocking up a simple Python version where we don't think too hard about efficiency?