multiple chromosomes (eg with SLiM v5)

[petrelharp]

In SLiM v5 it is easy to simulate multiple chromosomes at once; it would be nice to do this. Along the way we'd get sex chromosomes in (💯 ).

At first look, just allowing a list of contigs would suffice:

engine.simulate(model, [contig1, contigX, ...], samples)

since everything we'd need to do the simulation would be attributes of contigs.

However, @jeffspence notes that some things (like add_dfe) naturally act on a bunch of chromosomes at once: so, maybe we have a class like ContigSet that is basically a list of contigs but can do like

ContigSet.add_dfe(interval_dict, DFE)

where interval_dict is a dict of intervals, with keys the IDs of chromosomes.

[petrelharp]

Additional notes from the meeting today:

• we need a new class because there's going to be state shared across contigs for traits (eg the environment)
• the output of simulate will depend on whether it is passed a contig (outputs a tree sequence) or a list-of-contigs object (outputs a list of tree sequence)