msprime
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Support arbitrary rate maps for gene conversion
sim_ancestry supports providing an arbitrary rate map as input, but the underlying infrastructure currently assumes a single rate and will trip some assertions.
Waiting on #1196 first.
We're not going to get this implemented in time for the 1.0 release so I'm pushing it to 1.1. It's not critical, as it's a straightforward extension API wise.
As part of this, when fixing it we should
- note that the GC rate is absolute, not a fraction of the recombination rate (which is how is it sometimes parameterised in other simulators such as SLiM)
- provide a utility function to make a new RateMap by multiplying all the rate values by a constant, so that we can create GC maps that are simple multipliers of a passed-in recombination map. After all, the reason that SLiM encodes GC as a fraction of recombination is that GC rates and recombination rates are, to a first order, simple multiples of each other.
- document an example of creating a GC map like this.