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Support arbitrary rate maps for gene conversion

Open jeromekelleher opened this issue 3 years ago • 2 comments

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.

jeromekelleher avatar Sep 25 '20 15:09 jeromekelleher

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.

jeromekelleher avatar Mar 08 '21 08:03 jeromekelleher

As part of this, when fixing it we should

  1. 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)
  2. 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.
  3. document an example of creating a GC map like this.

hyanwong avatar Mar 29 '21 16:03 hyanwong