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Support arbitrary rate maps for gene conversion #1212

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jeromekelleher opened this issue Sep 25, 2020 · 2 comments
Open

Support arbitrary rate maps for gene conversion #1212

jeromekelleher opened this issue Sep 25, 2020 · 2 comments
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@jeromekelleher
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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
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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.

@hyanwong
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hyanwong commented Mar 29, 2021

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.

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