Most of the API/help for the recombination inputs say something like this (which I took from the CLI help)
-g , --genetic-map Specify a particular genetic map. If no genetic map is
specified use a flat map by default. Available maps:
A flat map is a uniform recombination rate, right? It's not clear where users can find out what this uniform rate is.
Subissue of #215 and #137
We could say "By default, we use a chromosome-specific uniform recombination rate." The recombination rates for each chromosome are in the catalog and online docs.
"flat map" is not a good choice of terminology though, we should change it.
Okay, I'll do this.
What's the status of this @gtsambos?
Sorry, haven't gotten round to this yet. I can submit a mini pull request and change a few lines of wording later tonight so we can close this --