Document RateMap etc

[hyanwong]

At the moment the documentation is in msprime under its own section within Utilities: Rate Maps. Since it is purely a python thing, I wonder if in tskit it should simply live in the Python API documentation. We already have a utility functions section: we could simply make it "Utility classes and functions" and put some of the explanatory stuff there? Some might want to stay in the msprime docs, I guess. There's quite a lot of material in the current msprime file.

[jeromekelleher]

Do we want to make this a blocker for 0.5.4?

[hyanwong]

No, I don't think that's necessary if we want to get 0.5.4 out soon. The msprime version will carry on working and is documented there. It will take some thought to get the docs right, so I think it can just be undocumented for the time being.

[jeromekelleher]

I think there are good reasons for not documented it yet actually - let's see how the process of cutting it out of msprime goes first and whether we need to make any minor API tweaks first.

[hyanwong]

Yes, I agree.

[hyanwong]

Just looking at the API for this again, in the light of wanting to be able to export a HapMap-style recombination rate. I wonder if we want to define class RecombinationMap(RateMap):, and then have read_hapmap (and maybe write_hapmap) as methods of the subclass?