While snp_frequencies and hap_frequencies each have their own file while cnv_frequencies is stuck in anopheles.py. It would probably make more sense to give it its own file as well.

This issue replaces the first part of #661.

Here is @leehart comment for this issue from #661:

I can certainly see the benefits to consistency putting cnv_frequencies into its own file. I'm not sure why that is currently different, but I guess it just hasn't been been moved over yet. I can't imagine a technical reason, yet. Maybe @alimanfoo has some knowledge of this?