Optional genomic-scale for popgen stats

See discussion in #888

Most methods within popgen.py are automatically applied over windows and default to variants if the dataset has not been windowed. It would be useful to optionally apply these methods over the whole genome and potentially per contig. Additionally, some methods such as identity_by_state and Weir_Goudet_beta are currently applied to the whole genome, but it would also be useful to apply them within windows/contigs.

An option to allow more user control, whist keeping sensible defaults, would be to introduce a by parameter which can be used to specify the genomic scale (e.g., one of {"genome", "windows", "variants"}). The specified scale would determine the genomic-dimension and shape of the resulting values.

[timothymillar]

SGTM also, but this may require some re-working of the identity_by_state and Weir_Goudet_beta methods if/when windowing is required.

[jeromekelleher]

SGTM @tomwhite, I’ll cast my vote for adding the window_by_genome function then.