Function to compare genotypes stored in xarray.dataset using sgkit

[szhan]

This function should help compare genotypes stored in two VCF files, e.g., one from BEAGLE containing imputed genotypes and the other containing ground-truth genotypes. The plan is to develop a version of this function to work for cases where only biallelic or monoallelic sites are compared before generalising it to be incorporated into sgkit.

[hyanwong]

Does this tie in to tskit-dev/tsinfer#739

On that note, we should probably try to push tskit-dev/tskit#2617 through. I think all the comments are addressed on that PR now, and it can probably be merged, right?

[szhan]

Ah, yes! Using SampleData to compare genotypes is an absolute nightmare.

[hyanwong]

Should probably be incorporated into SGkit, not SampleData.

[szhan]

Yes, I mean using SampleData to compare genotypes is inconvenient. Should definitely move onto sgkit.

[szhan]

If one or both of ds1 and ds2 is empty, then a ValueError exception should be raised, right? Since there are genotypes to be remapped. h/t @benjeffery for suggesting these tests.

[szhan]

Should also add tests involving cases where

1. Some site positions overlap.
2. No site positions are shared.

[szhan]

Leaving this open, although it is good enough for now.