Add variant/sample summary statistic methods

At a minimum, we need to be able to calculate these axis-wise aggregations (for GWAS QC):

• Variants (across samples)
  • genotype counts
  • allele counts and frequency
  • call count and rate
  • hwe p value (https://github.com/pystatgen/sgkit/issues/28)
• Samples (across variants)
  • call count and rate
  • genotype counts

I would propose that we start by making methods for each that take a single Dataset and return Dataset instances (it will be easier to define the frequencies/rates when the counts are defined in the same functions).

This should consider whatever the solution to https://github.com/pystatgen/sgkit/issues/3 ends up being.

[eric-czech]

What still needs doing to merge #102 and are there any other aggregations we should add?

It would be best to focus on getting those ones merged first and at a glance some remaining todos are:

• Count alleles should be based on https://github.com/pystatgen/sgkit/pull/114 instead
• This line should just sum instead of stack
• Some thought should be put into what happens when AN is 0 in allele_frequency
• Those methods could use more testing
• They also need documentation and examples

[eric-czech]

I believe #282 is related; @eric-czech as part of issue triage is it worth enumerating what’s left to close this issue out?

I think #282 can stay on its own since it’s not an aggregation. I turned the original bullet points into a checklist. All that’s left is to add functions that call the some of the same internal functions with a different dimension for the sample-wise stats. I.e. we need a sample_stats function like variant_stats.