Add AC and AN after tskit to zarr conversion

[duncanMR]

Currently, allele counts are not computed when converting from tskit:

It would be helpful to have AC and AN available in the zarr for filtering. It seems like sgkit's count_call_alleles function would be helpful here:

from bio2zarr import tskit as ts2zarr
import numpy as np
import tskit
import sgkit

zarr_path = "data/zarr/test.zarr"
ts_path = "data/simulated/test.trees"

arg = tskit.load(ts_path)
individuals_nodes = np.zeros((arg.num_individuals, 2), dtype=int)
for individual in arg.individuals():
    id = individual.id
    individuals_nodes[id] = individual.nodes
    
ts2zarr.convert(ts_path=ts_path, zarr_path=zarr_path, individuals_nodes=individuals_nodes)
ds = sgkit.load_dataset(zarr_path, consolidated=False)

AC = sgkit.count_call_alleles(ds)["call_allele_count"].sum(dim="samples").values

[jeromekelleher]

I think we should compute these on all conversions (unless already present, or explicitly disabled). We can add some code based on what we're using in vcztools to do this, using the same strategy as for computing local alleles