Genotype ploidy summary functions

It would be useful to be able to summarize ploidy along different dimensions when working with mixed ploidy data. Currently ploidy can only be inferred from the call_genotype array by the number of allele values > -1 at each call.

Methods could be implemented to calculate the following arrays:

• 'call_genotype_ploidy' of shape (variants, samples)
• 'variant_ploidy' of shape (variants, )
• 'sample_ploidy' of shape (samples, )

If ploidy is variable across a given variant or sample then -1 should be returned indicating mixed-ploidy along that dimension.

There was some discussion of this in #243 but it was agreed that this is better as a separate PR #373 (comment)

Example: call_genotype array:

[[[0, 0, -1, -1], [0, 0,  1,  1], [0, 0, 1, 1]],
 [[0, 0,  0, -1], [0, 1, -2, -2], [0, 1, 1, 1]],
 [[0, 0,  0,  1], [0, 0, -2, -2], [0, 0, 0, 0]],]

call_genotype_ploidy array:

[[4, 4, 4],
 [4, 2, 4],
 [4, 2, 4]]

variant_ploidy array:

[ 4,
 -1,
 -1]

sample_ploidy array:

[4, -1, 4]

[timothymillar]

@tomwhite I actually realized a couple of days ago that the methods in #472 still need to be added to the docs and top level API. I’ll put another PR together shortly.

[tomwhite]

Can this be closed now that #472 is merged?