Tim Millar

> do something a bit nicer if we're not restricted to ASCII That could be great for users who aren't familiar with VCF. I think there will still be some...

Defaulting to the most human readable option makes sense. I'm interested to see what that option would look like!

@tomwhite the freebayes variant caller is a good example for producing a range of allele lengths. The VCFs avialable [here](https://github.com/pfrnz/Example-Tetraploid-Potato-VCF-PRJNA414303) (see releases) were called with freebayes and have allele lengths...

Somewhat related, this is a simple function to get the frequency of each alternate allele in "long form" with shape (variant loci * alts at loci, samples). This works for...

Just noting that I started using `infer_` for the ploidy methods because `count_` didn't sound correct. I don't think `infer_` is great either, but it's the best verb I could...

It's also worth pointing out that in many cases in which the method doesn't have a prefix, the calculated variable has `stat_` as a prefix. E.g. `Tajimas_D` returns variable `stat_Tajimas_D`.

Somewhat related to this, I've been working on code to convert between indices and genotype calls for VCF fields of length `'G'`. These functions can handle arbitrary allele counts and...

A large enough combination of ploidy and n_alleles will result in an index that is too large for an int64. But this shouldn't be a problem for realistic values.

Maybe we should leave it open for now to document the `SGKIT_DISABLE_NUMBA_CACHE` variable. I also wondered if you had a suggestion for testing that setting that variable works as expected...

Just noting that the pca method also hasn't been added to `api.rst` yet.