Make sure that variant.count() returns alleles in an order

[hyanwong]

And document/test it.

We might want to match up the frequencies with the indexes in .genotypes. As we are simply looping over .alleles to make the counts (and frequencies), all we need to do is make sure the None entry is at the end.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.67%. Comparing base (300ea4f) to head (cae652f).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3471   +/-   ##
=======================================
  Coverage   91.67%   91.67%           
=======================================
  Files          38       38           
  Lines       32188    32188           
  Branches     5151     5151           
=======================================
  Hits        29509    29509           
  Misses       2346     2346           
  Partials      333      333           

Flag	Coverage Δ
C	82.23% <ø> (ø)
c-python	77.54% <ø> (ø)
python-tests	96.43% <100.00%> (ø)
python-tests-no-jit	33.19% <0.00%> (ø)

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Components	Coverage Δ
Python API	98.72% <100.00%> (ø)
Python C interface	91.23% <ø> (ø)
C library	91.24% <ø> (ø)

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