Always read alleles as strings (not bytes)

[hyanwong]

Fixes #810. Waiting to activate test until I understand what's wrong in #927

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 87.04%. Comparing base (e309fa4) to head (ac8eae9).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #928   +/-   ##
=======================================
  Coverage   87.04%   87.04%           
=======================================
  Files           5        5           
  Lines        1767     1767           
  Branches      310      310           
=======================================
  Hits         1538     1538           
  Misses        140      140           
  Partials       89       89           

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[jeromekelleher]

So this doesn't help with #927 then?

[hyanwong]

No, #927 is independent of this PR, it's just that I noticed the problem when trying to write the unit tests.

[jeromekelleher]

I think you'd be better off doing a quick msprime->Zarr wrapper here until tskit2zarr exists, the sgkit simulator is pretty primitive. This code here should basically do it.

[hyanwong]

This code here should basically do it.

Fab. Thanks Jerome. PR updated with this code. This is now for review (the actual change to formats.py is trivial: it's the test that takes most of the code)

[hyanwong]

@Mergifyio rebase

[mergify]

rebase

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[benjeffery]

@Mergifyio rebase

[mergify]

rebase

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[benjeffery]

@Mergifyio rebase

[mergify]

rebase

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