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Remove VCF support #1264

Merged
merged 9 commits into from
Oct 10, 2024
Merged

Remove VCF support #1264

merged 9 commits into from
Oct 10, 2024

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tomwhite
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@tomwhite tomwhite commented Sep 24, 2024

  • User visible changes (including notable bug fixes) are documented in changelog.rst

This removes the VCF reading and writing functionality from sgkit, since better implementations are available (and being actively developed) in the bio2zarr and vcztools projects.

I had hoped to remove only the VCF reading functions in this PR, but the writing side is quite entwined (e.g. due to testing), so it would be much easier to remove them both at once. We haven't deprecated the VCF write functions yet (#1245), since that is waiting on releasing vcztools.

So I've marked this as a draft as it's not ready to be merged yet. It would be good to get people's feedback though as this is quite a big change.

@tomwhite tomwhite added documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats labels Sep 24, 2024
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@jeromekelleher jeromekelleher left a comment

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+1 !!

It mainly looks like such a big diff because of all the tests, and data, but that's all ported to bio2zarr, pretty much.

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tomwhite commented Oct 2, 2024

We discussed this in the developers meeting and the consensus there was it would be good to merge this as it removes a lot of unsupported code.

All tests are now passing except for the ones that use NumPy 2, which will need a bio2zarr release (see sgkit-dev/bio2zarr#256).

@tomwhite tomwhite merged commit f64dddb into sgkit-dev:main Oct 10, 2024
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This was referenced Oct 10, 2024
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