Remove VCF support #1264
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Remove VCF support #1264
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tomwhite
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jeromekelleher
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Sep 24, 2024
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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). |
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changelog.rstThis 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.