Handle case where GT is defined in header, but not used in FORMAT

sgkit-dev / bio2zarr

Convert bioinformatics file formats to Zarr

Apache License 2.0

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Handle case where GT is defined in header, but not used in FORMAT #270

Closed tomwhite closed 2 weeks ago

tomwhite commented 2 weeks ago

Fixes #267

This is based on #269, which should be merged first.

tomwhite commented 2 weeks ago

I think this is failing due to variant_id and variant_ID clashing on macOS' case-sensitive filesystem.

Hopefully https://github.com/sgkit-dev/hypothesis-vcf/pull/4 will fix it.

jeromekelleher commented 2 weeks ago

Thanks @tomwhite - can you rebase on main please?

jeromekelleher commented 2 weeks ago

LGTM!

You'll need to update the numbers in the du test because of the newly added file (sorry, it was a stupid idea using this as the test data!)

coveralls commented 2 weeks ago

coverage: 98.855% (+0.001%) from 98.854% when pulling e0ce82a0485ce41a07cf5db8c404af49fcfb53eb on tomwhite:missing-gt into 02b595d0d3265473926bbb5a1acf9b077c0230e3 on sgkit-dev:main.