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

Merged
merged 3 commits into from
Jul 9, 2024
Merged

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

merged 3 commits into from
Jul 9, 2024

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tomwhite
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@tomwhite tomwhite commented Jul 8, 2024

Fixes #267

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

@tomwhite
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tomwhite commented Jul 8, 2024

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

Hopefully sgkit-dev/hypothesis-vcf#4 will fix it.

@jeromekelleher
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Thanks @tomwhite - can you rebase on main please?

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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!)

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coveralls commented Jul 9, 2024 •
edited
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Coverage Status

coverage: 98.855% (+0.001%) from 98.854%
when pulling e0ce82a on tomwhite:missing-gt
into 02b595d on sgkit-dev:main.

@jeromekelleher jeromekelleher merged commit 3e23768 into sgkit-dev:main Jul 9, 2024
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Parsing fails for VCF with GT in header but not in FORMAT field
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