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Add descriptions for the fixed fields #262

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merged 2 commits into from
Jul 1, 2024

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Will-Tyler
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Description

This pull request adds descriptions for the fixed fields in VCF Zarr. The fixed VCF Zarr fields are listed here, and descriptions for their corresponding VCF fields are found in the VCF specification. I consulted the specification for VCFv4.3 to come up with the short descriptions.

This pull request closes #124.

Approach

I add a dictionary relating the names of the fixed fields to their descriptions. ZarrArraySpec uses the dictionary during post-initialization to set the description field. The description is then set as an attribute of the Zarr array by the VcfZarrWriter in init_array, which is called by init.

Testing

So far, I have only updated a unit test in test_vcz.py that fails with the new changes.

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Coverage Status

coverage: 98.846% (-0.04%) from 98.887%
when pulling d8474e9 on Will-Tyler:fixed-field-descriptions
into d192054 on sgkit-dev:main.

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Coverage Status

coverage: 98.888% (+0.001%) from 98.887%
when pulling d8474e9 on Will-Tyler:fixed-field-descriptions
into d192054 on sgkit-dev:main.

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@jeromekelleher jeromekelleher left a comment

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Very nice, thanks

@jeromekelleher jeromekelleher merged commit 597b1fa into sgkit-dev:main Jul 1, 2024
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Add description to zarr arrays for fixed fields
3 participants