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sgkit-dev / bio2zarr

Convert bioinformatics file formats to Zarr
Apache License 2.0
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Add descriptions for the fixed fields #262

Closed Will-Tyler closed 3 weeks ago

Will-Tyler commented 3 weeks ago

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.

coveralls commented 3 weeks ago

Coverage Status

coverage: 98.846% (-0.04%) from 98.887% when pulling d8474e935025fdbb2590a8fe2d814213bcc4e849 on Will-Tyler:fixed-field-descriptions into d1920541bf36101d5e3aa7656094901182c0e98b on sgkit-dev:main.

coveralls commented 3 weeks ago

Coverage Status

coverage: 98.888% (+0.001%) from 98.887% when pulling d8474e935025fdbb2590a8fe2d814213bcc4e849 on Will-Tyler:fixed-field-descriptions into d1920541bf36101d5e3aa7656094901182c0e98b on sgkit-dev:main.