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feat: Genotypes.check_maf() method #124

Merged
merged 12 commits into from
Oct 25, 2022
Merged

feat: Genotypes.check_maf() method #124

merged 12 commits into from
Oct 25, 2022

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aryarm
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@aryarm aryarm commented Oct 19, 2022

See #19


This PR removes the to_MAC() method and the AAF field from the variants property of the Genotypes class. Both are breaking changes to the Genotypes API.

Instead, we introduce a new check_maf() method, which offers a cleaner, more streamlined interface.

genotypes = data.Genotypes.load('tests/data/simple.vcf.gz')
genotypes.check_maf(threshold=0.05)

This PR also uses black to reformat many of the files in our codebase to follow Python's PEP8 style standards. If I thought a file would require too many changes to bring it up to date with the standards, I just excluded it from formatting by listing it in the extend-exclude section of our pyproject.toml file.

Once this PR is merged, we'll be able to check the formatting of all of the code in our repository with a simple command (black .). Hopefully, this will make it easier to move forward with automated style checks in #117

@aryarm aryarm merged commit dd4fa9e into main Oct 25, 2022
@aryarm aryarm deleted the ref/genotypes-af branch October 25, 2022 17:03
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