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Methods doc categories #1146

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merged 1 commit into from
Nov 28, 2023
Merged

Methods doc categories #1146

merged 1 commit into from
Nov 28, 2023

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benjeffery
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@benjeffery benjeffery commented Nov 27, 2023 •
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I've had a go at subsections in the method list as it was getting unwieldy.

jeromekelleher
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LGTM, minor reshuffle suggested

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mergify bot commented Nov 27, 2023

This PR has conflicts, @benjeffery please rebase and push updated version 🙏

@mergify mergify bot added the conflict PR conflict label Nov 27, 2023
@benjeffery benjeffery force-pushed the methods-org branch 2 times, most recently from 409c94a to 383bcef Compare November 27, 2023 12:49
@mergify mergify bot removed the conflict PR conflict label Nov 27, 2023
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Good suggestions - fixed and rebased.

@benjeffery benjeffery marked this pull request as ready for review November 27, 2023 12:50
jeromekelleher
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LGTM

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Looks great - @timothymillar, @tomwhite what do you think of this sectioning?

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##              main     #1146   +/-   ##
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LGTM

timothymillar
timothymillar reviewed Nov 27, 2023
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docs/api.rst Outdated
@@ -95,34 +98,69 @@ Methods
count_cohort_alleles
count_variant_alleles
count_variant_genotypes
individual_heterozygosity
observed_heterozygosity
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@timothymillar timothymillar Nov 27, 2023 •
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observed_heterozygosity should really be in the pop-gen section.

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Probably also individual heterozygosity?

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It really depends how widely you want to cast the net. Currently, the pop-gen section only includes methods that generalize over 'cohorts' (and 'windows'). individual_heterozygosity is only for individuals and, in the diploid case, it just marks heterozygous and homozygous calls as 1 or 0 respectively.

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LGTM aside from the above suggestion. The "Pedigree and Relatedness" section fells a little awkward, but I can't think of a better suggestion. I would almost suggest renaming it to just "Relatedness" or "Kinship and Relatedness". But it's not clear where pedigree_contribution would go.

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LGTM aside from the above suggestion. The "Pedigree and Relatedness" section fells a little awkward, but I can't think of a better suggestion. I would almost suggest renaming it to just "Relatedness" or "Kinship and Relatedness". But it's not clear where pedigree_contribution would go.

Just “Relatedness” should cover it well - there are many facets behind that word

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OK, let's move heterozygosity to popgen for now, and rename the "pedigree.. " section to "Relatedness" and we're good to go I think.

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Suggestions applied!

@jeromekelleher jeromekelleher added the auto-merge Auto merge label for mergify test flight label Nov 28, 2023
@mergify mergify bot merged commit 298fbbc into sgkit-dev:main Nov 28, 2023
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@benjeffery @jeromekelleher @codecov-commenter @tomwhite @timothymillar @gregorgorjanc