fix(scripts): count Venn overlap by distinct variant key

[ameynert]

Summary

Analysis-script robustness fix (#88). compare_divref_gnomad.R computed n_gnomad_only = nrow(gnomad) - nrow(divref_in_gnomad), where the subtrahend is a left-join row count. A duplicate variant key in the gnomAD TSV would inflate the overlap and could make n_gnomad_only negative, which euler() rejects.

Now all three Venn counts come from distinct variant-key set operations (intersect / setdiff), which is robust to duplicate keys and identical on clean inputs. The joined frames are still used for the per-variant AF-difference plots.

Verification

• pixi run --environment analysis Rscript -e 'parse(...)' — parses cleanly.

Note

#86 (the other item originally grouped here) is being closed as won't-do per discussion: the untracked sweep config is left as-is, and the population enum is skipped (an incomplete enum would risk rejecting valid runs without an authoritative gnomAD ancestry-code list). So this PR is #88 only.

Closes #88

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Reviewing files that changed from the base of the PR and between 1736c06 and 370b7a1.

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• scripts/compare_divref_gnomad.R

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