docs(genotype): split the genotype guide into 4 pages + AIRR-reader clarity pass - #10
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… + benchmarking pages The genotype guide had grown to ~717 lines across five feature PRs. Split it into a focused overview (what a genotype is, building, recombination, receptor revision, novel alleles, ground truth) plus three companion pages — sampling & population priors, cohorts, and benchmarking inference — mirroring the clonal guide cluster. Nav updated; cross-links added; mkdocs build clean.
…RR-vs-extension columns, model-assumption limitations, VDJbase freq loading, partis output Address an AIRR-community review: explain the OGRDB-derived cartridge's gene/allele labels vs IMGT (sourced from ogrdb.airr-community.org; no invented F/G semantics), gloss 'cartridge'/manifest/checksum, flag GenAIRR extension columns vs AIRR-standard fields, clarify expose_provenance gating, surface model assumptions in Limitations, add a concrete population-frequency loading snippet, and give a verified partis output pointer.
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Summary
The genotype guide had grown to ~717 lines across the five genotype PRs (V1, population priors, cartridge plane, cohorts, receptor revision). This splits it into a focused 4-page cluster (mirroring the clonal guides) and applies a clarity pass based on an AIRR-community-reader review.
Docs-only change — no source/code touched.
Page split
genotype.md(overview)genotype-priors.mdGenotype.sample+ cartridge population-prior plane (author/estimate/draw/audit) + loading population frequenciesgenotype-cohorts.mdrun_cohort+CohortResultgenotype-benchmarking.mdNav updated to a 4-entry cluster; cross-links added; the figure asset still resolves.
AIRR-reader clarity pass
IGHVF1-G1*01labels vs IMGT (IGHV1-69*01), sourced from OGRDB; deliberately does not invent theF/Gsemantics (undocumented) and notes OGRDB's own published set uses IMGT names.cartridge(+ link), andmanifest/checksum.haplotype,truth_*,original_v_call,receptor_revision_applied) with a link to the AIRR Rearrangement schema.expose_provenancegating (always-on vs gated fields).--parameter-diroutput pointer.Test plan
mkdocs buildclean — all four pages render, no broken-link/genotype warnings.site/gitignored.