docs(genotype): split the genotype guide into 4 pages + AIRR-reader clarity pass (#10)

* docs(genotype): split the mega-guide into overview + priors + cohorts + 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.

* docs(genotype): AIRR-reader clarity pass — naming/cartridge gloss, AIRR-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.

Author: MuteJester

mkdocs.yml

@@ -208,6 +208,9 @@ nav:
       - Clonal lineage trees: guides/clonal-lineage.md
       - Clonal repertoires (TCR & abundance): guides/clonal-repertoire.md
       - Genotypes (per-individual diploid): guides/genotype.md
+      - Genotype sampling & population priors: guides/genotype-priors.md
+      - Genotype cohorts: guides/genotype-cohorts.md
+      - Benchmarking genotype inference: guides/genotype-benchmarking.md
       - Junction N/P additions: guides/junction-additions.md
       - Targeted SHM rates: guides/shm-targeting.md
       - Corruption + sequencing artefacts: guides/corruption-sequencing.md

site_docs/guides/genotype-benchmarking.md

@@ -0,0 +1,162 @@
+# Benchmarking genotype inference
+
+
+The point of simulating from a *known* genotype is that you can run a
+genotype-inference tool on the resulting repertoire and score it against the
+planted truth — with no real-data uncertainty about what the right answer is.
+
+The recipe is the same for any tool:
+
+1. Build a `Genotype`, simulate a repertoire, write the AIRR table
+   (`result.to_tsv(...)`) and/or reads FASTA, and the ground truth
+   (`genotype.to_tsv(...)`).
+2. Run the inference tool to recover the per-individual allele set.
+3. Compare recovered vs planted: presence/absence, zygosity, and (for
+   discovery tools) any novel alleles.
+
+### Worked example: TIgGER and IgDiscover recover a planted genotype
+
+To show this end to end we planted a diploid IGH genotype in `human_igh` —
+**3 heterozygous** V genes (two alleles each), **3 homozygous** (one allele),
+and **3 fully deleted** genes — and filled the rest from the reference. We
+simulated 4,000 reads with light SHM, then ran two independent AIRR
+genotype-inference tools on the result:
+[**TIgGER**](https://tigger.readthedocs.io) (Immcantation; consumes the AIRR
+table) and [**IgDiscover**](https://igdiscover.se) (germline discovery from the
+raw reads, with its own IgBLAST).
+
+Because GenAIRR already emits AIRR records with `v_call` **and**
+`sequence_alignment`, TIgGER's `inferGenotype` consumes the rearrangement table
+**directly — no separate IgBLAST step is needed**:
+
+```r
+library(tigger); library(airr)
+rep    <- read_rearrangement("repertoire.tsv")     # GenAIRR's AIRR output
+germ_v <- readIgFasta("germline_V.fasta")          # cartridge V germline (names match v_call)
+# find_unmutated=TRUE asks inferGenotype to base calls on unmutated reads per
+# allele; the light-SHM simulation below provides them.
+geno   <- inferGenotype(rep, germline_db = germ_v, find_unmutated = TRUE)
+plotGenotype(geno)
+```
+
+The `germline_V.fasta` written below is **ungapped** — fine for `inferGenotype`;
+if you go on to TIgGER's IMGT-gapped steps (`reassignAlleles`) supply a gapped V
+germline instead.
+
+TIgGER recovered the planted genotype **exactly**: every heterozygous gene → two
+alleles, every homozygous gene → one, every deleted gene → **absent**. Across all
+52 V genes, allele-presence **precision = 1.00**, **recall = 1.00**, and the
+per-gene allele count matched the truth for **52/52** genes.
+
+**IgDiscover**, run on the raw reads with the cartridge as its starting database,
+independently agreed: **precision = 1.00** (zero false-positive alleles),
+**recall = 0.96** (50/52 carried alleles), with **all three deletions correct**
+and **all heterozygous genes fully resolved** (both alleles recovered). The two
+missed alleles were low-expression single-copy genes below IgDiscover's default
+expression threshold — a tool-tuning matter, not a simulation artefact.
+
+!!! note "These are upper-bound numbers on idealised data"
+    Near-perfect recovery is expected here: the simulated germline names match the
+    scoring database exactly, SHM is light and substitution-only, and there are no
+    indels, chimeras, or contamination. Real data is harder — which is the point
+    of being able to **dial difficulty up** (heavier SHM via `mutate`, sequencing
+    artefacts via the corruption passes, lower per-allele depth) and re-measure
+    how each tool degrades against the same known truth.
+
+![GenAIRR-simulated genotype recovered by TIgGER and IgDiscover: planted vs inferred allele counts agree for every gene](../assets/genotype-tigger-recovery.png)
+
+*(A) The nine study genes: both tools' inferred allele counts match the planted
+zygosity for each (heterozygous → 2, homozygous → 1, deleted → 0). (B) All 52 V
+genes fall on the agreement diagonal; presence precision = 1.00 for both tools,
+recall 1.00 (TIgGER) / 0.96 (IgDiscover), zero false-positive alleles, all
+deletions correct.*
+
+### Reproduce it
+
+This builds the **exact** genotype behind the figure — 3 heterozygous, 3
+homozygous, and 3 deleted study V genes, the rest filled from the reference —
+simulates 4,000 reads with light SHM at `seed=7`, and writes every input the two
+tools need plus the ground truth to score against:
+
+```python
+import GenAIRR as ga
+import GenAIRR.data as gdata
+from GenAIRR.genotype import Genotype
+
+cfg = gdata.HUMAN_IGH_OGRDB
+HET = ["IGHVF1-G1", "IGHVF1-G2", "IGHVF1-G3"]   # 2 alleles each
+HOM = ["IGHVF2-G4", "IGHVF3-G5", "IGHVF3-G6"]   # 1 allele
+DEL = ["IGHVF3-G7", "IGHVF3-G8", "IGHVF3-G9"]   # deleted (both chromosomes)
+
+g = Genotype.from_dataconfig(cfg).complete_from_reference("homozygous_first_reference")
+for gene in HET:
+    a0, a1 = (a.name for a in cfg.v_alleles[gene][:2])
+    g.heterozygous(gene, a0, a1)
+for gene in HOM:
+    g.homozygous(gene, cfg.v_alleles[gene][0].name)
+for gene in DEL:
+    g.delete_gene(gene, haplotype="both")
+g.with_subject("DONOR01")
+
+res = (
+    ga.Experiment.on(cfg).with_genotype(g).recombine()
+      .mutate(rate=0.004)                       # light SHM, as in real data
+      .run_records(n=4000, seed=7, expose_provenance=True)
+)
+
+res.to_tsv("repertoire.tsv")                    # AIRR table → TIgGER
+g.to_tsv("truth_genotype.tsv")                  # ground truth to score against
+
+with open("reads.fasta", "w") as fh:            # raw reads → IgDiscover / partis
+    for r in res:
+        fh.write(f">{r['sequence_id']}\n{r['sequence'].upper()}\n")
+
+with open("germline_V.fasta", "w") as fh:       # cartridge V germline (names match v_call)
+    for gene, alleles in cfg.v_alleles.items():
+        for a in alleles:
+            fh.write(f">{a.name}\n{a.ungapped_seq.upper()}\n")
+```
+
+**Score it.** Run TIgGER (R snippet above) on `repertoire.tsv`, or IgDiscover on
+`reads.fasta` with the cartridge as its starting database
+(`igdiscover init --database db/ --single-reads reads.fasta project/ && cd project
+&& igdiscover run`). Then compare each tool's per-gene allele set against
+`g.to_table()` (the planted truth): allele-presence precision/recall, zygosity,
+and deletion calls. With the genotype above this yields TIgGER precision/recall
+1.00 (52/52 genes) and IgDiscover precision 1.00 / recall 0.96 — the figure.
+
+### Running other tools on the same data
+
+The only difference between tools is whether they consume the **AIRR table**
+(TIgGER) or the **raw reads** (`reads.fasta`, which you can write from `result`),
+running their own aligner:
+
+- **[IgDiscover](https://igdiscover.se)** — germline *discovery* from reads (its
+  own IgBLAST + iterative filtering). Initialise with the cartridge germline as
+  the starting database and the simulated reads, then run the pipeline; the
+  `final/database/V.fasta` expressed-allele set is the recovered genotype:
+
+  ```bash
+  igdiscover init --database db/ --single-reads reads.fasta project/
+  cd project && igdiscover run
+  ```
+
+- **[partis](https://github.com/psathyrella/partis)** — HMM annotation with
+  per-sample germline inference. Start from the cartridge germline and cache
+  parameters into a parameter directory:
+
+  ```bash
+  partis cache-parameters --infname reads.fa \
+      --initial-germline-dir db/ --parameter-dir out/
+  ```
+
+  partis infers a per-sample germline set during this step (starting from
+  `--initial-germline-dir`) and writes it under `--parameter-dir`; see partis's
+  [germline-inference docs](https://github.com/psathyrella/partis/blob/main/docs/germline-inference.md)
+  for the exact output location. Score that recovered allele set against
+  `g.to_table()` the same way.
+
+Because the genotype is planted, every tool is scored identically: recovered
+allele set vs `genotype.to_table()` — presence precision/recall, zygosity, and
+deletion calls.
+

site_docs/guides/genotype-cohorts.md

@@ -0,0 +1,60 @@
+# Genotype cohorts
+
+A single genotype models one subject. To simulate a **cohort** — many subjects,
+each with their own genotype — use `run_cohort`. It runs the single-subject path
+once per subject and collects the results:
+
+```python
+import GenAIRR as ga
+import GenAIRR.data as gdata
+from GenAIRR.genotype import Genotype
+
+cfg = gdata.HUMAN_IGH_OGRDB
+# one sampled genotype per donor
+donors = [Genotype.sample(cfg, seed=s, subject_id=f"donor_{s}") for s in range(5)]
+
+cohort = ga.Experiment.on(cfg).recombine().run_cohort(
+    donors, n_per_subject=200, seed=0, expose_provenance=True)
+
+cohort.subject_ids            # ['donor_0', ..., 'donor_4']
+len(cohort)                   # 1000 total records
+cohort.result_for("donor_2")  # that donor's SimulationResult
+cohort.to_csv("cohort.csv")   # combined, subject-tagged, unique sequence_id
+```
+
+`run_cohort` returns a `CohortResult`:
+
+- `.subject_ids` / `.genotypes` / `.results` — per-subject, in input order.
+- `.result_for(sid)` / `.refdata_for(sid)` — one subject's `SimulationResult` and
+  the reference it ran against. Each subject can carry different novel/private
+  alleles, so its *effective* germline (base catalogue + that subject's novels)
+  differs; keeping it per subject is what lets `validate_records` and
+  novel-allele truth calls stay correct across a heterogeneous cohort.
+- `.records` — a fresh, subject-tagged, `sequence_id`-namespaced concatenation
+  (each `sequence_id` is `"{subject_id}_{...}"`, so combined AIRR/FASTA export
+  never collides).
+- `.to_dataframe()` / `.to_csv()` / `.to_fasta()` — combined export over a stable
+  union of columns.
+
+**Record counts.** `n_per_subject` applies to all subjects; pass `counts` (a
+parallel list, same length as the genotypes) to vary per-subject repertoire
+sizes. A count of `0` is allowed — that subject appears in the cohort with zero
+records.
+
+```python
+cohort = ga.Experiment.on(cfg).recombine().run_cohort(
+    donors, counts=[500, 200, 0, 1000, 300], seed=0)
+```
+
+**Subject IDs.** Taken from each genotype's `subject_id`; if none are set they are
+auto-assigned `subject_0..N-1`. Mixed (some set, some not) or duplicate IDs raise.
+
+**Determinism.** Each subject gets an independent sub-seed derived from `seed`, so
+a cohort is fully reproducible and subjects are independent.
+
+`run_cohort` is mutually exclusive with `with_genotype`, `restrict_alleles`, and
+`recombine(*_allele_weights=...)` (the genotype owns allele expression). It
+**supports** `receptor_revision` (each subject's replacement V is restricted to
+its own carried alleles); clonal forks are not combined with a cohort in this
+release.
+