ArrayTrain (plan §12): simurg train — EGT cluster files from a cohort's GTCs

- simurg/train/clusters.py: vectorised per-locus θ mixture (AA/AB/BB + outlier component, θ-ordered bounds),
  cluster selection and merging, lone clusters homozygous, missing clusters imputed by cross-locus regression
  per assay type, cluster_sep and train (GenTrain-field) scores.
- formats/egt.py: write_egt (EGT v3, data block 9, round-trips through the reader).
- pipeline/train.py: normalised θ/R from GTC raw X/Y + transforms, sex-aware (X females, Y males, MT haploid),
  intensity-only loci as one R cluster.
- scripts/train/concordance_chr.py: array vs 1000G 30x on one chromosome.
Demo (36 GSA v4 PGx arrays, chr22 vs 1000G): trained 99.29 % / NRD 2.6 % vs vendor EGT 99.57 % / 1.55 %.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

src/simurg/core/errors.py

@@ -177,6 +177,7 @@ CATALOGUE: dict[str, MessageDef] = dict(
         _m("E_PGX_GUIDELINE", "error", "Guideline tables not present in the PGx DB", "PGX-025"),
         _m("W_PGX_NO_PROBE_MAP", "warning", "The PGx DB has no probe map for this manifest", "PGX-035"),
         _m("E_PGX_PLATFORM_UNKNOWN", "error", "PGx CN platform (LCG/EX) unknown: give --csv or --platform", "CLI-032"),
+        _m("E_TRAIN_TOO_SMALL", "error", "Too few GTCs to train a cluster file", "plan §12"),
         _m("E_PGX_SOURCE", "error", "PGx source tables missing; run scripts/pgx/fetch_sources.sh", "PGX-001"),
         # --- methylation control QC (MET-001 .. MET-018) -------------------------------------------------
         _m("E_METH_NO_ASSAY", "error", "Probe section not found", "MET-002"),