PGx star alleles: pgx star-allele call (PGX-011..021), probe masks vs 1000G, GeT-RM validation (K-029)

- simurg/pgx/star.py: solver-free diplotype enumeration incl. CN forms (deletion, xN), wildcards, array-equivalence
  classes, raw_score/score with CPIC frequency priors; calibrated error model (spec PGX-012 amended).
- pipeline/pgx_star.py: DB gene models, SNV + PGx CN VCF evidence, masks, diplotype_summary.tsv + pgx_calls.json.
- scripts/pgx: derive_masks.py (array vs 1000G 30x over HTTPS, GS calibration), getrm_truth.py,
  validate_star_getrm.py.
- GSA v4 PGx demo vs GeT-RM (16 CEPH): 100/109 gene calls; CYP2D6/2C19/2C9 41/45 (docs/validation/V2_pgx_star.md).

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

docs/messages.md

@@ -44,8 +44,11 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_OUTPUT_EXISTS` | error | Outputs already exist; use --force or --resume | CLI-010 |
 | `E_PGX_BATCH_TOO_SMALL` | error | Too few (passing) samples in the batch for PGx CN calling | PCN-004 |
 | `E_PGX_CN_FAILED` | error | PGx CN calling failed for the sample | PCN-002 |
+| `E_PGX_CN_MISSING` | error | A sample has no PGx CN VCF (give --no-cn to run without) | PGX-011 |
 | `E_PGX_SOURCE` | error | PGx source tables missing; run scripts/pgx/fetch_sources.sh | PGX-001 |
 | `E_PGX_TRAIN_TOO_SMALL` | error | Too few (passing) samples to train a PGx CN model | PCN-005 |
+| `E_PGX_VCF_UNINDEXED` | error | SNV VCFs for PGx must be bgzipped and indexed | PGX-011 |
+| `E_PGX_VCF_UNSUITABLE` | error | SNV VCF unsuitable for PGx (squashing/locus filters/foreign) | PGX-011 |
 | `E_QC_CONFIG_EXT` | error | QC config file must be .yaml or .yml | QC-021 |
 | `E_QC_CONFIG_MISSING` | error | QC config file does not exist | QC-021 |
 | `E_QC_CONFIG_PARSE` | error | QC config file is not valid YAML | QC-021 |