PGx DB: pgx db build from CPIC (PGX-001..005, IN-053, CLI-035)

- scripts/pgx/fetch_sources.sh: CPIC API tables (CC0) into a dated folder with version and hashes.
- simurg/pgx/db.py: CPIC HGVS locations and values -> left-normalised VCF variants (SNV, del, ins, dup,
  repeats, delins, chrM); IUPAC values are core-allele wildcards; alleles without definitions are flagged.
- pipeline/pgx_db.py: deterministic SQLite (content-hash name), probe_map via the SNV VCF site mapper;
  GSA v4 PGx: 22 genes, 1354 alleles, 5002 probe links; two builds byte-identical.

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

THIRD_PARTY_NOTICES.md

@@ -15,6 +15,7 @@ used only as external subprocess oracles and are not copied or linked.
 | [PyO3](https://github.com/PyO3/pyo3), [rust-numpy](https://github.com/PyO3/rust-numpy), [ndarray](https://github.com/rust-ndarray/ndarray) and their Rust dependencies | MIT / Apache-2.0 / BSD-2-Clause | Compiled into the optional `simurg_core` extension (`rust/simurg-core`); list with `cargo tree` |
 | [UCSC Genome Browser](https://genome.ucsc.edu/) `cytoBand` tables (hg38, hg19) and `ncbiRefSeq` (RefSeq transcripts, NCBI) | Free for all uses (UCSC data terms; RefSeq is public domain) | `simurg/cn/data/cytoBand_GRCh3{7,8}.txt.gz` and the derived centromere/acrocentric mask BEDs are shipped; `scripts/build_annotation_bundle.sh` downloads cytoBand + ncbiRefSeq for gene lists; `simurg/pgx/data/pgx_cn_regions.GRCh38.v1.bed` is derived from ncbiRefSeq exon coordinates (`scripts/pgx/build_cn_regions.py`) |
 | [illuminaio](https://github.com/HenrikBengtsson/illuminaio) | GPL-2 | Documentation of IDAT field codes only; oracle via subprocess |
+| [CPIC](https://cpicpgx.org) database via the CPIC API (allele definitions, allele function, diplotype→phenotype tables) | CC0 1.0 | downloaded by `scripts/pgx/fetch_sources.sh` into `data/` (never committed); `simurg pgx db build` derives the local PGx DB from it; source version and file hashes are recorded in the DB `meta` table |
 
 ## BSD-2-Clause (BeadArrayFiles, verbatim from its README)