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.
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kemal committed 2026-09-29 13:24:54 +01:00
1 parent cc8c934167
commit 82d6153a63
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@@ -171,6 +171,7 @@ CATALOGUE: dict[str, MessageDef] = dict(
_m("W_PGX_NO_ALT_CONTIG", "warning", "FASTA lacks a contig carrying a PGx region; REF written as N", "IN-062"),
_m("W_PGX_BATCH_COMPOSITION", "warning", "Batch spans several lots/batches or > 14 days of scans", "PCN-006"),
_m("E_PGX_CN_FAILED", "error", "PGx CN calling failed for the sample", "PCN-002"),
_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"),
_m("E_METH_NO_CONTROLS", "error", "Missing control probes in manifest", "MET-002"),