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PGx: full call detail (PGX-016..020, 027/028, 031), pgx coverage (PGX-009/035), full HGVS
ci / test (3.12) (push) Failing after 9s
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- supporting_variants.tsv, unresolved_variants.tsv, variants_not_covered.tsv with PGX-026 metadata; per-allele
  supporting/unresolved sites for both alleles of every candidate; variant_change vs top, distant_alternative,
  unexplained_variants, alleles_impacted_by_no_call, alleles_tested.
- simurg pgx coverage: callable / not_covered / masked / equivalent_to per allele and manifest.
- HGVS on GRCh38 RefSeq accessions (NC_...:g.).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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kemalandClaude Opus 5.5 committed 2026-09-29 16:16:39 +01:00
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commit 4dafce3f18
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src/simurg/core/errors.py
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@@ -175,6 +175,7 @@ CATALOGUE: dict[str, MessageDef] = dict(
_m("E_PGX_VCF_UNINDEXED", "error", "SNV VCFs for PGx must be bgzipped and indexed", "PGX-011"),
_m("E_PGX_VCF_UNSUITABLE", "error", "SNV VCF unsuitable for PGx (squashing/locus filters/foreign)", "PGX-011"),
_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_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"),