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PGx CN: scan-date batch warning (PCN-006), CN-consistent BAF evidence (PCN-010, --bafs-in-cn),
ci / test (3.12) (push) Failing after 9s
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ci / test (3.13) (push) Failing after 11s
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noise-outlier exclusion + robustness test (PCN-017/EDGE-026), platform from the CSV manifest (CLI-032)

Also: star-allele calls are checked for one manifest/build per run (PGX-011), duplications at the CN cap are
named xN (PGX-022), and tandem names attach supporting variants to their full copy.

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 17:11:34 +01:00
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commit baac9af5c5
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src/simurg/core/errors.py
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@@ -176,6 +176,7 @@ CATALOGUE: dict[str, MessageDef] = dict(
_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_PLATFORM_UNKNOWN", "error", "PGx CN platform (LCG/EX) unknown: give --csv or --platform", "CLI-032"),
_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"),