PGx CN: scan-date batch warning (PCN-006), CN-consistent BAF evidence (PCN-010, --bafs-in-cn),

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
2026-09-29 17:11:34 +01:00
1 parent aee8caa39e
commit baac9af5c5
@@ -46,6 +46,7 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `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_GUIDELINE` | error | Guideline tables not present in the PGx DB | PGX-025 |
+| `E_PGX_PLATFORM_UNKNOWN` | error | PGx CN platform (LCG/EX) unknown: give --csv or --platform | CLI-032 |
 | `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 |