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PGx phenotypes: pgx phenotype|annotate (PGX-024..028, CLI-034)
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CPIC lookups by allele function counts or activity values (duplications N x activity, *5/*0 = 0, total-score
fallback), Indeterminate when feasible solutions disagree or an allele is not in the guideline; per-sample
simurg.pgx/1 JSON and diplotype_annotations.tsv with PGX-026 metadata lines.

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 16:03:27 +01:00
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docs/messages.md
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@@ -45,6 +45,7 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
| `E_PGX_BATCH_TOO_SMALL` | error | Too few (passing) samples in the batch for PGx CN calling | PCN-004 |
| `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_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 |