PGx: full call detail (PGX-016..020, 027/028, 031), pgx coverage (PGX-009/035), full HGVS

- 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.).
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kemal committed 2026-09-29 16:16:39 +01:00
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@@ -106,6 +106,7 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
| `W_PGX_BATCH_BELOW_RECOMMENDED` | warning | Fewer passing samples than recommended | PCN-004 |
| `W_PGX_BATCH_COMPOSITION` | warning | Batch spans several lots/batches or > 14 days of scans | PCN-006 |
| `W_PGX_NO_ALT_CONTIG` | warning | FASTA lacks a contig carrying a PGx region; REF written as N | IN-062 |
| `W_PGX_NO_PROBE_MAP` | warning | The PGx DB has no probe map for this manifest | PGX-035 |
| `W_PGX_REGION_FEW_PROBES` | warning | PGx CN region has fewer than 10 unmasked probes | PCN-008 |
| `W_QC_LABEL_SANITIZED` | warning | Dataset label was sanitized | QC-042 |
| `W_QC_NO_BAF` | warning | GTC has no B-allele frequencies; contamination not estimated | QC-064 |