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.).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

src/simurg/cli/main.py

@@ -910,6 +910,22 @@ def pgx_annotate_cmd(
     _pgx_phenotype(calls, db, out, guideline, force, log_json, debug, quiet, "pgx annotate")
 
 
+@pgx_app.command("coverage")
+def pgx_coverage_cmd(
+    bpm: Annotated[Path, typer.Option("--bpm", help="BPM manifest (required).")],
+    db: Annotated[Path, typer.Option("--db", help="PGx DB built with this manifest (required).")],
+    out: Annotated[Path, typer.Option("--out", help="Output folder.")] = Path("."),
+    log_json: LogJson = False,
+    debug: Debug = False,
+    quiet: Quiet = False,
+) -> None:
+    """Which alleles this array can call: pgx_coverage.tsv (PGX-009, PGX-035)."""
+    from simurg.pipeline.pgx_db import run_coverage
+
+    rep = _reporter("pgx coverage", out, log_json, debug, quiet)
+    run_guarded(rep, lambda: run_coverage(bpm, db, out, rep))
+
+
 @pgx_cn_app.command("train")
 def pgx_cn_train_cmd(
     gtcs: Annotated[Path, typer.Option("--gtcs", help="Folder searched recursively for training GTCs (required).")],