v2 CN: cn annotate (JSON report, ISCN 2020, cytobands, genes) and the annotation bundle builder

cn call now records per-chromosome and sample statistics (percent het, LRR stats, BAF
deviations, robust LogR dev, call rate) in the sidecar; cn annotate writes
<sample>.cyto.json (CYTO-033) with ISCN microarray/traditional strings (CYTO-034), bands
and RefSeq gene lists (CYTO-035), LOH summaries, weighted median CN (CYTO-026); annotation
bundle from UCSC cytoBand + ncbiRefSeq (CYTO-036, IN-054). Tests for ISCN strings, gene
overlap, sidecar-missing error and an end-to-end call+annotate.

src/simurg/cli/main.py

@@ -767,6 +767,32 @@ def cn_call_cmd(
     run_guarded(rep, lambda: run_cn_call(opts, rep))
 
 
+@cn_app.command("annotate")
+def cn_annotate_cmd(
+    vcfs: Annotated[Path, typer.Option("--vcfs", help="Output folder of cn call (required).")],
+    bundle: Annotated[
+        Path | None, typer.Option("--annotation-bundle", help="Bundle from scripts/build_annotation_bundle.sh.")
+    ] = None,
+    out: Annotated[Path | None, typer.Option("--out", help="Output folder (default: --vcfs).")] = None,
+    min_qual: Annotated[int, typer.Option("--min-qual", min=0, max=60)] = 20,
+    size_basis: Annotated[str, typer.Option("--size-basis", help="effective|raw")] = "effective",
+    iscn_min_size: Annotated[int, typer.Option("--iscn-min-size", min=0, help="bp")] = 0,
+    force: ForceOpt = False,
+    log_json: LogJson = False,
+    debug: Debug = False,
+    quiet: Quiet = False,
+) -> None:
+    """cn call output -> per-sample JSON report with ISCN 2020 strings, cytobands and genes (CLI-029)."""
+    from simurg.pipeline.cn import CnAnnotateOptions, run_cn_annotate
+
+    if size_basis not in ("effective", "raw"):
+        raise typer.BadParameter("--size-basis effective|raw")
+    rep = _reporter("cn annotate", out or vcfs, log_json, debug, quiet)
+    opts = CnAnnotateOptions(vcfs=vcfs, bundle=bundle, out=out, min_qual=min_qual, size_basis=size_basis,
+                             iscn_min_size=iscn_min_size, force=force)  # fmt: skip
+    run_guarded(rep, lambda: run_cn_annotate(opts, rep))
+
+
 # --------------------------------------------------------------------------------------------------------
 methyl_app = typer.Typer(help="Methylation arrays: control QC, detection, beta values (MET-001).")
 app.add_typer(methyl_app, name="methyl")