CN: per-probe LRR noise from the batch reference (CYTO-042), --probe-lrr-sd/--no-probe-lrr-sd

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

src/simurg/cli/main.py

@@ -739,6 +739,9 @@ def cn_call_cmd(
     switch_distance: Annotated[
         float, typer.Option("--switch-distance", help="Advanced: HMM switch distance D (bp).")
     ] = 5e8,
+    probe_lrr_sd: Annotated[
+        bool, typer.Option("--probe-lrr-sd/--no-probe-lrr-sd", help="Advanced: per-probe LRR noise from the model.")
+    ] = True,
     threads: ThreadsOpt = 0,
     force: ForceOpt = False,
     log_json: LogJson = False,
@@ -768,7 +771,7 @@ def cn_call_cmd(
         out=out, bpm=bpm, model=model, gtcs=gtcs, summary=summary, fasta=fasta, thresholds=th, smoothing=smoothing,
         cn_cap=cn_cap, gc_correct=gc_correct, unknown_sex_policy=unknown_sex_policy, gt_mode=gt_mode,
         svlen_mode=svlen_mode, mask_bed=mask_bed, bgzip=not no_bgzip, mosaic_prior=mosaic_prior,
-        switch_d=switch_distance, threads=threads, force=force,
+        switch_d=switch_distance, probe_lrr_sd=probe_lrr_sd, threads=threads, force=force,
         argv=sys.argv[1:],
     )  # fmt: skip
     run_guarded(rep, lambda: run_cn_call(opts, rep))