CN: per-probe heterozygous BAF spread from the batch reference; --mosaic-prior/--switch-distance; Pi memory guard

scripts/pi_run.sh runs heavy jobs in their own process group and stops them when
MemAvailable drops below a floor (Raspberry Pi OS boots with cgroup_disable=memory, so a
systemd MemoryMax cap is not available); a 360-sample genotype run with cohort QC had
exhausted memory and the OOM killer took down the desktop session.

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

src/simurg/cli/main.py

@@ -733,6 +733,12 @@ def cn_call_cmd(
     svlen_mode: Annotated[str, typer.Option("--svlen-mode", help="signed|positive")] = "signed",
     mask_bed: Annotated[Path | None, typer.Option("--mask-bed", help="Mask BED (default: built-in).")] = None,
     no_bgzip: Annotated[bool, typer.Option("--no-bgzip", help="Plain VCF (cn annotate then refuses it).")] = False,
+    mosaic_prior: Annotated[
+        float, typer.Option("--mosaic-prior", help="Advanced: mosaic states' switch mass.")
+    ] = 0.004,
+    switch_distance: Annotated[
+        float, typer.Option("--switch-distance", help="Advanced: HMM switch distance D (bp).")
+    ] = 5e8,
     threads: ThreadsOpt = 0,
     force: ForceOpt = False,
     log_json: LogJson = False,
@@ -761,7 +767,8 @@ def cn_call_cmd(
     opts = CnCallOptions(
         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, threads=threads, force=force,
+        svlen_mode=svlen_mode, mask_bed=mask_bed, bgzip=not no_bgzip, mosaic_prior=mosaic_prior,
+        switch_d=switch_distance, threads=threads, force=force,
         argv=sys.argv[1:],
     )  # fmt: skip
     run_guarded(rep, lambda: run_cn_call(opts, rep))