CN: noise-corrected BAF split and complete-loss MF (CYTO-041); Pi tuning harness

Mosaic fraction from the BAF split now subtracts the heterozygous BAF noise (median |BAF-0.5| of unsplit
hets = 0.6745 sigma_b), and a mosaic loss lacking its expected heterozygotes gets MF 1 and is promoted to a
constitutional DEL (CYTO-020). Adds scripts/v2/cn_tune.sh + cn_tune_report.py (GSE165845 rounds on the Pi).

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

tests/unit/test_cn.py

@@ -12,7 +12,7 @@ from typer.testing import CliRunner
 
 from simurg.cli.main import app
 from simurg.cn import hmm
-from simurg.cn.events import Event, Thresholds, apply_thresholds, effective_size, extract
+from simurg.cn.events import Event, Thresholds, _mf_from_baf, apply_thresholds, effective_size, extract
 from simurg.cn.gcwave import gc_correct
 from simurg.cn.model import gc_fractions, population_bfreq
 from simurg.formats.gtc import Gtc, write_gtc
@@ -228,3 +228,21 @@ def test_packaged_cn_data() -> None:  # the built-in mask and cytobands ship wit
         m = read_mask(None, build)
         assert len(m) >= 24 and all(s <= e for iv in m.values() for s, e in iv)
         assert gzip.decompress(_builtin_file(f"cytoBand_{build}.txt.gz")).startswith(b"chr1\t0\t")
+
+
+def test_mf_refinements() -> None:  # CYTO-018 / CYTO-041
+    rng = np.random.default_rng(3)
+    sd = 0.04
+    # unsplit heterozygotes: noise alone must not look like a mosaic split
+    b = 0.5 + rng.normal(0, sd, 400)
+    mf = _mf_from_baf("MDEL", b, sd)
+    assert mf is not None and mf < 0.08
+    assert (_mf_from_baf("MDEL", b, 0.0) or 0) > 0.05  # uncorrected, the old estimate was biased upwards
+    # a true 40 % mosaic loss is still recovered
+    d = 0.4 / (2 * (2 - 0.4))
+    b = 0.5 + rng.choice([-d, d], 400) + rng.normal(0, sd, 400)
+    assert abs((_mf_from_baf("MDEL", b, sd) or 0) - 0.4) < 0.08
+    # no heterozygotes where ~50 are expected: a complete (constitutional) loss
+    b = rng.choice([0.0, 1.0], 100) + rng.normal(0, 0.01, 100)
+    assert _mf_from_baf("MDEL", np.clip(b, 0, 1), sd, np.full(100, 0.3)) == 1.0
+    assert _mf_from_baf("MDEL", np.clip(b, 0, 1), sd, np.full(100, 0.01)) is None  # too few expected