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

tests/unit/test_cn.py

@@ -249,3 +249,18 @@ def test_mf_refinements() -> None:  # CYTO-018 / CYTO-041
     mixed = hom.copy()
     mixed[:8] = 2
     assert not complete_loss(mixed, np.full(30, 0.3))
+
+
+def test_probe_lrr_noise() -> None:  # CYTO-042
+    from simurg.cn.model import reference_lrr_spread
+    from simurg.pipeline.cn import _lrr_noise
+
+    rng = np.random.default_rng(5)
+    sd = np.array([0.1] * 50 + [0.3] * 50)
+    lrr = (rng.normal(0, 1, (40, 100)) * sd + rng.normal(0, 0.2, (40, 1))).astype(np.float32)  # + sample offsets
+    spread = reference_lrr_spread(lrr, np.zeros(100, dtype=np.float32))
+    assert abs(float(np.median(spread[:50])) - 0.1) < 0.02 and abs(float(np.median(spread[50:])) - 0.3) < 0.05
+    auto = np.ones(100, dtype=np.bool_)
+    s = _lrr_noise(0.2, auto, spread)
+    assert np.median(s[50:]) / np.median(s[:50]) > 2
+    assert np.all(_lrr_noise(0.2, auto, None) == 0.2)