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

src/simurg/cn/hmm.py

@@ -8,7 +8,8 @@ weights, switch model]
 * Diploid regions: CN0, CN1, CN2, CN2-LOH, CN3, CN3-LOH, CN4 and mosaic loss / gain / CN-LOH at cell fractions
   0.2, 0.4, 0.6, 0.8. Haploid regions (male X outside PAR, male Y): CN0, CN1, CN2 and mosaic gain/loss relative to
   the region's median LRR.
-* LRR ~ (1−ε)·N(µ_state, σ) + ε·U(−5, 3); σ = 1.4826·MAD of the sample's autosomal LRR (floor 0.08); CN0 σ = 2.
+* LRR ~ (1−ε)·N(µ_state, σ) + ε·U(−5, 3); σ = 1.4826·MAD of the sample's autosomal LRR (floor 0.08), scaled per
+  probe by the reference's LRR spread (CYTO-042); CN0 σ = 2.
   Mosaic means interpolate linearly between the constitutional means by the cell fraction.
 * BAF ~ (1−ε)·Σ_g w_g N(b_g, σ_b) + ε·U(0, 1); genotype weights from the probe's PFB p (binomial in the copy
   number; LOH: {0: 1−p, 1: p}); mosaic heterozygotes split into the two bands 0.5 ± d(f).
@@ -106,7 +107,7 @@ def _norm(x: F64, mu: float, sd: float | F64) -> F64:
 
 @dataclass
 class Params:
-    lrr_sd: float
+    lrr_sd: float | F64  # scalar or per probe (CYTO-042)
     baf_sd: float
     lrr_offset: float = 0.0  # added to every state mean (haploid regions: the region's median LRR)
     switch_d: float = SWITCH_D