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

SIMURGARRAY_FUNCTIONAL_SPEC.md

@@ -2447,6 +2447,11 @@ about **algorithms or numerics**, the plan wins. Each such conflict found during
     (CYTO-020) to a constitutional DEL with `HIGHFRACTION`. This catches constitutional deletions whose LRR is
     compressed towards the mosaic states.
 
+- **CYTO-042** `§10.2 · v2` **Per-probe LRR noise [OURS].** A model built with `--reference-gtcs` stores each
+  probe's robust LRR SD across the reference (1.4826·MAD after removing each sample's median and the probe's
+  reference median). `cn call` scales the sample's LRR emission SD per probe by that spread relative to the autosomal
+  median spread, clipped to [0.5, 3]. Without the column, or with `--no-probe-lrr-sd`, every probe uses the sample SD.
+
 ---
 
 ## 7. Targeted PGx copy number (v2)
@@ -3723,6 +3728,7 @@ Generated from the item tags (`build.py`). Phases: P0–P10 as in plan §18; `v2
 | CYTO-039 | Batch scale | §10, §19 | v2 | D-9, E-35 |
 | CYTO-040 | Degenerate samples | §10 | v2 | E-35 |
 | CYTO-041 | MF refinements | §10.3 | v2 | K-027 |
+| CYTO-042 | Per-probe LRR noise | §10.2 | v2 | K-027 |
 | PCN-001 | Region catalogue | §11 | v2 | B-23, C-G25, D-10 |
 | PCN-002 | Genotype every region [EMU] | §11 | v2 | B-23 |
 | PCN-003 | Inputs | §11 | v2 | A-G37 |