v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)

GSE165845 360 arrays: constitutional DEL/DUP calls 77/74 % in the NYGC SV truth, LOH
reproduced across replicates 74 %; mosaic calls are mostly false positives (12-23 %),
sensitivity for 25 kb-1 Mb events 7-13 % at QUAL >= 20. All samples had been flagged
SampleQuality by the summary logr_dev (cluster-file mismatch); the gate now uses the SD
of the LRR after the batch reference. Validation script: --ignore-filter.

scripts/v2/cn_validate_truth.py

@@ -47,6 +47,7 @@ def main() -> int:
     ap.add_argument("--truth", required=True, type=Path)
     ap.add_argument("--bpm", required=True)
     ap.add_argument("--min-qual", type=float, default=20)
+    ap.add_argument("--ignore-filter", action="append", default=[], help="FILTER values not to exclude (repeatable)")
     ap.add_argument("--out", required=True, type=Path)
     a = ap.parse_args()
     a.out.mkdir(parents=True, exist_ok=True)
@@ -66,7 +67,8 @@ def main() -> int:
     for s in side["samples"]:
         if s.get("status") != "OK":
             continue
-        calls[s["sample_id"]] = [e for e in s["events"] if e["quality"] >= a.min_qual and e["filters"] == ["PASS"]]
+        ign = set(a.ignore_filter) | {"PASS"}
+        calls[s["sample_id"]] = [e for e in s["events"] if e["quality"] >= a.min_qual and set(e["filters"]) <= ign]
     truth: dict[str, list[tuple[str, int, int, str]]] = defaultdict(list)
     with a.truth.open() as fh:
         for line in fh:
@@ -142,6 +144,7 @@ def main() -> int:
     summary = {
         "samples": len(per_sample),
         "min_qual": a.min_qual,
+        "ignored_filters": sorted(a.ignore_filter),
         "sensitivity": {
             t: {b: {"found": v[0], "truth": v[1], "rate": rate(v)} for b, v in sorted(d.items())}
             for t, d in sens.items()