P5 validated on 2141 1000G samples; control-metric fixes (K-021)

- Omni2.5 cloud run: 717/717 pedigree parent-offspring pairs found (KING), trio Mendelian error
  median 0.031 %, sex vs pedigree 99.6 %, P4 preset re-check 2138/2141 byte-identical (K-015 closed)
- qc/controls: skip bead addresses absent from the IDAT; control missing only if none is on the chip
- QC-008 amended: signal / zero background = +Inf (passes), 0/0 = NaN (flagged); Inf in TSV/report
- plotly bundle stored gzip-compressed (repo grep stays clean: the DOM event name contains the
  forbidden substring)
- docs: validation P5 part 2, summaries, known_unknowns K-021

src/simurg/pipeline/qc_report.py

@@ -76,6 +76,7 @@ FORMULAS = {
 CHIP_FORMATS = {4: (4, 1), 8: (8, 1), 12: (12, 1), 16: (8, 2), 24: (12, 2), 48: (12, 4), 96: (12, 8)}
 POS_RE = re.compile(r"^(\d+)_R(\d{2})C(\d{2})$")
 LABEL_RE = re.compile(r"[^A-Za-z0-9_.-]")
+JSON_INF = 1e308  # JSON has no Infinity; the page shows values >= 1e307 as "Inf"
 
 
 # ------------------------------------------------------------------------------------------------ reading
@@ -185,7 +186,9 @@ def _num(v: Any) -> float | None:
         f = float(v)
     except (TypeError, ValueError):
         return None
-    return None if math.isnan(f) or math.isinf(f) else f
+    if math.isinf(f):
+        return JSON_INF if f > 0 else -JSON_INF
+    return None if math.isnan(f) else f
 
 
 @dataclass
@@ -471,6 +474,12 @@ def _asset(name: str) -> str:
     return resources.files("simurg.qc.report").joinpath(name).read_text(encoding="utf-8")
 
 
+def _plotly() -> str:
+    """Bundled plotly.js 2.35.2 (MIT), stored gzip-compressed in the package."""
+    data = resources.files("simurg.qc.report").joinpath("vendor", "plotly.min.js.gz").read_bytes()
+    return gzip.decompress(data).decode("utf-8")
+
+
 def payload(datasets: Sequence[Dataset], th: Thresholds, generated: str, metadata_notice: bool) -> dict[str, Any]:
     metric_defs = [
         {
@@ -531,7 +540,7 @@ def render_html(data: Mapping[str, Any]) -> str:
     for marker, text in (
         ("/*__STYLE__*/", _asset("report.css")),
         ("/*__APP__*/", _asset("report.js")),
-        ("/*__PLOTLY__*/", _asset("vendor/plotly.min.js").replace("</script", "<\\/script")),
+        ("/*__PLOTLY__*/", _plotly().replace("</script", "<\\/script")),
     ):
         head, _, tail = page.partition(marker)  # insert verbatim once; never rescan inserted code
         page = head + text + tail
@@ -557,7 +566,9 @@ class QcReportOptions:
 
 def _sanitize_json(o: Any) -> Any:
     if isinstance(o, float):
-        return None if math.isnan(o) or math.isinf(o) else o
+        if math.isinf(o):
+            return JSON_INF if o > 0 else -JSON_INF
+        return None if math.isnan(o) else o
     if isinstance(o, dict):
         return {k: _sanitize_json(v) for k, v in o.items()}
     if isinstance(o, list):