PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)

- simurg/pgx/cn.py: per-region CN mixture, mu_c = delta + gamma*log2((c+1)/3), free lower CN-0 component,
  Hardy-Weinberg-constrained weights over haplotype copy numbers, EM from a grid of label starts.
- pipeline/pgx_cn.py: model file (.simurg-pgxcn), batch rules (PCN-004), per-sample CN VCF + tbi, batch and
  sample summaries.
- The GSA v4 PGx demo arrays are 30 CEPH/1000G individuals (scripts/pgx/demo36_identity.tsv); against NYGC 30x
  SV RD_CN 224/240 region calls agree (GSTM1, UGT2B17 30/30), in-sample (docs/validation/V2_pgx_cn.md).

docs/validation/V2_pgx_cn_demo36.json

@@ -0,0 +1,89 @@
+{
+ "individuals": 30,
+ "regions": {
+  "GSTM1": {
+   "record": "HGSV_9691",
+   "concordant": 30,
+   "n": 30,
+   "rate": 1.0,
+   "truth_to_call_mismatches": {}
+  },
+  "UGT2B17": {
+   "record": "HGSV_63272",
+   "concordant": 30,
+   "n": 30,
+   "rate": 1.0,
+   "truth_to_call_mismatches": {}
+  },
+  "SULT1A1": {
+   "record": "HGSV_207805",
+   "concordant": 29,
+   "n": 30,
+   "rate": 0.9667,
+   "truth_to_call_mismatches": {
+    "2->1": 1
+   }
+  },
+  "CYP2A6.intron.7": {
+   "record": "HGSV_232737",
+   "concordant": 28,
+   "n": 30,
+   "rate": 0.9333,
+   "truth_to_call_mismatches": {
+    "3->2": 1,
+    "1->2": 1
+   }
+  },
+  "CYP2A6.exon.1": {
+   "record": "HGSV_232737",
+   "concordant": 29,
+   "n": 30,
+   "rate": 0.9667,
+   "truth_to_call_mismatches": {
+    "3->2": 1
+   }
+  },
+  "CYP2D6.exon.9": {
+   "record": "HGSV_247317",
+   "concordant": 25,
+   "n": 30,
+   "rate": 0.8333,
+   "truth_to_call_mismatches": {
+    "4->2": 1,
+    "3->2": 3,
+    "2->1": 1
+   }
+  },
+  "CYP2D6.intron.2": {
+   "record": "HGSV_247317",
+   "concordant": 25,
+   "n": 30,
+   "rate": 0.8333,
+   "truth_to_call_mismatches": {
+    "4->3": 1,
+    "3->2": 3,
+    "2->1": 1
+   }
+  },
+  "CYP2D6.p5": {
+   "record": "HGSV_247317",
+   "concordant": 28,
+   "n": 30,
+   "rate": 0.9333,
+   "truth_to_call_mismatches": {
+    "4->3": 1,
+    "2->1": 1
+   }
+  }
+ },
+ "overall": {
+  "concordant": 224,
+  "n": 240,
+  "rate": 0.9333
+ },
+ "gstt1_cn_distribution": {
+  "0": 5,
+  "1": 16,
+  "2": 9
+ }
+}