CHANGELOG: v2 CN/LOH/mosaicism and pharmacogenomics

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

CHANGELOG.md

@@ -7,6 +7,20 @@ CSV manifests, the 21 control metrics, pOOBAH detection p-values, noob, linear/n
 summary tsv/xlsx/html with a β PCA, per-sample tables; methylation folders load in `simurg qc report`;
 `qc controls --array-type methylation`. Checked against sesame (`docs/validation/V2_methylation.md`, K-026).
 
+**Copy number, LOH and mosaicism** (`simurg cn build-model|call|annotate`; CYTO-001 … CYTO-042): GC-wave
+correction, sex-aware batch reference, HMM with constitutional, LOH and mosaic states, event statistics and
+filters, CNV VCF + segments + sidecar, ISCN 2020 annotation from UCSC tables; noise-normalised mosaic fractions and
+complete-loss promotion (CYTO-041), per-probe LRR noise (CYTO-042). Validated on implanted events and on 360
+GSE165845 arrays against the NYGC 30x SV callset (`docs/validation/V2_cn.md`, K-027).
+
+**Pharmacogenomics** (`simurg pgx db build|coverage`, `pgx copy-number train|call`, `pgx star-allele call`,
+`pgx phenotype`; PCN-001 … PCN-017, PGX-001 … PGX-035): targeted CN for CYP2D6 sub-regions, CYP2A6, GSTM1, GSTT1,
+UGT2B17, SULT1A1, CYP2E1 (HWE-constrained compression mixture); a deterministic PGx DB from CPIC, PharmVar and
+ClinPGx (70 genes); solver-free diplotype calling with array-equivalence classes, CYP2D6 structures (*5, xN,
+*68+*4, *36+*10, *13), G6PD, HLA tags, variant-based and *0 genes; probe masks from 1000G 30x concordance; CPIC and
+DPWG phenotypes; per-sample JSON and the TSV set. The GSA v4 PGx demo arrays are 30 CEPH/1000G individuals: region
+CN 224/240 vs NYGC SV, gene calls 154/168 vs GeT-RM (`docs/validation/V2_pgx_cn.md`, `V2_pgx_star.md`, K-028, K-029).
+
 ## 1.1.0 — 2026-09-28 (P9, P10)
 
 **Packaging (P10).** `scripts/build_dist.sh` (sdist, pure wheel, manylinux_2_28 kernel wheels for x86_64 and