Release 2.0.0: v2 modules (ArrayTrain, CN/LOH, PGx, methylation QC)

User guide: ArrayTrain section, v2 commands in the table, v2 accuracy rows,
updated limitations. README status for v2.0.0. Version 2.0.0 (Python package);
the Rust kernels are unchanged and stay simurg_core 1.1.0. uv.lock committed
(uv lock --check clean).

Full suite on the Pi, file by file under the memory guard: 29 files exit 0
(unit: 282 passed), ruff and mypy clean.

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

README.md

@@ -1,7 +1,8 @@
 # SimurgArray
 
 Personal research toolkit for Illumina Infinium genotyping BeadChip data
-(IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; later CN/LOH, PGx, cluster training).
+(IDAT → normalization → genotype calling → BAF/LRR → QC → VCF/PLINK; CN/LOH/mosaicism, PGx, cluster training,
+methylation control QC).
 
 - **SIMURGARRAY_MASTER_PLAN.md** — architecture, algorithms, roadmap
 - **SIMURGARRAY_FUNCTIONAL_SPEC.md** — 416 itemised requirements (CLI, inputs, outputs, QC, CN, PGx, methylation, edge cases)
@@ -9,9 +10,10 @@ Personal research toolkit for Illumina Infinium genotyping BeadChip data
 
 ## Status
 
-**v1.1.0** (2026-09-28) — see `CHANGELOG.md`. IDAT → normalization → GenCall-equivalent genotype calling → GTC v5 →
-sample/control QC with an HTML report → plus-strand VCF/BCF → PLINK 1/2, bedGraph, final report; plus a
-differential-testing harness. Validation (`docs/validation/`):
+**v2.0.0** (2026-09-30) — see `CHANGELOG.md`. v1: IDAT → normalization → GenCall-equivalent genotype calling →
+GTC v5 → sample/control QC with an HTML report → plus-strand VCF/BCF → PLINK 1/2, bedGraph, final report; plus a
+differential-testing harness. v2 adds cluster training (ArrayTrain), genome-wide CN/LOH/mosaic calling,
+pharmacogenomics (targeted CN, star alleles, phenotypes) and methylation control QC. Validation (`docs/validation/`):
 
 | Check | Result |
 |---|---|
@@ -19,13 +21,17 @@ differential-testing harness. Validation (`docs/validation/`):
 | GSA demo vs gtc2vcf, GTCtoVCF, plink2 | zero unexplained differences |
 | 1000 Genomes pedigrees (Omni2.5) | 717/717 parent–offspring pairs; Mendel error median 0.031 % |
 | 360 GSA arrays (GSE165845) vs NYGC 30x WGS / GIAB HG001 | concordance 0.9934 / 0.9985; replicates 0.9966 |
+| ArrayTrain EGT, GSE165845 chr22 vs 1000G 30x | 99.44 % concordance (vendor EGT 99.46 %), call rate 99.61 % |
+| CN, 360 GSE165845 arrays vs NYGC 30x SV | PASS precision DEL 44 % / DUP 57 % |
+| PGx, GSA v4 demo vs GeT-RM | 154/168 gene calls |
+| Methylation QC vs sesame | β r = 0.99998 |
 
 Commands: `simurg inspect`, `ingest`, `normalize`, `genotype`, `qc controls|samples|contamination|relatedness|loci|report|suggest-thresholds`,
-`gtc-to-vcf`, `export plink|bedgraph|finalreport|locus-summary`, `compare`. **User guide: `docs/user_guide.md`**;
-worked example: `examples/gsa_demo.sh`. P9 (performance) is done: optional Rust kernels, byte-identical outputs,
-~80 GSA samples/min per server core (`docs/validation/P9.md`). P10 (packaging) is done: wheels, Docker image and
-conda recipes, verified on fresh x86_64 and aarch64 machines (`docs/validation/P10.md`). v2 in progress: methylation control QC (`simurg methyl qc`,
-`docs/validation/V2_methylation.md`); next CN/LOH, PGx, cluster training.
+`gtc-to-vcf`, `export plink|bedgraph|finalreport|locus-summary`, `compare`, `train`, `cn build-model|call|annotate`,
+`pgx db build|coverage|copy-number|star-allele|phenotype`, `methyl qc|convert-manifest`. **User guide:
+`docs/user_guide.md`**; worked example: `examples/gsa_demo.sh`. Optional Rust kernels (byte-identical outputs,
+~80 GSA samples/min per server core, `docs/validation/P9.md`); wheels, Docker image and conda recipes
+(`docs/validation/P10.md`).
 
 ## Quick start