v1.0.0: user guide, examples, changelog

docs/user_guide.md (install, inputs, complete run, commands, presets, QC, outputs,
accuracy, limitations, troubleshooting), examples/gsa_demo.sh (end-to-end run on the
public GSA demo, verified on the Pi), examples/sample_sheet.csv, CHANGELOG.md; version 1.0.0.

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

CHANGELOG.md

@@ -0,0 +1,33 @@
+# Changelog
+
+## 1.0.0 — 2026-09-28
+
+First release: the v1.0 goals of the master plan (§1.1), built and validated phase by phase (P0–P8).
+
+**Formats (P1–P2).** Readers for IDAT (plain or gzipped; encrypted v1 refused), BPM, CSV manifest, EGT, GTC v3–v5
+and sample sheets; `simurg inspect`; raw X/Y assembly into a canonical Parquet model (`simurg ingest`, resumable).
+
+**Signal and calling (P3–P4).** Per-bin affine normalization 1.2.0 and 1.1.2; GenCall-equivalent calling from an
+EGT with GenCall score; θ/R, BAF, LRR, LogR deviation, GC10/GC50, intensity percentiles, sex (rules 1 and 2);
+GTC v5/v3 writer (`simurg genotype`). Presets `current` and `autocall-1.6.2`.
+
+**QC (P5).** Control-probe metrics, threshold profiles and YAML, two-axis sample status and flags,
+BAF-regression contamination, KING-robust relatedness and Mendel errors, locus summary, threshold suggestion, a
+self-contained HTML QC report with xlsx/csv table (`simurg qc …`).
+
+**Outputs (P6).** Plus-strand harmonisation with an audit trail; per-sample VCF.gz + tabix or cohort BCF + CSI
+(`GT:GS:BAF:LRR`, optional INFO and intensity fields, merged multi-probe sites, indels from SourceSeq, SNV+indel
+merging, auxiliary MNV loci); PLINK 1 `.bed` and PLINK 2 `.pgen`; BAF/LRR bedGraph; final report and genotype matrix.
+
+**Testing (P7).** `simurg compare` (EXACT/NEAR/DISCREPANCY/UNKNOWN per field and locus class, HTML dashboard) and a
+nightly differential run against gtc2vcf, GTCtoVCF and vendor GTCs.
+
+**Validation (P8).** 360 GSA arrays of 120 1000 Genomes individuals vs NYGC 30x WGS (concordance 0.9934) and
+GIAB HG001 (0.9985, non-ref F1 0.997); replicate concordance 0.9966. Vendor-equivalence: 2138/2141 Omni2.5 GTCs
+byte-identical, zero unexplained VCF/PLINK differences vs gtc2vcf, GTCtoVCF and plink2.
+
+Documentation: `docs/user_guide.md`, `examples/`, `docs/validation/P1.md … P8.md`, `docs/known_unknowns.md`,
+`docs/messages.md`.
+
+Known limitations: needs an existing cluster file (training is v2); no CN/LOH/PGx yet; largest tested cohort
+2141 samples; pure NumPy speed.