kemal
87f9b3499c
P2 (WIP): raw X/Y assembly, canonical Parquet model, simurg ingest
...
- signal/raw_xy.py: vectorised Infinium I/II raw X/Y and control assembly
(plan §7.1) with a per-chip address-map cache; IN-027 coverage gate
- core/schemas.py: Arrow schemas (loci, sample_intensity, controls),
deterministic atomic Parquet writing
- pipeline/ingest.py + CLI: discovery, sheet, IN-010 naming, overwrite
check before any work, spawn-based workers, per-sample isolation,
--resume by input hashes, run manifest, exit codes 0/3/4
- matches gtc2vcf raw X/Y and controls exactly on 18 GSA samples;
outputs byte-identical across thread counts and layouts
2026-09-27 20:54:06 +01:00
kemal
a7a235beb5
P1 validated on 1000 Genomes Omni2.5 (2141 vendor GTCs + IDATs)
...
All 2141 vendor-written GTC v3 files match BeadArrayFiles field by field
and re-encode byte-identically; all IDAT pairs parse; the 2.45M-locus BPM,
dbv-7 EGT and CSV manifest agree with BeadArrayFiles and each other.
Run on a self-destructing AWS spot instance (42 min, ~$0.20).
2026-09-27 20:22:35 +01:00
kemal
8cd092460f
P1: file parsers, sample sheet, discovery, CLI inspect
...
Readers for IDAT v3, BPM (locus entries v4-v8), CSV manifest, EGT
(data blocks 5-9) and GTC v3-v5 (plus a layout-preserving GTC writer);
sample-sheet validation (IN-001..IN-014), IDAT discovery and pairing
(IN-020..IN-022), message catalogue and exit codes (CLI-014/016),
JSON Lines logging (CLI-007/008), atomic writes (CLI-011), run manifest,
and `simurg inspect`.
Validation (docs/validation/P1.md): GTC, BPM and EGT readers agree
exactly with Illumina BeadArrayFiles on GSA v4 / GDA v1 files; GTCs
round-trip byte-identically; BPM and CSV manifests are consistent.
2026-09-27 16:56:39 +01:00
kemal
91e97424c7
Add sanitized Phase-0 research archive under docs/research
...
Research notes R1-R4, documentation-study files A-E (source of the
functional spec's `src:` tags) and PGx coverage CSVs, rewritten to use
neutral naming and current project decisions (plan §2).
2026-09-27 16:27:34 +01:00
kemal