kemal/SimurgArray
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5c93e194e0b83a6313e7ed899b4420add1338e7b
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5 Commits
Author SHA1 Message Date
kemalandClaude Opus 5.5 5c93e194e0 P2 validated on 2141 vendor GTCs (1000 Genomes Omni2.5)
ci / test (3.12) (push) Failing after 8s
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ci / test (3.13) (push) Failing after 10s
Details 
Raw X/Y and controls assembled from IDATs equal the vendor GTC arrays for
2138/2141 samples x 2.45M loci; 3 single-locus differences are recorded
as K-009 (probable per-channel missing rule in AutoCall 1.6.2.2). Channel
order X=Red confirmed (U1). `simurg ingest` processed all 2141 samples in
19 min (I/O-bound). AWS run cost ~$0.34 and left no resources.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-27 22:19:28 +01:00
kemalandClaude Opus 5.5 a4faead6d7 P2 (WIP): raw X/Y assembly, canonical Parquet model, simurg ingest
ci / test (3.12) (push) Failing after 8s
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ci / test (3.13) (push) Failing after 10s
Details 
- 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

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-27 20:54:06 +01:00
kemalandClaude Opus 5.5 854fe132cc P1 validated on 1000 Genomes Omni2.5 (2141 vendor GTCs + IDATs)
ci / test (3.12) (push) Failing after 8s
Details
ci / test (3.13) (push) Failing after 10s
Details 
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).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-27 20:22:35 +01:00
kemalandClaude Opus 5.5 4357d3deef P1: file parsers, sample sheet, discovery, CLI inspect
ci / test (3.12) (push) Failing after 11s
Details
ci / test (3.13) (push) Failing after 12s
Details 
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.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-27 16:56:39 +01:00
kemalandClaude Opus 5.5 0861b27c2b 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).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-27 16:27:34 +01:00