2 Commits

Include renames

Author	SHA1	Message	Date
kemal	17bd0e8f78	P2 validation: oracle test and large-scale raw X/Y check ... - tests/oracle/test_p2_raw_xy.py: IDAT-assembled raw X/Y and controls equal the arrays in oracle GTCs - validate_p1_large.py: phase-P2 comparison against vendor GTCs with diagnostics (channel swap, bead-count disagreements) - cloud trial: also runs `simurg ingest` on all samples (time/memory), disk 250 GB	2026-09-27 20:57:42 +01:00
kemal	5a20e7131c	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