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).

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

docs/known_unknowns.md

@@ -4,10 +4,11 @@ Plan §20 lists the open questions; this file records what the implementation ha
 
 | ID | Date | Topic | Finding | Status |
 |---|---|---|---|---|
+| K-008 | 2026-09-27 | Vendor GTC layout | 2141 vendor GTC v3 files (AutoCall 1.6.2.2) re-encode byte-identically with the canonical v3 order, so the writer reproduces the vendor layout (no padding or reordering). | resolved |
 | K-007 | 2026-09-27 | Demo data | The "GDA v1 Demo 36" download is a GenomeStudio project (`.bsc` + `Data/*.bin`), not IDATs. The GSA v4 PGx demo (`idats_Demo_36.zip`) is used as the P0 IDAT fixture instead. Bioconductor `hapmap370k` is no longer in the current release. | resolved (plan §17 updated) |
 | K-006 | 2026-09-27 | Sample sheet | Recognised input columns (`Sample_ID`, `Sample_Name`, …) collide case-insensitively with output columns `sample_id`/`sample_name` (IN-005). Recognised columns are exempt from the reserved-name check and are passed through verbatim. | decision, revisit in P4 (OUT-060 pass-through) |
 | K-005 | 2026-09-27 | Sample sheet | Illumina's GSA v4 template sheet has an empty `Sample_Name` column → `E_SHEET_NAME_EMPTY` (IN-010 behaviour as specified). | as specified |
 | K-004 | 2026-09-27 | GTC scanner data | PMT gains are 4 bytes read as int32 by BeadArrayFiles and written as float by gtc2vcf. We keep the raw 4 bytes (byte-exact round-trip) and expose the int32 view. | resolved |
 | K-003 | 2026-09-27 | Assay type from sequences | gtc2vcf's rule for inferring Infinium I colour from probe/source sequences (needed only for BPM locus entries < v6) agrees with the explicit BPM value for 99.71 % of GSA v4 Infinium I loci. The BPM is authoritative whenever it carries the assay type. | documented; test threshold 99.5 % |
-| K-002 | 2026-09-27 | EGT data block (plan U3) | GSA v4 and GDA v1 EGTs are data-block v9 with 15 extra floats per record; the first extra float is the intensity threshold (non-zero for 16 015 GDA loci). The reader tries candidate record sizes and accepts the one whose trailing cluster counts match. dbv 7/8 files still untested. | partly resolved |
+| K-002 | 2026-09-27 | EGT data block (plan U3) | GSA v4 and GDA v1 EGTs are data-block v9 with 15 extra floats per record; the first extra float is the intensity threshold (non-zero for 16 015 GDA loci). The reader tries candidate record sizes and accepts the one whose trailing cluster counts match. The Omni2.5 EGT is dbv 7 with 15 extra floats (structure confirmed); whether its first extra float is an intensity threshold (gtc2vcf) or unused (BeadArrayFiles) is still open. | partly resolved |
-| K-001 | 2026-09-27 | IDAT MidBlock (plan U2) | In GSA v4 (BeadChip 48x4), HumanCNV370 (2x12) and 450k (12x8) IDATs the MidBlock count equals N and the section is 4 bytes per entry (int32, as in illuminaio). gtc2vcf reads uint8 but never uses the values. We infer the element size from the section length. | resolved for these chips |
+| K-001 | 2026-09-27 | IDAT MidBlock (plan U2) | In GSA v4 (BeadChip 48x4), HumanCNV370 (2x12) and 450k (12x8) IDATs the MidBlock count equals N and the section is 4 bytes per entry (int32, as in illuminaio). gtc2vcf reads uint8 but never uses the values. We infer the element size from the section length. | resolved for these chips + BeadChip 4x10 (Omni2.5, 2141 files) |

docs/validation/P1.md

@@ -37,6 +37,22 @@ Commands: `pytest tests/unit` (every CI run), `pytest tests/oracle -m "not slow"
 | Sample-sheet matrix EDGE-007 (27 cases) incl. 10 000 rows < 2 s (PERF-007) | synthetic | **pass** |
 | Locale independence of `inspect --json` (C, tr_TR, de_DE) | synthetic | **pass** |
 
+## Large-scale run: 1000 Genomes Omni2.5 (AWS, 2026-09-27)
+
+Self-destructing spot instance (`scripts/cloud/trial.sh`, m7g.4xlarge, 16 vCPU), run `run-20260927T183712Z`,
+summary in `P1_omni2141_summary.json`. 107 GB archive streamed from `s3://1000genomes` (extracted 170 GB) in
+22 min; validation 18 min; instance lifetime 42 min; cost ≈ $0.20.
+
+| Criterion | Result |
+|---|---|
+| 2141 **vendor-written** GTCs (v3, AutoCall 1.6.2.2): every field equal to BeadArrayFiles | **2141/2141 EXACT** |
+| Same GTCs: read → write byte-identical | **2141/2141** |
+| 2141 IDAT pairs (BeadChip 4x10) parse and pair; MidBlock int32 | **2141/2141** |
+| BPM HumanOmni2.5-4v1-Multi_B (2 450 000 loci, 51 normalization bins) vs BeadArrayFiles | **EXACT** |
+| EGT (data block v7, 2 450 000 records) vs BeadArrayFiles: all θ/R means and SDs, N | **0 mismatches** |
+| BPM ↔ CSV consistency | **0 differences** |
+| GTC transforms per sample = BPM bins (51) | **pass** |
+
 ## Performance on the Pi (single thread, pure Python/NumPy)
 
 | Operation | Time | Peak RSS |
@@ -51,8 +67,5 @@ BPM/CSV parsing is the only slow step; it is a one-off per run and moves to Rust
 
 ## Not yet covered (needs the larger machine / later phases)
 
-- GEO sweep of 254 genotyping IDAT series and the 1000 Genomes Omni2.5 set (plan §18 P1 wording) — P1 is
+- GEO sweep of 254 genotyping IDAT series (other chip generations, IDAT variants) — still open.
-  validated on P0 data only; rerun `tests/oracle` after `scripts/fetch_data.sh p1`.
-- GTCs written by vendor software (only gtc2vcf-written GTCs are available locally); the 1000 Genomes Broad set
-  contains vendor GTCs.
 - IN-027 (IDAT ↔ manifest coverage gate) is P2; the coverage computation is already exercised by a test.

docs/validation/P1_omni2141_summary.json

@@ -0,0 +1,53 @@
+{
+  "root": "/work/omni/data",
+  "started": "2026-09-27T19:00:42Z",
+  "n_gtc": 2141,
+  "n_idat_pairs": 2141,
+  "unpaired_idats": 0,
+  "gtc_ok": 2141,
+  "gtc_roundtrip_identical": 2141,
+  "gtc_versions": [
+    3
+  ],
+  "gtc_autocall_versions": [
+    "1.6.2.2"
+  ],
+  "gtc_failures": [],
+  "gtc_roundtrip_failures": [],
+  "idat_ok": 2141,
+  "idat_failures": [],
+  "idat_midblock_itemsizes": [
+    4
+  ],
+  "idat_chip_types": [
+    "BeadChip 4x10"
+  ],
+  "bpm": {
+    "num_loci": 2450000,
+    "names": true,
+    "snps": true,
+    "chroms": true,
+    "map_infos": true,
+    "address_a": true,
+    "assay_types": true,
+    "normalization_lookups": true,
+    "n_bins": 51
+  },
+  "egt": {
+    "num_records": 2450000,
+    "dbv": 7,
+    "extra_floats": 15,
+    "record_mismatches": 0
+  },
+  "bpm_csv_problems": [],
+  "gtc_vs_bpm_num_snps": [
+    2450000,
+    2450000
+  ],
+  "gtc_transforms_vs_bins": [
+    51,
+    51
+  ],
+  "seconds": 1098.7,
+  "passed": true
+}