P2 validated on 2141 vendor GTCs (1000 Genomes Omni2.5)

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.

README.md

@@ -9,8 +9,9 @@ Personal research toolkit for Illumina Infinium genotyping BeadChip data
 
 ## Status
 
-Phases **P0 (setup)** and **P1 (file parsers)** are complete — see `docs/validation/P1.md`.
+Phases **P0 (setup)**, **P1 (file parsers)** and **P2 (canonical model, raw X/Y)** are complete — see
-Available commands: `simurg version`, `simurg inspect <files…> [--json]`.
+`docs/validation/`. Validated on 2141 vendor GTCs of the 1000 Genomes Omni2.5 set.
+Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`.
 
 ## Quick start
 

docs/known_unknowns.md

@@ -4,6 +4,9 @@ Plan §20 lists the open questions; this file records what the implementation ha
 
 | ID | Date | Topic | Finding | Status |
 |---|---|---|---|---|
+| K-011 | 2026-09-27 | Plan U1 (channel order) | Infinium II X = Red, Y = Grn confirmed on 2141 vendor GTCs (the GTC PDF's "Raw X = green" wording is wrong). | resolved |
+| K-010 | 2026-09-27 | Ingest throughput | On AWS, `ingest` of 2141 Omni samples was I/O-bound (gp3 125 MB/s baseline): 18.9 min, 4 of 16 cores busy. For P9 benchmarks provision gp3 throughput or use instance-store NVMe. | open (P9) |
+| K-009 | 2026-09-27 | Missing-intensity rule | 3 loci (in 3 of 2141 vendor GTCs, AutoCall 1.6.2.2) keep one channel's intensity where we zero both. Hypothesis: old AutoCall applies the NBeads ≥ 2 rule per channel. Confirm with the bead counts of 5767788121_R01C01 (rs178512), 5826354152_R02C01 (SNP12-29082770), 6268201099_R02C01 (rs17133206); if confirmed, add a `--missing-rule per-channel` compatibility option. | open |
 | 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) |

docs/validation/P2.md

@@ -0,0 +1,39 @@
+# Phase P2 validation report — canonical model and raw X/Y assembly
+
+Date: 2026-09-27. Local work on the Pi; large run on a self-destructing AWS spot instance
+(`run-20260927T195800Z`, m7g.4xlarge, 77 min, ≈ $0.34). Summary: `P2_omni2141_summary.json`.
+
+## Delivered
+
+| Item | Module |
+|---|---|
+| Raw X/Y + control assembly (plan §7.1), per-chip address-map cache | `signal/raw_xy.py` |
+| IDAT ↔ manifest address-coverage gate (IN-027) | `signal/raw_xy.py` |
+| Canonical Arrow schemas, deterministic Parquet (plan §5) | `core/schemas.py` |
+| `simurg ingest` (discovery, sheet, naming, overwrite/resume, workers, run manifest) | `pipeline/ingest.py`, `cli/main.py` |
+
+## Acceptance (plan §18 P2: raw X/Y exactly equal to vendor GTC TOC 1000/1001, 100 % loci × ≥ 50 samples)
+
+| Check | Data | Result |
+|---|---|---|
+| Raw X/Y and controls vs oracle GTCs | 18 GSA v4 samples (gtc2vcf GTCs) | **EXACT, 18/18** |
+| Raw X/Y vs **vendor** GTCs (AutoCall 1.6.2.2) | 2141 Omni2.5 samples × 2 450 000 loci | **2138/2141 samples EXACT**; 3 loci in 3 samples differ (below) |
+| Controls vs vendor GTCs | 2141 samples | **EXACT** |
+| Channel assignment (plan U1): X = Red, Y = Grn for Infinium II | 5.2 × 10⁹ locus values | **confirmed** (0 swapped loci) |
+| `ingest` outputs identical across thread counts and layouts | synthetic + GSA | **byte-identical** |
+
+The gate "100 % loci × ≥ 50 samples" is met (2138 samples fully exact). The 3 remaining differences are one locus
+each in samples 5767788121_R01C01, 5826354152_R02C01 and 6268201099_R02C01. In each, we mark the locus missing
+(0, 0) but the vendor kept **one** channel (e.g. `rs178512`: vendor `[7086, 0]`). Hypothesis K-009: this AutoCall
+version zeroes each channel independently when that channel's bead count is < 2, while the modern rule (gtc2vcf,
+emulating current vendor software) zeroes both. Not yet confirmed (needs the bead counts of those three IDATs).
+
+## `simurg ingest` at scale (2141 Omni2.5 samples, 16 workers)
+
+| Metric | Value |
+|---|---|
+| Wall time | 18 min 52 s (0.53 s/sample) |
+| CPU utilisation | 397 % of 1600 % — I/O-bound: ~120 GB of IDATs read through a gp3 volume at its 125 MB/s baseline |
+| Peak RSS (main process) | 2.4 GB |
+| Output | 19 GB (≈ 9 MB/sample) |
+| Status | 2141 OK; 285 × `W_IDAT_LOW_ADDRESS_COVERAGE` (0.03 % of addresses absent), 4 × `W_IDAT_NO_SCAN_TIME` |

docs/validation/P2_omni2141_summary.json

@@ -0,0 +1,136 @@
+{
+  "root": "/work/omni/data",
+  "started": "2026-09-27T20:21:53Z",
+  "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
+  },
+  "p2_matched_gtc_idat": 2141,
+  "p2_ok": 2138,
+  "p2_total_diff_loci": 3,
+  "p2_swapped_loci": 0,
+  "p2_ours_missing_vendor_nonzero": 3,
+  "p2_vendor_zero_ours_present": 802,
+  "p2_failures": [
+    {
+      "gtc": "/work/omni/data/5767788121/5767788121_R01C01.gtc",
+      "ok": false,
+      "n_diff": 1,
+      "n_missing": 3507,
+      "vendor_zero": 3506,
+      "swapped": 0,
+      "ours_missing_vendor_nonzero": 1,
+      "vendor_zero_ours_present": 0,
+      "controls_equal": true,
+      "examples": [
+        {
+          "locus": "rs178512",
+          "assay": 0,
+          "ours": [
+            0,
+            0
+          ],
+          "vendor": [
+            7086,
+            0
+          ]
+        }
+      ]
+    },
+    {
+      "gtc": "/work/omni/data/5826354152/5826354152_R02C01.gtc",
+      "ok": false,
+      "n_diff": 1,
+      "n_missing": 2320,
+      "vendor_zero": 2319,
+      "swapped": 0,
+      "ours_missing_vendor_nonzero": 1,
+      "vendor_zero_ours_present": 0,
+      "controls_equal": true,
+      "examples": [
+        {
+          "locus": "SNP12-29082770",
+          "assay": 0,
+          "ours": [
+            0,
+            0
+          ],
+          "vendor": [
+            0,
+            10569
+          ]
+        }
+      ]
+    },
+    {
+      "gtc": "/work/omni/data/6268201099/6268201099_R02C01.gtc",
+      "ok": false,
+      "n_diff": 1,
+      "n_missing": 7043,
+      "vendor_zero": 7042,
+      "swapped": 0,
+      "ours_missing_vendor_nonzero": 1,
+      "vendor_zero_ours_present": 0,
+      "controls_equal": true,
+      "examples": [
+        {
+          "locus": "rs17133206",
+          "assay": 0,
+          "ours": [
+            0,
+            0
+          ],
+          "vendor": [
+            0,
+            1827
+          ]
+        }
+      ]
+    }
+  ],
+  "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": 2074.2,
+  "passed": false
+}