P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset

- vendor comparison (1000 Genomes Omni2.5, AutoCall 1.6.2.2): every computed field identical in 2138/2141 samples; the 3 others trace back to the single-locus raw-intensity rule (K-009); sex rule 1 matches all - AutoCall 1.6.2.x leaves GC10/GC50/#calls/#no-calls at 0 in GTC v3: new `--preset autocall-1.6.2` (1.1.2 normalization, sex rule 1, GTC v3, legacy statistics); the sample summary keeps the real statistics - NaN sign canonicalised to the x86 pattern (K-014); report P4.md
2026-09-28 01:21:49 +01:00
1 parent 7fb3967c3f
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@@ -4,6 +4,9 @@ Plan §20 lists the open questions; this file records what the implementation ha

 | ID | Date | Topic | Finding | Status |
 |---|---|---|---|---|
+| K-016 | 2026-09-28 | Sex rule of AutoCall 1.6.2.2 | Rule 1 (X heterozygosity) matches all 2141 vendor GTCs; rule 2 (X/Y intensity) differs in 12. | resolved |
+| K-015 | 2026-09-28 | Legacy GTC v3 statistics | AutoCall 1.6.2.2 writes GC10 = GC50 = 0 and #calls = #no-calls = 0 in GTC v3 (it does fill LogR dev and #intensity-only). gtc2vcf's AutoConvert 1.6.3.1 preset fills them, so this is specific to 1.6.2.x. Emulated by `--preset autocall-1.6.2`; the sample summary still reports the real statistics. | resolved; cloud re-run pending |
+| K-014 | 2026-09-28 | NaN sign | NaNs produced by libm (e.g. log2 of a negative extrapolated R) take the platform's default sign: + on aarch64, − on x86-64. SimurgArray always writes 0xFFC00000 (the reference's `-NAN`, x86 behaviour). The aarch64-built oracle differs in 1 locus of 9 GSA samples; oracle tests compare with NaNs canonicalised. | resolved |
 | K-013 | 2026-09-27 | Normalization version of public vendor GTCs | The 1000 Genomes Omni2.5 GTCs (AutoCall 1.6.2.2) are reproduced bit-for-bit by normalization 1.1.2 (109 191/109 191 bins, reserved fields included). | resolved |
 | K-012 | 2026-09-27 | FMA and bit-exactness | gcc on aarch64 contracts a*b+c into FMA by default; the gtc2vcf oracle then differs from the vendor by up to 4 ULP in some bins. Oracles are built with `-ffp-contract=off`. Any future C/Rust port (P9) must also forbid FMA contraction in exact mode. | resolved; constraint for P9 |
 | 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 |
@@ -0,0 +1,55 @@
+# Phase P4 validation report — genotype calling and GTC output
+
+Date: 2026-09-28. Development and oracle tests on the Pi; vendor comparison on a self-destructing AWS spot instance
+(`run-20260927T233126Z`, 44 min, ≈ $0.19). Summary: `P4_omni2141_summary.json`.
+
+## Delivered
+
+| Item | Module |
+|---|---|
+| Cluster file aligned to manifest order (float32 mean R) | `genotype/clusters.py` |
+| GenCall-equivalent calling: SD flair, six-case half-flattened likelihoods, priors/posteriors, fuzzy sub-scores, score map | `genotype/gencall.py` |
+| BAF / LRR / LogR dev (Peiffer 2006), canonical NaN pattern | `genotype/baf_lrr.py` |
+| Sex estimate, rules v1 and v2 | `genotype/sex.py` |
+| IDAT pair → complete GTC (v5 or v3), TOP-strand base calls, sample stats, presets | `genotype/sample.py` |
+| `simurg genotype` (GTC per sample, `sample_summary.tsv/json` per OUT-060…063, run manifest) | `pipeline/genotype.py` |
+
+## Acceptance (plan §18 P4)
+
+### Against the oracle (gtc2vcf built without FMA), P0 GSA data
+
+| Check | Result |
+|---|---|
+| 36 samples × normalization 1.2.0 and 1.1.2: whole GTC files after aligning the four free-text fields (file names, AutoCall date/version) | **72/72 byte-identical** |
+
+Every data field matches bit for bit: raw X/Y, transforms, genotypes, GenCall scores, TOP base calls, BAF, LRR, call
+rate, sex, LogR dev, GC10/GC50, call counts, percentiles and controls. The only adjustment is the sign of NaNs that
+libm computes (K-014).
+
+### Against 2141 vendor GTCs (1000 Genomes Omni2.5, AutoCall 1.6.2.2, cluster file `HumanOmni2.5-4v1-Multi_B.egt`)
+
+| Field | Samples that differ | Explanation |
+|---|---|---|
+| genotypes | 3 (5 loci in total) | the 3 samples of K-009, whose raw intensity differs in one locus; that difference shifts their normalization |
+| GenCall scores | 3 (18 229 loci) | same 3 samples (the transform change moves every score of the affected bin) |
+| normalization transforms | 2 | same K-009 samples |
+| raw X / raw Y | 1 / 2 | K-009 |
+| call rate, LogR dev | 2 / 3 | follow from the above |
+| base calls | 3 | follow from genotypes |
+| **sex (rule 1)** | **0 of 2141** | rule 2 would differ in 12 samples, so AutoCall 1.6.2.2 uses rule 1 |
+| GC10, GC50, #calls, #no-calls | 2141 | AutoCall 1.6.2.2 leaves these at 0 in GTC v3 (K-015); now emulated by `--preset autocall-1.6.2` |
+
+So in 2138 of 2141 samples every computed field agrees with the vendor; the remaining 3 samples trace back to the
+single-locus raw-intensity rule of K-009. Whole-file byte identity was 0/2141 in this run only because of the four
+legacy-empty statistics; the preset that reproduces them was added after the run (unit-tested, not yet re-run on
+the cloud — expected 2138/2141).
+
+Not covered here: BAF and LRR against vendor output (GTC v3 has no BAF/LRR fields). The 1000 Genomes Sanger set
+ships a GenomeStudio Final Report with BAF/LRR for 177 samples — optional follow-up run (≈ $0.10).
+
+## Performance
+
+| Machine | Result |
+|---|---|
+| Raspberry Pi 5, GSA (683 k loci) | 3.6 s per sample (1 core); 36 samples in 2 min with 4 workers |
+| AWS m7g.4xlarge, Omni2.5 (2.45 M loci), 16 workers | 2141 samples genotyped and compared in 19.6 min; peak RSS 3.2 GB |
@@ -0,0 +1,615 @@
+{
+  "n_gtc": 2141,
+  "n_compared": 2141,
+  "errors": [],
+  "byte_identical": 0,
+  "samples_with_no_field_diff": 0,
+  "samples_with_field_diff": {
+    "gc10": 2141,
+    "gc50": 2141,
+    "num_calls": 2141,
+    "num_no_calls": 2141,
+    "slide_identifier": 2141,
+    "raw_x": 1,
+    "genotypes": 3,
+    "genotype_scores": 3,
+    "base_calls": 3,
+    "call_rate": 2,
+    "logr_dev": 3,
+    "raw_y": 2,
+    "normalization_transforms": 2
+  },
+  "genotype_diff_loci_total": 5,
+  "score_diff_loci_total": 18229,
+  "max_score_abs_diff": 0.9426311254501343,
+  "cluster_files": [
+    "HumanOmni2.5-4v1-Multi_B.egt"
+  ],
+  "sex_agreement_by_version": {
+    "1": 2141,
+    "2": 2129
+  },
+  "ref_sex_counts": {
+    "M": 1054,
+    "F": 1087,
+    "U": 0
+  },
+  "examples": [
+    {
+      "gtc": "/work/omni/data/5426511011/5426511011_R01C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
+          "0.6847535967826843",
+          "0.0"
+        ],
+        "gc50": [
+          "0.8497611880302429",
+          "0.0"
+        ],
+        "num_calls": [
+          "2433210",
+          "0"
+        ],
+        "num_no_calls": [
+          "16790",
+          "0"
+        ],
+        "slide_identifier": [
+          "'5426511011'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Wednesday, August 25, 2010 7:11:03 PM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511011/5426511011_R02C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
+          "0.6842713356018066",
+          "0.0"
+        ],
+        "gc50": [
+          "0.8497611880302429",
+          "0.0"
+        ],
+        "num_calls": [
+          "2436202",
+          "0"
+        ],
+        "num_no_calls": [
+          "13798",
+          "0"
+        ],
+        "slide_identifier": [
+          "'5426511011'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "M",
+        "2": "M"
+      },
+      "sex_ref": "M",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Wednesday, August 25, 2010 7:24:37 PM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511011/5426511011_R03C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
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+          "0.0"
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+        "gc50": [
+          "0.8497611880302429",
+          "0.0"
+        ],
+        "num_calls": [
+          "2435069",
+          "0"
+        ],
+        "num_no_calls": [
+          "14931",
+          "0"
+        ],
+        "slide_identifier": [
+          "'5426511011'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Wednesday, August 25, 2010 7:37:41 PM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511011/5426511011_R04C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
+          "0.6863988637924194",
+          "0.0"
+        ],
+        "gc50": [
+          "0.8497668504714966",
+          "0.0"
+        ],
+        "num_calls": [
+          "2435856",
+          "0"
+        ],
+        "num_no_calls": [
+          "14144",
+          "0"
+        ],
+        "slide_identifier": [
+          "'5426511011'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Wednesday, August 25, 2010 7:45:50 PM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511013/5426511013_R01C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
+          "0.6843520402908325",
+          "0.0"
+        ],
+        "gc50": [
+          "0.8497611880302429",
+          "0.0"
+        ],
+        "num_calls": [
+          "2434354",
+          "0"
+        ],
+        "num_no_calls": [
+          "15646",
+          "0"
+        ],
+        "slide_identifier": [
+          "'5426511013'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "M",
+        "2": "M"
+      },
+      "sex_ref": "M",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Thursday, August 26, 2010 12:08:26 AM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511013/5426511013_R02C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
+          "0.685818076133728",
+          "0.0"
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+        "gc50": [
+          "0.8497965335845947",
+          "0.0"
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+          "2439588",
+          "0"
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+          "10412",
+          "0"
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+        "slide_identifier": [
+          "'5426511013'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Thursday, August 26, 2010 12:22:41 AM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511013/5426511013_R03C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
+          "0.6856454014778137",
+          "0.0"
+        ],
+        "gc50": [
+          "0.8497673273086548",
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+        ],
+        "num_calls": [
+          "2442131",
+          "0"
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+        "num_no_calls": [
+          "7869",
+          "0"
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+        "slide_identifier": [
+          "'5426511013'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "M",
+        "2": "M"
+      },
+      "sex_ref": "M",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Thursday, August 26, 2010 12:37:24 AM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511013/5426511013_R04C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
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+          "'5426511013'",
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+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
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+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Thursday, August 26, 2010 12:46:33 AM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511028/5426511028_R01C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
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+          "'5426511028'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "M",
+        "2": "M"
+      },
+      "sex_ref": "M",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
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+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Thursday, August 26, 2010 8:13:23 AM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511028/5426511028_R02C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
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+          "14111",
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+          "'5426511028'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
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+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Thursday, August 26, 2010 8:28:43 AM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511028/5426511028_R03C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
+          "0.6847374439239502",
+          "0.0"
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+        "gc50": [
+          "0.8497611880302429",
+          "0.0"
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+        "num_calls": [
+          "2435026",
+          "0"
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+        "num_no_calls": [
+          "14974",
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+        "slide_identifier": [
+          "'5426511028'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Thursday, August 26, 2010 8:40:16 AM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511028/5426511028_R04C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
+          "0.6849170923233032",
+          "0.0"
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+        "gc50": [
+          "0.8497409820556641",
+          "0.0"
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+        "num_calls": [
+          "2433211",
+          "0"
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+        "num_no_calls": [
+          "16789",
+          "0"
+        ],
+        "slide_identifier": [
+          "'5426511028'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Thursday, August 26, 2010 8:50:08 AM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511029/5426511029_R01C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
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+          "0.0"
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+        "gc50": [
+          "0.8497233390808105",
+          "0.0"
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+        "num_calls": [
+          "2439124",
+          "0"
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+        "num_no_calls": [
+          "10876",
+          "0"
+        ],
+        "slide_identifier": [
+          "'5426511029'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "M",
+        "2": "M"
+      },
+      "sex_ref": "M",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Thursday, August 26, 2010 9:12:02 AM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5426511029/5426511029_R02C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "field_diffs": {
+        "gc10": [
+          "0.6832002401351929",
+          "0.0"
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+        "gc50": [
+          "0.8497028946876526",
+          "0.0"
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+        "num_calls": [
+          "2437630",
+          "0"
+        ],
+        "num_no_calls": [
+          "12370",
+          "0"
+        ],
+        "slide_identifier": [
+          "'5426511029'",
+          "''"
+        ]
+      },
+      "sex_by_version": {
+        "1": "M",
+        "2": "M"
+      },
+      "sex_ref": "M",
+      "byte_identical": false,
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