{"abstract":"CDS exon phase mistakes remaining bases for consumed bases.","category":"Genomic coordinate mapping","checks":6,"contract":"Given lengths of preceding coding segments in transcript order, report GFF-like leading completion phase (3-total modulo 3) modulo 3. This model assumes the initial segment starts on a codon boundary.","evaluation_group":"model-2cc2bf1858752ef1","failed_approach":"Using three minus the remainder without modulo three invents a full-codon skip at aligned junctions.","family":"z-genetics_coordinates-splice-phase","id":"FA-12586","implementations":{"attempt":{"sha256":"8ea2b41e73dece5b57452933487b19d618cfed678f622610daab4ed293936755","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(lengths):\n    return 3-sum(lengths)%3\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('one carried base',solve([3*N+1]),2)\ncheck('two carried bases',solve([3*N+2]),1)\ncheck('aligned exon',solve([3*N]),0)\ncheck('no preceding exon',solve([]),0)\ncheck('multiple segments',solve([3*N+1,4]),1)\ncheck('split closes codon',solve([3*N+1,2]),0)\nprint(json.dumps({\"observations\": observations, \"passed\": all(x[\"passed\"] for x in observations)}, ensure_ascii=False))\nraise SystemExit(0 if all(x[\"passed\"] for x in observations) else 1)\n"},"broken":{"sha256":"95cb317d4b3a9ce87e46d6f229efe26a87e6bfe6be80115f27642745cf8d2551","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(lengths):\n    return sum(lengths)%3\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('one carried base',solve([3*N+1]),2)\ncheck('two carried bases',solve([3*N+2]),1)\ncheck('aligned exon',solve([3*N]),0)\ncheck('no preceding exon',solve([]),0)\ncheck('multiple segments',solve([3*N+1,4]),1)\ncheck('split closes codon',solve([3*N+1,2]),0)\nprint(json.dumps({\"observations\": observations, \"passed\": all(x[\"passed\"] for x in observations)}, ensure_ascii=False))\nraise SystemExit(0 if all(x[\"passed\"] for x in observations) else 1)\n"},"fixed":{"sha256":"6add019219780c9c0f9d3430c2f13102367449ea062a28e3a56abfca8dc05005","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(lengths):\n    return (-sum(lengths))%3\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('one carried base',solve([3*N+1]),2)\ncheck('two carried bases',solve([3*N+2]),1)\ncheck('aligned exon',solve([3*N]),0)\ncheck('no preceding exon',solve([]),0)\ncheck('multiple segments',solve([3*N+1,4]),1)\ncheck('split closes codon',solve([3*N+1,2]),0)\nprint(json.dumps({\"observations\": observations, \"passed\": all(x[\"passed\"] for x in observations)}, ensure_ascii=False))\nraise SystemExit(0 if all(x[\"passed\"] for x in observations) else 1)\n"}},"limitations":"Synthetic coordinate fixtures only; not a production annotation or alignment implementation. This reproducer isolates one failure mechanism. Results cover the supplied fixtures. Variants within a family share a test contract and should remain grouped when constructing evaluation splits. Related mechanisms with a shared evaluation_group must also remain together; these controlled models are not independent production incidents.","method":"Deterministic executable model with adversarial boundary fixtures.","provenance":{"created_by":"Failure Map","dependencies":"Python standard library","family":"z-genetics_coordinates-splice-phase","generated_at":"2026-09-29T14:38:58.146336+00:00","license":"CC0-1.0","python":"3.12.14","seed":1,"split":"open-access"},"relevance":"An abstract offline coordinate model isolates this software mapping defect; it does not model biological interpretation.","repair":"Return the number of leading bases needed to complete the split codon, modulo three.","root_cause":"The carried coding remainder is used directly as the next segment phase.","sha256":"2770de9ae26774de178c77f92c81c4cd974905ca34cd955b844dd25e20fb2c01","title":"CDS exon phase mistakes remaining bases for consumed bases · case 01","variant":1,"variant_policy":"Five numbered records share a model and may reuse boundary fixtures.","verification":{"attempt":{"elapsed_ms":40.596,"exit_code":1,"observations":[{"actual":2,"check":"one carried base","expected":2,"passed":true},{"actual":1,"check":"two carried bases","expected":1,"passed":true},{"actual":3,"check":"aligned exon","expected":0,"passed":false},{"actual":3,"check":"no preceding exon","expected":0,"passed":false},{"actual":1,"check":"multiple segments","expected":1,"passed":true},{"actual":3,"check":"split closes codon","expected":0,"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"one carried base\", \"actual\": 2, \"expected\": 2, \"passed\": true}, {\"check\": \"two carried bases\", \"actual\": 1, \"expected\": 1, \"passed\": true}, {\"check\": \"aligned exon\", \"actual\": 3, \"expected\": 0, \"passed\": false}, {\"check\": \"no preceding exon\", \"actual\": 3, \"expected\": 0, \"passed\": false}, {\"check\": \"multiple segments\", \"actual\": 1, \"expected\": 1, \"passed\": true}, {\"check\": \"split closes codon\", \"actual\": 3, \"expected\": 0, \"passed\": false}], \"passed\": false}\n"},"broken":{"elapsed_ms":40.894,"exit_code":1,"observations":[{"actual":1,"check":"one carried base","expected":2,"passed":false},{"actual":2,"check":"two carried bases","expected":1,"passed":false},{"actual":0,"check":"aligned exon","expected":0,"passed":true},{"actual":0,"check":"no preceding exon","expected":0,"passed":true},{"actual":2,"check":"multiple segments","expected":1,"passed":false},{"actual":0,"check":"split closes codon","expected":0,"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"one carried base\", \"actual\": 1, \"expected\": 2, \"passed\": false}, {\"check\": \"two carried bases\", \"actual\": 2, \"expected\": 1, \"passed\": false}, {\"check\": \"aligned exon\", \"actual\": 0, \"expected\": 0, \"passed\": true}, {\"check\": \"no preceding exon\", \"actual\": 0, \"expected\": 0, \"passed\": true}, {\"check\": \"multiple segments\", \"actual\": 2, \"expected\": 1, \"passed\": false}, {\"check\": \"split closes codon\", \"actual\": 0, \"expected\": 0, \"passed\": true}], \"passed\": false}\n"},"fixed":{"elapsed_ms":40.93,"exit_code":0,"observations":[{"actual":2,"check":"one carried base","expected":2,"passed":true},{"actual":1,"check":"two carried bases","expected":1,"passed":true},{"actual":0,"check":"aligned exon","expected":0,"passed":true},{"actual":0,"check":"no preceding exon","expected":0,"passed":true},{"actual":1,"check":"multiple segments","expected":1,"passed":true},{"actual":0,"check":"split closes codon","expected":0,"passed":true}],"passed":true,"stderr":"","stdout":"{\"observations\": [{\"check\": \"one carried base\", \"actual\": 2, \"expected\": 2, \"passed\": true}, {\"check\": \"two carried bases\", \"actual\": 1, \"expected\": 1, \"passed\": true}, {\"check\": \"aligned exon\", \"actual\": 0, \"expected\": 0, \"passed\": true}, {\"check\": \"no preceding exon\", \"actual\": 0, \"expected\": 0, \"passed\": true}, {\"check\": \"multiple segments\", \"actual\": 1, \"expected\": 1, \"passed\": true}, {\"check\": \"split closes codon\", \"actual\": 0, \"expected\": 0, \"passed\": true}], \"passed\": true}\n"}},"verified":true,"visibility":"public"}