{"abstract":"Coding coordinates include untranslated transcript prefix.","category":"Genomic coordinate mapping","checks":6,"contract":"For half-open coding transcript range [start,end), return [zero-based codon,within-codon offset]; outside coding range return None.","evaluation_group":"model-3acddd1498936eb2","failed_approach":"Subtracting the origin without excluding downstream untranslated bases invents codons.","family":"z-genetics_coordinates-cds-origin","id":"FA-12581","implementations":{"attempt":{"sha256":"caa6d361087fb4d5cfdedd2f337205db861887a829c20d3d25c2af2dcceff664","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(start, end, pos):\n    return [(pos-start)//3,(pos-start)%3] if pos>=start else None\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ns=N+4;e=s+9\ncheck('coding origin',solve(s,e,s),[0,0])\ncheck('second codon',solve(s,e,s+3),[1,0])\ncheck('within codon',solve(s,e,s+5),[1,2])\ncheck('last coding base',solve(s,e,e-1),[2,2])\ncheck('upstream untranslated',solve(s,e,s-1),None)\ncheck('downstream untranslated',solve(s,e,e),None)\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":"7e7d464c6c83d3f8d4d07feae7eacc4173bc2a25d6347de25e78162c15e08af0","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(start, end, pos):\n    return [pos//3,pos%3]\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ns=N+4;e=s+9\ncheck('coding origin',solve(s,e,s),[0,0])\ncheck('second codon',solve(s,e,s+3),[1,0])\ncheck('within codon',solve(s,e,s+5),[1,2])\ncheck('last coding base',solve(s,e,e-1),[2,2])\ncheck('upstream untranslated',solve(s,e,s-1),None)\ncheck('downstream untranslated',solve(s,e,e),None)\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":"2a893fd7930826e59ce7eadd34565584b7ca5a8e2646602bf3bc067bb3872913","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(start, end, pos):\n    return [(pos-start)//3,(pos-start)%3] if start<=pos<end else None\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ns=N+4;e=s+9\ncheck('coding origin',solve(s,e,s),[0,0])\ncheck('second codon',solve(s,e,s+3),[1,0])\ncheck('within codon',solve(s,e,s+5),[1,2])\ncheck('last coding base',solve(s,e,e-1),[2,2])\ncheck('upstream untranslated',solve(s,e,s-1),None)\ncheck('downstream untranslated',solve(s,e,e),None)\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-cds-origin","generated_at":"2026-09-29T14:38:58.145581+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":"Subtract coding start and reject both untranslated regions before calculating codon and within-codon offset.","root_cause":"Coding position uses full transcript offset as its origin.","sha256":"02a0f5c34e80558fc7dfdb2a7105c4a8cd834fcb75adb27159e5181bd3d889a1","title":"Coding coordinates include untranslated transcript prefix · case 01","variant":1,"variant_policy":"Five numbered records share a model and may reuse boundary fixtures.","verification":{"attempt":{"elapsed_ms":40.283,"exit_code":1,"observations":[{"actual":[0,0],"check":"coding origin","expected":[0,0],"passed":true},{"actual":[1,0],"check":"second codon","expected":[1,0],"passed":true},{"actual":[1,2],"check":"within codon","expected":[1,2],"passed":true},{"actual":[2,2],"check":"last coding base","expected":[2,2],"passed":true},{"actual":null,"check":"upstream untranslated","expected":null,"passed":true},{"actual":[3,0],"check":"downstream untranslated","expected":null,"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"coding origin\", \"actual\": [0, 0], \"expected\": [0, 0], \"passed\": true}, {\"check\": \"second codon\", \"actual\": [1, 0], \"expected\": [1, 0], \"passed\": true}, {\"check\": \"within codon\", \"actual\": [1, 2], \"expected\": [1, 2], \"passed\": true}, {\"check\": \"last coding base\", \"actual\": [2, 2], \"expected\": [2, 2], \"passed\": true}, {\"check\": \"upstream untranslated\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"downstream untranslated\", \"actual\": [3, 0], \"expected\": null, \"passed\": false}], \"passed\": false}\n"},"broken":{"elapsed_ms":40.966,"exit_code":1,"observations":[{"actual":[1,2],"check":"coding origin","expected":[0,0],"passed":false},{"actual":[2,2],"check":"second codon","expected":[1,0],"passed":false},{"actual":[3,1],"check":"within codon","expected":[1,2],"passed":false},{"actual":[4,1],"check":"last coding base","expected":[2,2],"passed":false},{"actual":[1,1],"check":"upstream untranslated","expected":null,"passed":false},{"actual":[4,2],"check":"downstream untranslated","expected":null,"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"coding origin\", \"actual\": [1, 2], \"expected\": [0, 0], \"passed\": false}, {\"check\": \"second codon\", \"actual\": [2, 2], \"expected\": [1, 0], \"passed\": false}, {\"check\": \"within codon\", \"actual\": [3, 1], \"expected\": [1, 2], \"passed\": false}, {\"check\": \"last coding base\", \"actual\": [4, 1], \"expected\": [2, 2], \"passed\": false}, {\"check\": \"upstream untranslated\", \"actual\": [1, 1], \"expected\": null, \"passed\": false}, {\"check\": \"downstream untranslated\", \"actual\": [4, 2], \"expected\": null, \"passed\": false}], \"passed\": false}\n"},"fixed":{"elapsed_ms":40.318,"exit_code":0,"observations":[{"actual":[0,0],"check":"coding origin","expected":[0,0],"passed":true},{"actual":[1,0],"check":"second codon","expected":[1,0],"passed":true},{"actual":[1,2],"check":"within codon","expected":[1,2],"passed":true},{"actual":[2,2],"check":"last coding base","expected":[2,2],"passed":true},{"actual":null,"check":"upstream untranslated","expected":null,"passed":true},{"actual":null,"check":"downstream untranslated","expected":null,"passed":true}],"passed":true,"stderr":"","stdout":"{\"observations\": [{\"check\": \"coding origin\", \"actual\": [0, 0], \"expected\": [0, 0], \"passed\": true}, {\"check\": \"second codon\", \"actual\": [1, 0], \"expected\": [1, 0], \"passed\": true}, {\"check\": \"within codon\", \"actual\": [1, 2], \"expected\": [1, 2], \"passed\": true}, {\"check\": \"last coding base\", \"actual\": [2, 2], \"expected\": [2, 2], \"passed\": true}, {\"check\": \"upstream untranslated\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"downstream untranslated\", \"actual\": null, \"expected\": null, \"passed\": true}], \"passed\": true}\n"}},"verified":true,"visibility":"public"}