{"abstract":"Inserted query bases acquire fabricated reference coordinates.","category":"Genomic coordinate mapping","checks":6,"contract":"Map query bases through M/I/D; query insertion bases have no reference coordinate.","contract_signature":"ops, start, pos","evaluation_group":"z-genetics_coordinates-query-reference-alignment","failed_approach":"Skipping insertion query advancement shifts all downstream query coordinates.","family":"z-genetics_coordinates-insertion-unmapped","id":"FA-12571","implementations":{"attempt":{"sha256":"033d2305a6f0e8b950b01c0881a6b25dbaa3be0e1230b10eb8f03a1e39beba62","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(ops, start, pos):\n    q=0;r=start\n    for op,size in ops:\n     if op=='M':\n      if q <= pos < q+size: return r+pos-q\n      q+=size;r+=size\n     elif op=='I':\n      if q <= pos < q+size: return None\n      q+=0\n     elif op=='D': r+=size\n    return None\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\no=[('M',2),('I',N+1),('M',3)]\ncheck('first inserted',solve(o,50,2),None)\ncheck('last inserted',solve(o,50,N+2),None)\ncheck('first downstream',solve(o,50,N+3),52)\ncheck('last downstream',solve(o,50,N+5),54)\ncheck('before insertion',solve(o,50,1),51)\ncheck('past end',solve(o,50,N+6),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":"f5114ae981bb83c0e684fd79753f35463659c95f07908c4caf17f185aa73b291","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(ops, start, pos):\n    q=0;r=start\n    for op,size in ops:\n     if op=='M':\n      if q <= pos < q+size: return r+pos-q\n      q+=size;r+=size\n     elif op=='I':\n      if q <= pos < q+size: return r\n      q+=size\n     elif op=='D': r+=size\n    return None\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\no=[('M',2),('I',N+1),('M',3)]\ncheck('first inserted',solve(o,50,2),None)\ncheck('last inserted',solve(o,50,N+2),None)\ncheck('first downstream',solve(o,50,N+3),52)\ncheck('last downstream',solve(o,50,N+5),54)\ncheck('before insertion',solve(o,50,1),51)\ncheck('past end',solve(o,50,N+6),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-insertion-unmapped","generated_at":"2026-09-29T14:38:58.145309+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.","root_cause":"Inserted bases are projected onto the next reference position.","sha256":"0ca878c2f7fd2f0e1836738e630d7ea82cf69fcc3759363f6bd3dac315f45785","title":"Inserted query bases acquire fabricated reference coordinates · case 01","variant":1,"variant_policy":"Five numbered records share a model and may reuse boundary fixtures.","verified":true,"visibility":"public","verification":{"attempt":{"elapsed_ms":43.367,"exit_code":1,"observations":[{"actual":null,"check":"first inserted","expected":null,"passed":true},{"actual":null,"check":"last inserted","expected":null,"passed":true},{"actual":54,"check":"first downstream","expected":52,"passed":false},{"actual":null,"check":"last downstream","expected":54,"passed":false},{"actual":51,"check":"before insertion","expected":51,"passed":true},{"actual":null,"check":"past end","expected":null,"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"first inserted\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"last inserted\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"first downstream\", \"actual\": 54, \"expected\": 52, \"passed\": false}, {\"check\": \"last downstream\", \"actual\": null, \"expected\": 54, \"passed\": false}, {\"check\": \"before insertion\", \"actual\": 51, \"expected\": 51, \"passed\": true}, {\"check\": \"past end\", \"actual\": null, \"expected\": null, \"passed\": true}], \"passed\": false}\n"},"broken":{"elapsed_ms":44.031,"exit_code":1,"observations":[{"actual":52,"check":"first inserted","expected":null,"passed":false},{"actual":52,"check":"last inserted","expected":null,"passed":false},{"actual":52,"check":"first downstream","expected":52,"passed":true},{"actual":54,"check":"last downstream","expected":54,"passed":true},{"actual":51,"check":"before insertion","expected":51,"passed":true},{"actual":null,"check":"past end","expected":null,"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"first inserted\", \"actual\": 52, \"expected\": null, \"passed\": false}, {\"check\": \"last inserted\", \"actual\": 52, \"expected\": null, \"passed\": false}, {\"check\": \"first downstream\", \"actual\": 52, \"expected\": 52, \"passed\": true}, {\"check\": \"last downstream\", \"actual\": 54, \"expected\": 54, \"passed\": true}, {\"check\": \"before insertion\", \"actual\": 51, \"expected\": 51, \"passed\": true}, {\"check\": \"past end\", \"actual\": null, \"expected\": null, \"passed\": true}], \"passed\": false}\n"}},"member_only":{"stages":["fixed"],"fields":["implementations.fixed","verification.fixed","harness","repair"],"note":"The verified repair, its recorded checks, the repair description, and the scoring harness are available to members."}}