{"abstract":"Lifted coordinates discard ambiguous chain mappings.","category":"Genomic coordinate mapping","checks":6,"contract":"Synthetic chain hits are [contig,base] mappings for one source base; return the unique destination pair or None.","evaluation_group":"model-608374259584c511","failed_approach":"Rejecting multiple hits discards redundant chains that agree exactly.","family":"z-genetics_coordinates-chain-multimap","id":"FA-12576","implementations":{"attempt":{"sha256":"6825a196308eac056d771402d4bec673cca05124e7a0f58724b9ab7cbba8a562","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(hits):\n    return hits[0] if len(hits)==1 else None\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('conflicting positions',solve([['a',N],['a',N+1]]),None)\ncheck('redundant chains',solve([['a',N],['a',N]]),['a',N])\ncheck('different contigs',solve([['a',N],['b',N]]),None)\ncheck('single hit',solve([['b',N]]),['b',N])\ncheck('no hit',solve([]),None)\ncheck('three agreeing',solve([['a',N]]*3),['a',N])\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":"2b99121db99ff4b2aa7fc5187133dadb476352eeb162e909fb109a2af63fde31","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(hits):\n    return hits[0] if hits else None\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('conflicting positions',solve([['a',N],['a',N+1]]),None)\ncheck('redundant chains',solve([['a',N],['a',N]]),['a',N])\ncheck('different contigs',solve([['a',N],['b',N]]),None)\ncheck('single hit',solve([['b',N]]),['b',N])\ncheck('no hit',solve([]),None)\ncheck('three agreeing',solve([['a',N]]*3),['a',N])\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":"78f0b3a143617a4c1b9015f266a0b81c8e07233ba0b5d37f0a32898deab3c315","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(hits):\n    unique=set(tuple(x) for x in hits)\n    return list(next(iter(unique))) if len(unique)==1 else None\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('conflicting positions',solve([['a',N],['a',N+1]]),None)\ncheck('redundant chains',solve([['a',N],['a',N]]),['a',N])\ncheck('different contigs',solve([['a',N],['b',N]]),None)\ncheck('single hit',solve([['b',N]]),['b',N])\ncheck('no hit',solve([]),None)\ncheck('three agreeing',solve([['a',N]]*3),['a',N])\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-chain-multimap","generated_at":"2026-09-29T14:38:58.144713+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 a coordinate only when the set of destination reference/base pairs has cardinality one.","root_cause":"First chain hit is returned even when alternative mappings disagree.","sha256":"4a96ee3dc8df796aa12865f63e7165e275162527126c6d3e308a471619c8230b","title":"Lifted coordinates discard ambiguous chain mappings · case 01","variant":1,"variant_policy":"Five numbered records share a model and may reuse boundary fixtures.","verification":{"attempt":{"elapsed_ms":43.407,"exit_code":1,"observations":[{"actual":null,"check":"conflicting positions","expected":null,"passed":true},{"actual":null,"check":"redundant chains","expected":["a",1],"passed":false},{"actual":null,"check":"different contigs","expected":null,"passed":true},{"actual":["b",1],"check":"single hit","expected":["b",1],"passed":true},{"actual":null,"check":"no hit","expected":null,"passed":true},{"actual":null,"check":"three agreeing","expected":["a",1],"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"conflicting positions\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"redundant chains\", \"actual\": null, \"expected\": [\"a\", 1], \"passed\": false}, {\"check\": \"different contigs\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"single hit\", \"actual\": [\"b\", 1], \"expected\": [\"b\", 1], \"passed\": true}, {\"check\": \"no hit\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"three agreeing\", \"actual\": null, \"expected\": [\"a\", 1], \"passed\": false}], \"passed\": false}\n"},"broken":{"elapsed_ms":40.81,"exit_code":1,"observations":[{"actual":["a",1],"check":"conflicting positions","expected":null,"passed":false},{"actual":["a",1],"check":"redundant chains","expected":["a",1],"passed":true},{"actual":["a",1],"check":"different contigs","expected":null,"passed":false},{"actual":["b",1],"check":"single hit","expected":["b",1],"passed":true},{"actual":null,"check":"no hit","expected":null,"passed":true},{"actual":["a",1],"check":"three agreeing","expected":["a",1],"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"conflicting positions\", \"actual\": [\"a\", 1], \"expected\": null, \"passed\": false}, {\"check\": \"redundant chains\", \"actual\": [\"a\", 1], \"expected\": [\"a\", 1], \"passed\": true}, {\"check\": \"different contigs\", \"actual\": [\"a\", 1], \"expected\": null, \"passed\": false}, {\"check\": \"single hit\", \"actual\": [\"b\", 1], \"expected\": [\"b\", 1], \"passed\": true}, {\"check\": \"no hit\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"three agreeing\", \"actual\": [\"a\", 1], \"expected\": [\"a\", 1], \"passed\": true}], \"passed\": false}\n"},"fixed":{"elapsed_ms":44.257,"exit_code":0,"observations":[{"actual":null,"check":"conflicting positions","expected":null,"passed":true},{"actual":["a",1],"check":"redundant chains","expected":["a",1],"passed":true},{"actual":null,"check":"different contigs","expected":null,"passed":true},{"actual":["b",1],"check":"single hit","expected":["b",1],"passed":true},{"actual":null,"check":"no hit","expected":null,"passed":true},{"actual":["a",1],"check":"three agreeing","expected":["a",1],"passed":true}],"passed":true,"stderr":"","stdout":"{\"observations\": [{\"check\": \"conflicting positions\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"redundant chains\", \"actual\": [\"a\", 1], \"expected\": [\"a\", 1], \"passed\": true}, {\"check\": \"different contigs\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"single hit\", \"actual\": [\"b\", 1], \"expected\": [\"b\", 1], \"passed\": true}, {\"check\": \"no hit\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"three agreeing\", \"actual\": [\"a\", 1], \"expected\": [\"a\", 1], \"passed\": true}], \"passed\": true}\n"}},"verified":true,"visibility":"public"}