{"abstract":"Ambiguous sequence symbols are compared as literal letters.","category":"Biological sequence representation","checks":6,"contract":"For equal-length strings over A,C,G,T,R,N, return whether every aligned pair has intersecting sets; R={A,G}, N={A,C,G,T}. Unequal lengths are false.","contract_signature":"a,b","evaluation_group":"model-d710fe8c7c9b1449","failed_approach":"Subset comparison requires certainty although the contract asks possibility.","family":"z-bio_sequences-ambiguity-overlap","id":"FA-12496","implementations":{"attempt":{"sha256":"40c7e4aeef86697e33f73f4508ec95597ee15e195c9f17317e5a2246ef8606d0","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(a,b):\n    m={'A':set('A'),'C':set('C'),'G':set('G'),'T':set('T'),'R':set('AG'),'N':set('ACGT')}\n    return len(a)==len(b) and all(m[x]<=m[y] for x,y in zip(a,b))\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('variable ambiguity', solve('R'*N,'A'*N), True)\ncheck('incompatible', solve('R','C'), False)\ncheck('unknown possible', solve('N','T'), True)\ncheck('empty', solve('',''), True)\ncheck('length', solve('A','AA'), False)\ncheck('late mismatch', solve('NA','TC'), False)\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":"3bf2cd4692ec36681cf8126d5913d42441359af72d056b987175bb551a397077","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(a,b):\n    return a==b\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('variable ambiguity', solve('R'*N,'A'*N), True)\ncheck('incompatible', solve('R','C'), False)\ncheck('unknown possible', solve('N','T'), True)\ncheck('empty', solve('',''), True)\ncheck('length', solve('A','AA'), False)\ncheck('late mismatch', solve('NA','TC'), False)\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 strings and explicit policies only; no biological interpretation or laboratory workflow. 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-bio_sequences-ambiguity-overlap","generated_at":"2026-09-29T14:38:57.484891+00:00","license":"CC0-1.0","python":"3.12.14","seed":1,"split":"open-access"},"relevance":"An offline abstract sequence-data model; useful for testing representation invariants without biological inference.","root_cause":"Literal equality ignores possible-base sets.","sha256":"a4a41eb948d9588d748a7d8c551f355b5b1e5c0b4f0445b0815bc267ac2d546f","title":"Ambiguous sequence symbols are compared as literal letters · 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":40.905,"exit_code":1,"observations":[{"actual":false,"check":"variable ambiguity","expected":true,"passed":false},{"actual":false,"check":"incompatible","expected":false,"passed":true},{"actual":false,"check":"unknown possible","expected":true,"passed":false},{"actual":true,"check":"empty","expected":true,"passed":true},{"actual":false,"check":"length","expected":false,"passed":true},{"actual":false,"check":"late mismatch","expected":false,"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"variable ambiguity\", \"actual\": false, \"expected\": true, \"passed\": false}, {\"check\": \"incompatible\", \"actual\": false, \"expected\": false, \"passed\": true}, {\"check\": \"unknown possible\", \"actual\": false, \"expected\": true, \"passed\": false}, {\"check\": \"empty\", \"actual\": true, \"expected\": true, \"passed\": true}, {\"check\": \"length\", \"actual\": false, \"expected\": false, \"passed\": true}, {\"check\": \"late mismatch\", \"actual\": false, \"expected\": false, \"passed\": true}], \"passed\": false}\n"},"broken":{"elapsed_ms":42.645,"exit_code":1,"observations":[{"actual":false,"check":"variable ambiguity","expected":true,"passed":false},{"actual":false,"check":"incompatible","expected":false,"passed":true},{"actual":false,"check":"unknown possible","expected":true,"passed":false},{"actual":true,"check":"empty","expected":true,"passed":true},{"actual":false,"check":"length","expected":false,"passed":true},{"actual":false,"check":"late mismatch","expected":false,"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"variable ambiguity\", \"actual\": false, \"expected\": true, \"passed\": false}, {\"check\": \"incompatible\", \"actual\": false, \"expected\": false, \"passed\": true}, {\"check\": \"unknown possible\", \"actual\": false, \"expected\": true, \"passed\": false}, {\"check\": \"empty\", \"actual\": true, \"expected\": true, \"passed\": true}, {\"check\": \"length\", \"actual\": false, \"expected\": false, \"passed\": true}, {\"check\": \"late mismatch\", \"actual\": false, \"expected\": false, \"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."}}