{"abstract":"Quality filtering separates scores from surviving bases.","category":"Biological sequence representation","checks":6,"contract":"Given sequence and same-length integer qualities, return [retained_string,retained_qualities] preserving pairs whose quality is >= cutoff.","contract_signature":"s,q,cut","evaluation_group":"model-710f106d558e1b8d","failed_approach":"Filtering scores by a strict threshold disagrees with inclusive base selection.","family":"z-bio_sequences-quality-mask-sync","id":"FA-12521","implementations":{"attempt":{"sha256":"cc83be163fc624e5f6efe4abb3ed4778bb9736bab484cc456b9d633aa81bb08f","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(s,q,cut):\n    return [''.join(c for c,v in zip(s,q) if v>=cut),[v for v in q if v>cut]]\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('variable threshold', solve('ACT',[N-1,N,N+1],N), ['CT',[N,N+1]])\ncheck('empty', solve('',[],2), ['',[]])\ncheck('all removed', solve('AC',[0,1],2), ['',[]])\ncheck('all retained', solve('AC',[2,3],2), ['AC',[2,3]])\ncheck('equality', solve('T',[0],0), ['T',[0]])\ncheck('internal hole', solve('ACT',[5,0,4],3), ['AT',[5,4]])\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":"9d37abcdaa34b9a94fc91d21b043a55cac7b453a8eb075520127f719764e04b3","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(s,q,cut):\n    return [''.join(c for c,v in zip(s,q) if v>=cut),q]\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('variable threshold', solve('ACT',[N-1,N,N+1],N), ['CT',[N,N+1]])\ncheck('empty', solve('',[],2), ['',[]])\ncheck('all removed', solve('AC',[0,1],2), ['',[]])\ncheck('all retained', solve('AC',[2,3],2), ['AC',[2,3]])\ncheck('equality', solve('T',[0],0), ['T',[0]])\ncheck('internal hole', solve('ACT',[5,0,4],3), ['AT',[5,4]])\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-quality-mask-sync","generated_at":"2026-09-29T14:38:57.529398+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":"Bases are selected but the original quality array is retained.","sha256":"f2e08982daafe4ee08f44b9de1f2fa54a374564cd859f27c9430969e9a7b94fe","title":"Quality filtering separates scores from surviving bases · 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":42.416,"exit_code":1,"observations":[{"actual":["CT",[2]],"check":"variable threshold","expected":["CT",[1,2]],"passed":false},{"actual":["",[]],"check":"empty","expected":["",[]],"passed":true},{"actual":["",[]],"check":"all removed","expected":["",[]],"passed":true},{"actual":["AC",[3]],"check":"all retained","expected":["AC",[2,3]],"passed":false},{"actual":["T",[]],"check":"equality","expected":["T",[0]],"passed":false},{"actual":["AT",[5,4]],"check":"internal hole","expected":["AT",[5,4]],"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"variable threshold\", \"actual\": [\"CT\", [2]], \"expected\": [\"CT\", [1, 2]], \"passed\": false}, {\"check\": \"empty\", \"actual\": [\"\", []], \"expected\": [\"\", []], \"passed\": true}, {\"check\": \"all removed\", \"actual\": [\"\", []], \"expected\": [\"\", []], \"passed\": true}, {\"check\": \"all retained\", \"actual\": [\"AC\", [3]], \"expected\": [\"AC\", [2, 3]], \"passed\": false}, {\"check\": \"equality\", \"actual\": [\"T\", []], \"expected\": [\"T\", [0]], \"passed\": false}, {\"check\": \"internal hole\", \"actual\": [\"AT\", [5, 4]], \"expected\": [\"AT\", [5, 4]], \"passed\": true}], \"passed\": false}\n"},"broken":{"elapsed_ms":38.68,"exit_code":1,"observations":[{"actual":["CT",[0,1,2]],"check":"variable threshold","expected":["CT",[1,2]],"passed":false},{"actual":["",[]],"check":"empty","expected":["",[]],"passed":true},{"actual":["",[0,1]],"check":"all removed","expected":["",[]],"passed":false},{"actual":["AC",[2,3]],"check":"all retained","expected":["AC",[2,3]],"passed":true},{"actual":["T",[0]],"check":"equality","expected":["T",[0]],"passed":true},{"actual":["AT",[5,0,4]],"check":"internal hole","expected":["AT",[5,4]],"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"variable threshold\", \"actual\": [\"CT\", [0, 1, 2]], \"expected\": [\"CT\", [1, 2]], \"passed\": false}, {\"check\": \"empty\", \"actual\": [\"\", []], \"expected\": [\"\", []], \"passed\": true}, {\"check\": \"all removed\", \"actual\": [\"\", [0, 1]], \"expected\": [\"\", []], \"passed\": false}, {\"check\": \"all retained\", \"actual\": [\"AC\", [2, 3]], \"expected\": [\"AC\", [2, 3]], \"passed\": true}, {\"check\": \"equality\", \"actual\": [\"T\", [0]], \"expected\": [\"T\", [0]], \"passed\": true}, {\"check\": \"internal hole\", \"actual\": [\"AT\", [5, 0, 4]], \"expected\": [\"AT\", [5, 4]], \"passed\": false}], \"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."}}