{"abstract":"Unknown bases are deleted before k-mer extraction.","category":"Biological sequence representation","checks":6,"contract":"For uppercase ACGTN input, return length-k contiguous windows containing no N, preserving repeats and order; k positive. N breaks eligibility without removing positions.","evaluation_group":"model-67dd59398dfb5d1f","failed_approach":"Replacing unknown bases with A fabricates concrete windows.","family":"z-bio_sequences-ambiguous-kmer-barrier","id":"FA-12536","implementations":{"attempt":{"sha256":"11a77f4be2844729bd0af09228aaeaaa3d3173641ce917db13ae5aa5241470b6","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(s,k):\n    s=s.replace('N','A')\n    return [s[i:i+k] for i in range(len(s)-k+1)]\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('variable barrier', solve('A'*N+'NC',2), ['AA']*max(0,N-1))\ncheck('unknown only', solve('NN',1), [])\ncheck('empty', solve('',2), [])\ncheck('too short', solve('A',2), [])\ncheck('valid duplicate', solve('AAA',2), ['AA','AA'])\ncheck('ends', solve('NACN',2), ['AC'])\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":"cc4b167a54edcf1baad73e7bf1b036b762402bb02f18e3788c09ed209787e330","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(s,k):\n    s=s.replace('N','')\n    return [s[i:i+k] for i in range(len(s)-k+1)]\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('variable barrier', solve('A'*N+'NC',2), ['AA']*max(0,N-1))\ncheck('unknown only', solve('NN',1), [])\ncheck('empty', solve('',2), [])\ncheck('too short', solve('A',2), [])\ncheck('valid duplicate', solve('AAA',2), ['AA','AA'])\ncheck('ends', solve('NACN',2), ['AC'])\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":"65e89aacefbeefd6cef1aaf3eec26e6e080f32dbaa6213d3c482bcb39b5a2b08","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(s,k):\n    return [s[i:i+k] for i in range(len(s)-k+1) if 'N' not in s[i:i+k]]\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\ncheck('variable barrier', solve('A'*N+'NC',2), ['AA']*max(0,N-1))\ncheck('unknown only', solve('NN',1), [])\ncheck('empty', solve('',2), [])\ncheck('too short', solve('A',2), [])\ncheck('valid duplicate', solve('AAA',2), ['AA','AA'])\ncheck('ends', solve('NACN',2), ['AC'])\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-ambiguous-kmer-barrier","generated_at":"2026-09-29T14:38:57.852817+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.","repair":"Implement the stated sequence contract while preserving its positional and symbol semantics.","root_cause":"Deletion joins flanking bases into nonexistent contiguous windows.","sha256":"ef806b58df459ed834b5719f5798764600531fbd51a7861ecdeff7df7fcb124a","title":"Unknown bases are deleted before k-mer extraction · case 01","variant":1,"variant_policy":"Five numbered records share a model and may reuse boundary fixtures.","verification":{"attempt":{"elapsed_ms":41.304,"exit_code":1,"observations":[{"actual":["AA","AC"],"check":"variable barrier","expected":[],"passed":false},{"actual":["A","A"],"check":"unknown only","expected":[],"passed":false},{"actual":[],"check":"empty","expected":[],"passed":true},{"actual":[],"check":"too short","expected":[],"passed":true},{"actual":["AA","AA"],"check":"valid duplicate","expected":["AA","AA"],"passed":true},{"actual":["AA","AC","CA"],"check":"ends","expected":["AC"],"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"variable barrier\", \"actual\": [\"AA\", \"AC\"], \"expected\": [], \"passed\": false}, {\"check\": \"unknown only\", \"actual\": [\"A\", \"A\"], \"expected\": [], \"passed\": false}, {\"check\": \"empty\", \"actual\": [], \"expected\": [], \"passed\": true}, {\"check\": \"too short\", \"actual\": [], \"expected\": [], \"passed\": true}, {\"check\": \"valid duplicate\", \"actual\": [\"AA\", \"AA\"], \"expected\": [\"AA\", \"AA\"], \"passed\": true}, {\"check\": \"ends\", \"actual\": [\"AA\", \"AC\", \"CA\"], \"expected\": [\"AC\"], \"passed\": false}], \"passed\": false}\n"},"broken":{"elapsed_ms":43.833,"exit_code":1,"observations":[{"actual":["AC"],"check":"variable barrier","expected":[],"passed":false},{"actual":[],"check":"unknown only","expected":[],"passed":true},{"actual":[],"check":"empty","expected":[],"passed":true},{"actual":[],"check":"too short","expected":[],"passed":true},{"actual":["AA","AA"],"check":"valid duplicate","expected":["AA","AA"],"passed":true},{"actual":["AC"],"check":"ends","expected":["AC"],"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"variable barrier\", \"actual\": [\"AC\"], \"expected\": [], \"passed\": false}, {\"check\": \"unknown only\", \"actual\": [], \"expected\": [], \"passed\": true}, {\"check\": \"empty\", \"actual\": [], \"expected\": [], \"passed\": true}, {\"check\": \"too short\", \"actual\": [], \"expected\": [], \"passed\": true}, {\"check\": \"valid duplicate\", \"actual\": [\"AA\", \"AA\"], \"expected\": [\"AA\", \"AA\"], \"passed\": true}, {\"check\": \"ends\", \"actual\": [\"AC\"], \"expected\": [\"AC\"], \"passed\": true}], \"passed\": false}\n"},"fixed":{"elapsed_ms":41.855,"exit_code":0,"observations":[{"actual":[],"check":"variable barrier","expected":[],"passed":true},{"actual":[],"check":"unknown only","expected":[],"passed":true},{"actual":[],"check":"empty","expected":[],"passed":true},{"actual":[],"check":"too short","expected":[],"passed":true},{"actual":["AA","AA"],"check":"valid duplicate","expected":["AA","AA"],"passed":true},{"actual":["AC"],"check":"ends","expected":["AC"],"passed":true}],"passed":true,"stderr":"","stdout":"{\"observations\": [{\"check\": \"variable barrier\", \"actual\": [], \"expected\": [], \"passed\": true}, {\"check\": \"unknown only\", \"actual\": [], \"expected\": [], \"passed\": true}, {\"check\": \"empty\", \"actual\": [], \"expected\": [], \"passed\": true}, {\"check\": \"too short\", \"actual\": [], \"expected\": [], \"passed\": true}, {\"check\": \"valid duplicate\", \"actual\": [\"AA\", \"AA\"], \"expected\": [\"AA\", \"AA\"], \"passed\": true}, {\"check\": \"ends\", \"actual\": [\"AC\"], \"expected\": [\"AC\"], \"passed\": true}], \"passed\": true}\n"}},"verified":true,"visibility":"public"}