{"abstract":"Equal read counts hide mismatched mate identities.","category":"Scientific pipeline provenance","checks":6,"contract":"Each mate stream has unique read IDs; return paired intersection and symmetric-difference orphan IDs as sorted lists.","contract_signature":"left, right","evaluation_group":"model-aa8c0cf8118e7a0d","failed_approach":"Comparing sorted IDs only checks equal counts and overlooks unmatched reads.","family":"z-scientific_pipelines-paired-read-identity","id":"FA-11896","implementations":{"attempt":{"sha256":"6d651f59d927a90846f5504aa21a376ae893fc11aac1584c02fada2c6fd80760","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(left, right):\n    return {'paired': sorted(left) if len(left)==len(right) else [], 'orphans': sorted(set(left)^set(right))}\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\na='read'+str(N)\ncheck('same size different mates', solve([a,'b'], [a,'c']), {'paired':[a], 'orphans':['b','c']})\ncheck('reordered mates', solve(['b',a], [a,'b']), {'paired':sorted(['b',a]), 'orphans':[]})\ncheck('left orphan', solve([a,'b'], [a]), {'paired':[a], 'orphans':['b']})\ncheck('right orphan', solve([a], [a,'b']), {'paired':[a], 'orphans':['b']})\ncheck('no reads', solve([], []), {'paired':[], 'orphans':[]})\ncheck('no overlap', solve(['a'], ['b']), {'paired':[], 'orphans':['a','b']})\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":"79caaaadb5ea23d6e9d0b4908cbedb116d6951b15749fe8e0caf84f3569c2644","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(left, right):\n    return {'paired': sorted(left[:min(len(left),len(right))]), 'orphans': []}\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\na='read'+str(N)\ncheck('same size different mates', solve([a,'b'], [a,'c']), {'paired':[a], 'orphans':['b','c']})\ncheck('reordered mates', solve(['b',a], [a,'b']), {'paired':sorted(['b',a]), 'orphans':[]})\ncheck('left orphan', solve([a,'b'], [a]), {'paired':[a], 'orphans':['b']})\ncheck('right orphan', solve([a], [a,'b']), {'paired':[a], 'orphans':['b']})\ncheck('no reads', solve([], []), {'paired':[], 'orphans':[]})\ncheck('no overlap', solve(['a'], ['b']), {'paired':[], 'orphans':['a','b']})\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":"In-memory symbolic records only; no instrument, assay, or production workflow validation. 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-scientific_pipelines-paired-read-identity","generated_at":"2026-09-29T14:38:51.961075+00:00","license":"CC0-1.0","python":"3.12.14","seed":1,"split":"open-access"},"relevance":"A deterministic offline model of scientific workflow bookkeeping; the fixtures test provenance contracts without modeling instruments or biological inference.","root_cause":"Pairing uses position without checking read identity.","sha256":"9d3f83fbc207282bf5d3f613b902ba5c3ad253316b792527ffba679dabdf1922","title":"Equal read counts hide mismatched mate identities · 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":41.26,"exit_code":1,"observations":[{"actual":{"orphans":["b","c"],"paired":["b","read1"]},"check":"same size different mates","expected":{"orphans":["b","c"],"paired":["read1"]},"passed":false},{"actual":{"orphans":[],"paired":["b","read1"]},"check":"reordered mates","expected":{"orphans":[],"paired":["b","read1"]},"passed":true},{"actual":{"orphans":["b"],"paired":[]},"check":"left orphan","expected":{"orphans":["b"],"paired":["read1"]},"passed":false},{"actual":{"orphans":["b"],"paired":[]},"check":"right orphan","expected":{"orphans":["b"],"paired":["read1"]},"passed":false},{"actual":{"orphans":[],"paired":[]},"check":"no reads","expected":{"orphans":[],"paired":[]},"passed":true},{"actual":{"orphans":["a","b"],"paired":["a"]},"check":"no overlap","expected":{"orphans":["a","b"],"paired":[]},"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"same size different mates\", \"actual\": {\"paired\": [\"b\", \"read1\"], \"orphans\": [\"b\", \"c\"]}, \"expected\": {\"paired\": [\"read1\"], \"orphans\": [\"b\", \"c\"]}, \"passed\": false}, {\"check\": \"reordered mates\", \"actual\": {\"paired\": [\"b\", \"read1\"], \"orphans\": []}, \"expected\": {\"paired\": [\"b\", \"read1\"], \"orphans\": []}, \"passed\": true}, {\"check\": \"left orphan\", \"actual\": {\"paired\": [], \"orphans\": [\"b\"]}, \"expected\": {\"paired\": [\"read1\"], \"orphans\": [\"b\"]}, \"passed\": false}, {\"check\": \"right orphan\", \"actual\": {\"paired\": [], \"orphans\": [\"b\"]}, \"expected\": {\"paired\": [\"read1\"], \"orphans\": [\"b\"]}, \"passed\": false}, {\"check\": \"no reads\", \"actual\": {\"paired\": [], \"orphans\": []}, \"expected\": {\"paired\": [], \"orphans\": []}, \"passed\": true}, {\"check\": \"no overlap\", \"actual\": {\"paired\": [\"a\"], \"orphans\": [\"a\", \"b\"]}, \"expected\": {\"paired\": [], \"orphans\": [\"a\", \"b\"]}, \"passed\": false}], \"passed\": false}\n"},"broken":{"elapsed_ms":39.118,"exit_code":1,"observations":[{"actual":{"orphans":[],"paired":["b","read1"]},"check":"same size different mates","expected":{"orphans":["b","c"],"paired":["read1"]},"passed":false},{"actual":{"orphans":[],"paired":["b","read1"]},"check":"reordered mates","expected":{"orphans":[],"paired":["b","read1"]},"passed":true},{"actual":{"orphans":[],"paired":["read1"]},"check":"left orphan","expected":{"orphans":["b"],"paired":["read1"]},"passed":false},{"actual":{"orphans":[],"paired":["read1"]},"check":"right orphan","expected":{"orphans":["b"],"paired":["read1"]},"passed":false},{"actual":{"orphans":[],"paired":[]},"check":"no reads","expected":{"orphans":[],"paired":[]},"passed":true},{"actual":{"orphans":[],"paired":["a"]},"check":"no overlap","expected":{"orphans":["a","b"],"paired":[]},"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"same size different mates\", \"actual\": {\"paired\": [\"b\", \"read1\"], \"orphans\": []}, \"expected\": {\"paired\": [\"read1\"], \"orphans\": [\"b\", \"c\"]}, \"passed\": false}, {\"check\": \"reordered mates\", \"actual\": {\"paired\": [\"b\", \"read1\"], \"orphans\": []}, \"expected\": {\"paired\": [\"b\", \"read1\"], \"orphans\": []}, \"passed\": true}, {\"check\": \"left orphan\", \"actual\": {\"paired\": [\"read1\"], \"orphans\": []}, \"expected\": {\"paired\": [\"read1\"], \"orphans\": [\"b\"]}, \"passed\": false}, {\"check\": \"right orphan\", \"actual\": {\"paired\": [\"read1\"], \"orphans\": []}, \"expected\": {\"paired\": [\"read1\"], \"orphans\": [\"b\"]}, \"passed\": false}, {\"check\": \"no reads\", \"actual\": {\"paired\": [], \"orphans\": []}, \"expected\": {\"paired\": [], \"orphans\": []}, \"passed\": true}, {\"check\": \"no overlap\", \"actual\": {\"paired\": [\"a\"], \"orphans\": []}, \"expected\": {\"paired\": [], \"orphans\": [\"a\", \"b\"]}, \"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."}}