{"abstract":"Contig aliases choose an arbitrary reference target.","category":"Genomic coordinate mapping","checks":6,"contract":"Names identify canonical contigs; aliases may collide. Exact canonical match wins; ambiguous or absent aliases return None.","contract_signature":"rows, name","evaluation_group":"model-5c39a43c83273d62","failed_approach":"Rejecting all multiple alias matches also rejects an exact canonical identifier.","family":"z-genetics_coordinates-alias-ambiguity","id":"FA-12551","implementations":{"attempt":{"sha256":"9e072018e34fe3eaf654832c0167d9c21f15dd164694b97525ddecb87d9fda3a","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(rows, name):\n    matches=[c for c,a in rows if name==c or name in a]\n    return matches[0] if len(matches)==1 else None\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\na='contig'+str(N)\nr=[(a,['x','shared']),('other',['shared',a]),('third',[])]\ncheck('ambiguous alias',solve(r,'shared'),None)\ncheck('canonical beats alias',solve(r,a),a)\ncheck('unique alias',solve(r,'x'),a)\ncheck('canonical other',solve(r,'other'),'other')\ncheck('canonical without alias',solve(r,'third'),'third')\ncheck('absent',solve(r,'missing'),None)\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":"ab6cd6653554e92579d64d567a96e3ecacfdb7cc0f7ffe5461d353a69367f3ab","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(rows, name):\n    return next((c for c,aliases in rows if name==c or name in aliases),None)\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\na='contig'+str(N)\nr=[(a,['x','shared']),('other',['shared',a]),('third',[])]\ncheck('ambiguous alias',solve(r,'shared'),None)\ncheck('canonical beats alias',solve(r,a),a)\ncheck('unique alias',solve(r,'x'),a)\ncheck('canonical other',solve(r,'other'),'other')\ncheck('canonical without alias',solve(r,'third'),'third')\ncheck('absent',solve(r,'missing'),None)\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-alias-ambiguity","generated_at":"2026-09-29T14:38:57.974745+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.","root_cause":"Alias normalization chooses the first candidate without detecting collisions.","sha256":"be46333441861d2b833f2015a83941386f9bc85e085427ea2ae9c125710deec4","title":"Contig aliases choose an arbitrary reference target · 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":43.135,"exit_code":1,"observations":[{"actual":null,"check":"ambiguous alias","expected":null,"passed":true},{"actual":null,"check":"canonical beats alias","expected":"contig1","passed":false},{"actual":"contig1","check":"unique alias","expected":"contig1","passed":true},{"actual":"other","check":"canonical other","expected":"other","passed":true},{"actual":"third","check":"canonical without alias","expected":"third","passed":true},{"actual":null,"check":"absent","expected":null,"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"ambiguous alias\", \"actual\": null, \"expected\": null, \"passed\": true}, {\"check\": \"canonical beats alias\", \"actual\": null, \"expected\": \"contig1\", \"passed\": false}, {\"check\": \"unique alias\", \"actual\": \"contig1\", \"expected\": \"contig1\", \"passed\": true}, {\"check\": \"canonical other\", \"actual\": \"other\", \"expected\": \"other\", \"passed\": true}, {\"check\": \"canonical without alias\", \"actual\": \"third\", \"expected\": \"third\", \"passed\": true}, {\"check\": \"absent\", \"actual\": null, \"expected\": null, \"passed\": true}], \"passed\": false}\n"},"broken":{"elapsed_ms":43.408,"exit_code":1,"observations":[{"actual":"contig1","check":"ambiguous alias","expected":null,"passed":false},{"actual":"contig1","check":"canonical beats alias","expected":"contig1","passed":true},{"actual":"contig1","check":"unique alias","expected":"contig1","passed":true},{"actual":"other","check":"canonical other","expected":"other","passed":true},{"actual":"third","check":"canonical without alias","expected":"third","passed":true},{"actual":null,"check":"absent","expected":null,"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"ambiguous alias\", \"actual\": \"contig1\", \"expected\": null, \"passed\": false}, {\"check\": \"canonical beats alias\", \"actual\": \"contig1\", \"expected\": \"contig1\", \"passed\": true}, {\"check\": \"unique alias\", \"actual\": \"contig1\", \"expected\": \"contig1\", \"passed\": true}, {\"check\": \"canonical other\", \"actual\": \"other\", \"expected\": \"other\", \"passed\": true}, {\"check\": \"canonical without alias\", \"actual\": \"third\", \"expected\": \"third\", \"passed\": true}, {\"check\": \"absent\", \"actual\": null, \"expected\": null, \"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."}}