{"abstract":"Intronic coordinate ties choose the wrong transcript anchor.","category":"Genomic coordinate mapping","checks":6,"contract":"For reference base p strictly inside the intron between exon-end base left and exon-start base right, return [anchor,signed distance]; upstream transcript boundary wins ties.","evaluation_group":"model-8c0d94376404fc31","failed_approach":"Nearest-boundary repair retains reference-left tie breaking on negative strands.","family":"z-genetics_coordinates-intronic-anchor","id":"FA-12561","implementations":{"attempt":{"sha256":"0f3563317350d8888a30dd70bce3894a1649988e57e4e5187bd1030a3fa2b463","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(left, right, p, strand):\n    anchor=left if p-left <= right-p else right\n    return [anchor,(p-anchor)*(1 if strand=='+' else -1)]\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\nl=10*N;r=l+8\ncheck('plus near right',solve(l,r,l+7,'+'),[r,-1])\ncheck('minus tie',solve(l,r,l+4,'-'),[r,4])\ncheck('plus tie',solve(l,r,l+4,'+'),[l,4])\ncheck('plus near left',solve(l,r,l+1,'+'),[l,1])\ncheck('minus near left',solve(l,r,l+1,'-'),[l,-1])\ncheck('minus near right',solve(l,r,l+7,'-'),[r,1])\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":"489b9e63aec8d1f6e5c49c285213c524b1c7f5fa5527b6801c4a4e230a6dba63","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(left, right, p, strand):\n    return [left,p-left]\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\nl=10*N;r=l+8\ncheck('plus near right',solve(l,r,l+7,'+'),[r,-1])\ncheck('minus tie',solve(l,r,l+4,'-'),[r,4])\ncheck('plus tie',solve(l,r,l+4,'+'),[l,4])\ncheck('plus near left',solve(l,r,l+1,'+'),[l,1])\ncheck('minus near left',solve(l,r,l+1,'-'),[l,-1])\ncheck('minus near right',solve(l,r,l+7,'-'),[r,1])\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":"fb38ecdfc24e60cffadec433d11e01f65818ff0f4c7428707e29c4f912648d8d","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(left, right, p, strand):\n    anchor=left if p-left < right-p or (p-left==right-p and strand=='+') else right\n    return [anchor,(p-anchor)*(1 if strand=='+' else -1)]\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\nl=10*N;r=l+8\ncheck('plus near right',solve(l,r,l+7,'+'),[r,-1])\ncheck('minus tie',solve(l,r,l+4,'-'),[r,4])\ncheck('plus tie',solve(l,r,l+4,'+'),[l,4])\ncheck('plus near left',solve(l,r,l+1,'+'),[l,1])\ncheck('minus near left',solve(l,r,l+1,'-'),[l,-1])\ncheck('minus near right',solve(l,r,l+7,'-'),[r,1])\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-intronic-anchor","generated_at":"2026-09-29T14:38:58.115700+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.","repair":"Choose the nearest boundary, break ties toward transcript upstream, and orient sign by strand.","root_cause":"Intronic notation always uses the left reference exon boundary.","sha256":"94348fa3b020da539c42745f97df580c36be95b5d730cf037dfab6b3238e2c24","title":"Intronic coordinate ties choose the wrong transcript anchor · case 01","variant":1,"variant_policy":"Five numbered records share a model and may reuse boundary fixtures.","verification":{"attempt":{"elapsed_ms":39.37,"exit_code":1,"observations":[{"actual":[18,-1],"check":"plus near right","expected":[18,-1],"passed":true},{"actual":[10,-4],"check":"minus tie","expected":[18,4],"passed":false},{"actual":[10,4],"check":"plus tie","expected":[10,4],"passed":true},{"actual":[10,1],"check":"plus near left","expected":[10,1],"passed":true},{"actual":[10,-1],"check":"minus near left","expected":[10,-1],"passed":true},{"actual":[18,1],"check":"minus near right","expected":[18,1],"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"plus near right\", \"actual\": [18, -1], \"expected\": [18, -1], \"passed\": true}, {\"check\": \"minus tie\", \"actual\": [10, -4], \"expected\": [18, 4], \"passed\": false}, {\"check\": \"plus tie\", \"actual\": [10, 4], \"expected\": [10, 4], \"passed\": true}, {\"check\": \"plus near left\", \"actual\": [10, 1], \"expected\": [10, 1], \"passed\": true}, {\"check\": \"minus near left\", \"actual\": [10, -1], \"expected\": [10, -1], \"passed\": true}, {\"check\": \"minus near right\", \"actual\": [18, 1], \"expected\": [18, 1], \"passed\": true}], \"passed\": false}\n"},"broken":{"elapsed_ms":42.438,"exit_code":1,"observations":[{"actual":[10,7],"check":"plus near right","expected":[18,-1],"passed":false},{"actual":[10,4],"check":"minus tie","expected":[18,4],"passed":false},{"actual":[10,4],"check":"plus tie","expected":[10,4],"passed":true},{"actual":[10,1],"check":"plus near left","expected":[10,1],"passed":true},{"actual":[10,1],"check":"minus near left","expected":[10,-1],"passed":false},{"actual":[10,7],"check":"minus near right","expected":[18,1],"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"plus near right\", \"actual\": [10, 7], \"expected\": [18, -1], \"passed\": false}, {\"check\": \"minus tie\", \"actual\": [10, 4], \"expected\": [18, 4], \"passed\": false}, {\"check\": \"plus tie\", \"actual\": [10, 4], \"expected\": [10, 4], \"passed\": true}, {\"check\": \"plus near left\", \"actual\": [10, 1], \"expected\": [10, 1], \"passed\": true}, {\"check\": \"minus near left\", \"actual\": [10, 1], \"expected\": [10, -1], \"passed\": false}, {\"check\": \"minus near right\", \"actual\": [10, 7], \"expected\": [18, 1], \"passed\": false}], \"passed\": false}\n"},"fixed":{"elapsed_ms":41.267,"exit_code":0,"observations":[{"actual":[18,-1],"check":"plus near right","expected":[18,-1],"passed":true},{"actual":[18,4],"check":"minus tie","expected":[18,4],"passed":true},{"actual":[10,4],"check":"plus tie","expected":[10,4],"passed":true},{"actual":[10,1],"check":"plus near left","expected":[10,1],"passed":true},{"actual":[10,-1],"check":"minus near left","expected":[10,-1],"passed":true},{"actual":[18,1],"check":"minus near right","expected":[18,1],"passed":true}],"passed":true,"stderr":"","stdout":"{\"observations\": [{\"check\": \"plus near right\", \"actual\": [18, -1], \"expected\": [18, -1], \"passed\": true}, {\"check\": \"minus tie\", \"actual\": [18, 4], \"expected\": [18, 4], \"passed\": true}, {\"check\": \"plus tie\", \"actual\": [10, 4], \"expected\": [10, 4], \"passed\": true}, {\"check\": \"plus near left\", \"actual\": [10, 1], \"expected\": [10, 1], \"passed\": true}, {\"check\": \"minus near left\", \"actual\": [10, -1], \"expected\": [10, -1], \"passed\": true}, {\"check\": \"minus near right\", \"actual\": [18, 1], \"expected\": [18, 1], \"passed\": true}], \"passed\": true}\n"}},"verified":true,"visibility":"public"}