FA-12551 / Genomic coordinate mapping / Open access

Contig aliases choose an arbitrary reference target · case 01

Contig aliases choose an arbitrary reference target.

Verified by executionVariant 1 · 6 checks per implementationDownload source bundle ↓JSON ↗

ROOT CAUSE

Alias normalization chooses the first candidate without detecting collisions.

THE FAILURE

Alias normalization chooses the first candidate without detecting collisions.

Unsuccessful approach: Rejecting all multiple alias matches also rejects an exact canonical identifier.

Case contract

Names identify canonical contigs; aliases may collide. Exact canonical match wins; ambiguous or absent aliases return None.

Why this case matters

An abstract offline coordinate model isolates this software mapping defect; it does not model biological interpretation.

1 / The failure

Exit 1

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(rows, name):
    return next((c for c,aliases in rows if name==c or name in aliases),None)
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
a='contig'+str(N)
r=[(a,['x','shared']),('other',['shared',a]),('third',[])]
check('ambiguous alias',solve(r,'shared'),None)
check('canonical beats alias',solve(r,a),a)
check('unique alias',solve(r,'x'),a)
check('canonical other',solve(r,'other'),'other')
check('canonical without alias',solve(r,'third'),'third')
check('absent',solve(r,'missing'),None)
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
ambiguous alias	`contig1`	`None`	Failed
canonical beats alias	`contig1`	`contig1`	Passed
unique alias	`contig1`	`contig1`	Passed
canonical other	`other`	`other`	Passed
canonical without alias	`third`	`third`	Passed
absent	`None`	`None`	Passed

SHA-256 / ab6cd6653554e92579d64d567a96e3ecacfdb7cc0f7ffe5461d353a69367f3ab

2 / The unsuccessful fix

Exit 1

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(rows, name):
    matches=[c for c,a in rows if name==c or name in a]
    return matches[0] if len(matches)==1 else None
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
a='contig'+str(N)
r=[(a,['x','shared']),('other',['shared',a]),('third',[])]
check('ambiguous alias',solve(r,'shared'),None)
check('canonical beats alias',solve(r,a),a)
check('unique alias',solve(r,'x'),a)
check('canonical other',solve(r,'other'),'other')
check('canonical without alias',solve(r,'third'),'third')
check('absent',solve(r,'missing'),None)
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
ambiguous alias	`None`	`None`	Passed
canonical beats alias	`None`	`contig1`	Failed
unique alias	`contig1`	`contig1`	Passed
canonical other	`other`	`other`	Passed
canonical without alias	`third`	`third`	Passed
absent	`None`	`None`	Passed

SHA-256 / 9e072018e34fe3eaf654832c0167d9c21f15dd164694b97525ddecb87d9fda3a

HELD IN THE MEMBER ARCHIVE

The verified repair and its recorded checks are member-only.

This mechanism has 6 recorded checks per implementation. The open-access tier publishes the failure and the unsuccessful fix; the repaired source that passes every check, and the observations that prove it, are available to members.

Every case sharing this mechanism uses the same contract and the same repair, so this one record is held back for all of them.

Member access is invitation-based. Sign in with your invited account to inspect the repair.

Verification & scope

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.

Observations recorded using Python 3.12.14 at 2026-09-29T14:38:57.974745+00:00.

Case digest / be46333441861d2b833f2015a83941386f9bc85e085427ea2ae9c125710deec4