FA-12506 / Biological sequence representation / Open access

K-mer windows span independent sequence records · case 01

K-mer windows span independent sequence records.

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

ROOT CAUSE

Concatenation creates windows across record boundaries.

THE FAILURE

Concatenation creates windows across record boundaries.

Unsuccessful approach: Adding an N separator leaks artificial separator windows.

Case contract

Return all length-k windows in record order, then position order, independently per record; k is positive and records contain ACGT only.

Why this case matters

An offline abstract sequence-data model; useful for testing representation invariants without biological inference.

1 / The failure

Exit 1

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

N = 1
observations = []
def solve(records,k):
    s=''.join(records)
    return [s[i:i+k] for i in range(len(s)-k+1)]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable records', solve(['A'*N,'C'],2), ['AA']*max(0,N-1))
check('empty collection', solve([],2), [])
check('short records', solve(['A','T'],2), [])
check('exact', solve(['AC','GT'],2), ['AC','GT'])
check('unit', solve(['A','','C'],1), ['A','C'])
check('overlap', solve(['ACG'],2), ['AC','CG'])
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
variable records	`['AC']`	`[]`	Failed
empty collection	`[]`	`[]`	Passed
short records	`['AT']`	`[]`	Failed
exact	`['AC', 'CG', 'GT']`	`['AC', 'GT']`	Failed
unit	`['A', 'C']`	`['A', 'C']`	Passed
overlap	`['AC', 'CG']`	`['AC', 'CG']`	Passed

SHA-256 / 8070ee98295dc60a2912a4f614c1e2cfe125211170efaa561323f35aac23b53c

2 / The unsuccessful fix

Exit 1

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

N = 1
observations = []
def solve(records,k):
    s='N'.join(records)
    return [s[i:i+k] for i in range(len(s)-k+1)]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable records', solve(['A'*N,'C'],2), ['AA']*max(0,N-1))
check('empty collection', solve([],2), [])
check('short records', solve(['A','T'],2), [])
check('exact', solve(['AC','GT'],2), ['AC','GT'])
check('unit', solve(['A','','C'],1), ['A','C'])
check('overlap', solve(['ACG'],2), ['AC','CG'])
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
variable records	`['AN', 'NC']`	`[]`	Failed
empty collection	`[]`	`[]`	Passed
short records	`['AN', 'NT']`	`[]`	Failed
exact	`['AC', 'CN', 'NG', 'GT']`	`['AC', 'GT']`	Failed
unit	`['A', 'N', 'N', 'C']`	`['A', 'C']`	Failed
overlap	`['AC', 'CG']`	`['AC', 'CG']`	Passed

SHA-256 / b364c3f5e71ca0cf2904616a6faed0d5f1ccaee7a90064d569a45dbafdc38022

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 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.

Observations recorded using Python 3.12.14 at 2026-09-29T14:38:57.488793+00:00.

Case digest / 6d457e663808713987d75835f6eaf762f2a70402e280bb6fdf68d09bd258129f