FA-12521 / Biological sequence representation / Open access

Quality filtering separates scores from surviving bases · case 01

Quality filtering separates scores from surviving bases.

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

ROOT CAUSE

Bases are selected but the original quality array is retained.

THE FAILURE

Bases are selected but the original quality array is retained.

Unsuccessful approach: Filtering scores by a strict threshold disagrees with inclusive base selection.

Case contract

Given sequence and same-length integer qualities, return [retained_string,retained_qualities] preserving pairs whose quality is >= cutoff.

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(s,q,cut):
    return [''.join(c for c,v in zip(s,q) if v>=cut),q]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable threshold', solve('ACT',[N-1,N,N+1],N), ['CT',[N,N+1]])
check('empty', solve('',[],2), ['',[]])
check('all removed', solve('AC',[0,1],2), ['',[]])
check('all retained', solve('AC',[2,3],2), ['AC',[2,3]])
check('equality', solve('T',[0],0), ['T',[0]])
check('internal hole', solve('ACT',[5,0,4],3), ['AT',[5,4]])
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 threshold	`['CT', [0, 1, 2]]`	`['CT', [1, 2]]`	Failed
empty	`['', []]`	`['', []]`	Passed
all removed	`['', [0, 1]]`	`['', []]`	Failed
all retained	`['AC', [2, 3]]`	`['AC', [2, 3]]`	Passed
equality	`['T', [0]]`	`['T', [0]]`	Passed
internal hole	`['AT', [5, 0, 4]]`	`['AT', [5, 4]]`	Failed

SHA-256 / 9d37abcdaa34b9a94fc91d21b043a55cac7b453a8eb075520127f719764e04b3

2 / The unsuccessful fix

Exit 1

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

N = 1
observations = []
def solve(s,q,cut):
    return [''.join(c for c,v in zip(s,q) if v>=cut),[v for v in q if v>cut]]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('variable threshold', solve('ACT',[N-1,N,N+1],N), ['CT',[N,N+1]])
check('empty', solve('',[],2), ['',[]])
check('all removed', solve('AC',[0,1],2), ['',[]])
check('all retained', solve('AC',[2,3],2), ['AC',[2,3]])
check('equality', solve('T',[0],0), ['T',[0]])
check('internal hole', solve('ACT',[5,0,4],3), ['AT',[5,4]])
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 threshold	`['CT', [2]]`	`['CT', [1, 2]]`	Failed
empty	`['', []]`	`['', []]`	Passed
all removed	`['', []]`	`['', []]`	Passed
all retained	`['AC', [3]]`	`['AC', [2, 3]]`	Failed
equality	`['T', []]`	`['T', [0]]`	Failed
internal hole	`['AT', [5, 4]]`	`['AT', [5, 4]]`	Passed

SHA-256 / cc83be163fc624e5f6efe4abb3ed4778bb9736bab484cc456b9d633aa81bb08f

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 2026-09-29T14:38:57.529398+00:00.

Case digest / f2e08982daafe4ee08f44b9de1f2fa54a374564cd859f27c9430969e9a7b94fe