FA-12546 / Genomic coordinate mapping / Open access

Reverse alignments apply soft clipping at the wrong query end · case 01

Original read positions map to the wrong reference base after reverse orientation and asymmetric soft clipping.

Verified by executionVariant 1 · 9 checks per implementationDownload source bundle ↓JSON ↗

ROOT CAUSE

Original query indexes are consumed directly in alignment orientation without accounting for reverse alignment.

VERIFIED REPAIR

Reverse the original query index over the full query length, then remove the alignment-leading soft clip and reject clipped bases.

Unsuccessful approach: Reversing only the unclipped aligned segment loses the position of asymmetric leading and trailing soft clips.

Case contract

For a synthetic ungapped alignment with leading/trailing soft clip lengths in alignment orientation, map a zero-based original read index to reference base or None. Query length is lead+aligned+trail. Reverse alignments reverse indexes across the entire query before clipping.

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(lead, aligned, trail, start, reverse, pos):
    q=pos-lead
    return start+q if 0<=q<aligned else None
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
lead=N; aligned=4; trail=N+2; length=lead+aligned+trail
check('reverse first aligned original base',solve(lead,aligned,trail,100,True,trail),103)
check('reverse last aligned original base',solve(lead,aligned,trail,100,True,trail+3),100)
check('reverse preceding clipped base',solve(lead,aligned,trail,100,True,trail-1),None)
check('reverse following clipped base',solve(lead,aligned,trail,100,True,trail+4),None)
check('forward first aligned base',solve(lead,aligned,trail,100,False,lead),100)
check('forward last aligned base',solve(lead,aligned,trail,100,False,lead+3),103)
check('forward leading clip',solve(lead,aligned,trail,100,False,lead-1),None)
check('outside original read',solve(lead,aligned,trail,100,True,length),None)
check('negative original index',solve(lead,aligned,trail,100,True,-1),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
reverse first aligned original base	`102`	`103`	Failed
reverse last aligned original base	`None`	`100`	Failed
reverse preceding clipped base	`101`	`None`	Failed
reverse following clipped base	`None`	`None`	Passed
forward first aligned base	`100`	`100`	Passed
forward last aligned base	`103`	`103`	Passed
forward leading clip	`None`	`None`	Passed
outside original read	`None`	`None`	Passed
negative original index	`None`	`None`	Passed

SHA-256 / 4f62f4a45243fa4e6a11df0ab1be380968f06b91e8351525113d0b5c026bbb50

2 / The unsuccessful fix

Exit 1

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

N = 1
observations = []
def solve(lead, aligned, trail, start, reverse, pos):
    q=pos-lead
    if reverse: q=aligned-1-q
    return start+q if 0<=q<aligned else None
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
lead=N; aligned=4; trail=N+2; length=lead+aligned+trail
check('reverse first aligned original base',solve(lead,aligned,trail,100,True,trail),103)
check('reverse last aligned original base',solve(lead,aligned,trail,100,True,trail+3),100)
check('reverse preceding clipped base',solve(lead,aligned,trail,100,True,trail-1),None)
check('reverse following clipped base',solve(lead,aligned,trail,100,True,trail+4),None)
check('forward first aligned base',solve(lead,aligned,trail,100,False,lead),100)
check('forward last aligned base',solve(lead,aligned,trail,100,False,lead+3),103)
check('forward leading clip',solve(lead,aligned,trail,100,False,lead-1),None)
check('outside original read',solve(lead,aligned,trail,100,True,length),None)
check('negative original index',solve(lead,aligned,trail,100,True,-1),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
reverse first aligned original base	`101`	`103`	Failed
reverse last aligned original base	`None`	`100`	Failed
reverse preceding clipped base	`102`	`None`	Failed
reverse following clipped base	`None`	`None`	Passed
forward first aligned base	`100`	`100`	Passed
forward last aligned base	`103`	`103`	Passed
forward leading clip	`None`	`None`	Passed
outside original read	`None`	`None`	Passed
negative original index	`None`	`None`	Passed

SHA-256 / 1a9fb2bca275c5c8b8150d563e8401ef7c8bf10fd9ae07ce8f1bb882446394ad

3 / The verified repair

Exit 0

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

N = 1
observations = []
def solve(lead, aligned, trail, start, reverse, pos):
    length=lead+aligned+trail
    if not 0<=pos<length: return None
    q=(length-1-pos if reverse else pos)-lead
    return start+q if 0<=q<aligned else None
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
lead=N; aligned=4; trail=N+2; length=lead+aligned+trail
check('reverse first aligned original base',solve(lead,aligned,trail,100,True,trail),103)
check('reverse last aligned original base',solve(lead,aligned,trail,100,True,trail+3),100)
check('reverse preceding clipped base',solve(lead,aligned,trail,100,True,trail-1),None)
check('reverse following clipped base',solve(lead,aligned,trail,100,True,trail+4),None)
check('forward first aligned base',solve(lead,aligned,trail,100,False,lead),100)
check('forward last aligned base',solve(lead,aligned,trail,100,False,lead+3),103)
check('forward leading clip',solve(lead,aligned,trail,100,False,lead-1),None)
check('outside original read',solve(lead,aligned,trail,100,True,length),None)
check('negative original index',solve(lead,aligned,trail,100,True,-1),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
reverse first aligned original base	`103`	`103`	Passed
reverse last aligned original base	`100`	`100`	Passed
reverse preceding clipped base	`None`	`None`	Passed
reverse following clipped base	`None`	`None`	Passed
forward first aligned base	`100`	`100`	Passed
forward last aligned base	`103`	`103`	Passed
forward leading clip	`None`	`None`	Passed
outside original read	`None`	`None`	Passed
negative original index	`None`	`None`	Passed

SHA-256 / 005ee3b887374d31474949dd01eff723bada96b1d3749feb08ccc2d75ee8f38e

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 2026-09-29T14:38:57.931391+00:00.

Case digest / 2f699373bfd326e5db43e6da2c0dc4eed38a6eab3cb4f688a51b931eba4072a0