FA-12549 / Genomic coordinate mapping / Member archive

Reverse alignments apply soft clipping at the wrong query end · case 04

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

Member previewVariant 4 · 3 implementations · 9 checks per implementation

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.

One recorded failure

Sample boundary fixture

This sample comes from the broken implementation of a controlled reproducer.

Boundary fixture	Actual	Expected	Outcome
reverse first aligned original base	`102`	`103`	Failed

MEMBER ARCHIVE

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This record includes three runnable implementations, regression fixtures, execution results, and source hashes.

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