fix: pair fa:Z extras with correct annotations on reverse-strand reads#103
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fix: pair fa:Z extras with correct annotations on reverse-strand reads#103
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FiberAnnotations::new re-orders fs/fl into aligned (reference) order when the record is reverse-complement aligned, but from_bam_tags was pairing the fa:Z extras in their original tag-storage order. Result: on reverse-strand reads the extras of adjacent annotations were silently swapped. ref_start /ref_end remained correct; only the extra columns were mis-paired, so the symptom looked like peak-size labels getting swapped between overlapping peaks. Fix: reverse the split fa:Z values when record.is_reverse() so they match FiberAnnotations::new's already-flipped order. Adds two regression tests covering a forward-strand baseline and a reverse-strand case with 5 peaks (last two overlapping) to catch any off-by-one pairing error. Confirmed the reverse-strand test fails without the fix.
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Summary
FiberAnnotations::newflips fs/fl viapositions_on_aligned_sequencebutfrom_bam_tagsleft the auxiliaryfa:Zvector in tag-storage order — causing extras to be paired with the wrong annotation (symmetric peak swap) whenever multiple peaks were present.ann_valsbefore zipping whenrecord.is_reverse()so extras align with the already-flipped annotations.Test plan
cargo testpasses with the fix