130 suboptimal alignment - #132

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sebschmi merged 13 commits into

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130-suboptimal-alignment

Dec 18, 2025

Commits on Dec 17, 2025

Compute statistics about gap fillings per chain.
sebschmi
committed
1fe99a2
Refactor and make exact chaining caching.
sebschmi
committed
ac405fb
Measure anchor computation time.
sebschmi
committed
3f8eb7c
Report chain gap filling ratio without percent.
sebschmi
committed
9c054e8
Refactor chain gap filling statistics.
sebschmi
committed
47b6581
Make anchor order into their natural order.
sebschmi
committed
13e05fe
Batch gap-affine chain evaluation.
sebschmi
committed
db1f8ed
Fix batched gap-affine chain evaluation.
sebschmi
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dd28907
Batch 12 jump chain evaluation.
sebschmi
committed
c128ed1
Batch 34 jump chain evaluation.
sebschmi
committed
deae26c
Update tests.
sebschmi
committed
a10b00d
Do not adjust Cost::max_value() in Ts34JumpAligner.
sebschmi
committed
3d02f71

Commits on Dec 18, 2025

Fix wrong exact alignment computation regarding non-matches.
sebschmi
committed
e0f3b79