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algbio / tsalign Public

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Chainalign#115

Merged

sebschmi merged 31 commits into

mainalgbio/tsalign:mainfrom

chainalignalgbio/tsalign:chainalignCopy head branch name to clipboard

Dec 8, 2025

Conversation Commits31 (31)Checks Files changed

Merged

Chainalign#115
sebschmi merged 31 commits into
mainfrom
chainalign

Commits

Commits on Nov 28, 2025

Add lib_ts_chainalign stub.
sebschmi
committed

Commits on Dec 1, 2025

Gap affine cost lower bound.
sebschmi
committed
Precompute TS jump lower bounds for 12-jump.
sebschmi
committed
Precompute lower bounds also for 34-jump.
sebschmi
committed
Implement gap filling for gap-affine alignment.
sebschmi
committed
Rename alignment modules.
sebschmi
committed

Commits on Dec 2, 2025

Restrict match runs in exact chaining.
sebschmi
committed
Refactor alignment coordinates.
sebschmi
committed
Implement TS 12-jump exact chaining.
sebschmi
committed
Fix gap filling for gap-affine secondary alignment.
sebschmi
committed
Fix TS ancestor coordinate interpretation.
sebschmi
committed
Test 12-jump exact chaining algo.
sebschmi
committed

Commits on Dec 3, 2025

Treat no target found as infinite costs.
sebschmi
committed
Implement TS 34-jump exact chaining.
sebschmi
committed
Connect tschainalign to tsalign (except AlignmentResult).
sebschmi
committed
Implement anchor finding.
sebschmi
committed

Commits on Dec 4, 2025

Initialise chaining cost function with lower bounds.
sebschmi
committed
Compute initial chain.
sebschmi
committed
Refine chain with primary alignments.
sebschmi
committed

Commits on Dec 5, 2025

Buggy complete version of tschainalign.
sebschmi
committed
Fix empty jumps.
sebschmi
committed
Fix k and more diagnostics.
sebschmi
committed

Commits on Dec 8, 2025

Add progress indicator to chainalign.
sebschmi
committed
More diagnostics.
sebschmi
committed
Automatically convert sequences to upper case.
sebschmi
committed
Fix anti-primary gap computation in chainalign.
sebschmi
committed
Evaluate each chained pair only once.
sebschmi
committed
Custom I/O implementation for chaining lower bounds.
sebschmi
committed
Use rust-analyzer from toolchain.
sebschmi
committed
Fix LowerBoundCostArray constructor.
sebschmi
committed
Fix.
sebschmi
committed

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