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e2e7e70
Add lib_ts_chainalign stub.
sebschmi Nov 28, 2025
d95cd02
Gap affine cost lower bound.
sebschmi Nov 28, 2025
0fc75c7
Precompute TS jump lower bounds for 12-jump.
sebschmi Dec 1, 2025
1b86a71
Precompute lower bounds also for 34-jump.
sebschmi Dec 1, 2025
d073f98
Implement gap filling for gap-affine alignment.
sebschmi Dec 1, 2025
ec3eaa2
Rename alignment modules.
sebschmi Dec 1, 2025
1d4d971
Restrict match runs in exact chaining.
sebschmi Dec 2, 2025
3821835
Refactor alignment coordinates.
sebschmi Dec 2, 2025
7040766
Implement TS 12-jump exact chaining.
sebschmi Dec 2, 2025
c32f72d
Fix gap filling for gap-affine secondary alignment.
sebschmi Dec 2, 2025
21df6b7
Fix TS ancestor coordinate interpretation.
sebschmi Dec 2, 2025
dff5724
Test 12-jump exact chaining algo.
sebschmi Dec 2, 2025
27294b9
Treat no target found as infinite costs.
sebschmi Dec 3, 2025
e17eb7d
Implement TS 34-jump exact chaining.
sebschmi Dec 3, 2025
d1b9fc7
Connect tschainalign to tsalign (except AlignmentResult).
sebschmi Dec 3, 2025
47c9b90
Implement anchor finding.
sebschmi Dec 3, 2025
af33335
Initialise chaining cost function with lower bounds.
sebschmi Dec 4, 2025
5b11578
Compute initial chain.
sebschmi Dec 4, 2025
82e3290
Refine chain with primary alignments.
sebschmi Dec 4, 2025
8f3ad66
Buggy complete version of tschainalign.
sebschmi Dec 5, 2025
46cc26b
Fix empty jumps.
sebschmi Dec 5, 2025
7ece69a
Fix k and more diagnostics.
sebschmi Dec 5, 2025
e9f2cb0
Add progress indicator to chainalign.
sebschmi Dec 8, 2025
15203ae
More diagnostics.
sebschmi Dec 8, 2025
8a630a8
Automatically convert sequences to upper case.
sebschmi Dec 8, 2025
120b144
Fix anti-primary gap computation in chainalign.
sebschmi Dec 8, 2025
6bf5e96
Evaluate each chained pair only once.
sebschmi Dec 8, 2025
d01f416
Custom I/O implementation for chaining lower bounds.
sebschmi Dec 8, 2025
70a3664
Use rust-analyzer from toolchain.
sebschmi Dec 8, 2025
ee205c8
Fix LowerBoundCostArray constructor.
sebschmi Dec 8, 2025
790570f
Fix.
sebschmi Dec 8, 2025
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,3 +2,4 @@
/tsa_config
/*.log
/callgrind.out.*
*.tsc
206 changes: 205 additions & 1 deletion Cargo.lock

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions Cargo.toml
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ members = [
"generic_a_star",
"seed_chain",
"lib_tsalign",
"lib_ts_chainalign",
"lib_tsshow",
"tsalign",

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