Commits · 4606588191350e4271ab5dc0edd76c02f7757e8f · Martin Larralde / LightMotif · GitLab

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Jun 14, 2024
- Release v0.7.2 · 46065881
  Martin Larralde authored 8 months ago
  
  View commits for tag v0.7.2 v0.7.2
  
  46065881
- Implement `__getitem__` for row access for matrices of `lightmotif-py` · d44e7b0e
  Martin Larralde authored 8 months ago
  
  d44e7b0e
- Allow changing log base in `WeightMatrix.log_odds` method · f7e791de
  Martin Larralde authored 8 months ago
  
  f7e791de
- Add `__len__` implementation for all matrix classes of `lightmotif-py` · 7b58f7e9
  Martin Larralde authored 8 months ago
  
  7b58f7e9
- Release v0.7.1 · d3cce922
  Martin Larralde authored 8 months ago
  
  View commits for tag v0.7.1 v0.7.1
  
  d3cce922
- Fix resizing of striped scores in NEON score implementation · 200d85ce
  Martin Larralde authored 8 months ago
  
  200d85ce
- Release v0.7.0 · d8e791db
  Martin Larralde authored 9 months ago
  
  View commits for tag v0.7.0 v0.7.0
  
  d8e791db
- Fix compilation of NEON code [ci skip] · 2fb9aad0
  Martin Larralde authored 9 months ago
  
  2fb9aad0
- Remove `lightmotif-transfac` from workspace [ci skip] · 4584268b
  Martin Larralde authored 9 months ago
  
  4584268b
- Remove the deprecated `lightmotif-transfac` crate · ce89359e
  Martin Larralde authored 9 months ago
  
  ce89359e
- Remove direct mutable access to `StripedSequence` attributes · f71b0485
  Martin Larralde authored 9 months ago
  
  f71b0485
- Replace direct attribute access with getters in `StripedSequence` · 85263f04
  Martin Larralde authored 9 months ago
  
  85263f04
- Update `cibuildwheel` used in Actions workflows to latest release · c2885e51
  Martin Larralde authored 9 months ago
  
  c2885e51
- Add benchmark for striping an encoded sequence · 751c9ac8
  Martin Larralde authored 9 months ago
  
  751c9ac8
- Fix issue in NEON platform code · 3fe9e36d
  Martin Larralde authored 9 months ago
  
  3fe9e36d
- Avoid consuming the scanner in `Scanner.best` method · 81971296
  Martin Larralde authored 9 months ago
  
  81971296
- Use a single `Scanner` type in `lightmotif::scan` · 355deaa0
  Martin Larralde authored 9 months ago
  
  355deaa0
- Implement a scanning algorithm for finding hits in a sequence · d48cbb3d
  Martin Larralde authored 9 months ago
  
  d48cbb3d
Jun 13, 2024
- Reorganize code for striped scores · 32508c48
  Martin Larralde authored 9 months ago
  
  32508c48
- Use a dedicated type for `ScoringMatrix.score` and refactor code · 840959f7
  Martin Larralde authored 9 months ago
  
  840959f7
- Revert book-keeping attributes used in `StripedScores` · 4d3145ff
  Martin Larralde authored 9 months ago
  
  4d3145ff
- Add method to build the reverse-complement of a PSSM · 87b63939
  Martin Larralde authored 9 months ago
  
  87b63939
- Implement back `StripedScores.__len__` and `StripedScores.__getitem__` · 984b5ea4
  Martin Larralde authored 9 months ago
  
  984b5ea4
May 08, 2024
- Fix release date in `CHANGELOG.md` [ci skip] · edb5e45b
  Martin Larralde authored 10 months ago
  
  edb5e45b
Mar 12, 2024
- Allow changing log base when building `ScoringMatrix` from `WeightMatrix` · fe89288a
  Martin Larralde authored 1 year ago
  
  fe89288a
Mar 11, 2024
- Make `StripedScores::sequence_index` take a `MatrixCoordinates` argument · 2f1eaa5d
  Martin Larralde authored 1 year ago
  
  2f1eaa5d
- Implement indexing by matrix coordinates in `DenseMatrix` · e003a705
  Martin Larralde authored 1 year ago
  
  e003a705
- Fix sequence rows not being updated in `StripedScores::resize` · 5a835042
  Martin Larralde authored 1 year ago
  
  5a835042
- Cache the number of sequence rows in `StripedScores` · e8811d8f
  Martin Larralde authored 1 year ago
  
  e8811d8f
- Fix tests and benchmarks to use the new `Maximum` API · 4cd84026
  Martin Larralde authored 1 year ago
  
  4cd84026
- Rewrite platform-specific code for updated `Maximum` trait · 978b6db3
  Martin Larralde authored 1 year ago
  
  978b6db3
- Update `Maximum::argmax` to return matrix coordinates in the `StripedScores` · 030c3bc7
  Martin Larralde authored 1 year ago
  
  030c3bc7
- Add method to `ScoringMatrix` to score a single sequence position · f2d4ebd8
  Martin Larralde authored 1 year ago
  
  f2d4ebd8
Mar 10, 2024
- Remove the `sequence_length` method from `StripedScores` · e995edbb
  Martin Larralde authored 1 year ago
  
  e995edbb
- Rewrite the `Threshold` operation to return matrix coordinates · e2fa2464
  Martin Larralde authored 1 year ago
  
  e2fa2464
- Fix issue with scoring in SSE2 implementation · e1d6cd05
  Martin Larralde authored 1 year ago
  
  e1d6cd05
- Remove platform-specific code for thresholding scores · 28adbffe
  Martin Larralde authored 1 year ago
  
  28adbffe
- Reorganize thresholding code so that indices are correct with regard to row range · f5bbcd67
  Martin Larralde authored 1 year ago
  
  f5bbcd67
- Add row-based scoring for other platforms and update benchmarks · 8b64a60d
  Martin Larralde authored 1 year ago
  
  8b64a60d
- Fix tests to use new `Score` argument order · 2faf505f
  Martin Larralde authored 1 year ago
  
  2faf505f