Commits · ba2386965944c5780376c5dc2a86e5cadae742b0 · Martin Larralde / LightMotif · GitLab

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Jun 16, 2024
- Use aligned loads in AVX2 implementation of `Score` · ba238696
  Martin Larralde authored 9 months ago
  
  ba238696
- Fix incorrect alignment handling in `DenseMatrix` · 18fccd31
  Martin Larralde authored 9 months ago
  
  18fccd31
- Fix default alignment used for x86-64 and Aarch64 · 72f42705
  Martin Larralde authored 9 months ago
  
  72f42705
- Manually implement `Clone` for `DenseMatrix` to enforce memory alignment · 8aab22de
  Martin Larralde authored 9 months ago
  
  8aab22de
- Hotfix issue with alignment of data in AVX2 code · 9b24165a
  Martin Larralde authored 9 months ago
  
  9b24165a
Jun 15, 2024
- Rename JASPAR (2016) benchmark in `lightmotif-io` · ed79dd5c
  Martin Larralde authored 9 months ago
  
  ed79dd5c
- Make AVX2 implementation of `score_into` with `gather` more generic · f57b3cdb
  Martin Larralde authored 9 months ago
  
  f57b3cdb
- Use `_mm256_permutevar8x32_ps` in AVX2 `Score` to avoid special case for default Dna symbol · ff811f37
  Martin Larralde authored 9 months ago
  
  ff811f37
- Add helper functions to read any format in `lightmotif-io` · a0bb4e2b
  Martin Larralde authored 9 months ago
  
  a0bb4e2b
- Add `lightmotif-io` module to parse the raw JASPAR format · 197d8059
  Martin Larralde authored 9 months ago
  
  197d8059
Jun 14, 2024
- Fix issue with scoring of an empty range of rows · ce993e6d
  Martin Larralde authored 9 months ago
  
  ce993e6d
- Fix striping of empty sequence panicking with AVX2 implementation · de67200a
  Martin Larralde authored 9 months ago
  
  de67200a
- Remove unused file from `lightmotif-tfmpvalue` [ci skip] · f4b262b7
  Martin Larralde authored 9 months ago
  
  f4b262b7
- Use substraction in `FrequencyMatrix.to_scoring` method · f0251cbf
  Martin Larralde authored 9 months ago
  
  f0251cbf
- Release v0.7.2 · 46065881
  Martin Larralde authored 9 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 9 months ago
  
  d44e7b0e
- Allow changing log base in `WeightMatrix.log_odds` method · f7e791de
  Martin Larralde authored 9 months ago
  
  f7e791de
- Add `__len__` implementation for all matrix classes of `lightmotif-py` · 7b58f7e9
  Martin Larralde authored 9 months ago
  
  7b58f7e9
- Release v0.7.1 · d3cce922
  Martin Larralde authored 9 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 9 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