Commits · 6927895afd8f52fd034fbc74216097e50c065950 · Martin Larralde / LightMotif · GitLab

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Dec 06, 2024
- Allow accessing and configuring the row capacity of a `DenseMatrix` · 6927895a
  Martin Larralde authored 3 months ago
  
  6927895a
Nov 13, 2024
- Make the `ravel` methods of `DenseMatrix` unsafe as they may expose uninitialized elements · db96b24a
  Martin Larralde authored 4 months ago
  
  db96b24a
- Add a trait to compute correlations for `lightmotif::pwm` matrices · 992b92b1
  Martin Larralde authored 4 months ago
  
  992b92b1
- Use macros to refactor common code in `lightmotif-py` · d88807aa
  Martin Larralde authored 4 months ago
  
  d88807aa
Nov 12, 2024
- Fix slow implementation of `SymbolCount::count_symbols` fo r `StripedSequence` · 83ea36ed
  Martin Larralde authored 4 months ago
  
  83ea36ed
- Inline some short functions in `lightmotif` core modules · b85be7e8
  Martin Larralde authored 4 months ago
  
  b85be7e8
- Use default column type based on current platform in most `lightmotif` types · 015ef4ad
  Martin Larralde authored 4 months ago
  
  015ef4ad
- Add dedicated trait for positive column dimensions in `lightmotif` · 58c4dc67
  Martin Larralde authored 4 months ago
  
  58c4dc67
- Add tests for `SymbolCount` for `EncodedSequence` and `StripedSequence` · dca3f923
  Martin Larralde authored 4 months ago
  
  dca3f923
- Use macros in `lightmotif-py` to reduce duplicated code between alphabets · c125bcc9
  Martin Larralde authored 4 months ago
  
  c125bcc9
Nov 08, 2024
- Allow accessing the sampled survival function distribution for a PSSM in `lightmotif-py` · 033bd157
  Martin Larralde authored 4 months ago
  
  033bd157
- Use the `Dispatch` columns for matrices in `lightmotif-py` · 43065afc
  Martin Larralde authored 4 months ago
  
  43065afc
- Add new `ScoreDistribution` Python type to help with p-value computation · 7f2251fe
  Martin Larralde authored 4 months ago
  
  7f2251fe
- Update type hints to show different p-value methods · 5ccfcbf6
  Martin Larralde authored 4 months ago
  
  5ccfcbf6
- Update `lightmotif-py` to use the MEME implementation of p-value computation · 9bb0a98b
  Martin Larralde authored 4 months ago
  
  9bb0a98b
- Mark most `ScoreDistribution` methods as `inline` · 69185a8a
  Martin Larralde authored 4 months ago
  
  69185a8a
- Add small example to `lightmotif::pwm::dist` documentation · bb8aab65
  Martin Larralde authored 4 months ago
  
  bb8aab65
- Add `ScoringMatrix::to_score_distribution` method and document `ScoreDistribution` methods · 07c0ef8c
  Martin Larralde authored 4 months ago
  
  07c0ef8c
- Implement `Distribution` from `rand` for `ScoreDistribution` · 5844591d
  Martin Larralde authored 4 months ago
  
  5844591d
- Improve documentation for `lightmotif::pwm::dist` module · a7ce3be3
  Martin Larralde authored 4 months ago
  
  a7ce3be3
- Store min and max score in `CumulativeDistribution` · d7880314
  Martin Larralde authored 4 months ago
  
  d7880314
- Move `lightmotif::pwm` into a module and move `CumulativeDistribution` to `lightmotif::pwm::cdf` · 22b43118
  Martin Larralde authored 4 months ago
  
  22b43118
- Implement cumulative distribution approximation for a `ScoringMatrix` · 409cb96b
  Martin Larralde authored 4 months ago
  
  409cb96b
- Make `lightmotif::scan::Hit` fields read-only · d6b320da
  Martin Larralde authored 4 months ago
  
  d6b320da
- Recycle `StripedScores` between `Sampler` iterations · c965d5f2
  Martin Larralde authored 4 months ago
  
  c965d5f2
- Implement `size_hint` for `StripedScores` iterator · 76cfe66b
  Martin Larralde authored 4 months ago
  
  76cfe66b
- Add method to take ownership of a `FrequencyMatrix` and converting it into a `ScoringMatrix` · a377df54
  Martin Larralde authored 4 months ago
  
  a377df54
- Avoid calling `log` twice in `FrequencyMatrix::to_scoring` · 2e71cbc2
  Martin Larralde authored 4 months ago
  
  2e71cbc2
Nov 07, 2024
- Fix missing `_mm_sfence` in `score_f32_avx2_permute` · 6559f76a
  Martin Larralde authored 4 months ago
  
  6559f76a
- Merge branch 'sampler' · f13cfdcf
  Martin Larralde authored 4 months ago
  
  f13cfdcf
- Add Gibbs sampler to `README.md` [ci skip] · 2206c13a
  Martin Larralde authored 4 months ago
  
  2206c13a
- Rename `sample` feature and make it a default · d3c9d576
  Martin Larralde authored 4 months ago
  
  d3c9d576
- Document public types of `lightmotif::sampler` · 74ae72c3
  Martin Larralde authored 4 months ago
  
  74ae72c3
- Add more documentation to `lightmotif::pwm` and `lightmotif::sampler` · 769f27d1
  Martin Larralde authored 4 months ago
  
  769f27d1
- Avoid encoding sequences twice in `lightmotif::sampler` tests · e3e338e2
  Martin Larralde authored 4 months ago
  
  e3e338e2
- Reorganize AVX2-specific code to keep indices as `__m256i` · b5108167
  Martin Larralde authored 4 months ago
  
  b5108167
- Implement `DenseMatrix` iterators without unsafe code · a81327fe
  Martin Larralde authored 4 months ago
  
  a81327fe
- Fix `ScoringMatrix::information_content` returning NaN on matrices with `-inf` scores · eb37f760
  Martin Larralde authored 4 months ago
  
  eb37f760
Nov 06, 2024
- Use dispatch based on `Alphabet::K` to decide implementation of `score_f32` on AVX2 · 3c5c16ff
  Martin Larralde authored 4 months ago
  
  3c5c16ff
Nov 04, 2024
- Add project homepage to `pyproject.toml` [ci skip] · 58484d43
  Martin Larralde authored 4 months ago
  
  58484d43