Commits · 32508c4824b2d08635eb08b8361a39a16ddbf940 · Martin Larralde / LightMotif · GitLab

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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
- Reorganize scoring trait and implement row-slice scoring for AVX2 and SSE2 · 39d4fa2c
  Martin Larralde authored 1 year ago
  
  39d4fa2c
- Update `Score` trait to allow scoring a range of rows for a striped sequence · d3ef7eef
  Martin Larralde authored 1 year ago
  
  d3ef7eef
Mar 09, 2024
- Add `ScoringMatrix::score_into` method · 9c739c99
  Martin Larralde authored 1 year ago
  
  9c739c99
- Use `Self::uninitialized` in `DenseMatrix::from_rows` · d1f5b7c8
  Martin Larralde authored 1 year ago
  
  d1f5b7c8
- Update `generic-array` dependency to `v1.0` · 8d805a4a
  Martin Larralde authored 1 year ago
  
  8d805a4a
- Fix trait bounds in `lightmotif-io` · 53c1d7a0
  Martin Larralde authored 1 year ago
  
  53c1d7a0
- Require alignment to be `PowerOfTwo` in `DenseMatrix` implementation · 10426833
  Martin Larralde authored 1 year ago
  
  10426833
- Implement sampling of random sequences using `rand` · 1b4f594e
  Martin Larralde authored 1 year ago
  
  1b4f594e
- Hide documentation for `lightmotif::pli` to encourage using the 'simple' API · 7c5403d4
  Martin Larralde authored 1 year ago
  
  7c5403d4
Mar 08, 2024
- Update example in `README.md` [ci skip] · 06764f8f
  Martin Larralde authored 1 year ago
  
  06764f8f
- Fix benchmark not compiling without explicit `Pipeline` · 8b6d7095
  Martin Larralde authored 1 year ago
  
  8b6d7095
- Use `Backend::LANES` in `Sse2` code · b0e78dc9
  Martin Larralde authored 1 year ago
  
  b0e78dc9
- Add `MultipleOf<N>` trait to simplify typenums in platform code signature · 3c6ce734
  Martin Larralde authored 1 year ago
  
  3c6ce734
- Streamline use of pipelined functions in `lightmotif-py` · cbd1dfbc
  Martin Larralde authored 1 year ago
  
  cbd1dfbc
- Add simple API to sequence and matrix types internally using a dispatch `Pipeline` · 174a5e0c
  Martin Larralde authored 1 year ago
  
  174a5e0c
- Make `EncodedSequence.stripe` use a `Pipeline` internally · 63d41d1b
  Martin Larralde authored 1 year ago
  
  63d41d1b
- Fix code issues with `cargo clippy` · 411c96d6
  Martin Larralde authored 1 year ago
  
  411c96d6
- Add constructor for Python `ScoringMatrix` class · f7862877
  Martin Larralde authored 1 year ago
  
  f7862877