Commits · f2d4ebd8e94eca66ce3dac998c426e81f8ae0cd3 · Martin Larralde / LightMotif · GitLab

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Mar 11, 2024
- 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
- Make sure `lightmotif-py` computes the right p-values · 093889bc
  Martin Larralde authored 1 year ago
  
  093889bc
- Clear dual-licensing of the `lightmotif-py` depending on the TFM-PVALUE dependency · ec8d85ea
  Martin Larralde authored 1 year ago
  
  ec8d85ea
- Add support for optional TFMPvalue interface in Python bindings · e85eb753
  Martin Larralde authored 1 year ago
  
  e85eb753
Jan 28, 2024
- Update `cibuildwheel` used in Actions workflows to latest release · 31aab51f
  Martin Larralde authored 1 year ago
  
  31aab51f
Dec 15, 2023
- Implement `FromIterator<A::Symbol>` for `EncodedSequence<A>` · fd2c564a
  Martin Larralde authored 1 year ago
  
  fd2c564a
- Add `Background` constructor computing frequencies from an array of symbol counts · 6e4d37c9
  Martin Larralde authored 1 year ago
  
  6e4d37c9
- Add `Background` constructor counting symbol occurences in a single sequence · 7acbd712
  Martin Larralde authored 1 year ago
  
  7acbd712
- Add `Background` constructor counting symbol occurences in several sequences · 1339bddc
  Martin Larralde authored 1 year ago
  
  1339bddc
- Add trait to count the number of symbol occurences in an arbitrary collection · b5ac2896
  Martin Larralde authored 1 year ago
  
  b5ac2896
- Add methods to compute the entropy and information content of a `CountMatrix` · 0a68afc6
  Martin Larralde authored 1 year ago
  
  0a68afc6
- Add `matrix` accessor to all matrix types in `lightmotif::pwm` · 1249af5f
  Martin Larralde authored 1 year ago
  
  1249af5f
- Fix `PartialEq` for `DenseMatrix` to only compare equality of data · 1e42f62f
  Martin Larralde authored 1 year ago
  
  1e42f62f
Dec 14, 2023
- Fix handling of unknown residues in `permute` impl of `Score` for `Avx2` · 72f19cc7
  Martin Larralde authored 1 year ago
  
  72f19cc7
- Allow indexing a `StripedSequence` to access symbols sequentially · 6b06ad64
  Martin Larralde authored 1 year ago
  
  6b06ad64