Commits · 66f43eee4fb75bb24499b608018c8f12375d2ab5 · Martin Larralde / LightMotif · GitLab

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Jun 25, 2023
- Refactor `lightmotif::pwm` and avoid infinite scores for columns with zero background frequencies · 66f43eee
  Martin Larralde authored 1 year ago
  
  66f43eee
- Move TFMPvalue implementation to a dedicated crate for licensing reasons · bdc2b248
  Martin Larralde authored 1 year ago
  
  bdc2b248
- Port TFMPvalue algorithm from original C++ implementation · a943ac37
  Martin Larralde authored 1 year ago
  
  a943ac37
- Require `Alphabet::K` associated type to be `Debug` · 1d3da419
  Martin Larralde authored 1 year ago
  
  1d3da419
- Add methods to compute the minimum and maximum scores of a PSSM · 4e62768a
  Martin Larralde authored 1 year ago
  
  4e62768a
Jun 20, 2023
- Add Python benchmarks against MOODS [ci skip] · 6de22b26
  Martin Larralde authored 1 year ago
  
  6de22b26
Jun 16, 2023
- Add dict-based constructor for `CountMatrix` Python class · 8d1d59e2
  Martin Larralde authored 1 year ago
  
  8d1d59e2
- Add `__eq__` method to matrices in `lightmotif-py` · 8da67d92
  Martin Larralde authored 1 year ago
  
  8da67d92
- Add `PartialEq` implementation to matrix types in `lightmotif` · 6868b68e
  Martin Larralde authored 1 year ago
  
  6868b68e
May 19, 2023
- Update instructions to use AVX2 in `README.md` [ci skip] · 2899bf15
  Martin Larralde authored 1 year ago
  
  2899bf15
May 17, 2023
- Update `README.md` with up-to-date benchmark results [ci skip] · cde4077c
  Martin Larralde authored 1 year ago
  
  cde4077c
- Rewrite the SSE2 maximum implementation using a generic number of columns · 4264ca28
  Martin Larralde authored 1 year ago
  
  4264ca28
- Release v0.2.0 · fc274e33
  Martin Larralde authored 1 year ago
  
  View commits for tag v0.2.0 v0.2.0
  
  fc274e33
- Re-export `typenum` crate in the `lightmotif::num` module · 6bb7ce31
  Martin Larralde authored 1 year ago
  
  6bb7ce31
- Add proper `Display` trait implementation for `EncodedSequence` · e7e76b1a
  Martin Larralde authored 1 year ago
  
  e7e76b1a
- Add tests to check the TRANSFAC parser works on TRANSFAC, JASPAR and PRODORIC matrices · 8e940621
  Martin Larralde authored 1 year ago
  
  8e940621
- Fix TRANSFAC parser to accept zero-decimal floats in the count matrix · 45e53759
  Martin Larralde authored 1 year ago
  
  45e53759
- Apply `clippy` suggestions · 2d131b9c
  Martin Larralde authored 1 year ago
  
  2d131b9c
- Disable warning about overflowing literals in AVX2 code · 068523db
  Martin Larralde authored 1 year ago
  
  068523db
- Use AVX2 broadcast instructions to load scores from the PSSM rows · 1464911a
  Martin Larralde authored 1 year ago
  
  1464911a
- Update Python wrapper to use NEON backend when supported · fee4ab59
  Martin Larralde authored 1 year ago
  
  fee4ab59
- Make NEON pipeline generic over the column count · c8f383dd
  Martin Larralde authored 1 year ago
  
  c8f383dd
May 16, 2023
- Add Arm NEON implementation of the scoring algorithm · 3ab0c763
  Martin Larralde authored 1 year ago
  
  3ab0c763
- Fix build of SSE2 tests · a1c02b8c
  Martin Larralde authored 1 year ago
  
  a1c02b8c
- Update `WeightMatrix.calculate` in Python version to use SSE2 as a fallback · a7970f44
  Martin Larralde authored 1 year ago
  
  a7970f44
- Fix build of `lightmotif-bench` and `lightmotif-transfac` tests · 87659cea
  Martin Larralde authored 1 year ago
  
  87659cea
- Use `typenum` to generate SSE2 functions accepting striped matrix with `16n` columns · c22a4a19
  Martin Larralde authored 1 year ago
  
  c22a4a19
- Update `lightmotif-py` and `lightmotif-transfac` with the new pipeline API · 12a2db0e
  Martin Larralde authored 1 year ago
  
  12a2db0e
- Add helper trait for strictly positive typenums · 6eb702e2
  Martin Larralde authored 1 year ago
  
  6eb702e2
- Reorganize code and add more documentation to individual modules · 271bd8d4
  Martin Larralde authored 1 year ago
  
  271bd8d4
- Refactor tests and benchmarks using generics · 2682fb6c
  Martin Larralde authored 1 year ago
  
  2682fb6c
- Remove unused imports from the `lightmotif` code · 1244dcfd
  Martin Larralde authored 1 year ago
  
  1244dcfd
- Reorganize pipeline code into several submodules · 0dee6009
  Martin Larralde authored 1 year ago
  
  0dee6009
- Move pipeline code to a new dedicated module · 0781efb0
  Martin Larralde authored 1 year ago
  
  0781efb0
- Rewrite swizzle of SSSE3 implementation to use SSE2 instructions · aae97369
  Martin Larralde authored 1 year ago
  
  aae97369
May 15, 2023
- Avoid initializing matrix before scoring in `Score` · 54c9e4dc
  Martin Larralde authored 1 year ago
  
  54c9e4dc
- Add an unsafe constructor to create an uninitialized `DenseMatrix` · b32502ea
  Martin Larralde authored 1 year ago
  
  b32502ea
- Fix benchmarks to work with new `typenum` API · 3929e16f
  Martin Larralde authored 1 year ago
  
  3929e16f
- Update `lightmotif-py` with the new `typenum` API · fd54401d
  Martin Larralde authored 1 year ago
  
  fd54401d
- Make `Score` trait generic over the striped sequence columns · 53b25d75
  Martin Larralde authored 1 year ago
  
  53b25d75