Commits · 90d3b2cb055142085c92802e5bec957243b6453b · Martin Larralde / LightMotif · GitLab

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Jul 18, 2023
- Avoid error on missing symbols in `CountMatrix.__init__` · 90d3b2cb
  Martin Larralde authored 1 year ago
  
  90d3b2cb
- Improve SIMD performance by using pointers in scan loops · 404a6b44
  Martin Larralde authored 1 year ago
  
  404a6b44
- Reorganize handling of column alignment in `DenseMatrix` · dc6bff68
  Martin Larralde authored 1 year ago
  
  dc6bff68
- Avoid storing indices in external vector in `DenseMatrix` · 9e52544c
  Martin Larralde authored 1 year ago
  
  9e52544c
Jun 28, 2023
- Use AVX2 masked stores instead of blend in `Avx2::threshold` · 46297c96
  Martin Larralde authored 1 year ago
  
  46297c96
Jun 27, 2023
- Add an AVX2 implementation of `Threshold` · e2b8403b
  Martin Larralde authored 1 year ago
  
  e2b8403b
- Fix `Sse2::threshold` to ignore last indices resulting from matrix padding · 56e97685
  Martin Larralde authored 1 year ago
  
  56e97685
- Add benchmarks for the different `Threshold` implementations · 174cca1c
  Martin Larralde authored 1 year ago
  
  174cca1c
- Add an SSE2 implementation of `Threshold` · b0ac0a6c
  Martin Larralde authored 1 year ago
  
  b0ac0a6c
- Mark `StripedScores.index` as `inline` to speed-up loop indexing · e1433747
  Martin Larralde authored 1 year ago
  
  e1433747
- Add new trait to search positions above threshold in `StripedScores` · 085a85c2
  Martin Larralde authored 1 year ago
  
  085a85c2
- Panic when the sequence is too long in AVX2 and SSE2 `best_position` code · a4c07b1f
  Martin Larralde authored 1 year ago
  
  a4c07b1f
Jun 26, 2023
- Simplify handling of `StripedScores` in base `lightmotif` crate · eaf43961
  Martin Larralde authored 1 year ago
  
  eaf43961
- Improve `DenseMatrix::resize` performance when downsizing · f095d516
  Martin Larralde authored 1 year ago
  
  f095d516
- Fix typos in main crate (#1) · c1401644
  Dirk Stolle authored 1 year ago
  
  Unverified
  
  c1401644
- Update actions/checkout in GitHub Actions workflows to v3 (#2) · b30792ac
  Dirk Stolle authored 1 year ago
  
  Unverified
  
  b30792ac
Jun 25, 2023
- Release v0.3.0 · 48ce08e6
  Martin Larralde authored 1 year ago
  
  View commits for tag v0.3.0 v0.3.0
  
  48ce08e6
- Add step to release `lightmotif-tfmpvalue` to `test.yml` Actions workflow · c7c77f0a
  Martin Larralde authored 1 year ago
  
  c7c77f0a
- Add tests for each iteration of `TfmPvalue::approximate_pvalue` · dfe858e1
  Martin Larralde authored 1 year ago
  
  dfe858e1
- Reorganize granularity handling in `TfmPvalue` · 6d89ab79
  Martin Larralde authored 1 year ago
  
  6d89ab79
- Add `fnv` as an optional dependency to speed-up maps in `TfmPvalue` · a42049fc
  Martin Larralde authored 1 year ago
  
  a42049fc
- Add benchmarks for exact computations in `lightmotif-tfmpvalue` · dad6a9e1
  Martin Larralde authored 1 year ago
  
  dad6a9e1
- Remove unused imports from `lightmotif-tfmpvalue` tests · 0e03075a
  Martin Larralde authored 1 year ago
  
  0e03075a
- Add usage example to `README.md` of `lightmotif-tfmpvalue` · ad8c9277
  Martin Larralde authored 1 year ago
  
  ad8c9277
- Add `DenseMatrix` constructor from an iterator of rows · df13aa38
  Martin Larralde authored 1 year ago
  
  df13aa38
- Add more documentation to `lightmotif-tfmpvalue` types · c87010a2
  Martin Larralde authored 1 year ago
  
  c87010a2
- Update workspace to use the 2021 resolver · 5740836b
  Martin Larralde authored 1 year ago
  
  5740836b
- Refactor `TfmPvalue` iterations into a single object for both algorithms · 33df90a6
  Martin Larralde authored 1 year ago
  
  33df90a6
- Rewrite `lightmotif-tfmpvalue` using an iterator pattern for the approximation · 49d9492d
  Martin Larralde authored 1 year ago
  
  49d9492d
- 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