Commits · 8b227e32aa3d70f63f5daf62477f407d0d06744e · Martin Larralde / LightMotif · GitLab

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Aug 07, 2023
- Add `Alphabet` methods to parse ASCII strings · 8b227e32
  Martin Larralde authored 1 year ago
  
  8b227e32
- Add `From<Vec<_>>` and `Default` traits to `EncodedSequence` · c35c1d89
  Martin Larralde authored 1 year ago
  
  c35c1d89
Jul 31, 2023
- Improve handling of pointers in SSE2 pipeline · b0a68a5e
  Martin Larralde authored 1 year ago
  
  b0a68a5e
- Use constant functions to setup the alphabet default in AVX2 pipeline · 2ee08cf0
  Martin Larralde authored 1 year ago
  
  2ee08cf0
- Remove unused variable from `lightmotif::pli::platform::avx2` · f6a3e626
  Martin Larralde authored 1 year ago
  
  f6a3e626
- Add `lightmotif` benchmarks for protein PSSMs · 3f545250
  Martin Larralde authored 1 year ago
  
  3f545250
- Add AVX2 scoring using `gather` instead of `permute` to support protein alphabets · 0640ebcb
  Martin Larralde authored 1 year ago
  
  0640ebcb
Jul 28, 2023
- Update benchmark results in `README.md` [ci skip] · 9bdb14ee
  Martin Larralde authored 1 year ago
  
  9bdb14ee
- Use streaming intrinsics for storing data in AVX2 and SSE2 extensions · 97bac0d7
  Martin Larralde authored 1 year ago
  
  97bac0d7
Jul 18, 2023
- Add `StripedScores.threshold` method to `lightmotif-py` · 2670dee0
  Martin Larralde authored 1 year ago
  
  2670dee0
- Rename `DenseMatrix::columns_effective` to `DenseMatrix::stride` · b9504e91
  Martin Larralde authored 1 year ago
  
  b9504e91
- Add documentation pages for missing `lightmotif-py` objects · 9fe5d5ae
  Martin Larralde authored 1 year ago
  
  9fe5d5ae
- Improve documentation of Python objects in `lightmotif-py` · f57957fd
  Martin Larralde authored 1 year ago
  
  f57957fd
- Add links to other crates in project `README.md` [ci skip] · a82ecced
  Martin Larralde authored 1 year ago
  
  a82ecced
- Add configuration files to build documentation on ReadTheDocs · 4b901d09
  Martin Larralde authored 1 year ago
  
  4b901d09
- 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
  
  c1401644
- Update actions/checkout in GitHub Actions workflows to v3 (#2) · b30792ac
  Dirk Stolle authored 1 year ago
  
  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