Commits · c22a4a195d781a4e192d0913bc2dae41549e2984 · Martin Larralde / LightMotif · GitLab

Snippets Groups Projects

May 16, 2023
- 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
- Update `lightmotif-transfac` with new `typenum` API · 5776de5f
  Martin Larralde authored 1 year ago
  
  5776de5f
- Select a default vector type for `Pipeline` based on compile-time features · 684b4091
  Martin Larralde authored 1 year ago
  
  684b4091
- Fix broken SSSE3 maximum position implementation · f7c39a37
  Martin Larralde authored 1 year ago
  
  f7c39a37
- Use `typenum` and `generic-array` crates to handle constant alphabet sizes · 3f0c8c94
  Martin Larralde authored 1 year ago
  
  3f0c8c94
- Update SSSE3 implementation to support `Protein` alphabet · 738b7e28
  Martin Larralde authored 1 year ago
  
  738b7e28
- Add `Protein` alphabet to base crate · c1ac593d
  Martin Larralde authored 1 year ago
  
  c1ac593d
May 11, 2023
- Add links to both versions of the library in `README.md` [ci skip] · c2042d29
  Martin Larralde authored 1 year ago
  
  c2042d29
- Add struct to iterate over the striped scores in order · ef89f554
  Martin Larralde authored 1 year ago
  
  ef89f554
- Add shortcut method to encode and stripe a text sequence · bf846770
  Martin Larralde authored 1 year ago
  
  bf846770
- Add `reverse_complement` method to all matrices · 0e1158aa
  Martin Larralde authored 1 year ago
  
  0e1158aa
- Add method to get all symbols of an alphabet · ae161e39
  Martin Larralde authored 1 year ago
  
  ae161e39
- Add traits for alphabet complementation to `lightmotif` · 83627fd6
  Martin Larralde authored 1 year ago
  
  83627fd6
May 10, 2023
- Use aligned loads in SSSE3 maximum search implementation · 5c306f61
  Martin Larralde authored 1 year ago
  
  5c306f61
- Add SSSE3 implementation of the maximum score search algorithm · b4408fc4
  Martin Larralde authored 1 year ago
  
  b4408fc4
- Add method to extract the best position from a `StripedScores` matrix with AVX2 · 7f70de3b
  Martin Larralde authored 1 year ago
  
  7f70de3b
- Add method accessors to `lightmotif_transfac::Matrix` · a43aefce
  Martin Larralde authored 1 year ago
  
  a43aefce
May 09, 2023
- Improve API for `lightmotif-transfac` · 278665a9
  Martin Larralde authored 1 year ago
  
  278665a9
- Add support for parsing more metadata from TRANSFAC files · 5c3f73c8
  Martin Larralde authored 1 year ago
  
  5c3f73c8
May 08, 2023
- Use `memchr` to parse lines faster in TRANSFAC parser · 4183f7d1
  Martin Larralde authored 1 year ago
  
  4183f7d1
- Rewrite TRANSFAC parser to support out-of-order line entries · 89c20190
  Martin Larralde authored 1 year ago
  
  89c20190
May 06, 2023
- Fix DNA benchmark and update results `README.md` [ci skip] · fa0657e5
  Martin Larralde authored 1 year ago
  
  fa0657e5
May 04, 2023
- Update `setup.py` to allow inplace extension compilation · d3813cad
  Martin Larralde authored 1 year ago
  
  d3813cad
- Add `target_feature` attributes for SSSE3 and AVX2 code · 98e005fb
  Martin Larralde authored 1 year ago
  
  98e005fb
- Remove multiple compilation units from `lightmotif-py` · 9beab6cd
  Martin Larralde authored 1 year ago
  
  9beab6cd
- Reorganize conditional compilation of AVX2 code in `lightmotif` crate · 9fbade7d
  Martin Larralde authored 1 year ago
  
  9fbade7d
- Fix permissions for the `release-a-changelog` action [ci skip] · 868f2198
  Martin Larralde authored 1 year ago
  
  868f2198