https://github.com/althonos/lightmotif - v0.10.0

Added

lightmotif

• Experimental Gibbs sampler implementation for motif detection in zoops and oops modes.
• IndexMut<MatrixCoordinates> trait implementation for DenseMatrix type.
• AsRef<Vec<T>> for Scores<T>.
• information_content methods to WeightMatrix and ScoringMatrix.
• consensus method to CountMatrix.
• FrequencyMatrix::into_scoring to take ownership of a frequency matrix and converting it inplace into a ScoringMatrix.
• Implement size_hint for StripedScores iterator.
• Cumulative distribution approximation for ScoringMatrix.
• Add ScoringMatrix::to_score_distribution method to compute a score distribution suitable for P-value estimation.
• Trait to compute correlations for lightmotif::pwm matrices.
• new_unchecked constructors to lightmotif::pwm types (undocumented).
• Efficient look-up table implementation for Aarch64 NEON f32-scoring.

lightmotif-io

• Reader for MEME format files.

Changed

lightmotif

• Implement DenseMatrix iterators without unsafe code.
• Make lightmotif::scan::Hit fields read-only.
• Inline short functions in lightmotif core moduels.
• Make the ravel methods of DenseMatrix unsafe.
• Allow accessing and configuring the row capacity of a DenseMatrix.
• Always pre-allocate additional rows when creating a new StripedSequence to avoid reallocation for wrap rows.
• Use pointers to avoid matrix indexing inside pipeline hot loops.
• Skip use of NEON for Score<Protein> since generic code is faster.

lightmotif-io

• Update nom dependency to 8.0.

lightmotif-py

• Update pyo3 dependency to 0.23.
• Use maturin instead of setuptools-rust to build Python bindings from source.

Fixed

lightmotif

• Use all columns of the matrix in CountMatrix::entropy.
• Fix missing _mm_sfence in score_f32_avx2_permute code.
• Avoid multiple log calls in FrequencyMatrix::to_scoring.

Removed

lightmotif

• Const method declaration for matrix traits not const in lightmotif::pwm.

- Rust
Published by github-actions[bot] about 1 year ago

https://github.com/althonos/lightmotif - v0.9.0

Added

lightmotif

• DenseMatrix::ravel to get the array of a DenseMatrix as a single continuous slice.

lightmotif-py

• Support for protein alphabets (#5).
• protein property to CountMatrix, WeightMatrix, ScoringMatrix, EncodedSequence and StripedSequence.
• Scanner class to use the new DNA scanning algorithm.
• Buffer protocol implmementation for ScoringMatrix objects.
• lightmotif.load function to load one or more Motif from a file-like object (#6).
• Motif.name property to store the optional name of a Motif.
• Several Motif subclasses to store motif and metadata loaded from a file.
• Type annotations for the lightmotif.lib package.

Fixed

lightmotif-io

• Parsing of floating-point numbers in JASPAR parser.
• Panic on error unwrapping in lightmotif-io.

Changed

lightmotif

• Rewrite DenseMatrix with constant platform-specific alignment to reduce amount of unsafe code.

Removed

lightmotif-py

• alphabet parameter of ScoringMatrix and EncodedSequence.

- Rust
Published by althonos over 1 year ago

https://github.com/althonos/lightmotif - v0.9.1

Added

lightmotif-py

• Arch User Repository package python-lightmotif to distribute the Python package on ArchLinux.

Fixed

lightmotif-py

• Fix issues with source distribution missing required files for compilation.
• Remove unused test data to reduce size of source distribution.

- Rust
Published by github-actions[bot] over 1 year ago

https://github.com/althonos/lightmotif - v0.8.0

Added

lightmotif

• lightmotif::pwm::DiscreteMatrix to store a discretized ScoringMatrix.
• MatrixElement marker trait for Default + Copy types that can be used as a DenseMatrix element.
• lightmotif::scores::Scores wrapper of Vec<T> with shortcut max, threshold and argmax methods.
• AVX2 and NEON implementations of Score<u8, Dna> pipeline operation.

Fixed

lightmotif

• Remove requirement for T: Debug in Clone implementation of DenseMatrix<T>.
• SSE2 and AVX2 implementations of Argmax not returning the last index in case of ties.

lightmotif-tfmpvalue

• Cache internal buffer for Q-values to avoid reallocation between iterations.

Changed

lightmotif

• Cache the Pipeline used in lightmotif::scan::Scanner.
• Make lightmotif::scores::StripedScores generic over the score type.
• Make Maximum and Threshold generic over the score type.
• Use a discrete matrix in Scanner to quickly eliminate blocks without candidate position above given threshold.
• Compile crate without the rand and rand-distr features by default.

lightmotif-py

• Update pyo3 dependency to v0.22.0.

- Rust
Published by github-actions[bot] almost 2 years ago

https://github.com/althonos/lightmotif - v0.7.3

Added

lightmotif-io

• lightmotif_io::jaspar to read matrices in raw JASPAR format.
• Implementation of Clone and Error for the lightmotif_io::error::Error type.

Changed

lightmotif

• Use logarithmic subtraction in FrequencyMatrix::to_scoring.
• Use _mm256_permutevara8x32_ps instead of _mm256_permutevar_ps in AVX2 implementation to avoid special handling of unknown matric character N.

Fixed

lightmotif

• Striping of empty sequences panicking on AVX2 implementation.
• Scoring of empty range of rows panicking.
• Invalid alignment of data in AVX2 code.
• Clone implementation of DenseMatrix not preserving memory alignment.

- Rust
Published by github-actions[bot] almost 2 years ago

https://github.com/althonos/lightmotif - v0.7.2

Added

lightmotif-py

• Add __len__ implementation for all matrix clases.
• Allow changing the logarithm base in WeightMatrix.log_odds method.
• Implement __getitem__ for row access for all matrix classes.

- Rust
Published by github-actions[bot] almost 2 years ago

https://github.com/althonos/lightmotif - v0.7.0

Added

lightmotif

• Implement indexing of StripedSequence by sequence index.
• matrix accessor to all matrix types in lightmotif::pwm and lightmotif::seq.
• entropy and information_content methods to CountMatrix.
• SymbolCount trait for counting the number of occurrences of a symbol in an iterable.
• Several Background constructors for counting occurences in one or more sequences.
• FromIterator<A::Symbol> constructor for EncodedSequence<A>.
• MultipleOf<N> trait to simplify typenums in platform code signatures.
• Sampling of random sequences using the rand dependency under a feature flag.
• ScoringMatrix.score_into method to re-use a StripedScores buffer.
• ScoringMatrix.score_position method to score a single sequence position.
• Indexing by MatrixCoordinates in DenseMatrix.
• Support for chanding logarithm base when building a ScoringMatrix from a WeightMatrix.
• Scanning algorithm for finding hits in a sequence with an iterator without allocating StripedScores for each sequence position.

lightmotif-py

• Support for optional TFMPvalue interface in Python bindings under GPLv3+ code.
• Constructor for ScoringMatrix class.
• ScoringMatrix.reverse_complement to compute the reverse-complement of a scoring matrix.

Changed

lightmotif

• Make EncodedSequence.stripe use a dispatching Pipeline internally.
• Require power-of-two alignment in DenseMatrix implementations.
• Update generic-array dependency to v1.0.
• Change order of parameters in ScoringMatrix.score.
• Reorganize scoring trait and implement row-slice scoring for AVX2 and SSE2.
• Rewrite Pipeline::threshold to return matrix coordinates instead of a sequence index.
• Rewrite Pipeline::argmax to return matrix coordinates instead of a sequence index.

lightmotif-py

• Streamline the use of pipelined functions in Python bindings.

Fixed

lightmotif

• Handling of unknown residues in permute implementation of Score on AVX2.
• PartialEq for DenseMatrix to ignore alignment padding in each row.

Removed

lightmotif

• Platform-specific code for thresholding a StripedScores matrix.
• Direct attribute access in StripedSequence.

lightmotif-transfac

• Remove crate from repository, superseded by the lightmotif-io crate.

- Rust
Published by github-actions[bot] almost 2 years ago

https://github.com/althonos/lightmotif - v0.6.0

Added

lightmotif

• Validating constructor ::pwm::FrequencyMatrix::new testing for frequencies on each ranks.
• Getter to the raw data matrix of a ::pwm::FrequencyMatrix.

lightmotif-io

New crate with JASPAR, TRANSFAC and UNIPROBE format parsers.

Changed

lightmotif

• Make max_score and min_score columns of ::pwm::ScoringMatrix ignore the wildcard symbol column.

lightmotif-tfmpvalue

• Invert decay in TfmPvalue to reduce rounding errors when computing granularity.
• Use a fast integer hashing algorithm for i64 keys in maps used for recording Q-values.
• Compute the optimal column permutation to accelerate the computation of score distributions.

Removed

lightmotif-transfac

Deprecate crate in favour of lightmotif-io.

- Rust
Published by github-actions[bot] over 2 years ago

https://github.com/althonos/lightmotif - v0.5.1

Fixed

lightmotif

• Compilation for Arm NEON platforms.

- Rust
Published by github-actions[bot] almost 3 years ago

https://github.com/althonos/lightmotif - v0.5.0

Added

lightmotif

• Arm NEON implementation of Threshold and Encode.
• Alphabet::as_str method to get the symbols of an alphabet as a string.
• DenseMatrix::fill method to fill a dense matrix with a constant value.
• Convenience getters and conversion traits to StripedSequence.
• Stripe trait to implement striping of an encoded sequence with SIMD.
• Dynamic dispatched pipeline selecting the best implementation as runtime.
• PartialEq implementation for EncodedSequence.

lightmotif-py

• Buffer and copy protocols for StripedSequence and EncodedSequence.
• Indexing support to EncodedSequence.

lightmotif-tfmpvalue

• Convenience methods to access the wrapped ScoringMatrix reference in TfmPvalue.

Changed

lightmotif

• Encode::encode now returns an EncodedSequence instead of a raw Vec.
• Performance improvements for Encode for AVX2 and NEON by removing non-const function calls in loop.
• Performance improvements for Threshold by skipping the index buffer initialization.
• Avoid buffer initialization when allocating a new buffer in EncodedSequence::encode.
• Require Symbol implementors to implement Eq.

lightmotif-py

• Use the dynamic dispatch pipeline to run vectorized operations.

lightmotif-tfmpvalue

• Make TfmPvalue generic over the type of reference to the wrapped ScoringMatrix.

Fixed

lightmotif

• Debug implementation of DenseMatrix crashing when attempting to render the padding bytes.

- Rust
Published by github-actions[bot] almost 3 years ago

https://github.com/althonos/lightmotif - v0.4.0

Changed

lightmotif

• Improve DenseMatrix::resize performance when downsizing.
• Explicitly panic when sequence is too long to be processed with u32 indices in AVX2 and SSE2.
• Reorganize DenseMatrix column alignment and index storage.
• Improve Score performance by using pointers instead of slices in SIMD loops.
• Rename DenseMatrix::columns_effective to DenseMatrix::stride.
• Use streaming intrinsics to store data in AVX2 and SSE2 implementations.
• Rename BestPosition trait to Maximum.

lightmotif-py

• Avoid error on missing symbols in CountMatrix.__init__

Added

lightmotif

• Threshold trait to find all position above a certain score in a StripedScores matrix.
• Encode trait to encode an ASCII sequence into a Vec<Symbol>.
• AVX2 implementation of Score using gather instead of permute for protein alphabets.
• From<Vec<_>> and Default trait implementations to EncodedSequence.
• Alphabet methods to operate on ASCII strings.
• StripedScores.is_empty method to check if a StripedScores contains any score.

lightmotif-py

• StripedScores.threshold method wrapping the Threshold pipeline operation.
• StripedScores.max and StripedScores.argmax methods to get the best score and best position.

Fixed

lightmotif

• Score causing an overflow when given a sequence shorter than the PSSM.
• Maximum trait returns the smallest position on equal maxima.

- Rust
Published by github-actions[bot] almost 3 years ago

https://github.com/althonos/lightmotif - v0.3.0

Changed

• Rewrite the SSE2 maximum search implementation using a generic number of columns.
• Refactor lightmotif::pwm to avoid infinite odds-ratio for columns with zero background frequencies.

Added

• lightmotif-tfmpvalue crate implementing the TFMPvalue for computing p-values for a ScoringMatrix.
• DenseMatrix::from_rows method to create a dense matrix from an iterable of rows.
• PartialEq implementation for matrices in lightmotif.
• Methods to compute the minimum and maximum scores of a ScoringMatrix.

- Rust
Published by github-actions[bot] almost 3 years ago

https://github.com/althonos/lightmotif - v0.2.0

Changed

• Crate structure to avoid cluttering the main lightmotif module namespace.
• Swizzling used in the SSSE3 implementation to make it require SSE2 only.
• TRANSFAC parser to support parsing sections in arbitrary order and accept additional metadata.
• Use memchr to parse lines faster in TRANSFAC parser.
• Use typenum and generic-array to handle constant matrix dimensions.
• Make Score trait generic over the number of columns in the striped sequence.

Added

• Accessors for some of the attributes of lightmotif_transfac::Matrix.
• Pipeline method to extract the best position from a StripedScore matrix.
• Child trait for alphabet complementation.
• Methods for reverse-complementing all matrices from lightmotif::pwm.
• Alphabet::symbols method to get all the symbols of an alphabet.
• StripedSequence::encode constructor to encode and stripe a text sequence without allocating an extra EncodedSequence.
• Iterator methods and helper struct for StripedScores.
• Protein alphabet to lightmotif::abc.
• DenseMatrix::uninitialized constructor to allocate a dense matrix without filling its contents.
• lightmotif::num module with typenum re-exports and additional StrictlyPositive marker trait.
• Arm NEON implementation of the position scoring algorithm.
• Display implementation for EncodedSequence instead of an arbitrary ToString implementation.

- Rust
Published by github-actions[bot] about 3 years ago

https://github.com/althonos/lightmotif - v0.1.1

Added

• Helper crate to detect CPU features support at runtime.

Fixed

• AVX2 code being imported on x86-64 platforms without checking for OS support.
• AVX2-enabled extension always being compiled even on platforms with no AVX2 support.

Removed

• built and pyo3-built build dependencies (causing issues with workspaces).

- Rust
Published by althonos about 3 years ago

https://github.com/althonos/lightmotif - v0.1.0

Initial release.

- Rust
Published by althonos about 3 years ago