v0.10.1

Added

lightmotif

• Lossy constructor for EncodedSequence replacing unknown characters with Alphabet::default_symbol.
• block_size option to change the number of rows of the block used in a Scanner.

Fixed

lightmotif

• ScoringMatrix::to_discrete failing conversion on cells with -inf scores (due to zero pseudocounts).
• Panic in Scanner::next caused by empty scores buffer.
• Non-saturating add being used in score_u8_neon causing Scanner to ignore some hits on Arm platforms.

Changed

lightmotif

• Update rand dependency to v0.10.0.

lightmotif-py

• Update pyo3 dependency to v0.28.0..

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.

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.

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.

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.

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.

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.

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.

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.

v0.5.1

Fixed

lightmotif

• Compilation for Arm NEON platforms.