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.