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.

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.

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).

v0.1.0

Initial release.