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.