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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

v0.6.0 - 2023-08-31

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 - 2023-08-31

Fixed

lightmotif

  • Compilation for Arm NEON platforms.

v0.5.0 - 2023-08-31

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.

v0.4.0 - 2023-08-10

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.

v0.3.0 - 2023-06-25

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 - 2023-05-15

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 - 2023-05-04

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 - 2023-05-04

Initial release.