Lightmotif

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`.

Fixed

`lightmotif`
- Compilation for Arm NEON platforms.

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.

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.

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`.

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.