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@github-actions github-actions released this 14 Jun 14:02
v0.7.0
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althonos Martin Larralde
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Added

lightmotif

  • Implement indexing of StripedSequence by sequence index.
  • matrix accessor to all matrix types in lightmotif::pwm and lightmotif::seq.
  • entropy and information_content methods to CountMatrix.
  • SymbolCount trait for counting the number of occurrences of a symbol in an iterable.
  • Several Background constructors for counting occurences in one or more sequences.
  • FromIterator<A::Symbol> constructor for EncodedSequence<A>.
  • MultipleOf<N> trait to simplify typenums in platform code signatures.
  • Sampling of random sequences using the rand dependency under a feature flag.
  • ScoringMatrix.score_into method to re-use a StripedScores buffer.
  • ScoringMatrix.score_position method to score a single sequence position.
  • Indexing by MatrixCoordinates in DenseMatrix.
  • Support for chanding logarithm base when building a ScoringMatrix from a WeightMatrix.
  • Scanning algorithm for finding hits in a sequence with an iterator without allocating StripedScores for each sequence position.

lightmotif-py

  • Support for optional TFMPvalue interface in Python bindings under GPLv3+ code.
  • Constructor for ScoringMatrix class.
  • ScoringMatrix.reverse_complement to compute the reverse-complement of a scoring matrix.

Changed

lightmotif

  • Make EncodedSequence.stripe use a dispatching Pipeline internally.
  • Require power-of-two alignment in DenseMatrix implementations.
  • Update generic-array dependency to v1.0.
  • Change order of parameters in ScoringMatrix.score.
  • Reorganize scoring trait and implement row-slice scoring for AVX2 and SSE2.
  • Rewrite Pipeline::threshold to return matrix coordinates instead of a sequence index.
  • Rewrite Pipeline::argmax to return matrix coordinates instead of a sequence index.

lightmotif-py

  • Streamline the use of pipelined functions in Python bindings.

Fixed

lightmotif

  • Handling of unknown residues in permute implementation of Score on AVX2.
  • PartialEq for DenseMatrix to ignore alignment padding in each row.

Removed

lightmotif

  • Platform-specific code for thresholding a StripedScores matrix.
  • Direct attribute access in StripedSequence.

lightmotif-transfac

  • Remove crate from repository, superseded by the lightmotif-io crate.
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