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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

[1.0.0]

  • Alphabet types is now inherited in the BioMarkovChain struct.
  • Operations with BMC (log_odds_ratio_score, log_odds_ratio_matrix...) have been updated for correctnes.
  • BioMarkovChain now has a logscale kwarg to calculate the log_odds_ratio_score using base 2.
  • Tests have been updated to reflect the changes.

[0.10.1]

  • Apply a more simple way to calculate the lors and more correct.
  • Update the log_odds_ratio_matrix so it can be simply generated with two BMC models
  • Update the docs.
  • Move the dnaseqprobability to markovprobability and gains the logscale kwarg.

[0.10.0]

  • New documentation framework.
  • log_odds_ratio_score now only requires the sequence and the model is a keyword argument.
  • Various improvements on the docs.
  • BioMarkovChain now is more cleanly displayed.

[0.9.0]

  • BioMarkovChain now has a compliant BioSequences alphabet.

[0.8.1]

  • Fix BioMarkovChain checks compats.

[0.8.0]

  • BioMarkovChain checks whether its row-stochastic.
  • New extended functions from the DiscreteMarkovChains packages are now available.
  • dnaseqprobability is much faster.
  • New methods to calculate the logg-odds-ratio-matrix and logg-odds-ratio-score of a BioSequences.
  • Improvementes on the docs.

[0.7.0]

  • Improve BioMarkoChain struct to be more flexible and distinguish DNA, RNA, AminoAcid #17

[0.6.0]

  • Update docs version to 1.0.
  • Update docs logo.
  • Add new methods for to calculate the log-odds ratio of a sequence and a model.
  • Extend new methods from the booleans/predicates of DiscreteMarkovChains.jl package.
  • Clean code and make it more lightweight by using weakdeps.

[0.5.0]

  • Improve count of transitions 10X thanks to VectorizedKmers.jl.

[0.4.1]

  • Internals changes, clean code and make it more flexible.

[0.4.0]

  • Clean documentation.
  • Add a randbmc methods.
  • Improve BMC printing.

[0.3.0]

  • Refactoring the TransitionModel to a BioMarkovChain construct and better interface.

[0.2.0]

  • Exapanding the alphabets to RNA and AA to its Markov chains.
  • Improving runtime and allocations.
  • Refacotring and renaming of internal functions.

[0.1.X]

  • This version has some clean ups and a new faster version of dinucleotides counts thanks to @gdalle. See here the discussion.

[0.1.0]

  • First release of BioMarkovChains