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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

[0.6.0]

  • The ORF type has been updated to hold a view of the sequence represented by the ORF.
  • Docs have been updated to reflect the new sequence method.
  • ORFs no longer hold score information directly. Instead, the Feature field has been added to hold this information in case a new finder method needs it.

[0.5.0]

  • The ORF type has been updated to handle the new finder argument type.
  • findorfs now has a new finder argument that can be used to select the gene finding method.
  • The getorf method has been removed in favor of having a simple sequence method for ORF instances.
  • The write_* API has been updated to handle the new finder argument.
  • A NaiveFinder method has been implemented with a scoring scheme directly.
  • iscoding has been updated to handle the new finder argument.
  • Documentation has been updated and improved.

[0.4.0]

  • findorfs now has a new method argument that can be used to select the gene finding method.
  • The getorf method has been updated to handle the new method argument.
  • The write_* API has been updated to handle the new method argument.
  • A NaiveFinder method has been implemented with a scoring scheme as well (NaiveFinderScored).
  • iscoding has been updated to handle the new method argument.

[0.3.0]

  • ORF has a new score field that can be used to rank ORFs.
  • findorfs is now felixible and can be expanded to more gene finding methods/algorithms.
  • A new (and quite simple) finding method with a scoring scheme has been implemented.
  • Docuemntation has been updated and improved.

[0.2.0]

  • A more stable ORF type that asserts for incorrect ORFs.
  • Extended Base.getindex method to better handle ORF enabling: seq[orf] regardless of the ORF strand.
  • The write_* API is much more stable and its been rewriten to handle IOStreams and IOBuffers as well.
  • The new record_orfs_fna and record_orfs_faa methods intearact with the FASTX interface.
  • Codebase has been reduced. Direct String manipulation is not enabled for findorfs and get_* methods.
  • Docstrings have been updated following method updates.
  • Better tests and now Aqua.jl is used for several tests as well.

[0.1.0]

  • GeneFinder is now more reliable and load faster.

[0.0.23]

  • Some cleanups and docs updates

[0.0.22]

  • Decoupling Markov chains to its own repo plus some general cleaning.

[0.0.21]

  • Improve the orf prediction and add frame information see #20

[0.0.20]

  • Better docs w/ MathJax

[0.0.19]

  • Improve docs on markov chains and transition models

[0.0.18]

  • Clean code and update methods for transition matrix

[0.0.17]

  • Add several methods towards HMMs in gene finding see PR #17

[0.0.16]

  • Fix a bug with importing FASTX.sequence() in write API

[0.0.15]

  • Add precompilation statement to findorfs()
  • Clean src and update docs

[0.0.14]

  • Implement a sorting method for the orfs (#16)

[0.0.13]

  • Add write_gff methods

[0.0.12]

  • some refactors

[0.0.11]

  • Fix a bug with @view
  • Improve cdsgenerator and getcds

[0.0.10]

  • Fix a bug in getcds

[0.0.9]

  • Improvements in findorfs (prev orf_finder). Main ideas: Dan also see this Post
  • Update some docs

[0.0.8]

  • Renaming functions in simple finder implementation
  • Better docs following some BluStyle guidelines

[0.0.7]

  • Clean up comments.
  • New write_bed function.
  • Document methods.
  • Add Zenodo badge.

[0.0.6]

  • Work on extended start codon for generators.
  • simplefind and its generators now can be fine tuned with alternative codons and orf length.
  • Work on the IO system
  • More on Docs

[0.0.5]

  • Changed in the internals of simplefinder.
  • Added a new logo.
  • Improved tests and docs.
  • Added generators orfgenerator and locationgenerator.
  • Included some helper functions.
  • The findcds and findproteins turned into generators (cdsgenerator and proteingenerator).
  • Add the Codon type and clean others.

[0.0.4]

  • Now registered: add GeneFinder to install from the REPL
  • Better docs

[0.0.3]

  • Clean simplefinder
  • Add references
  • Clean README
  • Clean initial structs
  • Make it public

[0.0.2]

  • Add findcds and findproteins function for the first algorithm
  • Add docs for simplefinder functions and structs
  • Add test using TestItems package

[0.0.1]

  • Add some basic structs like ORF
  • Add first ORF finder function simplefinder
  • Add package overview