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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.

[3.4.0]

  • Deprecate functions n_ambiguous, n_gaps and n_certain. Instead, use the equivalent methods count(f, seq) with the appropriate function f.
  • Deprecate method Base.count(::Function, ::BioSequence, ::BioSequence), and the other methods of count which are subtypes of this.
  • Deprecate use of functions matches and mismatches where the input seqs have different lengths.
  • Optimise count(==(biosymbol), biosequence) and count(==(biosymbol), biosequence)
  • Optimise contruction of LongSequence nucleotide sequences from sequences with a different bit-number (e.g. two-bit seqs from four-bit seqs)

[3.3.0]

  • Add functions bioseq and guess_alphabet to easily construct a biosequence of an unknown alphabet from e.g. a string.
  • Relax requirement of decode, such that it no longer needs to check for invalid data. Note that this change is not breaking, since it is not possible for correctly-implemented Alphabet and BioSequence to store invalid data.

[3.2.0]

  • Dropped support for Julia versions older than 1.10.0
  • Added a 'Recipes' page to the documentation
  • Add new genetic code: blepharisma_macronuclear_genetic_code
  • Improve documentation of sequence count methods and sequence string literals
  • Various performance improvements to counting, ExactSearchQuery and ispalindromic

[3.1.6]

  • The heuristics for translating sequences with ambiguous symbols is now improved. Now, translate does not rely on heuristics but uses an algorithm that always returns exactly the right amino acid in the face of ambiguous nucleotides.

[3.1.5]

  • Attempting to translate a nucleotide sequence with gap symbols now throws an error (#278, see #277)

[3.1.4]

  • Migrate from SnoopPrecompile to PrecompileTools (#273)

[3.1.3]

  • Improve error when mis-encoding LongDNA from byte-like inputs (#267)
  • Remove references to internal Random.GLOBAL_RNG (#265)

[3.1.2]

  • Fix bug in converting LongSubSeq to LongSequence (#261)

[3.1.1]

  • Add iterate method for Alphabets (#233)
  • Add SnoopPrecompile workload and dependency on SnoopPrecompile (#257)

[3.1.0]

Added

  • Add rand!([::AbstractRNG], ::LongSequence, [::Sampler]) methods

[3.0.2]

Added

  • It is now possible to join BioSymbols into a BioSequence.
  • Add findall methods to BioSequence

[3.0.1]

Release has been yanked from General Registry

[3.0]

Removed

  • Removed unsafe_setindex!. Instead, use normal setindex with @inbounds.
  • Removed minhashing functionality - see package MinHash.jl
  • Removed composition functionality - see package Kmers.jl
  • Removed ReferenceSequence functionality
  • Removed demultiplexer functionality
  • Removed kmer functionality - this is moved to Kmers.jl
  • Removed VoidAlphabet and CharAlphabet
  • Removed ConditionIterator

Added

  • Added type LongSubSeq, a view into a LongSequence.
  • Added method translate!(::LongAminoAcidSeq, ::LongNucleotideSeq; kwargs...)
  • Added method join(::Type{T<:BioSeuence}, it) to join an iterable of biosequences to a new instance of T.
  • Added method join!(s::BioSequence, it), an in-place version of join

Changed

  • LongSequence is no longer copy-on-write. For views, use LongSubSeq.
  • Renamed LongAminoAcidSeq -> LongAA, LongNucleotideSeq -> LongNuc LongRNASeq -> LongRNA and LongDNASeq -> LongDNA
  • The interface for Alphabet and BioSequence is now more clearly defined, documented, and tested.
  • The constructor LongSequence{A}(::Integer) has been removed in favor of LongSequence{A}(undef, ::Integer).
  • Biological sequences can no longer be converted to/from strings and vectors.
  • Updated the element and substring search API to conform to Base.find* patterns.

2.0.1

Changed

  • Fixed syntax errors where functions were marked with @inbounds instead of @inline.

[2.0]

Added

  • New subtypes of Random.Sampler, SamplerUniform and SamplerWeighted.
  • Random LongSequences can now be created with randseq, optionally using a sampler to specify element distribution.
  • All random LongSequence generator methods take an optional AbstractRNG argument.
  • Add methods to randseq to optimize random generation of NucleicAcid or AminoAcid LongSequences.
  • BioGenerics is now a dependency - replaces BioCore.
  • A SkipmerFactory iterator that allows iteration over the Skipmers in a nucleotide sequence. A Skipmer is a Mer (see changed below), that is generated using a certain cyclic nucleotide sampling pattern. See this paper for more details.
  • A BigMer parametric primitive type has been added, that has the same functionality as Mer (see changed section), but uses 128 bits instead of 64.
  • An abstract parametric type called AbstractMer has been added to unify Mer and BigMer.
  • Generators of bit-parallel iteration code have been introduced to help developers write bitparallel implementations of some methods. Counting GC content, matches and mismatches have been migrated to use these generators.
  • Added occursin methods for exact matching.

Changed

  • The abstract Sequence type is now called BioSequence{A}.
  • The type previously called BioSequence{A} is now LongSequence{A}.
  • Kmers are now a parametric primitive type: Mer{A<:NucleicAcidAlphabet{2},K}.
  • unsafe_setindex! has been made systematic for all setindex methods as a way of bypassing all bound checking and orphan! calls.
  • Kmer string literals have been updated, they are now mer"" string literals, and they have a flag to enforce the type of Mer e.g.: mer"ATCG"dna, mer"AUCG"rna
  • No longer use an old version of Twiddle and deprecated functions.
  • Using Base.count with certain functions and sequence combinations dispatches to highly optimized bit-parallel implementations, falling back to a default naive counting loop by default for all other predicate-sequence combinations.
  • No more implicit conversion from strings to biological sequences. The Base.convert methods have been renamed to Base.parse methods.

Removed

  • The FASTQ module.
  • The FASTA module.
  • The TwoBit module.
  • The ABIF module.
  • BioCore is no longer a dependency.
  • Automa is no longer a dependency.

1.1.0

Changed

  • Automatic conversion of LongDNASeq to LongRNASeq when translating sequences.
  • Add alternative_start keyword argument to translate().
  • Add abstract type for kmer iterators.
  • 🐎 Faster kmer iteration.
  • Fixed indexing in ABIF records.

1.0.0 - 2018-08-23

Added

  • Issue and PR templates.
  • Code of Conduct and Contributing files.
  • A changelog file.
  • Support for julia v0.7 and v1.0.

Removed

  • ❗ Support for julia v0.6.

0.8.3 - 2018-02-28

Changed

  • Fix the sequence method so as the sequence type can be specified, allowing type-stable efficient code generation.

0.8.2 - 2018-02-19

Changed

  • A bug fix for FASTA.Record writing where the width parameter of a FASTA.Writer is less than or equal to zero.

0.8.1 - 2017-11-10

Changed

  • Update documentation generation.
  • Fixes to type definition keywords.
  • Bit-parallel GC counting.

0.8.0 - 2017-08-16

Added

  • Position weight matrix search functionality.
  • A generalised composition method.
  • typemin and typemax methods for Kmer types.

Changed

  • MinHash function now generalised to Reader types.
  • Updates to doc tests.

0.7.0 - 2017-07-28

Added

  • Support for julia v0.6 only.

Removed

  • ❗ Dropped support for julia v0.5.

0.6.3 - 2017-07-06

Changed

  • Iterators.jl is not longer used as a dependency in favour of Itertools.jl.

0.6.1 - 2017-06-20

Changed

  • Bug-fix for site-counting algorithm.

0.6.0 - 2017-06-14

Added

  • ⬆️ Compatibility with julia v0.6.
  • The ungap and ungap! methods, that are shorthand for filtering gaps from biological sequences.

Changed

  • Bug fixes for Kmer iteration that were caused by gaps in 4-bit encoded sequences.

0.5.0 - 2017-06-07

Added

  • All files pertaining to the old Bio.Seq module.