v3.4.1

BioSequences v3.4.1

Diff since v3.4.0

Merged pull requests:

• WIP: Kmers.jl compatibility (#282) (@jakobnissen)
• Various internal code cleanup (#323) (@jakobnissen)
• Add tryencode (#324) (@jakobnissen)
• Speed up search operations for SeqOrView (#325) (@jakobnissen)
• Use part when counting over chunk iterators (#326) (@jakobnissen)
• Unroll == and some search functions (#327) (@jakobnissen)

Closed issues:

• add an ispermitted for Alphabets? (#219)
• PFM just accepts vectors? (#310)
• Optimise findnext for SeqOrView (#322)

v3.4.0

BioSequences v3.4.0

Diff since v3.3.0

Merged pull requests:

• Rewrite counting of BioSequence (#316) (@jakobnissen)
• Optimise some LongSequence constructors (#320) (@jakobnissen)

Closed issues:

• What's up with the strange two-argument counting methods? (#314)
• Rewrite bitpar compiler (#315)

v3.3.0

BioSequences v3.3.0

Diff since v3.2.0

Merged pull requests:

• [RFC]: Add functions guess_parse and guess_alphabet (#292) (@jakobnissen)
• More consistently throw EncodeError (#319) (@jakobnissen)

Closed issues:

• Record type inference (#268)

v3.2.0

BioSequences v3.2.0

Diff since v3.1.6

Merged pull requests:

• Update issue and PR template to match BioJulia guidelines (#298) (@jakobnissen)
• Document string literal macro (#300) (@jakobnissen)
• Update docs with recipes pages (#301) (@jakobnissen)
• Update ispalindromic (#304) (@jakobnissen)
• Precompute ExactSearchQuery faster (#305) (@jakobnissen)
• Drop CI for MacOS Julia 1.5 (#306) (@jakobnissen)
• Add new ncbi translation code (#307) (@camilogarciabotero)
• Flip sticker (#308) (@jakobnissen)
• Upgrade CI (#309) (@jakobnissen)
• Drop pre-LTS Julia support (#311) (@jakobnissen)
• Annotate const fields as const (#312) (@jakobnissen)
• Document bitpar counting (#313) (@jakobnissen)

Closed issues:

• Get this package back into PkgEval (#295)
• A strange behavior in approximate searches (#302)
• ispalindromic with respect to reverse or reverse_complement? (#303)

v3.1.6

BioSequences v3.1.6

Diff since v3.1.5

Merged pull requests:

• Improve heuristics of translating ambiguous nucs (#280) (@jakobnissen)
• Decode nocheck (#281) (@jakobnissen)
• Fix tests (#283) (@jakobnissen)
• A few fixes for tests (#285) (@jakobnissen)
• Bump Documenter to 1.0 (#286) (@jakobnissen)
• Remove downstream BioMakie CI (#287) (@jakobnissen)
• Allow translation of LongSubSeq (#288) (@jakobnissen)
• Define compat for Random (#290) (@jakobnissen)

Closed issues:

• Translate subsequence (#263)

v3.1.5

BioSequences v3.1.5

Diff since v3.1.4

Closed issues:

• Use lowercase in DNA sequences (#275)
• domain name of this repo should be updated (#276)
• Translation Issue arising from isambiguous(DNA_Gap) == false (#277)

Merged pull requests:

• Error when translating gaps (#278) (@jakobnissen)

v3.1.4

BioSequences v3.1.4

Diff since v3.1.3

Merged pull requests:

• Update URLs from biojulia.net to biojulia.dev (#272) (@kescobo)
• Migrate from SnoopPrecompile to PrecompileTools (#273) (@timholy)
• Bump version to v3.1.4 (#274) (@jakobnissen)

v3.1.3

BioSequences v3.1.3

Diff since v3.1.2

Closed issues:

• Improve error message on encoding error (#266)

Merged pull requests:

• Remove references to Random.GLOBAL_RNG (#265) (@jakobnissen)
• Improve error when mis-encoding LongDNA from byte-like inputs (#267) (@jakobnissen)
• Fix behavior of iterate on indices <= 0 (#271) (@cjprybol)

v3.1.2

BioSequences v3.1.2

Diff since v3.1.1

Closed issues:

• Converting a LongSubSeq to LongSequence can give weird results (#260)

Merged pull requests:

• Fix bug in zero_offset! called when materializing seqview (#261) (@jakobnissen)

v3.1.1

BioSequences v3.1.1

Diff since v3.1.0

Closed issues:

• Base.eltype(::Type{<:Alphabet}) violates eltype docstring (#231)
• Add doctests to CI (#252)
• Indexing with bool or integer vector does not work with seqview (#256)

Merged pull requests:

• Add iterate method for Alphabets (#233) (@SabrinaJaye)
• Documentation for findall method (#236) (@CiaranOMara)
• Doctests (#237) (@CiaranOMara)
• Improve robustness of rand tests (#255) (@jakobnissen)
• Add SnoopPrecompile (#257) (@jakobnissen)
• Fix typo (#258) (@cossio)
• Stop pirating BioSymbols (#259) (@jakobnissen)