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)

v2.0.6

BioSequences v2.0.6

Diff since v2.0.5

Closed issues:

• getindex not defined for arrays (#61)
• Problems installing BioSequences package (#71)
• Performance review before release (#86)
• julia 1.5: Time for views of a sequence? (#102)
• Erroneous reverse_complement behaviour? (#110)
• Slicing ReferenceSequences (#114)
• Failed push! adds empty bases (#115)
• Future of subsequences (#118)
• Demultiplexer fails for Levenshtein distance > 1 (#124)
• One-hot encoding of sequences (#130)
• Spring cleanup for v3 (#138)
• Fixup tests before v3 (#139)
• Check interfaces, remove NotImplemented errors (#140)
• Streamline find functions to behave like Base's (#141)
• [speculative] Remove BioSequence(::Integer)? (#142)
• Disallow construction of k-mers from integers (#145)
• Move to upcoming release of BioSymbols (#148)
• Add trait "iscomplete" to Alphabet (#151)
• ERROR: UndefVarError: FASTA not defined (#152)
• Export RE.Regex, and make constructors easier. (#167)
• Implement reverse translation (AminoAcid -> Codon) (#168)
• approxsearch and approxrsearch should return Union{Nothing, T} (#175)
• Default to dynamic allocation for string literals (#180)
• No version for Julia 1.6.1 (#185)
• No version for Julia 1.6.1 (#186)
• errors in docs: random kmers (#195)
• Don't recommend users engage in type piracy with stringbyte (#198)
• Include comparison example (#199)
• TagBot trigger issue (#209)
• findnext, findprev broken ... possible to add findall? (#215)
• LongDNA, LongRNA "not defined" (#216)
• Implement findall (#217)
• What happened to DNAMer? (#222)
• 🐛 in iscanonical / canonical (#225)
• join(LongRNA{2}, (RNA_A,)) should work (#230)
• Base.eltype(::Type{<:Alphabet}) violates eltype docstring (#231)
• Implement rand! (#249)
• FASTA module not defined (#251)
• Add doctests to CI (#252)
• Indexing with bool or integer vector does not work with seqview (#256)

Merged pull requests:

• Implement range slices over kmers (#112) (@cjprybol)
• Update links for this pull request template (#113) (@cjprybol)
• Fix push! (#116) (@jakobnissen)
• Fix StackOverflow error on Kmer instatiation (#117) (@jakobnissen)
• Remove LongSequence copy-on-write (#119) (@jakobnissen)
• Add sequence view (#120) (@jakobnissen)
• Remove Kmers (#121) (@SabrinaJaye)
• CompatHelper: bump compat for "StableRNGs" to "1.0" (#122) (@github-actions[bot])
• Make same-type conversion noop (#123) (@jakobnissen)
• Fix ReferenceSequence slicing bug (#125) (@lhnguyen-vn)
• Allow hamming circle around N (#126) (@tp2750)
• Fix reversing seq with unused data (#128) (@jakobnissen)
• Refactor translation (#131) (@jakobnissen)
• Deprecate minhash (#132) (@jakobnissen)
• Move some indexing logic from LongSequence to BioSequence (#133) (@jakobnissen)
• Add join and join! for BioSequence (#134) (@jakobnissen)
• Fix typo in genetic code show (#136) (@jakobnissen)
• Change semantics of find to match Base (#144) (@jakobnissen)
• Remove the constructor LongSequence{A}(::Integer) (#146) (@jakobnissen)
• Remove conversion to/from integers and kmers, and direct instantiatio… (#147) (@jakobnissen)
• Re-add construction between integer/kmer (#149) (@jakobnissen)
• Remove ConditionIterator (#150) (@jakobnissen)
• Remove financial backing and Gitter from README (#153) (@jakobnissen)
• Remove @sprintf dependency. (#156) (@SabrinaJaye)
• Remove BioGenerics dependency (#157) (@SabrinaJaye)
• Remove Combinatorics dependency (#158) (@SabrinaJaye)
• Remove IndexableBitVector dependency (#159) (@SabrinaJaye)
• Update user manual (#160) (@SabrinaJaye)
• Update interface to version 3. (#161) (@jakobnissen)
• Change sequence type aliases (#163) (@SabrinaJaye)
• Add fast equality for BioSequence (#164) (@jakobnissen)
• Add findfirst method for BioSymbol (#166) (@jakobnissen)
• Export RE.Regex and RE.RegexMatch as BioRegex and BioRegexMatch (#169) (@jakobnissen)
• Approximate search now returns nothing when no match is found (#176) (@jakobnissen)
• Remove undefined exports (#177) (@jakobnissen)
• Fix doctests after type alias renaming (#181) (@jakobnissen)
• Fix documenter warnings about broken links (#183) (@jakobnissen)
• Remove dependency on StableRNGs (#188) (@jakobnissen)
• Search API redo (#190) (@SabrinaJaye)
• Improve docstrings and changelog slightly (#191) (@jakobnissen)
• Add workflow for downstream tests (#192) (@CiaranOMara)
• Improve docstrings (#193) (@jakobnissen)
• Add parsing of BioSequence, simplify some printing (#194) (@jakobnissen)
• Remove sequence conversion to/from String and Vector (#196) (@jakobnissen)
• Fix REPL blocks in docs (#197) (@jakobnissen)
• Rename stringbyte and avoid pirating BioSymbols (#200) (@jakobnissen)
• Clarify comparison to sequences in docs (#201) (@jakobnissen)
• Add has_interface function (#202) (@jakobnissen)
• WIP: Test bonanza for v3 (#203) (@jakobnissen)
• Fix issues from v3/master merge (#207) (@jakobnissen)
• Fix bugs in minimal Alphabet interface example (#208) (@jakobnissen)
• Small internal refactors (#210) (@jakobnissen)
• Correct Julia compatibility entry (#214) (@CiaranOMara)
• Add findall method (#218) (@CiaranOMara)
• 🐛-fix iscanonical (#227) (@SabrinaJaye)
• Fix small errors (#228) (@jakobnissen)
• Sequence hashing: Bugfix and slight simplification (#229) (@jakobnissen)
• Add iterate method for Alphabets (#233) (@SabrinaJaye)
• Allow join to work with BioSymbol (#234) (@jakobnissen)
• Fix ambiguity errors (#235) (@jakobnissen)
• Documentation for findall method (#236) (@CiaranOMara)
• Doctests (#237) (@CiaranOMara)
• Use codeunits over unsafe_wrap (#239) (@jakobnissen)
• Cosmetic changes in constructors (#240) (@jakobnissen)
• Use naive hash fallback for BioSequence (#244) (@jakobnissen)
• Reset Julia compat to v1.5 (#245) (@jakobnissen)
• Improve hasinterface(::Type{BioSequence}) (#248) (@jakobnissen)
• Add rand!([::AbstractRNG], ::LongSequence, [::Sampler]) methods (#250) (@jakobnissen)
• Various small doc fixes (#253) (@jakobnissen)
• Vbump (#254) (@jakobnissen)
• Improve robustness of rand tests (#255) (@jakobnissen)
• Add SnoopPrecompile (#257) (@jakobnissen)