Releases | Open Source Science

https://github.com/biojulia/biosequences.jl - v3.5.0

Add spliceinto!. This function inserts a sequence into a biosequence, and optionally deletes part of the original sequence. The naming difference from Base.splice! reflects is slightly different API.
Optimise various methods

- Julia
Published by jakobnissen 11 months ago

https://github.com/biojulia/biosequences.jl - v3.4.2

BioSequences v3.4.2

Merged pull requests: - Add more optimised find methods for BioSequences (#331) (@jakobnissen) - Improve GC counting code (#332) (@jakobnissen) - Improve bit-twiddling for counting (#335) (@jakobnissen)

Closed issues: - Add optimised find functions (#330)

- Julia
Published by github-actions[bot] 12 months ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] over 2 years ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] almost 3 years ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] about 3 years ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/biojulia/biosequences.jl - 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)

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/biojulia/biosequences.jl - 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 reversecomplement 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}, (RNAA,))should work (#230) -Base.eltype(::Type{<:Alphabet})violateseltype` 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)

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/biojulia/biosequences.jl - v3.1.0

BioSequences v3.1.0

Diff since v3.0.2

Closed issues: - Implement rand! (#249) - FASTA module not defined (#251)

Merged pull requests: - Improve hasinterface(::Type{BioSequence}) (#248) (@jakobnissen) - Add rand!([::AbstractRNG], ::LongSequence, [::Sampler]) methods (#250) (@jakobnissen) - Various small doc fixes (#253) (@jakobnissen) - Vbump (#254) (@jakobnissen)

- Julia
Published by github-actions[bot] almost 4 years ago

https://github.com/biojulia/biosequences.jl - v3.0.2

BioSequences v3.0.2

Diff since v3.0.0

Closed issues: - Implement reverse translation (AminoAcid -> Codon) (#168) - 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)

Merged pull requests: - 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) - Allow join to work with BioSymbol (#234) (@jakobnissen) - Fix ambiguity errors (#235) (@jakobnissen) - 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)

- Julia
Published by github-actions[bot] almost 4 years ago

https://github.com/biojulia/biosequences.jl - v3.0.0

BioSequences v3.0.0

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) - 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)

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)

- Julia
Published by github-actions[bot] over 4 years ago

https://github.com/biojulia/biosequences.jl - v2.0.5

BioSequences v2.0.5

Diff since v2.0.4

Merged pull requests: - hotfix for reverse_complementing a slice of a longseq (#111) (@cjprybol)

- Julia
Published by github-actions[bot] almost 6 years ago