Tags: BioJulia/BioSequences.jl
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[Diff since v3.1.5](v3.1.5...v3.1.6) **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)
[Diff since v3.1.4](v3.1.4...v3.1.5) **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)
[Diff since v3.1.2](v3.1.2...v3.1.3) **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)
[Diff since v3.1.1](v3.1.1...v3.1.2) **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)
[Diff since v3.1.0](v3.1.0...v3.1.1) **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)
[Diff since v2.0.5](v2.0.5...v2.0.6) **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)
[Diff since v3.0.2](v3.0.2...v3.1.0) **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)
[Diff since v3.0.0](v3.0.0...v3.0.2) **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)
[Diff since v2.0.5](v2.0.5...v3.0.0) **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)
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