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Releases: BioJulia/BioSequences.jl

v2.0.6

23 Sep 12:00
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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:

v3.1.0

29 Jul 09:33
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BioSequences v3.1.0

Diff since v3.0.2

Closed issues:

  • Implement rand! (#249)
  • FASTA module not defined (#251)

Merged pull requests:

v3.0.2

07 Jul 07:55
f7ccb6b
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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:

v3.0.0

07 Jan 01:49
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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:

v2.0.5

25 Jun 00:11
93d9462
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BioSequences v2.0.5

Diff since v2.0.4

Merged pull requests:

  • hotfix for reverse_complementing a slice of a longseq (#111) (@cjprybol)

v2.0.4

06 Jun 00:10
01fbc26
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BioSequences v2.0.4

Diff since v2.0.3

v2.0.3

06 Jun 00:10
f084834
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BioSequences v2.0.3

Diff since v2.0.2

Merged pull requests:

v2.0.2

05 Jun 00:11
f8274b0
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BioSequences v2.0.2

Diff since v2.0.1

Closed issues:

  • Faster random LongSequence{NucleicAcidAlphabet{4}} generation (#77)

Merged pull requests:

v2.0.1

24 May 15:06
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BioSequences v2.0.1

Diff since v2.0.0

v2.0.0

24 May 14:06
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BioSequences v2.0.0

Diff since v1.1.0

Closed issues:

  • Change Varargs to vectors or array (#24)
  • Further generalise the bitparallel counting code (#27)
  • map(f, seq) raises an exception (#58)
  • Test Issue (#60)
  • FASTA.Reader doesn't recognize the correct alphabet with ambiguous sites (#64)

Merged pull requests: