BioJulia/BioSequences.jl

Issues

• Discussion: Make `LongSequence` fixed-length?

  #329 opened 4 months ago by jakobnissen
  6

• TagBot trigger issue

  #209 opened 3 years ago by JuliaTagBot
  15

• Document BioSequence interface(s)

  #328 opened 5 months ago by kescobo
  1

• Optimise findnext for SeqOrView

  #322 opened 5 months ago by jakobnissen
  1

• add an `ispermitted` for Alphabets?

  #219 opened 5 months ago by TransGirlCodes
  4

• PFM just accepts vectors?

  #310 opened 5 months ago by felipe-mansoldo
  2

• Remove `convert` for biosequences

  #321 opened 6 months ago by jakobnissen
  2

• What's up with the strange two-argument counting methods?

  #314 opened 6 months ago by jakobnissen
  0

• Rewrite bitpar compiler

  #315 opened 6 months ago by jakobnissen
  1

• Record type inference

  #268 opened 6 months ago by cjprybol
  3

• Hide inner constructors of objects in this package

  #318 opened 6 months ago by jakobnissen
  1

• Design of hash(::BioSequence). What to do?

  #243 opened 3 years ago by jakobnissen
  19

• `ispalindromic` with respect to `reverse` or `reverse_complement`?

  #303 opened a year ago by Seelengrab
  6

• A strange behavior in approximate searches

  #302 opened a year ago by panxiaoguang
  4

• How should one search for ORFs?

  #299 opened a year ago by jakobnissen
  5

• Create and export a generic test biosequence

  #296 opened a year ago by jakobnissen
  0

• Get this package back into PkgEval

  #295 opened a year ago by jakobnissen
  3

• Consider making Random a weak dep

  #289 opened a year ago by jakobnissen
  1

• Translate subsequence

  #263 opened 2 years ago by jakobnissen
  0

• Feature: concatenate bases with sequences

  #284 opened 2 years ago by BioTurboNick
  4

• Can we skip check in `decode`?

  #279 opened 2 years ago by jakobnissen
  0

• Translation Issue arising from `isambiguous(DNA_Gap) == false`

  #277 opened 2 years ago by chelate
  2

• New Feature: Molecular weight calculations for BioSequences

  #262 opened 2 years ago by benjaminlozanow
  8

• domain name of this repo should be updated

  #276 opened 2 years ago by ctarn
  4

• Use lowercase in DNA sequences

  #275 opened 2 years ago by ruysan
  1

• Improve error message on encoding error

  #266 opened 2 years ago by jakobnissen
  1

• Converting a LongSubSeq to LongSequence can give weird results

  #260 opened 2 years ago by ian-small
  1

• CenteredSequence{A} type for comparing short reads padding with AA_Gap

  #247 opened 3 years ago by gszep
  8

• `Base.eltype(::Type{<:Alphabet})` violates `eltype` docstring

  #231 opened 3 years ago by jakobnissen
  2

• Indexing with bool or integer vector does not work with seqview

  #256 opened 3 years ago by jakobnissen
  1

• Add doctests to CI

  #252 opened 3 years ago by jakobnissen
  2

• FASTA module not defined

  #251 opened 3 years ago by dinesh110598
  1

• Implement rand!

  #249 opened 3 years ago by jakobnissen
  1

• Add tryparse(::BioSequence, s::AbstractString) or similar

  #224 opened 3 years ago by jakobnissen
  3

• `join(LongRNA{2}, (RNA_A,))` should work

  #230 opened 3 years ago by jakobnissen
  0

• What happened to DNAMer?

  #222 opened 3 years ago by JokingHero
  1

• 🐛 in iscanonical / canonical

  #225 opened 3 years ago by TransGirlCodes
  2

• [FR] add `Query` versions for `Base.count`

  #223 opened 3 years ago by BeastyBlacksmith
  0

• Implement `findall`

  #217 opened 3 years ago by jakobnissen
  2

• LongDNA, LongRNA "not defined"

  #216 opened 3 years ago by fpmenninger
  5

• findnext, findprev broken ... possible to add findall?

  #215 opened 3 years ago by fpmenninger
  4

• Don't recommend users engage in type piracy with `stringbyte`

  #198 opened 3 years ago by jakobnissen
  1

• Include comparison example

  #199 opened 3 years ago by CiaranOMara
  1

• errors in docs: random kmers

  #195 opened 3 years ago by EvoArt
  0

• Should we make BioSequences <: AbstractVector?

  #173 opened 3 years ago by TransGirlCodes
  11

• Stop shipping with StableRNGs?

  #187 opened 4 years ago by jakobnissen
  3

• No version for Julia 1.6.1

  #185 opened 4 years ago by ammonite
  2

• No version for Julia 1.6.1

  #186 opened 4 years ago by ammonite
  1

• Default to dynamic allocation for string literals

  #180 opened 4 years ago by jakobnissen
  2

• `approxsearch` and `approxrsearch` should return `Union{Nothing, T}`

  #175 opened 4 years ago by jakobnissen
  1