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github.com/BioJulia/BioSequences.jl

Biological sequences for the julia language
https://github.com/BioJulia/BioSequences.jl

🐛 in iscanonical / canonical

SabrinaJaye opened this pull request over 2 years ago

🐛 in iscanonical / canonical

SabrinaJaye opened this issue over 2 years ago

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

jakobnissen opened this issue over 2 years ago

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

BeastyBlacksmith opened this issue almost 3 years ago

What happened to DNAMer?

JokingHero opened this issue almost 3 years ago

Loosen search iterator

CiaranOMara opened this pull request almost 3 years ago

Add `findall` method

CiaranOMara opened this pull request almost 3 years ago

add an `ispermitted` for Alphabets?

TransGirlCodes opened this issue almost 3 years ago

Add `findall` method

CiaranOMara opened this pull request almost 3 years ago

Implement `findall`

jakobnissen opened this issue almost 3 years ago

LongDNA, LongRNA "not defined"

fpmenninger opened this issue almost 3 years ago

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

fpmenninger opened this issue almost 3 years ago

Correct Julia compatibility entry

CiaranOMara opened this pull request almost 3 years ago

Small internal refactors

jakobnissen opened this pull request almost 3 years ago

TagBot trigger issue

JuliaTagBot opened this issue almost 3 years ago

Fix bugs in minimal Alphabet interface example

jakobnissen opened this pull request almost 3 years ago

Fix issues from v3/master merge

jakobnissen opened this pull request almost 3 years ago

Version 3 updates

SabrinaJaye opened this pull request almost 3 years ago

CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)

github-actions[bot] opened this pull request about 3 years ago

CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)

github-actions[bot] opened this pull request about 3 years ago

WIP: Test bonanza for v3

jakobnissen opened this pull request about 3 years ago

Add `has_interface` function

jakobnissen opened this pull request about 3 years ago

Clarify comparison to sequences in docs

jakobnissen opened this pull request about 3 years ago

Rename stringbyte and avoid pirating BioSymbols

jakobnissen opened this pull request about 3 years ago

Include comparison example

CiaranOMara opened this issue about 3 years ago

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

jakobnissen opened this issue about 3 years ago

Fix REPL blocks in docs

jakobnissen opened this pull request about 3 years ago

Remove sequence conversion to/from String and Vector

jakobnissen opened this pull request about 3 years ago

errors in docs: random kmers

EvoArt opened this issue about 3 years ago

Add parsing of BioSequence, simplify some printing

jakobnissen opened this pull request about 3 years ago

Improve docstrings

jakobnissen opened this pull request about 3 years ago

Add workflow for downstream tests

CiaranOMara opened this pull request about 3 years ago

Improve docstrings and changelog slightly

jakobnissen opened this pull request about 3 years ago

Search API redo

TransGirlCodes opened this pull request about 3 years ago

Add `findall` methods

CiaranOMara opened this pull request about 3 years ago

Remove dependency on StableRNGs

jakobnissen opened this pull request about 3 years ago

Stop shipping with StableRNGs?

jakobnissen opened this issue about 3 years ago

No version for Julia 1.6.1

ammonite opened this issue over 3 years ago

No version for Julia 1.6.1

ammonite opened this issue over 3 years ago

CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)

github-actions[bot] opened this pull request over 3 years ago

Make macro literals dynamic

jakobnissen opened this pull request over 3 years ago

Default to dynamic allocation for string literals

jakobnissen opened this issue over 3 years ago

CompatHelper: bump compat for "BioSymbols" to "5"

github-actions[bot] opened this pull request over 3 years ago

Should we make BioSequences <: AbstractVector?

SabrinaJaye opened this issue over 3 years ago

Implement broadcasting for BioSequences

SabrinaJaye opened this pull request over 3 years ago

Implement reverse translation (AminoAcid -> Codon)

BeastyBlacksmith opened this issue over 3 years ago

Update interface to version 3.

jakobnissen opened this pull request over 3 years ago

Streamline find functions to behave like Base's

jakobnissen opened this issue almost 4 years ago

Check interfaces, remove NotImplemented errors

jakobnissen opened this issue almost 4 years ago

Fixup tests before v3

jakobnissen opened this issue almost 4 years ago

Implement broadcasting for biosequences

jakobnissen opened this issue almost 4 years ago

Fixup addition with a BitIndex

SabrinaJaye opened this pull request over 4 years ago

Use stable RNG (take two)

jakobnissen opened this pull request over 4 years ago

Syntax error fix

SabrinaJaye opened this pull request almost 5 years ago

Improve performance of bit-parallel counting methods

SabrinaJaye opened this pull request almost 5 years ago

Test on julia 1.2 in travis

SabrinaJaye opened this pull request over 5 years ago

SkipmerFactory

SabrinaJaye opened this pull request almost 6 years ago