github.com/BioJulia/BioSequences.jl issues | Ecosyste.ms: OpenCollective

Discussion: Make `LongSequence` fixed-length?

jakobnissen opened this issue about 2 months ago

Document BioSequence interface(s)

kescobo opened this issue 3 months ago

Unroll == and some search functions

jakobnissen opened this pull request 4 months ago

Use part when counting over chunk iterators

jakobnissen opened this pull request 4 months ago

Speed up search operations for SeqOrView

jakobnissen opened this pull request 4 months ago

Add tryencode

jakobnissen opened this pull request 4 months ago

Various internal code cleanup

jakobnissen opened this pull request 4 months ago

Optimise findnext for SeqOrView

jakobnissen opened this issue 4 months ago

Remove `convert` for biosequences

jakobnissen opened this issue 4 months ago

Optimise some LongSequence constructors

jakobnissen opened this pull request 4 months ago

More consistently throw EncodeError

jakobnissen opened this pull request 4 months ago

Hide inner constructors of objects in this package

jakobnissen opened this issue 4 months ago

WIP Make LongSequence and LongSubSeq use Memory [DO NOT MERGE]

jakobnissen opened this pull request 4 months ago

Rewrite counting of BioSequence

jakobnissen opened this pull request 4 months ago

Rewrite bitpar compiler

jakobnissen opened this issue 4 months ago

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

jakobnissen opened this issue 4 months ago

Document bitpar counting

jakobnissen opened this pull request 4 months ago

Annotate const fields as const

jakobnissen opened this pull request 4 months ago

Drop pre-LTS Julia support

jakobnissen opened this pull request 4 months ago

PFM just accepts vectors?

felipe-mansoldo opened this issue 6 months ago

Upgrade CI

jakobnissen opened this pull request 8 months ago

Flip sticker

jakobnissen opened this pull request 8 months ago

Add new ncbi translation code

camilogarciabotero opened this pull request 8 months ago

Drop CI for MacOS Julia 1.5

jakobnissen opened this pull request 9 months ago

Precompute ExactSearchQuery faster

jakobnissen opened this pull request 9 months ago

Update `ispalindromic`

jakobnissen opened this pull request 11 months ago

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

Seelengrab opened this issue 11 months ago

A strange behavior in approximate searches

panxiaoguang opened this issue 12 months ago

Update docs with recipes pages

jakobnissen opened this pull request about 1 year ago

Document string literal macro

jakobnissen opened this pull request about 1 year ago

How should one search for ORFs?

jakobnissen opened this issue over 1 year ago

Update issue and PR template to match BioJulia guidelines

jakobnissen opened this pull request over 1 year ago

add predicate method and tests

camilogarciabotero opened this pull request over 1 year ago

Create and export a generic test biosequence

jakobnissen opened this issue over 1 year ago

Get this package back into PkgEval

jakobnissen opened this issue over 1 year ago

Run CI on Julia 1.5

jakobnissen opened this pull request over 1 year ago

Bump Julia compat to 1.6

jakobnissen opened this pull request over 1 year ago

[RFC]: Add functions `guess_parse` and `guess_alphabet`

jakobnissen opened this pull request over 1 year ago

Do not fail CI if codecov falls

jakobnissen opened this pull request over 1 year ago

Define compat for Random

jakobnissen opened this pull request over 1 year ago

Consider making Random a weak dep

jakobnissen opened this issue over 1 year ago

Allow translation of LongSubSeq

jakobnissen opened this pull request over 1 year ago

Remove downstream BioMakie CI

jakobnissen opened this pull request over 1 year ago

Bump Documenter to 1.0

jakobnissen opened this pull request over 1 year ago

A few fixes for tests

jakobnissen opened this pull request over 1 year ago

Feature: concatenate bases with sequences

BioTurboNick opened this issue over 1 year ago

Fix tests

jakobnissen opened this pull request over 1 year ago

WIP: Kmers.jl compatibility

jakobnissen opened this pull request over 1 year ago

Decode nocheck

jakobnissen opened this pull request over 1 year ago

Improve heuristics of translating ambiguous nucs

jakobnissen opened this pull request over 1 year ago

Can we skip check in `decode`?

jakobnissen opened this issue over 1 year ago

Error when translating gaps

jakobnissen opened this pull request over 1 year ago

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

chelate opened this issue over 1 year ago

domain name of this repo should be updated

ctarn opened this issue over 1 year ago

Use lowercase in DNA sequences

ruysan opened this issue over 1 year ago

Bump version to v3.1.4

jakobnissen opened this pull request over 1 year ago

Migrate from SnoopPrecompile to PrecompileTools

timholy opened this pull request almost 2 years ago

Update URLs from biojulia.net to biojulia.dev

kescobo opened this pull request almost 2 years ago

Fix behavior of iterate on indices <= 0

cjprybol opened this pull request almost 2 years ago

Add guessparse function

jakobnissen opened this pull request almost 2 years ago

Record type inference

cjprybol opened this issue almost 2 years ago

Improve error when mis-encoding LongDNA from byte-like inputs

jakobnissen opened this pull request almost 2 years ago

Improve error message on encoding error

jakobnissen opened this issue almost 2 years ago

Remove references to Random.GLOBAL_RNG

jakobnissen opened this pull request almost 2 years ago

Allow translation of sequence views

jakobnissen opened this pull request about 2 years ago

Translate subsequence

jakobnissen opened this issue about 2 years ago

New Feature: Molecular weight calculations for BioSequences

benjaminlozanow opened this issue about 2 years ago

Fix bug in zero_offset! called when materializing seqview

jakobnissen opened this pull request about 2 years ago

Converting a LongSubSeq to LongSequence can give weird results

ian-small opened this issue about 2 years ago

Stop pirating BioSymbols

jakobnissen opened this pull request about 2 years ago

Fix typo

cossio opened this pull request over 2 years ago

Add SnoopPrecompile

jakobnissen opened this pull request over 2 years ago

Indexing with bool or integer vector does not work with seqview

jakobnissen opened this issue over 2 years ago

Improve robustness of rand tests

jakobnissen opened this pull request over 2 years ago

Vbump

jakobnissen opened this pull request over 2 years ago

Various small doc fixes

jakobnissen opened this pull request over 2 years ago

Add doctests to CI

jakobnissen opened this issue over 2 years ago

FASTA module not defined

dinesh110598 opened this issue over 2 years ago

Add rand!([::AbstractRNG], ::LongSequence, [::Sampler]) methods

jakobnissen opened this pull request over 2 years ago

Implement rand!

jakobnissen opened this issue over 2 years ago

Improve hasinterface(::Type{BioSequence})

jakobnissen opened this pull request over 2 years ago

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

gszep opened this issue over 2 years ago

Reset Julia compat to v1.5

jakobnissen opened this pull request over 2 years ago

Use naive hash fallback for BioSequence

jakobnissen opened this pull request over 2 years ago

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

jakobnissen opened this issue over 2 years ago

Schedule method for removal

CiaranOMara opened this pull request over 2 years ago

WIP: Add tryparse

jakobnissen opened this pull request over 2 years ago

Cosmetic changes in constructors

jakobnissen opened this pull request over 2 years ago

Use codeunits over unsafe_wrap

jakobnissen opened this pull request over 2 years ago

Add tryencode and trydecode

jakobnissen opened this pull request over 2 years ago

Doctests

CiaranOMara opened this pull request over 2 years ago

Documentation for `findall` method

CiaranOMara opened this pull request over 2 years ago

Fix ambiguity errors

jakobnissen opened this pull request over 2 years ago

Allow join to work with BioSymbol

jakobnissen opened this pull request over 2 years ago

Add iterate method for Alphabets

SabrinaJaye opened this pull request over 2 years ago

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

jakobnissen opened this issue over 2 years ago

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

jakobnissen opened this issue over 2 years ago

Sequence hashing: Bugfix and slight simplification

jakobnissen opened this pull request over 2 years ago

Fix small errors

jakobnissen opened this pull request over 2 years ago

🐛-fix iscanonical

SabrinaJaye opened this pull request over 2 years ago