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BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

Add SnoopPrecompile

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Indexing with bool or integer vector does not work with seqview

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 2 years ago
Add SnoopPrecompile

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 2 years ago
Friendly request to `@deprecate` API changes via semver

github.com/BioJulia/BioAlignments.jl - dehann opened this issue over 2 years ago
Try to get preview build to work

github.com/BioJulia/FASTX.jl - kescobo opened this pull request over 2 years ago
Rollup of a few changes

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request over 2 years ago
hotfix/issue 31

github.com/BioJulia/XAM.jl - CiaranOMara opened this pull request over 2 years ago
TagBot trigger issue

github.com/BioJulia/FormatSpecimens.jl - JuliaTagBot opened this issue over 2 years ago
Add `index!(reader::Reader, path)`

github.com/BioJulia/XAM.jl - CiaranOMara opened this issue over 2 years ago
Use ReTest

github.com/BioJulia/FASTX.jl - kescobo opened this pull request over 2 years ago
Use ReTest or similar niceness?

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue over 2 years ago
Migrate to new Automa release

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue over 2 years ago
Make Documenter preview builds work.

github.com/BioJulia/FASTX.jl - kescobo opened this issue over 2 years ago
Make constructing records less horribly inefficient

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue over 2 years ago
Feature: Zero-dependency codegen

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Add rdr and wrt string macros and transcribe

github.com/BioJulia/BioGenerics.jl - jakobnissen opened this pull request over 2 years ago
CompatHelper: bump compat for MultivariateStats to 0.10, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 2 years ago
Slow compilation speed

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Add support for multi-byte transitions

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Remove unused files

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Better error on compiling null regex

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Remove StableSet and StableDict

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Make FSM generation deterministic by simply renaming nodes

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Consider making `.data` fields of records const

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue over 2 years ago
Remove BioSequences dependency

github.com/BioJulia/GFF3.jl - CiaranOMara opened this pull request over 2 years ago
Open BioSequences to allow v2 or v3

github.com/BioJulia/GFF3.jl - cjprybol opened this pull request over 2 years ago
Bug with regex set negation

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Keyerror on remove_dead_notes

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Improve robustness of rand tests

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Revamp BioGenerics.Automa.State: Recoverable readers

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Vbump

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Bump version

github.com/BioJulia/BioGenerics.jl - jakobnissen opened this pull request over 2 years ago
Various small doc fixes

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Add doctests to CI

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 2 years ago
Multiline FASTQ records?

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue over 2 years ago
Taking preconditions seriously

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Add varargs and kwargs to T(open(f, ::IO)) methods

github.com/BioJulia/BioGenerics.jl - jakobnissen opened this pull request over 2 years ago
Add getter methods (and forwarded getter methods) for alignment types

github.com/BioJulia/BioAlignments.jl - MillironX opened this pull request over 2 years ago
No good way to flush writers?

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue over 2 years ago
CompatHelper: bump compat for PopGenCore to 0.6, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 2 years ago
Enforce action dict symbols are same as machines

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Verify keys in RE.actions are correct on setindex!

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
FASTA module not defined

github.com/BioJulia/BioSequences.jl - dinesh110598 opened this issue over 2 years ago
Fix variables in generate_reader

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Release v0.1.1

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 2 years ago
Disable unambiguity check again

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Add constructor for Variant based on Variations

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 2 years ago
Use smaller integer width for table generator

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Remove ByteSet

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
TagBot trigger issue

github.com/BioJulia/SequenceVariation.jl - JuliaTagBot opened this issue over 2 years ago
Breaking changes for V1

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Fixup parse_class

github.com/BioJulia/Automa.jl - jakobnissen opened this pull request over 2 years ago
Add rand!([::AbstractRNG], ::LongSequence, [::Sampler]) methods

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Implement rand!

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 2 years ago
Make ambiguity errors easier to understand

github.com/BioJulia/Automa.jl - jakobnissen opened this issue over 2 years ago
Add reference and alternate base getters for Variation

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 2 years ago
CompatHelper: bump compat for BioSymbols to 5, (keep existing compat)

github.com/BioJulia/SequenceVariation.jl - github-actions[bot] opened this pull request over 2 years ago
CompatHelper: bump compat for BioSequences to 3, (keep existing compat)

github.com/BioJulia/SequenceVariation.jl - github-actions[bot] opened this pull request over 2 years ago
New version: v0.7.0

github.com/BioJulia/PopGenCore.jl - pdimens opened this pull request over 2 years ago
Improve hasinterface(::Type{BioSequence})

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
CenteredSequence{A} type for comparing short reads padding with AA_Gap

github.com/BioJulia/BioSequences.jl - gszep opened this issue over 2 years ago
Upgrade BioAlignments to v2.2 & BioSequences to v3

github.com/BioJulia/XAM.jl - MillironX opened this pull request over 2 years ago
Add Pkg to documentation’s package requirements

github.com/BioJulia/IntervalTrees.jl - CiaranOMara opened this pull request over 2 years ago
Getting string name of amino acids or other symbols (dna/rna)

github.com/BioJulia/BioSymbols.jl - anandijain opened this issue over 2 years ago
Feature: Create functions to get reference and alternate bases from `Variation`

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue over 2 years ago
Outdated documentation for SAM/BAM in BioAlignments is first hit in search

github.com/BioJulia/BioAlignments.jl - simon-anders opened this issue over 2 years ago
Prepare for package registration

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 2 years ago
Reset Julia compat to v1.5

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Use naive hash fallback for BioSequence

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Bump version

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request over 2 years ago
Add functions to get `Variation`s from `Variant`

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 2 years ago
Optimise hashing

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request over 2 years ago
Design of hash(::BioSequence). What to do?

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue over 2 years ago
Add Unsafe trait object

github.com/BioJulia/Kmers.jl - jakobnissen opened this pull request over 2 years ago
High level file processing

github.com/BioJulia/FASTX.jl - SabrinaJaye opened this issue over 2 years ago
Support HTTP.jl 1.0

github.com/BioJulia/BioServices.jl - quinnj opened this pull request over 2 years ago
CompatHelper: bump compat for Term to 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request over 2 years ago
Schedule method for removal

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this pull request over 2 years ago
Refactor tests

github.com/BioJulia/BioAlignments.jl - kescobo opened this issue over 2 years ago
WIP: Add tryparse

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Cosmetic changes in constructors

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Use codeunits over unsafe_wrap

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Add tryencode and trydecode

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Doctests

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this pull request over 2 years ago
Documentation for `findall` method

github.com/BioJulia/BioSequences.jl - CiaranOMara opened this pull request over 2 years ago
Weird error with `AffineGapScoreModel()`

github.com/BioJulia/BioAlignments.jl - jakobnissen opened this issue over 2 years ago
Resolve ambiguity error Kmer()

github.com/BioJulia/Kmers.jl - jakobnissen opened this pull request over 2 years ago
Add constructors

github.com/BioJulia/Kmers.jl - jakobnissen opened this pull request over 2 years ago
Add equality functions for Variation

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 2 years ago
Feature/variations-parse

github.com/BioJulia/SequenceVariation.jl - MillironX opened this pull request over 2 years ago
Fix ambiguity errors

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
Add translation of kmers

github.com/BioJulia/Kmers.jl - jakobnissen opened this pull request over 2 years ago
Roadmap to release

github.com/BioJulia/Kmers.jl - jakobnissen opened this issue over 2 years ago
Fix minor bugs

github.com/BioJulia/Kmers.jl - jakobnissen opened this pull request over 2 years ago
Small bugfixes

github.com/BioJulia/Kmers.jl - jakobnissen opened this pull request over 2 years ago
Add reverse translation

github.com/BioJulia/Kmers.jl - jakobnissen opened this pull request over 2 years ago
Proposal: Implement reverse translation

github.com/BioJulia/Kmers.jl - jakobnissen opened this issue over 2 years ago
Allow join to work with BioSymbol

github.com/BioJulia/BioSequences.jl - jakobnissen opened this pull request over 2 years ago
TagBot trigger issue

github.com/BioJulia/Kmers.jl - JuliaTagBot opened this issue over 2 years ago
Proposal: Allow zero-length kmers

github.com/BioJulia/Kmers.jl - jakobnissen opened this issue over 2 years ago