BioJulia issues | Ecosyste.ms: OpenCollective

Looping regex can be given a final action

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

tweak1

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request almost 2 years ago

Kmers.jl is unable to comply with `BioSequences.has_interface` as currently implemented

github.com/BioJulia/Kmers.jl - cjprybol opened this issue almost 2 years ago

consider removing kmer/sequence type inference from strings in favor of generalized version in BioSequences

github.com/BioJulia/Kmers.jl - cjprybol opened this issue almost 2 years ago

Add guessparse function

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

CompatHelper: add new compat entry for Aqua at version 0.6, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request almost 2 years ago

Add eachoverlap(reader::Reader, refname::String)

github.com/BioJulia/XAM.jl - apraga opened this issue almost 2 years ago

Dev

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request almost 2 years ago

Add docstrings and update docs

github.com/BioJulia/Kmers.jl - cjprybol opened this pull request almost 2 years ago

Record type inference

github.com/BioJulia/BioSequences.jl - cjprybol opened this issue almost 2 years ago

CompatHelper: bump compat for Meshes to 0.28, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request almost 2 years ago

Update hardware post

github.com/BioJulia/biojulia.github.io - jakobnissen opened this pull request almost 2 years ago

Domain name expired

github.com/BioJulia/biojulia.github.io - jakobnissen opened this issue almost 2 years ago

CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request almost 2 years ago

Fails to parse metadata with hypen in the key

github.com/BioJulia/GeneticVariation.jl - apraga opened this issue almost 2 years ago

devup

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request almost 2 years ago

better docstrings and struc update

github.com/BioJulia/BioMakie.jl - kool7d opened this pull request almost 2 years ago

CompatHelper: bump compat for BioAlignments to 3, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request almost 2 years ago

CompatHelper: add new compat entry for Meshes at version 0.27, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request almost 2 years ago

Improve error on predefined convert(::BioSymbol, ::Char)

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request almost 2 years ago

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

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

Improve error message on encoding error

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue almost 2 years ago

Fix Base.read!(::Reader, ::Record) and add tests

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 2 years ago

read! doesn't work in v2.0.0?

github.com/BioJulia/FASTX.jl - banhbio opened this issue almost 2 years ago

CompatHelper: bump compat for Term to 2, (keep existing compat)

github.com/BioJulia/PopGen.jl - github-actions[bot] opened this pull request almost 2 years ago

Remove references to Random.GLOBAL_RNG

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

Update BioAlignments and BioSequences compat. Change LongAminoAcidSeq to LongSequence{AminoAcidAlphabet}

github.com/BioJulia/BioStructures.jl - kool7d opened this pull request almost 2 years ago

Correctly finding matching double quotes when Unicode characters are present

github.com/BioJulia/Automa.jl - jagot opened this issue almost 2 years ago

Fix outdated tests

github.com/BioJulia/BioServices.jl - kescobo opened this issue almost 2 years ago

Release for expanding HTTP compat

github.com/BioJulia/BioServices.jl - kescobo opened this pull request almost 2 years ago

Document `read!(::Reader, ::Record)`

github.com/BioJulia/FASTX.jl - jonathanBieler opened this issue almost 2 years ago

TagBot trigger issue

github.com/BioJulia/SingleCellProjections.jl - JuliaTagBot opened this issue almost 2 years ago

Allow translation of sequence views

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

Release v0.2.2

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

CompatHelper: add new compat entry for NamedArrays at version 0.9, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request almost 2 years ago

CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request almost 2 years ago

CompatHelper: add new compat entry for Meshes at version 0.27, (keep existing compat)

github.com/BioJulia/BioMakie.jl - github-actions[bot] opened this pull request almost 2 years ago

Fix validation for Haplotypes

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

Translate subsequence

github.com/BioJulia/BioSequences.jl - jakobnissen opened this issue almost 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 almost 2 years ago

Multiple `Substitution`s doesn't invalidate `Haplotype`

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue almost 2 years ago

New Feature: Molecular weight calculations for BioSequences

github.com/BioJulia/BioSequences.jl - benjaminlozanow opened this issue almost 2 years ago

Release v0.2.1

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

Better error descriptions

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

Release v0.2.0

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

Add `isless` for `Edit` and `Variation`

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

Add `translate` functionality for haplotypes

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

Refactor `reconstruct` function

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

Rename `Variant` to `Haplotype`

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

Organize/stylize code and docs

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

Release v3.1.0

github.com/BioJulia/BioAlignments.jl - MillironX opened this pull request almost 2 years ago

Make BioSequences a weak dependency

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 2 years ago

Improve precompilation

github.com/BioJulia/FASTX.jl - jakobnissen opened this pull request almost 2 years ago

(Optionally) despecialize generated code on its IO

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

Consider despecializing AbstractFormattedIOs

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue almost 2 years ago

Correct way to add records to an array

github.com/BioJulia/XAM.jl - krishvishal opened this issue almost 2 years ago

Release v0.1.4

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

Reading whole file or FileIO integration ?

github.com/BioJulia/BED.jl - jonathanBieler opened this issue about 2 years ago

Make BioSequences an optional dependency

github.com/BioJulia/FASTX.jl - jakobnissen opened this issue about 2 years ago

Fix softclips causing Variant construction errors

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

Soft clips cause invalid Variants

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue about 2 years ago

Grantham's substitution matrix

github.com/BioJulia/BioAlignments.jl - KaparaNewbie opened this pull request about 2 years ago

Fix bug in zero_offset! called when materializing seqview

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

Converting a LongSubSeq to LongSequence can give weird results

github.com/BioJulia/BioSequences.jl - ian-small opened this issue about 2 years ago

Release v0.1.3

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

Add type parameterization to variations getter

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

How to write the function called findoverlaps with minoverlap>=1?

github.com/BioJulia/GenomicFeatures.jl - zhangchunyong999 opened this issue about 2 years ago

convert pdb to mol

github.com/BioJulia/BioStructures.jl - Nick-Mul opened this issue about 2 years ago

Stop pirating BioSymbols

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

Add `gap(::Type{Char})` to prevent piracy from BioSequences.

github.com/BioJulia/BioSymbols.jl - jakobnissen opened this pull request about 2 years ago

subset FASTX.FASTQ.Record

github.com/BioJulia/FASTX.jl - Liripo opened this issue about 2 years ago

bugfix for delete!(genes)

github.com/BioJulia/GenomicAnnotations.jl - hsianktin opened this pull request about 2 years ago

[feature] Merge all PopGen_.jl packages under PopGen.jl monorepo

github.com/BioJulia/PopGen.jl - pdimens opened this issue about 2 years ago

Add a `cigar` method and `BioAlignments.Alignment` constructor for XAM.jl optimisation

github.com/BioJulia/BioAlignments.jl - CiaranOMara opened this issue about 2 years ago

Release 0.3.1

github.com/BioJulia/XAM.jl - MillironX opened this pull request about 2 years ago

Fix typo

github.com/BioJulia/BioSequences.jl - cossio opened this pull request about 2 years ago

added method for handling different bam index types

github.com/BioJulia/XAM.jl - jonathanBieler opened this pull request about 2 years ago

Upgrade to BioAlignments v3

github.com/BioJulia/XAM.jl - MillironX opened this pull request about 2 years ago

GeneticVariation.VCF.Reader does not like output from the gatk tool: funcotator

github.com/BioJulia/GeneticVariation.jl - jackmo375 opened this issue about 2 years ago

Switch to Oneflow

github.com/BioJulia/XAM.jl - MillironX opened this issue about 2 years ago

Release v0.3.0

github.com/BioJulia/XAM.jl - MillironX opened this pull request about 2 years ago

`Base.parse` and `Base.tryparse` for `DNA` and `RNA`

github.com/BioJulia/BioSymbols.jl - warrenalphonso opened this pull request about 2 years ago

Release v0.1.2

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

Update dependencies

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

Release v3.0.0

github.com/BioJulia/BioAlignments.jl - MillironX opened this pull request about 2 years ago

Release v2.3.0

github.com/BioJulia/BioAlignments.jl - MillironX opened this pull request about 2 years ago

Can GenomicAnnotations.jl deal with multi-exon genes?

github.com/BioJulia/GenomicAnnotations.jl - Xiao-Zhong opened this issue about 2 years ago

Do you have the plan to add the pileup functions?

github.com/BioJulia/XAM.jl - panxiaoguang opened this issue about 2 years ago

Unambiguate type nomenclature

github.com/BioJulia/SequenceVariation.jl - MillironX opened this issue about 2 years ago

Better conversion from 2 to 4 bit nucleic kmers

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

Fix hashing

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

Improve type stability slightly

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

Write to treemix allele count format

github.com/BioJulia/PopGenCore.jl - pdimens opened this issue over 2 years ago

Add SnoopPrecompile

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

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