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

Flip sticker

jakobnissen opened this pull request 7 months ago

[Feature]: Add method to remove sequence match info from cigar

MillironX opened this issue almost 2 years ago

Release v3.1.0

MillironX opened this pull request about 2 years ago

Grantham's substitution matrix

KaparaNewbie opened this pull request about 2 years ago

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

CiaranOMara opened this issue about 2 years ago

Release v3.0.0

MillironX opened this pull request over 2 years ago

Release v2.3.0

MillironX opened this pull request over 2 years ago

Friendly request to `@deprecate` API changes via semver

dehann opened this issue over 2 years ago

Add getter methods (and forwarded getter methods) for alignment types

MillironX opened this pull request over 2 years ago

Outdated documentation for SAM/BAM in BioAlignments is first hit in search

simon-anders opened this issue over 2 years ago

Refactor tests

kescobo opened this issue over 2 years ago

Weird error with `AffineGapScoreModel()`

jakobnissen opened this issue over 2 years ago

Doctests

CiaranOMara opened this pull request over 2 years ago

Housekeeping

CiaranOMara opened this pull request over 2 years ago

Hotfix/2.2.0

CiaranOMara opened this pull request over 2 years ago

Alignment of 2 LongAminoAcidSeq with AffineGapScoreModel from docs goes out of bounds

kool7d opened this issue over 2 years ago

Do these methods work and are they tested?

CiaranOMara opened this issue over 2 years ago

Extract start and end positions from a PairwiseAlignment

rohanmaddamsetti opened this issue almost 3 years ago

BioSequences v3 and BioSymbols v5

CiaranOMara opened this pull request almost 3 years ago

Add ssh key to TagBot workflow

CiaranOMara opened this pull request almost 3 years ago

Add downstream tests

CiaranOMara opened this pull request almost 3 years ago

`AlignmentAnchor` method signature

CiaranOMara opened this issue almost 3 years ago

TagBot trigger issue

JuliaTagBot opened this issue almost 3 years ago

TagBot not triggering.

kescobo opened this issue almost 3 years ago

Zenodo Prep

kescobo opened this pull request almost 3 years ago

Lack of an article to cite BioAlignments.jl

Hugemiler opened this issue almost 3 years ago

Add support for 'meta' alignment operations (`OP_PAD` and `OP_HARD_CLIP`)

MillironX opened this pull request almost 3 years ago

OP_BACK has no use?

jakobnissen opened this issue almost 3 years ago

Update the alignment figure

alyst opened this pull request about 3 years ago

Update docs with alignment position

alyst opened this pull request about 3 years ago

Add more SubstitutionMatrix operations

timholy opened this pull request about 3 years ago

Bug in `OverlapAlignment`

jakobnissen opened this issue about 3 years ago

The API of accessing fields of BioAlignments

jakobnissen opened this issue about 3 years ago

What does the two integer fields in `Alignment` do?

jakobnissen opened this issue about 3 years ago

`ref2seq` returns a position outside of the sequence length

MillironX opened this issue over 3 years ago

Get reference and query from `PairwiseAlignment`

jakobnissen opened this issue over 3 years ago

Inconsistent when aligning distinct sequence types

jakobnissen opened this issue over 3 years ago

Allow compact printing of alignments

jakobnissen opened this pull request over 3 years ago

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

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

Multiple alignment manipulation

BioTurboNick opened this issue over 3 years ago

Prepare for minor release

alyst opened this pull request almost 4 years ago

"master" vs "develop" branches

alyst opened this issue almost 4 years ago

Remove BioJuliaRegistry

alyst opened this pull request almost 4 years ago

New CI based on GH-actions

alyst opened this pull request almost 4 years ago

Obscure error when aligning sequences with gaps

jakobnissen opened this issue almost 4 years ago

Add alignment string position support

alyst opened this pull request over 4 years ago

How to get the score of two alignments?

aadimator opened this issue over 4 years ago

Allow BioSequences 2.0

DilumAluthge opened this pull request almost 5 years ago

Release/v2.0.0

CiaranOMara opened this pull request almost 5 years ago

CompatHelper: bump compat for "Automa" to "0.8"

github-actions[bot] opened this pull request almost 5 years ago

Release/v1.0.1

CiaranOMara opened this pull request almost 5 years ago

Fix SAM.alignlength(record::Record)::Int

herbstk opened this pull request about 5 years ago

Incorrect calculation of alignment length in SAM.alignlength()

herbstk opened this issue about 5 years ago

@info instead of info

tanhevg opened this pull request about 5 years ago

Registering BioAlignments.jl to BioRegistry?

bicycle1885 opened this issue over 5 years ago

Update CI

CiaranOMara opened this pull request over 5 years ago

improve BAM.quality performance

jonathanBieler opened this pull request over 5 years ago

Sequence logo plots

cossio opened this issue over 5 years ago

Can't compiled by PackageCompile

aqzas opened this issue over 5 years ago

Fix reading BAM files from processes.

dcjones opened this pull request almost 6 years ago

find() instead of findall() in hts-files.md

aalexandersson opened this issue almost 6 years ago

LocalAlignment find lower score than biopython/scikit-bio implementations

diegozea opened this issue almost 6 years ago

Fix haskey(x::BAM.Record, y::String) (issue #20)

jakobnissen opened this pull request about 6 years ago

:bug: Update covert(BAM.Record x::Vector{UInt8} to Julia v. 1.0

jakobnissen opened this pull request about 6 years ago

Base.convert(BAM.Record, x::Vector{UInt8}) not updated to Julia v 1.0

jakobnissen opened this issue about 6 years ago

Cap Documenter.jl to 0.19 on Travis

mortenpi opened this pull request about 6 years ago

Bug in extracting auxiliary data fields from BAM file

jakobnissen opened this issue about 6 years ago

Julia 1.0 support

dcjones opened this pull request over 6 years ago

Version trouble with IntervalTrees. Only able to install "BioAlignments" after removing package "Bio"

kopperud opened this issue over 6 years ago

Support the mpileup format

SabrinaJaye opened this issue over 6 years ago

Fix deprecations

femtocleaner[bot] opened this pull request over 6 years ago

Add flag test for alignment to the positive strand

phaverty opened this pull request over 6 years ago

Support for >65535 CIGAR op-codes in BAM files

SabrinaJaye opened this pull request over 6 years ago

New BAM files can support more than 65535 cigar opcodes

ghuls opened this issue over 6 years ago

Contributing files rollout

SabrinaJaye opened this pull request over 6 years ago

How does one access the strand information?

phaverty opened this issue over 6 years ago

use where clause for type parameters