BioJulia/BioAlignments.jl

Issues

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

  #90 opened 2 years ago by MillironX
  1

• TagBot trigger issue

  #68 opened 3 years ago by JuliaTagBot
  5

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

  #87 opened 2 years ago by CiaranOMara
  0

• `ref2seq` returns a position outside of the sequence length

  #56 opened 2 years ago by MillironX
  0

• Friendly request to `@deprecate` API changes via semver

  #84 opened 2 years ago by dehann
  2

• Outdated documentation for SAM/BAM in BioAlignments is first hit in search

  #82 opened 2 years ago by simon-anders
  6

• Get reference and query from `PairwiseAlignment`

  #55 opened 3 years ago by jakobnissen
  2

• Refactor tests

  #81 opened 2 years ago by kescobo
  0

• Do these methods work and are they tested?

  #74 opened 2 years ago by CiaranOMara
  1

• Weird error with `AffineGapScoreModel()`

  #79 opened 2 years ago by jakobnissen
  0

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

  #75 opened 3 years ago by kool7d
  1

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

  #57 opened 3 years ago by jakobnissen
  1

• Extract start and end positions from a PairwiseAlignment

  #73 opened 3 years ago by rohanmaddamsetti
  1

• TagBot not triggering.

  #67 opened 3 years ago by kescobo
  0

• `AlignmentAnchor` method signature

  #69 opened 3 years ago by CiaranOMara
  1

• OP_BACK has no use?

  #63 opened 3 years ago by jakobnissen
  2

• Lack of an article to cite BioAlignments.jl

  #65 opened 3 years ago by Hugemiler
  1

• Bug in `OverlapAlignment`

  #59 opened 3 years ago by jakobnissen
  1

• The API of accessing fields of BioAlignments

  #58 opened 3 years ago by jakobnissen
  0

• Inconsistent when aligning distinct sequence types

  #54 opened 3 years ago by jakobnissen
  1

• Multiple alignment manipulation

  #51 opened 4 years ago by BioTurboNick
  3

• "master" vs "develop" branches

  #49 opened 4 years ago by alyst
  1

• Obscure error when aligning sequences with gaps

  #46 opened 4 years ago by jakobnissen
  0

• How to get the score of two alignments?

  #43 opened 4 years ago by aadimator
  0

• Incorrect calculation of alignment length in SAM.alignlength()

  #37 opened 4 years ago by herbstk
  1

• Registering BioAlignments.jl to BioRegistry?

  #35 opened 4 years ago by bicycle1885
  6

• Sequence logo plots

  #31 opened 5 years ago by cossio
  1

• Can't compiled by PackageCompile

  #30 opened 5 years ago by aqzas
  0

• LocalAlignment find lower score than biopython/scikit-bio implementations

  #27 opened 6 years ago by diegozea
  5

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

  #28 opened 6 years ago by aalexandersson
  0

• Bug in extracting auxiliary data fields from BAM file

  #20 opened 6 years ago by jakobnissen
  1

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

  #22 opened 6 years ago by jakobnissen
  1

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

  #17 opened 6 years ago by kopperud
  1

• Support the mpileup format

  #16 opened 6 years ago by TransGirlCodes
  0

• New BAM files can support more than 65535 cigar opcodes

  #12 opened 6 years ago by ghuls
  2

• How does one access the strand information?

  #9 opened 6 years ago by phaverty
  5