BioAlignments.jl
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BioJulia
Sequence alignment tools
The following was caught as an unrelated error in a [BGZFStreams.jl downstream test](https://github.com/BioJulia/BGZFStreams.jl/runs/5163487858?check_suite_focus=true). ``` MethodError: no method matching AlignmentAnchor(::Int64, ::Int64, ::BioAlignments.Operation) [243](https://github.com/BioJulia/BGZFStreams.jl/runs/5163487858?check_suite_focus=true#step:6:243) Closest candidates are: [244](https://github.com/BioJulia/BGZFStreams.jl/runs/5163487858?check_suite_focus=true#step:6:244) AlignmentAnchor(::Any, ::Any, ::Any, ::Any)...
@MillironX discovered that `OP_BACK` is not used in BioAlignments.jl, but listed as being present for compatibility with the SAM specs. However, as he also discovered, the operation is not listed...
For context, please read https://discourse.julialang.org/t/accessing-type-internal-fields-in-package-interfaces/70263 In brief, I was teaching some students about `BioAlignments` recently. My fellow teachers, who did not know about the package, were surprised at the workflow...
## Expected Behavior The `ref2seq` function should give a valid index that can be used to find the corresponding base in a `BAM.sequence`. ## Current Behavior `ref2seq` returns an invalid...
So I was surprised to find you can align Strings to each other: ``` julia> x= pairalign(LocalAlignment(), "ACA", "AAA", model) PairwiseAlignmentResult{Int64, String, String}: score: 6 seq: 1 ACA 3 |...
This pull request changes the compat entry for the `BioSymbols` package from `4` to `4, 5`. This keeps the compat entries for earlier versions. Note: I have not tested your...
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Need capability to manipulate a multiple sequence alignment, seems like the right place to put it. I started working on this but it may need more thought about how it...
MWE: ``` model = AffineGapScoreModel(EDNAFULL, gap_open=-12, gap_extend=-2) pairalign(LocalAlignment(), dna"A-A", dna"AAA", model) ``` Errors with: `ERROR: LoadError: BoundsError: attempt to access 15×15 Matrix{Int64} at index [0, 1] ` It seems clear...
Is there a way to only get the score of two alignments? Let's say that I have two alignments; `"MQD--RV--KRP"` and `"MKKL-K-K-H-P"` and I want to get there score. Currently,...
Is there a way to plot a sequence logo? See http://weblogo.threeplusone.com/, for example. If there isn't, maybe a plots recipe can be defined that takes letter weights and does this?
