BioAlignments.jl

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Friendly request to `@deprecate` API changes via semver

2

Hi BioAlignments, Just wanted to put in a friendly request for API changes to [follow Julia's `@deprecate`](https://docs.julialang.org/en/v1/base/base/#Base.@deprecate) pattern for API changes please, so for example in package v0.1.x: ```julia #...

dehann

## Types of changes This PR implements the following changes: * [x] :sparkles: New feature (A non-breaking change which adds functionality). * [ ] :bug: Bug fix (A non-breaking change,...

MillironX

Get reference and query from `PairwiseAlignment`

2

It would be nice if there were exported methods to get the reference and query form an alignment. Something like `ref(aln)` and `seq(aln)`.

jakobnissen

Update the alignment figure

1

# Update the alignment figure in the documentation > _This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any...

alyst

Related to https://github.com/BioJulia/BioAlignments.jl/discussions/80

kescobo

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

4

## Types of changes This PR implements the following changes: * [x] :sparkles: New feature (A non-breaking change which adds functionality). * [x] :bug: Bug fix (A non-breaking change, which...

MillironX

``` julia> AffineGapScoreModel() ERROR: KeyError: key :match not found Stacktrace: [1] getindex(h::Dict{Symbol, Union{}}, key::Symbol) @ Base ./dict.jl:498 [2] AffineGapScoreModel(; scores::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ BioAlignments ~/code/BioAlignments.jl/src/models.jl:97 [3] AffineGapScoreModel() @...

jakobnissen

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

1

Affine alignment is not working, but simple edit distance works. ``` strucseq = "KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL" msaseq = "KIFERCEFARTLKRNGMGGYHGIRLADWVCLARWESSYNTKATNYNSKSTDYGIFQINSRYWCNDGKTPGAVNACGISCNVLLQDDITQAIACAKRVVDPQGIRAWVAWKKHCEQDLTQYQGC" ``` ## Expected Behavior Something like ``` costmodel = CostModel(match=0, mismatch=1, insertion=1, deletion=1)...

kool7d

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

1

It looks like the `firstref` and `lastref` fields aren't actually used for anything. Can they be removed?

jakobnissen

Extract start and end positions from a PairwiseAlignment

1

Hello, I have a feature request, that is related to some other open issues related to the API of this package. Currently, there is no API to extract the start...

rohanmaddamsetti