millironx/SequenceVariation.jl
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Add docstrings for Variation functions

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This commit is contained in:
Thomas A. Christensen II 2022-12-31 14:45:33 -06:00
parent 673481b40f
commit 2a7d61e43d
1 changed files with 44 additions and 0 deletions
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src/Variation.jl
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@ -50,14 +50,37 @@ function Variant(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence,T<:
return Variant{S,T}(ref, edits)
end
"""
reference(v::Variation)
Gets the reference sequence of `v`
"""
reference(v::Variation) = v.ref
"""
_edit(v::Variation)
Gets the underlying [`Edit`](@ref) of `v`
"""
_edit(v::Variation) = v.edit
"""
mutation(v::Variation)
Gets the underlying [`Substitution`](@ref), [`Insertion`](@ref), or [`Deletion`](@ref) of
`v`.
"""
mutation(v::Variation) = _mutation(_edit(v))
BioGenerics.leftposition(v::Variation) = leftposition(_edit(v))
BioGenerics.rightposition(v::Variation) = rightposition(_edit(v))
Base.:(==)(x::Variation, y::Variation) = x.ref == y.ref && x.edit == y.edit
Base.hash(x::Variation, h::UInt) = hash(Variation, hash((x.ref, x.edit), h))
"""
_is_valid(v::Variation)
Validate `v`. `v` is invalid if its opertation is out of bounds.
"""
function _is_valid(v::Variation)
isempty(v.ref) && return false
op = v.edit.x
@ -92,6 +115,13 @@ function Base.in(v::Variation, var::Variant)
return any(v.edit == edit for edit in var.edits)
end
"""
translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
Convert the difference in `var` to a new reference sequence based upon `aln`. `aln` is the
alignment of the old reference (`aln.b`) and the new reference sequence (`aln.seq`). Returns
the new [`Variation`](@ref).
"""
function translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
kind = mutation(var)
pos = leftposition(var)
@ -153,10 +183,24 @@ function variations(v::Variant{S,T}) where {S,T}
return vs
end
"""
refbases(v::Variation)
Get the reference bases of `v`. Note that for deletions, `refbases` also returns the base
_before_ the deletion in accordance with the `REF` field of the
[VCF v4 specification](https://samtools.github.io/hts-specs/VCFv4.3.pdf).
"""
function refbases(v::Variation)
return _refbases(mutation(v), reference(v), leftposition(v))
end
"""
altbases(v::Variation)
Get the alternate bases of `v`. Note that for insertions, `altbases` also returns the base
_before_ the insertion in accordance with the `ALT` field of the
[VCF v4 specification](https://samtools.github.io/hts-specs/VCFv4.3.pdf).
"""
function altbases(v::Variation)
return _altbases(mutation(v), reference(v), leftposition(v))
end