mirror of
https://github.com/MillironX/SequenceVariation.jl.git
synced 2024-11-25 06:39:55 +00:00
Move Edit-related code to Edit.jl
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parent
a6ad47a568
commit
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2 changed files with 143 additions and 142 deletions
142
src/Edit.jl
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142
src/Edit.jl
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@ -0,0 +1,142 @@
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"""
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Substitution
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Represents the presence of a `T` at a given position. The position is stored
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outside this struct.
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"""
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struct Substitution{T<:BioSymbol}
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x::T
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end
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Base.:(==)(x::Substitution, y::Substitution) = x.x == y.x
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Base.hash(x::Substitution, h::UInt) = hash(Substitution, hash(x.x, h))
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"""
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Deletion
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Represents the deletion of N symbols. The location of the deletion is stored
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outside this struct
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"""
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struct Deletion
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len::UInt
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function Deletion(len::UInt)
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iszero(len) && error("Deletion must be at least 1 symbol")
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return new(len)
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end
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end
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Deletion(x::Integer) = Deletion(convert(UInt, x))
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Base.length(x::Deletion) = Int(x.len)
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Base.hash(x::Deletion, h::UInt) = hash(Deletion, hash(x.len, h))
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"""
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Insertion{S <: BioSequence}
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Represents the insertion of a `S` into a sequence. The location of the insertion
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is stored outside the struct.
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"""
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struct Insertion{S<:BioSequence}
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seq::S
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function Insertion{S}(x::S) where {S<:BioSequence}
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isempty(x) && error("Insertion must be at least 1 symbol")
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return new(x)
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end
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end
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Insertion(s::BioSequence) = Insertion{typeof(s)}(s)
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Base.length(x::Insertion) = length(x.seq)
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Base.:(==)(x::Insertion, y::Insertion) = x.seq == y.seq
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Base.hash(x::Insertion, h::UInt) = hash(Insertion, hash(x.seq, h))
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"""
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Edit{S <: BioSequence, T <: BioSymbol}
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An edit of either `Substitution{T}`, `Insertion{S}` or `Deletion` at a position.
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If deletion: Deletion of length L at ref pos `pos:pos+L-1`
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If insertion: Insertion of length L b/w ref pos `pos:pos+1`
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"""
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struct Edit{S<:BioSequence,T<:BioSymbol}
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x::Union{Substitution{T},Deletion,Insertion{S}}
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pos::UInt
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end
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Base.:(==)(e1::Edit, e2::Edit) = e1.pos == e2.pos && e1.x == e2.x
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Base.hash(x::Edit, h::UInt) = hash(Edit, hash((x.x, x.pos), h))
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Base.length(e::Edit) = e isa Substitution ? 1 : length(mutation(e))
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function Base.parse(::Type{T}, s::AbstractString) where {T<:Edit{Se,Sy}} where {Se,Sy}
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return parse(T, String(s))
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end
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function Base.parse(::Type{<:Edit{Se,Sy}}, s::Union{String,SubString{String}}) where {Se,Sy}
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# Either "Δ1-2", "11T" or "G16C"
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if (m = match(r"^Δ(\d+)-(\d+)$", s); m) !== nothing
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pos = parse(UInt, m[1])
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stop = parse(UInt, m[2])
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stop ≥ pos || throw(ArgumentError("Non-positive deletion length: \"" * s * "\""))
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Edit{Se,Sy}(Deletion(stop - pos + 1), pos)
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elseif (m = match(r"^(\d+)([A-Za-z]+)$", s); m) !== nothing
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pos = parse(UInt, m[1])
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seq = Se(m[2])
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Edit{Se,Sy}(Insertion(seq), pos)
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elseif (m = match(r"^[A-Za-z](\d+)([A-Za-z])$", s); m) !== nothing
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pos = parse(UInt, m[1])
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sym = Sy(first(m[2]))
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Edit{Se,Sy}(Substitution(sym), pos)
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else
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throw(ArgumentError("Failed to parse edit \"" * s * '"'))
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end
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end
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mutation(e::Edit) = e.x
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BioGenerics.leftposition(e::Edit) = e.pos
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function BioGenerics.rightposition(e::Edit)
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if mutation(e) isa Substitution
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return leftposition(e)
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elseif mutation(e) isa Insertion
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return leftposition(e) + 1
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elseif mutation(e) isa Deletion
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return leftposition(e) + length(e) - 1
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else
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error("Unknown mutation type $(typeof(mutation(e)))")
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end
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end
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function lendiff(edit::Edit)
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x = edit.x
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return x isa Substitution ? 0 : (x isa Deletion ? -length(x) : length(x.x))
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end
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function _refbases(s::Substitution, reference::S, pos::UInt) where {S<:BioSequence}
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return S([reference[pos]])
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end
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function _altbases(s::Substitution, reference::S, pos::UInt) where {S<:BioSequence}
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return S([s.x])
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end
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function _refbases(d::Deletion, reference::S, pos::UInt) where {S<:BioSequence}
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if pos == 1
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return S(reference[UnitRange{Int}(pos, pos + length(d))])
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else
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return S(reference[UnitRange{Int}(pos - 1, pos + length(d) - 1)])
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end
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end
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function _altbases(d::Deletion, reference::S, pos::UInt) where {S<:BioSequence}
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if pos == 1
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return S([reference[pos + 1]])
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else
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return S([reference[pos - 1]])
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end
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end
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function _refbases(i::Insertion, reference::S, pos::UInt) where {S<:BioSequence}
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return S([reference[pos]])
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end
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function _altbases(i::Insertion, reference::S, pos::UInt) where {S<:BioSequence}
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if pos == 1
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return S([i.seq..., reference[pos]])
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else
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return S([reference[pos], i.seq...])
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end
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end
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@ -31,107 +31,7 @@ const BS = BioSequences
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struct Unsafe end
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struct Inapplicable end
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"""
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Substitution
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Represents the presence of a `T` at a given position. The position is stored
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outside this struct.
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"""
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struct Substitution{T <: BioSymbol}
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x::T
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end
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Base.:(==)(x::Substitution, y::Substitution) = x.x == y.x
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Base.hash(x::Substitution, h::UInt) = hash(Substitution, hash(x.x, h))
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"""
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Deletion
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Represents the deletion of N symbols. The location of the deletion is stored
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outside this struct
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"""
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struct Deletion
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len::UInt
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function Deletion(len::UInt)
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iszero(len) && error("Deletion must be at least 1 symbol")
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new(len)
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end
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end
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Deletion(x::Integer) = Deletion(convert(UInt, x))
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Base.length(x::Deletion) = Int(x.len)
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Base.hash(x::Deletion, h::UInt) = hash(Deletion, hash(x.len, h))
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"""
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Insertion{S <: BioSequence}
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Represents the insertion of a `S` into a sequence. The location of the insertion
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is stored outside the struct.
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"""
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struct Insertion{S <: BioSequence}
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seq::S
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function Insertion{S}(x::S) where {S <: BioSequence}
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isempty(x) && error("Insertion must be at least 1 symbol")
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new(x)
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end
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end
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Insertion(s::BioSequence) = Insertion{typeof(s)}(s)
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Base.length(x::Insertion) = length(x.seq)
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Base.:(==)(x::Insertion, y::Insertion) = x.seq == y.seq
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Base.hash(x::Insertion, h::UInt) = hash(Insertion, hash(x.seq, h))
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"""
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Edit{S <: BioSequence, T <: BioSymbol}
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An edit of either `Substitution{T}`, `Insertion{S}` or `Deletion` at a position.
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If deletion: Deletion of length L at ref pos `pos:pos+L-1`
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If insertion: Insertion of length L b/w ref pos `pos:pos+1`
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"""
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struct Edit{S <: BioSequence, T <: BioSymbol}
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x::Union{Substitution{T}, Deletion, Insertion{S}}
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pos::UInt
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end
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Base.:(==)(e1::Edit, e2::Edit) = e1.pos == e2.pos && e1.x == e2.x
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Base.hash(x::Edit, h::UInt) = hash(Edit, hash((x.x, x.pos), h))
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Base.length(e::Edit) = e isa Substitution ? 1 : length(mutation(e))
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function Base.parse(::Type{T}, s::AbstractString) where {T <: Edit{Se, Sy}} where {Se, Sy}
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parse(T, String(s))
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end
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function Base.parse(::Type{<:Edit{Se, Sy}}, s::Union{String, SubString{String}}) where {Se, Sy}
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# Either "Δ1-2", "11T" or "G16C"
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if (m = match(r"^Δ(\d+)-(\d+)$", s); m) !== nothing
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pos = parse(UInt, m[1])
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stop = parse(UInt, m[2])
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stop ≥ pos || throw(ArgumentError("Non-positive deletion length: \"" * s * "\""))
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Edit{Se, Sy}(Deletion(stop - pos + 1), pos)
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elseif (m = match(r"^(\d+)([A-Za-z]+)$", s); m) !== nothing
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pos = parse(UInt, m[1])
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seq = Se(m[2])
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Edit{Se, Sy}(Insertion(seq), pos)
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elseif (m = match(r"^[A-Za-z](\d+)([A-Za-z])$", s); m) !== nothing
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pos = parse(UInt, m[1])
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sym = Sy(first(m[2]))
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Edit{Se, Sy}(Substitution(sym), pos)
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else
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throw(ArgumentError("Failed to parse edit \"" * s * '"'))
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end
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end
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mutation(e::Edit) = e.x
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BioGenerics.leftposition(e::Edit) = e.pos
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function BioGenerics.rightposition(e::Edit)
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if mutation(e) isa Substitution
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return leftposition(e)
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elseif mutation(e) isa Insertion
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return leftposition(e) + 1
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elseif mutation(e) isa Deletion
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return leftposition(e) + length(e) - 1
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else
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error("Unknown mutation type $(typeof(mutation(e)))")
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end
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end
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include("Edit.jl")
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# Edits are applied sequentially from first to last pos.
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# The vector must always be sorted by pos.
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@ -260,11 +160,6 @@ edits(v::Variant) = v.edits
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reference(v::Variant) = v.ref
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Base.:(==)(x::Variant, y::Variant) = x.ref == y.ref && x.edits == y.edits
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function lendiff(edit::Edit)
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x = edit.x
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x isa Substitution ? 0 : (x isa Deletion ? -length(x) : length(x.x))
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end
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function reconstruct!(seq::S, x::Variant{S}) where S
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len = length(x.ref) + sum(edit -> lendiff(edit), x.edits)
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resize!(seq, len % UInt)
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@ -422,42 +317,6 @@ function variations(v::Variant{S,T}) where {S,T}
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return vs
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end
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function _refbases(s::Substitution, reference::S, pos::UInt) where S <: BioSequence
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return S([reference[pos]])
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end
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function _altbases(s::Substitution, reference::S, pos::UInt) where S <: BioSequence
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return S([s.x])
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end
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function _refbases(d::Deletion, reference::S, pos::UInt) where S <: BioSequence
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if pos == 1
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return S(reference[UnitRange{Int}(pos, pos+length(d))])
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else
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return S(reference[UnitRange{Int}(pos-1, pos+length(d)-1)])
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end
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end
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function _altbases(d::Deletion, reference::S, pos::UInt) where S <: BioSequence
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if pos == 1
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return S([reference[pos+1]])
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else
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return S([reference[pos-1]])
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end
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end
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function _refbases(i::Insertion, reference::S, pos::UInt) where S <: BioSequence
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return S([reference[pos]])
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end
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function _altbases(i::Insertion, reference::S, pos::UInt) where S <: BioSequence
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if pos == 1
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return S([i.seq..., reference[pos]])
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else
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return S([reference[pos], i.seq...])
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end
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end
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function refbases(v::Variation)
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return _refbases(mutation(v), reference(v), leftposition(v))
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end
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