millironx/SequenceVariation.jl
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Fix show function for Variations with Insertion edits (#3)

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Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
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Thomas A. Christensen II 2022-05-06 05:25:07 -05:00 committed by GitHub
parent 92a2d40553
commit d0f0f65d7f
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1 changed files with 7 additions and 5 deletions
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src/SequenceVariation.jl
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@ -66,7 +66,7 @@ outside this struct
""" """
struct Deletion struct Deletion
len::UInt len::UInt
function Deletion(len::UInt) function Deletion(len::UInt)
iszero(len) && error("Deletion must be at least 1 symbol") iszero(len) && error("Deletion must be at least 1 symbol")
new(len) new(len)
@ -156,7 +156,7 @@ let
lastsymbol = symbol lastsymbol = symbol
end end
end, end,
:digit => :(num = UInt(10)*num + (byte - 0x30) % UInt), :digit => :(num = UInt(10)*num + (byte - 0x30) % UInt),
) )
@eval begin @eval begin
function Base.parse(::Type{Edit{S, T}}, data::BYTES) where {S, T} function Base.parse(::Type{Edit{S, T}}, data::BYTES) where {S, T}
@ -180,7 +180,7 @@ end
struct Variant{S <: BioSequence, T <: BioSymbol} struct Variant{S <: BioSequence, T <: BioSymbol}
ref::S ref::S
edits::Vector{Edit{S, T}} edits::Vector{Edit{S, T}}
Variant{S, T}(ref::S, edits::Vector{Edit{S, T}}, ::Unsafe) where {S, T} = new(ref, edits) Variant{S, T}(ref::S, edits::Vector{Edit{S, T}}, ::Unsafe) where {S, T} = new(ref, edits)
end end
@ -360,6 +360,8 @@ function Base.show(io::IO, x::Variation)
print(io, x.ref[pos], pos, content.x) print(io, x.ref[pos], pos, content.x)
elseif content isa Deletion elseif content isa Deletion
print(io, 'Δ', pos, '-', pos + content.len - 1) print(io, 'Δ', pos, '-', pos + content.len - 1)
elseif content isa Insertion
print(io, pos, content.seq)
else else
print(io, pos, content.x) print(io, pos, content.x)
end end
@ -384,7 +386,7 @@ function translate(var::Variation{S, T}, aln::PairwiseAlignment{S, S}) where {S,
(isgap(s) | isgap(r)) && return Inapplicable() (isgap(s) | isgap(r)) && return Inapplicable()
return Variation{S, T}(seq, Edit{S, T}(Insertion(var.edit.x), 0)) return Variation{S, T}(seq, Edit{S, T}(Insertion(var.edit.x), 0))
end end
(seqpos, op) = BA.ref2seq(aln, pos) (seqpos, op) = BA.ref2seq(aln, pos)
if kind isa Substitution if kind isa Substitution
# If it's a substitution, return nothing if it maps to a deleted # If it's a substitution, return nothing if it maps to a deleted
@ -416,7 +418,7 @@ function translate(var::Variation{S, T}, aln::PairwiseAlignment{S, S}) where {S,
else else
return Inapplicable() return Inapplicable()
end end
end end
end end
export Insertion, export Insertion,