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Fix show function for Variations with Insertion edits (#3)
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
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1 changed files with 7 additions and 5 deletions
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@ -66,7 +66,7 @@ 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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@ -156,7 +156,7 @@ let
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lastsymbol = symbol
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end
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end,
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:digit => :(num = UInt(10)*num + (byte - 0x30) % UInt),
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:digit => :(num = UInt(10)*num + (byte - 0x30) % UInt),
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)
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@eval begin
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function Base.parse(::Type{Edit{S, T}}, data::BYTES) where {S, T}
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@ -180,7 +180,7 @@ end
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struct Variant{S <: BioSequence, T <: BioSymbol}
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ref::S
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edits::Vector{Edit{S, T}}
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Variant{S, T}(ref::S, edits::Vector{Edit{S, T}}, ::Unsafe) where {S, T} = new(ref, edits)
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end
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@ -360,6 +360,8 @@ function Base.show(io::IO, x::Variation)
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print(io, x.ref[pos], pos, content.x)
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elseif content isa Deletion
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print(io, 'Δ', pos, '-', pos + content.len - 1)
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elseif content isa Insertion
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print(io, pos, content.seq)
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else
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print(io, pos, content.x)
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end
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@ -384,7 +386,7 @@ function translate(var::Variation{S, T}, aln::PairwiseAlignment{S, S}) where {S,
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(isgap(s) | isgap(r)) && return Inapplicable()
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return Variation{S, T}(seq, Edit{S, T}(Insertion(var.edit.x), 0))
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end
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(seqpos, op) = BA.ref2seq(aln, pos)
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if kind isa Substitution
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# If it's a substitution, return nothing if it maps to a deleted
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@ -416,7 +418,7 @@ function translate(var::Variation{S, T}, aln::PairwiseAlignment{S, S}) where {S,
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else
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return Inapplicable()
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end
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end
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end
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end
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export Insertion,
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