CHANGELOG.md

@@ -15,7 +15,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Code now follows [Blue style](https://github.com/invenia/BlueStyle) ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
 - :bomb: [BREAKING] Public and private API defined based on Blue style guidelines ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
-- :bomb: [BREAKING] Renamed type `Variant` to `Haplotype` ([#20](https://github.com/BioJulia/SequenceVariation.jl/issues/20)/[#29](https://github.com/BioJulia/SequenceVariation.jl/pull/29))
 
 ### Removed
 

docs/make.jl

@@ -14,7 +14,7 @@ makedocs(;
     modules=[SequenceVariation],
     pages=[
         "Home" => "index.md",
-        "Working with haplotypes" => "haplotypes.md",
+        "Working with variants" => "variants.md",
         "Working with variations" => "variations.md",
         "Comparing variations" => "compare.md",
         "API Reference" => "api.md",

docs/src/api.md

@@ -18,8 +18,8 @@ Insertion
 ## Variants
 
 ```@docs
-Haplotype
+Variant
-reference(::Haplotype)
+reference(::Variant)
 variations
 reconstruct!
 ```
@@ -49,7 +49,7 @@ _lendiff
 
 ```@docs
 _edits
-_is_valid(::Haplotype)
+_is_valid(::Variant)
 ```
 
 ### Variations

docs/src/compare.md

@@ -4,9 +4,9 @@ CurrentModule = SequenceVariation
 
 # Comparing variations in sequences
 
-## Checking for variations in a known haplotype
+## Checking for variations in a known variant
 
-Looking for a known [`Variation`](@ref) within a [`Haplotype`](@ref) is
+Looking for a known [`Variation`](@ref) within a [`Variant`](@ref) is
 efficiently accomplished using the `in` operator.
 
 ```@setup call_variants
@@ -21,27 +21,27 @@ bos_ovis_alignment =
 bos_human_alignment =
     PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
 
-bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
+bos_ovis_variant = Variant(bos_ovis_alignment)
-bos_human_haplotype = Haplotype(bos_human_alignment)
+bos_human_variant = Variant(bos_human_alignment)
 ```
 
 ```@example call_variants
 println("\tOvis aires\tHomo sapiens")
-for v in vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype))
+for v in vcat(variations(bos_ovis_variant), variations(bos_human_variant))
-    is_sheep = v in bos_ovis_haplotype
+    is_sheep = v in bos_ovis_variant
-    is_human = v in bos_human_haplotype
+    is_human = v in bos_human_variant
     println("$v\t$is_sheep\t\t$is_human")
 end
 ```
 
-## Constructing new haplotypes based on other variations
+## Constructing new variants based on other variations
 
-New haplotypes can be constructed using variations. This might be useful to pool
+New variants can be constructed using variations. This might be useful to pool
-variations found on different reads or to filter variations from a haplotype
+variations found on different reads or to filter variations from a variant
-that aren't validated by another haplotype.
+that aren't validated by another variant.
 
 ```@repl call_variants
-sheeple = vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype));
+sheeple = vcat(variations(bos_ovis_variant), variations(bos_human_variant));
-Haplotype(bovine, sheeple)
+Variant(bovine, sheeple)
 reconstruct!(bovine, ans)
 ```

docs/src/variants.md

@@ -2,14 +2,13 @@
 CurrentModule = SequenceVariation
 ```
 
-# Working with haplotypes
+# Working with variants
 
 ## Calling variants
 
 The first step in working with sequence variation is to identify (call)
-variations between two sequences. SequenceVariation can directly call variants
+variations. SequenceVariation can directly call variants using the
-using the `Haplotype(::PairwiseAlignment)` constructor of the
+`Variant(::PairwiseAlignment)` constructor of the [`Variant`](@ref) type.
-[`Haplotype`](@ref) type.
 
 ```@repl call_variants
 using SequenceVariation, BioAlignments, BioSequences
@@ -23,19 +22,19 @@ bos_ovis_alignment =
 bos_human_alignment =
     PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
 
-bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
+bos_ovis_variant = Variant(bos_ovis_alignment)
-bos_human_haplotype = Haplotype(bos_human_alignment)
+bos_human_variant = Variant(bos_human_alignment)
 ```
 
 ## Sequence reconstruction
 
-If the alternate sequence of a haplotype is no longer available (as is often the
+If the alternate sequence of a variant is no longer available (as is often the
 case when calling variants from alignment files), then the sequence can be
 retrieved using the [`reconstruct!`](@ref) function.
 
 ```@repl call_variants
 human2 = copy(bovine);
-reconstruct!(human2, bos_human_haplotype)
+reconstruct!(human2, bos_human_variant)
 human2 == bovine
 human2 == human
 ```

docs/src/variations.md

@@ -27,7 +27,7 @@ mutation(Variation(bovine_ins, "25ACA"))
 
 ## Extraction
 
-Sequence variations may also be extracted wholesale from a [`Haplotype`](@ref)
+Sequence variations may also be extracted wholesale from a [`Variant`](@ref)
 using the [`variations`](@ref) function.
 
 ```@setup call_variants
@@ -42,13 +42,13 @@ bos_ovis_alignment =
 bos_human_alignment =
     PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
 
-bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
+bos_ovis_variant = Variant(bos_ovis_alignment)
-bos_human_haplotype = Haplotype(bos_human_alignment)
+bos_human_variant = Variant(bos_human_alignment)
 ```
 
 ```@repl call_variants
-variations(bos_ovis_haplotype)
+variations(bos_ovis_variant)
-variations(bos_human_haplotype)
+variations(bos_human_variant)
 ```
 
 ## Reference switching
@@ -59,8 +59,8 @@ alignment between the new and old references using the [`translate`](@ref).
 ```@repl call_variants
 ovis_human_alignment =
     PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)
-human_variation = first(variations(bos_ovis_haplotype))
+human_variation = first(variations(bos_ovis_variant))
 reference(ans) == bovine
-SequenceVariation.translate(human_variation, ovis_human_haplotype)
+SequenceVariation.translate(human_variation, ovis_human_alignment)
 reference(ans) == bovine
 ```

src/SequenceVariation.jl

@@ -2,10 +2,10 @@ module SequenceVariation
 
 """
 Needs to be able to:
-* Given a sequence and a reference, create a `Haplotype` that unambiguously represents
+* Given a sequence and a reference, create a `Variant` that unambiguously represents
 the sequence
 
-* Given a `Haplotype` and a new reference, translate the variant to the new reference.
+* Given a `Variant` and a new reference, translate the variant to the new reference.
 
 * Given a mutation and a reference and a sequence, determine if the sequence has that
 mutation
@@ -26,9 +26,9 @@ using BioSequences: BioSequences, BioSequence, NucleotideSeq, LongSequence, isga
 using BioSymbols: BioSymbol
 
 export Deletion
-export Haplotype
 export Insertion
 export Substitution
+export Variant
 export Variation
 export altbases
 export mutation
@@ -45,7 +45,7 @@ struct Unsafe end
 struct Inapplicable end
 
 include("Edit.jl")
-include("Haplotype.jl")
+include("Variant.jl")
 include("Variation.jl")
 
 end # module

src/Variant.jl

@@ -1,43 +1,41 @@
 """
-    Haplotype{S<:BioSequence,T<:BioSymbol}
+    Variant{S<:BioSequence,T<:BioSymbol}
 
 A set of variations within a given sequence that are all found together. Depending on the
-field, it might also be referred to as a "genotype" or "strain."
+field, it might also be referred to as a "genotype," "haplotype," or "strain."
 
 # Constructors
 
-    Haplotype(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
+    Variant(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
-    Haplotype(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence,T<:BioSymbol}
+    Variant(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence,T<:BioSymbol}
-    Haplotype(
+    Variant(
         aln::PairwiseAlignment{T,T}
     ) where {T<:LongSequence{<:Union{BS.AminoAcidAlphabet,BS.NucleicAcidAlphabet}}}
 
-When constructing a `Haplotype` from a vector of [`Edit`](@ref)s or [`Variation`](@ref)s,
+When constructing a `Variant` from a vector of [`Edit`](@ref)s or [`Variation`](@ref)s, the
-the edits are applied sequentially from first to last position, therefore the vector must
+edits are applied sequentially from first to last position, therefore the vector must always
-always be sorted by position. These edits are sorted automatically if constructing from an
+be sorted by position. These edits are sorted automatically if constructing from an
 alignment.
 """
-struct Haplotype{S<:BioSequence,T<:BioSymbol}
+struct Variant{S<:BioSequence,T<:BioSymbol}
     ref::S
     edits::Vector{Edit{S,T}}
 
-    Haplotype{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
 
-function Haplotype{S,T}(
+function Variant{S,T}(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
-    ref::S, edits::Vector{Edit{S,T}}
-) where {S<:BioSequence,T<:BioSymbol}
     sort!(edits; by=x -> x.pos)
-    result = Haplotype{S,T}(ref, edits, Unsafe())
+    result = Variant{S,T}(ref, edits, Unsafe())
     _is_valid(result) || error("TODO") # report what kind of error message?
     return result
 end
 
-function Haplotype(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
+function Variant(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
-    return Haplotype{S,T}(ref, edits)
+    return Variant{S,T}(ref, edits)
 end
 
-function Base.show(io::IO, x::Haplotype)
+function Base.show(io::IO, x::Variant)
     n = length(x.edits)
     print(io, summary(x), " with $n edit$(n > 1 ? "s" : ""):")
     for i in x.edits
@@ -48,21 +46,21 @@ function Base.show(io::IO, x::Haplotype)
 end
 
 """
-    is_valid(h::Haplotype)
+    is_valid(v::Variant)
 
-Validate `h`. `h` is invalid if any of its operations are out of bounds, or the same
+Validate `v`. `v` is invalid if any of its operations are out of bounds, or the same
 position is affected by multiple edits.
 """
-function _is_valid(h::Haplotype)
+function _is_valid(v::Variant)
-    isempty(h.ref) && return false
+    isempty(v.ref) && return false
-    valid_positions = 1:length(h.ref)
+    valid_positions = 1:length(v.ref)
     last_was_insert = false
-    for edit in h.edits
+    for edit in v.edits
         pos = edit.pos
         op = edit.x
         # Sanity check: for this to be a valid variant, it must be comprised of valid
         # variations
-        _is_valid(Variation(h.ref, edit)) || return false
+        _is_valid(Variation(v.ref, edit)) || return false
 
         # For substitutions we simply do not allow another modification of the same base
         if op isa Substitution
@@ -89,7 +87,7 @@ function _is_valid(h::Haplotype)
     return true
 end
 
-function Haplotype(
+function Variant(
     aln::PairwiseAlignment{T,T}
 ) where {T<:LongSequence{<:Union{BS.AminoAcidAlphabet,BS.NucleicAcidAlphabet}}}
     ref = aln.b
@@ -143,30 +141,30 @@ function Haplotype(
         end
     end
 
-    return Haplotype(ref, edits)
+    return Variant(ref, edits)
 end
 
 """
-    _edits(h::Haplotype)
+    _edits(v::Variant)
 
-Gets the [`Edit`](@ref)s that comprise `h`
+Gets the [`Edit`](@ref)s that comprise `v`
 """
-_edits(h::Haplotype) = h.edits
+_edits(v::Variant) = v.edits
 
 """
-    reference(h::Haplotype)
+    reference(v::Variant)
 
-Gets the reference sequence of `h`.
+Gets the reference sequence of `v`.
 """
-reference(h::Haplotype) = h.ref
+reference(v::Variant) = v.ref
-Base.:(==)(x::Haplotype, y::Haplotype) = x.ref == y.ref && x.edits == y.edits
+Base.:(==)(x::Variant, y::Variant) = x.ref == y.ref && x.edits == y.edits
 
 """
-    reconstruct!(seq::S, x::Haplotype{S}) where {S}
+    reconstruct!(seq::S, x::Variant{S}) where {S}
 
 Apply the edits in `x` to `seq` and return the mutated sequence
 """
-function reconstruct!(seq::S, x::Haplotype{S}) where {S}
+function reconstruct!(seq::S, x::Variant{S}) where {S}
     len = length(x.ref) + sum(edit -> _lendiff(edit), _edits(x))
     resize!(seq, len % UInt)
     refpos = seqpos = 1

src/Variation.jl

@@ -12,7 +12,7 @@ and built-in validation.
     Variation(ref::S, edit::AbstractString) where {S<:BioSequence}
 
 Generally speaking, the `Edit` constructor should be avoided to ensure corectness: use of
-[`variations(::Haplotype)`](@ref) is encouraged, instead.
+[`variations(::Variant)`](@ref) is encouraged, instead.
 
 Constructing a `Variation` from an `AbstractString` will parse the from `edit` using the
 following syntax:
@@ -45,9 +45,9 @@ function Variation(ref::S, edit::AbstractString) where {S<:BioSequence}
     return Variation{S,T}(ref, e)
 end
 
-function Haplotype(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence,T<:BioSymbol}
+function Variant(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence,T<:BioSymbol}
     edits = _edit.(vars)
-    return Haplotype{S,T}(ref, edits)
+    return Variant{S,T}(ref, edits)
 end
 
 """
@@ -108,7 +108,7 @@ function Base.show(io::IO, x::Variation)
     end
 end
 
-function Base.in(v::Variation, var::Haplotype)
+function Base.in(v::Variation, var::Variant)
     if v.ref != var.ref
         error("References must be equal")
     end
@@ -171,14 +171,14 @@ function translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
 end
 
 """
-    variations(h::Haplotype{S,T}) where {S,T}
+    variations(v::Variant{S,T}) where {S,T}
 
-Converts the [`Edit`](@ref)s of `h` into a vector of [`Variation`](@ref)s.
+Converts the [`Edit`](@ref)s of `v` into a vector of [`Variation`](@ref)s.
 """
-function variations(h::Haplotype{S,T}) where {S,T}
+function variations(v::Variant{S,T}) where {S,T}
-    vs = Vector{Variation{S,T}}(undef, length(_edits(h)))
+    vs = Vector{Variation{S,T}}(undef, length(_edits(v)))
-    for (i, e) in enumerate(_edits(h))
+    for (i, e) in enumerate(_edits(v))
-        vs[i] = Variation{S,T}(reference(h), e)
+        vs[i] = Variation{S,T}(reference(v), e)
     end
     return vs
 end

test/runtests.jl

@@ -1,9 +1,9 @@
 """
 Needs to be able to:
-* Given a sequence and a reference, create a `Haplotype` that unambiguously represents
+* Given a sequence and a reference, create a `Variant` that unambiguously represents
 the sequence
 
-* Given a `Haplotype` and a new reference, translate the variant to the new reference.
+* Given a `Variant` and a new reference, translate the variant to the new reference.
 
 * Given a mutation and a reference and a sequence, determine if the sequence has that
 mutation
@@ -34,12 +34,12 @@ const DNA_MODEL = BioAlignments.AffineGapScoreModel(EDNAFULL; gap_open=-25, gap_
 align(a::BioSequence, b::BioSequence) = pairalign(GlobalAlignment(), a, b, DNA_MODEL).aln
 seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG")
 seq2 = ungap!(dna"TGATGCGTGT-AGCAACACTTATAGCG")
-var = Haplotype(align(seq1, seq2))
+var = Variant(align(seq1, seq2))
 
-@testset "HaplotypeRoundtrip" begin
+@testset "VariantRoundtrip" begin
     for v in variations(var)
         @test v in var
-        @test v in Haplotype(seq2, [v])
+        @test v in Variant(seq2, [v])
     end
 end
 
@@ -51,7 +51,7 @@ end
     read02 = AlignedSequence(mutseq[3:12], Alignment("10M", 1, 3))
     aln01 = PairwiseAlignment(read01, refseq)
     aln02 = PairwiseAlignment(read02, refseq)
-    @test Haplotype(aln01).edits == Haplotype(aln02).edits
+    @test Variant(aln01).edits == Variant(aln02).edits
 end
 
 @testset "VariationParsing" begin
@@ -72,7 +72,7 @@ end
 
     read = AlignedSequence(mutseq[1:10], Alignment("10M", 1, 1))
     aln = PairwiseAlignment(read, refseq)
-    var = Haplotype(aln)
+    var = Variant(aln)
 
     sub = Variation(refseq, "A4T")
     @test first(variations(var)) == sub
@@ -108,31 +108,31 @@ end
     @test altbases(Variation(dna"ATCGA", "1C")) == dna"CA"
 end
 
-@testset "SoftclipHaplotype" begin
+@testset "SoftclipVariant" begin
     refseq = dna"GATTACA"
     mutseq = dna"GATTACAAAA"
 
-    refvar = Haplotype(refseq, SequenceVariation.Edit{typeof(refseq),eltype(refseq)}[])
+    refvar = Variant(refseq, SequenceVariation.Edit{typeof(refseq),eltype(refseq)}[])
 
     # Test for ending soft clip
-    @test Haplotype(
+    @test Variant(
         PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S", 1, 1)), refseq)
     ) == refvar
 
     # Test for ending soft+hard clip
-    @test Haplotype(
+    @test Variant(
         PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S2H", 1, 1)), refseq)
     ) == refvar
 
     # Test that ending insertions are still valid
     @test length(
-        Haplotype(
+        Variant(
             PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3I", 1, 1)), refseq)
         ).edits,
     ) == 1
 
     # Test that out-of-bounds bases are still caught
-    @test_throws BoundsError Haplotype(
+    @test_throws BoundsError Variant(
         PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3X", 1, 1)), refseq)
     )
 end