CHANGELOG.md

@@ -16,7 +16,6 @@ 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))
-- :bomb: [BREAKING] Refactored `reconstruct` function to use `Haplotype`'s reference sequence ([#30](https://github.com/BioJulia/SequenceVariation.jl/pull/30))
 
 ### Removed
 

docs/src/api.md

@@ -21,7 +21,7 @@ Insertion
 Haplotype
 reference(::Haplotype)
 variations
-reconstruct
+reconstruct!
 ```
 
 ## Variations

docs/src/haplotypes.md

@@ -31,10 +31,11 @@ bos_human_haplotype = Haplotype(bos_human_alignment)
 
 If the alternate sequence of a haplotype 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.
+retrieved using the [`reconstruct!`](@ref) function.
 
 ```@repl call_variants
-human2 = reconstruct(bos_human_haplotype)
+human2 = copy(bovine);
+reconstruct!(human2, bos_human_haplotype)
 human2 == bovine
 human2 == human
 ```

src/Haplotype.jl

@@ -162,22 +162,21 @@ reference(h::Haplotype) = h.ref
 Base.:(==)(x::Haplotype, y::Haplotype) = x.ref == y.ref && x.edits == y.edits
 
 """
-    reconstruct(h::Haplotype)
+    reconstruct!(seq::S, x::Haplotype{S}) where {S}
 
-Apply the edits in `h` to the reference sequence of `h` and return the mutated sequence
+Apply the edits in `x` to `seq` and return the mutated sequence
 """
-function reconstruct(h::Haplotype)
+function reconstruct!(seq::S, x::Haplotype{S}) where {S}
-    len = length(reference(h)) + sum(edit -> _lendiff(edit), _edits(h))
+    len = length(x.ref) + sum(edit -> _lendiff(edit), _edits(x))
-    seq = copy(reference(h))
     resize!(seq, len % UInt)
     refpos = seqpos = 1
-    for edit in _edits(h)
+    for edit in x.edits
-        while refpos < leftposition(edit)
+        while refpos < edit.pos
-            seq[seqpos] = reference(h)[refpos]
+            seq[seqpos] = x.ref[refpos]
             refpos += 1
             seqpos += 1
         end
-        editx = _mutation(edit)
+        editx = edit.x
         if editx isa Substitution
             seq[seqpos] = editx.x
             seqpos += 1
@@ -185,14 +184,14 @@ function reconstruct(h::Haplotype)
         elseif editx isa Deletion
             refpos += editx.len
         elseif editx isa Insertion
-            for i in editx.seq
+            for i in editx.x
                 seq[seqpos] = i
                 seqpos += 1
             end
         end
     end
     while seqpos ≤ length(seq)
-        seq[seqpos] = reference(h)[refpos]
+        seq[seqpos] = x.ref[refpos]
         refpos += 1
         seqpos += 1
     end

src/SequenceVariation.jl

@@ -32,7 +32,7 @@ export Substitution
 export Variation
 export altbases
 export mutation
-export reconstruct
+export reconstruct!
 export refbases
 export reference
 export translate

src/edits/Deletion.jl

@@ -15,7 +15,7 @@ end
 Deletion(x::Integer) = Deletion(convert(UInt, x))
 
 Base.length(x::Deletion) = Int(x.len)
-Base.:(==)(x::Deletion, y::Deletion) = length(x) == length(y)
+Base.:(==)(x::Substitution, y::Substitution) = length(x) == length(y)
 Base.hash(x::Deletion, h::UInt) = hash(Deletion, hash(x.len, h))
 
 function _refbases(d::Deletion, reference::S, pos::UInt) where {S<:BioSequence}

test/runtests.jl

@@ -43,10 +43,6 @@ var = Haplotype(align(seq1, seq2))
     end
 end
 
-@testset "HaplotypeReconstruction" begin
-    @test reconstruct(var) == seq1
-end
-
 @testset "VariationPosition" begin
     refseq = dna"ACAACTTTATCT"
     mutseq = dna"ACATCTTTATCT"