CHANGELOG.md

@@ -7,19 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [0.1.3] - 2022-11-22
-
 ## Changed
 
 - Variations getter now returns type-parameterized vector ([#23](https://github.com/BioJulia/SequenceVariation.jl/pull/23))
 
-### Fixed
-
-- Soft clips at end of alignment causing invalid `Variant`s ([#25](https://github.com/BioJulia/SequenceVariation.jl/issues/25)/[#26](https://github.com/BioJulia/SequenceVariation.jl/pull/26))
-
 ## [0.1.2] - 2022-10-04
 
-## Changed
+- ## Changed
 
 - Updated dependency compats ([#21](https://github.com/BioJulia/SequenceVariation.jl/pull/21))
   - BioAlignments: 2 -> 2,3
@@ -43,8 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `Variant` constructor to automatically detect mutations from a `BioAlignments.PairwiseAlignment`
 - Methods to get reference and alternate bases from a `Variation`
 
-[unreleased]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.3...HEAD
+[unreleased]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.2...HEAD
-[0.1.3]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.2...v0.1.3
 [0.1.2]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.1...v0.1.2
 [0.1.1]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.0...v0.1.1
 [0.1.0]: https://github.com/BioJulia/SequenceVariation.jl/releases/tag/v0.1.0

Project.toml

@@ -1,7 +1,7 @@
 name = "SequenceVariation"
 uuid = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
 authors = ["Jakob Nybo Nissen <jakobnybonissen@gmail.com>", "Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>"]
-version = "0.1.3"
+version = "0.1.2"
 
 [deps]
 BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"

src/SequenceVariation.jl

@@ -20,7 +20,7 @@ TODO now:
 * Add tests
 """
 
-using BioAlignments: BioAlignments, PairwiseAlignment, OP_SOFT_CLIP
+using BioAlignments: BioAlignments, PairwiseAlignment
 using BioGenerics: BioGenerics, leftposition, rightposition
 using BioSequences: BioSequences, BioSequence, NucleotideSeq, LongSequence, isgap
 using BioSymbols: BioSymbol
@@ -233,10 +233,6 @@ function is_valid(v::Variant)
     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(v.ref, edit)) || return false
-
         # For substitutions we simply do not allow another modification of the same base
         if op isa Substitution
             pos in valid_positions || return false
@@ -246,7 +242,7 @@ function is_valid(v::Variant)
         # for next op. However, we cannot have two insertions at the same position, because
         # then the order of them is ambiguous
         elseif op isa Insertion
-            pos in (first(valid_positions)-1+last_was_insert:last(valid_positions)+1) || return false
+            pos in (first(valid_positions)-1+last_was_insert:last(valid_positions)) || return false
             last_was_insert = true
         # Deletions obviously invalidate the reference bases that are deleted.
         elseif op isa Deletion
@@ -263,6 +259,7 @@ function Variant(aln::PairwiseAlignment{T, T}) where {T <: LongSequence{<:Union{
     ref = aln.b
     E = eltype(typeof(ref))
     edits = Edit{T, E}[]
+    result = Variant(ref, edits)
     refpos = first(aln.a.aln.anchors).refpos
     seqpos = first(aln.a.aln.anchors).seqpos
     markpos = 0
@@ -299,24 +296,18 @@ function Variant(aln::PairwiseAlignment{T, T}) where {T <: LongSequence{<:Union{
         end
     end
 
-    # Check for clips at the end of the alignment
-    last_anchors = aln.a.aln.anchors[end-1:end]
-
     # Final indel, if applicable
-    if !any(anchor -> anchor.op == OP_SOFT_CLIP, last_anchors)
+    if !iszero(n_gaps)
-        if !iszero(n_gaps)
+        push!(edits, Edit{T, E}(Deletion(UInt(n_gaps)), UInt(markpos)))
-            push!(edits, Edit{T, E}(Deletion(UInt(n_gaps)), UInt(markpos)))
+    elseif !iszero(n_ins)
-        elseif !iszero(n_ins)
+        push!(edits, Edit{T, E}(Insertion(T(insertion_buffer)), UInt(markpos)))
-            push!(edits, Edit{T, E}(Insertion(T(insertion_buffer)), UInt(markpos)))
-        end
     end
 
-    return Variant(ref, edits)
+    return result
 end
 
 edits(v::Variant) = v.edits
 reference(v::Variant) = v.ref
-Base.:(==)(x::Variant, y::Variant) = x.ref == y.ref && x.edits == y.edits
 
 function lendiff(edit::Edit)
     x = edit.x
@@ -398,7 +389,7 @@ function is_valid(v::Variation)
     if op isa Substitution
         return pos in eachindex(v.ref)
     elseif op isa Insertion
-        return pos in 0:lastindex(v.ref)+1
+        return pos in 0:lastindex(v.ref)
     elseif op isa Deletion
         return pos in 1:(lastindex(v.ref)-length(op) + 1)
     end

test/runtests.jl

@@ -106,22 +106,3 @@ end
     @test refbases(Variation(dna"ATCGA", "1C")) == dna"A"
     @test altbases(Variation(dna"ATCGA", "1C")) == dna"CA"
 end
-
-@testset "SoftclipVariant" begin
-    refseq = dna"GATTACA"
-    mutseq = dna"GATTACAAAA"
-
-    refvar = Variant(refseq, SequenceVariation.Edit{typeof(refseq), eltype(refseq)}[])
-
-    # Test for ending soft clip
-    @test Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S", 1, 1)), refseq)) == refvar
-
-    # Test for ending soft+hard clip
-    @test Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S2H", 1, 1)), refseq)) == refvar
-
-    # Test that ending insertions are still valid
-    @test length(Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3I", 1, 1)), refseq)).edits) == 1
-
-    # Test that out-of-bounds bases are still caught
-    @test_throws BoundsError Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3X", 1, 1)), refseq))
-end