Bump version number to 0.2.0 in Project.toml

CHANGELOG.md

@@ -7,9 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.2.0] - 2023-01-10
+
 ### Added
 
 - Tutorial-type documentation ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
+- `Base.isless` implementation for `Edit` and `Variation` ([#31](https://github.com/BioJulia/SequenceVariation.jl/pull/31))
 
 ### Changed
 
@@ -60,7 +63,8 @@ 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/v0.1.4...HEAD
+[unreleased]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.2.0...HEAD
+[0.2.0]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.4...v0.2.0
 [0.1.4]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.3...v0.1.4
 [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

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 = "0.1.4"
+version = "0.2.0"
 
 [deps]
 BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"

README.md

@@ -5,6 +5,7 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/SequenceVariation.jl/blob/master/LICENSE)
 [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/stable)
 [![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/dev/)
+[![DOI](https://zenodo.org/badge/343847382.svg)](https://zenodo.org/badge/latestdoi/343847382)
 
 > This project follows the [semver](https://semver.org) _pro forma_ and uses the [OneFlow branching model](https://www.endoflineblog.com/oneflow-a-git-branching-model-and-workflow).
 
@@ -23,7 +24,7 @@ add SequenceVariation
 
 ## Testing
 
-SequenceVariation is tested against Julia `1.X` on Linux, OS X, and Windows.
+SequenceVariation is tested against Julia `1.6` (LTS), `1.X` (release) and nightly on Linux.
 
 **Latest build status:**
 

docs/src/index.md

@@ -23,7 +23,7 @@ add SequenceVariation
 
 ## Testing
 
-SequenceVariation is tested against Julia `1.X` on Linux, OS X, and Windows.
+SequenceVariation is tested against Julia `1.6` (LTS), `1.X` (release) and nightly on Linux.
 
 **Latest build status:**
 

src/Edit.jl

@@ -17,6 +17,13 @@ end
 Base.length(e::Edit) = length(_mutation(e))
 Base.:(==)(e1::Edit, e2::Edit) = e1.pos == e2.pos && e1.x == e2.x
 Base.hash(x::Edit, h::UInt) = hash(Edit, hash((x.x, x.pos), h))
+function Base.isless(x::Edit, y::Edit)
+    if leftposition(x) == leftposition(y)
+        return length(x) < length(y)
+    end
+
+    return leftposition(x) < leftposition(y)
+end
 
 function Base.parse(::Type{T}, s::AbstractString) where {T<:Edit{Se,Sy}} where {Se,Sy}
     return parse(T, String(s))

src/Variation.jl

@@ -75,6 +75,11 @@ BioGenerics.leftposition(v::Variation) = leftposition(_edit(v))
 BioGenerics.rightposition(v::Variation) = rightposition(_edit(v))
 Base.:(==)(x::Variation, y::Variation) = x.ref == y.ref && x.edit == y.edit
 Base.hash(x::Variation, h::UInt) = hash(Variation, hash((x.ref, x.edit), h))
+function Base.isless(x::Variation, y::Variation)
+    reference(x) == reference(y) ||
+        error("Variations cannot be compared if their reference sequences aren't equal")
+    return leftposition(x) < leftposition(y)
+end
 
 """
     _is_valid(v::Variation)

test/runtests.jl

@@ -36,6 +36,15 @@ seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG")
 seq2 = ungap!(dna"TGATGCGTGT-AGCAACACTTATAGCG")
 var = Haplotype(align(seq1, seq2))
 
+@testset "EditSorting" begin
+    S = typeof(seq1)
+    T = eltype(seq1)
+    @test SequenceVariation.Edit{S,T}(Deletion(1), 1) <
+        SequenceVariation.Edit{S,T}(Deletion(1), 2)
+    @test SequenceVariation.Edit{S,T}(Deletion(1), 1) <
+        SequenceVariation.Edit{S,T}(Deletion(2), 1)
+end
+
 @testset "HaplotypeRoundtrip" begin
     for v in variations(var)
         @test v in var
@@ -47,6 +56,10 @@ end
     @test reconstruct(var) == seq1
 end
 
+@testset "VariationSorting" begin
+    @test Variation(seq2, "A3T") < Variation(seq2, "T4A")
+end
+
 @testset "VariationPosition" begin
     refseq = dna"ACAACTTTATCT"
     mutseq = dna"ACATCTTTATCT"