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Add tests for _is_valid(::Haplotype)
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@ -45,6 +45,9 @@ seq2 = ungap!(dna"TGATGCGTGT-AGCAACACTTATAGCG")
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seq3 = ungap!(dna"-GATGCGTGT-AGCAACACTTATCGC-")
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var = Haplotype(align(seq1, seq2))
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const SEQ = typeof(seq1)
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const BSE = eltype(seq1)
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@testset "EditSorting" begin
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S = typeof(seq1)
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T = eltype(seq1)
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@ -55,6 +58,11 @@ var = Haplotype(align(seq1, seq2))
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end
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@testset "HaplotypeValidation" begin
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# Test that we can't use an empty reference
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@test_throws ErrorException Haplotype(
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dna"", [SequenceVariation.Edit{SEQ,BSE}(Insertion{SEQ}(dna"A"), 0)]
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)
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# Test that substitutions cannot share the same position
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@test_throws ErrorException Haplotype(
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seq2, [Variation(seq2, "T2A"), Variation(seq2, "T2C")]
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@ -87,6 +95,21 @@ end
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@test_throws ErrorException Haplotype(
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seq2, [Variation(seq2, "Δ2-6"), Variation(seq2, "Δ3-5")]
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)
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# Test that a complicated (but valid) Haplotype still checks out
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@test first(
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SequenceVariation._is_valid(
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Haplotype(
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seq2,
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[
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Variation(seq2, "0AAA"),
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Variation(seq2, "T2A"),
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Variation(seq2, "Δ5-8"),
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Variation(seq2, "G26A"),
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],
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),
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),
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)
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end
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@testset "HaplotypeRoundtrip" begin
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