millironx/SequenceVariation.jl
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Add tests for _is_valid(::Haplotype)

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Thomas A. Christensen II 2023-01-21 18:10:04 -06:00
parent 9776d5a31e
commit 2a5a5389ec
1 changed files with 35 additions and 0 deletions
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35
test/runtests.jl
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@ -54,6 +54,41 @@ var = Haplotype(align(seq1, seq2))
SequenceVariation.Edit{S,T}(Deletion(2), 1) SequenceVariation.Edit{S,T}(Deletion(2), 1)
end end
@testset "HaplotypeValidation" begin
# Test that substitutions cannot share the same position
@test_throws ErrorException Haplotype(
seq2, [Variation(seq2, "T2A"), Variation(seq2, "T2C")]
)
@test_throws ErrorException Haplotype(
seq2, [Variation(seq2, "G2A"), Variation(seq2, "G2T")]
)
@test_throws ErrorException Haplotype(
seq2, [Variation(seq2, "G26A"), Variation(seq2, "G26T")]
)
# Test that insertions cannot share the same position
@test_throws ErrorException Haplotype(
seq2, [Variation(seq2, "0AAA"), Variation(seq2, "0TTT")]
)
@test_throws ErrorException Haplotype(
seq2, [Variation(seq2, "2AAA"), Variation(seq2, "2TTT")]
)
@test_throws ErrorException Haplotype(
seq2, [Variation(seq2, "26AAA"), Variation(seq2, "26TTT")]
)
# Test that deletions invalidate further operations within the deleted positions
@test_throws ErrorException Haplotype(
seq2, [Variation(seq2, "Δ2-2"), Variation(seq2, "G2A")]
)
@test_throws ErrorException Haplotype(
seq2, [Variation(seq2, "G2A"), Variation(seq2, "Δ2-2")]
)
@test_throws ErrorException Haplotype(
seq2, [Variation(seq2, "Δ2-6"), Variation(seq2, "Δ3-5")]
)
end
@testset "HaplotypeRoundtrip" begin @testset "HaplotypeRoundtrip" begin
for v in variations(var) for v in variations(var)
@test v in var @test v in var