millironx/SequenceVariation.jl
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Apply Blue style to tests file

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This commit is contained in:
Thomas A. Christensen II 2023-01-03 21:59:42 -06:00
parent fb9ab68cca
commit d29764d2bc
1 changed files with 17 additions and 7 deletions
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20
test/runtests.jl
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@ -29,7 +29,7 @@ using BioSequences
using SequenceVariation using SequenceVariation
using Test using Test
const DNA_MODEL = BioAlignments.AffineGapScoreModel(EDNAFULL, gap_open=-25, gap_extend=-2) const DNA_MODEL = BioAlignments.AffineGapScoreModel(EDNAFULL; gap_open=-25, gap_extend=-2)
align(a::BioSequence, b::BioSequence) = pairalign(GlobalAlignment(), a, b, DNA_MODEL).aln align(a::BioSequence, b::BioSequence) = pairalign(GlobalAlignment(), a, b, DNA_MODEL).aln
seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG") seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG")
@ -115,16 +115,26 @@ end
refvar = Variant(refseq, SequenceVariation.Edit{typeof(refseq),eltype(refseq)}[]) refvar = Variant(refseq, SequenceVariation.Edit{typeof(refseq),eltype(refseq)}[])
# Test for ending soft clip # Test for ending soft clip
@test Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S", 1, 1)), refseq)) == refvar @test Variant(
PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S", 1, 1)), refseq)
) == refvar
# Test for ending soft+hard clip # Test for ending soft+hard clip
@test Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S2H", 1, 1)), refseq)) == refvar @test Variant(
PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3S2H", 1, 1)), refseq)
) == refvar
# Test that ending insertions are still valid # Test that ending insertions are still valid
@test length(Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3I", 1, 1)), refseq)).edits) == 1 @test length(
Variant(
PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3I", 1, 1)), refseq)
).edits,
) == 1
# Test that out-of-bounds bases are still caught # Test that out-of-bounds bases are still caught
@test_throws BoundsError Variant(PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3X", 1, 1)), refseq)) @test_throws BoundsError Variant(
PairwiseAlignment(AlignedSequence(mutseq, Alignment("7=3X", 1, 1)), refseq)
)
end end
@testset "Aqua" begin @testset "Aqua" begin