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Allow hamming circle around N #126

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Nov 10, 2020
Merged

Allow hamming circle around N #126

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4f2a9b9
Allow hamming circle around N
tp2750 Oct 31, 2020
4e1bda1
add more tests
tp2750 Nov 10, 2020
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2 changes: 1 addition & 1 deletion src/demultiplexer.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,7 @@ function hamming_circle(seq, m)
for rs in Iterators.product(fill(1:4, m)...)
seq′ = copy(seq)
for (p, r) in zip(ps, rs)
if findfirst(isequal(seq[p]), ACGT) ≤ r
if findfirst(isequal(seq[p]), ACGTN) ≤ r
r += 1
end
seq′[p] = ACGTN[r]
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18 changes: 18 additions & 0 deletions test/demultiplexer.jl
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Expand Up @@ -118,4 +118,22 @@
@test n_ok / 10_000 > 0.99
@test n_ok < n_ok_with_fallback
end

@testset "Hamming circle" begin
@test sort(BioSequences.hamming_circle(dna"A",1)) == [dna"C",dna"G",dna"T",dna"N"]
@test sort(BioSequences.hamming_circle(dna"N",1)) == [dna"A",dna"C",dna"G",dna"T"]
end
@testset "Levenshtein circle" begin
@test sort(BioSequences.levenshtein_circle(dna"A",1)) == [dna"", dna"C", dna"CA", dna"G", dna"GA", dna"T", dna"TA", dna"N", dna"NA"]
@test sort(BioSequences.levenshtein_circle(dna"N",1)) == [dna"", dna"A", dna"AN", dna"C", dna"CN", dna"G", dna"GN", dna"T", dna"TN"]
end
@testset "Levenshtein distance 2" begin
barcodes = [dna"ATGGC", dna"GGAAG"]
dplxr2 = Demultiplexer(barcodes, n_max_errors=2, distance=:levenshtein)

@test demultiplex(dplxr2, dna"ATGGC") === (1, 0)
@test demultiplex(dplxr2, dna"ATGG") === (1, 1)
@test demultiplex(dplxr2, dna"ATG") === (1, 2)
@test demultiplex(dplxr2, dna"TACG") === (0, -1)
end
end