millironx/SequenceVariation.jl
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Add translate function for Haplotypes

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This commit is contained in:
Thomas A. Christensen II 2023-01-05 13:09:12 -06:00
parent e251b292a7
commit a61a80d586
1 changed files with 20 additions and 0 deletions
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src/Haplotype.jl
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@ -198,3 +198,23 @@ function reconstruct(h::Haplotype)
end
return seq
end
"""
translate(hap::Haplotype{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
Convert the variations in `hap` to a new reference sequence based upon `aln`. The alignment
rules follow the conventions of
[`translate(::Variation, PairwiseAlignment)`](@ref translate(::Variation{S,T}, ::PairwiseAlignment{S,S}) where {S,T}).
Indels at the beginning or end may not be preserved. Returns a new
[`Haplotype`](@ref)
"""
function translate(hap::Haplotype{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
vars = variations(hap)
new_ref = BA.sequence(aln)
translated_vars = Variation{S,T}[]
for v in vars
new_v = translate(v, aln)
isnothing(new_v) || push!(translated_vars, new_v)
end
return Haplotype(new_ref, translated_vars)
end