millironx/SequenceVariation.jl
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Fix tests for translate(::Variation)

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Thomas A. Christensen II 2023-01-05 14:34:22 -06:00
parent 239b366a1c
commit e251b292a7
1 changed files with 7 additions and 6 deletions
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src/Variation.jl
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@ -138,7 +138,7 @@ function translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
if iszero(pos) if iszero(pos)
(s, r), _ = iterate(aln) (s, r), _ = iterate(aln)
(isgap(s) | isgap(r)) && return Inapplicable() (isgap(s) | isgap(r)) && return Inapplicable()
return Variation{S,T}(seq, Edit{S,T}(Insertion(var.edit.x), 0)) return Variation{S,T}(seq, Edit{S,T}(Insertion(kind.seq), 0))
end end
(seqpos, op) = BA.ref2seq(aln, pos) (seqpos, op) = BA.ref2seq(aln, pos)
@ -153,18 +153,19 @@ function translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
# If it's a deletion, return nothing if the deleted part is already missing # If it's a deletion, return nothing if the deleted part is already missing
# from the new reference. # from the new reference.
(stop, op2) = BA.ref2seq(aln, pos + length(kind) - 1) (stop, op2) = BA.ref2seq(aln, pos + length(kind) - 1)
start = seqpos + op == BA.OP_DELETE start = seqpos + (op == BA.OP_DELETE)
start < stop && return nothing del_len = stop - start + 1
edit = Edit{S,T}(Deletion(stop - start + 1), start) del_len > 0 || return nothing
edit = Edit{S,T}(Deletion(del_len), start)
return Variation{S,T}(seq, edit, Unsafe()) return Variation{S,T}(seq, edit, Unsafe())
else else
# If it maps directly to a symbol, just insert # If it maps directly to a symbol, just insert
if op in (BA.OP_MATCH, BA.OP_SEQ_MATCH, BA.OP_SEQ_MISMATCH) if op in (BA.OP_MATCH, BA.OP_SEQ_MATCH, BA.OP_SEQ_MISMATCH)
# This happens if there is already an insertion at the position # This happens if there is already an insertion at the position
if pos != lastindex(ref) && first(ref2seq(aln, pos + 1)) != seqpos + 1 if pos != lastindex(ref) && first(BA.ref2seq(aln, pos + 1)) != seqpos + 1
return Inapplicable() return Inapplicable()
else else
edit = Edit{S,T}(Insertion(var.edit.x), seqpos) edit = Edit{S,T}(Insertion(mutation(var).seq), seqpos)
return Variation{S,T}(seq, edit, Unsafe()) return Variation{S,T}(seq, edit, Unsafe())
end end
# Alternatively, it can map to a deletion. In that case, it become really # Alternatively, it can map to a deletion. In that case, it become really