millironx/SequenceVariation.jl
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Add more informative errors to _is_valid

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This commit is contained in:
Thomas A. Christensen II 2023-01-11 16:21:16 -06:00
parent 4e6c781c60
commit 2fa5782719
1 changed files with 8 additions and 6 deletions
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14
src/Haplotype.jl
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@ -29,7 +29,8 @@ function Haplotype{S,T}(
) where {S<:BioSequence,T<:BioSymbol} ) where {S<:BioSequence,T<:BioSymbol}
sort!(edits; by=x -> x.pos) sort!(edits; by=x -> x.pos)
result = Haplotype{S,T}(ref, edits, Unsafe()) result = Haplotype{S,T}(ref, edits, Unsafe())
_is_valid(result) || error("TODO") # report what kind of error message? valid, message = _is_valid(result)
valid || error(message)
return result return result
end end
@ -62,11 +63,12 @@ function _is_valid(h::Haplotype)
op = edit.x op = edit.x
# Sanity check: for this to be a valid variant, it must be comprised of valid # Sanity check: for this to be a valid variant, it must be comprised of valid
# variations # variations
_is_valid(Variation(h.ref, edit)) || return false _is_valid(Variation(h.ref, edit)) || return (false, "Invalid Variation")
# For substitutions we simply do not allow another modification of the same base # For substitutions we simply do not allow another modification of the same base
if op isa Substitution if op isa Substitution
pos in valid_positions || return false pos in valid_positions ||
return (false, "Multiple modifications at same position")
valid_positions = (first(valid_positions) + 1):last(valid_positions) valid_positions = (first(valid_positions) + 1):last(valid_positions)
last_was_insert = false last_was_insert = false
# Insertions affect 0 reference bases, so it does not modify the valid positions # Insertions affect 0 reference bases, so it does not modify the valid positions
@ -75,18 +77,18 @@ function _is_valid(h::Haplotype)
elseif op isa Insertion elseif op isa Insertion
pos in pos in
((first(valid_positions) - 1 + last_was_insert):(last(valid_positions) + 1)) || ((first(valid_positions) - 1 + last_was_insert):(last(valid_positions) + 1)) ||
return false return (false, "Multiple insertions at same position")
last_was_insert = true last_was_insert = true
# Deletions obviously invalidate the reference bases that are deleted. # Deletions obviously invalidate the reference bases that are deleted.
elseif op isa Deletion elseif op isa Deletion
len = length(op) len = length(op)
pos in (first(valid_positions):(last(valid_positions) - len + 1)) || pos in (first(valid_positions):(last(valid_positions) - len + 1)) ||
return false return (false, "Deletion out of range")
valid_positions = (first(valid_positions) + len):last(valid_positions) valid_positions = (first(valid_positions) + len):last(valid_positions)
last_was_insert = false last_was_insert = false
end end
end end
return true return (true, "")
end end
function Haplotype( function Haplotype(