millironx/SequenceVariation.jl
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Add Variation-level validation for Variants

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Testing indicates that some Variants (particularly those with insertions
and/or clips at the send of the query sequence) will validate fine as a
Variant, but will fail validation as a Variation. This problem is
particularly annoying when constructing Variants in the REPL, as the
creation will complete successfully, but the show of the Variant will
error out. To fix this, leverage the existing validation of Variation to
check each Edit within a Variant upon construction.
This commit is contained in:
Thomas A. Christensen II 2022-12-06 11:04:23 -06:00
parent 91c3acc85e
commit d8435be115
1 changed files with 4 additions and 0 deletions
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src/SequenceVariation.jl
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@ -233,6 +233,10 @@ function is_valid(v::Variant)
for edit in v.edits for edit in v.edits
pos = edit.pos pos = edit.pos
op = edit.x op = edit.x
# Sanity check: for this to be a valid variant, it must be comprised of valid
# variations
is_valid(Variation(v.ref, edit)) || return false
# 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