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Add Variation-level validation for Variants
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.
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@ -233,6 +233,10 @@ function is_valid(v::Variant)
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for edit in v.edits
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pos = edit.pos
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op = edit.x
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# Sanity check: for this to be a valid variant, it must be comprised of valid
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# variations
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is_valid(Variation(v.ref, edit)) || return false
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# For substitutions we simply do not allow another modification of the same base
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if op isa Substitution
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pos in valid_positions || return false
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