From d8435be115d38d450a283f2ed4a8b212b192dce0 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 6 Dec 2022 11:04:23 -0600
Subject: [PATCH] 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.
---
 src/SequenceVariation.jl | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 18db51a..de19df1 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -233,6 +233,10 @@ function is_valid(v::Variant)
     for edit in v.edits
         pos = edit.pos
         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
         if op isa Substitution
             pos in valid_positions || return false