From cb1c429610e214de017cb57726ecc539669dc24b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 3 Jan 2023 15:01:31 -0600
Subject: [PATCH] Update getter usage in translate function

---
 src/SequenceVariation.jl | 2 +-
 src/Variation.jl         | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 10f0839..c3b476b 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -20,7 +20,7 @@ TODO now:
 * Add tests
 """
 
-using BioAlignments: BioAlignments, PairwiseAlignment, OP_SOFT_CLIP
+using BioAlignments: BioAlignments, PairwiseAlignment, OP_SOFT_CLIP, sequence
 using BioGenerics: BioGenerics, leftposition, rightposition
 using BioSequences: BioSequences, BioSequence, NucleotideSeq, LongSequence, isgap
 using BioSymbols: BioSymbol
diff --git a/src/Variation.jl b/src/Variation.jl
index 9f0ac17..6f70e90 100644
--- a/src/Variation.jl
+++ b/src/Variation.jl
@@ -71,9 +71,10 @@ function Base.in(v::Variation, var::Variant)
 end
 
 function translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
-    kind = var.edit.x
-    pos = var.edit.pos
-    seq, ref = aln.seq, aln.b
+    kind = mutation(var)
+    pos = leftposition(var)
+    seq = sequence(aln)
+    ref = aln.b
 
     # Special case: Insertions may have a pos of 0, which cannot be mapped to
     # the seq using ref2seq