From ba9f0e8fb155b810771ea6261b6526145d8e6215 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Fri, 30 Dec 2022 14:35:55 -0600
Subject: [PATCH] Move Substitution-related code to edits/Substitution.jl

---
 src/Edit.jl               | 20 +-------------------
 src/edits/Substitution.jl | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+), 19 deletions(-)
 create mode 100644 src/edits/Substitution.jl

diff --git a/src/Edit.jl b/src/Edit.jl
index ecf2094..35dc062 100644
--- a/src/Edit.jl
+++ b/src/Edit.jl
@@ -1,14 +1,4 @@
-"""
-    Substitution
-
-Represents the presence of a `T` at a given position. The position is stored
-outside this struct.
-"""
-struct Substitution{T<:BioSymbol}
-    x::T
-end
-Base.:(==)(x::Substitution, y::Substitution) = x.x == y.x
-Base.hash(x::Substitution, h::UInt) = hash(Substitution, hash(x.x, h))
+include("edits/Substitution.jl")
 
 """
     Deletion
@@ -105,14 +95,6 @@ function lendiff(edit::Edit)
     return x isa Substitution ? 0 : (x isa Deletion ? -length(x) : length(x.x))
 end
 
-function _refbases(s::Substitution, reference::S, pos::UInt) where {S<:BioSequence}
-    return S([reference[pos]])
-end
-
-function _altbases(s::Substitution, reference::S, pos::UInt) where {S<:BioSequence}
-    return S([s.x])
-end
-
 function _refbases(d::Deletion, reference::S, pos::UInt) where {S<:BioSequence}
     if pos == 1
         return S(reference[UnitRange{Int}(pos, pos + length(d))])
diff --git a/src/edits/Substitution.jl b/src/edits/Substitution.jl
new file mode 100644
index 0000000..e8101da
--- /dev/null
+++ b/src/edits/Substitution.jl
@@ -0,0 +1,20 @@
+"""
+    Substitution
+
+Represents the presence of a `T` at a given position. The position is stored
+outside this struct.
+"""
+struct Substitution{T<:BioSymbol}
+    x::T
+end
+
+Base.:(==)(x::Substitution, y::Substitution) = x.x == y.x
+Base.hash(x::Substitution, h::UInt) = hash(Substitution, hash(x.x, h))
+
+function _refbases(s::Substitution, reference::S, pos::UInt) where {S<:BioSequence}
+    return S([reference[pos]])
+end
+
+function _altbases(s::Substitution, reference::S, pos::UInt) where {S<:BioSequence}
+    return S([s.x])
+end