Move Deletion-related code to edits/Deletion.jl

src/Edit.jl

@@ -1,22 +1,5 @@
 include("edits/Substitution.jl")
-
+include("edits/Deletion.jl")
-"""
-    Deletion
-
-Represents the deletion of N symbols. The location of the deletion is stored
-outside this struct
-"""
-struct Deletion
-    len::UInt
-
-    function Deletion(len::UInt)
-        iszero(len) && error("Deletion must be at least 1 symbol")
-        return new(len)
-    end
-end
-Deletion(x::Integer) = Deletion(convert(UInt, x))
-Base.length(x::Deletion) = Int(x.len)
-Base.hash(x::Deletion, h::UInt) = hash(Deletion, hash(x.len, h))
 
 """
     Insertion{S <: BioSequence}
@@ -95,22 +78,6 @@ function lendiff(edit::Edit)
     return x isa Substitution ? 0 : (x isa Deletion ? -length(x) : length(x.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))])
-    else
-        return S(reference[UnitRange{Int}(pos - 1, pos + length(d) - 1)])
-    end
-end
-
-function _altbases(d::Deletion, reference::S, pos::UInt) where {S<:BioSequence}
-    if pos == 1
-        return S([reference[pos + 1]])
-    else
-        return S([reference[pos - 1]])
-    end
-end
-
 function _refbases(i::Insertion, reference::S, pos::UInt) where {S<:BioSequence}
     return S([reference[pos]])
 end

src/edits/Deletion.jl

@@ -0,0 +1,34 @@
+"""
+    Deletion
+
+Represents the deletion of N symbols. The location of the deletion is stored
+outside this struct
+"""
+struct Deletion
+    len::UInt
+
+    function Deletion(len::UInt)
+        iszero(len) && error("Deletion must be at least 1 symbol")
+        return new(len)
+    end
+end
+Deletion(x::Integer) = Deletion(convert(UInt, x))
+
+Base.length(x::Deletion) = Int(x.len)
+Base.hash(x::Deletion, h::UInt) = hash(Deletion, hash(x.len, h))
+
+function _refbases(d::Deletion, reference::S, pos::UInt) where {S<:BioSequence}
+    if pos == 1
+        return S(reference[UnitRange{Int}(pos, pos + length(d))])
+    else
+        return S(reference[UnitRange{Int}(pos - 1, pos + length(d) - 1)])
+    end
+end
+
+function _altbases(d::Deletion, reference::S, pos::UInt) where {S<:BioSequence}
+    if pos == 1
+        return S([reference[pos + 1]])
+    else
+        return S([reference[pos - 1]])
+    end
+end