Refactor `reconstruct!` to use the built-in reference sequence

reconstruct! previously allow changing of _any_ sequence to match a
haplotype, with no check to see if that sequence is compatible with the
reference sequence the haplotype is based on. Change that to only allow
reconstructing sequences from the reference sequence itself, making this a
non-mutating function.

src/Haplotype.jl

@@ -162,21 +162,22 @@ reference(h::Haplotype) = h.ref
 Base.:(==)(x::Haplotype, y::Haplotype) = x.ref == y.ref && x.edits == y.edits
 
 """
-    reconstruct!(seq::S, x::Haplotype{S}) where {S}
+    reconstruct!(h::Haplotype)
 
-Apply the edits in `x` to `seq` and return the mutated sequence
+Apply the edits in `h` to the reference sequence of `h` and return the mutated sequence
 """
-function reconstruct!(seq::S, x::Haplotype{S}) where {S}
-    len = length(x.ref) + sum(edit -> _lendiff(edit), _edits(x))
+function reconstruct!(h::Haplotype)
+    len = length(reference(h)) + sum(edit -> _lendiff(edit), _edits(h))
+    seq = copy(reference(h))
     resize!(seq, len % UInt)
     refpos = seqpos = 1
-    for edit in x.edits
-        while refpos < edit.pos
-            seq[seqpos] = x.ref[refpos]
+    for edit in _edits(h)
+        while refpos < leftposition(edit)
+            seq[seqpos] = reference(h)[refpos]
             refpos += 1
             seqpos += 1
         end
-        editx = edit.x
+        editx = _mutation(edit)
         if editx isa Substitution
             seq[seqpos] = editx.x
             seqpos += 1
@@ -184,14 +185,14 @@ function reconstruct!(seq::S, x::Haplotype{S}) where {S}
         elseif editx isa Deletion
             refpos += editx.len
         elseif editx isa Insertion
-            for i in editx.x
+            for i in editx.seq
                 seq[seqpos] = i
                 seqpos += 1
             end
         end
     end
     while seqpos ≤ length(seq)
-        seq[seqpos] = x.ref[refpos]
+        seq[seqpos] = reference(h)[refpos]
         refpos += 1
         seqpos += 1
     end