From b80dd8c9501cff1e87760233f77cc823b7069ae5 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 5 Jan 2023 12:32:54 -0600
Subject: [PATCH] Rename reconstruct! function to reconstruct

The exclamation mark is conventionally used to mark mutating functions, but
reconstruct is no longer mutating, so change the notation.
---
 docs/src/api.md          | 2 +-
 docs/src/haplotypes.md   | 4 ++--
 src/Haplotype.jl         | 4 ++--
 src/SequenceVariation.jl | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/src/api.md b/docs/src/api.md
index 693b315..8dcb67a 100644
--- a/docs/src/api.md
+++ b/docs/src/api.md
@@ -21,7 +21,7 @@ Insertion
 Haplotype
 reference(::Haplotype)
 variations
-reconstruct!
+reconstruct
 ```
 
 ## Variations
diff --git a/docs/src/haplotypes.md b/docs/src/haplotypes.md
index 251670a..fe47bfe 100644
--- a/docs/src/haplotypes.md
+++ b/docs/src/haplotypes.md
@@ -31,11 +31,11 @@ bos_human_haplotype = Haplotype(bos_human_alignment)
 
 If the alternate sequence of a haplotype is no longer available (as is often the
 case when calling variants from alignment files), then the sequence can be
-retrieved using the [`reconstruct!`](@ref) function.
+retrieved using the [`reconstruct`](@ref) function.
 
 ```@repl call_variants
 human2 = copy(bovine);
-reconstruct!(human2, bos_human_haplotype)
+reconstruct(human2, bos_human_haplotype)
 human2 == bovine
 human2 == human
 ```
diff --git a/src/Haplotype.jl b/src/Haplotype.jl
index 7a4842b..fc36362 100644
--- a/src/Haplotype.jl
+++ b/src/Haplotype.jl
@@ -162,11 +162,11 @@ reference(h::Haplotype) = h.ref
 Base.:(==)(x::Haplotype, y::Haplotype) = x.ref == y.ref && x.edits == y.edits
 
 """
-    reconstruct!(h::Haplotype)
+    reconstruct(h::Haplotype)
 
 Apply the edits in `h` to the reference sequence of `h` and return the mutated sequence
 """
-function reconstruct!(h::Haplotype)
+function reconstruct(h::Haplotype)
     len = length(reference(h)) + sum(edit -> _lendiff(edit), _edits(h))
     seq = copy(reference(h))
     resize!(seq, len % UInt)
diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 93305e6..0e8cadd 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -32,7 +32,7 @@ export Substitution
 export Variation
 export altbases
 export mutation
-export reconstruct!
+export reconstruct
 export refbases
 export reference
 export translate