From 8a71715cd9fa3826da930f0caa965c109810232f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 4 Jan 2023 14:16:48 -0600
Subject: [PATCH] Change `v::Haplotype` function arguments to `h::Haplotype`

`v` made sense for a `Variant`, but doesn't for a `Haplotype`, so pretty
things up.
---
 src/Haplotype.jl | 26 +++++++++++++-------------
 src/Variation.jl | 12 ++++++------
 2 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/src/Haplotype.jl b/src/Haplotype.jl
index 7412331..b989186 100644
--- a/src/Haplotype.jl
+++ b/src/Haplotype.jl
@@ -48,21 +48,21 @@ function Base.show(io::IO, x::Haplotype)
 end
 
 """
-    is_valid(v::Haplotype)
+    is_valid(h::Haplotype)
 
-Validate `v`. `v` is invalid if any of its operations are out of bounds, or the same
+Validate `h`. `h` is invalid if any of its operations are out of bounds, or the same
 position is affected by multiple edits.
 """
-function _is_valid(v::Haplotype)
-    isempty(v.ref) && return false
-    valid_positions = 1:length(v.ref)
+function _is_valid(h::Haplotype)
+    isempty(h.ref) && return false
+    valid_positions = 1:length(h.ref)
     last_was_insert = false
-    for edit in v.edits
+    for edit in h.edits
         pos = edit.pos
         op = edit.x
         # Sanity check: for this to be a valid variant, it must be comprised of valid
         # variations
-        _is_valid(Variation(v.ref, edit)) || return false
+        _is_valid(Variation(h.ref, edit)) || return false
 
         # For substitutions we simply do not allow another modification of the same base
         if op isa Substitution
@@ -147,18 +147,18 @@ function Haplotype(
 end
 
 """
-    _edits(v::Haplotype)
+    _edits(h::Haplotype)
 
-Gets the [`Edit`](@ref)s that comprise `v`
+Gets the [`Edit`](@ref)s that comprise `h`
 """
-_edits(v::Haplotype) = v.edits
+_edits(h::Haplotype) = h.edits
 
 """
-    reference(v::Haplotype)
+    reference(h::Haplotype)
 
-Gets the reference sequence of `v`.
+Gets the reference sequence of `h`.
 """
-reference(v::Haplotype) = v.ref
+reference(h::Haplotype) = h.ref
 Base.:(==)(x::Haplotype, y::Haplotype) = x.ref == y.ref && x.edits == y.edits
 
 """
diff --git a/src/Variation.jl b/src/Variation.jl
index 5121707..9be5d3a 100644
--- a/src/Variation.jl
+++ b/src/Variation.jl
@@ -171,14 +171,14 @@ function translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
 end
 
 """
-    variations(v::Haplotype{S,T}) where {S,T}
+    variations(h::Haplotype{S,T}) where {S,T}
 
-Converts the [`Edit`](@ref)s of `v` into a vector of [`Variation`](@ref)s.
+Converts the [`Edit`](@ref)s of `h` into a vector of [`Variation`](@ref)s.
 """
-function variations(v::Haplotype{S,T}) where {S,T}
-    vs = Vector{Variation{S,T}}(undef, length(_edits(v)))
-    for (i, e) in enumerate(_edits(v))
-        vs[i] = Variation{S,T}(reference(v), e)
+function variations(h::Haplotype{S,T}) where {S,T}
+    vs = Vector{Variation{S,T}}(undef, length(_edits(h)))
+    for (i, e) in enumerate(_edits(h))
+        vs[i] = Variation{S,T}(reference(h), e)
     end
     return vs
 end