From a80ff869ce1243a2c832abebbfc26fcf6c97fc24 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 11 Jul 2022 12:53:35 -0500
Subject: [PATCH 01/11] Fix reference(::Variation)

`reference(::Variation)` used the wrong field name. Fix that so I can use
it downstream.
---
 src/SequenceVariation.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 06c8aa7..aeae059 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -367,7 +367,7 @@ function Variation(ref::S, edit::AbstractString) where {S<:BioSequence}
     return Variation{S,T}(ref, e)
 end
 
-reference(v::Variation) = v.reference
+reference(v::Variation) = v.ref
 edit(v::Variation) = v.edit
 mutation(v::Variation) = mutation(edit(v))
 BioGenerics.leftposition(v::Variation) = leftposition(edit(v))

From 73c2c2764f520e8e2b963bfae6b6371fd1c2c0fe Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 11 Jul 2022 12:50:20 -0500
Subject: [PATCH 02/11] Add private reference base getter for Substitution

---
 src/SequenceVariation.jl | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index aeae059..b7d6fb8 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -464,6 +464,10 @@ function variations(v::Variant)
     return vs
 end
 
+function _refbases(s::Substitution, reference::S, pos::UInt) where S <: BioSequence
+    return S([reference[pos]])
+end
+
 export Insertion,
     Deletion,
     Substitution,

From c1f47c7b223ff789091b170b4e8ce48e7d69bbb4 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 11 Jul 2022 12:50:40 -0500
Subject: [PATCH 03/11] Add private alternate base getter for Substitution

---
 src/SequenceVariation.jl | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index b7d6fb8..785384a 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -468,6 +468,10 @@ function _refbases(s::Substitution, reference::S, pos::UInt) where S <: BioSeque
     return S([reference[pos]])
 end
 
+function _altbases(s::Substitution, reference::S, pos::UInt) where S <: BioSequence
+    return S([s.x])
+end
+
 export Insertion,
     Deletion,
     Substitution,

From bc073eaf20b807cb4c4be8a36f6b5c5eda069bc0 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 11 Jul 2022 12:51:13 -0500
Subject: [PATCH 04/11] Add private reference base getter for Deletion

---
 src/SequenceVariation.jl | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 785384a..8ad2972 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -472,6 +472,14 @@ function _altbases(s::Substitution, reference::S, pos::UInt) where S <: BioSeque
     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))])
+    else
+        return S(reference[UnitRange{Int}(pos-1, pos+length(d)-1)])
+    end
+end
+
 export Insertion,
     Deletion,
     Substitution,

From 145e9e5f8853072c47b3cd004d0a3783810c9372 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 11 Jul 2022 12:51:35 -0500
Subject: [PATCH 05/11] Add private alternate base getter for Deletion

---
 src/SequenceVariation.jl | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 8ad2972..3bb4f73 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -480,6 +480,14 @@ function _refbases(d::Deletion, reference::S, pos::UInt) where S <: BioSequence
     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
+
 export Insertion,
     Deletion,
     Substitution,

From 1b7c7f86d78ef68020810595e273515e018b2273 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 11 Jul 2022 12:51:58 -0500
Subject: [PATCH 06/11] Add private reference base getter for Insertion

---
 src/SequenceVariation.jl | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 3bb4f73..6ae7b54 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -488,6 +488,10 @@ function _altbases(d::Deletion, reference::S, pos::UInt) where S <: BioSequence
     end
 end
 
+function _refbases(i::Insertion, reference::S, pos::UInt) where S <: BioSequence
+    return S([reference[pos]])
+end
+
 export Insertion,
     Deletion,
     Substitution,

From ccbe6eed62ff2c96b115323d50d6faaa70655cf3 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 11 Jul 2022 12:52:16 -0500
Subject: [PATCH 07/11] Add private alternate base getter for Insertion

---
 src/SequenceVariation.jl | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 6ae7b54..7012c33 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -492,6 +492,14 @@ function _refbases(i::Insertion, reference::S, pos::UInt) where S <: BioSequence
     return S([reference[pos]])
 end
 
+function _altbases(i::Insertion, reference::S, pos::UInt) where S <: BioSequence
+    if pos == 1
+        return S([i.seq..., reference[pos]])
+    else
+        return S([reference[pos], i.seq...])
+    end
+end
+
 export Insertion,
     Deletion,
     Substitution,

From cab314ec0baaa8b076cea5b8cbcfd86ce0aa71b1 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 11 Jul 2022 12:54:51 -0500
Subject: [PATCH 08/11] Add public reference base getter for Variation

---
 src/SequenceVariation.jl | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 7012c33..ca5b1f9 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -500,6 +500,10 @@ function _altbases(i::Insertion, reference::S, pos::UInt) where S <: BioSequence
     end
 end
 
+function refbases(v::Variation)
+    return _refbases(mutation(v), reference(v), leftposition(v))
+end
+
 export Insertion,
     Deletion,
     Substitution,
@@ -507,6 +511,7 @@ export Insertion,
     Variation,
     reference,
     mutation,
-    variations
+    variations,
+    refbases
 
 end # module

From b8e44c7b815f2021fddc022822737f02a46503e3 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 11 Jul 2022 12:56:33 -0500
Subject: [PATCH 09/11] Add public alternate base getter for Variation

---
 src/SequenceVariation.jl | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index ca5b1f9..0237a15 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -504,6 +504,10 @@ function refbases(v::Variation)
     return _refbases(mutation(v), reference(v), leftposition(v))
 end
 
+function altbases(v::Variation)
+    return _altbases(mutation(v), reference(v), leftposition(v))
+end
+
 export Insertion,
     Deletion,
     Substitution,
@@ -512,6 +516,7 @@ export Insertion,
     reference,
     mutation,
     variations,
-    refbases
+    refbases,
+    altbases
 
 end # module

From 97e1d193a64b06f298c990076dc83aeaf3b87e44 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 7 Jul 2022 10:38:15 -0500
Subject: [PATCH 10/11] Add VCF spec tests for reference and alternate bases

---
 test/runtests.jl | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/test/runtests.jl b/test/runtests.jl
index cad0d7f..9982a55 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -69,3 +69,33 @@ end
     sub = Variation(refseq, "A4T")
     @test first(variations(var)) == sub
 end
+
+@testset "VariationBases" begin
+    # Test substition bases
+    @test refbases(Variation(dna"ATCGA", "C3G")) == dna"C"
+    @test altbases(Variation(dna"ATCGA", "C3G")) == dna"G"
+
+    # Test single deletion bases
+    @test refbases(Variation(dna"ATCGA", "Δ3-3")) == dna"TC"
+    @test altbases(Variation(dna"ATCGA", "Δ3-3")) == dna"T"
+
+    # Test multiple deletion bases
+    @test refbases(Variation(dna"ATCGA", "Δ3-4")) == dna"TCG"
+    @test altbases(Variation(dna"ATCGA", "Δ3-4")) == dna"T"
+
+    # Test first position deletion
+    @test refbases(Variation(dna"ATCGA", "Δ1-1")) == dna"AT"
+    @test altbases(Variation(dna"ATCGA", "Δ1-1")) == dna"T"
+
+    # Test single insertion bases
+    @test refbases(Variation(dna"ATCGA", "3A")) == dna"C"
+    @test altbases(Variation(dna"ATCGA", "3A")) == dna"CA"
+
+    # Test multiple insertion bases
+    @test refbases(Variation(dna"ATCGA", "3TAG")) == dna"C"
+    @test altbases(Variation(dna"ATCGA", "3TAG")) == dna"CTAG"
+
+    # Test first position insertion
+    @test refbases(Variation(dna"ATCGA", "1C")) == dna"A"
+    @test altbases(Variation(dna"ATCGA", "1C")) == dna"CA"
+end

From 1cfe128070f55c582688abf11ce081cc7112ee52 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 13 Jul 2022 16:52:11 -0500
Subject: [PATCH 11/11] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 61da4e8..802a674 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,5 +14,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `Variation` type to store and compare individual mutations
 - `reconstruct!` function to build mutated sequences from `Variant`s
 - `Variant` constructor to automatically detect mutations from a `BioAlignments.PairwiseAlignment`
+- Methods to get reference and alternate bases from a `Variation`
 
 [unreleased]: https://github.com/BioJulia/SequenceVariation.jl