From ade9b7e41d2f28bc36850ed4c1e72d7e913e8937 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Fri, 6 May 2022 05:26:49 -0500
Subject: [PATCH] Fix inconsistent Variation positions (#4)

* Change Variant constructor to use alignment positions

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>

* Add test for positions of Variations

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
---
 src/SequenceVariation.jl |  3 ++-
 test/runtests.jl         | 13 ++++++++++++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 8b4ea6e..b8a630a 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -242,7 +242,8 @@ function Variant(aln::PairwiseAlignment{T, T}) where {T <: LongSequence{<:Union{
     E = eltype(typeof(ref))
     edits = Edit{T, E}[]
     result = Variant(ref, edits)
-    refpos = seqpos = 0
+    refpos = first(aln.a.aln.anchors).refpos
+    seqpos = first(aln.a.aln.anchors).seqpos
     markpos = 0
     n_gaps = n_ins = 0
     insertion_buffer = E[]
diff --git a/test/runtests.jl b/test/runtests.jl
index 89947cd..78e4d0b 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -32,4 +32,15 @@ const DNA_MODEL = BioAlignments.AffineGapScoreModel(EDNAFULL, gap_open=-25, gap_
 align(a::BioSequence, b::BioSequence) = pairalign(GlobalAlignment(), a, b, DNA_MODEL).aln
 seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG")
 seq2 = ungap!(dna"TGATGCGTGT-AGCAACACTTATAGCG")
-var = Variant(align(seq1, seq2))
\ No newline at end of file
+var = Variant(align(seq1, seq2))
+
+@testset "VariationPosition" begin
+    refseq = dna"ACAACTTTATCT"
+    mutseq = dna"ACATCTTTATCT"
+
+    read01 = AlignedSequence(mutseq[1:10], Alignment("10M", 1, 1))
+    read02 = AlignedSequence(mutseq[3:12], Alignment("10M", 1, 3))
+    aln01 = PairwiseAlignment(read01, refseq)
+    aln02 = PairwiseAlignment(read02, refseq)
+    @test Variant(aln01).edits == Variant(aln02).edits
+end