From 4817c8016add1e47e88f8eff9782407488d38a90 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 4 Apr 2023 11:50:24 -0500
Subject: [PATCH] feat: Add alignment(::Haplotype) function

---
 src/Haplotype.jl         | 11 +++++++++++
 src/SequenceVariation.jl | 10 +++++++++-
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/Haplotype.jl b/src/Haplotype.jl
index f5cf985..9164455 100644
--- a/src/Haplotype.jl
+++ b/src/Haplotype.jl
@@ -250,6 +250,17 @@ function BioAlignments.cigar(hap::Haplotype{S,T}) where {S,T}
     return join(cigar_string, "")
 end
 
+"""
+    alignment(hap::Haplotype)
+
+Gets a `PairwiseAlignment` of the mutated sequence of `hap` mapped to its refernce sequence
+"""
+function BioAlignments.alignment(hap::Haplotype)
+    return PairwiseAlignment(
+        AlignedSequence(reconstruct(hap), Alignment(cigar(hap))), reference(hap)
+    )
+end
+
 """
     translate(hap::Haplotype{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}
 
diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 37b0a42..e8e7210 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -20,7 +20,15 @@ TODO now:
 * Add tests
 """
 
-using BioAlignments: BioAlignments, PairwiseAlignment, OP_SOFT_CLIP, cigar, sequence
+using BioAlignments:
+    BioAlignments,
+    Alignment,
+    AlignedSequence,
+    PairwiseAlignment,
+    OP_SOFT_CLIP,
+    alignment,
+    cigar,
+    sequence
 using BioGenerics: BioGenerics, leftposition, rightposition
 using BioSequences: BioSequences, BioSequence, NucleotideSeq, LongSequence, isgap
 using BioSymbols: BioSymbol