From c3a7788dbd3e5881877c3e5bba5ce19eb0b8959c Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 4 Apr 2023 11:30:59 -0500
Subject: [PATCH] feat: Add _cigar(::Variation) function

Add a function that can convert the information contained in an
Insertion or a Deletion into a CIGAR operator.
---
 src/Variation.jl | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/Variation.jl b/src/Variation.jl
index 8af22bd..af9f4df 100644
--- a/src/Variation.jl
+++ b/src/Variation.jl
@@ -120,6 +120,21 @@ function Base.in(v::Variation, var::Haplotype)
     return any(v.edit == edit for edit in var.edits)
 end
 
+"""
+    _cigar(var::Variation{S,T}) where {S,T}
+
+Returns a CIGAR operation for `var`. Only supports insertions and deletions.
+
+See also [`_cigar_between`](@ref)
+"""
+function _cigar(var::Variation{S,T}) where {S,T}
+    mut = mutation(var)
+    mut isa Union{Deletion,Insertion} ||
+        throw(ArgumentError("var must be an Insertion or Deletion"))
+    cigar_letter = mut isa Deletion ? 'D' : 'I'
+    return string(length(mut), cigar_letter)
+end
+
 """
     translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}