From e84f765357f4ff4fed39260d063f366395561af9 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 4 Apr 2023 11:32:21 -0500
Subject: [PATCH] feat: Add _cigar_between(::Variation, ::Variation) function

Add a function that can calculate the matching bases between two
(non-matching) Variations and return a matching (M) CIGAR operation
---
 src/Variation.jl | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/src/Variation.jl b/src/Variation.jl
index af9f4df..851650a 100644
--- a/src/Variation.jl
+++ b/src/Variation.jl
@@ -135,6 +135,26 @@ function _cigar(var::Variation{S,T}) where {S,T}
     return string(length(mut), cigar_letter)
 end
 
+"""
+    _cigar_between(x::Variation{S,T}, y::Variation{S,T}) where {S,T}
+
+Returns a CIGAR operation for the (assumed) matching bases between `x` and `y`.
+
+See also [`_cigar`](@ref)
+"""
+function _cigar_between(x::Variation{S,T}, y::Variation{S,T}) where {S,T}
+    x == y && return ""
+    match_length = leftposition(y) - rightposition(x)
+    if mutation(y) isa Insertion
+        match_length -= 1
+    end
+    if mutation(y) isa Deletion
+        match_length += 1
+    end
+    match_length > 0 || return ""
+    return "$(match_length)M"
+end
+
 """
     translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}