From 5ffb11439ea80d5e5bd180711bf91c0b7cf5e9b3 Mon Sep 17 00:00:00 2001
From: Alexey Stukalov <astukalov@gmail.com>
Date: Tue, 22 Sep 2020 20:48:01 +0200
Subject: [PATCH] count_aligned(): optimize with agnpos

---
 src/pairwise/alignment.jl | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/src/pairwise/alignment.jl b/src/pairwise/alignment.jl
index 4e7989c5..0ddf572b 100644
--- a/src/pairwise/alignment.jl
+++ b/src/pairwise/alignment.jl
@@ -118,16 +118,7 @@ Count the number of aligned positions.
 """
 function count_aligned(aln::PairwiseAlignment)
     anchors = aln.a.aln.anchors
-    n = 0
-    for i in 2:lastindex(anchors)
-        op = anchors[i].op
-        if ismatchop(op) || isinsertop(op)
-            n += anchors[i].seqpos - anchors[i-1].seqpos
-        elseif isdeleteop(op)
-            n += anchors[i].refpos - anchors[i-1].refpos
-        end
-    end
-    return n
+    return isempty(anchors) ? 0 : last(anchors).agnpos
 end
 
 seq2ref(aln::PairwiseAlignment, i::Integer) = seq2ref(aln.a, i)