count_aligned(): optimize with alnpos

Author: alyst

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).alnpos
 end
 
 seq2ref(aln::PairwiseAlignment, i::Integer) = seq2ref(aln.a, i)