From ba978f425cd527b3b02f0940cdf3c0aec3ea5f6c Mon Sep 17 00:00:00 2001
From: Arthur Lu <root@tronnet.net>
Date: Tue, 5 Nov 2024 19:24:07 +0000
Subject: [PATCH] minor optimization to traceback

---
 pkg/utils.go |  4 ----
 pkg/wfa.go   | 18 ++++++++++++------
 2 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/pkg/utils.go b/pkg/utils.go
index a806159..deb4e76 100644
--- a/pkg/utils.go
+++ b/pkg/utils.go
@@ -62,10 +62,6 @@ func Reverse(s string) string {
 	return string(buf)
 }
 
-func Splice(s string, c rune, idx int) string {
-	return s[:idx] + string(c) + s[idx:]
-}
-
 func NextLoHi(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) (int, int) {
 	x := penalties.X
 	o := penalties.O
diff --git a/pkg/wfa.go b/pkg/wfa.go
index 1bc52d5..1aad469 100644
--- a/pkg/wfa.go
+++ b/pkg/wfa.go
@@ -1,5 +1,9 @@
 package wfa
 
+import (
+	"strings"
+)
+
 func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 	n := len(s1)
 	m := len(s2)
@@ -115,28 +119,30 @@ func WFBacktrace(M WavefrontComponent, I WavefrontComponent, D WavefrontComponen
 	}
 
 	CIGAR_part := Reverse(CIGAR_rev)
+	CIGAR_full := strings.Builder{}
 	c := 0
 	i := 0
 	j := 0
-	for i < len(s1) && j < len(s2) {
-		if s1[i] == s2[j] {
-			//CIGAR_part.splice(c, 0, "M")
-			CIGAR_part = Splice(CIGAR_part, 'M', c)
-			c++
+	for (i < len(s1) && j < len(s2)) || (c < len(CIGAR_part)) {
+		if i < len(s1) && j < len(s2) && s1[i] == s2[j] {
+			CIGAR_full.WriteByte('M')
 			i++
 			j++
 		} else if CIGAR_part[c] == 'X' {
+			CIGAR_full.WriteByte('X')
 			c++
 			i++
 			j++
 		} else if CIGAR_part[c] == 'I' {
+			CIGAR_full.WriteByte('I')
 			c++
 			j++
 		} else if CIGAR_part[c] == 'D' {
+			CIGAR_full.WriteByte('D')
 			c++
 			i++
 		}
 	}
 
-	return CIGAR_part
+	return CIGAR_full.String()
 }