fix issue in WFBacktrace and change format to proper CIGAR,

add test to ensure CIGAR correctness in the case of different traceback results,
add DecodeCIGAR function to exports

pkg/utils.go

@@ -2,11 +2,55 @@ package wfa
 
 import (
 	"math"
-	"unicode/utf8"
+	"strings"
 
 	"golang.org/x/exp/constraints"
 )
 
+func UIntToString(num uint) string { // num assumed to be positive
+	var builder strings.Builder
+
+	for num > 0 {
+		digit := num % 10
+		builder.WriteRune(rune('0' + digit))
+		num /= 10
+	}
+
+	// Reverse the string as we built it in reverse order
+	str := []rune(builder.String())
+	for i, j := 0, len(str)-1; i < j; i, j = i+1, j-1 {
+		str[i], str[j] = str[j], str[i]
+	}
+
+	return string(str)
+}
+
+func RunLengthDecode(encoded string) string {
+	decoded := strings.Builder{}
+	length := len(encoded)
+	i := 0
+
+	for i < length {
+		// If the current character is a digit, we need to extract the run length
+		runLength := 0
+		for i < length && encoded[i] >= '0' && encoded[i] <= '9' {
+			runLength = runLength*10 + int(encoded[i]-'0')
+			i++
+		}
+
+		// The next character will be the character to repeat
+		if i < length {
+			char := encoded[i]
+			for j := 0; j < runLength; j++ {
+				decoded.WriteByte(char)
+			}
+			i++ // Move past the character
+		}
+	}
+
+	return decoded.String()
+}
+
 func SafeMin[T constraints.Integer](values []T, idx int) T {
 	return values[idx]
 }
@@ -51,21 +95,6 @@ func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
 	}
 }
 
-func Reverse(s string) string {
-	size := len(s)
-	buf := make([]byte, size)
-	for start := 0; start < size; {
-		r, n := utf8.DecodeRuneInString(s[start:])
-		start += n
-		utf8.EncodeRune(buf[size-start:], r)
-	}
-	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
@@ -117,11 +146,8 @@ func NextD(M WavefrontComponent, D WavefrontComponent, score int, k int, penalti
 	a_ok, a, _ := M.GetVal(score-o-e, k+1)
 	b_ok, b, _ := D.GetVal(score-e, k+1)
 
-	ok, nextDTraceback := SafeArgMax(
-		[]bool{a_ok, b_ok},
-		[]uint32{a, b},
-	)
-	nextDVal := SafeMax([]uint32{a, b}, nextDTraceback) // nothing special
+	ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint32{a, b})
+	nextDVal := SafeMax([]uint32{a, b}, nextDTraceback)
 	if ok {
 		D.SetVal(score, k, nextDVal, []Traceback{OpenDel, ExtdDel}[nextDTraceback])
 	}
@@ -137,7 +163,6 @@ func NextM(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, sco
 
 	ok, nextMTraceback := SafeArgMax([]bool{a_ok, b_ok, c_ok}, []uint32{a, b, c})
 	nextMVal := SafeMax([]uint32{a, b, c}, nextMTraceback)
-
 	if ok {
 		M.SetVal(score, k, nextMVal, []Traceback{Sub, Ins, Del}[nextMTraceback])
 	}