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

test/wfa_test.go

@@ -3,6 +3,7 @@ package tests
 import (
 	"bufio"
 	"encoding/json"
+	"log"
 	"math/rand/v2"
 	"os"
 	"strconv"
@@ -46,6 +47,71 @@ func TestWavefrontPacking(t *testing.T) {
 	}
 }
 
+func GetScoreFromCIGAR(CIGAR string, penalties wfa.Penalty) int {
+	unpackedCIGAR := wfa.RunLengthDecode(CIGAR)
+	previousOp := '~'
+	score := 0
+	for _, Op := range unpackedCIGAR {
+		if Op == 'M' {
+			score = score + penalties.M
+		} else if Op == 'X' {
+			score = score + penalties.X
+		} else if (Op == 'I' && previousOp != 'I') || (Op == 'D' && previousOp != 'D') {
+			score = score + penalties.O + penalties.E
+		} else if (Op == 'I' && previousOp == 'I') || (Op == 'D' && previousOp == 'D') {
+			score = score + penalties.E
+		}
+		previousOp = Op
+	}
+	return score
+}
+
+func CheckCIGARCorrectness(s1 string, s2 string, CIGAR string) bool {
+	unpackedCIGAR := wfa.RunLengthDecode(CIGAR)
+	i := 0
+	j := 0
+
+	s1Aligned := strings.Builder{}
+	alignment := strings.Builder{}
+	s2Aligned := strings.Builder{}
+
+	for c := 0; c < len(unpackedCIGAR); c++ {
+		Op := unpackedCIGAR[c]
+		if Op == 'M' {
+			s1Aligned.WriteByte(s1[i])
+			alignment.WriteRune('|')
+			s2Aligned.WriteByte(s2[j])
+			i++
+			j++
+		} else if Op == 'X' {
+			s1Aligned.WriteByte(s1[i])
+			alignment.WriteRune(' ')
+			s2Aligned.WriteByte(s2[j])
+			i++
+			j++
+		} else if Op == 'I' {
+
+			s1Aligned.WriteRune('-')
+			alignment.WriteRune(' ')
+			s2Aligned.WriteByte(s2[j])
+
+			j++
+		} else if Op == 'D' {
+			s1Aligned.WriteByte(s1[i])
+			alignment.WriteRune('|')
+			s2Aligned.WriteRune('-')
+			i++
+		}
+	}
+
+	if i == len(s1) && j == len(s2) {
+		return true
+	} else {
+		log.Printf("\n%s\n%s\n%s\n i=%d, j=%d, |s1|=%d, |s2|=%d\n", s1Aligned.String(), alignment.String(), s2Aligned.String(), i, j, len(s1), len(s2))
+		return false
+	}
+}
+
 func TestWFA(t *testing.T) {
 	content, _ := os.ReadFile(testJsonPath)
 
@@ -73,7 +139,9 @@ func TestWFA(t *testing.T) {
 
 		for solutions.Scan() {
 			solution := solutions.Text()
+
 			expectedScore, _ := strconv.Atoi(strings.Split(solution, "\t")[0])
+			expectedCIGAR := strings.Split(solution, "\t")[1]
 
 			sequences.Scan()
 			s1 := sequences.Text()
@@ -85,9 +153,25 @@ func TestWFA(t *testing.T) {
 
 			x := wfa.WFAlign(s1, s2, testPenalties, true)
 			gotScore := x.Score
+			gotCIGAR := x.CIGAR
 
 			if gotScore != -1*expectedScore {
-				t.Errorf(`test: %s#%d, s1: %s, s2: %s, got: %d, expected: %d\n`, testName, idx, s1, s2, gotScore, expectedScore)
+				t.Errorf(`test: %s#%d, s1: %s, s2: %s, got: %d, expected: %d`, testName, idx, s1, s2, gotScore, expectedScore)
+				os.Exit(1)
+			}
+
+			if gotCIGAR != expectedCIGAR {
+				checkScore := GetScoreFromCIGAR(gotCIGAR, testPenalties)
+				CIGARCorrectness := CheckCIGARCorrectness(s1, s2, gotCIGAR)
+				if checkScore != gotScore && checkScore != -1*expectedScore { // nonequivalent alignment
+					t.Errorf(`test: %s#%d, s1: %s, s2: %s, got: [%s], expected: [%s]`, testName, idx, s1, s2, gotCIGAR, expectedCIGAR)
+					t.Errorf(`test: %s#%d, recalculated score: %d`, testName, idx, checkScore)
+					os.Exit(1)
+				}
+				if !CIGARCorrectness {
+					t.Errorf(`test: %s#%d, s1: %s, s2: %s, got: [%s], expected: [%s]`, testName, idx, s1, s2, gotCIGAR, expectedCIGAR)
+					os.Exit(1)
+				}
 			}
 
 			idx++