rewrite in go and compile to wasm

pkg/wfa.go

@@ -0,0 +1,146 @@
+package wfa
+
+func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
+	n := len(s1)
+	m := len(s2)
+	A_k := m - n
+	A_offset := m
+	score := 0
+	M := NewWavefrontComponent()
+	M.SetVal(0, 0, 0)
+	M.SetHi(0, 0)
+	M.SetLo(0, 0)
+	M.SetTraceback(0, 0, End)
+	I := NewWavefrontComponent()
+	D := NewWavefrontComponent()
+
+	for {
+		WFExtend(M, s1, n, s2, m, score)
+		ok, val := M.GetVal(score, A_k)
+		if ok && val >= A_offset {
+			break
+		}
+		score = score + 1
+		WFNext(M, I, D, score, penalties)
+	}
+
+	CIGAR := ""
+	if doCIGAR {
+		CIGAR = WFBacktrace(M, I, D, score, penalties, A_k, s1, s2)
+	}
+
+	return Result{
+		Score: score,
+		CIGAR: CIGAR,
+	}
+}
+
+func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score int) {
+	_, lo := M.GetLo(score)
+	_, hi := M.GetHi(score)
+	for k := lo; k <= hi; k++ {
+		// v = M[score][k] - k
+		// h = M[score][k]
+		ok, h := M.GetVal(score, k)
+		v := h - k
+
+		// exit early if v or h are invalid
+		if !ok {
+			continue
+		}
+		for v < n && h < m && s1[v] == s2[h] {
+			_, val := M.GetVal(score, k)
+			M.SetVal(score, k, val+1)
+			v++
+			h++
+		}
+	}
+}
+
+func WFNext(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) {
+	// get this score's lo
+	lo := NextLo(M, I, D, score, penalties)
+
+	// get this score's hi
+	hi := NextHi(M, I, D, score, penalties)
+
+	for k := lo; k <= hi; k++ {
+		NextI(M, I, score, k, penalties)
+		NextD(M, D, score, k, penalties)
+		NextM(M, I, D, score, k, penalties)
+	}
+}
+
+func WFBacktrace(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty, A_k int, s1 string, s2 string) string {
+	traceback_CIGAR := []string{"I", "I", "D", "D", "X", "", "", ""}
+	x := penalties.X
+	o := penalties.O
+	e := penalties.E
+	CIGAR_rev := ""
+	tb_s := score
+	tb_k := A_k
+	_, current_traceback := M.GetTraceback(tb_s, tb_k)
+	done := false
+
+	for !done {
+		CIGAR_rev = CIGAR_rev + traceback_CIGAR[current_traceback]
+		switch current_traceback {
+		case OpenIns:
+			tb_s = tb_s - o - e
+			tb_k = tb_k - 1
+			_, current_traceback = M.GetTraceback(tb_s, tb_k)
+		case ExtdIns:
+			tb_s = tb_s - e
+			tb_k = tb_k - 1
+			_, current_traceback = I.GetTraceback(tb_s, tb_k)
+		case OpenDel:
+			tb_s = tb_s - o - e
+			tb_k = tb_k + 1
+			_, current_traceback = M.GetTraceback(tb_s, tb_k)
+		case ExtdDel:
+			tb_s = tb_s - e
+			tb_k = tb_k + 1
+			_, current_traceback = D.GetTraceback(tb_s, tb_k)
+		case Sub:
+			tb_s = tb_s - x
+			// tb_k = tb_k;
+			_, current_traceback = M.GetTraceback(tb_s, tb_k)
+		case Ins:
+			// tb_s = tb_s;
+			// tb_k = tb_k;
+			_, current_traceback = I.GetTraceback(tb_s, tb_k)
+		case Del:
+			// tb_s = tb_s;
+			// tb_k = tb_k;
+			_, current_traceback = D.GetTraceback(tb_s, tb_k)
+		case End:
+			done = true
+		}
+	}
+
+	CIGAR_part := Reverse(CIGAR_rev)
+	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++
+			i++
+			j++
+		} else if CIGAR_part[c] == 'X' {
+			c++
+			i++
+			j++
+		} else if CIGAR_part[c] == 'I' {
+			c++
+			j++
+		} else if CIGAR_part[c] == 'D' {
+			c++
+			i++
+		}
+	}
+
+	return CIGAR_part
+}