minor optimization switching to wavefront pointers

pkg/types.go

@@ -101,13 +101,13 @@ type WavefrontComponent struct {
 }
 
 // NewWavefrontComponent: returns initialized WavefrontComponent
-func NewWavefrontComponent(preallocateSize int) WavefrontComponent {
+func NewWavefrontComponent(preallocateSize int) *WavefrontComponent {
 	// new wavefront component = {
 	// lo = [0]
 	// hi = [0]
 	// W = []
 	// }
-	w := WavefrontComponent{
+	w := &WavefrontComponent{
 		lo: &PositiveSlice[int]{
 			data:  []int{0},
 			valid: []bool{true},

pkg/utils.go

@@ -95,7 +95,7 @@ func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
 	}
 }
 
-func NextLoHi(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) (int, int) {
+func NextLoHi(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty) (int, int) {
 	x := penalties.X
 	o := penalties.O
 	e := penalties.E
@@ -125,7 +125,7 @@ func NextLoHi(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent,
 	return lo, hi
 }
 
-func NextI(M WavefrontComponent, I WavefrontComponent, score int, k int, penalties Penalty) {
+func NextI(M *WavefrontComponent, I *WavefrontComponent, score int, k int, penalties Penalty) {
 	o := penalties.O
 	e := penalties.E
 
@@ -139,7 +139,7 @@ func NextI(M WavefrontComponent, I WavefrontComponent, score int, k int, penalti
 	}
 }
 
-func NextD(M WavefrontComponent, D WavefrontComponent, score int, k int, penalties Penalty) {
+func NextD(M *WavefrontComponent, D *WavefrontComponent, score int, k int, penalties Penalty) {
 	o := penalties.O
 	e := penalties.E
 
@@ -153,7 +153,7 @@ func NextD(M WavefrontComponent, D WavefrontComponent, score int, k int, penalti
 	}
 }
 
-func NextM(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, k int, penalties Penalty) {
+func NextM(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, k int, penalties Penalty) {
 	x := penalties.X
 
 	a_ok, a, _ := M.GetVal(score-x, k)

pkg/wfa.go

@@ -38,7 +38,7 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 	}
 }
 
-func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score int) {
+func WFExtend(M *WavefrontComponent, s1 string, n int, s2 string, m int, score int) {
 	_, lo, hi := M.GetLoHi(score)
 	for k := lo; k <= hi; k++ {
 		// v = M[score][k] - k
@@ -60,7 +60,7 @@ func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score in
 	}
 }
 
-func WFNext(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) {
+func WFNext(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty) {
 	// get this score's lo, hi
 	lo, hi := NextLoHi(M, I, D, score, penalties)
 
@@ -71,7 +71,7 @@ func WFNext(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, sc
 	}
 }
 
-func WFBacktrace(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty, A_k int, A_offset uint32, s1 string, s2 string) string {
+func WFBacktrace(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty, A_k int, A_offset uint32, s1 string, s2 string) string {
 	x := penalties.X
 	o := penalties.O
 	e := penalties.E