README.md

@@ -5,9 +5,7 @@ Download `wfa.js` and `wfa.wasm`from [releases](https://git.tronnet.net/tronnet/
 ```
 import wfa from "./wfa.js"
 await wfa("<path to wasm>")
-let result = wfAlign(...)
+console.log(wfAlign(...))
-operations = DecodeCIGAR(result.CIGAR)
-// ...
 ```
 
 Where `<path to wasm>` is the path from the site root ie. `./scripts/wfa.wasm`. This will depend on your project structure.

go.mod

@@ -3,13 +3,13 @@ module wfa
 go 1.23.2
 
 require (
-	github.com/schollz/progressbar/v3 v3.17.1
+	github.com/schollz/progressbar/v3 v3.17.0
-	golang.org/x/exp v0.0.0-20241108190413-2d47ceb2692f
+	golang.org/x/exp v0.0.0-20241009180824-f66d83c29e7c
 )
 
 require (
 	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
 	github.com/rivo/uniseg v0.4.7 // indirect
-	golang.org/x/sys v0.27.0 // indirect
+	golang.org/x/sys v0.26.0 // indirect
-	golang.org/x/term v0.26.0 // indirect
+	golang.org/x/term v0.25.0 // indirect
 )

main.go

@@ -1,6 +1,7 @@
 package main
 
 import (
+	"fmt"
 	"syscall/js"
 	wfa "wfa/pkg"
 )
@@ -14,47 +15,32 @@ func main() {
 
 func wfAlign(this js.Value, args []js.Value) interface{} {
 	if len(args) != 4 {
-		resultMap := map[string]interface{}{
+		fmt.Println("invalid number of args, requires 4: s1, s2, penalties, doCIGAR")
-			"ok":    false,
+		return nil
-			"error": "invalid number of args, requires 4: s1, s2, penalties, doCIGAR",
-		}
-		return js.ValueOf(resultMap)
 	}
 
 	if args[0].Type() != js.TypeString {
-		resultMap := map[string]interface{}{
+		fmt.Println("s1 should be a string")
-			"ok":    false,
+		return nil
-			"error": "s1 should be a string",
-		}
-		return js.ValueOf(resultMap)
 	}
 
 	s1 := args[0].String()
 
 	if args[1].Type() != js.TypeString {
-		resultMap := map[string]interface{}{
+		fmt.Println("s2 should be a string")
-			"ok":    false,
+		return nil
-			"error": "s2 should be a string",
-		}
-		return js.ValueOf(resultMap)
 	}
 
 	s2 := args[1].String()
 
 	if args[2].Type() != js.TypeObject {
-		resultMap := map[string]interface{}{
+		fmt.Println("penalties should be a map with key values m, x, o, e")
-			"ok":    false,
+		return nil
-			"error": "penalties should be a map with key values m, x, o, e",
-		}
-		return js.ValueOf(resultMap)
 	}
 
 	if args[2].Get("m").IsUndefined() || args[2].Get("x").IsUndefined() || args[2].Get("o").IsUndefined() || args[2].Get("e").IsUndefined() {
-		resultMap := map[string]interface{}{
+		fmt.Println("penalties should be a map with key values m, x, o, e")
-			"ok":    false,
+		return nil
-			"error": "penalties should be a map with key values m, x, o, e",
-		}
-		return js.ValueOf(resultMap)
 	}
 
 	m := args[2].Get("m").Int()
@@ -70,11 +56,8 @@ func wfAlign(this js.Value, args []js.Value) interface{} {
 	}
 
 	if args[3].Type() != js.TypeBoolean {
-		resultMap := map[string]interface{}{
+		fmt.Println("doCIGAR should be a boolean")
-			"ok":    false,
+		return nil
-			"error": "doCIGAR should be a boolean",
-		}
-		return js.ValueOf(resultMap)
 	}
 
 	doCIGAR := args[3].Bool()
@@ -82,10 +65,8 @@ func wfAlign(this js.Value, args []js.Value) interface{} {
 	// Call the actual func.
 	result := wfa.WFAlign(s1, s2, penalties, doCIGAR)
 	resultMap := map[string]interface{}{
-		"ok":    true,
 		"score": result.Score,
 		"CIGAR": result.CIGAR,
-		"error": "",
 	}
 
 	return js.ValueOf(resultMap)
@@ -93,12 +74,12 @@ func wfAlign(this js.Value, args []js.Value) interface{} {
 
 func DecodeCIGAR(this js.Value, args []js.Value) interface{} {
 	if len(args) != 1 {
-		println("invalid number of args, requires 1: CIGAR")
+		fmt.Println("invalid number of args, requires 1: CIGAR")
 		return nil
 	}
 
 	if args[0].Type() != js.TypeString {
-		println("CIGAR should be a string")
+		fmt.Println("CIGAR should be a string")
 		return nil
 	}
 

pkg/custom_slice.go

@@ -41,3 +41,15 @@ func (a *PositiveSlice[T]) Set(idx int, value T) {
 	a.data[actualIdx] = value
 	a.valid[actualIdx] = true
 }
+
+func (a *PositiveSlice[T]) Preallocate(hi int) {
+	size := hi
+
+	// expand data array to actualIdx
+	newData := make([]T, size+1)
+	a.data = newData
+
+	// expand valid array to actualIdx
+	newValid := make([]bool, size+1)
+	a.valid = newValid
+}

pkg/debug.go

@@ -1,5 +1,3 @@
-//go:build debug
-
 package wfa
 
 import (
@@ -14,13 +12,11 @@ func (w *WavefrontComponent) String(score int) string {
 	max_hi := math.MinInt
 
 	for i := 0; i <= score; i++ {
-		valid := w.W.Valid(i)
+		if w.lo.Valid(i) && w.lo.Get(i) < min_lo {
-		lo, hi := UnpackWavefrontLoHi(w.W.Get(i).lohi)
+			min_lo = w.lo.Get(i)
-		if valid && lo < min_lo {
-			min_lo = lo
 		}
-		if valid && hi > max_hi {
+		if w.hi.Valid(i) && w.hi.Get(i) > max_hi {
-			max_hi = hi
+			max_hi = w.hi.Get(i)
 		}
 	}
 
@@ -44,7 +40,9 @@ func (w *WavefrontComponent) String(score int) string {
 
 	for i := 0; i <= score; i++ {
 		s = s + "["
-		lo, hi := UnpackWavefrontLoHi(w.W.Get(i).lohi)
+		lo := w.lo.Get(i)
+		hi := w.hi.Get(i)
+		// print out wavefront matrix
 		for k := min_lo; k <= max_hi; k++ {
 			valid, val, _ := UnpackWavefrontValue(w.W.Get(i).Get(k))
 			if valid {

pkg/types.go

@@ -25,55 +25,39 @@ const (
 	End
 )
 
-// bitpacked wavefront lo/hi values with 32 bits each
-type WavefrontLoHi uint64
-
-func PackWavefrontLoHi(lo int, hi int) WavefrontLoHi {
-	loBM := int64(int32(lo)) & 0x0000_0000_FFFF_FFFF
-	hiBM := int64(int64(hi) << 32)
-	return WavefrontLoHi(hiBM | loBM)
-}
-
-func UnpackWavefrontLoHi(lohi WavefrontLoHi) (int, int) {
-	loBM := int(int32(lohi & 0x0000_0000_FFFF_FFFF))
-	hiBM := int(int32(lohi & 0xFFFF_FFFF_0000_0000 >> 32))
-	return loBM, hiBM
-}
-
 // bitpacked wavefront values with 1 valid bit, 3 traceback bits, and 28 bits for the diag distance
-// technically this restricts to alignments with less than 268 million characters but that should be sufficient for most cases
+// technically this restricts to solutions within 268 million score but that should be sufficient for most cases
 type WavefrontValue uint32
 
-// TODO: add 64 bit packed value in case more than 268 million characters are needed
+// TODO: add 64 bit packed value in case more than 268 million score is needed
 
 // PackWavefrontValue: packs a diag value and traceback into a WavefrontValue
 func PackWavefrontValue(value uint32, traceback Traceback) WavefrontValue {
-	validBM := uint32(0x8000_0000)
-	tracebackBM := uint32(traceback&0x0000_0007) << 28
 	valueBM := value & 0x0FFF_FFFF
-	return WavefrontValue(validBM | tracebackBM | valueBM)
+	tracebackBM := uint32(traceback&0x0000_0007) << 28
+	return WavefrontValue(0x8000_0000 | valueBM | tracebackBM)
 }
 
 // UnpackWavefrontValue: opens a WavefrontValue into a valid bool, diag value and traceback
 func UnpackWavefrontValue(wfv WavefrontValue) (bool, uint32, Traceback) {
-	validBM := wfv&0x8000_0000 != 0
-	tracebackBM := uint8(wfv & 0x7000_0000 >> 28)
 	valueBM := uint32(wfv & 0x0FFF_FFFF)
+	tracebackBM := uint8(wfv & 0x7000_0000 >> 28)
+	validBM := wfv&0x8000_0000 != 0
 	return validBM, valueBM, Traceback(tracebackBM)
 }
 
 // Wavefront: stores a single wavefront, stores wavefront's lo value and hi is naturally lo + len(data)
 type Wavefront struct { // since wavefronts store diag distance, they should never be negative, and traceback data can be stored as uint8
 	data []WavefrontValue
-	lohi WavefrontLoHi
+	lo   int
 }
 
 // NewWavefront: returns a new wavefront with size accomodating lo and hi (inclusive)
 func NewWavefront(lo int, hi int) *Wavefront {
 	a := &Wavefront{}
 
-	a.lohi = PackWavefrontLoHi(lo, hi)
+	a.lo = lo
-	size := hi - lo
+	size := a.TranslateIndex(hi)
 
 	newData := make([]WavefrontValue, size+1)
 	a.data = newData
@@ -83,8 +67,7 @@ func NewWavefront(lo int, hi int) *Wavefront {
 
 // TranslateIndex: utility function for getting the data index given a diagonal
 func (a *Wavefront) TranslateIndex(diagonal int) int {
-	lo := int(int32(a.lohi & 0x0000_0000_FFFF_FFFF))
+	return diagonal - a.lo
-	return diagonal - lo
 }
 
 // Get: returns WavefrontValue for given diagonal
@@ -112,17 +95,27 @@ func (a *Wavefront) Set(diagonal int, value WavefrontValue) {
 
 // WavefrontComponent: each M/I/D wavefront matrix including the wavefront data, lo and hi
 type WavefrontComponent struct {
-	W *PositiveSlice[*Wavefront] // wavefront diag distance and traceback for each wavefront
+	lo *PositiveSlice[int]        // lo for each wavefront
+	hi *PositiveSlice[int]        // hi for each wavefront
+	W  *PositiveSlice[*Wavefront] // wavefront diag distance and traceback for each wavefront
 }
 
 // NewWavefrontComponent: returns initialized WavefrontComponent
-func NewWavefrontComponent() *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},
+		},
+		hi: &PositiveSlice[int]{
+			data:  []int{0},
+			valid: []bool{true},
+		},
 		W: &PositiveSlice[*Wavefront]{
 			defaultValue: &Wavefront{
 				data: []WavefrontValue{0},
@@ -130,6 +123,10 @@ func NewWavefrontComponent() *WavefrontComponent {
 		},
 	}
 
+	w.lo.Preallocate(preallocateSize)
+	w.hi.Preallocate(preallocateSize)
+	w.W.Preallocate(preallocateSize)
+
 	return w
 }
 
@@ -145,12 +142,23 @@ func (w *WavefrontComponent) SetVal(score int, k int, val uint32, tb Traceback)
 
 // GetLoHi: get lo and hi for wavefront=score
 func (w *WavefrontComponent) GetLoHi(score int) (bool, int, int) {
-	lo, hi := UnpackWavefrontLoHi(w.W.Get(score).lohi)
+	// if lo[score] and hi[score] are valid
-	return w.W.Valid(score), lo, hi
+	if w.lo.Valid(score) && w.hi.Valid(score) {
+		// return lo[score] hi[score]
+		return true, w.lo.Get(score), w.hi.Get(score)
+	} else {
+		return false, 0, 0
+	}
 }
 
 // SetLoHi: set lo and hi for wavefront=score
 func (w *WavefrontComponent) SetLoHi(score int, lo int, hi int) {
+	// lo[score] = lo
+	w.lo.Set(score, lo)
+	// hi[score] = hi
+	w.hi.Set(score, hi)
+
+	// preemptively setup w.W
 	b := NewWavefront(lo, hi)
 	w.W.Set(score, b)
 }

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 *WavefrontComponen
 	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, penal
 	}
 }
 
-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, penal
 	}
 }
 
-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

@@ -10,11 +10,12 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 	A_k := m - n
 	A_offset := uint32(m)
 	score := 0
-	M := NewWavefrontComponent()
+	estimatedScore := (max(n, m) * max(penalties.M, penalties.X, penalties.O, penalties.E)) / 4
+	M := NewWavefrontComponent(estimatedScore)
 	M.SetLoHi(0, 0, 0)
 	M.SetVal(0, 0, 0, End)
-	I := NewWavefrontComponent()
+	I := NewWavefrontComponent(estimatedScore)
-	D := NewWavefrontComponent()
+	D := NewWavefrontComponent(estimatedScore)
 
 	for {
 		WFExtend(M, s1, n, s2, m, score)
@@ -37,7 +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
@@ -59,7 +60,7 @@ func WFExtend(M *WavefrontComponent, s1 string, n int, s2 string, m int, score i
 	}
 }
 
-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)
 
@@ -70,7 +71,7 @@ func WFNext(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent,
 	}
 }
 
-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

test/wfa_test.go

@@ -12,7 +12,6 @@ import (
 	wfa "wfa/pkg"
 
 	"github.com/schollz/progressbar/v3"
-	"golang.org/x/exp/constraints"
 )
 
 const testJsonPath = "tests.json"
@@ -30,14 +29,14 @@ type TestCase struct {
 	Solutions string      `json:"solutions"`
 }
 
-func randRange[T constraints.Integer](min, max int) T {
+func randRange(min, max int) uint32 {
-	return T(rand.IntN(max-min) + min)
+	return uint32(rand.IntN(max-min) + min)
 }
 
 func TestWavefrontPacking(t *testing.T) {
 	for range 1000 {
-		val := randRange[uint32](0, 1000)
+		val := randRange(0, 1000)
-		tb := wfa.Traceback(randRange[uint32](0, 7))
+		tb := wfa.Traceback(randRange(0, 7))
 		v := wfa.PackWavefrontValue(val, tb)
 
 		valid, gotVal, gotTB := wfa.UnpackWavefrontValue(v)
@@ -48,20 +47,6 @@ func TestWavefrontPacking(t *testing.T) {
 	}
 }
 
-func TestLoHiPacking(t *testing.T) {
-	for range 1000 {
-		lo := randRange[int](-1000, 1000)
-		hi := randRange[int](-1000, 1000)
-		v := wfa.PackWavefrontLoHi(lo, hi)
-
-		gotLo, gotHi := wfa.UnpackWavefrontLoHi(v)
-
-		if gotLo != lo || gotHi != hi {
-			t.Errorf(`test WavefrontPack/Unpack, lo: %d, hi: %d, packedval: %x, gotlo: %d, gothi: %d`, lo, hi, v, gotLo, gotHi)
-		}
-	}
-}
-
 func GetScoreFromCIGAR(CIGAR string, penalties wfa.Penalty) int {
 	unpackedCIGAR := wfa.RunLengthDecode(CIGAR)
 	previousOp := '~'