remove unused PositiveSlice Preallocate

pack lo/hi values into Wavefront

Makefile

@@ -2,16 +2,25 @@
 
 build: clean
 	@echo "======================== Building Binary ======================="
-	GOOS=js GOARCH=wasm CGO_ENABLED=0 tinygo build -no-debug -opt=2 -target=wasm -o dist/wfa.wasm .
+	minify wfa.js > dist/wfa.js
+	GOOS=js GOARCH=wasm CGO_ENABLED=0 tinygo build -panic=trap -no-debug -opt=2 -target=wasm -o dist/wfa.wasm .
 
 clean:
 	@echo "======================== Cleaning Project ======================"
 	go clean
-	rm -f dist/wfa.wasm
+	rm -f dist/wfa.wasm dist/wfa.js cover.prof cpu.prof mem.prof test.test
 
 test:
 	@echo "======================== Running Tests ========================="
-	go test -v -cover -coverpkg=./pkg/ -coverprofile coverage ./test/
+	go test -v -cover -coverpkg=./pkg/ -coverprofile cover.prof -cpuprofile cpu.prof -memprofile mem.prof ./test/
 	@echo "======================= Coverage Report ========================"
-	go tool cover -func=coverage
+	go tool cover -func=cover.prof
-	@rm -f coverage
+	@rm -f cover.prof
+	@echo "==================== CPU Performance Report ===================="
+	go tool pprof -top cpu.prof
+	@rm -f cpu.prof
+	@echo "=================== Memory Performance Report =================="
+	go tool pprof -top mem.prof
+	@rm -f mem.prof
+
+	@rm -f test.test

README.md

@@ -5,7 +5,9 @@ Download `wfa.js` and `wfa.wasm`from [releases](https://git.tronnet.net/tronnet/
 ```
 import wfa from "./wfa.js"
 await wfa("<path to wasm>")
-console.log(wfAlign(...))
+let result = 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

@@ -2,10 +2,14 @@ module wfa
 
 go 1.23.2
 
+require (
+	github.com/schollz/progressbar/v3 v3.17.1
+	golang.org/x/exp v0.0.0-20241108190413-2d47ceb2692f
+)
+
 require (
 	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
 	github.com/rivo/uniseg v0.4.7 // indirect
-	github.com/schollz/progressbar/v3 v3.16.1 // 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

@@ -1,7 +1,6 @@
 package main
 
 import (
-	"fmt"
 	"syscall/js"
 	wfa "wfa/pkg"
 )
@@ -9,37 +8,53 @@ import (
 func main() {
 	c := make(chan bool)
 	js.Global().Set("wfAlign", js.FuncOf(wfAlign))
+	js.Global().Set("DecodeCIGAR", js.FuncOf(DecodeCIGAR))
 	<-c
 }
 
 func wfAlign(this js.Value, args []js.Value) interface{} {
 	if len(args) != 4 {
-		fmt.Println("invalid number of args, requires 4: s1, s2, penalties, doCIGAR")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "invalid number of args, requires 4: s1, s2, penalties, doCIGAR",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	if args[0].Type() != js.TypeString {
-		fmt.Println("s1 should be a string")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "s1 should be a string",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	s1 := args[0].String()
 
 	if args[1].Type() != js.TypeString {
-		fmt.Println("s2 should be a string")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "s2 should be a string",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	s2 := args[1].String()
 
 	if args[2].Type() != js.TypeObject {
-		fmt.Println("penalties should be a map with key values m, x, o, e")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"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() {
-		fmt.Println("penalties should be a map with key values m, x, o, e")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "penalties should be a map with key values m, x, o, e",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	m := args[2].Get("m").Int()
@@ -55,8 +70,11 @@ func wfAlign(this js.Value, args []js.Value) interface{} {
 	}
 
 	if args[3].Type() != js.TypeBoolean {
-		fmt.Println("doCIGAR should be a boolean")
+		resultMap := map[string]interface{}{
-		return nil
+			"ok":    false,
+			"error": "doCIGAR should be a boolean",
+		}
+		return js.ValueOf(resultMap)
 	}
 
 	doCIGAR := args[3].Bool()
@@ -64,9 +82,29 @@ 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)
 }
+
+func DecodeCIGAR(this js.Value, args []js.Value) interface{} {
+	if len(args) != 1 {
+		println("invalid number of args, requires 1: CIGAR")
+		return nil
+	}
+
+	if args[0].Type() != js.TypeString {
+		println("CIGAR should be a string")
+		return nil
+	}
+
+	CIGAR := args[0].String()
+
+	decoded := wfa.RunLengthDecode(CIGAR)
+
+	return js.ValueOf(decoded)
+}

pkg/custom_slice.go

@@ -1,55 +1,5 @@
 package wfa
 
-type IntegerSlice[T any] struct {
-	data         []T
-	valid        []bool
-	defaultValue T
-}
-
-func (a *IntegerSlice[T]) TranslateIndex(idx int) int {
-	if idx >= 0 { // 0 -> 0, 1 -> 2, 2 -> 4, 3 -> 6, ...
-		return 2 * idx
-	} else { // -1 -> 1, -2 -> 3, -3 -> 5, ...
-		return (-2 * idx) - 1
-	}
-}
-
-func (a *IntegerSlice[T]) Valid(idx int) bool {
-	actualIdx := a.TranslateIndex(idx)
-	if actualIdx < len(a.valid) { // idx is in the slice
-		return a.valid[actualIdx]
-	} else { // idx is out of the slice
-		return false
-	}
-}
-
-func (a *IntegerSlice[T]) Get(idx int) T {
-	actualIdx := a.TranslateIndex(idx)
-	if actualIdx < len(a.valid) { // idx is in the slice
-		return a.data[actualIdx]
-	} else { // idx is out of the slice
-		return a.defaultValue
-	}
-}
-
-func (a *IntegerSlice[T]) Set(idx int, value T) {
-	actualIdx := a.TranslateIndex(idx)
-	if actualIdx >= len(a.valid) { // idx is outside the slice
-		// expand data array to actualIdx
-		newData := make([]T, actualIdx+1)
-		copy(newData, a.data)
-		a.data = newData
-
-		// expand valid array to actualIdx
-		newValid := make([]bool, actualIdx+1)
-		copy(newValid, a.valid)
-		a.valid = newValid
-	}
-
-	a.data[actualIdx] = value
-	a.valid[actualIdx] = true
-}
-
 type PositiveSlice[T any] struct {
 	data         []T
 	valid        []bool
@@ -62,16 +12,12 @@ func (a *PositiveSlice[T]) TranslateIndex(idx int) int {
 
 func (a *PositiveSlice[T]) Valid(idx int) bool {
 	actualIdx := a.TranslateIndex(idx)
-	if actualIdx >= 0 && actualIdx < len(a.valid) { // idx is in the slice
+	return 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx]
-		return a.valid[actualIdx]
-	} else { // idx is out of the slice
-		return false
-	}
 }
 
 func (a *PositiveSlice[T]) Get(idx int) T {
 	actualIdx := a.TranslateIndex(idx)
-	if actualIdx >= 0 && actualIdx < len(a.valid) { // idx is in the slice
+	if 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx] { // idx is in the slice
 		return a.data[actualIdx]
 	} else { // idx is out of the slice
 		return a.defaultValue
@@ -82,12 +28,12 @@ func (a *PositiveSlice[T]) Set(idx int, value T) {
 	actualIdx := a.TranslateIndex(idx)
 	if actualIdx < 0 || actualIdx >= len(a.valid) { // idx is outside the slice
 		// expand data array to actualIdx
-		newData := make([]T, actualIdx+1)
+		newData := make([]T, 2*actualIdx+1)
 		copy(newData, a.data)
 		a.data = newData
 
 		// expand valid array to actualIdx
-		newValid := make([]bool, actualIdx+1)
+		newValid := make([]bool, 2*actualIdx+1)
 		copy(newValid, a.valid)
 		a.valid = newValid
 	}

pkg/debug.go

@@ -0,0 +1,81 @@
+//go:build debug
+
+package wfa
+
+import (
+	"fmt"
+	"math"
+)
+
+func (w *WavefrontComponent) String(score int) string {
+	traceback_str := []string{"OI", "EI", "OD", "ED", "SB", "IN", "DL", "EN"}
+	s := "<"
+	min_lo := math.MaxInt
+	max_hi := math.MinInt
+
+	for i := 0; i <= score; i++ {
+		valid := w.W.Valid(i)
+		lo, hi := UnpackWavefrontLoHi(w.W.Get(i).lohi)
+		if valid && lo < min_lo {
+			min_lo = lo
+		}
+		if valid && hi > max_hi {
+			max_hi = hi
+		}
+	}
+
+	for k := min_lo; k <= max_hi; k++ {
+		s = s + fmt.Sprintf("%02d", k)
+		if k < max_hi {
+			s = s + "|"
+		}
+	}
+
+	s = s + ">\t<"
+
+	for k := min_lo; k <= max_hi; k++ {
+		s = s + fmt.Sprintf("%02d", k)
+		if k < max_hi {
+			s = s + "|"
+		}
+	}
+
+	s = s + ">\n"
+
+	for i := 0; i <= score; i++ {
+		s = s + "["
+		lo, hi := UnpackWavefrontLoHi(w.W.Get(i).lohi)
+		for k := min_lo; k <= max_hi; k++ {
+			valid, val, _ := UnpackWavefrontValue(w.W.Get(i).Get(k))
+			if valid {
+				s = s + fmt.Sprintf("%02d", val)
+			} else if k < lo || k > hi {
+				s = s + "--"
+			} else {
+				s = s + "  "
+			}
+
+			if k < max_hi {
+				s = s + "|"
+			}
+		}
+		s = s + "]\t["
+		// print out traceback matrix
+		for k := min_lo; k <= max_hi; k++ {
+			valid, _, tb := UnpackWavefrontValue(w.W.Get(i).Get(k))
+			if valid {
+				s = s + traceback_str[tb]
+			} else if k < lo || k > hi {
+				s = s + "--"
+			} else {
+				s = s + "  "
+			}
+
+			if k < max_hi {
+				s = s + "|"
+			}
+		}
+		s = s + "]\n"
+	}
+	return s
+}

pkg/types.go

@@ -1,9 +1,9 @@
 package wfa
 
-import (
+type Result struct {
-	"fmt"
+	Score int
-	"math"
+	CIGAR string
-)
+}
 
 type Penalty struct {
 	M int
@@ -12,10 +12,10 @@ type Penalty struct {
 	E int
 }
 
-type traceback byte
+type Traceback byte
 
 const (
-	OpenIns traceback = iota
+	OpenIns Traceback = iota
 	ExtdIns
 	OpenDel
 	ExtdDel
@@ -25,190 +25,132 @@ const (
 	End
 )
 
-type WavefrontComponent struct {
+// bitpacked wavefront lo/hi values with 32 bits each
-	lo *PositiveSlice[int]                      // lo for each wavefront
+type WavefrontLoHi uint64
-	hi *PositiveSlice[int]                      // hi for each wavefront
+
-	W  *PositiveSlice[*IntegerSlice[int]]       // wavefront diag distance for each wavefront
+func PackWavefrontLoHi(lo int, hi int) WavefrontLoHi {
-	A  *PositiveSlice[*IntegerSlice[traceback]] // compact CIGAR for backtrace for each wavefront
+	loBM := int64(int32(lo)) & 0x0000_0000_FFFF_FFFF
+	hiBM := int64(int64(hi) << 32)
+	return WavefrontLoHi(hiBM | loBM)
 }
 
-func NewWavefrontComponent() WavefrontComponent {
+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
+type WavefrontValue uint32
+
+// TODO: add 64 bit packed value in case more than 268 million characters are 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)
+}
+
+// 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)
+	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
+}
+
+// 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)
+	size := hi - lo
+
+	newData := make([]WavefrontValue, size+1)
+	a.data = newData
+
+	return a
+}
+
+// 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 - lo
+}
+
+// Get: returns WavefrontValue for given diagonal
+func (a *Wavefront) Get(diagonal int) WavefrontValue {
+	actualIdx := a.TranslateIndex(diagonal)
+	if 0 <= actualIdx && actualIdx < len(a.data) { // idx is in the slice
+		return a.data[actualIdx]
+	} else { // idx is out of the slice
+		return 0
+	}
+}
+
+// Set: the diagonal to a WavefrontValue
+func (a *Wavefront) Set(diagonal int, value WavefrontValue) {
+	actualIdx := a.TranslateIndex(diagonal)
+
+	/* in theory idx is always in bounds because the wavefront is preallocated
+	if actualIdx < 0 || actualIdx >= len(a.data) {
+		return
+	}
+	*/
+
+	a.data[actualIdx] = value
+}
+
+// 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
+}
+
+// NewWavefrontComponent: returns initialized WavefrontComponent
+func NewWavefrontComponent() *WavefrontComponent {
 	// new wavefront component = {
 	// lo = [0]
 	// hi = [0]
 	// W = []
-	// A = []
 	// }
-	return WavefrontComponent{
+	w := &WavefrontComponent{
-		lo: &PositiveSlice[int]{
+		W: &PositiveSlice[*Wavefront]{
-			data:  []int{0},
+			defaultValue: &Wavefront{
-			valid: []bool{true},
+				data: []WavefrontValue{0},
 			},
-		hi: &PositiveSlice[int]{
-			data:  []int{0},
-			valid: []bool{true},
 		},
-		W: &PositiveSlice[*IntegerSlice[int]]{},
-		A: &PositiveSlice[*IntegerSlice[traceback]]{},
-	}
 	}
 
-// get value for wavefront=score, diag=k => returns ok, value
+	return w
-func (w *WavefrontComponent) GetVal(score int, k int) (bool, int) {
-	// if W[score][k] is valid
-	if w.W.Valid(score) && w.W.Get(score).Valid(k) {
-		// return W[score][k]
-		return true, w.W.Get(score).Get(k)
-	} else {
-		return false, 0
-	}
 }
 
-// set value for wavefront=score, diag=k
+// GetVal: get value for wavefront=score, diag=k => returns ok, value, traceback
-func (w *WavefrontComponent) SetVal(score int, k int, val int) {
+func (w *WavefrontComponent) GetVal(score int, k int) (bool, uint32, Traceback) {
-	// if W[score] is valid
+	return UnpackWavefrontValue(w.W.Get(score).Get(k))
-	if w.W.Valid(score) {
-		// W[score][k] = val
-		w.W.Get(score).Set(k, val)
-	} else {
-		// W[score] = []
-		w.W.Set(score, &IntegerSlice[int]{})
-		// W[score][k] = val
-		w.W.Get(score).Set(k, val)
-	}
 }
 
-// get alignment traceback for wavefront=score, diag=k => returns ok, value
+// SetVal: set value, traceback for wavefront=score, diag=k
-func (w *WavefrontComponent) GetTraceback(score int, k int) (bool, traceback) {
+func (w *WavefrontComponent) SetVal(score int, k int, val uint32, tb Traceback) {
-	// if W[score][k] is valid
+	w.W.Get(score).Set(k, PackWavefrontValue(val, tb))
-	if w.A.Valid(score) && w.A.Get(score).Valid(k) {
-		// return W[score][k]
-		return true, w.A.Get(score).Get(k)
-	} else {
-		return false, 0
-	}
 }
 
-// set alignment traceback for wavefront=score, diag=k
+// GetLoHi: get lo and hi for wavefront=score
-func (w *WavefrontComponent) SetTraceback(score int, k int, val traceback) {
+func (w *WavefrontComponent) GetLoHi(score int) (bool, int, int) {
-	// if A[score] is valid
+	lo, hi := UnpackWavefrontLoHi(w.W.Get(score).lohi)
-	if w.A.Valid(score) {
+	return w.W.Valid(score), lo, hi
-		// A[score][k] = val
-		w.A.Get(score).Set(k, val)
-	} else {
-		// W[score] = []
-		w.A.Set(score, &IntegerSlice[traceback]{})
-		// W[score][k] = val
-		w.A.Get(score).Set(k, val)
-	}
 }
 
-// get hi for wavefront=score
+// SetLoHi: set lo and hi for wavefront=score
-func (w *WavefrontComponent) GetHi(score int) (bool, int) {
+func (w *WavefrontComponent) SetLoHi(score int, lo int, hi int) {
-	// if hi[score] is valid
+	b := NewWavefront(lo, hi)
-	if w.hi.Valid(score) {
+	w.W.Set(score, b)
-		// return hi[score]
-		return true, w.hi.Get(score)
-	} else {
-		return false, 0
-	}
-}
-
-// set hi for wavefront=score
-func (w *WavefrontComponent) SetHi(score int, hi int) {
-	// hi[score] = hi
-	w.hi.Set(score, hi)
-}
-
-// get lo for wavefront=score
-func (w *WavefrontComponent) GetLo(score int) (bool, int) {
-	// if lo[score] is valid
-	if w.lo.Valid(score) {
-		// return lo[score]
-		return true, w.lo.Get(score)
-	} else {
-		return false, 0
-	}
-}
-
-// set hi for wavefront=score
-func (w *WavefrontComponent) SetLo(score int, lo int) {
-	// lo[score] = lo
-	w.lo.Set(score, lo)
-}
-
-type Result struct {
-	Score int
-	CIGAR string
-}
-
-func (w *WavefrontComponent) String(score int) string {
-	traceback_str := []string{"OI", "EI", "OD", "ED", "SB", "IN", "DL", "EN"}
-	s := "<"
-	min_lo := math.MaxInt
-	max_hi := math.MinInt
-
-	for i := 0; i <= score; i++ {
-		if w.lo.Valid(i) && w.lo.Get(i) < min_lo {
-			min_lo = w.lo.Get(i)
-		}
-		if w.hi.Valid(i) && w.hi.Get(i) > max_hi {
-			max_hi = w.hi.Get(i)
-		}
-	}
-
-	for k := min_lo; k <= max_hi; k++ {
-		s = s + fmt.Sprintf("%02d", k)
-		if k < max_hi {
-			s = s + "|"
-		}
-	}
-
-	s = s + ">\t<"
-
-	for k := min_lo; k <= max_hi; k++ {
-		s = s + fmt.Sprintf("%02d", k)
-		if k < max_hi {
-			s = s + "|"
-		}
-	}
-
-	s = s + ">\n"
-
-	for i := 0; i <= score; i++ {
-		s = s + "["
-		lo := w.lo.Get(i)
-		hi := w.hi.Get(i)
-		// print out wavefront matrix
-		for k := min_lo; k <= max_hi; k++ {
-			if w.W.Valid(i) && w.W.Get(i).Valid(k) {
-				s = s + fmt.Sprintf("%02d", w.W.Get(i).Get(k))
-			} else if k < lo || k > hi {
-				s = s + "--"
-			} else {
-				s = s + "  "
-			}
-
-			if k < max_hi {
-				s = s + "|"
-			}
-		}
-		s = s + "]\t["
-		// print out traceback matrix
-		for k := min_lo; k <= max_hi; k++ {
-			if w.A.Valid(i) && w.A.Get(i).Valid(k) {
-				s = s + traceback_str[w.A.Get(i).Get(k)]
-			} else if k < lo || k > hi {
-				s = s + "--"
-			} else {
-				s = s + "  "
-			}
-
-			if k < max_hi {
-				s = s + "|"
-			}
-		}
-		s = s + "]\n"
-	}
-	return s
 }

pkg/utils.go

@@ -2,28 +2,72 @@ package wfa
 
 import (
 	"math"
-	"unicode/utf8"
+	"strings"
+
+	"golang.org/x/exp/constraints"
 )
 
-func SafeMin(valids []bool, values []int) (bool, int) {
+func UIntToString(num uint) string { // num assumed to be positive
-	ok, idx := SafeArgMin(valids, values)
+	var builder strings.Builder
-	return ok, values[idx]
+
+	for num > 0 {
+		digit := num % 10
+		builder.WriteRune(rune('0' + digit))
+		num /= 10
 	}
 
-func SafeMax(valids []bool, values []int) (bool, int) {
+	// Reverse the string as we built it in reverse order
-	ok, idx := SafeArgMax(valids, values)
+	str := []rune(builder.String())
-	return ok, values[idx]
+	for i, j := 0, len(str)-1; i < j; i, j = i+1, j-1 {
+		str[i], str[j] = str[j], str[i]
 	}
 
-func SafeArgMax(valids []bool, values []int) (bool, int) {
+	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]
+}
+
+func SafeMax[T constraints.Integer](values []T, idx int) T {
+	return values[idx]
+}
+
+func SafeArgMax[T constraints.Integer](valids []bool, values []T) (bool, int) {
 	hasValid := false
 	maxIndex := 0
 	maxValue := math.MinInt
 	for i := 0; i < len(valids); i++ {
-		if valids[i] && values[i] > maxValue {
+		if valids[i] && int(values[i]) > maxValue {
 			hasValid = true
 			maxIndex = i
-			maxValue = values[i]
+			maxValue = int(values[i])
 		}
 	}
 	if hasValid {
@@ -33,15 +77,15 @@ func SafeArgMax(valids []bool, values []int) (bool, int) {
 	}
 }
 
-func SafeArgMin(valids []bool, values []int) (bool, int) {
+func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
 	hasValid := false
 	minIndex := 0
 	minValue := math.MaxInt
 	for i := 0; i < len(valids); i++ {
-		if valids[i] && values[i] < minValue {
+		if valids[i] && int(values[i]) < minValue {
 			hasValid = true
 			minIndex = i
-			minValue = values[i]
+			minValue = int(values[i])
 		}
 	}
 	if hasValid {
@@ -51,118 +95,75 @@ func SafeArgMin(valids []bool, values []int) (bool, int) {
 	}
 }
 
-func Reverse(s string) string {
+func NextLoHi(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty) (int, int) {
-	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 NextLo(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) int {
 	x := penalties.X
 	o := penalties.O
 	e := penalties.E
 
-	a_ok, a := M.GetLo(score - x)
+	a_ok, a_lo, a_hi := M.GetLoHi(score - x)
-	b_ok, b := M.GetLo(score - o - e)
+	b_ok, b_lo, b_hi := M.GetLoHi(score - o - e)
-	c_ok, c := I.GetLo(score - e)
+	c_ok, c_lo, c_hi := I.GetLoHi(score - e)
-	d_ok, d := D.GetLo(score - e)
+	d_ok, d_lo, d_hi := D.GetLoHi(score - e)
 
-	ok, lo := SafeMin(
+	ok_lo, idx := SafeArgMin(
 		[]bool{a_ok, b_ok, c_ok, d_ok},
-		[]int{a, b, c, d},
+		[]int{a_lo, b_lo, c_lo, d_lo},
 	)
-	lo--
+	lo := SafeMin([]int{a_lo, b_lo, c_lo, d_lo}, idx) - 1
-	if ok {
-		M.SetLo(score, lo)
-		I.SetLo(score, lo)
-		D.SetLo(score, lo)
-	}
-	return lo
-}
 
-func NextHi(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) int {
+	ok_hi, idx := SafeArgMax(
-	x := penalties.X
-	o := penalties.O
-	e := penalties.E
-
-	a_ok, a := M.GetHi(score - x)
-	b_ok, b := M.GetHi(score - o - e)
-	c_ok, c := I.GetHi(score - e)
-	d_ok, d := D.GetHi(score - e)
-
-	ok, hi := SafeMax(
 		[]bool{a_ok, b_ok, c_ok, d_ok},
-		[]int{a, b, c, d},
+		[]int{a_hi, b_hi, c_hi, d_hi},
 	)
-	hi++
+	hi := SafeMax([]int{a_hi, b_hi, c_hi, d_hi}, idx) + 1
-	if ok {
+
-		M.SetHi(score, hi)
+	if ok_lo && ok_hi {
-		I.SetHi(score, hi)
+		M.SetLoHi(score, lo, hi)
-		D.SetHi(score, hi)
+		I.SetLoHi(score, lo, hi)
+		D.SetLoHi(score, lo, hi)
 	}
-	return hi
+	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
 
-	a_ok, a := M.GetVal(score-o-e, k-1)
+	a_ok, a, _ := M.GetVal(score-o-e, k-1)
-	b_ok, b := I.GetVal(score-e, k-1)
+	b_ok, b, _ := I.GetVal(score-e, k-1)
 
-	ok, nextIVal := SafeMax([]bool{a_ok, b_ok}, []int{a, b})
+	ok, nextITraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint32{a, b})
+	nextIVal := SafeMax([]uint32{a, b}, nextITraceback) + 1 // important that the +1 is here
 	if ok {
-		I.SetVal(score, k, nextIVal+1) // important that the +1 is here
+		I.SetVal(score, k, nextIVal, []Traceback{OpenIns, ExtdIns}[nextITraceback])
-	}
-
-	ok, nextITraceback := SafeArgMax([]bool{a_ok, b_ok}, []int{a, b})
-	if ok {
-		I.SetTraceback(score, k, []traceback{OpenIns, ExtdIns}[nextITraceback])
 	}
 }
 
-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
 
-	a_ok, a := M.GetVal(score-o-e, k+1)
+	a_ok, a, _ := M.GetVal(score-o-e, k+1)
-	b_ok, b := D.GetVal(score-e, k+1)
+	b_ok, b, _ := D.GetVal(score-e, k+1)
 
-	ok, nextDVal := SafeMax([]bool{a_ok, b_ok}, []int{a, b})
+	ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint32{a, b})
+	nextDVal := SafeMax([]uint32{a, b}, nextDTraceback)
 	if ok {
-		D.SetVal(score, k, nextDVal) // nothing special
+		D.SetVal(score, k, nextDVal, []Traceback{OpenDel, ExtdDel}[nextDTraceback])
-	}
-
-	ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []int{a, b})
-	if ok {
-		D.SetTraceback(score, k, []traceback{OpenDel, ExtdDel}[nextDTraceback])
 	}
 }
 
-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)
+	a_ok, a, _ := M.GetVal(score-x, k)
 	a++ // important to have +1 here
-	b_ok, b := I.GetVal(score, k)
+	b_ok, b, _ := I.GetVal(score, k)
-	c_ok, c := D.GetVal(score, k)
+	c_ok, c, _ := D.GetVal(score, k)
 
-	ok, nextMVal := SafeMax([]bool{a_ok, b_ok, c_ok}, []int{a, b, c})
+	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)
+		M.SetVal(score, k, nextMVal, []Traceback{Sub, Ins, Del}[nextMTraceback])
-	}
-
-	ok, nextMTraceback := SafeArgMax([]bool{a_ok, b_ok, c_ok}, []int{a, b, c})
-	if ok {
-		M.SetTraceback(score, k, []traceback{Sub, Ins, Del}[nextMTraceback])
 	}
 }

pkg/wfa.go

@@ -1,22 +1,24 @@
 package wfa
 
+import (
+	"strings"
+)
+
 func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 	n := len(s1)
 	m := len(s2)
 	A_k := m - n
-	A_offset := m
+	A_offset := uint32(m)
 	score := 0
 	M := NewWavefrontComponent()
-	M.SetVal(0, 0, 0)
+	M.SetLoHi(0, 0, 0)
-	M.SetHi(0, 0)
+	M.SetVal(0, 0, 0, End)
-	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)
+		ok, val, _ := M.GetVal(score, A_k)
 		if ok && val >= A_offset {
 			break
 		}
@@ -26,7 +28,7 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 
 	CIGAR := ""
 	if doCIGAR {
-		CIGAR = WFBacktrace(M, I, D, score, penalties, A_k, s1, s2)
+		CIGAR = WFBacktrace(M, I, D, score, penalties, A_k, A_offset, s1, s2)
 	}
 
 	return Result{
@@ -35,13 +37,13 @@ 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 := M.GetLo(score)
+	_, lo, hi := M.GetLoHi(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)
+		ok, hu, _ := M.GetVal(score, k)
+		h := int(hu)
 		v := h - k
 
 		// exit early if v or h are invalid
@@ -49,20 +51,17 @@ func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score in
 			continue
 		}
 		for v < n && h < m && s1[v] == s2[h] {
-			_, val := M.GetVal(score, k)
+			_, val, tb := M.GetVal(score, k)
-			M.SetVal(score, k, val+1)
+			M.SetVal(score, k, val+1, tb)
 			v++
 			h++
 		}
 	}
 }
 
-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
+	// get this score's lo, hi
-	lo := NextLo(M, I, D, score, penalties)
+	lo, hi := NextLoHi(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)
@@ -71,76 +70,128 @@ func WFNext(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, sc
 	}
 }
 
-func WFBacktrace(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty, A_k int, 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 {
-	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
 
+	_, current_dist, current_traceback := M.GetVal(tb_s, tb_k)
+
+	Ops := []rune{'~'}
+	Counts := []uint{0}
+	idx := 0
+
 	for !done {
-		CIGAR_rev = CIGAR_rev + traceback_CIGAR[current_traceback]
 		switch current_traceback {
 		case OpenIns:
+			if Ops[idx] == 'I' {
+				Counts[idx]++
+			} else {
+				Ops = append(Ops, 'I')
+				Counts = append(Counts, 1)
+				idx++
+			}
+
 			tb_s = tb_s - o - e
 			tb_k = tb_k - 1
-			_, current_traceback = M.GetTraceback(tb_s, tb_k)
+			_, current_dist, current_traceback = M.GetVal(tb_s, tb_k)
 		case ExtdIns:
+			if Ops[idx] == 'I' {
+				Counts[idx]++
+			} else {
+				Ops = append(Ops, 'I')
+				Counts = append(Counts, 1)
+				idx++
+			}
+
 			tb_s = tb_s - e
 			tb_k = tb_k - 1
-			_, current_traceback = I.GetTraceback(tb_s, tb_k)
+			_, current_dist, current_traceback = I.GetVal(tb_s, tb_k)
 		case OpenDel:
+			if Ops[idx] == 'D' {
+				Counts[idx]++
+			} else {
+				Ops = append(Ops, 'D')
+				Counts = append(Counts, 1)
+				idx++
+			}
+
 			tb_s = tb_s - o - e
 			tb_k = tb_k + 1
-			_, current_traceback = M.GetTraceback(tb_s, tb_k)
+			_, current_dist, current_traceback = M.GetVal(tb_s, tb_k)
 		case ExtdDel:
+			if Ops[idx] == 'D' {
+				Counts[idx]++
+			} else {
+				Ops = append(Ops, 'D')
+				Counts = append(Counts, 1)
+				idx++
+			}
+
 			tb_s = tb_s - e
 			tb_k = tb_k + 1
-			_, current_traceback = D.GetTraceback(tb_s, tb_k)
+			_, current_dist, current_traceback = D.GetVal(tb_s, tb_k)
 		case Sub:
 			tb_s = tb_s - x
 			// tb_k = tb_k;
-			_, current_traceback = M.GetTraceback(tb_s, tb_k)
+			_, next_dist, next_traceback := M.GetVal(tb_s, tb_k)
+
+			if int(current_dist-next_dist)-1 > 0 {
+				Ops = append(Ops, 'M')
+				Counts = append(Counts, uint(current_dist-next_dist)-1)
+				idx++
+			}
+
+			if Ops[idx] == 'X' {
+				Counts[idx]++
+			} else {
+				Ops = append(Ops, 'X')
+				Counts = append(Counts, 1)
+				idx++
+			}
+
+			current_dist = next_dist
+			current_traceback = next_traceback
 		case Ins:
 			// tb_s = tb_s;
 			// tb_k = tb_k;
-			_, current_traceback = I.GetTraceback(tb_s, tb_k)
+			_, next_dist, next_traceback := I.GetVal(tb_s, tb_k)
+
+			Ops = append(Ops, 'M')
+			Counts = append(Counts, uint(current_dist-next_dist))
+			idx++
+
+			current_dist = next_dist
+			current_traceback = next_traceback
 		case Del:
 			// tb_s = tb_s;
 			// tb_k = tb_k;
-			_, current_traceback = D.GetTraceback(tb_s, tb_k)
+			_, next_dist, next_traceback := D.GetVal(tb_s, tb_k)
+
+			Ops = append(Ops, 'M')
+			Counts = append(Counts, uint(current_dist-next_dist))
+			idx++
+
+			current_dist = next_dist
+			current_traceback = next_traceback
 		case End:
+			Ops = append(Ops, 'M')
+			Counts = append(Counts, uint(current_dist))
+			idx++
+
 			done = true
 		}
 	}
 
-	CIGAR_part := Reverse(CIGAR_rev)
+	CIGAR := strings.Builder{}
-	c := 0
+	for i := len(Ops) - 1; i > 0; i-- {
-	i := 0
+		CIGAR.WriteString(UIntToString(Counts[i]))
-	j := 0
+		CIGAR.WriteRune(Ops[i])
-	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
+	return CIGAR.String()
 }

test/wfa_test.go

@@ -3,6 +3,8 @@ package tests
 import (
 	"bufio"
 	"encoding/json"
+	"log"
+	"math/rand/v2"
 	"os"
 	"strconv"
 	"strings"
@@ -10,6 +12,7 @@ import (
 	wfa "wfa/pkg"
 
 	"github.com/schollz/progressbar/v3"
+	"golang.org/x/exp/constraints"
 )
 
 const testJsonPath = "tests.json"
@@ -27,6 +30,103 @@ type TestCase struct {
 	Solutions string      `json:"solutions"`
 }
 
+func randRange[T constraints.Integer](min, max int) T {
+	return T(rand.IntN(max-min) + min)
+}
+
+func TestWavefrontPacking(t *testing.T) {
+	for range 1000 {
+		val := randRange[uint32](0, 1000)
+		tb := wfa.Traceback(randRange[uint32](0, 7))
+		v := wfa.PackWavefrontValue(val, tb)
+
+		valid, gotVal, gotTB := wfa.UnpackWavefrontValue(v)
+
+		if !valid || gotVal != val || gotTB != tb {
+			t.Errorf(`test WavefrontPack/Unpack, val: %d, tb: %d, packedval: %x, gotok: %t, gotval: %d, gottb: %d\n`, val, tb, v, valid, gotVal, gotTB)
+		}
+	}
+}
+
+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 := '~'
+	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)
 
@@ -54,7 +154,9 @@ 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()
@@ -64,11 +166,27 @@ func TestWFA(t *testing.T) {
 			s2 := sequences.Text()
 			s2 = s2[1:]
 
-			x := wfa.WFAlign(s1, s2, testPenalties, false)
+			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++

wfa.js

@@ -0,0 +1,560 @@
+// wasm_exec.js from tinygo
+
+// Copyright 2018 The Go Authors. All rights reserved.
+// Use of this source code is governed by a BSD-style
+// license that can be found in the LICENSE file.
+//
+// This file has been modified for use by the TinyGo compiler.
+
+(() => {
+	// Map multiple JavaScript environments to a single common API,
+	// preferring web standards over Node.js API.
+	//
+	// Environments considered:
+	// - Browsers
+	// - Node.js
+	// - Electron
+	// - Parcel
+
+	if (typeof global !== "undefined") {
+		// global already exists
+	} else if (typeof window !== "undefined") {
+		window.global = window;
+	} else if (typeof self !== "undefined") {
+		self.global = self;
+	} else {
+		throw new Error("cannot export Go (neither global, window nor self is defined)");
+	}
+
+	if (!global.require && typeof require !== "undefined") {
+		global.require = require;
+	}
+
+	if (!global.fs && global.require) {
+		global.fs = require("node:fs");
+	}
+
+	const enosys = () => {
+		const err = new Error("not implemented");
+		err.code = "ENOSYS";
+		return err;
+	};
+
+	if (!global.fs) {
+		let outputBuf = "";
+		global.fs = {
+			constants: { O_WRONLY: -1, O_RDWR: -1, O_CREAT: -1, O_TRUNC: -1, O_APPEND: -1, O_EXCL: -1 }, // unused
+			writeSync(fd, buf) {
+				outputBuf += decoder.decode(buf);
+				const nl = outputBuf.lastIndexOf("\n");
+				if (nl != -1) {
+					console.log(outputBuf.substr(0, nl));
+					outputBuf = outputBuf.substr(nl + 1);
+				}
+				return buf.length;
+			},
+			write(fd, buf, offset, length, position, callback) {
+				if (offset !== 0 || length !== buf.length || position !== null) {
+					callback(enosys());
+					return;
+				}
+				const n = this.writeSync(fd, buf);
+				callback(null, n);
+			},
+			chmod(path, mode, callback) { callback(enosys()); },
+			chown(path, uid, gid, callback) { callback(enosys()); },
+			close(fd, callback) { callback(enosys()); },
+			fchmod(fd, mode, callback) { callback(enosys()); },
+			fchown(fd, uid, gid, callback) { callback(enosys()); },
+			fstat(fd, callback) { callback(enosys()); },
+			fsync(fd, callback) { callback(null); },
+			ftruncate(fd, length, callback) { callback(enosys()); },
+			lchown(path, uid, gid, callback) { callback(enosys()); },
+			link(path, link, callback) { callback(enosys()); },
+			lstat(path, callback) { callback(enosys()); },
+			mkdir(path, perm, callback) { callback(enosys()); },
+			open(path, flags, mode, callback) { callback(enosys()); },
+			read(fd, buffer, offset, length, position, callback) { callback(enosys()); },
+			readdir(path, callback) { callback(enosys()); },
+			readlink(path, callback) { callback(enosys()); },
+			rename(from, to, callback) { callback(enosys()); },
+			rmdir(path, callback) { callback(enosys()); },
+			stat(path, callback) { callback(enosys()); },
+			symlink(path, link, callback) { callback(enosys()); },
+			truncate(path, length, callback) { callback(enosys()); },
+			unlink(path, callback) { callback(enosys()); },
+			utimes(path, atime, mtime, callback) { callback(enosys()); },
+		};
+	}
+
+	if (!global.process) {
+		global.process = {
+			getuid() { return -1; },
+			getgid() { return -1; },
+			geteuid() { return -1; },
+			getegid() { return -1; },
+			getgroups() { throw enosys(); },
+			pid: -1,
+			ppid: -1,
+			umask() { throw enosys(); },
+			cwd() { throw enosys(); },
+			chdir() { throw enosys(); },
+		}
+	}
+
+	if (!global.crypto) {
+		const nodeCrypto = require("node:crypto");
+		global.crypto = {
+			getRandomValues(b) {
+				nodeCrypto.randomFillSync(b);
+			},
+		};
+	}
+
+	if (!global.performance) {
+		global.performance = {
+			now() {
+				const [sec, nsec] = process.hrtime();
+				return sec * 1000 + nsec / 1000000;
+			},
+		};
+	}
+
+	if (!global.TextEncoder) {
+		global.TextEncoder = require("node:util").TextEncoder;
+	}
+
+	if (!global.TextDecoder) {
+		global.TextDecoder = require("node:util").TextDecoder;
+	}
+
+	// End of polyfills for common API.
+
+	const encoder = new TextEncoder("utf-8");
+	const decoder = new TextDecoder("utf-8");
+	let reinterpretBuf = new DataView(new ArrayBuffer(8));
+	var logLine = [];
+
+	global.Go = class {
+		constructor() {
+			this._callbackTimeouts = new Map();
+			this._nextCallbackTimeoutID = 1;
+
+			const mem = () => {
+				// The buffer may change when requesting more memory.
+				return new DataView(this._inst.exports.memory.buffer);
+			}
+
+			const unboxValue = (v_ref) => {
+				reinterpretBuf.setBigInt64(0, v_ref, true);
+				const f = reinterpretBuf.getFloat64(0, true);
+				if (f === 0) {
+					return undefined;
+				}
+				if (!isNaN(f)) {
+					return f;
+				}
+
+				const id = v_ref & 0xffffffffn;
+				return this._values[id];
+			}
+
+
+			const loadValue = (addr) => {
+				let v_ref = mem().getBigUint64(addr, true);
+				return unboxValue(v_ref);
+			}
+
+			const boxValue = (v) => {
+				const nanHead = 0x7FF80000n;
+
+				if (typeof v === "number") {
+					if (isNaN(v)) {
+						return nanHead << 32n;
+					}
+					if (v === 0) {
+						return (nanHead << 32n) | 1n;
+					}
+					reinterpretBuf.setFloat64(0, v, true);
+					return reinterpretBuf.getBigInt64(0, true);
+				}
+
+				switch (v) {
+					case undefined:
+						return 0n;
+					case null:
+						return (nanHead << 32n) | 2n;
+					case true:
+						return (nanHead << 32n) | 3n;
+					case false:
+						return (nanHead << 32n) | 4n;
+				}
+
+				let id = this._ids.get(v);
+				if (id === undefined) {
+					id = this._idPool.pop();
+					if (id === undefined) {
+						id = BigInt(this._values.length);
+					}
+					this._values[id] = v;
+					this._goRefCounts[id] = 0;
+					this._ids.set(v, id);
+				}
+				this._goRefCounts[id]++;
+				let typeFlag = 1n;
+				switch (typeof v) {
+					case "string":
+						typeFlag = 2n;
+						break;
+					case "symbol":
+						typeFlag = 3n;
+						break;
+					case "function":
+						typeFlag = 4n;
+						break;
+				}
+				return id | ((nanHead | typeFlag) << 32n);
+			}
+
+			const storeValue = (addr, v) => {
+				let v_ref = boxValue(v);
+				mem().setBigUint64(addr, v_ref, true);
+			}
+
+			const loadSlice = (array, len, cap) => {
+				return new Uint8Array(this._inst.exports.memory.buffer, array, len);
+			}
+
+			const loadSliceOfValues = (array, len, cap) => {
+				const a = new Array(len);
+				for (let i = 0; i < len; i++) {
+					a[i] = loadValue(array + i * 8);
+				}
+				return a;
+			}
+
+			const loadString = (ptr, len) => {
+				return decoder.decode(new DataView(this._inst.exports.memory.buffer, ptr, len));
+			}
+
+			const timeOrigin = Date.now() - performance.now();
+			this.importObject = {
+				wasi_snapshot_preview1: {
+					// https://github.com/WebAssembly/WASI/blob/main/phases/snapshot/docs.md#fd_write
+					fd_write: function(fd, iovs_ptr, iovs_len, nwritten_ptr) {
+						let nwritten = 0;
+						if (fd == 1) {
+							for (let iovs_i=0; iovs_i<iovs_len;iovs_i++) {
+								let iov_ptr = iovs_ptr+iovs_i*8; // assuming wasm32
+								let ptr = mem().getUint32(iov_ptr + 0, true);
+								let len = mem().getUint32(iov_ptr + 4, true);
+								nwritten += len;
+								for (let i=0; i<len; i++) {
+									let c = mem().getUint8(ptr+i);
+									if (c == 13) { // CR
+										// ignore
+									} else if (c == 10) { // LF
+										// write line
+										let line = decoder.decode(new Uint8Array(logLine));
+										logLine = [];
+										console.log(line);
+									} else {
+										logLine.push(c);
+									}
+								}
+							}
+						} else {
+							console.error('invalid file descriptor:', fd);
+						}
+						mem().setUint32(nwritten_ptr, nwritten, true);
+						return 0;
+					},
+					fd_close: () => 0,      // dummy
+					fd_fdstat_get: () => 0, // dummy
+					fd_seek: () => 0,       // dummy
+					"proc_exit": (code) => {
+						if (global.process) {
+							// Node.js
+							process.exit(code);
+						} else {
+							// Can't exit in a browser.
+							throw 'trying to exit with code ' + code;
+						}
+					},
+					random_get: (bufPtr, bufLen) => {
+						crypto.getRandomValues(loadSlice(bufPtr, bufLen));
+						return 0;
+					},
+				},
+				gojs: {
+					// func ticks() float64
+					"runtime.ticks": () => {
+						return timeOrigin + performance.now();
+					},
+
+					// func sleepTicks(timeout float64)
+					"runtime.sleepTicks": (timeout) => {
+						// Do not sleep, only reactivate scheduler after the given timeout.
+						setTimeout(this._inst.exports.go_scheduler, timeout);
+					},
+
+					// func finalizeRef(v ref)
+					"syscall/js.finalizeRef": (v_ref) => {
+						const id = mem().getUint32(unboxValue(v_ref), true);
+						this._goRefCounts[id]--;
+						if (this._goRefCounts[id] === 0) {
+							const v = this._values[id];
+							this._values[id] = null;
+							this._ids.delete(v);
+							this._idPool.push(id);
+						}
+					},
+
+					// func stringVal(value string) ref
+					"syscall/js.stringVal": (value_ptr, value_len) => {
+						const s = loadString(value_ptr, value_len);
+						return boxValue(s);
+					},
+
+					// func valueGet(v ref, p string) ref
+					"syscall/js.valueGet": (v_ref, p_ptr, p_len) => {
+						let prop = loadString(p_ptr, p_len);
+						let v = unboxValue(v_ref);
+						let result = Reflect.get(v, prop);
+						return boxValue(result);
+					},
+
+					// func valueSet(v ref, p string, x ref)
+					"syscall/js.valueSet": (v_ref, p_ptr, p_len, x_ref) => {
+						const v = unboxValue(v_ref);
+						const p = loadString(p_ptr, p_len);
+						const x = unboxValue(x_ref);
+						Reflect.set(v, p, x);
+					},
+
+					// func valueDelete(v ref, p string)
+					"syscall/js.valueDelete": (v_ref, p_ptr, p_len) => {
+						const v = unboxValue(v_ref);
+						const p = loadString(p_ptr, p_len);
+						Reflect.deleteProperty(v, p);
+					},
+
+					// func valueIndex(v ref, i int) ref
+					"syscall/js.valueIndex": (v_ref, i) => {
+						return boxValue(Reflect.get(unboxValue(v_ref), i));
+					},
+
+					// valueSetIndex(v ref, i int, x ref)
+					"syscall/js.valueSetIndex": (v_ref, i, x_ref) => {
+						Reflect.set(unboxValue(v_ref), i, unboxValue(x_ref));
+					},
+
+					// func valueCall(v ref, m string, args []ref) (ref, bool)
+					"syscall/js.valueCall": (ret_addr, v_ref, m_ptr, m_len, args_ptr, args_len, args_cap) => {
+						const v = unboxValue(v_ref);
+						const name = loadString(m_ptr, m_len);
+						const args = loadSliceOfValues(args_ptr, args_len, args_cap);
+						try {
+							const m = Reflect.get(v, name);
+							storeValue(ret_addr, Reflect.apply(m, v, args));
+							mem().setUint8(ret_addr + 8, 1);
+						} catch (err) {
+							storeValue(ret_addr, err);
+							mem().setUint8(ret_addr + 8, 0);
+						}
+					},
+
+					// func valueInvoke(v ref, args []ref) (ref, bool)
+					"syscall/js.valueInvoke": (ret_addr, v_ref, args_ptr, args_len, args_cap) => {
+						try {
+							const v = unboxValue(v_ref);
+							const args = loadSliceOfValues(args_ptr, args_len, args_cap);
+							storeValue(ret_addr, Reflect.apply(v, undefined, args));
+							mem().setUint8(ret_addr + 8, 1);
+						} catch (err) {
+							storeValue(ret_addr, err);
+							mem().setUint8(ret_addr + 8, 0);
+						}
+					},
+
+					// func valueNew(v ref, args []ref) (ref, bool)
+					"syscall/js.valueNew": (ret_addr, v_ref, args_ptr, args_len, args_cap) => {
+						const v = unboxValue(v_ref);
+						const args = loadSliceOfValues(args_ptr, args_len, args_cap);
+						try {
+							storeValue(ret_addr, Reflect.construct(v, args));
+							mem().setUint8(ret_addr + 8, 1);
+						} catch (err) {
+							storeValue(ret_addr, err);
+							mem().setUint8(ret_addr+ 8, 0);
+						}
+					},
+
+					// func valueLength(v ref) int
+					"syscall/js.valueLength": (v_ref) => {
+						return unboxValue(v_ref).length;
+					},
+
+					// valuePrepareString(v ref) (ref, int)
+					"syscall/js.valuePrepareString": (ret_addr, v_ref) => {
+						const s = String(unboxValue(v_ref));
+						const str = encoder.encode(s);
+						storeValue(ret_addr, str);
+						mem().setInt32(ret_addr + 8, str.length, true);
+					},
+
+					// valueLoadString(v ref, b []byte)
+					"syscall/js.valueLoadString": (v_ref, slice_ptr, slice_len, slice_cap) => {
+						const str = unboxValue(v_ref);
+						loadSlice(slice_ptr, slice_len, slice_cap).set(str);
+					},
+
+					// func valueInstanceOf(v ref, t ref) bool
+					"syscall/js.valueInstanceOf": (v_ref, t_ref) => {
+ 						return unboxValue(v_ref) instanceof unboxValue(t_ref);
+					},
+
+					// func copyBytesToGo(dst []byte, src ref) (int, bool)
+					"syscall/js.copyBytesToGo": (ret_addr, dest_addr, dest_len, dest_cap, src_ref) => {
+						let num_bytes_copied_addr = ret_addr;
+						let returned_status_addr = ret_addr + 4; // Address of returned boolean status variable
+
+						const dst = loadSlice(dest_addr, dest_len);
+						const src = unboxValue(src_ref);
+						if (!(src instanceof Uint8Array || src instanceof Uint8ClampedArray)) {
+							mem().setUint8(returned_status_addr, 0); // Return "not ok" status
+							return;
+						}
+						const toCopy = src.subarray(0, dst.length);
+						dst.set(toCopy);
+						mem().setUint32(num_bytes_copied_addr, toCopy.length, true);
+						mem().setUint8(returned_status_addr, 1); // Return "ok" status
+					},
+
+					// copyBytesToJS(dst ref, src []byte) (int, bool)
+					// Originally copied from upstream Go project, then modified:
+					//   https://github.com/golang/go/blob/3f995c3f3b43033013013e6c7ccc93a9b1411ca9/misc/wasm/wasm_exec.js#L404-L416
+					"syscall/js.copyBytesToJS": (ret_addr, dst_ref, src_addr, src_len, src_cap) => {
+						let num_bytes_copied_addr = ret_addr;
+						let returned_status_addr = ret_addr + 4; // Address of returned boolean status variable
+
+						const dst = unboxValue(dst_ref);
+						const src = loadSlice(src_addr, src_len);
+						if (!(dst instanceof Uint8Array || dst instanceof Uint8ClampedArray)) {
+							mem().setUint8(returned_status_addr, 0); // Return "not ok" status
+							return;
+						}
+						const toCopy = src.subarray(0, dst.length);
+						dst.set(toCopy);
+						mem().setUint32(num_bytes_copied_addr, toCopy.length, true);
+						mem().setUint8(returned_status_addr, 1); // Return "ok" status
+					},
+				}
+			};
+
+			// Go 1.20 uses 'env'. Go 1.21 uses 'gojs'.
+			// For compatibility, we use both as long as Go 1.20 is supported.
+			this.importObject.env = this.importObject.gojs;
+		}
+
+		async run(instance) {
+			this._inst = instance;
+			this._values = [ // JS values that Go currently has references to, indexed by reference id
+				NaN,
+				0,
+				null,
+				true,
+				false,
+				global,
+				this,
+			];
+			this._goRefCounts = []; // number of references that Go has to a JS value, indexed by reference id
+			this._ids = new Map();  // mapping from JS values to reference ids
+			this._idPool = [];      // unused ids that have been garbage collected
+			this.exited = false;    // whether the Go program has exited
+
+			while (true) {
+				const callbackPromise = new Promise((resolve) => {
+					this._resolveCallbackPromise = () => {
+						if (this.exited) {
+							throw new Error("bad callback: Go program has already exited");
+						}
+						setTimeout(resolve, 0); // make sure it is asynchronous
+					};
+				});
+				this._inst.exports._start();
+				if (this.exited) {
+					break;
+				}
+				await callbackPromise;
+			}
+		}
+
+		_resume() {
+			if (this.exited) {
+				throw new Error("Go program has already exited");
+			}
+			this._inst.exports.resume();
+			if (this.exited) {
+				this._resolveExitPromise();
+			}
+		}
+
+		_makeFuncWrapper(id) {
+			const go = this;
+			return function () {
+				const event = { id: id, this: this, args: arguments };
+				go._pendingEvent = event;
+				go._resume();
+				return event.result;
+			};
+		}
+	}
+
+	if (
+		global.require &&
+		global.require.main === module &&
+		global.process &&
+		global.process.versions &&
+		!global.process.versions.electron
+	) {
+		if (process.argv.length != 3) {
+			console.error("usage: go_js_wasm_exec [wasm binary] [arguments]");
+			process.exit(1);
+		}
+
+		const go = new Go();
+		WebAssembly.instantiate(fs.readFileSync(process.argv[2]), go.importObject).then((result) => {
+			return go.run(result.instance);
+		}).catch((err) => {
+			console.error(err);
+			process.exit(1);
+		});
+	}
+})();
+
+// wasm setup code
+export default function init (path) {
+	return new Promise ((res) => {
+		const go = new Go();
+		var wasm;
+		
+		if ('instantiateStreaming' in WebAssembly) {
+			WebAssembly.instantiateStreaming(fetch(path), go.importObject).then(function (obj) {
+				wasm = obj.instance;
+				go.run(wasm);
+				res()
+			})
+		} else {
+			fetch(path).then(resp =>
+				resp.arrayBuffer()
+			).then(bytes =>
+				WebAssembly.instantiate(bytes, go.importObject).then(function (obj) {
+					wasm = obj.instance;
+					go.run(wasm);
+					res()
+				})
+			)
+		}
+	}) 
+}