update README

add test to ensure CIGAR correctness in the case of different traceback results,
add DecodeCIGAR function to exports

.eslintrc.json

@@ -1,43 +0,0 @@
-{
-	"env": {
-		"es2021": true,
-		"node": true
-	},
-	"extends": "standard",
-	"parserOptions": {
-		"ecmaVersion": "latest",
-		"sourceType": "module"
-	},
-	"rules": {
-		"no-tabs": [
-			"error",
-			{
-				"allowIndentationTabs": true
-			}
-		],
-		"indent": [
-			"error",
-			"tab"
-		],
-		"linebreak-style": [
-			"error",
-			"unix"
-		],
-		"quotes": [
-			"error",
-			"double"
-		],
-		"semi": [
-			"error",
-			"always"
-		],
-		"brace-style": [
-			"error",
-			"stroustrup",
-			{
-				"allowSingleLine": false
-			}
-		],
-		"camelcase": 0
-	}
-}

.gitignore

@@ -1,2 +1,2 @@
-**/package-lock.json
+go.sum
-**/node_modules
+dist/*

Makefile

@@ -0,0 +1,26 @@
+.PHONY: build clean test
+
+build: clean
+	@echo "======================== Building Binary ======================="
+	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 dist/wfa.js cover.prof cpu.prof mem.prof test.test
+
+test:
+	@echo "======================== Running Tests ========================="
+	go test -v -cover -coverpkg=./pkg/ -coverprofile cover.prof -cpuprofile cpu.prof -memprofile mem.prof ./test/
+	@echo "======================= Coverage Report ========================"
+	go tool cover -func=cover.prof
+	@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

@@ -0,0 +1,13 @@
+# Using WFA-JS
+
+Download `wfa.js` and `wfa.wasm`from [releases](https://git.tronnet.net/tronnet/WFA-JS/releases) to your project. Add to your script:
+
+```
+import wfa from "./wfa.js"
+await wfa("<path to wasm>")
+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

@@ -0,0 +1,15 @@
+module wfa
+
+go 1.23.2
+
+require (
+	github.com/schollz/progressbar/v3 v3.17.0
+	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 v0.26.0 // indirect
+	golang.org/x/term v0.25.0 // indirect
+)

main.go

@@ -0,0 +1,91 @@
+package main
+
+import (
+	"fmt"
+	"syscall/js"
+	wfa "wfa/pkg"
+)
+
+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")
+		return nil
+	}
+
+	if args[0].Type() != js.TypeString {
+		fmt.Println("s1 should be a string")
+		return nil
+	}
+
+	s1 := args[0].String()
+
+	if args[1].Type() != js.TypeString {
+		fmt.Println("s2 should be a string")
+		return nil
+	}
+
+	s2 := args[1].String()
+
+	if args[2].Type() != js.TypeObject {
+		fmt.Println("penalties should be a map with key values m, x, o, e")
+		return nil
+	}
+
+	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")
+		return nil
+	}
+
+	m := args[2].Get("m").Int()
+	x := args[2].Get("x").Int()
+	o := args[2].Get("o").Int()
+	e := args[2].Get("e").Int()
+
+	penalties := wfa.Penalty{
+		M: m,
+		X: x,
+		O: o,
+		E: e,
+	}
+
+	if args[3].Type() != js.TypeBoolean {
+		fmt.Println("doCIGAR should be a boolean")
+		return nil
+	}
+
+	doCIGAR := args[3].Bool()
+
+	// Call the actual func.
+	result := wfa.WFAlign(s1, s2, penalties, doCIGAR)
+	resultMap := map[string]interface{}{
+		"score": result.Score,
+		"CIGAR": result.CIGAR,
+	}
+
+	return js.ValueOf(resultMap)
+}
+
+func DecodeCIGAR(this js.Value, args []js.Value) interface{} {
+	if len(args) != 1 {
+		fmt.Println("invalid number of args, requires 1: CIGAR")
+		return nil
+	}
+
+	if args[0].Type() != js.TypeString {
+		fmt.Println("CIGAR should be a string")
+		return nil
+	}
+
+	CIGAR := args[0].String()
+
+	decoded := wfa.RunLengthDecode(CIGAR)
+
+	return js.ValueOf(decoded)
+}

package.json

@@ -1,18 +0,0 @@
-{
-	"name": "wfa-js",
-	"version": "0.0.1",
-	"description": "Wavefront alignment algorithm in JS",
-	"main": "src/main.js",
-	"type": "module",
-	"devDependencies": {
-		"eslint": "^8.43.0",
-		"eslint-config-standard": "^17.1.0",
-		"eslint-plugin-import": "^2.27.5",
-		"eslint-plugin-n": "^16.0.1",
-		"eslint-plugin-promise": "^6.1.1",
-		"progress": "^2.0.3"
-	},
-	"scripts": {
-		"lint": "DEBUG=eslint:cli-engine eslint --fix ."
-	}
-}

pkg/custom_slice.go

@@ -0,0 +1,55 @@
+package wfa
+
+type PositiveSlice[T any] struct {
+	data         []T
+	valid        []bool
+	defaultValue T
+}
+
+func (a *PositiveSlice[T]) TranslateIndex(idx int) int {
+	return idx
+}
+
+func (a *PositiveSlice[T]) Valid(idx int) bool {
+	actualIdx := a.TranslateIndex(idx)
+	return 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx]
+}
+
+func (a *PositiveSlice[T]) Get(idx int) T {
+	actualIdx := a.TranslateIndex(idx)
+	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
+	}
+}
+
+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, 2*actualIdx+1)
+		copy(newData, a.data)
+		a.data = newData
+
+		// expand valid array to actualIdx
+		newValid := make([]bool, 2*actualIdx+1)
+		copy(newValid, a.valid)
+		a.valid = newValid
+	}
+
+	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

@@ -0,0 +1,79 @@
+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++ {
+		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++ {
+			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

@@ -0,0 +1,164 @@
+package wfa
+
+type Result struct {
+	Score int
+	CIGAR string
+}
+
+type Penalty struct {
+	M int
+	X int
+	O int
+	E int
+}
+
+type Traceback byte
+
+const (
+	OpenIns Traceback = iota
+	ExtdIns
+	OpenDel
+	ExtdDel
+	Sub
+	Ins
+	Del
+	End
+)
+
+// bitpacked wavefront values with 1 valid bit, 3 traceback bits, and 28 bits for the diag distance
+// 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 score is needed
+
+// PackWavefrontValue: packs a diag value and traceback into a WavefrontValue
+func PackWavefrontValue(value uint32, traceback Traceback) WavefrontValue {
+	valueBM := value & 0x0FFF_FFFF
+	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) {
+	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
+	lo   int
+}
+
+// NewWavefront: returns a new wavefront with size accomodating lo and hi (inclusive)
+func NewWavefront(lo int, hi int) *Wavefront {
+	a := &Wavefront{}
+
+	a.lo = lo
+	size := a.TranslateIndex(hi)
+
+	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 {
+	return diagonal - a.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 {
+	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(preallocateSize int) *WavefrontComponent {
+	// new wavefront component = {
+	// lo = [0]
+	// hi = [0]
+	// W = []
+	// }
+	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},
+			},
+		},
+	}
+
+	w.lo.Preallocate(preallocateSize)
+	w.hi.Preallocate(preallocateSize)
+	w.W.Preallocate(preallocateSize)
+
+	return w
+}
+
+// GetVal: get value for wavefront=score, diag=k => returns ok, value, traceback
+func (w *WavefrontComponent) GetVal(score int, k int) (bool, uint32, Traceback) {
+	return UnpackWavefrontValue(w.W.Get(score).Get(k))
+}
+
+// SetVal: set value, traceback for wavefront=score, diag=k
+func (w *WavefrontComponent) SetVal(score int, k int, val uint32, tb Traceback) {
+	w.W.Get(score).Set(k, PackWavefrontValue(val, tb))
+}
+
+// GetLoHi: get lo and hi for wavefront=score
+func (w *WavefrontComponent) GetLoHi(score int) (bool, int, int) {
+	// if lo[score] and hi[score] are valid
+	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

@@ -0,0 +1,169 @@
+package wfa
+
+import (
+	"math"
+	"strings"
+
+	"golang.org/x/exp/constraints"
+)
+
+func UIntToString(num uint) string { // num assumed to be positive
+	var builder strings.Builder
+
+	for num > 0 {
+		digit := num % 10
+		builder.WriteRune(rune('0' + digit))
+		num /= 10
+	}
+
+	// Reverse the string as we built it in reverse order
+	str := []rune(builder.String())
+	for i, j := 0, len(str)-1; i < j; i, j = i+1, j-1 {
+		str[i], str[j] = str[j], str[i]
+	}
+
+	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] && int(values[i]) > maxValue {
+			hasValid = true
+			maxIndex = i
+			maxValue = int(values[i])
+		}
+	}
+	if hasValid {
+		return true, maxIndex
+	} else {
+		return false, 0
+	}
+}
+
+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] && int(values[i]) < minValue {
+			hasValid = true
+			minIndex = i
+			minValue = int(values[i])
+		}
+	}
+	if hasValid {
+		return true, minIndex
+	} else {
+		return false, 0
+	}
+}
+
+func NextLoHi(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, penalties Penalty) (int, int) {
+	x := penalties.X
+	o := penalties.O
+	e := penalties.E
+
+	a_ok, a_lo, a_hi := M.GetLoHi(score - x)
+	b_ok, b_lo, b_hi := M.GetLoHi(score - o - e)
+	c_ok, c_lo, c_hi := I.GetLoHi(score - e)
+	d_ok, d_lo, d_hi := D.GetLoHi(score - e)
+
+	ok_lo, idx := SafeArgMin(
+		[]bool{a_ok, b_ok, c_ok, d_ok},
+		[]int{a_lo, b_lo, c_lo, d_lo},
+	)
+	lo := SafeMin([]int{a_lo, b_lo, c_lo, d_lo}, idx) - 1
+
+	ok_hi, idx := SafeArgMax(
+		[]bool{a_ok, b_ok, c_ok, d_ok},
+		[]int{a_hi, b_hi, c_hi, d_hi},
+	)
+	hi := SafeMax([]int{a_hi, b_hi, c_hi, d_hi}, idx) + 1
+
+	if ok_lo && ok_hi {
+		M.SetLoHi(score, lo, hi)
+		I.SetLoHi(score, lo, hi)
+		D.SetLoHi(score, lo, hi)
+	}
+	return lo, hi
+}
+
+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)
+	b_ok, b, _ := I.GetVal(score-e, k-1)
+
+	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, []Traceback{OpenIns, ExtdIns}[nextITraceback])
+	}
+}
+
+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)
+	b_ok, b, _ := D.GetVal(score-e, k+1)
+
+	ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint32{a, b})
+	nextDVal := SafeMax([]uint32{a, b}, nextDTraceback)
+	if ok {
+		D.SetVal(score, k, nextDVal, []Traceback{OpenDel, ExtdDel}[nextDTraceback])
+	}
+}
+
+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++ // important to have +1 here
+	b_ok, b, _ := I.GetVal(score, k)
+	c_ok, c, _ := D.GetVal(score, k)
+
+	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, []Traceback{Sub, Ins, Del}[nextMTraceback])
+	}
+}

pkg/wfa.go

@@ -0,0 +1,198 @@
+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 := uint32(m)
+	score := 0
+	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(estimatedScore)
+	D := NewWavefrontComponent(estimatedScore)
+
+	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, A_offset, s1, s2)
+	}
+
+	return Result{
+		Score: score,
+		CIGAR: CIGAR,
+	}
+}
+
+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
+		// h = M[score][k]
+		ok, hu, _ := M.GetVal(score, k)
+		h := int(hu)
+		v := h - k
+
+		// exit early if v or h are invalid
+		if !ok {
+			continue
+		}
+		for v < n && h < m && s1[v] == s2[h] {
+			_, val, tb := M.GetVal(score, k)
+			M.SetVal(score, k, val+1, tb)
+			v++
+			h++
+		}
+	}
+}
+
+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)
+
+	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, A_offset uint32, s1 string, s2 string) string {
+	x := penalties.X
+	o := penalties.O
+	e := penalties.E
+
+	tb_s := score
+	tb_k := A_k
+	done := false
+
+	_, current_dist, current_traceback := M.GetVal(tb_s, tb_k)
+
+	Ops := []rune{'~'}
+	Counts := []uint{0}
+	idx := 0
+
+	for !done {
+		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_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_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_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_dist, current_traceback = D.GetVal(tb_s, tb_k)
+		case Sub:
+			tb_s = tb_s - x
+			// tb_k = 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;
+			_, 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;
+			_, 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 := strings.Builder{}
+	for i := len(Ops) - 1; i > 0; i-- {
+		CIGAR.WriteString(UIntToString(Counts[i]))
+		CIGAR.WriteRune(Ops[i])
+	}
+
+	return CIGAR.String()
+}

src/main.js

@@ -1,31 +0,0 @@
-import wf_align from "./wfa.js";
-import fs from "fs";
-import ProgressBar from "progress";
-
-let data = fs.readFileSync("./tests/tests.json");
-data = JSON.parse(data);
-const sequences = fs.readFileSync("./tests/sequences").toString().split("\n");
-// const total = sequences.length;
-const total = 500; // skip the later tests because of memory usage
-
-for (const test_name of Object.keys(data)) {
-	const test = data[test_name];
-	const penalties = test.penalties;
-	const solutions = fs.readFileSync(test.solutions).toString().split("\n");
-	const bar = new ProgressBar(":bar :current/:total", { total: total / 2 });
-	console.log(`test: ${test_name}`);
-	let correct = 0;
-	let j = 0;
-	for (let i = 0; i < total; i += 2) {
-		const s1 = sequences[i].replace(">");
-		const s2 = sequences[i + 1].replace("<");
-		const { CIGAR, score } = wf_align(s1, s2, penalties);
-		const solution_score = Number(solutions[j].split("\t")[0]);
-		if (solution_score === -score) {
-			correct += 1;
-		}
-		j += 1;
-		bar.tick();
-	}
-	console.log(`correct: ${correct}\ntotal: ${total / 2}\n`);
-}

src/wfa.js

@@ -1,328 +0,0 @@
-class WavefrontComponent {
-	constructor () {
-		this.lo = [0]; // lo for each wavefront
-		this.hi = [0]; // hi for each wavefront
-		this.W = []; // wavefront diag distance for each wavefront
-		this.A = []; // compact CIGAR for backtrace
-	}
-
-	// get value for wavefront=score, diag=k
-	get_val (score, k) {
-		if (this.W[score] !== undefined && this.W[score][k] !== undefined) {
-			return this.W[score][k];
-		}
-		else {
-			return NaN;
-		}
-	}
-
-	// set value for wavefront=score, diag=k
-	set_val (score, k, val) {
-		if (this.W[score]) {
-			this.W[score][k] = val;
-		}
-		else {
-			this.W[score] = [];
-			this.W[score][k] = val;
-		}
-	}
-
-	// get alignment traceback
-	get_traceback (score, k) {
-		if (this.A[score] !== undefined && this.A[score][k] !== undefined) {
-			return this.A[score][k];
-		}
-		else {
-			return undefined;
-		}
-	}
-
-	// set alignment traceback
-	set_traceback (score, k, traceback) {
-		if (this.A[score]) {
-			this.A[score][k] = traceback;
-		}
-		else {
-			this.A[score] = [];
-			this.A[score][k] = traceback;
-		}
-	}
-
-	// get hi for wavefront=score
-	get_hi (score) {
-		const hi = this.hi[score];
-		return isNaN(hi) ? 0 : hi;
-	}
-
-	// set hi for wavefront=score
-	set_hi (score, hi) {
-		this.hi[score] = hi;
-	}
-
-	// get lo for wavefront=score
-	get_lo (score) {
-		const lo = this.lo[score];
-		return isNaN(lo) ? 0 : lo;
-	}
-
-	// set lo for wavefront=score
-	set_lo (score, lo) {
-		this.lo[score] = lo;
-	}
-
-	// string representation of all wavefronts
-	toString () {
-		const traceback_str = ["OI", "EI", "OD", "ED", "SB", "IN", "DL", "EN"];
-		let s = "<";
-		let min_lo = Infinity;
-		let max_hi = -Infinity;
-		// get the min lo and max hi values across all wavefronts
-		for (let i = 0; i < this.W.length; i++) {
-			const lo = this.lo[i];
-			const hi = this.hi[i];
-			if (lo < min_lo) {
-				min_lo = lo;
-			}
-			if (hi > max_hi) {
-				max_hi = hi;
-			}
-		}
-		// print out two headers, one for wavefront and one for traceback
-		for (let k = min_lo; k <= max_hi; k++) {
-			s += FormatNumberLength(k, 2);
-			if (k < max_hi) {
-				s += "|";
-			}
-		}
-		s += ">\t<";
-		for (let k = min_lo; k <= max_hi; k++) {
-			s += FormatNumberLength(k, 2);
-			if (k < max_hi) {
-				s += "|";
-			}
-		}
-		s += ">\n";
-		// for each wavefront
-		for (let i = 0; i < this.W.length; i++) {
-			s += "[";
-			const lo = this.lo[i];
-			const hi = this.hi[i];
-			// print out the wavefront matrix
-			for (let k = min_lo; k <= max_hi; k++) {
-				if (this.W[i] !== undefined && this.W[i][k] !== undefined && !isNaN(this.W[i][k])) {
-					s += FormatNumberLength(this.W[i][k], 2);
-				}
-				else if (k < lo || k > hi) {
-					s += "--";
-				}
-				else {
-					s += "  ";
-				}
-				if (k < max_hi) {
-					s += "|";
-				}
-			}
-			s += "]\t[";
-			// print out the traceback matrix
-			for (let k = min_lo; k <= max_hi; k++) {
-				if (this.A[i] !== undefined && this.A[i][k] !== undefined) {
-					s += traceback_str[this.A[i][k].toString()];
-				}
-				else if (k < lo || k > hi) {
-					s += "--";
-				}
-				else {
-					s += "  ";
-				}
-				if (k < max_hi) {
-					s += "|";
-				}
-			}
-			s += "]\n";
-		}
-		return s;
-	}
-}
-
-const traceback = {
-	OpenIns: 0,
-	ExtdIns: 1,
-	OpenDel: 2,
-	ExtdDel: 3,
-	Sub: 4,
-	Ins: 5,
-	Del: 6,
-	End: 7
-};
-
-function FormatNumberLength (num, length) {
-	let r = "" + num;
-	while (r.length < length) {
-		r = " " + r;
-	}
-	return r;
-}
-
-function min (args) {
-	args.forEach((el, idx, arr) => {
-		arr[idx] = isNaN(el) ? Infinity : el;
-	});
-	const min = Math.min.apply(Math, args);
-	return min === Infinity ? NaN : min;
-}
-
-function max (args) {
-	args.forEach((el, idx, arr) => {
-		arr[idx] = isNaN(el) ? -Infinity : el;
-	});
-	const max = Math.max.apply(Math, args);
-	return max === -Infinity ? NaN : max;
-}
-
-function argmax (args) {
-	const val = max(args);
-	return args.indexOf(val);
-}
-
-export default function wf_align (s1, s2, penalties) {
-	const n = s1.length;
-	const m = s2.length;
-	const A_k = m - n;
-	const A_offset = m;
-	let score = 0;
-	const M = new WavefrontComponent();
-	M.set_val(0, 0, 0);
-	M.set_hi(0, 0);
-	M.set_lo(0, 0);
-	M.set_traceback(0, 0, traceback.End);
-	const I = new WavefrontComponent();
-	const D = new WavefrontComponent();
-	while (true) {
-		wf_extend(M, s1, n, s2, m, score);
-		if (M.get_val(score, A_k) >= A_offset) {
-			break;
-		}
-		score++;
-		wf_next(M, I, D, score, penalties);
-	}
-	return wf_backtrace(M, I, D, score, penalties, A_k, A_offset);
-}
-
-function wf_extend (M, s1, n, s2, m, score) {
-	const lo = M.get_lo(score);
-	const hi = M.get_hi(score);
-	for (let k = lo; k <= hi; k++) {
-		let v = M.get_val(score, k) - k;
-		let h = M.get_val(score, k);
-		if (isNaN(v) || isNaN(h)) {
-			continue;
-		}
-		while (s1[v] === s2[h]) {
-			M.set_val(score, k, M.get_val(score, k) + 1);
-			v++;
-			h++;
-			if (v > n || h > m) {
-				break;
-			}
-		}
-	}
-}
-
-function wf_next (M, I, D, score, penalties) {
-	const x = penalties.x;
-	const o = penalties.o;
-	const e = penalties.e;
-	const lo = min([M.get_lo(score - x), M.get_lo(score - o - e), I.get_lo(score - e), D.get_lo(score - e)]) - 1;
-	const hi = max([M.get_hi(score - x), M.get_hi(score - o - e), I.get_hi(score - e), D.get_hi(score - e)]) + 1;
-	M.set_hi(score, hi);
-	I.set_hi(score, hi);
-	D.set_hi(score, hi);
-	M.set_lo(score, lo);
-	I.set_lo(score, lo);
-	D.set_lo(score, lo);
-	for (let k = lo; k <= hi; k++) {
-		I.set_val(score, k, max([
-			M.get_val(score - o - e, k - 1),
-			I.get_val(score - e, k - 1)
-		]) + 1);
-		I.set_traceback(score, k, [traceback.OpenIns, traceback.ExtdIns][argmax([
-			M.get_val(score - o - e, k - 1),
-			I.get_val(score - e, k - 1)
-		])]);
-		D.set_val(score, k, max([
-			M.get_val(score - o - e, k + 1),
-			D.get_val(score - e, k + 1)
-		]));
-		D.set_traceback(score, k, [traceback.OpenDel, traceback.ExtdDel][argmax([
-			M.get_val(score - o - e, k + 1),
-			D.get_val(score - e, k + 1)
-		])]);
-		M.set_val(score, k, max([
-			M.get_val(score - x, k) + 1,
-			I.get_val(score, k),
-			D.get_val(score, k)
-		]));
-		M.set_traceback(score, k, [traceback.Sub, traceback.Ins, traceback.Del][argmax([
-			M.get_val(score - x, k) + 1,
-			I.get_val(score, k),
-			D.get_val(score, k)
-		])]);
-	}
-}
-
-function wf_backtrace (M, I, D, score, penalties, A_k) {
-	const traceback_CIGAR = ["I", "I", "D", "D", "X", "", "", ""];
-	const x = penalties.x;
-	const o = penalties.o;
-	const e = penalties.e;
-	let CIGAR_rev = ""; // reversed CIGAR
-	let tb_s = score; // traceback score
-	let tb_k = A_k; // traceback diag k
-	let current_traceback = M.get_traceback(tb_s, tb_k);
-	let done = false;
-	while (!done) {
-		CIGAR_rev += traceback_CIGAR[current_traceback];
-		switch (current_traceback) {
-		case traceback.OpenIns:
-			tb_s = tb_s - o - e;
-			tb_k = tb_k - 1;
-			current_traceback = M.get_traceback(tb_s, tb_k);
-			break;
-		case traceback.ExtdIns:
-			tb_s = tb_s - e;
-			tb_k = tb_k - 1;
-			current_traceback = I.get_traceback(tb_s, tb_k);
-			break;
-		case traceback.OpenDel:
-			tb_s = tb_s - o - e;
-			tb_k = tb_k + 1;
-			current_traceback = M.get_traceback(tb_s, tb_k);
-			break;
-		case traceback.ExtdDel:
-			tb_s = tb_s - e;
-			tb_k = tb_k + 1;
-			current_traceback = D.get_traceback(tb_s, tb_k);
-			break;
-		case traceback.Sub:
-			tb_s = tb_s - x;
-			// tb_k = tb_k;
-			current_traceback = M.get_traceback(tb_s, tb_k);
-			break;
-		case traceback.Ins:
-			// tb_s = tb_s;
-			// tb_k = tb_k;
-			current_traceback = I.get_traceback(tb_s, tb_k);
-			break;
-		case traceback.Del:
-			// tb_s = tb_s;
-			// tb_k = tb_k;
-			current_traceback = D.get_traceback(tb_s, tb_k);
-			break;
-		case traceback.End:
-			done = true;
-			break;
-		}
-	}
-	const CIGAR = Array.from(CIGAR_rev).reverse().join("");
-	return { CIGAR, score };
-}

test/tests.json

@@ -6,7 +6,7 @@
             "o": 2,
             "e": 1
         },
-        "solutions": "./tests/test_affine_p0_sol"
+        "solutions": "test_affine_p0_sol"
     },
     "p1": {
         "penalties": {
@@ -15,7 +15,7 @@
             "o": 1,
             "e": 4
         },
-        "solutions": "./tests/test_affine_p1_sol"
+        "solutions": "test_affine_p1_sol"
     },
     "p2": {
         "penalties": {
@@ -24,6 +24,6 @@
             "o": 3,
             "e": 2
         },
-        "solutions": "./tests/test_affine_p2_sol"
+        "solutions": "test_affine_p2_sol"
     }
 }

test/wfa_test.go

@@ -0,0 +1,181 @@
+package tests
+
+import (
+	"bufio"
+	"encoding/json"
+	"log"
+	"math/rand/v2"
+	"os"
+	"strconv"
+	"strings"
+	"testing"
+	wfa "wfa/pkg"
+
+	"github.com/schollz/progressbar/v3"
+)
+
+const testJsonPath = "tests.json"
+const testSequences = "sequences"
+
+type TestPenalty struct {
+	M int `json:"m"`
+	X int `json:"x"`
+	O int `json:"o"`
+	E int `json:"e"`
+}
+
+type TestCase struct {
+	Penalties TestPenalty `json:"penalties"`
+	Solutions string      `json:"solutions"`
+}
+
+func randRange(min, max int) uint32 {
+	return uint32(rand.IntN(max-min) + min)
+}
+
+func TestWavefrontPacking(t *testing.T) {
+	for range 1000 {
+		val := randRange(0, 1000)
+		tb := wfa.Traceback(randRange(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 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)
+
+	var testMap map[string]TestCase
+	json.Unmarshal(content, &testMap)
+
+	for k, v := range testMap {
+		testName := k
+
+		testPenalties := wfa.Penalty{
+			M: v.Penalties.M,
+			X: v.Penalties.X,
+			O: v.Penalties.O,
+			E: v.Penalties.E,
+		}
+
+		sequencesFile, _ := os.Open(testSequences)
+		sequences := bufio.NewScanner(sequencesFile)
+		solutionsFile, _ := os.Open(v.Solutions)
+		solutions := bufio.NewScanner(solutionsFile)
+
+		bar := progressbar.Default(305, k)
+
+		idx := 0
+
+		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()
+			s1 = s1[1:]
+
+			sequences.Scan()
+			s2 := sequences.Text()
+			s2 = s2[1:]
+
+			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`, 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++
+			bar.Add(1)
+		}
+	}
+}

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()
+				})
+			)
+		}
+	}) 
+}