update dev-init

fix missing dist dir make issue
remove minification of wasm.js
2026-07-06 20:47:09 +00:00 · 2026-07-06 20:40:48 +00:00 · 2026-07-06 20:36:42 +00:00 · 2026-07-06 18:44:32 +00:00 · 2025-10-02 21:56:39 +00:00 · 2025-09-30 17:41:14 +00:00
22 changed files with 1616 additions and 468 deletions
@@ -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
-	}
-}
@@ -1,3 +1,2 @@
-**/package-lock.json
-**/node_modules
+go.sum
 dist/*
@@ -0,0 +1,30 @@
+.PHONY: build clean test dev-init
+
+build: clean
+	@echo "======================== Building Binary ======================="
+	mkdir -p dist
+	cp wfa.js dist/wfa.js
+	GOOS=js GOARCH=wasm CGO_ENABLED=0 tinygo build -panic=trap -no-debug -opt=s -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
+
+dev-init:
+	go get -t wfa/test
@@ -0,0 +1,13 @@
+# Using WFA-JS
+
+Download `wfa.js` and `wfa.wasm`from [releases](https://git.tronnet.net/alu/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.
@@ -0,0 +1,15 @@
+module wfa
+
+go 1.26.4
+
+require (
+	github.com/schollz/progressbar/v3 v3.19.1
+	golang.org/x/exp v0.0.0-20260611194520-c48552f49976
+)
+
+require (
+	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
+	github.com/rivo/uniseg v0.4.7 // indirect
+	golang.org/x/sys v0.46.0 // indirect
+	golang.org/x/term v0.44.0 // indirect
+)
@@ -0,0 +1,31 @@
+<!DOCTYPE html>
+<html>
+    <head>
+        <script src="wfa.js" type="module"></script>
+        <script type="module">
+            import wfaInit from "./wfa.js";
+            wfaInit("dist/wfa.wasm");
+            window.addEventListener("DOMContentLoaded", () => {
+                document.querySelector("#submit").addEventListener("click", () => {
+                    a = document.querySelector("#a").value
+                    b = document.querySelector("#b").value
+                    const penalties = {
+                        m: 0,
+                        x: 1,
+                        o: 0,
+                        e: 1
+                    };
+                    const { score, CIGAR } = global.wfa.wfAlign(a, b, penalties, true);
+                    const alignment = global.wfa.DecodeCIGAR(CIGAR);
+                    document.querySelector("#result").innerText = `${score}, ${CIGAR}, ${alignment}`;
+                })
+            });            
+        </script>
+    </head>
+    <body>
+        <label>A: </label><input id="a">
+        <label>B: </label><input id="b">
+        <button id="submit">Submit</button>
+        <p><span>Result: </span><span id="result"></span></p>
+    </body>
+</html>
@@ -0,0 +1,110 @@
+package main
+
+import (
+	"syscall/js"
+	wfa "wfa/pkg"
+)
+
+func main() {
+	c := make(chan bool)
+	js.Global().Get("wfa").Set("wfAlign", js.FuncOf(wfAlign))
+	js.Global().Get("wfa").Set("DecodeCIGAR", js.FuncOf(DecodeCIGAR))
+	<-c
+}
+
+func wfAlign(this js.Value, args []js.Value) interface{} {
+	if len(args) != 4 {
+		resultMap := map[string]interface{}{
+			"ok":    false,
+			"error": "invalid number of args, requires 4: s1, s2, penalties, doCIGAR",
+		}
+		return js.ValueOf(resultMap)
+	}
+
+	if args[0].Type() != js.TypeString {
+		resultMap := map[string]interface{}{
+			"ok":    false,
+			"error": "s1 should be a string",
+		}
+		return js.ValueOf(resultMap)
+	}
+
+	s1 := args[0].String()
+
+	if args[1].Type() != js.TypeString {
+		resultMap := map[string]interface{}{
+			"ok":    false,
+			"error": "s2 should be a string",
+		}
+		return js.ValueOf(resultMap)
+	}
+
+	s2 := args[1].String()
+
+	if args[2].Type() != js.TypeObject {
+		resultMap := map[string]interface{}{
+			"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() {
+		resultMap := map[string]interface{}{
+			"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()
+	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 {
+		resultMap := map[string]interface{}{
+			"ok":    false,
+			"error": "doCIGAR should be a boolean",
+		}
+		return js.ValueOf(resultMap)
+	}
+
+	doCIGAR := args[3].Bool()
+
+	// 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)
+}
@@ -1,20 +0,0 @@
-{
-	"name": "wfa-js",
-	"version": "1.0.0",
-	"description": "Wavefront alignment algorithm in JS",
-	"main": "tests/test.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": {
-		"test": "node tests/test.js",
-		"lint": "DEBUG=eslint:cli-engine eslint --fix src/*.js tests/*.js",
-		"minify": "sed -ze 's/\\t//g; s/\\/\\/[[:print:]]*//g;s/\\n//g;' src/wfa.js > dist/wfa.js"
-	}
-}
@@ -0,0 +1,36 @@
+package wfa
+
+type PositiveSlice[T any] struct {
+	data         []T
+	valid        []bool
+	defaultValue T
+}
+
+func (a *PositiveSlice[T]) Valid(idx int) bool {
+	return 0 <= idx && idx < len(a.valid) && a.valid[idx]
+}
+
+func (a *PositiveSlice[T]) Get(idx int) T {
+	if 0 <= idx && idx < len(a.valid) && a.valid[idx] { // idx is in the slice
+		return a.data[idx]
+	} else { // idx is out of the slice
+		return a.defaultValue
+	}
+}
+
+func (a *PositiveSlice[T]) Set(idx int, value T) {
+	if idx >= len(a.valid) { // idx is outside the slice
+		// expand data array to 2*idx
+		newData := make([]T, 2*idx+1)
+		copy(newData, a.data)
+		a.data = newData
+
+		// expand valid array to 2*idx
+		newValid := make([]bool, 2*idx+1)
+		copy(newValid, a.valid)
+		a.valid = newValid
+	}
+
+	a.data[idx] = value
+	a.valid[idx] = true
+}
@@ -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
+}
@@ -0,0 +1,154 @@
+package wfa
+
+type Integer interface {
+	~int | ~int8 | ~int16 | ~int32 | ~int64 | ~uint | ~uint8 | ~uint16 | ~uint32 | ~uint64 | ~uintptr
+}
+
+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 lo/hi values with 32 bits each
+type WavefrontLoHi uint64
+
+func PackWavefrontLoHi(lo int, hi int) WavefrontLoHi {
+	loBM := int64(int32(lo)) & 0x0000_0000_FFFF_FFFF
+	hiBM := int64(int64(hi) << 32)
+	return WavefrontLoHi(hiBM | loBM)
+}
+
+func UnpackWavefrontLoHi(lohi WavefrontLoHi) (int, int) {
+	loBM := int(int32(lohi & 0x0000_0000_FFFF_FFFF))
+	hiBM := int(int32(lohi & 0xFFFF_FFFF_0000_0000 >> 32))
+	return loBM, hiBM
+}
+
+// bitpacked wavefront values with 1 valid bit, 3 traceback bits, and 60 bits for the diag distance
+type WavefrontValue uint64
+
+// PackWavefrontValue: packs a diag value and traceback into a WavefrontValue
+func PackWavefrontValue(value uint64, traceback Traceback) WavefrontValue {
+	validBM := uint64(0x8000_0000_0000_0000)
+	tracebackBM := uint64(traceback&0x0000_0007) << 60
+	valueBM := uint64(value) & 0x0FFF_FFFF_FFFF_FFFF
+	return WavefrontValue(validBM | tracebackBM | valueBM)
+}
+
+// UnpackWavefrontValue: opens a WavefrontValue into a valid bool, diag value and traceback
+func UnpackWavefrontValue(wfv WavefrontValue) (bool, uint64, Traceback) {
+	validBM := wfv&0x8000_0000_0000_0000 != 0
+	tracebackBM := uint8(wfv & 0x7000_0000_0000_0000 >> 60)
+	valueBM := uint64(wfv & 0x0000_0000_FFFF_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
+	a.data = make([]WavefrontValue, size+1)
+
+	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 = []
+	// }
+	w := &WavefrontComponent{
+		W: &PositiveSlice[*Wavefront]{
+			defaultValue: &Wavefront{
+				data: []WavefrontValue{0},
+			},
+		},
+	}
+
+	return w
+}
+
+// GetVal: get value for wavefront=score, diag=k => returns ok, value, traceback
+func (w *WavefrontComponent) GetVal(score int, k int) (bool, uint64, 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 uint64, 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) {
+	lo, hi := UnpackWavefrontLoHi(w.W.Get(score).lohi)
+	return w.W.Valid(score), lo, hi
+}
+
+// SetLoHi: set lo and hi for wavefront=score
+func (w *WavefrontComponent) SetLoHi(score int, lo int, hi int) {
+	b := NewWavefront(lo, hi)
+	w.W.Set(score, b)
+}
@@ -0,0 +1,169 @@
+package wfa
+
+const MaxInt = int(^uint(0) >> 1)
+const MinInt = -MaxInt - 1
+
+// convert an unsigned into to string
+func UIntToString(num uint) string { // num assumed to be positive
+	str := []rune{}
+
+	for num > 0 {
+		digit := num % 10
+		str = append(str, rune('0'+digit))
+		num /= 10
+	}
+
+	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)
+}
+
+// decode runlength encoded string such as CIGARs
+func RunLengthDecode(encoded string) string {
+	decoded := []rune{}
+	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 = append(decoded, rune(char))
+			}
+			i++ // Move past the character
+		}
+	}
+
+	return string(decoded)
+}
+
+// given the min index, return the item in values at that index
+func SafeMin[T Integer](values []T, idx int) T {
+	return values[idx]
+}
+
+// given the max index, return the item in values at that index
+func SafeMax[T Integer](values []T, idx int) T {
+	return values[idx]
+}
+
+// given array of values and corresponding array of valid flags, find the min of value which is valid or return false if there does not exist any
+func SafeArgMin[T Integer](valids []bool, values []T) (bool, int) {
+	hasValid := false
+	minIndex := 0
+	minValue := 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
+	}
+}
+
+// given array of values and corresponding array of valid flags, find the max of value which is valid or return false if there does not exist any
+func SafeArgMax[T Integer](valids []bool, values []T) (bool, int) {
+	hasValid := false
+	maxIndex := 0
+	maxValue := MinInt
+	for i := range valids {
+		if valids[i] && int(values[i]) > maxValue {
+			hasValid = true
+			maxIndex = i
+			maxValue = int(values[i])
+		}
+	}
+	return hasValid, maxIndex
+}
+
+// set the lext lo and hi bounds for wavefronts M, I, D
+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
+}
+
+// set the traceback and diag value for the next I wavefront
+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}, []uint64{a, b})
+	nextIVal := SafeMax([]uint64{a, b}, nextITraceback) + 1 // important that the +1 is here
+	if ok {
+		I.SetVal(score, k, nextIVal, []Traceback{OpenIns, ExtdIns}[nextITraceback])
+	}
+}
+
+// set the traceback and diag value for the next D wavefront
+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}, []uint64{a, b})
+	nextDVal := SafeMax([]uint64{a, b}, nextDTraceback)
+	if ok {
+		D.SetVal(score, k, nextDVal, []Traceback{OpenDel, ExtdDel}[nextDTraceback])
+	}
+}
+
+// set the traceback and diag value for the next M wavefront
+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}, []uint64{a, b, c})
+	nextMVal := SafeMax([]uint64{a, b, c}, nextMTraceback)
+	if ok {
+		M.SetVal(score, k, nextMVal, []Traceback{Sub, Ins, Del}[nextMTraceback])
+	}
+}
@@ -0,0 +1,195 @@
+package wfa
+
+// WFAlign takes strings s1, s2, penalties, and returns the score and CIGAR if doCIGAR is true
+func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
+	n := len(s1)
+	m := len(s2)
+	A_k := m - n          // diagonal where both sequences end
+	A_offset := uint64(m) // offset along a_k diagonal corresponding to end
+	score := 0
+	M := NewWavefrontComponent()
+	M.SetLoHi(0, 0, 0)
+	M.SetVal(0, 0, 0, End)
+	I := NewWavefrontComponent()
+	D := NewWavefrontComponent()
+
+	for {
+		WFExtend(M, s1, n, s2, m, score)
+		ok, val, _ := M.GetVal(score, A_k)
+		if ok && val >= A_offset { // exit when M_(s,a_k) >= A_offset, ie the wavefront has reached the end
+			break
+		}
+		score = score + 1
+		WFNext(M, I, D, score, penalties)
+	}
+
+	CIGAR := ""
+	if doCIGAR { // if doCIGAR, then perform backtrace, otherwise just return the score
+		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++ { // for each diagonal in current wavefront
+		// v = M[score][k] - k
+		// h = M[score][k]
+		ok, uh, tb := M.GetVal(score, k)
+		// exit early if M_(s,l) is invalid
+		if !ok {
+			continue
+		}
+		h := int(uh)
+		v := h - k
+		// in the paper, we do v++, h++, M_(s,k)++
+		// however, note that h = M_(s,k) so instead we just do v++, h++ and set M_(s,k) at the end
+		// this saves a some memory reads and writes
+		for v < n && h < m && s1[v] == s2[h] { // extend diagonal for the next set of matches
+			v++
+			h++
+		}
+		M.SetVal(score, k, uint64(h), tb)
+	}
+}
+
+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++ { // for each diagonal, extend the matrices for the next wavefronts
+		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 uint64, 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 := ""
+	for i := len(Ops) - 1; i > 0; i-- {
+		CIGAR += UIntToString(Counts[i])
+		CIGAR += string(Ops[i])
+	}
+
+	return CIGAR
+}
@@ -1,356 +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
-	getVal (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
-	setVal (score, k, val) {
-		if (this.W[score]) {
-			this.W[score][k] = val;
-		}
-		else {
-			this.W[score] = [];
-			this.W[score][k] = val;
-		}
-	}
-
-	// get alignment traceback
-	getTraceback (score, k) {
-		if (this.A[score] !== undefined && this.A[score][k] !== undefined) {
-			return this.A[score][k];
-		}
-		else {
-			return undefined;
-		}
-	}
-
-	// set alignment traceback
-	setTraceback (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
-	getHi (score) {
-		const hi = this.hi[score];
-		return isNaN(hi) ? 0 : hi;
-	}
-
-	// set hi for wavefront=score
-	setHi (score, hi) {
-		this.hi[score] = hi;
-	}
-
-	// get lo for wavefront=score
-	getLo (score) {
-		const lo = this.lo[score];
-		return isNaN(lo) ? 0 : lo;
-	}
-
-	// set lo for wavefront=score
-	setLo (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 wfAlign (s1, s2, penalties, doCIGAR = false) {
-	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.setVal(0, 0, 0);
-	M.setHi(0, 0);
-	M.setLo(0, 0);
-	M.setTraceback(0, 0, traceback.End);
-	const I = new WavefrontComponent();
-	const D = new WavefrontComponent();
-	while (true) {
-		wfExtend(M, s1, n, s2, m, score);
-		if (M.getVal(score, A_k) >= A_offset) {
-			break;
-		}
-		score++;
-		wfNext(M, I, D, score, penalties);
-	}
-	let CIGAR = null;
-	if (doCIGAR) {
-		CIGAR = wfBacktrace(M, I, D, score, penalties, A_k, s1, s2);
-	}
-	return { score, CIGAR };
-}
-
-function wfExtend (M, s1, n, s2, m, score) {
-	const lo = M.getLo(score);
-	const hi = M.getHi(score);
-	for (let k = lo; k <= hi; k++) {
-		let v = M.getVal(score, k) - k;
-		let h = M.getVal(score, k);
-		if (isNaN(v) || isNaN(h)) {
-			continue;
-		}
-		while (s1[v] === s2[h]) {
-			M.setVal(score, k, M.getVal(score, k) + 1);
-			v++;
-			h++;
-			if (v > n || h > m) {
-				break;
-			}
-		}
-	}
-}
-
-function wfNext (M, I, D, score, penalties, do_traceback) {
-	const x = penalties.x;
-	const o = penalties.o;
-	const e = penalties.e;
-	const lo = min([M.getLo(score - x), M.getLo(score - o - e), I.getLo(score - e), D.getLo(score - e)]) - 1;
-	const hi = max([M.getHi(score - x), M.getHi(score - o - e), I.getHi(score - e), D.getHi(score - e)]) + 1;
-	M.setHi(score, hi);
-	I.setHi(score, hi);
-	D.setHi(score, hi);
-	M.setLo(score, lo);
-	I.setLo(score, lo);
-	D.setLo(score, lo);
-	for (let k = lo; k <= hi; k++) {
-		I.setVal(score, k, max([
-			M.getVal(score - o - e, k - 1),
-			I.getVal(score - e, k - 1)
-		]) + 1);
-		I.setTraceback(score, k, [traceback.OpenIns, traceback.ExtdIns][argmax([
-			M.getVal(score - o - e, k - 1),
-			I.getVal(score - e, k - 1)
-		])]);
-		D.setVal(score, k, max([
-			M.getVal(score - o - e, k + 1),
-			D.getVal(score - e, k + 1)
-		]));
-		D.setTraceback(score, k, [traceback.OpenDel, traceback.ExtdDel][argmax([
-			M.getVal(score - o - e, k + 1),
-			D.getVal(score - e, k + 1)
-		])]);
-		M.setVal(score, k, max([
-			M.getVal(score - x, k) + 1,
-			I.getVal(score, k),
-			D.getVal(score, k)
-		]));
-		M.setTraceback(score, k, [traceback.Sub, traceback.Ins, traceback.Del][argmax([
-			M.getVal(score - x, k) + 1,
-			I.getVal(score, k),
-			D.getVal(score, k)
-		])]);
-	}
-}
-
-function wfBacktrace (M, I, D, score, penalties, A_k, s1, s2) {
-	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.getTraceback(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.getTraceback(tb_s, tb_k);
-			break;
-		case traceback.ExtdIns:
-			tb_s = tb_s - e;
-			tb_k = tb_k - 1;
-			current_traceback = I.getTraceback(tb_s, tb_k);
-			break;
-		case traceback.OpenDel:
-			tb_s = tb_s - o - e;
-			tb_k = tb_k + 1;
-			current_traceback = M.getTraceback(tb_s, tb_k);
-			break;
-		case traceback.ExtdDel:
-			tb_s = tb_s - e;
-			tb_k = tb_k + 1;
-			current_traceback = D.getTraceback(tb_s, tb_k);
-			break;
-		case traceback.Sub:
-			tb_s = tb_s - x;
-			// tb_k = tb_k;
-			current_traceback = M.getTraceback(tb_s, tb_k);
-			break;
-		case traceback.Ins:
-			// tb_s = tb_s;
-			// tb_k = tb_k;
-			current_traceback = I.getTraceback(tb_s, tb_k);
-			break;
-		case traceback.Del:
-			// tb_s = tb_s;
-			// tb_k = tb_k;
-			current_traceback = D.getTraceback(tb_s, tb_k);
-			break;
-		case traceback.End:
-			done = true;
-			break;
-		}
-	}
-	const CIGAR_part = Array.from(CIGAR_rev).reverse(); // still missing Match positions
-	let c = 0;
-	let i = 0;
-	let j = 0;
-	while (i < s1.length && j < s2.length) { // iterate through the strings to back-solve match positions
-		if (s1[i] === s2[j]) { // match, insert M and then increment c, i, j
-			CIGAR_part.splice(c, 0, "M");
-			c++;
-			i++;
-			j++;
-		}
-		else if (CIGAR_part[c] === "X") { // mismatch, increment c, i, j
-			c++;
-			i++;
-			j++;
-		}
-		else if (CIGAR_part[c] === "I") { // insertion of character to s1 to reach s2, increment c,j
-			c++;
-			j++;
-		}
-		else if (CIGAR_part[c] === "D") { // deletion of character from s1 to reach s2, increment c,i
-			c++;
-			i++;
-		}
-	}
-	return CIGAR_part.join("");
-}
@@ -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"
    }
 }
@@ -0,0 +1,196 @@
+package tests
+
+import (
+	"bufio"
+	"encoding/json"
+	"log"
+	"math/rand/v2"
+	"os"
+	"strconv"
+	"strings"
+	"testing"
+	wfa "wfa/pkg"
+
+	"github.com/schollz/progressbar/v3"
+	"golang.org/x/exp/constraints"
+)
+
+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[T constraints.Integer](min, max int) T {
+	return T(rand.IntN(max-min) + min)
+}
+
+func TestWavefrontPacking(t *testing.T) {
+	for range 1000 {
+		val := randRange[uint64](0, 1000)
+		tb := wfa.Traceback(randRange[uint64](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)
+
+	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)
+		}
+	}
+}
@@ -1,41 +0,0 @@
-import wfAlign from "../src/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
-const timePerChar = [];
-
-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 start = process.hrtime()[1];
-		const { score } = wfAlign(s1, s2, penalties, false);
-		const elapsed = process.hrtime()[1] - start;
-		timePerChar.push((elapsed / 1e9) / (s1.length + s2.length));
-		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`);
-	console.log(`average time per character (ms): ${average(timePerChar) * 1000}`);
-}
-
-function average (arr) {
-	const sum = arr.reduce((a, b) => a + b, 0);
-	return sum / arr.length;
-}
@@ -0,0 +1,579 @@
+// 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 = [];
+	const wasmExit = {}; // thrown to exit via proc_exit (not an error)
+
+	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) => {
+						this.exited = true;
+						this.exitCode = code;
+						this._resolveExitPromise();
+						throw wasmExit;
+					},
+					random_get: (bufPtr, bufLen) => {
+						crypto.getRandomValues(loadSlice(bufPtr, bufLen));
+						return 0;
+					},
+				},
+				gojs: {
+					// func ticks() int64
+					"runtime.ticks": () => {
+						return BigInt((timeOrigin + performance.now()) * 1e6);
+					},
+
+					// func sleepTicks(timeout int64)
+					"runtime.sleepTicks": (timeout) => {
+						// Do not sleep, only reactivate scheduler after the given timeout.
+						setTimeout(() => {
+							if (this.exited) return;
+							try {
+								this._inst.exports.go_scheduler();
+							} catch (e) {
+								if (e !== wasmExit) throw e;
+							}
+						}, Number(timeout)/1e6);
+					},
+
+					// func finalizeRef(v ref)
+					"syscall/js.finalizeRef": (v_ref) => {
+						// Note: TinyGo does not support finalizers so this is only called
+						// for one specific case, by js.go:jsString. and can/might leak memory.
+						const id = v_ref & 0xffffffffn;
+						if (this._goRefCounts?.[id] !== undefined) {
+							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);
+							}
+						} else {
+							console.error("syscall/js.finalizeRef: unknown id", id);
+						}
+					},
+
+					// func stringVal(value string) ref
+					"syscall/js.stringVal": (value_ptr, value_len) => {
+						value_ptr >>>= 0;
+						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
+			this.exitCode = 0;
+
+			if (this._inst.exports._start) {
+				let exitPromise = new Promise((resolve, reject) => {
+					this._resolveExitPromise = resolve;
+				});
+
+				// Run program, but catch the wasmExit exception that's thrown
+				// to return back here.
+				try {
+					this._inst.exports._start();
+				} catch (e) {
+					if (e !== wasmExit) throw e;
+				}
+
+				await exitPromise;
+				return this.exitCode;
+			} else {
+				this._inst.exports._initialize();
+			}
+		}
+
+		_resume() {
+			if (this.exited) {
+				throw new Error("Go program has already exited");
+			}
+			try {
+				this._inst.exports.resume();
+			} catch (e) {
+				if (e !== wasmExit) throw e;
+			}
+			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(async (result) => {
+			let exitCode = await go.run(result.instance);
+			process.exit(exitCode);
+		}).catch((err) => {
+			console.error(err);
+			process.exit(1);
+		});
+	}
+})();
+
+// wasm setup code
+export default function init (path) {
+	return new Promise ((res) => {
+		const go = new Go();
+		const run = (obj) => {
+			const wasm = obj.instance;
+			global.wfa = wasm
+			go.run(wasm);
+			res()
+		}
+		if ('instantiateStreaming' in WebAssembly) {
+			WebAssembly.instantiateStreaming(fetch(path), go.importObject).then(function (obj) {
+				run(obj)				
+			})
+		} else {
+			fetch(path).then(resp =>
+				resp.arrayBuffer()
+			).then(bytes =>
+				WebAssembly.instantiate(bytes, go.importObject).then(function (obj) {
+					run(obj)	
+				})
+			)
+		}
+	}) 
+}
Author	SHA1	Message	Date
alu	f8f8636cc3	update dev-init	2026-07-06 20:47:09 +00:00
alu	13b522f6a0	fix missing dist dir make issue	2026-07-06 20:40:48 +00:00
alu	05cd2d79df	remove minification of wasm.js	2026-07-06 20:36:42 +00:00
alu	bc52a250a4	update go mod	2026-07-06 18:44:32 +00:00
=	830c0a7586	update wfa.js, reduce clobbering of global namespaces	2025-10-02 21:56:39 +00:00
=	c94a7902c0	remove imports, switch to opt=s, add debug index.html	2025-09-30 17:41:14 +00:00
alu	8ccb45748d	update go mod	2025-09-17 06:13:27 +00:00
alu	63a375995c	minor code cleanup, use uint64 for wavefront values	2025-05-07 21:20:13 +00:00
alu	2351faf2d7	cleanup code	2025-05-01 18:04:42 +00:00
alu	a446bbd923	fix readme, update go mod	2025-03-12 00:09:18 +00:00
alu	f1407fd045	remove unused PositiveSlice Preallocate	2024-11-12 19:04:02 +00:00
alu	ce635cc2b1	remove wavefront component preallocation	2024-11-12 18:53:03 +00:00
alu	f5d2528e20	fix comment	2024-11-12 18:47:25 +00:00
alu	6f78825876	optimize build size by avoiding fmt, pack lo/hi values into Wavefront	2024-11-12 18:44:12 +00:00
alu	a878da42a3	update README	2024-11-08 22:49:37 +00:00
alu	bd720f06fb	minor optimization switching to wavefront pointers	2024-11-08 21:51:17 +00:00
alu	1bbf38aaab	fix DecodeCIGAR argument hint	2024-11-07 20:58:17 +00:00
alu	cde429cb80	fix issue in WFBacktrace and change format to proper CIGAR, add test to ensure CIGAR correctness in the case of different traceback results, add DecodeCIGAR function to exports	2024-11-07 19:01:01 +00:00
alu	3da3ddf10c	major optimization by packing wavefront values	2024-11-05 18:28:28 +00:00
alu	8679c51fb0	update go mod, move Wavefront String method to debug file, minor optimizations	2024-11-05 05:35:46 +00:00
alu	2c7adbef06	implement missing finalizeRef implementation from go wasm_exec.js	2024-11-01 17:23:04 +00:00
alu	65516fbd50	move wfa.js glue script to root, add minify wfa.js job to build command	2024-10-29 17:36:25 +00:00
alu	a3beca4ed2	various optimizations to compute time, add more profiling options to make test	2024-10-29 17:03:19 +00:00
alu	aed3ac6f8f	add import instructions to README	2024-10-24 18:29:50 +00:00
alu	547dffd8ee	rewrite in go and compile to wasm	2024-10-24 18:07:10 +00:00