fix missing dist dir make issue

remove minification of wasm.js
update go mod
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 · 2025-09-17 06:13:27 +00:00
8 changed files with 125 additions and 80 deletions
@@ -2,8 +2,9 @@

 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 .
+	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 ======================"
@@ -1,15 +1,15 @@
 module wfa

-go 1.23.6
+go 1.26.4

 require (
-	github.com/schollz/progressbar/v3 v3.17.1
-	golang.org/x/exp v0.0.0-20241108190413-2d47ceb2692f
+	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 v0.27.0 // indirect
-	golang.org/x/term v0.26.0 // 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>
@@ -7,8 +7,8 @@ import (

 func main() {
 	c := make(chan bool)
-	js.Global().Set("wfAlign", js.FuncOf(wfAlign))
-	js.Global().Set("DecodeCIGAR", js.FuncOf(DecodeCIGAR))
+	js.Global().Get("wfa").Set("wfAlign", js.FuncOf(wfAlign))
+	js.Global().Get("wfa").Set("DecodeCIGAR", js.FuncOf(DecodeCIGAR))
 	<-c
 }

@@ -1,5 +1,9 @@
 package wfa

+type Integer interface {
+	~int | ~int8 | ~int16 | ~int32 | ~int64 | ~uint | ~uint8 | ~uint16 | ~uint32 | ~uint64 | ~uintptr
+}
+
 type Result struct {
 	Score int
 	CIGAR string
@@ -1,24 +1,18 @@
 package wfa

-import (
-	"math"
-	"strings"
-
-	"golang.org/x/exp/constraints"
-)
+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
-	var builder strings.Builder
+	str := []rune{}

 	for num > 0 {
 		digit := num % 10
-		builder.WriteRune(rune('0' + digit))
+		str = append(str, 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]
 	}
@@ -28,7 +22,7 @@ func UIntToString(num uint) string { // num assumed to be positive

 // decode runlength encoded string such as CIGARs
 func RunLengthDecode(encoded string) string {
-	decoded := strings.Builder{}
+	decoded := []rune{}
 	length := len(encoded)
 	i := 0

@@ -44,30 +38,30 @@ func RunLengthDecode(encoded string) string {
 		if i < length {
 			char := encoded[i]
 			for j := 0; j < runLength; j++ {
-				decoded.WriteByte(char)
+				decoded = append(decoded, rune(char))
 			}
 			i++ // Move past the character
 		}
 	}

-	return decoded.String()
+	return string(decoded)
 }

 // given the min index, return the item in values at that index
-func SafeMin[T constraints.Integer](values []T, idx int) T {
+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 constraints.Integer](values []T, idx int) T {
+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 constraints.Integer](valids []bool, values []T) (bool, int) {
+func SafeArgMin[T Integer](valids []bool, values []T) (bool, int) {
 	hasValid := false
 	minIndex := 0
-	minValue := math.MaxInt
+	minValue := MaxInt
 	for i := 0; i < len(valids); i++ {
 		if valids[i] && int(values[i]) < minValue {
 			hasValid = true
@@ -83,10 +77,10 @@ func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
 }

 // 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 constraints.Integer](valids []bool, values []T) (bool, int) {
+func SafeArgMax[T Integer](valids []bool, values []T) (bool, int) {
 	hasValid := false
 	maxIndex := 0
-	maxValue := math.MinInt
+	maxValue := MinInt
 	for i := range valids {
 		if valids[i] && int(values[i]) > maxValue {
 			hasValid = true
@@ -1,9 +1,5 @@
 package wfa

-import (
-	"strings"
-)
-
 // 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)
@@ -189,11 +185,11 @@ func WFBacktrace(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontCompo
 		}
 	}

-	CIGAR := strings.Builder{}
+	CIGAR := ""
 	for i := len(Ops) - 1; i > 0; i-- {
-		CIGAR.WriteString(UIntToString(Counts[i]))
-		CIGAR.WriteRune(Ops[i])
+		CIGAR += UIntToString(Counts[i])
+		CIGAR += string(Ops[i])
 	}

-	return CIGAR.String()
+	return CIGAR
 }
@@ -1,5 +1,3 @@
-// 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.
@@ -134,6 +132,7 @@
 	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() {
@@ -272,14 +271,11 @@
 					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;
-						}
+					proc_exit: (code) => {
+						this.exited = true;
+						this.exitCode = code;
+						this._resolveExitPromise();
+						throw wasmExit;
 					},
 					random_get: (bufPtr, bufLen) => {
 						crypto.getRandomValues(loadSlice(bufPtr, bufLen));
@@ -287,31 +283,45 @@
 					},
 				},
 				gojs: {
-					// func ticks() float64
+					// func ticks() int64
 					"runtime.ticks": () => {
-						return timeOrigin + performance.now();
+						return BigInt((timeOrigin + performance.now()) * 1e6);
 					},

-					// func sleepTicks(timeout float64)
+					// func sleepTicks(timeout int64)
 					"runtime.sleepTicks": (timeout) => {
 						// Do not sleep, only reactivate scheduler after the given timeout.
-						setTimeout(this._inst.exports.go_scheduler, 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) => {
-						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);
+						// 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);
 					},
@@ -472,21 +482,25 @@
 			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;

-			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
-					};
+			if (this._inst.exports._start) {
+				let exitPromise = new Promise((resolve, reject) => {
+					this._resolveExitPromise = resolve;
 				});
-				this._inst.exports._start();
-				if (this.exited) {
-					break;
+
+				// 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 callbackPromise;
+
+				await exitPromise;
+				return this.exitCode;
+			} else {
+				this._inst.exports._initialize();
 			}
 		}

@@ -494,7 +508,11 @@
 			if (this.exited) {
 				throw new Error("Go program has already exited");
 			}
-			this._inst.exports.resume();
+			try {
+				this._inst.exports.resume();
+			} catch (e) {
+				if (e !== wasmExit) throw e;
+			}
 			if (this.exited) {
 				this._resolveExitPromise();
 			}
@@ -524,8 +542,9 @@
 		}

 		const go = new Go();
-		WebAssembly.instantiate(fs.readFileSync(process.argv[2]), go.importObject).then((result) => {
-			return go.run(result.instance);
+		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);
@@ -537,22 +556,22 @@
 export default function init (path) {
 	return new Promise ((res) => {
 		const go = new Go();
-		var wasm;
-		
+		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) {
-				wasm = obj.instance;
-				go.run(wasm);
-				res()
+				run(obj)				
 			})
 		} else {
 			fetch(path).then(resp =>
 				resp.arrayBuffer()
 			).then(bytes =>
 				WebAssembly.instantiate(bytes, go.importObject).then(function (obj) {
-					wasm = obj.instance;
-					go.run(wasm);
-					res()
+					run(obj)	
 				})
 			)
 		}
Author	SHA1	Message	Date
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