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base: alu/WFA-JS:v2.0.4
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alu/WFA-JS:main
alu/WFA-JS:v2.0.5 alu/WFA-JS:v2.0.4 alu/WFA-JS:v2.0.3 alu/WFA-JS:v2.0.2 alu/WFA-JS:v2.0.1 alu/WFA-JS:v2.0.0 alu/WFA-JS:v1.0.0 alu/WFA-JS:v0.0.2 alu/WFA-JS:0.0.1
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compare: alu/WFA-JS:f8f8636cc3f00e3fa0c379b490b7df05b9df3d2c
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alu/WFA-JS:main
alu/WFA-JS:v2.0.5 alu/WFA-JS:v2.0.4 alu/WFA-JS:v2.0.3 alu/WFA-JS:v2.0.2 alu/WFA-JS:v2.0.1 alu/WFA-JS:v2.0.0 alu/WFA-JS:v1.0.0 alu/WFA-JS:v0.0.2 alu/WFA-JS:0.0.1

7 Commits
v2.0.4 .. f8f8636cc3

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
8 changed files with 125 additions and 81 deletions
Expand all files Collapse all files
Makefile
+3 -3
View File
@@ -2,8 +2,9 @@
build: clean build: clean
@echo "======================== Building Binary =======================" @echo "======================== Building Binary ======================="
minify wfa.js > dist/wfa.js mkdir -p dist
GOOS=js GOARCH=wasm CGO_ENABLED=0 tinygo build -panic=trap -no-debug -opt=2 -target=wasm -o dist/wfa.wasm . 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: clean:
@echo "======================== Cleaning Project ======================" @echo "======================== Cleaning Project ======================"
@@ -26,5 +27,4 @@ test:
@rm -f test.test @rm -f test.test
dev-init: dev-init:
apt install minify
go get -t wfa/test go get -t wfa/test
go.mod
+5 -5
View File
@@ -1,15 +1,15 @@
module wfa module wfa
go 1.23.6 go 1.26.4
require ( require (
github.com/schollz/progressbar/v3 v3.17.1 github.com/schollz/progressbar/v3 v3.19.1
golang.org/x/exp v0.0.0-20241108190413-2d47ceb2692f golang.org/x/exp v0.0.0-20260611194520-c48552f49976
) )
require ( require (
github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
github.com/rivo/uniseg v0.4.7 // indirect github.com/rivo/uniseg v0.4.7 // indirect
golang.org/x/sys v0.27.0 // indirect golang.org/x/sys v0.46.0 // indirect
golang.org/x/term v0.26.0 // indirect golang.org/x/term v0.44.0 // indirect
) )
index.html
+31
View File
@@ -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>
main.go
+2 -2
View File
@@ -7,8 +7,8 @@ import (
func main() { func main() {
c := make(chan bool) c := make(chan bool)
js.Global().Set("wfAlign", js.FuncOf(wfAlign)) js.Global().Get("wfa").Set("wfAlign", js.FuncOf(wfAlign))
js.Global().Set("DecodeCIGAR", js.FuncOf(DecodeCIGAR)) js.Global().Get("wfa").Set("DecodeCIGAR", js.FuncOf(DecodeCIGAR))
<-c <-c
} }
pkg/types.go
+4
View File
@@ -1,5 +1,9 @@
package wfa package wfa
type Integer interface {
~int | ~int8 | ~int16 | ~int32 | ~int64 | ~uint | ~uint8 | ~uint16 | ~uint32 | ~uint64 | ~uintptr
}
type Result struct { type Result struct {
Score int Score int
CIGAR string CIGAR string
pkg/utils.go
+13 -19
View File
@@ -1,24 +1,18 @@
package wfa package wfa
import ( const MaxInt = int(^uint(0) >> 1)
"math" const MinInt = -MaxInt - 1
"strings"
"golang.org/x/exp/constraints"
)
// convert an unsigned into to string // convert an unsigned into to string
func UIntToString(num uint) string { // num assumed to be positive func UIntToString(num uint) string { // num assumed to be positive
var builder strings.Builder str := []rune{}
for num > 0 { for num > 0 {
digit := num % 10 digit := num % 10
builder.WriteRune(rune('0' + digit)) str = append(str, rune('0'+digit))
num /= 10 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 { for i, j := 0, len(str)-1; i < j; i, j = i+1, j-1 {
str[i], str[j] = str[j], str[i] 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 // decode runlength encoded string such as CIGARs
func RunLengthDecode(encoded string) string { func RunLengthDecode(encoded string) string {
decoded := strings.Builder{} decoded := []rune{}
length := len(encoded) length := len(encoded)
i := 0 i := 0
@@ -44,30 +38,30 @@ func RunLengthDecode(encoded string) string {
if i < length { if i < length {
char := encoded[i] char := encoded[i]
for j := 0; j < runLength; j++ { for j := 0; j < runLength; j++ {
decoded.WriteByte(char) decoded = append(decoded, rune(char))
} }
i++ // Move past the character i++ // Move past the character
} }
} }
return decoded.String() return string(decoded)
} }
// given the min index, return the item in values at that index // 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] return values[idx]
} }
// given the max index, return the item in values at that index // 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] 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 // 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 hasValid := false
minIndex := 0 minIndex := 0
minValue := math.MaxInt minValue := MaxInt
for i := 0; i < len(valids); i++ { for i := 0; i < len(valids); i++ {
if valids[i] && int(values[i]) < minValue { if valids[i] && int(values[i]) < minValue {
hasValid = true 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 // 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 hasValid := false
maxIndex := 0 maxIndex := 0
maxValue := math.MinInt maxValue := MinInt
for i := range valids { for i := range valids {
if valids[i] && int(values[i]) > maxValue { if valids[i] && int(values[i]) > maxValue {
hasValid = true hasValid = true
pkg/wfa.go
+4 -8
View File
@@ -1,9 +1,5 @@
package wfa package wfa
import (
"strings"
)
// WFAlign takes strings s1, s2, penalties, and returns the score and CIGAR if doCIGAR is true // 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 { func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
n := len(s1) 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-- { for i := len(Ops) - 1; i > 0; i-- {
CIGAR.WriteString(UIntToString(Counts[i])) CIGAR += UIntToString(Counts[i])
CIGAR.WriteRune(Ops[i]) CIGAR += string(Ops[i])
} }
return CIGAR.String() return CIGAR
} }
wfa.js
+63 -44
View File
@@ -1,5 +1,3 @@
// wasm_exec.js from tinygo
// Copyright 2018 The Go Authors. All rights reserved. // Copyright 2018 The Go Authors. All rights reserved.
// Use of this source code is governed by a BSD-style // Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file. // license that can be found in the LICENSE file.
@@ -134,6 +132,7 @@
const decoder = new TextDecoder("utf-8"); const decoder = new TextDecoder("utf-8");
let reinterpretBuf = new DataView(new ArrayBuffer(8)); let reinterpretBuf = new DataView(new ArrayBuffer(8));
var logLine = []; var logLine = [];
const wasmExit = {}; // thrown to exit via proc_exit (not an error)
global.Go = class { global.Go = class {
constructor() { constructor() {
@@ -272,14 +271,11 @@
fd_close: () => 0, // dummy fd_close: () => 0, // dummy
fd_fdstat_get: () => 0, // dummy fd_fdstat_get: () => 0, // dummy
fd_seek: () => 0, // dummy fd_seek: () => 0, // dummy
"proc_exit": (code) => { proc_exit: (code) => {
if (global.process) { this.exited = true;
// Node.js this.exitCode = code;
process.exit(code); this._resolveExitPromise();
} else { throw wasmExit;
// Can't exit in a browser.
throw 'trying to exit with code ' + code;
}
}, },
random_get: (bufPtr, bufLen) => { random_get: (bufPtr, bufLen) => {
crypto.getRandomValues(loadSlice(bufPtr, bufLen)); crypto.getRandomValues(loadSlice(bufPtr, bufLen));
@@ -287,31 +283,45 @@
}, },
}, },
gojs: { gojs: {
// func ticks() float64 // func ticks() int64
"runtime.ticks": () => { "runtime.ticks": () => {
return timeOrigin + performance.now(); return BigInt((timeOrigin + performance.now()) * 1e6);
}, },
// func sleepTicks(timeout float64) // func sleepTicks(timeout int64)
"runtime.sleepTicks": (timeout) => { "runtime.sleepTicks": (timeout) => {
// Do not sleep, only reactivate scheduler after the given 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) // func finalizeRef(v ref)
"syscall/js.finalizeRef": (v_ref) => { "syscall/js.finalizeRef": (v_ref) => {
const id = mem().getUint32(unboxValue(v_ref), true); // Note: TinyGo does not support finalizers so this is only called
this._goRefCounts[id]--; // for one specific case, by js.go:jsString. and can/might leak memory.
if (this._goRefCounts[id] === 0) { const id = v_ref & 0xffffffffn;
const v = this._values[id]; if (this._goRefCounts?.[id] !== undefined) {
this._values[id] = null; this._goRefCounts[id]--;
this._ids.delete(v); if (this._goRefCounts[id] === 0) {
this._idPool.push(id); 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 // func stringVal(value string) ref
"syscall/js.stringVal": (value_ptr, value_len) => { "syscall/js.stringVal": (value_ptr, value_len) => {
value_ptr >>>= 0;
const s = loadString(value_ptr, value_len); const s = loadString(value_ptr, value_len);
return boxValue(s); return boxValue(s);
}, },
@@ -472,21 +482,25 @@
this._ids = new Map(); // mapping from JS values to reference ids this._ids = new Map(); // mapping from JS values to reference ids
this._idPool = []; // unused ids that have been garbage collected this._idPool = []; // unused ids that have been garbage collected
this.exited = false; // whether the Go program has exited this.exited = false; // whether the Go program has exited
this.exitCode = 0;
while (true) { if (this._inst.exports._start) {
const callbackPromise = new Promise((resolve) => { let exitPromise = new Promise((resolve, reject) => {
this._resolveCallbackPromise = () => { this._resolveExitPromise = resolve;
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) { // Run program, but catch the wasmExit exception that's thrown
break; // 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) { if (this.exited) {
throw new Error("Go program has already 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) { if (this.exited) {
this._resolveExitPromise(); this._resolveExitPromise();
} }
@@ -524,8 +542,9 @@
} }
const go = new Go(); const go = new Go();
WebAssembly.instantiate(fs.readFileSync(process.argv[2]), go.importObject).then((result) => { WebAssembly.instantiate(fs.readFileSync(process.argv[2]), go.importObject).then(async (result) => {
return go.run(result.instance); let exitCode = await go.run(result.instance);
process.exit(exitCode);
}).catch((err) => { }).catch((err) => {
console.error(err); console.error(err);
process.exit(1); process.exit(1);
@@ -537,22 +556,22 @@
export default function init (path) { export default function init (path) {
return new Promise ((res) => { return new Promise ((res) => {
const go = new Go(); const go = new Go();
var wasm; const run = (obj) => {
const wasm = obj.instance;
global.wfa = wasm
go.run(wasm);
res()
}
if ('instantiateStreaming' in WebAssembly) { if ('instantiateStreaming' in WebAssembly) {
WebAssembly.instantiateStreaming(fetch(path), go.importObject).then(function (obj) { WebAssembly.instantiateStreaming(fetch(path), go.importObject).then(function (obj) {
wasm = obj.instance; run(obj)
go.run(wasm);
res()
}) })
} else { } else {
fetch(path).then(resp => fetch(path).then(resp =>
resp.arrayBuffer() resp.arrayBuffer()
).then(bytes => ).then(bytes =>
WebAssembly.instantiate(bytes, go.importObject).then(function (obj) { WebAssembly.instantiate(bytes, go.importObject).then(function (obj) {
wasm = obj.instance; run(obj)
go.run(wasm);
res()
}) })
) )
} }