remove imports,
switch to opt=s, add debug index.html
This commit is contained in:
=
2
Makefile
2
Makefile
@@ -3,7 +3,7 @@
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build: clean
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@echo "======================== Building Binary ======================="
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minify wfa.js > dist/wfa.js
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GOOS=js GOARCH=wasm CGO_ENABLED=0 tinygo build -panic=trap -no-debug -opt=2 -target=wasm -o dist/wfa.wasm .
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GOOS=js GOARCH=wasm CGO_ENABLED=0 tinygo build -panic=trap -no-debug -opt=s -target=wasm -o dist/wfa.wasm .
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clean:
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@echo "======================== Cleaning Project ======================"
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31
index.html
Normal file
31
index.html
Normal file
@@ -0,0 +1,31 @@
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<!DOCTYPE html>
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<html>
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<head>
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<script src="dist/wfa.js" type="module"></script>
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<script type="module">
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import wfaInit from "./dist/wfa.js";
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window.addEventListener("DOMContentLoaded", () => {
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wfaInit("dist/wfa.wasm");
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document.querySelector("#submit").addEventListener("click", () => {
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a = document.querySelector("#a").value
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b = document.querySelector("#b").value
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const penalties = {
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m: 0,
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x: 1,
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o: 0,
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e: 1
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};
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const { score, CIGAR } = global.wfAlign(a, b, penalties, true);
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const alignment = global.DecodeCIGAR(CIGAR);
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document.querySelector("#result").innerText = `${score}, ${CIGAR}, ${alignment}`;
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})
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});
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</script>
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</head>
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<body>
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<label>A: </label><input id="a">
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<label>B: </label><input id="b">
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<button id="submit">Submit</button>
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<p><span>Result: </span><span id="result"></span></p>
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</body>
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</html>
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@@ -1,5 +1,9 @@
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package wfa
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type Integer interface {
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~int | ~int8 | ~int16 | ~int32 | ~int64 | ~uint | ~uint8 | ~uint16 | ~uint32 | ~uint64 | ~uintptr
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}
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type Result struct {
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Score int
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CIGAR string
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32
pkg/utils.go
32
pkg/utils.go
@@ -1,24 +1,18 @@
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package wfa
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import (
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"math"
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"strings"
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"golang.org/x/exp/constraints"
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)
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const MaxInt = int(^uint(0) >> 1)
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const MinInt = -MaxInt - 1
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// convert an unsigned into to string
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func UIntToString(num uint) string { // num assumed to be positive
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var builder strings.Builder
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str := []rune{}
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for num > 0 {
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digit := num % 10
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builder.WriteRune(rune('0' + digit))
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str = append(str, rune('0'+digit))
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num /= 10
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}
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// Reverse the string as we built it in reverse order
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str := []rune(builder.String())
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for i, j := 0, len(str)-1; i < j; i, j = i+1, j-1 {
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str[i], str[j] = str[j], str[i]
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}
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@@ -28,7 +22,7 @@ func UIntToString(num uint) string { // num assumed to be positive
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// decode runlength encoded string such as CIGARs
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func RunLengthDecode(encoded string) string {
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decoded := strings.Builder{}
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decoded := []rune{}
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length := len(encoded)
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i := 0
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@@ -44,30 +38,30 @@ func RunLengthDecode(encoded string) string {
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if i < length {
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char := encoded[i]
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for j := 0; j < runLength; j++ {
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decoded.WriteByte(char)
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decoded = append(decoded, rune(char))
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}
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i++ // Move past the character
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}
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}
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return decoded.String()
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return string(decoded)
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}
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// given the min index, return the item in values at that index
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func SafeMin[T constraints.Integer](values []T, idx int) T {
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func SafeMin[T Integer](values []T, idx int) T {
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return values[idx]
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}
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// given the max index, return the item in values at that index
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func SafeMax[T constraints.Integer](values []T, idx int) T {
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func SafeMax[T Integer](values []T, idx int) T {
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return values[idx]
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}
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// 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
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func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
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func SafeArgMin[T Integer](valids []bool, values []T) (bool, int) {
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hasValid := false
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minIndex := 0
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minValue := math.MaxInt
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minValue := MaxInt
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for i := 0; i < len(valids); i++ {
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if valids[i] && int(values[i]) < minValue {
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hasValid = true
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@@ -83,10 +77,10 @@ func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) {
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}
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// 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
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func SafeArgMax[T constraints.Integer](valids []bool, values []T) (bool, int) {
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func SafeArgMax[T Integer](valids []bool, values []T) (bool, int) {
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hasValid := false
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maxIndex := 0
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maxValue := math.MinInt
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maxValue := MinInt
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for i := range valids {
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if valids[i] && int(values[i]) > maxValue {
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hasValid = true
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12
pkg/wfa.go
12
pkg/wfa.go
@@ -1,9 +1,5 @@
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package wfa
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import (
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"strings"
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)
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// WFAlign takes strings s1, s2, penalties, and returns the score and CIGAR if doCIGAR is true
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func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
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n := len(s1)
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@@ -189,11 +185,11 @@ func WFBacktrace(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontCompo
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}
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}
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CIGAR := strings.Builder{}
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CIGAR := ""
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for i := len(Ops) - 1; i > 0; i-- {
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CIGAR.WriteString(UIntToString(Counts[i]))
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CIGAR.WriteRune(Ops[i])
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CIGAR += UIntToString(Counts[i])
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CIGAR += string(Ops[i])
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}
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return CIGAR.String()
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return CIGAR
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}
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