.gitignore

@@ -1,3 +1,2 @@
 **/package-lock.json
 **/node_modules
-dist/*

package.json

@@ -1,8 +1,8 @@
 {
 	"name": "wfa-js",
-	"version": "1.0.0",
+	"version": "0.0.1",
 	"description": "Wavefront alignment algorithm in JS",
-	"main": "tests/test.js",
+	"main": "src/main.js",
 	"type": "module",
 	"devDependencies": {
 		"eslint": "^8.43.0",
@@ -13,8 +13,6 @@
 		"progress": "^2.0.3"
 	},
 	"scripts": {
-		"test": "node tests/test.js",
+		"lint": "DEBUG=eslint:cli-engine eslint --fix ."
-		"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"
 	}
 }

src/main.js

@@ -1,4 +1,4 @@
-import wfAlign from "../src/wfa.js";
+import wf_align from "./wfa.js";
 import fs from "fs";
 import ProgressBar from "progress";
 
@@ -7,7 +7,6 @@ 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];
@@ -20,10 +19,7 @@ for (const test_name of Object.keys(data)) {
 	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 { CIGAR, score } = wf_align(s1, s2, penalties);
-		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;
@@ -32,10 +28,4 @@ for (const test_name of Object.keys(data)) {
 		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;
 }

src/wfa.js

@@ -7,7 +7,7 @@ class WavefrontComponent {
 	}
 
 	// get value for wavefront=score, diag=k
-	getVal (score, k) {
+	get_val (score, k) {
 		if (this.W[score] !== undefined && this.W[score][k] !== undefined) {
 			return this.W[score][k];
 		}
@@ -17,7 +17,7 @@ class WavefrontComponent {
 	}
 
 	// set value for wavefront=score, diag=k
-	setVal (score, k, val) {
+	set_val (score, k, val) {
 		if (this.W[score]) {
 			this.W[score][k] = val;
 		}
@@ -28,7 +28,7 @@ class WavefrontComponent {
 	}
 
 	// get alignment traceback
-	getTraceback (score, k) {
+	get_traceback (score, k) {
 		if (this.A[score] !== undefined && this.A[score][k] !== undefined) {
 			return this.A[score][k];
 		}
@@ -38,7 +38,7 @@ class WavefrontComponent {
 	}
 
 	// set alignment traceback
-	setTraceback (score, k, traceback) {
+	set_traceback (score, k, traceback) {
 		if (this.A[score]) {
 			this.A[score][k] = traceback;
 		}
@@ -49,24 +49,24 @@ class WavefrontComponent {
 	}
 
 	// get hi for wavefront=score
-	getHi (score) {
+	get_hi (score) {
 		const hi = this.hi[score];
 		return isNaN(hi) ? 0 : hi;
 	}
 
 	// set hi for wavefront=score
-	setHi (score, hi) {
+	set_hi (score, hi) {
 		this.hi[score] = hi;
 	}
 
 	// get lo for wavefront=score
-	getLo (score) {
+	get_lo (score) {
 		const lo = this.lo[score];
 		return isNaN(lo) ? 0 : lo;
 	}
 
 	// set lo for wavefront=score
-	setLo (score, lo) {
+	set_lo (score, lo) {
 		this.lo[score] = lo;
 	}
 
@@ -184,45 +184,41 @@ function argmax (args) {
 	return args.indexOf(val);
 }
 
-export default function wfAlign (s1, s2, penalties, doCIGAR = false) {
+export default function wf_align (s1, s2, penalties) {
 	const n = s1.length;
 	const m = s2.length;
 	const A_k = m - n;
 	const A_offset = m;
 	let score = 0;
 	const M = new WavefrontComponent();
-	M.setVal(0, 0, 0);
+	M.set_val(0, 0, 0);
-	M.setHi(0, 0);
+	M.set_hi(0, 0);
-	M.setLo(0, 0);
+	M.set_lo(0, 0);
-	M.setTraceback(0, 0, traceback.End);
+	M.set_traceback(0, 0, traceback.End);
 	const I = new WavefrontComponent();
 	const D = new WavefrontComponent();
 	while (true) {
-		wfExtend(M, s1, n, s2, m, score);
+		wf_extend(M, s1, n, s2, m, score);
-		if (M.getVal(score, A_k) >= A_offset) {
+		if (M.get_val(score, A_k) >= A_offset) {
 			break;
 		}
 		score++;
-		wfNext(M, I, D, score, penalties);
+		wf_next(M, I, D, score, penalties);
 	}
-	let CIGAR = null;
+	return wf_backtrace(M, I, D, score, penalties, A_k, A_offset);
-	if (doCIGAR) {
-		CIGAR = wfBacktrace(M, I, D, score, penalties, A_k, s1, s2);
-	}
-	return { score, CIGAR };
 }
 
-function wfExtend (M, s1, n, s2, m, score) {
+function wf_extend (M, s1, n, s2, m, score) {
-	const lo = M.getLo(score);
+	const lo = M.get_lo(score);
-	const hi = M.getHi(score);
+	const hi = M.get_hi(score);
 	for (let k = lo; k <= hi; k++) {
-		let v = M.getVal(score, k) - k;
+		let v = M.get_val(score, k) - k;
-		let h = M.getVal(score, k);
+		let h = M.get_val(score, k);
 		if (isNaN(v) || isNaN(h)) {
 			continue;
 		}
 		while (s1[v] === s2[h]) {
-			M.setVal(score, k, M.getVal(score, k) + 1);
+			M.set_val(score, k, M.get_val(score, k) + 1);
 			v++;
 			h++;
 			if (v > n || h > m) {
@@ -232,49 +228,49 @@ function wfExtend (M, s1, n, s2, m, score) {
 	}
 }
 
-function wfNext (M, I, D, score, penalties, do_traceback) {
+function wf_next (M, I, D, score, penalties) {
 	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 lo = min([M.get_lo(score - x), M.get_lo(score - o - e), I.get_lo(score - e), D.get_lo(score - e)]) - 1;
-	const hi = max([M.getHi(score - x), M.getHi(score - o - e), I.getHi(score - e), D.getHi(score - e)]) + 1;
+	const hi = max([M.get_hi(score - x), M.get_hi(score - o - e), I.get_hi(score - e), D.get_hi(score - e)]) + 1;
-	M.setHi(score, hi);
+	M.set_hi(score, hi);
-	I.setHi(score, hi);
+	I.set_hi(score, hi);
-	D.setHi(score, hi);
+	D.set_hi(score, hi);
-	M.setLo(score, lo);
+	M.set_lo(score, lo);
-	I.setLo(score, lo);
+	I.set_lo(score, lo);
-	D.setLo(score, lo);
+	D.set_lo(score, lo);
 	for (let k = lo; k <= hi; k++) {
-		I.setVal(score, k, max([
+		I.set_val(score, k, max([
-			M.getVal(score - o - e, k - 1),
+			M.get_val(score - o - e, k - 1),
-			I.getVal(score - e, k - 1)
+			I.get_val(score - e, k - 1)
 		]) + 1);
-		I.setTraceback(score, k, [traceback.OpenIns, traceback.ExtdIns][argmax([
+		I.set_traceback(score, k, [traceback.OpenIns, traceback.ExtdIns][argmax([
-			M.getVal(score - o - e, k - 1),
+			M.get_val(score - o - e, k - 1),
-			I.getVal(score - e, k - 1)
+			I.get_val(score - e, k - 1)
 		])]);
-		D.setVal(score, k, max([
+		D.set_val(score, k, max([
-			M.getVal(score - o - e, k + 1),
+			M.get_val(score - o - e, k + 1),
-			D.getVal(score - e, k + 1)
+			D.get_val(score - e, k + 1)
 		]));
-		D.setTraceback(score, k, [traceback.OpenDel, traceback.ExtdDel][argmax([
+		D.set_traceback(score, k, [traceback.OpenDel, traceback.ExtdDel][argmax([
-			M.getVal(score - o - e, k + 1),
+			M.get_val(score - o - e, k + 1),
-			D.getVal(score - e, k + 1)
+			D.get_val(score - e, k + 1)
 		])]);
-		M.setVal(score, k, max([
+		M.set_val(score, k, max([
-			M.getVal(score - x, k) + 1,
+			M.get_val(score - x, k) + 1,
-			I.getVal(score, k),
+			I.get_val(score, k),
-			D.getVal(score, k)
+			D.get_val(score, k)
 		]));
-		M.setTraceback(score, k, [traceback.Sub, traceback.Ins, traceback.Del][argmax([
+		M.set_traceback(score, k, [traceback.Sub, traceback.Ins, traceback.Del][argmax([
-			M.getVal(score - x, k) + 1,
+			M.get_val(score - x, k) + 1,
-			I.getVal(score, k),
+			I.get_val(score, k),
-			D.getVal(score, k)
+			D.get_val(score, k)
 		])]);
 	}
 }
 
-function wfBacktrace (M, I, D, score, penalties, A_k, s1, s2) {
+function wf_backtrace (M, I, D, score, penalties, A_k) {
 	const traceback_CIGAR = ["I", "I", "D", "D", "X", "", "", ""];
 	const x = penalties.x;
 	const o = penalties.o;
@@ -282,7 +278,7 @@ function wfBacktrace (M, I, D, score, penalties, A_k, s1, s2) {
 	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 current_traceback = M.get_traceback(tb_s, tb_k);
 	let done = false;
 	while (!done) {
 		CIGAR_rev += traceback_CIGAR[current_traceback];
@@ -290,67 +286,43 @@ function wfBacktrace (M, I, D, score, penalties, A_k, s1, s2) {
 		case traceback.OpenIns:
 			tb_s = tb_s - o - e;
 			tb_k = tb_k - 1;
-			current_traceback = M.getTraceback(tb_s, tb_k);
+			current_traceback = M.get_traceback(tb_s, tb_k);
 			break;
 		case traceback.ExtdIns:
 			tb_s = tb_s - e;
 			tb_k = tb_k - 1;
-			current_traceback = I.getTraceback(tb_s, tb_k);
+			current_traceback = I.get_traceback(tb_s, tb_k);
 			break;
 		case traceback.OpenDel:
 			tb_s = tb_s - o - e;
 			tb_k = tb_k + 1;
-			current_traceback = M.getTraceback(tb_s, tb_k);
+			current_traceback = M.get_traceback(tb_s, tb_k);
 			break;
 		case traceback.ExtdDel:
 			tb_s = tb_s - e;
 			tb_k = tb_k + 1;
-			current_traceback = D.getTraceback(tb_s, tb_k);
+			current_traceback = D.get_traceback(tb_s, tb_k);
 			break;
 		case traceback.Sub:
 			tb_s = tb_s - x;
 			// tb_k = tb_k;
-			current_traceback = M.getTraceback(tb_s, tb_k);
+			current_traceback = M.get_traceback(tb_s, tb_k);
 			break;
 		case traceback.Ins:
 			// tb_s = tb_s;
 			// tb_k = tb_k;
-			current_traceback = I.getTraceback(tb_s, tb_k);
+			current_traceback = I.get_traceback(tb_s, tb_k);
 			break;
 		case traceback.Del:
 			// tb_s = tb_s;
 			// tb_k = tb_k;
-			current_traceback = D.getTraceback(tb_s, tb_k);
+			current_traceback = D.get_traceback(tb_s, tb_k);
 			break;
 		case traceback.End:
 			done = true;
 			break;
 		}
 	}
-	const CIGAR_part = Array.from(CIGAR_rev).reverse(); // still missing Match positions
+	const CIGAR = Array.from(CIGAR_rev).reverse().join("");
-	let c = 0;
+	return { CIGAR, score };
-	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("");
 }