@genome-spy/app 0.89.0 → 1.0.0

package/dist/{esm-lwYrRdbg.js → esm-Bv7Frz7C.js}

@@ -6,49 +6,46 @@ function e(e) {
 	}
 	return -1;
 }
-function t(t, n, r, i) {
-	let a = n.length, o = 0;
+function t(t, n, r, i, a = 0, o = n.length) {
+	let s = o, c = a;
 	if (t === "GT") {
 		for (let e = 0; e < r; e++) {
-			let t = o;
-			for (; o < a && n.charCodeAt(o) !== 9;) o++;
-			i(n, t, o, e), o++;
+			let t = c;
+			for (; c < s && n.charCodeAt(c) !== 9;) c++;
+			i(n, t, c, e), c++;
 		}
 		return;
 	}
-	let s = e(t);
-	if (s !== -1) {
-		if (s === 0) {
+	let l = e(t);
+	if (l !== -1) {
+		if (l === 0) {
 			for (let e = 0; e < r; e++) {
-				let t = o;
-				for (; o < a && n.charCodeAt(o) !== 58 && n.charCodeAt(o) !== 9;) o++;
-				for (i(n, t, o, e); o < a && n.charCodeAt(o) !== 9;) o++;
-				o++;
+				let t = c;
+				for (; c < s && n.charCodeAt(c) !== 58 && n.charCodeAt(c) !== 9;) c++;
+				i(n, t, c, e);
+				let r = n.indexOf("	", c);
+				c = (r === -1 || r > s ? s : r) + 1;
 			}
 			return;
 		}
 		for (let e = 0; e < r; e++) {
-			let t = o, r = o;
-			for (; r < a && n.charCodeAt(r) !== 9;) r++;
-			let c = 0, l = t;
-			for (let a = t; a <= r; a++) if (a === r || n.charCodeAt(a) === 58) {
-				if (c === s) {
-					i(n, l, a, e);
-					break;
-				}
-				c++, l = a + 1;
+			let t = 0, r = c, a = -1, o = -1;
+			for (; c < s;) {
+				let e = n.charCodeAt(c);
+				if (e === 9) break;
+				e === 58 && a === -1 && (t === l ? (a = r, o = c) : (t++, r = c + 1)), c++;
 			}
-			o = r + 1;
+			a === -1 && (a = t === l ? r : c, o = c), i(n, a, o, e), c++;
 		}
 	}
 }
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/parseGenotypesOnly.js
-function n(e, n, r) {
-	let i = Object.create(null);
-	return t(e, n, r.length, (e, t, n, a) => {
-		i[r[a] ?? ""] = e.slice(t, n);
-	}), i;
+function n(e, n, r, i = 0, a = n.length) {
+	let o = Object.create(null);
+	return t(e, n, r.length, (e, t, n, i) => {
+		o[r[i] ?? ""] = e.slice(t, n);
+	}, i, a), o;
 }
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/parseInfo.js
@@ -79,9 +76,61 @@ function i(e, t) {
 	}
 	return n;
 }
+function a(e, t) {
+	let n = new Int32Array(t.length).fill(-1), r = 0, i = 0, a = e.length;
+	for (let o = 0; o <= a; o++) if (o === a || e.charCodeAt(o) === 58) {
+		let a = o - i;
+		for (let o = 0; o < t.length; o++) {
+			let s = t[o];
+			if (n[o] === -1 && s.length === a) {
+				let t = !0;
+				for (let n = 0; n < a; n++) if (e.charCodeAt(i + n) !== s.charCodeAt(n)) {
+					t = !1;
+					break;
+				}
+				t && (n[o] = r);
+			}
+		}
+		r++, i = o + 1;
+	}
+	return n;
+}
+function o(e, t, n, r, i, o = 0, s = t.length) {
+	let c = r.length;
+	if (c === 0) return;
+	let l = a(e, r), u = -1;
+	for (let e = 0; e < c; e++) l[e] > u && (u = l[e]);
+	if (u === -1) return;
+	let d = new Int32Array(c * 2), f = s, p = o;
+	for (let e = 0; e < n; e++) {
+		d.fill(-1);
+		let n = 0, r = p, a = !1;
+		for (; p < f;) {
+			let e = t.charCodeAt(p);
+			if (e === 9) break;
+			if (e === 58) {
+				for (let e = 0; e < c; e++) l[e] === n && (d[e * 2] = r, d[e * 2 + 1] = p);
+				if (n++, r = p + 1, n > u) {
+					a = !0;
+					let e = t.indexOf("	", p);
+					p = e === -1 || e > f ? f : e;
+					break;
+				}
+			}
+			p++;
+		}
+		if (!a) for (let e = 0; e < c; e++) l[e] === n && (d[e * 2] = r, d[e * 2 + 1] = p);
+		i(t, d, e), p++;
+	}
+}
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/Variant.js
-var a = class {
+var s = class {
+	formatMeta;
+	line;
+	restStart;
+	restEnd;
+	sampleNames;
 	CHROM;
 	POS;
 	ID;
@@ -91,15 +140,22 @@ var a = class {
 	FILTER;
 	INFO;
 	FORMAT;
-	formatMeta;
-	rest;
-	sampleNames;
 	constructor(e, t, n, r, a) {
-		let o = e.length, s = 0, c = 0;
+		let o = e.length;
+		for (; o > 0;) {
+			let t = e.charCodeAt(o - 1);
+			if (t !== 10 && t !== 13) break;
+			--o;
+		}
+		let s = 0, c = 0;
 		for (; s < o && c < 9;) e.charCodeAt(s) === 9 && (c += 1), s += 1;
-		let l = c === 9 ? s - 1 : s, u = e.slice(0, l).split("	"), d = e.slice(l + 1), [f, p, m, h, g, _, v] = u, y = v === "." ? void 0 : v?.split(";");
+		let l = c === 9 ? s - 1 : s, u = e.slice(0, l).split("	"), [d, f, p, m, h, g, _] = u;
 		if (a && !u[7]) throw Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
-		this.CHROM = f, this.POS = p === void 0 ? 0 : +p, this.ID = m === "." ? void 0 : m?.split(";"), this.REF = h, this.ALT = g === "." ? void 0 : g?.split(","), this.QUAL = _ === void 0 || _ === "." ? void 0 : +_, this.FILTER = y?.length === 1 && y[0] === "PASS" ? "PASS" : y, this.INFO = u[7] === void 0 || u[7] === "." ? {} : i(u[7], t), this.FORMAT = u[8], this.formatMeta = n, this.rest = d, this.sampleNames = r;
+		let v = _ === "." ? void 0 : _?.split(";");
+		this.CHROM = d, this.POS = f === void 0 ? 0 : +f, this.ID = p === "." ? void 0 : p?.split(";"), this.REF = m, this.ALT = h === "." ? void 0 : h?.split(","), this.QUAL = g === void 0 || g === "." ? void 0 : +g, this.FILTER = v?.length === 1 && v[0] === "PASS" ? "PASS" : v, this.INFO = u[7] === void 0 || u[7] === "." ? {} : i(u[7], t), this.FORMAT = u[8], this.formatMeta = n, this.line = e, this.restStart = Math.min(l + 1, o), this.restEnd = o, this.sampleNames = r;
+	}
+	get rest() {
+		return this.line.slice(this.restStart, this.restEnd);
 	}
 	SAMPLES() {
 		let e = {}, t = this.FORMAT;
@@ -110,16 +166,17 @@ var a = class {
 			}), a = r.length, o = this.sampleNames.length;
 			for (let t = 0; t < o; t++) {
 				let o = this.sampleNames[t] ?? "", s = {}, c = n[t] ?? "", l = c.length, u = 0, d = 0;
-				for (let e = 0; e <= l; e++) if (e === l || c[e] === ":") {
-					let t = r[d] ?? "", n = c.slice(u, e);
+				for (let e = 0; e <= l; e++) if (e === l || c.charCodeAt(e) === 58) {
+					let t = r[d] ?? "", n = c.slice(u, e), o = i[d];
 					if (n === "" || n === ".") s[t] = void 0;
+					else if (!n.includes(",")) s[t] = [o ? +n : n];
 					else {
-						let e = n.split(","), r = e.length, a = i[d], o = [];
+						let e = n.split(","), r = e.length, i = [];
 						for (let t = 0; t < r; t++) {
 							let n = e[t] ?? "";
-							o.push(n === "." ? void 0 : a ? +n : n);
+							i.push(n === "." ? void 0 : o ? +n : n);
 						}
-						s[t] = o;
+						s[t] = i;
 					}
 					if (u = e + 1, d += 1, d >= a) break;
 				}
@@ -129,10 +186,13 @@ var a = class {
 		return e;
 	}
 	GENOTYPES() {
-		return n(this.FORMAT ?? "", this.rest, this.sampleNames);
+		return n(this.FORMAT ?? "", this.line, this.sampleNames, this.restStart, this.restEnd);
 	}
 	processGenotypes(e) {
-		t(this.FORMAT ?? "", this.rest, this.sampleNames.length, e);
+		t(this.FORMAT ?? "", this.line, this.sampleNames.length, e, this.restStart, this.restEnd);
+	}
+	processFormatFields(e, t) {
+		o(this.FORMAT ?? "", this.line, this.sampleNames.length, e, t, this.restStart, this.restEnd);
 	}
 	toJSON() {
 		return {
@@ -150,37 +210,37 @@ var a = class {
 };
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/parseMetaString.js
-function o(e) {
-	let t = [], n = [], r = !1, i = !1, a = e.length;
+function c(e) {
+	let t = [], n = !1, r = !1, i = 0, a = e.length;
 	for (let o = 0; o < a; o++) {
-		let a = e[o] ?? "";
-		a === "\"" ? (r = !r, n.push(a)) : a === "[" ? (i = !0, n.push(a)) : a === "]" ? (i = !1, n.push(a)) : a === "," && !r && !i ? (t.push(n.join("").trim()), n.length = 0) : n.push(a);
+		let a = e[o];
+		a === "\"" ? n = !n : a === "[" ? r = !0 : a === "]" ? r = !1 : a === "," && !n && !r && (t.push(e.slice(i, o).trim()), i = o + 1);
 	}
-	return n.length > 0 && t.push(n.join("").trim()), t;
+	return i < a && t.push(e.slice(i).trim()), t;
 }
-function s(e, t) {
+function l(e, t) {
 	let n = e.indexOf(t);
-	return [e.slice(0, n), e.slice(n + 1)];
+	return n === -1 ? [e, ""] : [e.slice(0, n), e.slice(n + 1)];
 }
-function c(e) {
-	let t = l(e), n = t.ID;
+function u(e) {
+	let t = d(e), n = t.ID;
 	if (delete t.ID, "Number" in t) {
 		let e = Number(t.Number);
 		Number.isNaN(e) || (t.Number = e);
 	}
 	return [n, t];
 }
-function l(e) {
-	let t = o(e.slice(1, -1)), n = {};
+function d(e) {
+	let t = c(e.slice(1, -1)), n = {};
 	for (let e of t) {
-		let [t, r] = s(e, "=");
-		r && r.startsWith("[") && r.endsWith("]") ? n[t] = r.slice(1, -1).split(",").map((e) => e.trim()) : r && r.startsWith("\"") && r.endsWith("\"") ? n[t] = r.slice(1, -1) : n[t] = r;
+		let [t, r] = l(e, "=");
+		n[t] = r && r.startsWith("[") && r.endsWith("]") ? r.slice(1, -1).split(",").map((e) => e.trim()) : r && r.startsWith("\"") && r.endsWith("\"") ? r.slice(1, -1) : r;
 	}
 	return n;
 }
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/vcfReserved.js
-var u = {
+var f = {
 	InfoFields: {
 		AA: {
 			Number: 1,
@@ -489,7 +549,20 @@ var u = {
 		"*": { Description: "Represents any possible alternative allele at this location" }
 	},
 	FilterTypes: { PASS: { Description: "Passed all filters" } }
-}, d = class {
+}, p = [
+	"#CHROM",
+	"POS",
+	"ID",
+	"REF",
+	"ALT",
+	"QUAL",
+	"FILTER",
+	"INFO"
+];
+function m(e) {
+	return typeof e == "object" && !!e;
+}
+var h = class {
 	metadata;
 	strict;
 	samples;
@@ -498,30 +571,20 @@ var u = {
 		let n = e.split(/[\r\n]+/).filter(Boolean);
 		if (!n.length) throw Error("no non-empty header lines specified");
 		this.strict = t, this.metadata = {
-			INFO: { ...u.InfoFields },
-			FORMAT: { ...u.GenotypeFields },
-			ALT: { ...u.AltTypes },
-			FILTER: { ...u.FilterTypes }
+			INFO: { ...f.InfoFields },
+			FORMAT: { ...f.GenotypeFields },
+			ALT: { ...f.AltTypes },
+			FILTER: { ...f.FilterTypes }
 		};
 		let r;
-		for (let e = 0; e < n.length; e++) {
-			let t = n[e] ?? "";
-			if (t.startsWith("#")) t.startsWith("##") ? this.parseMetadata(t) : r = t;
-			else throw Error(`Bad line in header:\n${t}`);
+		for (let e of n) {
+			if (!e.startsWith("#")) throw Error(`Bad line in header:\n${e}`);
+			e.startsWith("##") ? this.parseMetadata(e) : r = e;
 		}
 		if (!r) throw Error("No format line found in header");
-		let i = r.trim().split("	"), a = i.slice(0, 8), o = [
-			"#CHROM",
-			"POS",
-			"ID",
-			"REF",
-			"ALT",
-			"QUAL",
-			"FILTER",
-			"INFO"
-		];
+		let i = r.trim().split("	");
 		if (i.length < 8) throw Error(`VCF header missing columns:\n${r}`);
-		if (a.length !== o.length || !a.every((e, t) => e === o[t])) throw Error(`VCF column headers not correct:\n${r}`);
+		if (p.some((e, t) => i[t] !== e)) throw Error(`VCF column headers not correct:\n${r}`);
 		this.samples = i.slice(9);
 	}
 	parseMetadata(e) {
@@ -529,18 +592,18 @@ var u = {
 		if (!t) throw Error(`Line is not a valid metadata line: ${e}`);
 		let n = t[1] ?? "", r = t[2];
 		if (r?.startsWith("<")) {
-			let e = this.metadata[n], t = e && typeof e == "object" ? e : {}, [i, a] = c(r);
+			let e = this.metadata[n], t = e && typeof e == "object" ? e : {}, [i, a] = u(r);
 			typeof i == "string" ? (t[i] = a, this.metadata[n] = t) : this.metadata[n] = a;
 		} else this.metadata[n] = r;
 	}
 	getMetadata(...e) {
 		let t = this.metadata;
-		for (let n of e) if (typeof t != "object" || !t || (t = t[n], t === void 0)) return;
+		for (let n of e) t = m(t) ? t[n] : void 0;
 		return t;
 	}
 	parseLine(e) {
-		return new a(e, this.metadata.INFO, this.metadata.FORMAT, this.samples, this.strict);
+		return new s(e, this.metadata.INFO, this.metadata.FORMAT, this.samples, this.strict);
 	}
 };
 //#endregion
-export { d as default };
+export { h as default };

package/dist/{esm-VvpZ9hsq.js → esm-C3A-AuRi.js}

@@ -76,7 +76,7 @@ var e = function(e, t, n, r, i) {
 	*[(r = /* @__PURE__ */ new WeakMap(), i = /* @__PURE__ */ new WeakMap(), a = /* @__PURE__ */ new WeakMap(), o = /* @__PURE__ */ new WeakMap(), s = /* @__PURE__ */ new WeakMap(), c = /* @__PURE__ */ new WeakMap(), n = /* @__PURE__ */ new WeakSet(), l = function(e) {
 		if (typeof t(this, c, "f") == "function") for (let [n, r] of e) t(this, c, "f").call(this, n, r.value);
 	}, u = function(e, n) {
-		return typeof n.expiry == "number" && n.expiry <= Date.now() ? (typeof t(this, c, "f") == "function" && t(this, c, "f").call(this, e, n.value), this.delete(e)) : !1;
+		return typeof n.expiry == "number" && n.expiry <= Date.now() && (typeof t(this, c, "f") == "function" && t(this, c, "f").call(this, e, n.value), this.delete(e));
 	}, d = function(e, r) {
 		if (!t(this, n, "m", u).call(this, e, r)) return r.value;
 	}, f = function(e, r) {