@genome-spy/app 0.81.0 → 0.83.0

package/dist/{esm-CWd6i_cL.js → esm-D8vvQAP3.js}

@@ -1,4 +1,4 @@
-import { n as e, r as t } from "./esm-Cx-EbkOj.js";
+import { n as e, r as t } from "./esm-CGLz7idZ.js";
 import { t as n } from "./esm-VvpZ9hsq.js";
 import { n as r, r as i } from "./esm-BdT7qUL-.js";
 import { t as a } from "./AbortablePromiseCache-BTmAcN-t.js";

package/dist/{esm-Bn4VTHqw.js → esm-DQ3lJSQN.js}

@@ -1,4 +1,4 @@
-import { t as e } from "./esm-Cx-EbkOj.js";
+import { t as e } from "./esm-CGLz7idZ.js";
 import { n as t } from "./esm-BdT7qUL-.js";
 //#region ../core/node_modules/@gmod/indexedfasta/esm/fetchableSmallFasta.js
 var n = new TextDecoder("utf8");

package/dist/{esm-k9p3oHkt.js → esm-lwYrRdbg.js}

@@ -1,78 +1,76 @@
-//#region ../../node_modules/@gmod/vcf/esm/processGenotypes.js
-var e = 9, t = 58;
-function n(e) {
-	let n = 0, r = 0, i = e.length;
-	for (let a = 0; a <= i; a++) if (a === i || e.charCodeAt(a) === t) {
-		if (a - r === 2 && e.charCodeAt(r) === 71 && e.charCodeAt(r + 1) === 84) return n;
-		n++, r = a + 1;
+function e(e) {
+	let t = 0, n = 0, r = e.length;
+	for (let i = 0; i <= r; i++) if (i === r || e.charCodeAt(i) === 58) {
+		if (i - n === 2 && e.charCodeAt(n) === 71 && e.charCodeAt(n + 1) === 84) return t;
+		t++, n = i + 1;
 	}
 	return -1;
 }
-function r(r, i, a, o) {
-	let s = i.length, c = 0;
-	if (r === "GT") {
-		for (let t = 0; t < a; t++) {
-			let n = c;
-			for (; c < s && i.charCodeAt(c) !== e;) c++;
-			o(i, n, c, t), c++;
+function t(t, n, r, i) {
+	let a = n.length, o = 0;
+	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++;
 		}
 		return;
 	}
-	let l = n(r);
-	if (l !== -1) {
-		if (l === 0) {
-			for (let n = 0; n < a; n++) {
-				let r = c;
-				for (; c < s && i.charCodeAt(c) !== t && i.charCodeAt(c) !== e;) c++;
-				for (o(i, r, c, n); c < s && i.charCodeAt(c) !== e;) c++;
-				c++;
+	let s = e(t);
+	if (s !== -1) {
+		if (s === 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++;
 			}
 			return;
 		}
-		for (let n = 0; n < a; n++) {
-			let r = c, a = c;
-			for (; a < s && i.charCodeAt(a) !== e;) a++;
-			let u = 0, d = r;
-			for (let e = r; e <= a; e++) if (e === a || i.charCodeAt(e) === t) {
-				if (u === l) {
-					o(i, d, e, n);
+		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;
 				}
-				u++, d = e + 1;
+				c++, l = a + 1;
 			}
-			c = a + 1;
+			o = r + 1;
 		}
 	}
 }
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/parseGenotypesOnly.js
-function i(e, t, n) {
+function n(e, n, r) {
 	let i = Object.create(null);
-	return r(e, t, n.length, (e, t, r, a) => {
-		i[n[a] ?? ""] = e.slice(t, r);
+	return t(e, n, r.length, (e, t, n, a) => {
+		i[r[a] ?? ""] = e.slice(t, n);
 	}), i;
 }
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/parseInfo.js
-function a(e) {
+function r(e) {
 	try {
 		return decodeURIComponent(e);
 	} catch {
 		return e;
 	}
 }
-function o(e, t) {
-	let n = {}, r = e.includes("%"), i = e.split(";"), o = i.length;
+function i(e, t) {
+	let n = {}, i = e.includes("%"), a = e.split(";"), o = a.length;
 	for (let e = 0; e < o; e++) {
-		let o = i[e] ?? "", s = o.indexOf("="), c = s === -1 ? o : o.slice(0, s), l = s === -1 ? void 0 : o.slice(s + 1), u = t[c]?.Type;
+		let o = a[e] ?? "", s = o.indexOf("="), c = s === -1 ? o : o.slice(0, s), l = s === -1 ? void 0 : o.slice(s + 1), u = t[c]?.Type;
 		if (u === "Flag" || !l) n[c] = !0;
 		else {
-			let e = u === "Integer" || u === "Float", t = l.split(","), i = t.length, o = [];
-			for (let n = 0; n < i; n++) {
-				let i = t[n] ?? "";
-				if (i === ".") o.push(void 0);
+			let e = u === "Integer" || u === "Float", t = l.split(","), a = t.length, o = [];
+			for (let n = 0; n < a; n++) {
+				let a = t[n] ?? "";
+				if (a === ".") o.push(void 0);
 				else {
-					let t = r ? a(i) : i;
+					let t = i ? r(a) : a;
 					o.push(e ? Number(t) : t);
 				}
 			}
@@ -83,7 +81,7 @@ function o(e, t) {
 }
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/Variant.js
-var s = class {
+var a = class {
 	CHROM;
 	POS;
 	ID;
@@ -96,12 +94,12 @@ var s = class {
 	formatMeta;
 	rest;
 	sampleNames;
-	constructor(e, t, n, r, i) {
-		let a = e.length, s = 0, c = 0;
-		for (; s < a && c < 9;) e.charCodeAt(s) === 9 && (c += 1), s += 1;
+	constructor(e, t, n, r, a) {
+		let o = e.length, 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(";");
-		if (i && !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] === "." ? {} : o(u[7], t), this.FORMAT = u[8], this.formatMeta = n, this.rest = d, this.sampleNames = r;
+		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;
 	}
 	SAMPLES() {
 		let e = {}, t = this.FORMAT;
@@ -131,10 +129,10 @@ var s = class {
 		return e;
 	}
 	GENOTYPES() {
-		return i(this.FORMAT ?? "", this.rest, this.sampleNames);
+		return n(this.FORMAT ?? "", this.rest, this.sampleNames);
 	}
 	processGenotypes(e) {
-		r(this.FORMAT ?? "", this.rest, this.sampleNames.length, e);
+		t(this.FORMAT ?? "", this.rest, this.sampleNames.length, e);
 	}
 	toJSON() {
 		return {
@@ -152,7 +150,7 @@ var s = class {
 };
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/parseMetaString.js
-function c(e) {
+function o(e) {
 	let t = [], n = [], r = !1, i = !1, a = e.length;
 	for (let o = 0; o < a; o++) {
 		let a = e[o] ?? "";
@@ -160,29 +158,29 @@ function c(e) {
 	}
 	return n.length > 0 && t.push(n.join("").trim()), t;
 }
-function l(e, t) {
+function s(e, t) {
 	let n = e.indexOf(t);
 	return [e.slice(0, n), e.slice(n + 1)];
 }
-function u(e) {
-	let t = d(e), n = t.ID;
+function c(e) {
+	let t = l(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 d(e) {
-	let t = c(e.slice(1, -1)), n = {};
+function l(e) {
+	let t = o(e.slice(1, -1)), n = {};
 	for (let e of t) {
-		let [t, r] = l(e, "=");
+		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;
 	}
 	return n;
 }
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/vcfReserved.js
-var f = {
+var u = {
 	InfoFields: {
 		AA: {
 			Number: 1,
@@ -491,7 +489,7 @@ var f = {
 		"*": { Description: "Represents any possible alternative allele at this location" }
 	},
 	FilterTypes: { PASS: { Description: "Passed all filters" } }
-}, p = class {
+}, d = class {
 	metadata;
 	strict;
 	samples;
@@ -500,10 +498,10 @@ var f = {
 		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: { ...f.InfoFields },
-			FORMAT: { ...f.GenotypeFields },
-			ALT: { ...f.AltTypes },
-			FILTER: { ...f.FilterTypes }
+			INFO: { ...u.InfoFields },
+			FORMAT: { ...u.GenotypeFields },
+			ALT: { ...u.AltTypes },
+			FILTER: { ...u.FilterTypes }
 		};
 		let r;
 		for (let e = 0; e < n.length; e++) {
@@ -531,7 +529,7 @@ var f = {
 		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] = u(r);
+			let e = this.metadata[n], t = e && typeof e == "object" ? e : {}, [i, a] = c(r);
 			typeof i == "string" ? (t[i] = a, this.metadata[n] = t) : this.metadata[n] = a;
 		} else this.metadata[n] = r;
 	}
@@ -541,8 +539,8 @@ var f = {
 		return t;
 	}
 	parseLine(e) {
-		return new s(e, this.metadata.INFO, this.metadata.FORMAT, this.samples, this.strict);
+		return new a(e, this.metadata.INFO, this.metadata.FORMAT, this.samples, this.strict);
 	}
 };
 //#endregion
-export { p as default };
+export { d as default };