@genome-spy/core 0.77.0 → 0.79.0

package/dist/bundle/esm-DlYGqi79.js

@@ -0,0 +1,128 @@
+import { t as e } from "./esm-Cx-EbkOj.js";
+import { t } from "./browser-CETrb2cm.js";
+//#region node_modules/@gmod/indexedfasta/esm/fetchableSmallFasta.js
+var n = new TextDecoder("utf8");
+function r(e) {
+	return e.split(">").filter((e) => /\S/.test(e)).map((e) => {
+		let [t, ...n] = e.split("\n"), [r, ...i] = t.split(" "), a = n.join("").replace(/\s/g, "");
+		return {
+			id: r,
+			description: i.join(" "),
+			sequence: a
+		};
+	});
+}
+var i = class {
+	data;
+	indexed;
+	constructor({ fasta: e, path: i }) {
+		let a;
+		if (e) a = e;
+		else if (i) a = new t(i);
+		else throw Error("Need to pass fasta or path");
+		this.data = a.readFile().then((e) => r(n.decode(e)));
+	}
+	getIndexed() {
+		return this.indexed ??= this.data.then((e) => new Map(e.map((e) => [e.id, e]))), this.indexed;
+	}
+	async fetch(e, t, n) {
+		let r = (await this.getIndexed()).get(e);
+		if (!r) throw Error(`no sequence with id ${e} exists`);
+		return r.sequence.slice(t, n);
+	}
+	async getSequenceNames() {
+		return (await this.data).map((e) => e.id);
+	}
+}, a = new TextDecoder("utf8");
+function o(e, t, n, r) {
+	return e + t * Math.floor(r / n) + r % n;
+}
+async function s(e, t = {}) {
+	let n = a.decode(await e.readFile(t)), r = /* @__PURE__ */ new Map();
+	for (let e of n.split("\n")) {
+		let t = e.trim();
+		if (!t) continue;
+		let n = t.split("	");
+		if (n.length < 5) throw Error(`Malformed FAI line (expected 5 tab-separated columns, got ${String(n.length)}): ${t}`);
+		let [i, a, o, s, c] = n;
+		if (i.startsWith(">")) throw Error("found > in sequence name, might have supplied FASTA file for the FASTA index");
+		let l = +a, u = +s;
+		if (l > 0 && u === 0) throw Error(`Invalid FAI index for "${i}": LINEBASES is 0, FASTA likely missing trailing newline; regenerate the .fai index`);
+		r.set(i, {
+			length: l,
+			offset: +o,
+			lineLength: u,
+			lineBytes: +c
+		});
+	}
+	return r;
+}
+async function c(e, t, n = 0, r, i) {
+	if (n < 0) throw TypeError("regionStart cannot be less than 0");
+	let s = Math.min(r ?? t.length, t.length);
+	if (n >= s) return "";
+	let c = o(t.offset, t.lineBytes, t.lineLength, n), l = o(t.offset, t.lineBytes, t.lineLength, s) - c, u = a.decode(await e.read(l, c, i)).replace(/\s+/g, "");
+	if (/[^\x20-\x7e]/.test(u.slice(0, 1e3))) throw Error("Non-ASCII bytes in sequence; file may be gzip — use BgzipIndexedFasta or decompress");
+	return u;
+}
+var l = class {
+	fasta;
+	fai;
+	indexes;
+	constructor({ fasta: e, fai: n, path: r, faiPath: i }) {
+		if (e) this.fasta = e;
+		else if (r) this.fasta = new t(r);
+		else throw Error("Need to pass filehandle for fasta or path to localfile");
+		if (n) this.fai = n;
+		else if (i) this.fai = new t(i);
+		else if (r) this.fai = new t(`${r}.fai`);
+		else throw Error("Need to pass filehandle for fai or path to localfile");
+	}
+	async getIndexes(e) {
+		return this.indexes ??= s(this.fai, e).catch((e) => {
+			throw this.indexes = void 0, e;
+		}), this.indexes;
+	}
+	async getSequenceNames(e) {
+		return [...(await this.getIndexes(e)).keys()];
+	}
+	async getSequenceSizes(e) {
+		let t = {};
+		for (let [n, r] of await this.getIndexes(e)) t[n] = r.length;
+		return t;
+	}
+	async getSequenceSize(e, t) {
+		return (await this.getIndexes(t)).get(e)?.length;
+	}
+	async hasReferenceSequence(e, t) {
+		return (await this.getIndexes(t)).has(e);
+	}
+	async getResiduesByName(e, t, n, r) {
+		let i = (await this.getIndexes(r)).get(e);
+		if (i !== void 0) return c(this.fasta, i, t, n, r);
+	}
+	async getSequence(e, t, n, r) {
+		return this.getResiduesByName(e, t, n, r);
+	}
+}, u = class extends l {
+	constructor({ fasta: n, path: r, fai: i, faiPath: a, gzi: o, gziPath: s }) {
+		let c;
+		if (n && o) c = new e({
+			filehandle: n,
+			gziFilehandle: o
+		});
+		else if (r && s) c = new e({
+			filehandle: new t(r),
+			gziFilehandle: new t(s)
+		});
+		else throw Error("BgzipIndexedFasta requires either {fasta, gzi} or {path, gziPath}");
+		super({
+			fasta: c,
+			fai: i,
+			faiPath: a,
+			path: r
+		});
+	}
+};
+//#endregion
+export { u as BgzipIndexedFasta, i as FetchableSmallFasta, l as IndexedFasta, r as parseSmallFasta };

package/dist/bundle/{esm-BygJiwh0.js → esm-k9p3oHkt.js}

@@ -1,154 +1,127 @@
-//#region ../../node_modules/@gmod/vcf/esm/parseGenotypesOnly.js
-function e(e, t, n) {
-	let r = Object.create(null), i = n.length, a = t.length, o = 0;
-	if (e === "GT") {
-		for (let e = 0; e < i; e++) {
-			let i = o;
-			for (; o < a && t.charCodeAt(o) !== 9;) o++;
-			r[n[e]] = t.slice(i, o), o++;
-		}
-		return r;
-	}
-	let s = e.indexOf("GT");
-	if (s === -1) return r;
-	if (s === 0) {
-		for (let e = 0; e < i; e++) {
-			let i = o;
-			for (; o < a && t.charCodeAt(o) !== 58 && t.charCodeAt(o) !== 9;) o++;
-			for (r[n[e]] = t.slice(i, o); o < a && t.charCodeAt(o) !== 9;) o++;
-			o++;
-		}
-		return r;
-	}
-	let c = 0;
-	for (let t = 0; t < s; t++) e.charCodeAt(t) === 58 && c++;
-	for (let e = 0; e < i; e++) {
-		let i = o, s = o;
-		for (; s < a && t.charCodeAt(s) !== 9;) s++;
-		let l = 0, u = i;
-		for (let a = i; a <= s; a++) if (a === s || t.charCodeAt(a) === 58) {
-			if (l === c) {
-				r[n[e]] = t.slice(u, a);
-				break;
-			}
-			l++, u = a + 1;
-		}
-		o = s + 1;
+//#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;
 	}
-	return r;
+	return -1;
 }
-//#endregion
-//#region ../../node_modules/@gmod/vcf/esm/processGenotypes.js
-function t(e, t, n, r) {
-	let i = t.length, a = 0;
-	if (e === "GT") {
-		for (let e = 0; e < n; e++) {
-			let e = a;
-			for (; a < i && t.charCodeAt(a) !== 9;) a++;
-			r(t, e, a), a++;
+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++;
 		}
 		return;
 	}
-	let o = e.indexOf("GT");
-	if (o === -1) return;
-	if (o === 0) {
-		for (let e = 0; e < n; e++) {
-			let e = a;
-			for (; a < i && t.charCodeAt(a) !== 58 && t.charCodeAt(a) !== 9;) a++;
-			for (r(t, e, a); a < i && t.charCodeAt(a) !== 9;) a++;
-			a++;
+	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++;
+			}
+			return;
 		}
-		return;
-	}
-	let s = 0;
-	for (let t = 0; t < o; t++) e.charCodeAt(t) === 58 && s++;
-	for (let e = 0; e < n; e++) {
-		let e = a, n = a;
-		for (; n < i && t.charCodeAt(n) !== 9;) n++;
-		let o = 0, c = e;
-		for (let i = e; i <= n; i++) if (i === n || t.charCodeAt(i) === 58) {
-			if (o === s) {
-				r(t, c, i);
-				break;
+		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);
+					break;
+				}
+				u++, d = e + 1;
 			}
-			o++, c = i + 1;
+			c = a + 1;
 		}
-		a = n + 1;
 	}
 }
 //#endregion
-//#region ../../node_modules/@gmod/vcf/esm/Variant.js
-function n(e) {
+//#region ../../node_modules/@gmod/vcf/esm/parseGenotypesOnly.js
+function i(e, t, n) {
+	let i = Object.create(null);
+	return r(e, t, n.length, (e, t, r, a) => {
+		i[n[a] ?? ""] = e.slice(t, r);
+	}), i;
+}
+//#endregion
+//#region ../../node_modules/@gmod/vcf/esm/parseInfo.js
+function a(e) {
 	try {
 		return decodeURIComponent(e);
 	} catch {
 		return e;
 	}
 }
-var r = class {
-	constructor(e, t, n, r, i) {
-		let a = 0, o = 0;
-		for (; a < e.length && o < 9;) e[a] === "	" && (o += 1), a += 1;
-		let s = o === 9 ? a - 1 : a, c = e.slice(0, s).split("	"), l = e.slice(s + 1), [u, d, f, p, m, h, g] = c, _ = g === "." ? void 0 : g.split(";");
-		if (i && !c[7]) throw Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
-		this.CHROM = u, this.POS = +d, this.ID = f === "." ? void 0 : f.split(";"), this.REF = p, this.ALT = m === "." ? void 0 : m.split(","), this.QUAL = h === "." ? void 0 : +h, this.FILTER = _?.length === 1 && _[0] === "PASS" ? "PASS" : _, this.INFO = c[7] === void 0 || c[7] === "." ? {} : this.parseInfo(c[7], t), this.FORMAT = c[8], this.formatMeta = n, this.rest = l, this.sampleNames = r;
-	}
-	parseInfo(e, t) {
-		let r = {}, i = e.includes("%"), a = e.split(";"), o = a.length;
-		for (let e = 0; e < o; e++) {
-			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") r[c] = !0;
-			else if (!l) r[c] = !0;
-			else {
-				let e = u === "Integer" || u === "Float", t = l.split(","), a = t.length;
-				if (i) {
-					let i = [];
-					for (let r = 0; r < a; r++) {
-						let a = t[r];
-						if (a === ".") i.push(void 0);
-						else {
-							let t = n(a);
-							i.push(e ? Number(t) : t);
-						}
-					}
-					r[c] = i;
-				} else {
-					let n = [];
-					for (let r = 0; r < a; r++) {
-						let i = t[r];
-						i === "." ? n.push(void 0) : n.push(e ? Number(i) : i);
-					}
-					r[c] = n;
+function o(e, t) {
+	let n = {}, r = e.includes("%"), i = e.split(";"), o = i.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;
+		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);
+				else {
+					let t = r ? a(i) : i;
+					o.push(e ? Number(t) : t);
 				}
 			}
+			n[c] = o;
 		}
-		return r;
+	}
+	return n;
+}
+//#endregion
+//#region ../../node_modules/@gmod/vcf/esm/Variant.js
+var s = class {
+	CHROM;
+	POS;
+	ID;
+	REF;
+	ALT;
+	QUAL;
+	FILTER;
+	INFO;
+	FORMAT;
+	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;
+		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;
 	}
 	SAMPLES() {
 		let e = {}, t = this.FORMAT;
 		if (t) {
-			let n = this.rest.split("	"), r = t.split(":"), i = [];
-			for (let e = 0; e < r.length; e++) {
-				let t = this.formatMeta[r[e]]?.Type;
-				i.push(t === "Integer" || t === "Float");
-			}
-			let a = r.length, o = this.sampleNames.length;
+			let n = this.rest.split("	"), r = t.split(":"), i = r.map((e) => {
+				let t = this.formatMeta[e]?.Type;
+				return t === "Integer" || t === "Float";
+			}), 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;
+				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 = c.slice(u, e);
-					if (t === "" || t === ".") s[r[d]] = void 0;
+					let t = r[d] ?? "", n = c.slice(u, e);
+					if (n === "" || n === ".") s[t] = void 0;
 					else {
-						let e = t.split(","), n = [];
-						if (i[d]) for (let t = 0; t < e.length; t++) {
-							let r = e[t];
-							n.push(r === "." ? void 0 : +r);
+						let e = n.split(","), r = e.length, a = i[d], o = [];
+						for (let t = 0; t < r; t++) {
+							let n = e[t] ?? "";
+							o.push(n === "." ? void 0 : a ? +n : n);
 						}
-						else for (let t = 0; t < e.length; t++) {
-							let r = e[t];
-							n.push(r === "." ? void 0 : r);
-						}
-						s[r[d]] = n;
+						s[t] = o;
 					}
 					if (u = e + 1, d += 1, d >= a) break;
 				}
@@ -158,10 +131,10 @@ var r = class {
 		return e;
 	}
 	GENOTYPES() {
-		return e(this.FORMAT ?? "", this.rest, this.sampleNames);
+		return i(this.FORMAT ?? "", this.rest, this.sampleNames);
 	}
 	processGenotypes(e) {
-		t(this.FORMAT ?? "", this.rest, this.sampleNames.length, e);
+		r(this.FORMAT ?? "", this.rest, this.sampleNames.length, e);
 	}
 	toJSON() {
 		return {
@@ -179,33 +152,37 @@ var r = class {
 };
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/parseMetaString.js
-function i(e) {
+function c(e) {
 	let t = [], n = [], r = !1, i = !1, a = e.length;
 	for (let o = 0; o < a; o++) {
-		let a = e[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);
 	}
 	return n.length > 0 && t.push(n.join("").trim()), t;
 }
-function a(e, t) {
+function l(e, t) {
 	let n = e.indexOf(t);
 	return [e.slice(0, n), e.slice(n + 1)];
 }
-function o(e) {
-	let t = i(e.slice(1, -1)), n = [];
-	for (let e = 0; e < t.length; e++) {
-		let r = t[e], [i, o] = a(r, "=");
-		if (o && o.startsWith("[") && o.endsWith("]")) {
-			let e = o.slice(1, -1).split(",");
-			for (let t = 0; t < e.length; t++) e[t] = e[t].trim();
-			n.push([i, e]);
-		} else o && o.startsWith("\"") && o.endsWith("\"") ? n.push([i, o.slice(1, -1)]) : n.push([i, o]);
+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 d(e) {
+	let t = c(e.slice(1, -1)), n = {};
+	for (let e of t) {
+		let [t, r] = l(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 Object.fromEntries(n);
+	return n;
 }
 //#endregion
 //#region ../../node_modules/@gmod/vcf/esm/vcfReserved.js
-var s = {
+var f = {
 	InfoFields: {
 		AA: {
 			Number: 1,
@@ -514,20 +491,23 @@ var s = {
 		"*": { Description: "Represents any possible alternative allele at this location" }
 	},
 	FilterTypes: { PASS: { Description: "Passed all filters" } }
-}, c = class {
+}, p = class {
+	metadata;
+	strict;
+	samples;
 	constructor({ header: e, strict: t = !0 }) {
 		if (!e.length) throw Error("empty header received");
 		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: { ...s.InfoFields },
-			FORMAT: { ...s.GenotypeFields },
-			ALT: { ...s.AltTypes },
-			FILTER: { ...s.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];
+			let t = n[e] ?? "";
 			if (t.startsWith("#")) t.startsWith("##") ? this.parseMetadata(t) : r = t;
 			else throw Error(`Bad line in header:\n${t}`);
 		}
@@ -549,25 +529,20 @@ var s = {
 	parseMetadata(e) {
 		let t = /^##(.+?)=(.*)/.exec(e.trim());
 		if (!t) throw Error(`Line is not a valid metadata line: ${e}`);
-		let [n, r] = t.slice(1, 3), i = n;
+		let n = t[1] ?? "", r = t[2];
 		if (r?.startsWith("<")) {
-			i in this.metadata || (this.metadata[i] = {});
-			let [e, t] = this.parseStructuredMetaVal(r);
-			e ? this.metadata[i][e] = t : this.metadata[i] = t;
-		} else this.metadata[i] = r;
-	}
-	parseStructuredMetaVal(e) {
-		let t = o(e), n = t.ID;
-		return delete t.ID, "Number" in t && (Number.isNaN(Number(t.Number)) || (t.Number = Number(t.Number))), [n, t];
+			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, n = e.length;
-		for (let r = 0; r < n; r++) if (t = t[e[r]], !t) return t;
+		let t = this.metadata;
+		for (let n of e) if (typeof t != "object" || !t || (t = t[n], t === void 0)) return;
 		return t;
 	}
 	parseLine(e) {
-		return new r(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 { c as default };
+export { p as default };