@genome-spy/app 0.73.0 → 0.75.0

package/dist/esm-n0auOe11.js

@@ -0,0 +1,121 @@
+import { t as e } from "./esm-BDFRLEuD.js";
+import { t } from "./browser-Dvlo92rx.js";
+//#region ../core/node_modules/@gmod/indexedfasta/esm/indexedFasta.js
+function n(e, t, n, r) {
+	return e + t * Math.floor(r / n) + r % n;
+}
+async function r(e, t = {}) {
+	let n = new TextDecoder("utf8").decode(await e.readFile(t)), r = [], i = [], a = [], o = [], s = [], c = {}, l = 0, u = n.length, d = 0;
+	for (; l < u;) {
+		let e = n.indexOf("\n", l);
+		e === -1 && (e = u);
+		let t = n.slice(l, e);
+		if (t.endsWith("\r") && (t = t.slice(0, -1)), t = t.trim(), l = e + 1, t.length === 0) continue;
+		let f = t.indexOf("	"), p = t.indexOf("	", f + 1), m = t.indexOf("	", p + 1), h = t.indexOf("	", m + 1), g = t.slice(0, f);
+		if (g.startsWith(">")) throw Error("found > in sequence name, might have supplied FASTA file for the FASTA index");
+		r.push(g), a.push(+t.slice(f + 1, p)), i.push(+t.slice(p + 1, m)), o.push(+t.slice(m + 1, h)), s.push(+t.slice(h + 1)), c[g] = d, d++;
+	}
+	return {
+		names: r,
+		nameToIndex: c,
+		offsets: i,
+		lengths: a,
+		lineLengths: o,
+		lineBytes: s
+	};
+}
+var i = class {
+	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  or path to localfile");
+	}
+	async _getIndexes(e) {
+		return this.indexes ||= r(this.fai, e).catch((e) => {
+			throw this.indexes = void 0, e;
+		}), this.indexes;
+	}
+	async getSequenceNames(e) {
+		return (await this._getIndexes(e)).names;
+	}
+	async getSequenceSizes(e) {
+		let t = await this._getIndexes(e);
+		if (!t.sizesCache) {
+			let e = {};
+			for (let n = 0; n < t.names.length; n++) e[t.names[n]] = t.lengths[n];
+			t.sizesCache = e;
+		}
+		return t.sizesCache;
+	}
+	async getSequenceSize(e, t) {
+		let n = await this._getIndexes(t), r = n.nameToIndex[e];
+		return r === void 0 ? void 0 : n.lengths[r];
+	}
+	async hasReferenceSequence(e, t) {
+		return (await this._getIndexes(t)).nameToIndex[e] !== void 0;
+	}
+	async getResiduesByName(e, t, n, r) {
+		let i = await this._getIndexes(r), a = i.nameToIndex[e];
+		if (a !== void 0) return this._fetchFromIndex(i.offsets[a], i.lineBytes[a], i.lineLengths[a], i.lengths[a], t, n, r);
+	}
+	async getSequence(e, t, n, r) {
+		return this.getResiduesByName(e, t, n, r);
+	}
+	async _fetchFromIndex(e, t, r, i, a = 0, o, s) {
+		let c = o;
+		if (a < 0) throw TypeError("regionStart cannot be less than 0");
+		if ((c === void 0 || c > i) && (c = i), a >= c) return "";
+		let l = n(e, t, r, a), u = n(e, t, r, c) - l, d = new TextDecoder("utf8").decode(await this.fasta.read(u, l, s)).replace(/\s+/g, "");
+		if (/[^\x20-\x7e]/.test(d.slice(0, 1e3))) throw Error("Non-ASCII characters detected in sequence. The file may be gzip compressed. Use BgzipIndexedFasta for bgzip files, or decompress the file.");
+		return d;
+	}
+}, a = class extends i {
+	constructor({ fasta: n, path: r, fai: i, faiPath: a, gzi: o, gziPath: s }) {
+		super({
+			fasta: n,
+			path: r,
+			fai: i,
+			faiPath: a
+		}), n && o ? this.fasta = new e({
+			filehandle: n,
+			gziFilehandle: o
+		}) : r && s && (this.fasta = new e({
+			filehandle: new t(r),
+			gziFilehandle: new t(s)
+		}));
+	}
+};
+//#endregion
+//#region ../core/node_modules/@gmod/indexedfasta/esm/index.js
+function o(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 s = class {
+	constructor({ fasta: e, path: n }) {
+		if (e) this.fasta = e;
+		else if (n) this.fasta = new t(n);
+		else throw Error("Need to pass fasta or path");
+		this.data = this.fasta.readFile().then((e) => o(new TextDecoder("utf8").decode(e)));
+	}
+	async fetch(e, t, n) {
+		let r = (await this.data).find((t) => t.id === e), i = n - t;
+		if (!r) throw Error(`no sequence with id ${e} exists`);
+		return r.sequence.slice(t, i);
+	}
+	async getSequenceNames() {
+		return (await this.data).map((e) => e.id);
+	}
+};
+//#endregion
+export { a as BgzipIndexedFasta, s as FetchableSmallFasta, i as IndexedFasta, o as parseSmallFasta };