@genome-spy/app 0.79.1 → 0.80.0

package/dist/esm-WxH0jQt4.js

@@ -1,128 +0,0 @@
-import { t as e } from "./esm-Cx-EbkOj.js";
-import { n as t } from "./esm-C3k-CPce.js";
-//#region ../core/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 };