@genome-spy/app 0.75.0 → 0.77.0

package/dist/esm-CZvS2Ldm.js

@@ -0,0 +1,155 @@
+//#region ../../node_modules/@jbrowse/quick-lru/esm/index.js
+var e = function(e, t, n, r, i) {
+	if (r === "m") throw TypeError("Private method is not writable");
+	if (r === "a" && !i) throw TypeError("Private accessor was defined without a setter");
+	if (typeof t == "function" ? e !== t || !i : !t.has(e)) throw TypeError("Cannot write private member to an object whose class did not declare it");
+	return r === "a" ? i.call(e, n) : i ? i.value = n : t.set(e, n), n;
+}, t = function(e, t, n, r) {
+	if (n === "a" && !r) throw TypeError("Private accessor was defined without a getter");
+	if (typeof t == "function" ? e !== t || !r : !t.has(e)) throw TypeError("Cannot read private member from an object whose class did not declare it");
+	return n === "m" ? r : n === "a" ? r.call(e) : r ? r.value : t.get(e);
+}, n, r, i, a, o, s, c, l, u, d, f, p, m, h, g, _ = class extends Map {
+	constructor(t = {}) {
+		if (super(), n.add(this), r.set(this, 0), i.set(this, /* @__PURE__ */ new Map()), a.set(this, /* @__PURE__ */ new Map()), o.set(this, void 0), s.set(this, void 0), c.set(this, void 0), !(t.maxSize && t.maxSize > 0)) throw TypeError("`maxSize` must be a number greater than 0");
+		if (typeof t.maxAge == "number" && t.maxAge === 0) throw TypeError("`maxAge` must be a number greater than 0");
+		e(this, o, t.maxSize, "f"), e(this, s, t.maxAge || Infinity, "f"), e(this, c, t.onEviction, "f");
+	}
+	get __oldCache() {
+		return t(this, a, "f");
+	}
+	get(e) {
+		if (t(this, i, "f").has(e)) {
+			let r = t(this, i, "f").get(e);
+			return t(this, n, "m", f).call(this, e, r);
+		}
+		if (t(this, a, "f").has(e)) {
+			let r = t(this, a, "f").get(e);
+			if (!t(this, n, "m", u).call(this, e, r)) return t(this, n, "m", h).call(this, e, r), r.value;
+		}
+	}
+	set(e, r, { maxAge: a = t(this, s, "f") } = {}) {
+		let o = typeof a == "number" && a !== Infinity ? Date.now() + a : void 0;
+		return t(this, i, "f").has(e) ? t(this, i, "f").set(e, {
+			value: r,
+			expiry: o
+		}) : t(this, n, "m", m).call(this, e, {
+			value: r,
+			expiry: o
+		}), this;
+	}
+	has(e) {
+		return t(this, i, "f").has(e) ? !t(this, n, "m", u).call(this, e, t(this, i, "f").get(e)) : t(this, a, "f").has(e) ? !t(this, n, "m", u).call(this, e, t(this, a, "f").get(e)) : !1;
+	}
+	peek(e) {
+		if (t(this, i, "f").has(e)) return t(this, n, "m", p).call(this, e, t(this, i, "f"));
+		if (t(this, a, "f").has(e)) return t(this, n, "m", p).call(this, e, t(this, a, "f"));
+	}
+	expiresIn(e) {
+		let n = t(this, i, "f").get(e) ?? t(this, a, "f").get(e);
+		if (n) return n.expiry ? n.expiry - Date.now() : Infinity;
+	}
+	delete(n) {
+		var o;
+		let s = t(this, i, "f").delete(n);
+		return s && e(this, r, (o = t(this, r, "f"), o--, o), "f"), t(this, a, "f").delete(n) || s;
+	}
+	clear() {
+		t(this, i, "f").clear(), t(this, a, "f").clear(), e(this, r, 0, "f");
+	}
+	resize(s) {
+		if (!(s && s > 0)) throw TypeError("`maxSize` must be a number greater than 0");
+		let c = [...t(this, n, "m", g).call(this)], u = c.length - s;
+		u < 0 ? (e(this, i, new Map(c), "f"), e(this, a, /* @__PURE__ */ new Map(), "f"), e(this, r, c.length, "f")) : (u > 0 && t(this, n, "m", l).call(this, c.slice(0, u)), e(this, a, new Map(c.slice(u)), "f"), e(this, i, /* @__PURE__ */ new Map(), "f"), e(this, r, 0, "f")), e(this, o, s, "f");
+	}
+	evict(o = 1) {
+		let s = o;
+		if (!s || s <= 0) return;
+		let c = [...t(this, n, "m", g).call(this)], u = Math.trunc(Math.min(s, Math.max(c.length - 1, 0)));
+		u <= 0 || (t(this, n, "m", l).call(this, c.slice(0, u)), e(this, a, new Map(c.slice(u)), "f"), e(this, i, /* @__PURE__ */ new Map(), "f"), e(this, r, 0, "f"));
+	}
+	*keys() {
+		for (let [e] of this) yield e;
+	}
+	*values() {
+		for (let [, e] of this) yield e;
+	}
+	*[(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;
+	}, d = function(e, r) {
+		if (!t(this, n, "m", u).call(this, e, r)) return r.value;
+	}, f = function(e, r) {
+		return r.expiry ? t(this, n, "m", d).call(this, e, r) : r.value;
+	}, p = function(e, r) {
+		let i = r.get(e);
+		return t(this, n, "m", f).call(this, e, i);
+	}, m = function(s, c) {
+		var u;
+		t(this, i, "f").set(s, c), e(this, r, (u = t(this, r, "f"), u++, u), "f"), t(this, r, "f") >= t(this, o, "f") && (e(this, r, 0, "f"), t(this, n, "m", l).call(this, t(this, a, "f")), e(this, a, t(this, i, "f"), "f"), e(this, i, /* @__PURE__ */ new Map(), "f"));
+	}, h = function(e, r) {
+		t(this, a, "f").delete(e), t(this, n, "m", m).call(this, e, r);
+	}, g = function* () {
+		for (let e of t(this, a, "f")) {
+			let [r, a] = e;
+			t(this, i, "f").has(r) || t(this, n, "m", u).call(this, r, a) || (yield e);
+		}
+		for (let e of t(this, i, "f")) {
+			let [r, i] = e;
+			t(this, n, "m", u).call(this, r, i) || (yield e);
+		}
+	}, Symbol.iterator)]() {
+		for (let e of t(this, i, "f")) {
+			let [r, i] = e;
+			t(this, n, "m", u).call(this, r, i) || (yield [r, i.value]);
+		}
+		for (let e of t(this, a, "f")) {
+			let [r, a] = e;
+			t(this, i, "f").has(r) || t(this, n, "m", u).call(this, r, a) || (yield [r, a.value]);
+		}
+	}
+	*entriesDescending() {
+		let e = [...t(this, i, "f")];
+		for (let r = e.length - 1; r >= 0; --r) {
+			let [i, a] = e[r];
+			t(this, n, "m", u).call(this, i, a) || (yield [i, a.value]);
+		}
+		e = [...t(this, a, "f")];
+		for (let r = e.length - 1; r >= 0; --r) {
+			let [a, o] = e[r];
+			t(this, i, "f").has(a) || t(this, n, "m", u).call(this, a, o) || (yield [a, o.value]);
+		}
+	}
+	*entriesAscending() {
+		for (let [e, r] of t(this, n, "m", g).call(this)) yield [e, r.value];
+	}
+	get size() {
+		if (!t(this, r, "f")) return t(this, a, "f").size;
+		let e = 0;
+		for (let n of t(this, a, "f").keys()) t(this, i, "f").has(n) || e++;
+		return Math.min(t(this, r, "f") + e, t(this, o, "f"));
+	}
+	get maxSize() {
+		return t(this, o, "f");
+	}
+	get maxAge() {
+		return t(this, s, "f");
+	}
+	entries() {
+		return this.entriesAscending();
+	}
+	forEach(e, t = this) {
+		for (let [n, r] of this.entriesAscending()) e.call(t, r, n, this);
+	}
+	get [Symbol.toStringTag]() {
+		return "QuickLRU";
+	}
+	toString() {
+		return `QuickLRU(${this.size}/${this.maxSize})`;
+	}
+	[Symbol.for("nodejs.util.inspect.custom")]() {
+		return this.toString();
+	}
+};
+//#endregion
+export { _ as t };

package/dist/esm-C_XrKaCY.js

@@ -0,0 +1,137 @@
+import { n as e, t } from "./chunk-CPXzm0be.js";
+//#region ../../node_modules/generic-filehandle2/esm/util.js
+async function n(e) {
+	return e.bytes ? e.bytes() : new Uint8Array(await e.arrayBuffer());
+}
+//#endregion
+//#region ../../node_modules/generic-filehandle2/esm/blobFile.js
+var r = class {
+	blob;
+	constructor(e) {
+		this.blob = e;
+	}
+	async read(e, t = 0) {
+		return e === 0 ? new Uint8Array() : n(this.blob.slice(t, t + e));
+	}
+	async readFile(e) {
+		let t = typeof e == "string" ? e : e?.encoding;
+		if (t === "utf8") return this.blob.text();
+		if (t) throw Error(`unsupported encoding: ${t}`);
+		return n(this.blob);
+	}
+	stat() {
+		return Promise.resolve({ size: this.blob.size });
+	}
+	close() {
+		return Promise.resolve();
+	}
+};
+//#endregion
+//#region ../../node_modules/generic-filehandle2/esm/remoteFile.js
+function i(e) {
+	return (typeof e == "object" && e && "message" in e && typeof e.message == "string" ? e.message : `${e}`).replace(/\.$/, "");
+}
+var a = class {
+	url;
+	_stat;
+	fetchImplementation;
+	baseHeaders;
+	baseOverrides;
+	constructor(e, t = {}) {
+		this.url = e, this.baseHeaders = t.headers ?? {}, this.baseOverrides = t.overrides ?? {}, this.fetchImplementation = t.fetch ?? globalThis.fetch.bind(globalThis);
+	}
+	buildRequest(e, t) {
+		return {
+			...this.baseOverrides,
+			...e.overrides,
+			headers: {
+				...this.baseHeaders,
+				...e.headers,
+				...t
+			},
+			method: "GET",
+			redirect: "follow",
+			mode: "cors",
+			signal: e.signal
+		};
+	}
+	async fetch(e, t) {
+		let n = (t) => Error(`${i(t)} fetching ${e}`, { cause: t }), r;
+		try {
+			r = await this.fetchImplementation(e, t);
+		} catch (i) {
+			if (`${i}`.includes("Failed to fetch")) {
+				console.warn(`generic-filehandle: refetching ${e} to attempt to work around chrome CORS header caching bug`);
+				try {
+					r = await this.fetchImplementation(e, {
+						...t,
+						cache: "reload"
+					});
+				} catch (e) {
+					throw n(e);
+				}
+			} else throw n(i);
+		}
+		return r;
+	}
+	async read(e, t, r = {}) {
+		if (e === 0) return new Uint8Array();
+		if (Number.isNaN(e) || Number.isNaN(t)) throw TypeError(`read() called with NaN length or position (length=${e}, position=${t}). The index file may be corrupt.`);
+		let i = await this.fetch(this.url, this.buildRequest(r, { range: `bytes=${t}-${t + e - 1}` }));
+		if (i.status === 416) return new Uint8Array();
+		if (!i.ok) throw Error(`HTTP ${i.status} fetching ${this.url}`);
+		if (i.status === 200 && t === 0 || i.status === 206) {
+			let t = i.headers.get("content-range"), r = /\/(\d+)$/.exec(t ?? "");
+			r?.[1] && (this._stat = { size: parseInt(r[1], 10) });
+			let a = await n(i);
+			return !this._stat && i.status === 200 && (this._stat = { size: a.byteLength }), a.byteLength <= e ? a : a.subarray(0, e);
+		}
+		throw Error(i.status === 200 ? `${this.url} fetch returned status 200, expected 206` : `HTTP ${i.status} fetching ${this.url}`);
+	}
+	async readFile(e = {}) {
+		let t = typeof e == "string" ? e : e.encoding, r = typeof e == "string" ? {} : e, i = await this.fetch(this.url, this.buildRequest(r));
+		if (!i.ok) throw Error(`HTTP ${i.status} fetching ${this.url}`);
+		if (t === "utf8") return i.text();
+		if (t) throw Error(`unsupported encoding: ${t}`);
+		return n(i);
+	}
+	async stat() {
+		return this._stat || await this.read(10, 0), this._stat ?? { size: 0 };
+	}
+	close() {
+		return Promise.resolve();
+	}
+}, o = (/* @__PURE__ */ t(((e, t) => {
+	t.exports = {};
+})))(), s = class {
+	filename;
+	constructor(e) {
+		this.filename = e;
+	}
+	async read(e, t = 0) {
+		if (e === 0) return new Uint8Array();
+		let n = new Uint8Array(e), r;
+		try {
+			r = await (0, o.open)(this.filename, "r");
+			let i = await r.read(n, 0, e, t);
+			return i.buffer.subarray(0, i.bytesRead);
+		} finally {
+			if (r) try {
+				await r.close();
+			} catch {}
+		}
+	}
+	async readFile(e) {
+		return (0, o.readFile)(this.filename, e);
+	}
+	async stat() {
+		return (0, o.stat)(this.filename);
+	}
+	async close() {}
+}, c = /* @__PURE__ */ e({
+	BlobFile: () => r,
+	LocalFile: () => s,
+	RemoteFile: () => a
+});
+//#endregion
+export { s as n, a as r, c as t };

package/dist/{esm-DCCYNvaz.js → esm-CqrZuhTF.js}

@@ -1,6 +1,6 @@
-import { t as e } from "./esm-CGX-qz1d.js";
-import { n as t, r as n } from "./esm-BDFRLEuD.js";
-import { r, t as i } from "./browser-Dvlo92rx.js";
+import { n as e, r as t } from "./esm-BDFRLEuD.js";
+import { t as n } from "./esm-CZvS2Ldm.js";
+import { n as r, r as i } from "./esm-id9DWBZW.js";
 //#region ../../node_modules/@gmod/bam/esm/chunk.js
 var a = class {
 	constructor(e, t, n, r) {
@@ -145,8 +145,8 @@ var T = class extends v {
 	async lineCount(e, t) {
 		return (await this.parse(t)).indices(e)?.stats?.lineCount || 0;
 	}
-	async _parse(t) {
-		let n = await this.filehandle.readFile(), r = new DataView(n.buffer);
+	async _parse(e) {
+		let t = await this.filehandle.readFile(), r = new DataView(t.buffer);
 		if (r.getUint32(0, !0) !== x) throw Error("Not a BAI file");
 		let i = r.getInt32(4, !0), o = ((1 << 18) - 1) / 7, s = 8, c, l = [];
 		for (let e = 0; e < i; e++) {
@@ -163,44 +163,44 @@ var T = class extends v {
 					for (let t = 0; t < e; t++) s += 8, s += 8;
 				}
 			}
-			let t = r.getInt32(s, !0);
+			let n = r.getInt32(s, !0);
 			s += 4;
-			let i = Array(t);
-			for (let e = 0; e < t; e++) {
-				let t = b(n, s);
-				s += 8, c = f(c, t), i[e] = t;
+			let i = Array(n);
+			for (let e = 0; e < n; e++) {
+				let n = b(t, s);
+				s += 8, c = f(c, n), i[e] = n;
 			}
 		}
-		let u = new e({ maxSize: 5 });
+		let u = new n({ maxSize: 5 });
 		function p(e) {
-			let t = l[e];
-			if (t === void 0) return;
-			let i = r.getInt32(t, !0), s;
-			t += 4;
+			let n = l[e];
+			if (n === void 0) return;
+			let i = r.getInt32(n, !0), s;
+			n += 4;
 			let u = {};
 			for (let e = 0; e < i; e += 1) {
-				let e = r.getUint32(t, !0);
-				if (t += 4, e === o + 1) t += 4, s = d(n, t + 16), t += 32;
+				let e = r.getUint32(n, !0);
+				if (n += 4, e === o + 1) n += 4, s = d(t, n + 16), n += 32;
 				else if (e > o + 1) throw Error("bai index contains too many bins, please use CSI");
 				else {
-					let i = r.getInt32(t, !0);
-					t += 4;
+					let i = r.getInt32(n, !0);
+					n += 4;
 					let o = Array(i);
 					for (let r = 0; r < i; r++) {
-						let i = b(n, t);
-						t += 8;
-						let s = b(n, t);
-						t += 8, c = f(c, i), o[r] = new a(i, s, e);
+						let i = b(t, n);
+						n += 8;
+						let s = b(t, n);
+						n += 8, c = f(c, i), o[r] = new a(i, s, e);
 					}
 					u[e] = o;
 				}
 			}
-			let p = r.getInt32(t, !0);
-			t += 4;
+			let p = r.getInt32(n, !0);
+			n += 4;
 			let m = Array(p);
 			for (let e = 0; e < p; e++) {
-				let r = b(n, t);
-				t += 8, c = f(c, r), m[e] = r;
+				let r = b(t, n);
+				n += 8, c = f(c, r), m[e] = r;
 			}
 			return {
 				binIndex: u,
@@ -565,8 +565,8 @@ var M = class extends v {
 			...p(e.subarray(t + 28, t + 28 + u), this.renameRefSeq)
 		};
 	}
-	async _parse(n) {
-		let r = await t(await this.filehandle.readFile(n)), i = new DataView(r.buffer), o, s = i.getUint32(0, !0);
+	async _parse(t) {
+		let r = await e(await this.filehandle.readFile(t)), i = new DataView(r.buffer), o, s = i.getUint32(0, !0);
 		if (s === O) o = 1;
 		else if (s === k) o = 2;
 		else throw Error(`Not a CSI file ${s}`);
@@ -590,7 +590,7 @@ var M = class extends v {
 				}
 			}
 		}
-		let _ = new e({ maxSize: 5 });
+		let _ = new n({ maxSize: 5 });
 		function v(e) {
 			let t = g[e];
 			if (t === void 0) return;
@@ -1126,38 +1126,38 @@ function B(e) {
 	return n;
 }
 var V = 65536, H = class {
-	constructor({ bamFilehandle: t, bamPath: n, bamUrl: a, baiPath: o, baiFilehandle: s, baiUrl: c, csiPath: l, csiFilehandle: u, csiUrl: d, htsget: f, renameRefSeqs: p = (e) => e, recordClass: m }) {
-		if (this.htsget = !1, this.chunkFeatureCache = new e({ maxSize: 100 }), this.renameRefSeq = p, this.RecordClass = m ?? z, t) this.bam = t;
-		else if (n) this.bam = new i(n);
-		else if (a) this.bam = new r(a);
+	constructor({ bamFilehandle: e, bamPath: t, bamUrl: a, baiPath: o, baiFilehandle: s, baiUrl: c, csiPath: l, csiFilehandle: u, csiUrl: d, htsget: f, renameRefSeqs: p = (e) => e, recordClass: m }) {
+		if (this.htsget = !1, this.chunkFeatureCache = new n({ maxSize: 100 }), this.renameRefSeq = p, this.RecordClass = m ?? z, e) this.bam = e;
+		else if (t) this.bam = new r(t);
+		else if (a) this.bam = new i(a);
 		else if (f) this.htsget = !0, this.bam = new N();
 		else throw Error("unable to initialize bam");
 		if (u) this.index = new M({ filehandle: u });
-		else if (l) this.index = new M({ filehandle: new i(l) });
-		else if (d) this.index = new M({ filehandle: new r(d) });
+		else if (l) this.index = new M({ filehandle: new r(l) });
+		else if (d) this.index = new M({ filehandle: new i(d) });
 		else if (s) this.index = new T({ filehandle: s });
-		else if (o) this.index = new T({ filehandle: new i(o) });
-		else if (c) this.index = new T({ filehandle: new r(c) });
-		else if (n) this.index = new T({ filehandle: new i(`${n}.bai`) });
-		else if (a) this.index = new T({ filehandle: new r(`${a}.bai`) });
+		else if (o) this.index = new T({ filehandle: new r(o) });
+		else if (c) this.index = new T({ filehandle: new i(c) });
+		else if (t) this.index = new T({ filehandle: new r(`${t}.bai`) });
+		else if (a) this.index = new T({ filehandle: new i(`${a}.bai`) });
 		else if (f) this.htsget = !0;
 		else throw Error("unable to infer index format");
 	}
-	async getHeaderPre(e) {
-		let n = l(e);
+	async getHeaderPre(t) {
+		let n = l(t);
 		if (!this.index) return;
-		let r = await this.index.parse(n), i = r.firstDataLine === void 0 ? void 0 : r.firstDataLine.blockPosition + V, a = await t(i === void 0 ? await this.bam.readFile() : await this.bam.read(i, 0)), o = new DataView(a.buffer);
+		let r = await this.index.parse(n), i = r.firstDataLine === void 0 ? void 0 : r.firstDataLine.blockPosition + V, a = await e(i === void 0 ? await this.bam.readFile() : await this.bam.read(i, 0)), o = new DataView(a.buffer);
 		if (o.getInt32(0, !0) !== 21840194) throw Error("Not a BAM file");
 		let s = o.getInt32(4, !0);
 		this.header = new TextDecoder("utf8").decode(a.subarray(8, 8 + s));
 		let c = s + 8;
-		for (let e = 0; e < 5; e++) {
+		for (let t = 0; t < 5; t++) {
 			if (this._hasEnoughRefSeqData(a, c)) {
 				let { chrToIndex: e, indexToChr: t } = this._parseRefSeqs(a, c);
 				return this.chrToIndex = e, this.indexToChr = t, B(this.header);
 			}
 			if (i === void 0) throw Error(`Insufficient data for reference sequences in ${a.length} bytes`);
-			i *= 2, a = await t(await this.bam.read(i, 0));
+			i *= 2, a = await e(await this.bam.read(i, 0));
 		}
 		throw Error("Insufficient data for reference sequences after 5 retries");
 	}
@@ -1281,8 +1281,8 @@ var V = 65536, H = class {
 			return c;
 		}))).flat();
 	}
-	async _readChunk({ chunk: e, opts: t }) {
-		let { buffer: r, cpositions: i, dpositions: a } = await n(await this.bam.read(e.fetchedSize(), e.minv.blockPosition, t), e);
+	async _readChunk({ chunk: e, opts: n }) {
+		let { buffer: r, cpositions: i, dpositions: a } = await t(await this.bam.read(e.fetchedSize(), e.minv.blockPosition, n), e);
 		return {
 			data: r,
 			cpositions: i,
@@ -1352,8 +1352,8 @@ var V = 65536, H = class {
 };
 //#endregion
 //#region ../../node_modules/@gmod/bam/esm/htsget.js
-async function U(e, n) {
-	let r = await Promise.all(e.map(async (e) => {
+async function U(t, n) {
+	let r = await Promise.all(t.map(async (e) => {
 		let { url: t, headers: r } = e;
 		if (t.startsWith("data:")) {
 			let e = await fetch(t);
@@ -1372,7 +1372,7 @@ async function U(e, n) {
 			return new Uint8Array(await a.arrayBuffer());
 		}
 	}));
-	return m(await Promise.all(r.map((e) => t(e))));
+	return m(await Promise.all(r.map((t) => e(t))));
 }
 var W = class extends H {
 	constructor(e) {

package/dist/{esm-D-WfYOx7.js → esm-Cz4iCfzF.js}

@@ -1,7 +1,7 @@
-import { t as e } from "./esm-CGX-qz1d.js";
-import { n as t, r as n } from "./esm-BDFRLEuD.js";
-import { r, t as i } from "./browser-Dvlo92rx.js";
-import { t as a } from "./AbortablePromiseCache-3gHJdF3E.js";
+import { n as e, r as t } from "./esm-BDFRLEuD.js";
+import { t as n } from "./esm-CZvS2Ldm.js";
+import { n as r, r as i } from "./esm-id9DWBZW.js";
+import { t as a } from "./AbortablePromiseCache-beUIcZcW.js";
 //#region ../../node_modules/@gmod/tabix/esm/chunk.js
 var o = class {
 	constructor(e, t, n, r) {
@@ -132,8 +132,8 @@ var b = class extends s {
 			coordinateType: i
 		};
 	}
-	async _parse(e = {}) {
-		let n = await t(await this.filehandle.readFile(e)), r = new DataView(n.buffer), i;
+	async _parse(t = {}) {
+		let n = await e(await this.filehandle.readFile(t)), r = new DataView(n.buffer), i;
 		if (r.getUint32(0, !0) === h) i = 1;
 		else if (r.getUint32(0, !0) === g) i = 2;
 		else throw Error("Not a CSI file");
@@ -226,8 +226,8 @@ var w = class extends s {
 		let n = await this.parse(t), r = n.refNameToId[e];
 		return r === void 0 || !n.indices[r] ? -1 : n.indices[r].stats?.lineCount ?? -1;
 	}
-	async _parse(e = {}) {
-		let n = await t(await this.filehandle.readFile(e)), r = new DataView(n.buffer);
+	async _parse(t = {}) {
+		let n = await e(await this.filehandle.readFile(t)), r = new DataView(n.buffer);
 		if (r.getUint32(0, !0) !== x) throw Error("Not a TBI file");
 		let i = r.getUint32(4, !0), a = r.getUint32(8, !0), s = a & 65536 ? "zero-based-half-open" : "1-based-closed", c = {
 			0: "generic",
@@ -305,12 +305,12 @@ var w = class extends s {
 		return f(l, d);
 	}
 }, T = class {
-	constructor({ path: t, filehandle: n, url: o, tbiPath: s, tbiUrl: c, tbiFilehandle: l, csiPath: u, csiUrl: d, csiFilehandle: f, renameRefSeqs: p, chunkCacheSize: m = 5 * 2 ** 20 }) {
-		this.cache = new e({ maxSize: 1e3 });
+	constructor({ path: e, filehandle: t, url: o, tbiPath: s, tbiUrl: c, tbiFilehandle: l, csiPath: u, csiUrl: d, csiFilehandle: f, renameRefSeqs: p, chunkCacheSize: m = 5 * 2 ** 20 }) {
+		this.cache = new n({ maxSize: 1e3 });
 		let h = p ?? ((e) => e);
-		if (n) this.filehandle = n;
-		else if (t) this.filehandle = new i(t);
-		else if (o) this.filehandle = new r(o);
+		if (t) this.filehandle = t;
+		else if (e) this.filehandle = new r(e);
+		else if (o) this.filehandle = new i(o);
 		else throw TypeError("must provide either filehandle or path");
 		if (l) this.index = new w({
 			filehandle: l,
@@ -321,23 +321,23 @@ var w = class extends s {
 			renameRefSeqs: h
 		});
 		else if (s) this.index = new w({
-			filehandle: new i(s),
+			filehandle: new r(s),
 			renameRefSeqs: h
 		});
 		else if (u) this.index = new b({
-			filehandle: new i(u),
+			filehandle: new r(u),
 			renameRefSeqs: h
 		});
-		else if (t) this.index = new w({
-			filehandle: new i(`${t}.tbi`),
+		else if (e) this.index = new w({
+			filehandle: new r(`${e}.tbi`),
 			renameRefSeqs: h
 		});
-		else if (d) this.index = new b({ filehandle: new r(d) });
-		else if (c) this.index = new w({ filehandle: new r(c) });
-		else if (o) this.index = new w({ filehandle: new r(`${o}.tbi`) });
+		else if (d) this.index = new b({ filehandle: new i(d) });
+		else if (c) this.index = new w({ filehandle: new i(c) });
+		else if (o) this.index = new w({ filehandle: new i(`${o}.tbi`) });
 		else throw TypeError("must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl");
 		this.renameRefSeq = h, this.hasCustomRenameRefSeq = p !== void 0, this.chunkCache = new a({
-			cache: new e({ maxSize: Math.floor(m / 65536) }),
+			cache: new n({ maxSize: Math.floor(m / 65536) }),
 			fill: (e, t) => this.readChunk(e, { signal: t })
 		});
 	}
@@ -386,8 +386,8 @@ var w = class extends s {
 	async getMetadata(e = {}) {
 		return this.index.getMetadata(e);
 	}
-	async getHeaderBuffer(e = {}) {
-		let { firstDataLine: n, metaChar: r, maxBlockSize: i } = await this.getMetadata(e), a = (n?.blockPosition || 0) + i, o = await t(await this.filehandle.read(a, 0, e));
+	async getHeaderBuffer(t = {}) {
+		let { firstDataLine: n, metaChar: r, maxBlockSize: i } = await this.getMetadata(t), a = (n?.blockPosition || 0) + i, o = await e(await this.filehandle.read(a, 0, t));
 		if (r) {
 			let e = -1, t = r.charCodeAt(0);
 			for (let n = 0, r = o.length; n < r; n++) {
@@ -453,8 +453,8 @@ var w = class extends s {
 	async lineCount(e, t = {}) {
 		return this.index.lineCount(e, t);
 	}
-	async readChunk(e, t = {}) {
-		return n(await this.filehandle.read(e.fetchedSize(), e.minv.blockPosition, t), e, this.cache);
+	async readChunk(e, n = {}) {
+		return t(await this.filehandle.read(e.fetchedSize(), e.minv.blockPosition, n), e, this.cache);
 	}
 };
 //#endregion