@genome-spy/app 1.2.0 → 1.3.0

package/dist/esm-Dls41IbZ.js

@@ -0,0 +1,787 @@
+import { n as e, r as t } from "./esm-nzwgJFGz.js";
+import { t as n } from "./SharedReadCache-9sT2aIxW.js";
+import { n as r, r as i } from "./esm-BUkWqSr2.js";
+//#region ../../node_modules/@gmod/tabix/esm/chunk.js
+var a = class {
+	minv;
+	maxv;
+	bin;
+	endPosition;
+	constructor(e, t, n, r = t.blockPosition + 65536) {
+		this.minv = e, this.maxv = t, this.bin = n, this.endPosition = r;
+	}
+	toString() {
+		return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
+	}
+	fetchedSize() {
+		return this.endPosition - this.minv.blockPosition;
+	}
+};
+//#endregion
+//#region ../../node_modules/@gmod/tabix/node_modules/@jbrowse/quick-lru/esm/index.js
+function o(e, t) {
+	if (!(t > 0)) throw TypeError(`\`${e}\` must be a number greater than 0`);
+}
+var s = class {
+	#e = /* @__PURE__ */ new Map();
+	#t = /* @__PURE__ */ new Map();
+	#n;
+	#r;
+	#i;
+	constructor(e) {
+		let t = e.maxAge ?? Infinity;
+		o("maxSize", e.maxSize), o("maxAge", t), this.#n = e.maxSize, this.#r = t, this.#i = e.onEviction;
+	}
+	#a(e) {
+		let t = this.#i;
+		if (t) for (let [n, r] of e) t(n, r.value);
+	}
+	#o(e, t) {
+		return t.expiry !== void 0 && t.expiry <= Date.now() && (this.#i?.(e, t.value), this.delete(e), !0);
+	}
+	#s(e, t) {
+		return this.#o(e, t) ? void 0 : t.value;
+	}
+	#c(e, t) {
+		if (this.#t.delete(e), this.#e.set(e, t), this.#e.size >= this.#n) {
+			let e = this.#t;
+			this.#t = this.#e, this.#e = /* @__PURE__ */ new Map(), this.#a(e);
+		}
+	}
+	#l(e) {
+		this.#t = new Map(e), this.#e = /* @__PURE__ */ new Map();
+	}
+	*#u() {
+		for (let e of [this.#t, this.#e]) for (let t of e) this.#o(...t) || (yield t);
+	}
+	get(e) {
+		let t = this.#e.get(e);
+		if (t) return this.#s(e, t);
+		let n = this.#t.get(e);
+		if (n && !this.#o(e, n)) return this.#c(e, n), n.value;
+	}
+	set(e, t, { maxAge: n = this.#r } = {}) {
+		let r = {
+			value: t,
+			expiry: n === Infinity ? void 0 : Date.now() + n
+		};
+		return this.#e.has(e) ? this.#e.set(e, r) : this.#c(e, r), this;
+	}
+	has(e) {
+		let t = this.#e.get(e) ?? this.#t.get(e);
+		return t !== void 0 && !this.#o(e, t);
+	}
+	peek(e) {
+		let t = this.#e.get(e) ?? this.#t.get(e);
+		return t ? this.#s(e, t) : void 0;
+	}
+	expiresIn(e) {
+		let t = this.#e.get(e) ?? this.#t.get(e);
+		if (t) return t.expiry === void 0 ? Infinity : t.expiry - Date.now();
+	}
+	delete(e) {
+		return this.#e.delete(e) || this.#t.delete(e);
+	}
+	clear() {
+		this.#e.clear(), this.#t.clear();
+	}
+	resize(e) {
+		o("maxSize", e);
+		let t = [...this.#u()], n = t.length - e;
+		n < 0 ? (this.#e = new Map(t), this.#t = /* @__PURE__ */ new Map()) : (this.#a(t.slice(0, n)), this.#l(t.slice(n))), this.#n = e;
+	}
+	evict(e = 1) {
+		if (!(e > 0)) return;
+		let t = [...this.#u()], n = Math.trunc(Math.min(e, t.length - 1));
+		n > 0 && (this.#a(t.slice(0, n)), this.#l(t.slice(n)));
+	}
+	get size() {
+		return Math.min(this.#e.size + this.#t.size, this.#n);
+	}
+	get maxSize() {
+		return this.#n;
+	}
+	get maxAge() {
+		return this.#r;
+	}
+	*entriesAscending() {
+		for (let [e, t] of this.#u()) yield [e, t.value];
+	}
+	*entriesDescending() {
+		for (let e of [this.#e, this.#t]) for (let [t, n] of [...e].reverse()) this.#o(t, n) || (yield [t, n.value]);
+	}
+	entries() {
+		return this.entriesAscending();
+	}
+	[Symbol.iterator]() {
+		return this.entriesAscending();
+	}
+	*keys() {
+		for (let [e] of this) yield e;
+	}
+	*values() {
+		for (let [, e] of this) yield e;
+	}
+	forEach(e, t = this) {
+		for (let [n, r] of this) 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();
+	}
+}, c = 2 ** 32;
+function l(e, t = 0) {
+	let n = e[t] | e[t + 1] << 8 | e[t + 2] << 16 | e[t + 3] << 24;
+	return ((e[t + 4] | e[t + 5] << 8 | e[t + 6] << 16 | e[t + 7] << 24) >>> 0) * c + (n >>> 0);
+}
+//#endregion
+//#region ../../node_modules/@gmod/tabix/esm/virtualOffset.js
+var u = class {
+	blockPosition;
+	dataPosition;
+	constructor(e, t) {
+		this.blockPosition = e, this.dataPosition = t;
+	}
+	toString() {
+		return `${this.blockPosition}:${this.dataPosition}`;
+	}
+	compareTo(e) {
+		return this.blockPosition - e.blockPosition || this.dataPosition - e.dataPosition;
+	}
+};
+function d(e, t = 0) {
+	return new u(e[t + 7] * 1099511627776 + e[t + 6] * 4294967296 + e[t + 5] * 16777216 + e[t + 4] * 65536 + e[t + 3] * 256 + e[t + 2], e[t + 1] << 8 | e[t]);
+}
+//#endregion
+//#region ../../node_modules/@gmod/tabix/esm/util.js
+function f(e, t) {
+	let n = e.length;
+	if (n === 0) return e;
+	let r;
+	if (t) {
+		let i = t.blockPosition, a = t.dataPosition;
+		r = [];
+		for (let t = 0; t < n; t++) {
+			let n = e[t];
+			(n.maxv.blockPosition - i || n.maxv.dataPosition - a) > 0 && r.push(n);
+		}
+		if (r.length === 0) return r;
+	} else r = e;
+	r.sort((e, t) => {
+		let n = e.minv.blockPosition - t.minv.blockPosition;
+		return n === 0 ? e.minv.dataPosition - t.minv.dataPosition : n;
+	});
+	let i = [r[0]], o = r[0].minv.blockPosition, s = r[0].maxv.blockPosition;
+	for (let e = 1; e < r.length; e++) {
+		let t = r[e], n = t.minv.blockPosition, c = t.maxv.blockPosition;
+		if (n - s < 65e3 && c - o < 5e6) {
+			let e = i.at(-1);
+			(c - s || t.maxv.dataPosition - e.maxv.dataPosition) > 0 && (i[i.length - 1] = new a(e.minv, t.maxv, e.bin, t.endPosition), s = c);
+		} else i.push(t), o = n, s = c;
+	}
+	return p(i);
+}
+function p(e) {
+	let t = [e[0]];
+	for (let n = 1; n < e.length; n++) {
+		let r = e[n], i = t.at(-1).maxv;
+		(r.minv.blockPosition - i.blockPosition || r.minv.dataPosition - i.dataPosition) >= 0 ? t.push(r) : (r.maxv.blockPosition - i.blockPosition || r.maxv.dataPosition - i.dataPosition) > 0 && t.push(new a(i, r.maxv, r.bin, r.endPosition));
+	}
+	return t;
+}
+function m(e, t = []) {
+	let n = [...t];
+	for (let t of e) n.push(t.minv.blockPosition, t.maxv.blockPosition);
+	n.sort((e, t) => e - t);
+	for (let t of e) {
+		let e = t.maxv.blockPosition, r = 0, i = n.length;
+		for (; r < i;) {
+			let t = r + i >>> 1;
+			n[t] > e ? i = t : r = t + 1;
+		}
+		r < n.length && (t.endPosition = Math.min(t.endPosition, n[r]));
+	}
+}
+function h(e, t, n, r) {
+	let i = r ? r.blockPosition : Infinity, a = r ? r.dataPosition : 0, o = !1;
+	for (let r = 0; r < n; r++) {
+		let n = t + r * 8, s = e[n + 7] * 1099511627776 + e[n + 6] * 4294967296 + e[n + 5] * 16777216 + e[n + 4] * 65536 + e[n + 3] * 256 + e[n + 2], c = e[n + 1] << 8 | e[n];
+		(s < i || s === i && c < a) && (i = s, a = c, o = !0);
+	}
+	return o ? new u(i, a) : r;
+}
+function g(e) {
+	let t = new TextDecoder("utf-8"), n = [], r = {}, i = 0, a = 0;
+	for (; a < e.length;) {
+		let o = e.indexOf(0, a);
+		if (o === -1) break;
+		if (o > a) {
+			let s = t.decode(e.subarray(a, o));
+			n[i] = s, r[s] = i;
+		}
+		a = o + 1, i++;
+	}
+	return {
+		refNameToId: r,
+		refIdToName: n
+	};
+}
+var _ = {
+	0: "generic",
+	1: "SAM",
+	2: "VCF",
+	3: "GAF"
+};
+function v(e, t) {
+	let n = new DataView(e.buffer, e.byteOffset, e.byteLength), r = n.getInt32(t, !0), i = r & 65536 ? "zero-based-half-open" : "1-based-closed", a = _[r & 15];
+	if (!a) throw Error(`invalid Tabix preset format flags ${r}`);
+	let o = {
+		ref: n.getInt32(t + 4, !0),
+		start: n.getInt32(t + 8, !0),
+		end: n.getInt32(t + 12, !0)
+	}, s = n.getInt32(t + 16, !0), c = s ? String.fromCharCode(s) : void 0, l = n.getInt32(t + 20, !0), u = n.getInt32(t + 24, !0), { refIdToName: d, refNameToId: f } = g(e.subarray(t + 28, t + 28 + u));
+	return {
+		refIdToName: d,
+		refNameToId: f,
+		skipLines: l,
+		metaChar: c,
+		columnNumbers: o,
+		format: a,
+		coordinateType: i
+	};
+}
+function y(e, t) {
+	return { lineCount: l(e, t) };
+}
+function b(e, t = 5) {
+	let n = new s({ maxSize: t });
+	return (t) => {
+		let r = n.get(t);
+		if (r !== void 0) return r;
+		let i = e(t);
+		return i !== void 0 && n.set(t, i), i;
+	};
+}
+//#endregion
+//#region ../../node_modules/@gmod/tabix/esm/indexFile.js
+function x(e, t, n, r) {
+	if (t > 2 ** (n + r * 3)) return;
+	let i = (8 ** (r + 1) - 1) / 7, a = (8 ** r - 1) / 7 + Math.floor((t - 1) / 2 ** n) + 1;
+	for (a >= i && (a = 0);;) {
+		for (; a % 8 == 1;) a = (a - 1) / 8;
+		if (a === 0) return;
+		let t = e[a];
+		if (t?.length) {
+			let e = t[0].minv;
+			for (let n = 1; n < t.length; n++) {
+				let r = t[n].minv;
+				r.compareTo(e) < 0 && (e = r);
+			}
+			return e;
+		}
+		a++;
+	}
+}
+function S(e, t) {
+	return e.format === "GAF" ? 0 : e.refNameToId[t];
+}
+var C = class {
+	filehandle;
+	parseCache = new n({});
+	constructor({ filehandle: e }) {
+		this.filehandle = e;
+	}
+	async readIndexBytes(e) {
+		let t = await this.filehandle.readFile({
+			signal: e.signal,
+			onProgress: e.onProgress
+		}), n = await r(t);
+		return {
+			bytes: n,
+			dataView: new DataView(n.buffer, n.byteOffset, n.byteLength)
+		};
+	}
+	async lineCount(e, t = {}) {
+		let n = await this.parse(t), r = S(n, e);
+		return r === void 0 ? -1 : n.indices(r)?.stats?.lineCount ?? -1;
+	}
+	async getMetadata(e = {}) {
+		let { indices: t, ...n } = await this.parse(e);
+		return n;
+	}
+	async blocksForRange(e, t, n, r = {}) {
+		let i = await this.parse(r), a = S(i, e);
+		if (a === void 0) return [];
+		let o = i.indices(a);
+		if (!o) return [];
+		i.format === "GAF" && (t = Math.max(t - 1, 0));
+		let s = [];
+		for (let [e, r] of this.reg2bins(t, n, i)) for (let t = e; t <= r; t++) {
+			let e = o.binIndex[t];
+			if (e) for (let t of e) s.push(t);
+		}
+		let c = f(s, this.lowestOffset(o, t, i)), l = x(o.binIndex, n, i.minShift, i.depth);
+		if (l) {
+			let e = c.length;
+			for (; e > 0 && c[e - 1].minv.compareTo(l) >= 0;) e--;
+			c.length = e;
+		}
+		return c;
+	}
+	parse(e = {}) {
+		return this.parseCache.get("index", e.signal, (t) => this._parse({
+			...e,
+			signal: t
+		}));
+	}
+	async hasRefSeq(e, t = {}) {
+		return !!(await this.parse(t)).indices(e)?.binIndex;
+	}
+}, w = 21582659, T = 38359875;
+function E(e, t) {
+	return e * 2 ** t;
+}
+function D(e, t) {
+	return Math.floor(e / 2 ** t);
+}
+var O = class extends C {
+	async _parse(e = {}) {
+		let { bytes: t, dataView: n } = await this.readIndexBytes(e), r = n.getUint32(0, !0), i;
+		if (r === w) i = 1;
+		else if (r === T) i = 2;
+		else throw Error(`Not a CSI file (magic=${r})`);
+		let o = n.getInt32(4, !0), s = n.getInt32(8, !0), c = (8 ** (s + 1) - 1) / 7, l = 2 ** (o + s * 3), u = n.getInt32(12, !0), f = u >= 28 && (n.getInt32(16, !0) & 15) == 3, p = u >= 30 || f ? v(t, 16) : {
+			refIdToName: [],
+			refNameToId: {},
+			metaChar: void 0,
+			columnNumbers: {
+				ref: 0,
+				start: 1,
+				end: 2
+			},
+			coordinateType: "zero-based-half-open",
+			format: "generic"
+		}, g = n.getInt32(16 + u, !0), _ = 16 + u + 4, x, S = [];
+		for (let e = 0; e < g; e++) {
+			S.push(_);
+			let e = n.getInt32(_, !0);
+			_ += 4;
+			for (let r = 0; r < e; r++) {
+				let e = n.getUint32(_, !0);
+				if (_ += 4, e > c) _ += 44;
+				else {
+					x = h(t, _, 1, x), _ += 8;
+					let e = n.getInt32(_, !0);
+					_ += 4 + 16 * e;
+				}
+			}
+		}
+		function C(e) {
+			let r = S[e];
+			if (r === void 0) return;
+			let i = r, o = n.getInt32(i, !0);
+			i += 4;
+			let s = {}, l = {}, u;
+			for (let e = 0; e < o; e++) {
+				let e = n.getUint32(i, !0);
+				if (i += 4, e > c) u = y(t, i + 28), i += 44;
+				else {
+					l[e] = d(t, i), i += 8;
+					let r = n.getInt32(i, !0);
+					i += 4;
+					let o = Array.from({ length: r });
+					for (let n = 0; n < r; n++) o[n] = new a(d(t, i), d(t, i + 8), e), i += 16;
+					s[e] = o;
+				}
+			}
+			return m(Object.values(s).flat()), {
+				binIndex: s,
+				loffsets: l,
+				stats: u
+			};
+		}
+		return {
+			...p,
+			csi: !0,
+			refCount: g,
+			maxBlockSize: 65536,
+			firstDataLine: x,
+			csiVersion: i,
+			indices: b(C),
+			minShift: o,
+			depth: s,
+			maxBinNumber: c,
+			maxRefLength: l
+		};
+	}
+	lowestOffset(e, t, { minShift: n, depth: r }) {
+		let { loffsets: i } = e, a;
+		if (i) {
+			let e = (E(1, 3 * r) - 1) / 7 + D(Math.max(t, 0), n);
+			for (; a === void 0 && e > 0;) if (a = i[e], a === void 0) {
+				let t = Math.floor((e - 1) / 8), n = t * 8 + 1;
+				e = e > n ? e - 1 : t;
+			}
+			a ??= i[0];
+		}
+		return a;
+	}
+	reg2bins(e, t, { minShift: n, depth: r, maxBinNumber: i }) {
+		e = Math.max(e, 0);
+		let a = 2 ** (n + r * 3);
+		t > a && (t = a), --t;
+		let o = 0, s = 0, c = n + r * 3, l = [];
+		for (; o <= r; c -= 3, s += E(1, o * 3), o += 1) {
+			let a = s + D(e, c), o = s + D(t, c);
+			if (o - a + l.length > i) throw Error(`query ${e}-${t} is too large for current binning scheme (shift ${n}, depth ${r}), try a smaller query or a coarser index binning scheme`);
+			l.push([a, o]);
+		}
+		return l;
+	}
+}, k = 21578324, A = 5, j = 14, M = 2 ** 29;
+function N(e) {
+	return Math.min(Math.max(e, 0), M);
+}
+var P = class extends C {
+	reg2bins(e, t) {
+		e > M && console.warn("querying outside of possible tabix range");
+		let n = N(e), r = Math.min(t, M) - 1, i = [];
+		return n <= r && i.push([0, 0], [1 + (n >> 26), 1 + (r >> 26)], [9 + (n >> 23), 9 + (r >> 23)], [73 + (n >> 20), 73 + (r >> 20)], [585 + (n >> 17), 585 + (r >> 17)], [4681 + (n >> 14), 4681 + (r >> 14)]), i;
+	}
+	lowestOffset(e, t) {
+		let n = e.linearIndex;
+		return n?.[Math.min(N(t) >> j, n.length - 1)];
+	}
+	async _parse(e = {}) {
+		let { bytes: t, dataView: n } = await this.readIndexBytes(e);
+		if (n.getUint32(0, !0) !== k) throw Error("Not a TBI file");
+		let r = n.getUint32(4, !0), { refNameToId: i, refIdToName: o, coordinateType: s, format: c, columnNumbers: l, metaChar: u, skipLines: f } = v(t, 8), p = 36 + n.getInt32(32, !0), g, _ = [];
+		for (let e = 0; e < r; e++) {
+			_.push(p);
+			let e = n.getInt32(p, !0);
+			p += 4;
+			for (let t = 0; t < e; t++) {
+				let e = n.getUint32(p, !0);
+				p += 4;
+				let t = n.getInt32(p, !0);
+				if (p += 4, e > 37450) throw Error("tabix index contains too many bins, please use a CSI index");
+				p += 16 * t;
+			}
+			let r = n.getInt32(p, !0);
+			p += 4, g = h(t, p, r, g), p += 8 * r;
+		}
+		function x(e) {
+			let r = _[e];
+			if (r === void 0) return;
+			let i = r, o = n.getInt32(i, !0);
+			i += 4;
+			let s = {}, c;
+			for (let e = 0; e < o; e++) {
+				let e = n.getUint32(i, !0);
+				if (i += 4, e > 37450) throw Error("tabix index contains too many bins, please use a CSI index");
+				if (e === 37450) {
+					let e = n.getInt32(i, !0);
+					i += 4, e === 2 && (c = y(t, i + 16)), i += 16 * e;
+				} else {
+					let r = n.getInt32(i, !0);
+					i += 4;
+					let o = Array.from({ length: r });
+					for (let n = 0; n < r; n++) o[n] = new a(d(t, i), d(t, i + 8), e), i += 16;
+					s[e] = o;
+				}
+			}
+			let l = n.getInt32(i, !0);
+			i += 4;
+			let u = Array.from({ length: l });
+			for (let e = 0; e < l; e++) u[e] = d(t, i), i += 8;
+			return m(Object.values(s).flat(), u.map((e) => e.blockPosition)), {
+				binIndex: s,
+				linearIndex: u,
+				stats: c
+			};
+		}
+		return {
+			indices: b(x),
+			metaChar: u,
+			minShift: j,
+			depth: A,
+			maxBinNumber: 37449,
+			maxRefLength: M,
+			skipLines: f,
+			firstDataLine: g,
+			columnNumbers: l,
+			coordinateType: s,
+			format: c,
+			refIdToName: o,
+			refNameToId: i,
+			maxBlockSize: 65536
+		};
+	}
+}, F = 9, I = 10, L = 13, R = 59, z = 60, B = 62, V = 6, H = 1024 * 2 ** 20, U = 18e4;
+function W(n, r, i) {
+	if (n) return n;
+	if (r) return new e(r);
+	if (i) return new t(i);
+	throw TypeError("must provide either filehandle, path, or url");
+}
+function G({ tbiFilehandle: n, csiFilehandle: r, tbiPath: i, csiPath: a, tbiUrl: o, csiUrl: s, path: c, url: l }) {
+	if (n) return new P({ filehandle: n });
+	if (r) return new O({ filehandle: r });
+	if (i) return new P({ filehandle: new e(i) });
+	if (a) return new O({ filehandle: new e(a) });
+	if (s) return new O({ filehandle: new t(s) });
+	if (o) return new P({ filehandle: new t(o) });
+	if (c) return new P({ filehandle: new e(`${c}.tbi`) });
+	if (l) return new P({ filehandle: new t(`${l}.tbi`) });
+	throw TypeError("must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl");
+}
+function K(e, t, n, r, i) {
+	return e[n] * 256 + (r - t[n]) + i + 1;
+}
+function q(e, t, n, r, i, a) {
+	let o = t + (r - n);
+	if (e[i] === 46) return o;
+	let s = i;
+	for (let n = i; n <= a; n++) if (n === a || e[n] === R) {
+		let r = n - s;
+		if (r >= 10 && e[s] === 83 && e[s + 1] === 86 && e[s + 2] === 84 && e[s + 3] === 89 && e[s + 4] === 80 && e[s + 5] === 69 && e[s + 6] === 61 && e[s + 7] === 84 && e[s + 8] === 82 && e[s + 9] === 65) return t + 1;
+		r >= 4 && e[s] === 69 && e[s + 1] === 78 && e[s + 2] === 68 && e[s + 3] === 61 && (o = Z(e, s + 4, n)), s = n + 1;
+	}
+	return o;
+}
+var J = new TextDecoder();
+function Y(e, t) {
+	let n = -1, r = t.charCodeAt(0);
+	for (let t = 0, i = e.length; t < i; t++) {
+		let i = e[t];
+		if (t === n + 1 && i !== r) break;
+		i === I && (n = t);
+	}
+	return e.subarray(0, n + 1);
+}
+function X(e, t) {
+	let n = 0;
+	for (let r = 0; r < t; r++) {
+		let t = e.indexOf(I, n);
+		if (t === -1) {
+			n = e.length;
+			break;
+		}
+		n = t + 1;
+	}
+	return J.decode(e.subarray(0, n)).split(/\r?\n/).slice(0, t);
+}
+function Z(e, t, n) {
+	let r = 0;
+	for (let i = t; i < n; i++) {
+		let t = e[i];
+		if (t >= 48 && t <= 57) r = r * 10 + (t - 48);
+		else break;
+	}
+	return r;
+}
+function Q(e, t, n, r, { start: i, end: a, pathCol: o, metaCharCode: s, decoder: c, callback: l }) {
+	let u = 0, d = 0;
+	for (; u < e.length;) {
+		let f = e.indexOf(I, u);
+		if (f === -1) break;
+		let p = u;
+		u = f + 1;
+		let m = p + r;
+		for (; d < n.length && m >= n[d];) d++;
+		if (e[p] === s) continue;
+		let h = p;
+		for (let t = 1; t < o; t++) {
+			let t = e.indexOf(F, h);
+			if (t === -1 || t >= f) {
+				h = f;
+				break;
+			}
+			h = t + 1;
+		}
+		let g = e[h];
+		if (g !== B && g !== z) continue;
+		let _ = e.indexOf(F, h);
+		(_ === -1 || _ > f) && (_ = f);
+		let v = Infinity, y = -1, b = h;
+		for (; b < _;) {
+			let t = 0, n = b + 1;
+			for (; n < _; n++) {
+				let r = e[n] - 48;
+				if (r < 0 || r > 9) break;
+				t = t * 10 + r;
+			}
+			t < v && (v = t), t > y && (y = t), b = n;
+		}
+		if (v >= a) return !0;
+		if (y >= i) {
+			let i = e[f - 1] === L ? f - 1 : f;
+			l(c.decode(e.subarray(p, i)), K(t, n, d, p, r), v, y + 1);
+		}
+	}
+	return !1;
+}
+var $ = class {
+	filehandle;
+	index;
+	chunkCache;
+	headerCache = new n({});
+	bgzfWorkerPool;
+	constructor({ path: e, filehandle: t, url: r, tbiPath: i, tbiUrl: a, tbiFilehandle: o, csiPath: s, csiUrl: c, csiFilehandle: l, chunkCacheSize: u = H, chunkCacheIdleTimeoutMs: d = U, chunkCacheBudget: f, bgzfWorkerPool: p }) {
+		this.bgzfWorkerPool = p, this.filehandle = W(t, e, r), this.index = G({
+			tbiFilehandle: o,
+			csiFilehandle: l,
+			tbiPath: i,
+			csiPath: s,
+			tbiUrl: a,
+			csiUrl: c,
+			path: e,
+			url: r
+		}), this.chunkCache = new n({
+			maxSize: u,
+			sizeOf: (e) => e.buffer.byteLength,
+			cacheKey: (e) => e.toString(),
+			idleTimeoutMs: d,
+			budget: f,
+			fill: (e, t) => this.readChunk(e, { signal: t })
+		});
+	}
+	clearChunkCache() {
+		this.chunkCache.clear();
+	}
+	async bytesForRegions(e, t = {}) {
+		let n = [];
+		for (let { refName: r, start: i, end: a } of e) {
+			let e = await this.index.blocksForRange(r, i, a, t);
+			for (let t of e) n.push(t);
+		}
+		let r = 0;
+		for (let e of f(n)) r += e.fetchedSize();
+		return r;
+	}
+	async getLines(e, t, n, r) {
+		let i, a = {}, o, s;
+		typeof r == "function" ? o = r : (a = r, o = r.lineCallback, i = r.signal, s = r.onProgress);
+		let c = await this.index.getMetadata(a), l = t ?? 0, u = n ?? c.maxRefLength;
+		if (l > u) throw TypeError("invalid start and end coordinates. start must be less than or equal to end");
+		if (l === u) return;
+		let d = await this.index.blocksForRange(e, l, u, a), f = c.format === "VCF", p = c.columnNumbers.ref || 0, m = c.columnNumbers.start || 0, h = f ? 8 : c.columnNumbers.end || 0, g = Math.max(p, m, h), _ = c.metaChar?.charCodeAt(0), v = c.coordinateType === "1-based-closed" ? -1 : 0, y = new TextEncoder(), b = new TextDecoder(), x = y.encode(e), S = new Int32Array(g + 1), C = c.format === "GAF" ? {
+			start: l,
+			end: u,
+			pathCol: m,
+			metaCharCode: _,
+			decoder: b,
+			callback: o
+		} : void 0, w = 0;
+		for (let e of d) w += e.fetchedSize();
+		let T = 0;
+		s?.(0, w);
+		let E = 1, D = [], O = (e) => {
+			for (; D.length < Math.min(e, d.length);) {
+				let e = d[D.length], t = this.chunkCache.get(e, i);
+				t.catch(() => {}), D.push(t);
+			}
+		};
+		O(1);
+		for (let e = 0, t = d.length; e < t; e++) {
+			let t = d[e], { buffer: n, cpositions: r, dpositions: i } = await D[e];
+			T += t.fetchedSize(), s?.(T, w);
+			let a = t.minv.dataPosition;
+			if (C) {
+				if (Q(n, r, i, a, C)) return;
+			} else {
+				let e = 0, t = 0;
+				for (; e < n.length;) {
+					let s = n.indexOf(I, e);
+					if (s === -1) break;
+					let c = e + a;
+					for (; t < i.length && c >= i[t];) t++;
+					if (_ !== void 0 && n[e] === _) {
+						e = s + 1;
+						continue;
+					}
+					S[0] = e - 1;
+					for (let e = 0; e < g; e++) {
+						let t = S[e], r = t < s ? n.indexOf(F, t + 1) : -1;
+						S[e + 1] = r === -1 || r >= s ? s : r;
+					}
+					let d = S[p - 1] + 1, y = S[p] - d;
+					if (y !== x.length) {
+						e = s + 1;
+						continue;
+					}
+					let C = !0;
+					for (let e = 0; e < y; e++) if (n[d + e] !== x[e]) {
+						C = !1;
+						break;
+					}
+					if (!C) {
+						e = s + 1;
+						continue;
+					}
+					let w = Z(n, S[m - 1] + 1, S[m]) + v;
+					if (w >= u) return;
+					let T;
+					if (T = h === 0 || h === m ? w + 1 : f ? q(n, w, S[3] + 1, S[4], S[h - 1] + 1, S[h]) : Z(n, S[h - 1] + 1, S[h]), T > l) {
+						let c = n[s - 1] === L ? s - 1 : s, l = b.decode(n.subarray(e, c));
+						o(l, K(r, i, t, e, a), w, T);
+					}
+					e = s + 1;
+				}
+			}
+			E = Math.min(E * 2, V), O(e + 1 + E);
+		}
+	}
+	async getMetadata(e = {}) {
+		return this.index.getMetadata(e);
+	}
+	async readHeaderBytes(e) {
+		let { firstDataLine: t, maxBlockSize: n } = await this.getMetadata(e), i = (t?.blockPosition ?? 0) + n, a = await this.filehandle.read(i, 0, e);
+		return r(a);
+	}
+	async parseHeader(e) {
+		let { metaChar: t, skipLines: n = 0 } = await this.getMetadata(e), r = await this.readHeaderBytes(e);
+		return {
+			header: J.decode(t ? Y(r, t) : r),
+			skippedLines: n > 0 ? X(r, n) : []
+		};
+	}
+	getParsedHeader(e = {}) {
+		return this.headerCache.get("header", e.signal, (t) => this.parseHeader({
+			...e,
+			signal: t
+		}));
+	}
+	async getHeaderBuffer(e = {}) {
+		let { metaChar: t } = await this.getMetadata(e), n = await this.readHeaderBytes(e);
+		return t ? Y(n, t) : n;
+	}
+	async getSkippedLines(e = {}) {
+		let { skipLines: t = 0 } = await this.getMetadata(e);
+		return t <= 0 ? [] : (await this.getParsedHeader(e)).skippedLines;
+	}
+	async getHeader(e = {}) {
+		return (await this.getParsedHeader(e)).header;
+	}
+	async getHeaderLines(e = {}) {
+		let { header: t, skippedLines: n } = await this.getParsedHeader(e);
+		return (t ? t.split(/\r?\n/) : n).filter(Boolean);
+	}
+	async getReferenceSequenceNames(e = {}) {
+		return (await this.getMetadata(e)).refIdToName;
+	}
+	async lineCount(e, t = {}) {
+		return this.index.lineCount(e, t);
+	}
+	async readChunk(e, t = {}) {
+		let n = await this.filehandle.read(e.fetchedSize(), e.minv.blockPosition, t), r = await this.bgzfWorkerPool;
+		return i(n, e, r);
+	}
+};
+//#endregion
+export { O as CSI, P as TBI, $ as TabixIndexedFile, u as VirtualOffset };