@genome-spy/app 0.79.0 → 0.80.0

package/dist/esm-CfsFQHsf.js

@@ -1,1367 +0,0 @@
-import { n as e, r as t } from "./esm-Cx-EbkOj.js";
-import { t as n } from "./esm-VvpZ9hsq.js";
-import { n as r, r as i } from "./esm-BLPinjwY.js";
-//#region ../../node_modules/@gmod/bam/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()})`;
-	}
-	compareTo(e) {
-		return this.minv.compareTo(e.minv) || this.maxv.compareTo(e.maxv) || this.bin - e.bin;
-	}
-	fetchedSize() {
-		return this.endPosition - this.minv.blockPosition;
-	}
-}, o = 65536, s = o * o;
-function c(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) * s + (n >>> 0);
-}
-//#endregion
-//#region ../../node_modules/@gmod/bam/esm/util.js
-function l(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], o = n.maxv;
-			(o.blockPosition - i || o.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[i.length - 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 i;
-}
-function u(e, t) {
-	return { lineCount: c(e, t) };
-}
-function d(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 f(e, t, n) {
-	if (t + 4 > e.length) return;
-	let r = new DataView(e.buffer), i = r.getInt32(t, !0), a = {}, o = [], s = new TextDecoder("utf8"), c = t + 4;
-	for (let t = 0; t < i; t++) {
-		if (c + 8 > e.length) return;
-		let i = r.getInt32(c, !0);
-		if (c + 8 + i > e.length) return;
-		let l = n(s.decode(e.subarray(c + 4, c + 4 + i - 1))), u = r.getInt32(c + i + 4, !0);
-		a[l] = t, o.push({
-			refName: l,
-			length: u
-		}), c += 8 + i;
-	}
-	return {
-		chrToIndex: a,
-		indexToChr: o
-	};
-}
-function p(e, t) {
-	return e ? e.compareTo(t) > 0 ? t : e : t;
-}
-function m(e, t = (e) => e) {
-	let n = new TextDecoder(), r = 0, i = 0, a = [], o = {};
-	for (let s = 0; s < e.length; s++) if (!e[s]) {
-		if (i < s) {
-			let c = t(n.decode(e.subarray(i, s)));
-			a[r] = c, o[c] = r;
-		}
-		i = s + 1, r++;
-	}
-	return {
-		refNameToId: o,
-		refIdToName: a
-	};
-}
-function h(e) {
-	let t = 0;
-	for (let n of e) t += n.length;
-	let n = new Uint8Array(t), r = 0;
-	for (let t of e) n.set(t, r), r += t.length;
-	return n;
-}
-function g(e, t, n) {
-	return (e & t) !== t || (e & n) !== 0;
-}
-function _(e, t) {
-	return t === "*" ? e === void 0 : `${e}` != `${t}`;
-}
-function v(e) {
-	if (!e) return "";
-	let { flagInclude: t = 0, flagExclude: n = 0, tagFilter: r } = e;
-	return `:f${t}x${n}${r ? `:${r.tag}=${r.value ?? "*"}` : ""}`;
-}
-function y(e, t) {
-	let { flagInclude: n = 0, flagExclude: r = 0, tagFilter: i } = t, a = [];
-	for (let t = 0, o = e.length; t < o; t++) {
-		let o = e[t];
-		!g(o.flags, n, r) && !(i && _(o.tags[i.tag], i.value)) && a.push(o);
-	}
-	return a;
-}
-function b(e, t, n, r, i = []) {
-	for (let a = 0, o = e.length; a < o; a++) {
-		let o = e[a];
-		if (o.ref_id === t) {
-			if (o.start >= r) break;
-			o.end >= n && i.push(o);
-		} else if (o.ref_id > t) break;
-	}
-	return i;
-}
-//#endregion
-//#region ../../node_modules/@gmod/bam/esm/indexFile.js
-function x(e, t = 5) {
-	let r = new n({ maxSize: t });
-	return (t) => {
-		if (r.has(t)) return r.get(t);
-		let n = e(t);
-		return n && r.set(t, n), n;
-	};
-}
-var S = class {
-	filehandle;
-	renameRefSeq;
-	setupP;
-	constructor({ filehandle: e, renameRefSeq: t = (e) => e }) {
-		this.filehandle = e, this.renameRefSeq = t;
-	}
-	async blocksForRange(e, t, n, r = {}) {
-		t < 0 && (t = 0);
-		let i = (await this.parse(r)).indices(e);
-		if (!i) return [];
-		let a = this.reg2bins(t, n);
-		if (a.length === 0) return [];
-		let o = [], { binIndex: s } = i;
-		for (let [e, t] of a) for (let n = e; n <= t; n++) {
-			let e = s[n];
-			if (e) for (let t = 0, n = e.length; t < n; t++) o.push(e[t]);
-		}
-		return l(o, this.getLowestChunk(i, t));
-	}
-	parse(e = {}) {
-		return this.setupP ||= this._parse(e).catch((e) => {
-			throw this.setupP = void 0, e;
-		}), this.setupP;
-	}
-	async lineCount(e, t) {
-		return (await this.parse(t)).indices(e)?.stats?.lineCount ?? 0;
-	}
-	async hasRefSeq(e, t) {
-		return !!(await this.parse(t)).indices(e);
-	}
-	async estimatedBytesForRegions(e, t) {
-		let n = l((await Promise.all(e.map((e) => this.blocksForRange(e.refId, e.start, e.end, t)))).flat()), r = 0;
-		for (let e of n) r += e.fetchedSize();
-		return r;
-	}
-}, C = 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 w(e, t = 0, n = !1) {
-	if (n) throw Error("big-endian virtual file offsets not implemented");
-	return new C(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/bam/esm/bai.js
-var ee = 21578050, T = 14, E = 1 << T;
-function te(e, t) {
-	return e - e % t;
-}
-function D(e, t) {
-	return e - e % t + t;
-}
-function O(e, t) {
-	return --t, [
-		[0, 0],
-		[1 + (e >> 26), 1 + (t >> 26)],
-		[9 + (e >> 23), 9 + (t >> 23)],
-		[73 + (e >> 20), 73 + (t >> 20)],
-		[585 + (e >> 17), 585 + (t >> 17)],
-		[4681 + (e >> T), 4681 + (t >> T)]
-	];
-}
-var k = class extends S {
-	async _parse(e) {
-		let t = await this.filehandle.readFile(e), n = new DataView(t.buffer);
-		if (n.getUint32(0, !0) !== ee) throw Error("Not a BAI file");
-		let r = n.getInt32(4, !0), i = 8, o, s = [];
-		for (let e = 0; e < r; e++) {
-			s.push(i);
-			let e = n.getInt32(i, !0);
-			i += 4;
-			for (let t = 0; t < e; t += 1) {
-				let e = n.getUint32(i, !0);
-				if (i += 4, e === 37450) i += 4, i += 32;
-				else if (e > 37450) throw Error("bai index contains too many bins, please use CSI");
-				else {
-					let e = n.getInt32(i, !0);
-					i += 4;
-					for (let t = 0; t < e; t++) i += 8, i += 8;
-				}
-			}
-			let r = n.getInt32(i, !0);
-			i += 4;
-			for (let e = 0; e < r; e++) o = p(o, w(t, i)), i += 8;
-		}
-		function c(e) {
-			let r = s[e];
-			if (r === void 0) return;
-			let i = n.getInt32(r, !0), o;
-			r += 4;
-			let c = {};
-			for (let e = 0; e < i; e += 1) {
-				let e = n.getUint32(r, !0);
-				if (r += 4, e === 37450) r += 4, o = u(t, r + 16), r += 32;
-				else if (e > 37450) throw Error("bai index contains too many bins, please use CSI");
-				else {
-					let i = n.getInt32(r, !0);
-					r += 4;
-					let o = Array(i);
-					for (let n = 0; n < i; n++) {
-						let i = w(t, r);
-						r += 8;
-						let s = w(t, r);
-						r += 8, o[n] = new a(i, s, e);
-					}
-					c[e] = o;
-				}
-			}
-			let l = n.getInt32(r, !0);
-			r += 4;
-			let f = Array(l);
-			for (let e = 0; e < l; e++) f[e] = w(t, r), r += 8;
-			return d(Object.values(c).flat(), f.map((e) => e.blockPosition)), {
-				binIndex: c,
-				linearIndex: f,
-				stats: o
-			};
-		}
-		return {
-			bai: !0,
-			firstDataLine: o,
-			maxBlockSize: 65536,
-			indices: x(c),
-			refCount: r
-		};
-	}
-	async indexCov(e, t, n, r) {
-		let i = E, a = t !== void 0, o = (await this.parse(r)).indices(e);
-		if (!o) return [];
-		let { linearIndex: s, stats: c } = o;
-		if (s.length === 0) return [];
-		let l = n === void 0 ? (s.length - 1) * i : D(n, i), u = t === void 0 ? 0 : te(t, i), d = Array(a ? (l - u) / i : s.length - 1), f = s[s.length - 1].blockPosition;
-		if (l > (s.length - 1) * i) throw Error("query outside of range of linear index");
-		let p = s[u / i].blockPosition;
-		for (let e = u / i, t = 0; e < l / i; e++, t++) d[t] = {
-			score: s[e + 1].blockPosition - p,
-			start: e * i,
-			end: e * i + i
-		}, p = s[e + 1].blockPosition;
-		return d.map((e) => ({
-			...e,
-			score: e.score * (c?.lineCount ?? 0) / f
-		}));
-	}
-	reg2bins(e, t) {
-		return O(e, t);
-	}
-	getLowestChunk(e, t) {
-		let { linearIndex: n } = e, r = n.length;
-		return n[Math.min(t >> T, r - 1)];
-	}
-}, A = [
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-];
-typeof Int32Array < "u" && (A = new Int32Array(A));
-var j = (e, t) => {
-	let n = t === 0 ? 0 : ~~t ^ -1;
-	for (let t = 0; t < e.length; t++) n = A[(n ^ e[t]) & 255] ^ n >>> 8;
-	return n ^ -1;
-}, M = 21582659, N = 38359875, P = new C(0, 0);
-function F(e, t) {
-	return e * 2 ** t;
-}
-function I(e, t) {
-	return Math.floor(e / 2 ** t);
-}
-var L = class extends S {
-	maxBinNumber = 0;
-	depth = 0;
-	minShift = 0;
-	async indexCov() {
-		return [];
-	}
-	parseAuxData(e, t) {
-		let n = new DataView(e.buffer), r = n.getUint32(t, !0), i = r & 65536 ? "zero-based-half-open" : "1-based-closed", a = [
-			"generic",
-			"SAM",
-			"VCF"
-		][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) : "", l = n.getInt32(t + 20, !0), u = n.getInt32(t + 24, !0);
-		return {
-			columnNumbers: o,
-			coordinateType: i,
-			metaValue: s,
-			metaChar: c,
-			skipLines: l,
-			format: a,
-			formatFlags: r,
-			...m(e.subarray(t + 28, t + 28 + u), this.renameRefSeq)
-		};
-	}
-	async _parse(t) {
-		let n = await e(await this.filehandle.readFile(t)), r = new DataView(n.buffer), i, o = r.getUint32(0, !0);
-		if (o === M) i = 1;
-		else if (o === N) i = 2;
-		else throw Error(`Not a CSI file ${o}`);
-		this.minShift = r.getInt32(4, !0), this.depth = r.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-		let s = this.maxBinNumber, c = r.getInt32(12, !0), l = c >= 30 ? this.parseAuxData(n, 16) : void 0, f = r.getInt32(16 + c, !0), m = 16 + c + 4, h, g = [];
-		for (let e = 0; e < f; e++) {
-			g.push(m);
-			let e = r.getInt32(m, !0);
-			m += 4;
-			for (let t = 0; t < e; t++) {
-				let e = r.getUint32(m, !0);
-				if (m += 4, e > this.maxBinNumber) m += 44;
-				else {
-					m += 8;
-					let e = r.getInt32(m, !0);
-					m += 4;
-					for (let t = 0; t < e; t += 1) {
-						let e = w(n, m);
-						m += 8, m += 8, h = p(h, e);
-					}
-				}
-			}
-		}
-		function _(e) {
-			let t = g[e];
-			if (t === void 0) return;
-			let i = r.getInt32(t, !0);
-			t += 4;
-			let o = {}, c;
-			for (let e = 0; e < i; e++) {
-				let e = r.getUint32(t, !0);
-				if (t += 4, e > s) c = u(n, t + 28), t += 44;
-				else {
-					t += 8;
-					let i = r.getInt32(t, !0);
-					t += 4;
-					let s = Array(i);
-					for (let r = 0; r < i; r += 1) {
-						let i = w(n, t);
-						t += 8;
-						let o = w(n, t);
-						t += 8, s[r] = new a(i, o, e);
-					}
-					o[e] = s;
-				}
-			}
-			return d(Object.values(o).flat()), {
-				binIndex: o,
-				stats: c
-			};
-		}
-		return {
-			csiVersion: i,
-			firstDataLine: h,
-			indices: x(_),
-			refCount: f,
-			csi: !0,
-			maxBlockSize: 65536,
-			...l
-		};
-	}
-	getLowestChunk() {
-		return P;
-	}
-	reg2bins(e, t) {
-		let n = 2 ** (this.minShift + this.depth * 3);
-		t > n && (t = n), --t;
-		let r = 0, i = 0, a = this.minShift + this.depth * 3, o = [];
-		for (; r <= this.depth; a -= 3, i += F(1, r * 3), r += 1) {
-			let n = i + I(e, a), r = i + I(t, a);
-			if (r - n + o.length > this.maxBinNumber) throw Error(`query ${e}-${t} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
-			o.push([n, r]);
-		}
-		return o;
-	}
-}, ne = class {
-	read() {
-		throw Error("never called");
-	}
-	stat() {
-		throw Error("never called");
-	}
-	readFile() {
-		throw Error("never called");
-	}
-	close() {
-		throw Error("never called");
-	}
-}, R = {
-	BAM_FPAIRED: 1,
-	BAM_FPROPER_PAIR: 2,
-	BAM_FUNMAP: 4,
-	BAM_FMUNMAP: 8,
-	BAM_FREVERSE: 16,
-	BAM_FMREVERSE: 32,
-	BAM_FREAD1: 64,
-	BAM_FREAD2: 128,
-	BAM_FSECONDARY: 256,
-	BAM_FQCFAIL: 512,
-	BAM_FDUP: 1024,
-	BAM_FSUPPLEMENTARY: 2048
-}, z = "=ACMGRSVTWYHKDBN".split(""), B = /* @__PURE__ */ "F F .F R .R F .R R .F2F1.F2R1.R2F1.R2R1.F1F2.F1R2.R1F2.R1R2.F2F1.F2R1.R2F1.R2R1.F F .R F .F R .R R .F1F2.R1F2.F1R2.R1R2.F2F1.R2F1.F2R1.R2R1.F1F2.R1F2.F1R2.R1R2".split("."), V = [
-	77,
-	73,
-	68,
-	78,
-	83,
-	72,
-	80,
-	61,
-	88,
-	63,
-	63,
-	63,
-	63,
-	63,
-	63,
-	63
-], H = new TextDecoder(), U = 461;
-function W(e, t, n, r, i) {
-	let a = e.byteOffset + n;
-	switch (r) {
-		case 105: {
-			if (a % 4 == 0) return new Int32Array(e.buffer, a, i);
-			let r = Array(i);
-			for (let e = 0; e < i; e++) r[e] = t.getInt32(n + e * 4, !0);
-			return r;
-		}
-		case 73: {
-			if (a % 4 == 0) return new Uint32Array(e.buffer, a, i);
-			let r = Array(i);
-			for (let e = 0; e < i; e++) r[e] = t.getUint32(n + e * 4, !0);
-			return r;
-		}
-		case 115: {
-			if (a % 2 == 0) return new Int16Array(e.buffer, a, i);
-			let r = Array(i);
-			for (let e = 0; e < i; e++) r[e] = t.getInt16(n + e * 2, !0);
-			return r;
-		}
-		case 83: {
-			if (a % 2 == 0) return new Uint16Array(e.buffer, a, i);
-			let r = Array(i);
-			for (let e = 0; e < i; e++) r[e] = t.getUint16(n + e * 2, !0);
-			return r;
-		}
-		case 99: return new Int8Array(e.buffer, a, i);
-		case 67: return new Uint8Array(e.buffer, a, i);
-		case 102: {
-			if (a % 4 == 0) return new Float32Array(e.buffer, a, i);
-			let r = Array(i);
-			for (let e = 0; e < i; e++) r[e] = t.getFloat32(n + e * 4, !0);
-			return r;
-		}
-		default: return;
-	}
-}
-function G(e, t) {
-	return e === 105 || e === 73 || e === 102 ? t << 2 : e === 115 || e === 83 ? t << 1 : t;
-}
-var K = class {
-	fileOffset;
-	_byteArray;
-	_start;
-	_end;
-	_dataView;
-	_cachedEnd;
-	_cachedTags;
-	_cachedLengthOnRef;
-	_cachedNumericCigar;
-	_cachedNUMERIC_MD;
-	_cachedSeqStart;
-	constructor(e) {
-		this._byteArray = e.bytes.byteArray, this._start = e.bytes.start, this._end = e.bytes.end, this.fileOffset = e.fileOffset, this._dataView = e.dataView;
-	}
-	get byteArray() {
-		return this._byteArray;
-	}
-	get flags() {
-		return this._dataView.getUint16(this._start + 18, !0);
-	}
-	get ref_id() {
-		return this._dataView.getInt32(this._start + 4, !0);
-	}
-	get start() {
-		return this._dataView.getInt32(this._start + 8, !0);
-	}
-	get end() {
-		return this._cachedEnd === void 0 && (this._cachedEnd = this.start + this.length_on_ref), this._cachedEnd;
-	}
-	get mq() {
-		let e = (this.bin_mq_nl & 65280) >> 8;
-		return e === 255 ? void 0 : e;
-	}
-	get score() {
-		return this.mq;
-	}
-	get qual() {
-		let e = this.seq_length;
-		if (e === 0) return null;
-		{
-			let t = this.seqStart + (e + 1 >> 1);
-			return this._byteArray.subarray(t, t + e);
-		}
-	}
-	get strand() {
-		return this.isReverseComplemented() ? -1 : 1;
-	}
-	get b0() {
-		return this._start + 36;
-	}
-	get seqStart() {
-		return this._cachedSeqStart === void 0 && (this._cachedSeqStart = this.b0 + this.read_name_length + this.num_cigar_bytes), this._cachedSeqStart;
-	}
-	get tagsStart() {
-		let e = this.seq_length;
-		return this.seqStart + (e + 1 >> 1) + e;
-	}
-	get name() {
-		let e = this.read_name_length - 1, t = this.b0, n = this._byteArray, r = Array(e);
-		for (let i = 0; i < e; i++) r[i] = n[t + i];
-		return String.fromCharCode(...r);
-	}
-	get NUMERIC_MD() {
-		if (this._cachedNUMERIC_MD === void 0) {
-			let e = this.getTagRaw("MD");
-			this._cachedNUMERIC_MD = e instanceof Uint8Array ? e : null;
-		}
-		return this._cachedNUMERIC_MD === null ? void 0 : this._cachedNUMERIC_MD;
-	}
-	get tags() {
-		return this._cachedTags === void 0 && (this._cachedTags = this._computeTags()), this._cachedTags;
-	}
-	getTag(e) {
-		return this._cachedTags === void 0 ? this._findTag(e, !1) : this._cachedTags[e];
-	}
-	getTagRaw(e) {
-		return this._findTag(e, !0);
-	}
-	_findTag(e, t) {
-		let n = e.charCodeAt(0), r = e.charCodeAt(1), i = this.tagsStart, a = this._end, o = this._byteArray;
-		for (; i < a;) {
-			let e = o[i], s = o[i + 1], c = o[i + 2];
-			i += 3;
-			let l = e === n && s === r;
-			switch (c) {
-				case 65:
-					if (l) return String.fromCharCode(o[i]);
-					i += 1;
-					break;
-				case 105:
-					if (l) return this._dataView.getInt32(i, !0);
-					i += 4;
-					break;
-				case 73:
-					if (l) return this._dataView.getUint32(i, !0);
-					i += 4;
-					break;
-				case 99:
-					if (l) return this._dataView.getInt8(i);
-					i += 1;
-					break;
-				case 67:
-					if (l) return this._dataView.getUint8(i);
-					i += 1;
-					break;
-				case 115:
-					if (l) return this._dataView.getInt16(i, !0);
-					i += 2;
-					break;
-				case 83:
-					if (l) return this._dataView.getUint16(i, !0);
-					i += 2;
-					break;
-				case 102:
-					if (l) return this._dataView.getFloat32(i, !0);
-					i += 4;
-					break;
-				case 90:
-				case 72: {
-					let e = i;
-					for (; i < a && o[i] !== 0;) i++;
-					if (l) return t ? o.subarray(e, i) : H.decode(o.subarray(e, i));
-					i++;
-					break;
-				}
-				case 66: {
-					let e = o[i++], t = this._dataView.getInt32(i, !0);
-					if (i += 4, l) return W(o, this._dataView, i, e, t);
-					i += G(e, t);
-					break;
-				}
-				default:
-					c !== void 0 && console.error("Unknown BAM tag type", c);
-					break;
-			}
-		}
-	}
-	_computeTags() {
-		let e = this.tagsStart, t = this._end, n = this._byteArray, r = {};
-		for (; e < t;) {
-			let i = String.fromCharCode(n[e], n[e + 1]), a = n[e + 2];
-			switch (e += 3, a) {
-				case 65:
-					r[i] = String.fromCharCode(n[e]), e += 1;
-					break;
-				case 105:
-					r[i] = this._dataView.getInt32(e, !0), e += 4;
-					break;
-				case 73:
-					r[i] = this._dataView.getUint32(e, !0), e += 4;
-					break;
-				case 99:
-					r[i] = this._dataView.getInt8(e), e += 1;
-					break;
-				case 67:
-					r[i] = this._dataView.getUint8(e), e += 1;
-					break;
-				case 115:
-					r[i] = this._dataView.getInt16(e, !0), e += 2;
-					break;
-				case 83:
-					r[i] = this._dataView.getUint16(e, !0), e += 2;
-					break;
-				case 102:
-					r[i] = this._dataView.getFloat32(e, !0), e += 4;
-					break;
-				case 90:
-				case 72: {
-					let a = e;
-					for (; e < t && n[e] !== 0;) e++;
-					r[i] = H.decode(n.subarray(a, e)), e++;
-					break;
-				}
-				case 66: {
-					let t = n[e++], a = this._dataView.getInt32(e, !0);
-					e += 4, r[i] = W(n, this._dataView, e, t, a), e += G(t, a);
-					break;
-				}
-				default:
-					console.error("Unknown BAM tag type", a);
-					break;
-			}
-		}
-		return r;
-	}
-	isPaired() {
-		return !!(this.flags & R.BAM_FPAIRED);
-	}
-	isProperlyPaired() {
-		return !!(this.flags & R.BAM_FPROPER_PAIR);
-	}
-	isSegmentUnmapped() {
-		return !!(this.flags & R.BAM_FUNMAP);
-	}
-	isMateUnmapped() {
-		return !!(this.flags & R.BAM_FMUNMAP);
-	}
-	isReverseComplemented() {
-		return !!(this.flags & R.BAM_FREVERSE);
-	}
-	isMateReverseComplemented() {
-		return !!(this.flags & R.BAM_FMREVERSE);
-	}
-	isRead1() {
-		return !!(this.flags & R.BAM_FREAD1);
-	}
-	isRead2() {
-		return !!(this.flags & R.BAM_FREAD2);
-	}
-	isSecondary() {
-		return !!(this.flags & R.BAM_FSECONDARY);
-	}
-	isFailedQc() {
-		return !!(this.flags & R.BAM_FQCFAIL);
-	}
-	isDuplicate() {
-		return !!(this.flags & R.BAM_FDUP);
-	}
-	isSupplementary() {
-		return !!(this.flags & R.BAM_FSUPPLEMENTARY);
-	}
-	_isCGTagPattern(e, t) {
-		if (t === 2) {
-			let t = this._dataView.getInt32(e, !0);
-			return (t & 15) == 4 && t >> 4 === this.seq_length;
-		} else return !1;
-	}
-	_computeLengthOnRef() {
-		let e = this._dataView.getInt32(this._start + 16, !0);
-		if (e & R.BAM_FUNMAP << 16) return 0;
-		let t = e & 65535, n = this.b0 + this.read_name_length;
-		if (this._isCGTagPattern(n, t)) {
-			let e = this._dataView.getInt32(n + 4, !0);
-			return (e & 15) != 3 && console.warn("CG tag with no N tag"), e >> 4;
-		}
-		let r = this._byteArray.byteOffset + n;
-		if (r % 4 == 0 && t > 50) {
-			let e = new Uint32Array(this._byteArray.buffer, r, t);
-			this._cachedNumericCigar = e;
-			let n = 0;
-			for (let r = 0; r < t; ++r) {
-				let t = e[r];
-				n += (t >> 4) * (U >> (t & 15) & 1);
-			}
-			return n;
-		}
-		let i = 0;
-		for (let e = 0; e < t; ++e) {
-			let t = this._dataView.getInt32(n + e * 4, !0);
-			i += (t >> 4) * (U >> (t & 15) & 1);
-		}
-		return i;
-	}
-	_computeNumericCigar() {
-		let e = this._dataView.getInt32(this._start + 16, !0);
-		if (e & R.BAM_FUNMAP << 16) return /* @__PURE__ */ new Uint32Array();
-		let t = e & 65535, n = this.b0 + this.read_name_length;
-		if (this._isCGTagPattern(n, t)) return this.tags.CG ?? /* @__PURE__ */ new Uint32Array();
-		let r = this._byteArray.byteOffset + n;
-		if (r % 4 == 0 && t > 50) return new Uint32Array(this._byteArray.buffer, r, t);
-		let i = Array(t);
-		for (let e = 0; e < t; ++e) i[e] = this._dataView.getInt32(n + e * 4, !0) | 0;
-		return i;
-	}
-	get length_on_ref() {
-		return this._cachedLengthOnRef === void 0 && (this._cachedLengthOnRef = this._computeLengthOnRef()), this._cachedLengthOnRef;
-	}
-	get NUMERIC_CIGAR() {
-		return this._cachedNumericCigar === void 0 && (this._cachedNumericCigar = this._computeNumericCigar()), this._cachedNumericCigar;
-	}
-	get CIGAR() {
-		let e = this.NUMERIC_CIGAR, t = "";
-		for (let n = 0, r = e.length; n < r; n++) {
-			let r = e[n], i = r >> 4, a = V[r & 15];
-			t += i + String.fromCharCode(a);
-		}
-		return t;
-	}
-	get num_cigar_ops() {
-		return this.flag_nc & 65535;
-	}
-	get num_cigar_bytes() {
-		return this.num_cigar_ops << 2;
-	}
-	get read_name_length() {
-		return this.bin_mq_nl & 255;
-	}
-	get num_seq_bytes() {
-		return this.seq_length + 1 >> 1;
-	}
-	get NUMERIC_SEQ() {
-		let e = this.seqStart;
-		return this._byteArray.subarray(e, e + this.num_seq_bytes);
-	}
-	get seq() {
-		let e = this.seq_length, t = this.seqStart, n = this._byteArray, r = Array(e), i = 0, a = e >> 1;
-		for (let e = 0; e < a; ++e) {
-			let a = n[t + e];
-			r[i++] = z[(a & 240) >> 4], r[i++] = z[a & 15];
-		}
-		return i < e && (r[i] = z[(n[t + a] & 240) >> 4]), r.join("");
-	}
-	get pair_orientation() {
-		let e = this.flags;
-		if (!(e & 12 || this.ref_id !== this.next_refid)) return B[e >> 4 & 15 | (this.template_length > 0 ? 16 : 0)];
-	}
-	get bin_mq_nl() {
-		return this._dataView.getInt32(this._start + 12, !0);
-	}
-	get flag_nc() {
-		return this._dataView.getInt32(this._start + 16, !0);
-	}
-	get seq_length() {
-		return this._dataView.getInt32(this._start + 20, !0);
-	}
-	get next_refid() {
-		return this._dataView.getInt32(this._start + 24, !0);
-	}
-	get next_pos() {
-		return this._dataView.getInt32(this._start + 28, !0);
-	}
-	get template_length() {
-		return this._dataView.getInt32(this._start + 32, !0);
-	}
-	seqAt(e) {
-		if (e < this.seq_length) {
-			let t = this._byteArray[this.seqStart + (e >> 1)];
-			return e % 2 == 0 ? z[(t & 240) >> 4] : z[t & 15];
-		} else return;
-	}
-	toJSON() {
-		return {
-			fileOffset: this.fileOffset,
-			ref_id: this.ref_id,
-			start: this.start,
-			end: this.end,
-			name: this.name,
-			flags: this.flags,
-			mq: this.mq,
-			CIGAR: this.CIGAR,
-			seq: this.seq,
-			next_refid: this.next_refid,
-			next_pos: this.next_pos,
-			template_length: this.template_length,
-			tags: this.tags
-		};
-	}
-};
-//#endregion
-//#region ../../node_modules/@gmod/bam/esm/sam.js
-function q(e) {
-	let t = e.split(/\r?\n/), n = [];
-	for (let e of t) {
-		let [t, ...r] = e.split(/\t/);
-		t && n.push({
-			tag: t.slice(1),
-			data: r.map((e) => {
-				let t = e.indexOf(":");
-				return {
-					tag: e.slice(0, t),
-					value: e.slice(t + 1)
-				};
-			})
-		});
-	}
-	return n;
-}
-var J = 65536;
-function Y(e, t, n) {
-	return e ?? (t ? new r(t) : n ? new i(n) : void 0);
-}
-function X(e, t) {
-	let { minv: n, maxv: r } = e;
-	return `${n.blockPosition}:${n.dataPosition}-${r.blockPosition}:${r.dataPosition}${v(t)}`;
-}
-var Z = class {
-	renameRefSeq;
-	bam;
-	header;
-	chrToIndex;
-	indexToChr;
-	index;
-	htsget = !1;
-	headerP;
-	chunkFeatureCache = new n({ maxSize: 100 });
-	RecordClass;
-	constructor({ bamFilehandle: e, bamPath: t, bamUrl: n, baiPath: r, baiFilehandle: i, baiUrl: a, csiPath: o, csiFilehandle: s, csiUrl: c, htsget: l, renameRefSeqs: u = (e) => e, recordClass: d }) {
-		this.renameRefSeq = u, this.RecordClass = d ?? K;
-		let f = Y(e, t, n);
-		if (f) this.bam = f;
-		else if (l) this.htsget = !0, this.bam = new ne();
-		else throw Error("no bam source: pass bamFilehandle, bamPath, bamUrl, or htsget: true");
-		let p = Y(s, o, c), m = Y(i, r, a) ?? Y(void 0, t ? `${t}.bai` : void 0, n ? `${n}.bai` : void 0);
-		if (p) this.index = new L({ filehandle: p });
-		else if (m) this.index = new k({ filehandle: m });
-		else if (!l) throw Error("no index source: pass csi*/bai* options or a bamPath/bamUrl so the .bai sibling can be inferred");
-	}
-	async getHeaderPre(t = {}) {
-		if (!this.index) return;
-		let n = await this.index.parse(t), r = n.firstDataLine === void 0 ? void 0 : n.firstDataLine.blockPosition + J, i = await e(r === void 0 ? await this.bam.readFile() : await this.bam.read(r, 0)), a = new DataView(i.buffer);
-		if (a.getInt32(0, !0) !== 21840194) throw Error("Not a BAM file");
-		let o = a.getInt32(4, !0);
-		this.header = new TextDecoder("utf8").decode(i.subarray(8, 8 + o));
-		let s = o + 8, c = f(i, s, this.renameRefSeq);
-		if (c ||= (i = await e(await this.bam.readFile()), f(i, s, this.renameRefSeq)), !c) throw Error("Insufficient data for reference sequences");
-		return this.chrToIndex = c.chrToIndex, this.indexToChr = c.indexToChr, q(this.header);
-	}
-	getHeader(e) {
-		return this.headerP ||= this.getHeaderPre(e).catch((e) => {
-			throw this.headerP = void 0, e;
-		}), this.headerP;
-	}
-	async getHeaderText(e = {}) {
-		return await this.getHeader(e), this.header;
-	}
-	async getSeqId(e, t) {
-		return await this.getHeader(t), this.chrToIndex?.[e];
-	}
-	async getRecordsForRange(e, t, n, r) {
-		let i = await this.getSeqId(e, r);
-		if (i === void 0 || !this.index) return [];
-		let a = await this.index.blocksForRange(i, t - 1, n, r);
-		return this._fetchChunkFeaturesDirect(a, i, t, n, r);
-	}
-	evictOverlappingChunks(e, t) {
-		for (let [n, r] of this.chunkFeatureCache) e <= r.maxBlock && t >= r.minBlock && this.chunkFeatureCache.delete(n);
-	}
-	async _fetchChunkFeaturesDirect(e, t, n, r, i = {}) {
-		let { viewAsPairs: a, filterBy: o, onProgress: s } = i, c = [], l = 0;
-		for (let t = 0, n = e.length; t < n; t++) l += e[t].fetchedSize();
-		let u = 0;
-		s?.(0, l);
-		for (let a = 0, d = e.length; a < d; a++) {
-			let d = e[a], f = X(d, o), p = d.minv.blockPosition, m = d.maxv.blockPosition, h, g = this.chunkFeatureCache.get(f);
-			if (g) h = g.features;
-			else {
-				this.evictOverlappingChunks(p, m);
-				let e = await this._readChunkFeatures(d, i);
-				h = o ? y(e, o) : e, this.chunkFeatureCache.set(f, {
-					minBlock: p,
-					maxBlock: m,
-					features: h
-				});
-			}
-			u += d.fetchedSize(), s?.(u, l), b(h, t, n, r, c);
-		}
-		if (a) {
-			let e = await this.fetchPairs(t, c, i);
-			for (let t = 0, n = e.length; t < n; t++) c.push(e[t]);
-		}
-		return c;
-	}
-	async fetchPairs(e, t, n) {
-		let { pairAcrossChr: r, maxInsertSize: i = 2e5 } = n, a = {}, o = /* @__PURE__ */ new Set();
-		for (let e = 0, n = t.length; e < n; e++) {
-			let n = t[e], r = n.name;
-			a[r] = (a[r] ?? 0) + 1, o.add(n.fileOffset);
-		}
-		let s = [];
-		for (let o = 0, c = t.length; o < c; o++) {
-			let c = t[o], l = c.name;
-			this.index && a[l] === 1 && (r || c.next_refid === e && Math.abs(c.start - c.next_pos) < i) && s.push(this.index.blocksForRange(c.next_refid, c.next_pos, c.next_pos + 1, n));
-		}
-		let c = /* @__PURE__ */ new Map(), l = await Promise.all(s);
-		for (let e = 0, t = l.length; e < t; e++) {
-			let t = l[e];
-			for (let e = 0, n = t.length; e < n; e++) {
-				let n = t[e];
-				c.set(n.toString(), n);
-			}
-		}
-		return (await Promise.all([...c.values()].map(async (e) => {
-			let t = await this._readChunkFeatures(e, n), r = [];
-			for (let e = 0, n = t.length; e < n; e++) {
-				let n = t[e];
-				a[n.name] === 1 && !o.has(n.fileOffset) && r.push(n);
-			}
-			return r;
-		}))).flat();
-	}
-	async _readChunkFeatures(e, n) {
-		let { buffer: r, cpositions: i, dpositions: a } = await t(await this.bam.read(e.fetchedSize(), e.minv.blockPosition, { signal: n.signal }), e);
-		return this.readBamFeatures(r, i, a, e);
-	}
-	async readBamFeatures(e, t, n, r) {
-		let i = 0, a = [], o = 0, s = new DataView(e.buffer), c = n.length > 0, l = t.length > 0;
-		for (; i + 4 < e.length;) {
-			let u = s.getInt32(i, !0), d = i + 4 + u - 1;
-			if (c) {
-				let e = i + r.minv.dataPosition;
-				for (; o < n.length && e >= n[o];) o++;
-			}
-			if (d < e.length) {
-				let c = new this.RecordClass({
-					bytes: {
-						byteArray: e,
-						start: i,
-						end: d
-					},
-					fileOffset: l ? t[o] * 256 + (i - n[o]) + r.minv.dataPosition + 1 : j(e.subarray(i, d)) >>> 0,
-					dataView: s
-				});
-				a.push(c);
-			}
-			i = d + 1;
-		}
-		return a;
-	}
-	async hasRefSeq(e, t) {
-		let n = await this.getSeqId(e, t);
-		return !this.index || n === void 0 ? !1 : this.index.hasRefSeq(n);
-	}
-	async lineCount(e, t) {
-		let n = await this.getSeqId(e, t);
-		return !this.index || n === void 0 ? 0 : this.index.lineCount(n);
-	}
-	async indexCov(e, t, n) {
-		let r = await this.getSeqId(e);
-		return !this.index || r === void 0 ? [] : this.index.indexCov(r, t, n);
-	}
-	async blocksForRange(e, t, n, r) {
-		let i = await this.getSeqId(e, r);
-		return !this.index || i === void 0 ? [] : this.index.blocksForRange(i, t, n, r);
-	}
-	clearFeatureCache() {
-		this.chunkFeatureCache.clear();
-	}
-	async estimatedBytesForRegions(e, t) {
-		if (!this.index) return 0;
-		await this.getHeader(t);
-		let n = e.flatMap((e) => {
-			let t = this.chrToIndex?.[e.refName];
-			return t === void 0 ? [] : [{
-				refId: t,
-				start: e.start,
-				end: e.end
-			}];
-		});
-		return this.index.estimatedBytesForRegions(n, t);
-	}
-};
-//#endregion
-//#region ../../node_modules/@gmod/bam/esm/htsget.js
-async function Q(e, t) {
-	let n = await fetch(e, t);
-	if (!n.ok) throw Error(`HTTP ${n.status} fetching ${e}: ${await n.text()}`);
-	return n;
-}
-async function re({ url: e, headers: t }, n) {
-	let { referer: r, ...i } = t ?? {}, a = e.startsWith("data:") ? await Q(e) : await Q(e, {
-		...n,
-		headers: i
-	});
-	return new Uint8Array(await a.arrayBuffer());
-}
-async function $(t, n) {
-	return h(await Promise.all(t.map(async (t) => e(await re(t, n)))));
-}
-var ie = class extends Z {
-	baseUrl;
-	trackId;
-	constructor(e) {
-		super({
-			htsget: !0,
-			recordClass: e.recordClass
-		}), this.baseUrl = e.baseUrl, this.trackId = e.trackId;
-	}
-	async getRecordsForRange(e, t, n, r) {
-		await this.getHeader(r);
-		let i = `${`${this.baseUrl}/${this.trackId}`}?referenceName=${e}&start=${t}&end=${n}&format=BAM`, o = this.chrToIndex?.[e];
-		if (o === void 0) return [];
-		let s = await $((await (await Q(i, r)).json()).htsget.urls.slice(1), { signal: r?.signal }), c = new C(0, 0);
-		return b(await this.readBamFeatures(s, [], [], new a(c, c, 0)), o, t, n);
-	}
-	async getHeaderPre(e = {}) {
-		let t = await $((await (await Q(`${this.baseUrl}/${this.trackId}?referenceName=na&class=header`, e)).json()).htsget.urls, { signal: e.signal }), n = new DataView(t.buffer);
-		if (n.getInt32(0, !0) !== 21840194) throw Error("Not a BAM file");
-		let r = n.getInt32(4, !0), i = q(new TextDecoder().decode(t.subarray(8, 8 + r))), a = [], o = {}, s = i.filter((e) => e.tag === "SQ");
-		for (let [e, t] of s.entries()) {
-			let n = "", r = 0;
-			for (let e of t.data) e.tag === "SN" ? n = e.value : e.tag === "LN" && (r = +e.value);
-			o[n] = e, a[e] = {
-				refName: n,
-				length: r
-			};
-		}
-		return this.chrToIndex = o, this.indexToChr = a, i;
-	}
-};
-//#endregion
-export { k as BAI, Z as BamFile, K as BamRecord, L as CSI, ie as HtsgetFile };