@genome-spy/app 0.79.0 → 0.80.0

package/dist/esm-EyvsqUZz.js

@@ -1,461 +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";
-import { t as a } from "./AbortablePromiseCache-BTmAcN-t.js";
-//#region ../core/node_modules/@gmod/tabix/esm/chunk.js
-var o = class {
-	constructor(e, t, n, r) {
-		this.minv = e, this.maxv = t, this.bin = n, this._fetchedSize = r;
-	}
-	toUniqueString() {
-		return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
-	}
-	toString() {
-		return this.toUniqueString();
-	}
-	compareTo(e) {
-		return this.minv.compareTo(e.minv) || this.maxv.compareTo(e.maxv) || this.bin - e.bin;
-	}
-	fetchedSize() {
-		return this._fetchedSize === void 0 ? this.maxv.blockPosition + 65536 - this.minv.blockPosition : this._fetchedSize;
-	}
-}, s = class {
-	constructor({ filehandle: e, renameRefSeqs: t = (e) => e }) {
-		this.filehandle = e, this.renameRefSeq = t;
-	}
-	async getMetadata(e = {}) {
-		let { indices: t, ...n } = await this.parse(e);
-		return n;
-	}
-	_findFirstData(e, t) {
-		return e ? e.compareTo(t) > 0 ? t : e : t;
-	}
-	async parse(e = {}) {
-		return this.parseP ||= this._parse(e).catch((e) => {
-			throw this.parseP = void 0, e;
-		}), this.parseP;
-	}
-	async hasRefSeq(e, t = {}) {
-		return !!(await this.parse(t)).indices[e]?.binIndex;
-	}
-	_parseNameBytes(e) {
-		let t = 0, n = 0, r = [], i = {}, a = new TextDecoder("utf8");
-		for (let o = 0; o < e.length; o += 1) if (!e[o]) {
-			if (n < o) {
-				let s = this.renameRefSeq(a.decode(e.subarray(n, o)));
-				r[t] = s, i[s] = t;
-			}
-			n = o + 1, t += 1;
-		}
-		return {
-			refNameToId: i,
-			refIdToName: r
-		};
-	}
-}, c = 65536, l = c * c;
-function u(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) * l + (n >>> 0);
-}
-//#endregion
-//#region ../core/node_modules/@gmod/tabix/esm/util.js
-function d(e, t) {
-	return t.minv.blockPosition - e.maxv.blockPosition < 65e3 && t.maxv.blockPosition - e.minv.blockPosition < 5e6;
-}
-function f(e, t) {
-	let n = [], r;
-	if (e.length === 0) return e;
-	e.sort(function(e, t) {
-		let n = e.minv.blockPosition - t.minv.blockPosition;
-		return n === 0 ? e.minv.dataPosition - t.minv.dataPosition : n;
-	});
-	for (let i of e) (!t || i.maxv.compareTo(t) > 0) && (r === void 0 ? (n.push(i), r = i) : d(r, i) ? i.maxv.compareTo(r.maxv) > 0 && (r.maxv = i.maxv) : (n.push(i), r = i));
-	return n;
-}
-//#endregion
-//#region ../core/node_modules/@gmod/tabix/esm/virtualOffset.js
-var p = class {
-	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 m(e, t = 0) {
-	return new p(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 ../core/node_modules/@gmod/tabix/esm/csi.js
-var h = 21582659, g = 38359875, _ = {
-	0: "generic",
-	1: "SAM",
-	2: "VCF"
-};
-function v(e, t) {
-	return e * 2 ** t;
-}
-function y(e, t) {
-	return Math.floor(e / 2 ** t);
-}
-var b = class extends s {
-	constructor(e) {
-		super(e), this.maxBinNumber = 0, this.depth = 0, this.minShift = 0;
-	}
-	async lineCount(e, t = {}) {
-		let n = await this.parse(t), r = n.refNameToId[e];
-		if (r === void 0 || !n.indices[r]) return -1;
-		let { stats: i } = n.indices[r];
-		return i ? i.lineCount : -1;
-	}
-	indexCov() {
-		throw Error("CSI indexes do not support indexcov");
-	}
-	parseAuxData(e, t) {
-		let n = new DataView(e.buffer), 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 } = this._parseNameBytes(e.subarray(t + 28, t + 28 + u));
-		return {
-			refIdToName: d,
-			refNameToId: f,
-			skipLines: l,
-			metaChar: c,
-			columnNumbers: o,
-			format: a,
-			coordinateType: 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");
-		this.minShift = r.getInt32(4, !0), this.depth = r.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-		let a = 2 ** (this.minShift + this.depth * 3), s = r.getInt32(12, !0), c = s && s >= 30 ? this.parseAuxData(n, 16) : {
-			refIdToName: [],
-			refNameToId: {},
-			metaChar: void 0,
-			columnNumbers: {
-				ref: 0,
-				start: 1,
-				end: 2
-			},
-			coordinateType: "zero-based-half-open",
-			format: "generic"
-		}, l = r.getInt32(16 + s, !0), u, d = 16 + s + 4, f = Array(l).fill(0).map(() => {
-			let e = r.getInt32(d, !0);
-			d += 4;
-			let t = {}, i;
-			for (let a = 0; a < e; a += 1) {
-				let e = r.getUint32(d, !0);
-				if (e > this.maxBinNumber) i = this.parsePseudoBin(n, d + 4), d += 48;
-				else {
-					let i = m(n, d + 4);
-					u = this._findFirstData(u, i);
-					let a = r.getInt32(d + 12, !0);
-					d += 16;
-					let s = Array(a);
-					for (let t = 0; t < a; t += 1) {
-						let r = m(n, d), i = m(n, d + 8);
-						d += 16, s[t] = new o(r, i, e);
-					}
-					t[e] = s;
-				}
-			}
-			return {
-				binIndex: t,
-				stats: i
-			};
-		});
-		return {
-			...c,
-			csi: !0,
-			refCount: l,
-			maxBlockSize: 65536,
-			firstDataLine: u,
-			csiVersion: i,
-			indices: f,
-			depth: this.depth,
-			maxBinNumber: this.maxBinNumber,
-			maxRefLength: a
-		};
-	}
-	parsePseudoBin(e, t) {
-		return { lineCount: u(e, t + 28) };
-	}
-	async blocksForRange(e, t, n, r = {}) {
-		t < 0 && (t = 0);
-		let i = await this.parse(r), a = i.refNameToId[e];
-		if (a === void 0) return [];
-		let s = i.indices[a];
-		if (!s) return [];
-		let c = this.reg2bins(t, n), l = [];
-		for (let [e, t] of c) for (let n = e; n <= t; n++) if (s.binIndex[n]) for (let e of s.binIndex[n]) l.push(new o(e.minv, e.maxv, n));
-		return f(l, new p(0, 0));
-	}
-	reg2bins(e, t) {
-		--e, e < 1 && (e = 1), t > 2 ** 50 && (t = 2 ** 34), --t;
-		let n = 0, r = 0, i = this.minShift + this.depth * 3, a = [];
-		for (; n <= this.depth; i -= 3, r += v(1, n * 3), n += 1) {
-			let n = r + y(e, i), o = r + y(t, i);
-			if (o - n + a.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`);
-			a.push([n, o]);
-		}
-		return a;
-	}
-}, x = 21578324, S = 14;
-function C(e, t) {
-	return e += 1, --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 >> 14), 4681 + (t >> 14)]
-	];
-}
-var w = class extends s {
-	async lineCount(e, t = {}) {
-		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(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",
-			1: "SAM",
-			2: "VCF"
-		}[a & 15];
-		if (!c) throw Error(`invalid Tabix preset format flags ${a}`);
-		let l = {
-			ref: r.getInt32(12, !0),
-			start: r.getInt32(16, !0),
-			end: r.getInt32(20, !0)
-		}, u = r.getInt32(24, !0), d = 2 ** 29, f = u ? String.fromCharCode(u) : void 0, p = r.getInt32(28, !0), h = r.getInt32(32, !0), { refNameToId: g, refIdToName: _ } = this._parseNameBytes(n.slice(36, 36 + h)), v = 36 + h, y;
-		return {
-			indices: Array(i).fill(0).map(() => {
-				let e = r.getInt32(v, !0);
-				v += 4;
-				let t = {}, i;
-				for (let a = 0; a < e; a += 1) {
-					let e = r.getUint32(v, !0);
-					if (v += 4, e > 37450) throw Error("tabix index contains too many bins, please use a CSI index");
-					if (e === 37450) {
-						let e = r.getInt32(v, !0);
-						v += 4, e === 2 && (i = this.parsePseudoBin(n, v)), v += 16 * e;
-					} else {
-						let i = r.getInt32(v, !0);
-						v += 4;
-						let a = Array(i);
-						for (let t = 0; t < i; t += 1) {
-							let r = m(n, v), i = m(n, v + 8);
-							v += 16, y = this._findFirstData(y, r), a[t] = new o(r, i, e);
-						}
-						t[e] = a;
-					}
-				}
-				let a = r.getInt32(v, !0);
-				v += 4;
-				let s = Array(a);
-				for (let e = 0; e < a; e += 1) s[e] = m(n, v), v += 8, y = this._findFirstData(y, s[e]);
-				return {
-					binIndex: t,
-					linearIndex: s,
-					stats: i
-				};
-			}),
-			metaChar: f,
-			maxBinNumber: 37449,
-			maxRefLength: d,
-			skipLines: p,
-			firstDataLine: y,
-			columnNumbers: l,
-			coordinateType: s,
-			format: c,
-			refIdToName: _,
-			refNameToId: g,
-			maxBlockSize: 65536
-		};
-	}
-	parsePseudoBin(e, t) {
-		return { lineCount: u(e, t + 16) };
-	}
-	async blocksForRange(e, t, n, r = {}) {
-		t < 0 && (t = 0);
-		let i = await this.parse(r), a = i.refNameToId[e];
-		if (a === void 0) return [];
-		let s = i.indices[a];
-		if (!s) return [];
-		(s.linearIndex.length > 0 ? s.linearIndex[t >> S >= s.linearIndex.length ? s.linearIndex.length - 1 : t >> S] : new p(0, 0)) || console.warn("querying outside of possible tabix range");
-		let c = C(t, n), l = [];
-		for (let [e, t] of c) for (let n = e; n <= t; n++) if (s.binIndex[n]) for (let e of s.binIndex[n]) l.push(new o(e.minv, e.maxv, n));
-		let u = s.linearIndex.length, d, m = Math.min(t >> 14, u - 1), h = Math.min(n >> 14, u - 1);
-		for (let e = m; e <= h; ++e) {
-			let t = s.linearIndex[e];
-			t && (!d || t.compareTo(d) < 0) && (d = t);
-		}
-		return f(l, d);
-	}
-}, T = class {
-	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 (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,
-			renameRefSeqs: h
-		});
-		else if (f) this.index = new b({
-			filehandle: f,
-			renameRefSeqs: h
-		});
-		else if (s) this.index = new w({
-			filehandle: new r(s),
-			renameRefSeqs: h
-		});
-		else if (u) this.index = new b({
-			filehandle: new r(u),
-			renameRefSeqs: h
-		});
-		else if (e) this.index = new w({
-			filehandle: new r(`${e}.tbi`),
-			renameRefSeqs: h
-		});
-		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 n({ maxSize: Math.floor(m / 65536) }),
-			fill: (e, t) => this.readChunk(e, { signal: t })
-		});
-	}
-	calculateFileOffset(e, t, n, r, i) {
-		return e[n] * 256 + (r - t[n]) + i + 1;
-	}
-	async getLines(e, t, n, r) {
-		let i, a = {}, o;
-		typeof r == "function" ? o = r : (a = r, o = r.lineCallback, i = r.signal);
-		let s = await this.index.getMetadata(a), c = t ?? 0, l = n ?? s.maxRefLength;
-		if (!(c <= l)) throw TypeError("invalid start and end coordinates. start must be less than or equal to end");
-		if (c === l) return;
-		let u = await this.index.blocksForRange(e, c, l, a), d = new TextDecoder("utf8"), f = s.format === "VCF", p = {
-			ref: s.columnNumbers.ref || 0,
-			start: s.columnNumbers.start || 0,
-			end: f ? 8 : s.columnNumbers.end || 0
-		}, m = Math.max(p.ref, p.start, p.end), h = s.metaChar?.charCodeAt(0), g = s.coordinateType === "1-based-closed" ? -1 : 0, _ = !this.hasCustomRenameRefSeq;
-		for (let t of u) {
-			let { buffer: n, cpositions: r, dpositions: a } = await this.chunkCache.get(t.toString(), t, i), s = 0, u = 0, v = d.decode(n);
-			if (n.length == v.length) for (; s < v.length;) {
-				let n = v.indexOf("\n", s);
-				if (n === -1) break;
-				let i = v.slice(s, n);
-				if (a) {
-					let e = s + t.minv.dataPosition;
-					for (; u < a.length && e >= a[u];) u++;
-				}
-				let d = this.checkLine(e, c, l, i, p.ref, p.start, p.end, m, h, g, f, _);
-				if (d === null) return;
-				d !== void 0 && o(i, this.calculateFileOffset(r, a, u, s, t.minv.dataPosition), d.start, d.end), s = n + 1;
-			}
-			else for (; s < n.length;) {
-				let i = n.indexOf(10, s);
-				if (i === -1) break;
-				let v = n.slice(s, i), y = d.decode(v);
-				if (a) {
-					let e = s + t.minv.dataPosition;
-					for (; u < a.length && e >= a[u];) u++;
-				}
-				let b = this.checkLine(e, c, l, y, p.ref, p.start, p.end, m, h, g, f, _);
-				if (b === null) return;
-				b !== void 0 && o(y, this.calculateFileOffset(r, a, u, s, t.minv.dataPosition), b.start, b.end), s = i + 1;
-			}
-		}
-	}
-	async getMetadata(e = {}) {
-		return this.index.getMetadata(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++) {
-				let r = o[n];
-				if (n === e + 1 && r !== t) break;
-				r === 10 && (e = n);
-			}
-			return o.subarray(0, e + 1);
-		}
-		return o;
-	}
-	async getHeader(e = {}) {
-		let t = new TextDecoder("utf8"), n = await this.getHeaderBuffer(e);
-		return t.decode(n);
-	}
-	async getReferenceSequenceNames(e = {}) {
-		return (await this.getMetadata(e)).refIdToName;
-	}
-	checkLine(e, t, n, r, i, a, o, s, c, l, u, d) {
-		if (c !== void 0 && r.charCodeAt(0) === c) return;
-		if (r.length < 500) {
-			let s = r.split("	"), c = s[i - 1];
-			if (!(d ? c === e : this.renameRefSeq(c) === e)) return;
-			let f = +s[a - 1] + l;
-			if (f >= n) return null;
-			let p;
-			return p = o === 0 || o === a ? f + 1 : u ? this._getVcfEnd(f, s[3], s[o - 1]) : +s[o - 1], p <= t ? void 0 : {
-				start: f,
-				end: p
-			};
-		}
-		let f = -1, p = [-1];
-		for (let e = 0; e < s; e++) {
-			let e = r.indexOf("	", f + 1);
-			if (e === -1) {
-				p.push(r.length);
-				break;
-			}
-			p.push(e), f = e;
-		}
-		let m = r.slice(p[i - 1] + 1, p[i]);
-		if (!(d ? m === e : this.renameRefSeq(m) === e)) return;
-		let h = +r.slice(p[a - 1] + 1, p[a]) + l;
-		if (h >= n) return null;
-		let g;
-		if (g = o === 0 || o === a ? h + 1 : u ? this._getVcfEnd(h, r.slice(p[3] + 1, p[4]), r.slice(p[o - 1] + 1, p[o])) : +r.slice(p[o - 1] + 1, p[o]), !(g <= t)) return {
-			start: h,
-			end: g
-		};
-	}
-	_getVcfEnd(e, t, n) {
-		let r = e + t.length;
-		if (n.includes("SVTYPE=TRA")) return e + 1;
-		if (n[0] !== ".") {
-			let e = n.indexOf("END=");
-			if (e !== -1 && (e === 0 || n[e - 1] === ";")) {
-				let t = e + 4, i = n.indexOf(";", t);
-				i === -1 && (i = n.length), r = Number.parseInt(n.slice(t, i), 10);
-			}
-		}
-		return r;
-	}
-	async lineCount(e, t = {}) {
-		return this.index.lineCount(e, t);
-	}
-	async readChunk(e, n = {}) {
-		return t(await this.filehandle.read(e.fetchedSize(), e.minv.blockPosition, n), e, this.cache);
-	}
-};
-//#endregion
-export { b as CSI, w as TBI, T as TabixIndexedFile };