@genome-spy/app 0.78.0 → 0.79.1

package/dist/esm-D2_c7lXY.js

@@ -1,298 +0,0 @@
-//#region ../../node_modules/gff-nostream/esm/util.js
-var e = {};
-for (let t = 0; t < 256; t++) {
-	let n = t.toString(16).toUpperCase().padStart(2, "0");
-	e[n] = String.fromCharCode(t), e[n.toLowerCase()] = String.fromCharCode(t);
-}
-function t(t) {
-	let n = t.indexOf("%");
-	if (n === -1) return t;
-	let r = "", i = 0, a = n;
-	for (; a < t.length;) if (t[a] === "%" && a + 2 < t.length) {
-		r += t.slice(i, a);
-		let n = e[t.slice(a + 1, a + 3)];
-		n === void 0 ? r += t.slice(a, a + 3) : r += n, a += 3, i = a;
-	} else a++;
-	return r + t.slice(i);
-}
-function n(e) {
-	if (e.length === 0 || e === ".") return {};
-	let n = {}, r = e.length;
-	e[r - 1] === "\n" && (r = e[r - 2] === "\r" ? r - 2 : r - 1, e = e.slice(0, r));
-	let i = 0;
-	for (; i < r;) {
-		let a = e.indexOf(";", i);
-		if (a === -1 && (a = r), a > i) {
-			let r = e.indexOf("=", i);
-			if (r !== -1 && r < a && r + 1 < a) {
-				let o = e.slice(i, r), s = n[o];
-				s || (s = [], n[o] = s);
-				let c = r + 1;
-				for (; c < a;) {
-					let n = e.indexOf(",", c);
-					if ((n === -1 || n > a) && (n = a), n > c) {
-						let r = e.slice(c, n);
-						s.push(t(r));
-					}
-					c = n + 1;
-				}
-			}
-		}
-		i = a + 1;
-	}
-	return n;
-}
-function r(e) {
-	if (e.length === 0 || e === ".") return {};
-	let t = {}, n = e.length;
-	e[n - 1] === "\n" && (n = e[n - 2] === "\r" ? n - 2 : n - 1, e = e.slice(0, n));
-	let r = 0;
-	for (; r < n;) {
-		let i = e.indexOf(";", r);
-		if (i === -1 && (i = n), i > r) {
-			let n = e.indexOf("=", r);
-			if (n !== -1 && n < i && n + 1 < i) {
-				let a = e.slice(r, n), o = t[a];
-				o || (o = [], t[a] = o);
-				let s = n + 1;
-				for (; s < i;) {
-					let t = e.indexOf(",", s);
-					(t === -1 || t > i) && (t = i), t > s && o.push(e.slice(s, t)), s = t + 1;
-				}
-			}
-		}
-		r = i + 1;
-	}
-	return t;
-}
-function i(e) {
-	return e.length === 0 || e === "." ? null : t(e);
-}
-function a(e) {
-	return e.length === 0 || e === "." ? null : e;
-}
-function o(e) {
-	let t = e.split("	"), r = t[0], o = t[1], s = t[2], c = t[3], l = t[4], u = t[5], d = t[6], f = t[7], p = t[8];
-	return {
-		seq_id: i(r),
-		source: i(o),
-		type: i(s),
-		start: c.length === 0 || c === "." ? null : +c,
-		end: l.length === 0 || l === "." ? null : +l,
-		score: u.length === 0 || u === "." ? null : +u,
-		strand: a(d),
-		phase: a(f),
-		attributes: p.length === 0 || p === "." ? null : n(p)
-	};
-}
-function s(e) {
-	let t = e.split("	"), n = t[0], i = t[1], o = t[2], s = t[3], c = t[4], l = t[5], u = t[6], d = t[7], f = t[8];
-	return {
-		seq_id: a(n),
-		source: a(i),
-		type: a(o),
-		start: s.length === 0 || s === "." ? null : +s,
-		end: c.length === 0 || c === "." ? null : +c,
-		score: l.length === 0 || l === "." ? null : +l,
-		strand: a(u),
-		phase: a(d),
-		attributes: f.length === 0 || f === "." ? null : r(f)
-	};
-}
-var c = new Set([
-	"start",
-	"end",
-	"seq_id",
-	"score",
-	"type",
-	"source",
-	"phase",
-	"strand"
-]);
-function l(e) {
-	if (e === "+") return 1;
-	if (e === "-") return -1;
-	if (e === ".") return 0;
-}
-function u(e, n) {
-	if (e.length === 0 || e === ".") return;
-	let r = e.length;
-	e[r - 1] === "\n" && (r = e[r - 2] === "\r" ? r - 2 : r - 1, e = e.slice(0, r));
-	let i = 0;
-	for (; i < r;) {
-		let a = e.indexOf(";", i);
-		if (a === -1 && (a = r), a > i) {
-			let r = e.indexOf("=", i);
-			if (r !== -1 && r < a && r + 1 < a) {
-				let o = e.slice(i, r);
-				if (o === "_lineHash") {
-					i = a + 1;
-					continue;
-				}
-				let s = o.toLowerCase();
-				c.has(s) && (s += "2");
-				let l = [], u = r + 1;
-				for (; u < a;) {
-					let n = e.indexOf(",", u);
-					if ((n === -1 || n > a) && (n = a), n > u) {
-						let r = e.slice(u, n);
-						l.push(t(r));
-					}
-					u = n + 1;
-				}
-				n[s] = l.length === 1 ? l[0] : l;
-			}
-		}
-		i = a + 1;
-	}
-}
-function d(e, t) {
-	if (e.length === 0 || e === ".") return;
-	let n = e.length;
-	e[n - 1] === "\n" && (n = e[n - 2] === "\r" ? n - 2 : n - 1, e = e.slice(0, n));
-	let r = 0;
-	for (; r < n;) {
-		let i = e.indexOf(";", r);
-		if (i === -1 && (i = n), i > r) {
-			let n = e.indexOf("=", r);
-			if (n !== -1 && n < i && n + 1 < i) {
-				let a = e.slice(r, n);
-				if (a === "_lineHash") {
-					r = i + 1;
-					continue;
-				}
-				let o = a.toLowerCase();
-				c.has(o) && (o += "2");
-				let s = [], l = n + 1;
-				for (; l < i;) {
-					let t = e.indexOf(",", l);
-					(t === -1 || t > i) && (t = i), t > l && s.push(e.slice(l, t)), l = t + 1;
-				}
-				t[o] = s.length === 1 ? s[0] : s;
-			}
-		}
-		r = i + 1;
-	}
-}
-function f(e) {
-	let n = e.split("	"), r = n[0], i = n[1], a = n[2], o = n[3], s = n[4], c = n[5], d = n[6], f = n[7], p = n[8], m = {
-		refName: r.length === 0 || r === "." ? "" : t(r),
-		source: i.length === 0 || i === "." ? null : t(i),
-		type: a.length === 0 || a === "." ? null : t(a),
-		start: o.length === 0 || o === "." ? 0 : o - 1,
-		end: s.length === 0 || s === "." ? 0 : +s,
-		score: c.length === 0 || c === "." ? void 0 : +c,
-		strand: l(d),
-		phase: f.length === 0 || f === "." ? void 0 : +f,
-		subfeatures: []
-	};
-	return u(p, m), m;
-}
-function p(e) {
-	let t = e.split("	"), n = t[0], r = t[1], i = t[2], a = t[3], o = t[4], s = t[5], c = t[6], u = t[7], f = t[8], p = {
-		refName: n.length === 0 || n === "." ? "" : n,
-		source: r.length === 0 || r === "." ? null : r,
-		type: i.length === 0 || i === "." ? null : i,
-		start: a.length === 0 || a === "." ? 0 : a - 1,
-		end: o.length === 0 || o === "." ? 0 : +o,
-		score: s.length === 0 || s === "." ? void 0 : +s,
-		strand: l(c),
-		phase: u.length === 0 || u === "." ? void 0 : +u,
-		subfeatures: []
-	};
-	return d(f, p), p;
-}
-//#endregion
-//#region ../../node_modules/gff-nostream/esm/api.js
-function m(e) {
-	return _(g(e));
-}
-function h(e) {
-	return v(g(e));
-}
-function g(e) {
-	let t = e.split(/\r?\n/), n = [];
-	for (let e = 0; e < t.length; e++) {
-		let r = t[e];
-		if (r.length === 0 || r[0] === "#") {
-			if (r.startsWith("##FASTA")) break;
-			continue;
-		}
-		if (r[0] === ">") break;
-		n.push({
-			line: r,
-			start: 0,
-			end: 0,
-			hasEscapes: r.includes("%")
-		});
-	}
-	return n;
-}
-function _(e) {
-	let t = [], n = /* @__PURE__ */ new Map(), r = /* @__PURE__ */ new Map();
-	for (let i = 0; i < e.length; i++) {
-		let a = e[i], c = a.hasEscapes ? o(a.line) : s(a.line);
-		c.child_features = [], c.derived_features = [], a.lineHash !== void 0 && (c.attributes ||= {}, c.attributes._lineHash = [String(a.lineHash)]);
-		let l = c.attributes, u = l?.ID, d = l?.Parent;
-		if (!u && !d) {
-			t.push([c]);
-			continue;
-		}
-		let f;
-		if (u) {
-			let e = u[0], i = n.get(e);
-			if (i) i.push(c), f = i;
-			else {
-				f = [c], d || t.push(f), n.set(e, f);
-				let i = r.get(e);
-				if (i) {
-					for (let e = 0; e < i.length; e++) c.child_features.push(i[e]);
-					r.delete(e);
-				}
-			}
-		} else f = [c];
-		if (d) for (let e = 0; e < d.length; e++) {
-			let t = d[e], i = n.get(t);
-			if (i) for (let e = 0; e < i.length; e++) i[e].child_features.push(f);
-			else {
-				let e = r.get(t);
-				e || (e = [], r.set(t, e)), e.push(f);
-			}
-		}
-	}
-	return t;
-}
-function v(e) {
-	let t = [], n = /* @__PURE__ */ new Map(), r = /* @__PURE__ */ new Map();
-	for (let i = 0; i < e.length; i++) {
-		let a = e[i], o = a.hasEscapes ? f(a.line) : p(a.line);
-		a.lineHash !== void 0 && (o._lineHash = String(a.lineHash));
-		let s = o.id, c = o.parent;
-		if (!s && !c) {
-			t.push(o);
-			continue;
-		}
-		if (s && !n.get(s)) {
-			c || t.push(o), n.set(s, o);
-			let e = r.get(s);
-			if (e) {
-				for (let t = 0; t < e.length; t++) o.subfeatures.push(e[t]);
-				r.delete(s);
-			}
-		}
-		if (c) {
-			let e = Array.isArray(c) ? c : [c];
-			for (let t = 0; t < e.length; t++) {
-				let i = e[t], a = n.get(i);
-				if (a) a.subfeatures.push(o);
-				else {
-					let e = r.get(i);
-					e || (e = [], r.set(i, e)), e.push(o);
-				}
-			}
-		}
-	}
-	return t;
-}
-//#endregion
-export { _ as parseRecords, v as parseRecordsJBrowse, m as parseStringSync, h as parseStringSyncJBrowse };

package/dist/esm-Daho46bY.js

@@ -1,121 +0,0 @@
-import { t as e } from "./esm-BgpwI2cq.js";
-import { n as t } from "./esm-C_XrKaCY.js";
-//#region ../core/node_modules/@gmod/indexedfasta/esm/indexedFasta.js
-function n(e, t, n, r) {
-	return e + t * Math.floor(r / n) + r % n;
-}
-async function r(e, t = {}) {
-	let n = new TextDecoder("utf8").decode(await e.readFile(t)), r = [], i = [], a = [], o = [], s = [], c = {}, l = 0, u = n.length, d = 0;
-	for (; l < u;) {
-		let e = n.indexOf("\n", l);
-		e === -1 && (e = u);
-		let t = n.slice(l, e);
-		if (t.endsWith("\r") && (t = t.slice(0, -1)), t = t.trim(), l = e + 1, t.length === 0) continue;
-		let f = t.indexOf("	"), p = t.indexOf("	", f + 1), m = t.indexOf("	", p + 1), h = t.indexOf("	", m + 1), g = t.slice(0, f);
-		if (g.startsWith(">")) throw Error("found > in sequence name, might have supplied FASTA file for the FASTA index");
-		r.push(g), a.push(+t.slice(f + 1, p)), i.push(+t.slice(p + 1, m)), o.push(+t.slice(m + 1, h)), s.push(+t.slice(h + 1)), c[g] = d, d++;
-	}
-	return {
-		names: r,
-		nameToIndex: c,
-		offsets: i,
-		lengths: a,
-		lineLengths: o,
-		lineBytes: s
-	};
-}
-var i = class {
-	constructor({ fasta: e, fai: n, path: r, faiPath: i }) {
-		if (e) this.fasta = e;
-		else if (r) this.fasta = new t(r);
-		else throw Error("Need to pass filehandle for fasta or path to localfile");
-		if (n) this.fai = n;
-		else if (i) this.fai = new t(i);
-		else if (r) this.fai = new t(`${r}.fai`);
-		else throw Error("Need to pass filehandle for  or path to localfile");
-	}
-	async _getIndexes(e) {
-		return this.indexes ||= r(this.fai, e).catch((e) => {
-			throw this.indexes = void 0, e;
-		}), this.indexes;
-	}
-	async getSequenceNames(e) {
-		return (await this._getIndexes(e)).names;
-	}
-	async getSequenceSizes(e) {
-		let t = await this._getIndexes(e);
-		if (!t.sizesCache) {
-			let e = {};
-			for (let n = 0; n < t.names.length; n++) e[t.names[n]] = t.lengths[n];
-			t.sizesCache = e;
-		}
-		return t.sizesCache;
-	}
-	async getSequenceSize(e, t) {
-		let n = await this._getIndexes(t), r = n.nameToIndex[e];
-		return r === void 0 ? void 0 : n.lengths[r];
-	}
-	async hasReferenceSequence(e, t) {
-		return (await this._getIndexes(t)).nameToIndex[e] !== void 0;
-	}
-	async getResiduesByName(e, t, n, r) {
-		let i = await this._getIndexes(r), a = i.nameToIndex[e];
-		if (a !== void 0) return this._fetchFromIndex(i.offsets[a], i.lineBytes[a], i.lineLengths[a], i.lengths[a], t, n, r);
-	}
-	async getSequence(e, t, n, r) {
-		return this.getResiduesByName(e, t, n, r);
-	}
-	async _fetchFromIndex(e, t, r, i, a = 0, o, s) {
-		let c = o;
-		if (a < 0) throw TypeError("regionStart cannot be less than 0");
-		if ((c === void 0 || c > i) && (c = i), a >= c) return "";
-		let l = n(e, t, r, a), u = n(e, t, r, c) - l, d = new TextDecoder("utf8").decode(await this.fasta.read(u, l, s)).replace(/\s+/g, "");
-		if (/[^\x20-\x7e]/.test(d.slice(0, 1e3))) throw Error("Non-ASCII characters detected in sequence. The file may be gzip compressed. Use BgzipIndexedFasta for bgzip files, or decompress the file.");
-		return d;
-	}
-}, a = class extends i {
-	constructor({ fasta: n, path: r, fai: i, faiPath: a, gzi: o, gziPath: s }) {
-		super({
-			fasta: n,
-			path: r,
-			fai: i,
-			faiPath: a
-		}), n && o ? this.fasta = new e({
-			filehandle: n,
-			gziFilehandle: o
-		}) : r && s && (this.fasta = new e({
-			filehandle: new t(r),
-			gziFilehandle: new t(s)
-		}));
-	}
-};
-//#endregion
-//#region ../core/node_modules/@gmod/indexedfasta/esm/index.js
-function o(e) {
-	return e.split(">").filter((e) => /\S/.test(e)).map((e) => {
-		let [t, ...n] = e.split("\n"), [r, ...i] = t.split(" "), a = n.join("").replace(/\s/g, "");
-		return {
-			id: r,
-			description: i.join(" "),
-			sequence: a
-		};
-	});
-}
-var s = class {
-	constructor({ fasta: e, path: n }) {
-		if (e) this.fasta = e;
-		else if (n) this.fasta = new t(n);
-		else throw Error("Need to pass fasta or path");
-		this.data = this.fasta.readFile().then((e) => o(new TextDecoder("utf8").decode(e)));
-	}
-	async fetch(e, t, n) {
-		let r = (await this.data).find((t) => t.id === e), i = n - t;
-		if (!r) throw Error(`no sequence with id ${e} exists`);
-		return r.sequence.slice(t, i);
-	}
-	async getSequenceNames() {
-		return (await this.data).map((e) => e.id);
-	}
-};
-//#endregion
-export { a as BgzipIndexedFasta, s as FetchableSmallFasta, i as IndexedFasta, o as parseSmallFasta };