@genome-spy/app 1.0.0 → 1.1.0

package/dist/esm-CjkeZi__.js

@@ -0,0 +1,238 @@
+import { i as e, n as t } from "./esm-Dndm-NaA.js";
+import { n } from "./esm-VFJeyk9i.js";
+import { t as r } from "./SharedReadCache-Ey5QIiPM.js";
+//#endregion
+//#region ../../node_modules/@gmod/bgzf-filehandle/esm/long.js
+function i(e, t = 0) {
+	let n = e.getUint32(t, !0);
+	return e.getUint32(t + 4, !0) * 4294967296 + n;
+}
+//#endregion
+//#region ../../node_modules/@gmod/bgzf-filehandle/esm/gziIndex.js
+var a = 16, o = {
+	compressed: /* @__PURE__ */ new Float64Array(),
+	uncompressed: /* @__PURE__ */ new Float64Array()
+};
+function s(e, t) {
+	let n = new Float64Array(t + 1), r = new Float64Array(t + 1), o = new DataView(e.buffer, e.byteOffset, e.byteLength);
+	for (let e = 0; e < t; e += 1) {
+		let t = e * a;
+		n[e + 1] = i(o, t), r[e + 1] = i(o, t + 8);
+	}
+	return {
+		compressed: n,
+		uncompressed: r
+	};
+}
+function c(e, t) {
+	let n = 0, r = e.length;
+	for (; n < r;) {
+		let i = n + r >>> 1;
+		e[i] <= t ? n = i + 1 : r = i;
+	}
+	return n;
+}
+var l = class {
+	filehandle;
+	index;
+	constructor({ filehandle: e }) {
+		this.filehandle = e;
+	}
+	_getIndex() {
+		return this.index ||= this._readIndex().catch((e) => {
+			throw this.index = void 0, e;
+		}), this.index;
+	}
+	async _readIndex() {
+		let e = await this.filehandle.read(8, 0), t = i(new DataView(e.buffer, e.byteOffset, e.byteLength));
+		if (t === 0) return s(/* @__PURE__ */ new Uint8Array(), 0);
+		if (t > (2 ** 53 - 1) / a) throw TypeError("integer overflow");
+		return s(await this.filehandle.read(a * t, 8), t);
+	}
+	async getRelevantBlocksForRead(e, t) {
+		if (e === 0) return {
+			...o,
+			nextCompressedPosition: void 0
+		};
+		let { compressed: n, uncompressed: r } = await this._getIndex(), i = c(r, t) - 1, a = c(r, t + e - 1);
+		return {
+			compressed: n.subarray(i, a),
+			uncompressed: r.subarray(i, a),
+			nextCompressedPosition: a < n.length ? n[a] : void 0
+		};
+	}
+}, u = 10, d = 33554432;
+function f(e) {
+	let t = 0, n = [], r = () => {
+		t--, n.shift()?.();
+	};
+	return async (i) => {
+		t >= e && await new Promise((e) => {
+			n.push(e);
+		}), t++;
+		try {
+			return await i();
+		} finally {
+			r();
+		}
+	};
+}
+function p(e, t, n) {
+	let r = [], i = e.length, a = 0;
+	for (; a < i;) {
+		let o = a + 1;
+		for (; o < i && t[o] - t[a] < d;) o += 1;
+		r.push({
+			compressedStart: e[a],
+			compressedEnd: o < i ? e[o] : n ?? e[i - 1] + 65536,
+			uncompressedStart: t[a]
+		}), a = o;
+	}
+	return r;
+}
+function m(e, t, n, r) {
+	let i = Math.max(0, n - t), a = Math.min(r, t + e.length) - t;
+	return i < e.length ? e.subarray(i, a) : /* @__PURE__ */ new Uint8Array();
+}
+var h = class {
+	filehandle;
+	gzi;
+	limit;
+	constructor({ filehandle: e, gziFilehandle: t, blockConcurrency: n = u }) {
+		this.filehandle = e, this.gzi = new l({ filehandle: t }), this.limit = f(n);
+	}
+	async read(n, r) {
+		let { compressed: i, uncompressed: a, nextCompressedPosition: o } = await this.gzi.getRelevantBlocksForRead(n, r);
+		if (i.length === 0) return /* @__PURE__ */ new Uint8Array();
+		let s = r + n, c = p(i, a, o), l = await Promise.all(c.map((e) => this.limit(async () => {
+			let n = await this.filehandle.read(e.compressedEnd - e.compressedStart, e.compressedStart);
+			return m(await t(n), e.uncompressedStart, r, s);
+		})));
+		return e(l);
+	}
+}, g = new TextDecoder("utf8");
+function _(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 v = class {
+	data;
+	indexed;
+	constructor({ fasta: e, path: t }) {
+		let r;
+		if (e) r = e;
+		else if (t) r = new n(t);
+		else throw Error("Need to pass fasta or path");
+		this.data = r.readFile().then((e) => _(g.decode(e)));
+	}
+	getIndexed() {
+		return this.indexed ??= this.data.then((e) => new Map(e.map((e) => [e.id, e]))), this.indexed;
+	}
+	async fetch(e, t, n) {
+		let r = (await this.getIndexed()).get(e);
+		if (!r) throw Error(`no sequence with id ${e} exists`);
+		return r.sequence.slice(t, n);
+	}
+	async getSequenceNames() {
+		return (await this.data).map((e) => e.id);
+	}
+}, y = new TextDecoder("utf8");
+function b(e, t, n, r) {
+	return e + t * Math.floor(r / n) + r % n;
+}
+async function x(e, t = {}) {
+	let n = y.decode(await e.readFile(t)), r = /* @__PURE__ */ new Map();
+	for (let e of n.split("\n")) {
+		let t = e.trim();
+		if (!t) continue;
+		let n = t.split("	");
+		if (n.length < 5) throw Error(`Malformed FAI line (expected 5 tab-separated columns, got ${String(n.length)}): ${t}`);
+		let [i, a, o, s, c] = n;
+		if (i.startsWith(">")) throw Error("found > in sequence name, might have supplied FASTA file for the FASTA index");
+		let l = +a, u = +s;
+		if (l > 0 && u === 0) throw Error(`Invalid FAI index for "${i}": LINEBASES is 0, FASTA likely missing trailing newline; regenerate the .fai index`);
+		r.set(i, {
+			length: l,
+			offset: +o,
+			lineLength: u,
+			lineBytes: +c
+		});
+	}
+	return r;
+}
+async function S(e, t, n = 0, r, i) {
+	if (n < 0) throw TypeError("regionStart cannot be less than 0");
+	let a = Math.min(r ?? t.length, t.length);
+	if (n >= a) return "";
+	let o = b(t.offset, t.lineBytes, t.lineLength, n), s = b(t.offset, t.lineBytes, t.lineLength, a) - o, c = y.decode(await e.read(s, o, i)).replace(/\s+/g, "");
+	if (/[^\x20-\x7e]/.test(c.slice(0, 1e3))) throw Error("Non-ASCII bytes in sequence; file may be gzip — use BgzipIndexedFasta or decompress");
+	return c;
+}
+var C = class {
+	fasta;
+	fai;
+	indexCache = new r({});
+	constructor({ fasta: e, fai: t, path: r, faiPath: i }) {
+		if (e) this.fasta = e;
+		else if (r) this.fasta = new n(r);
+		else throw Error("Need to pass filehandle for fasta or path to localfile");
+		if (t) this.fai = t;
+		else if (i) this.fai = new n(i);
+		else if (r) this.fai = new n(`${r}.fai`);
+		else throw Error("Need to pass filehandle for fai or path to localfile");
+	}
+	getIndexes(e) {
+		return this.indexCache.get("fai", e?.signal, (t) => x(this.fai, {
+			...e,
+			signal: t
+		}));
+	}
+	async getSequenceNames(e) {
+		return [...(await this.getIndexes(e)).keys()];
+	}
+	async getSequenceSizes(e) {
+		let t = {};
+		for (let [n, r] of await this.getIndexes(e)) t[n] = r.length;
+		return t;
+	}
+	async getSequenceSize(e, t) {
+		return (await this.getIndexes(t)).get(e)?.length;
+	}
+	async hasReferenceSequence(e, t) {
+		return (await this.getIndexes(t)).has(e);
+	}
+	async getResiduesByName(e, t, n, r) {
+		let i = (await this.getIndexes(r)).get(e);
+		if (i !== void 0) return S(this.fasta, i, t, n, r);
+	}
+	async getSequence(e, t, n, r) {
+		return this.getResiduesByName(e, t, n, r);
+	}
+}, w = class extends C {
+	constructor({ fasta: e, path: t, fai: r, faiPath: i, gzi: a, gziPath: o }) {
+		let s;
+		if (e && a) s = new h({
+			filehandle: e,
+			gziFilehandle: a
+		});
+		else if (t && o) s = new h({
+			filehandle: new n(t),
+			gziFilehandle: new n(o)
+		});
+		else throw Error("BgzipIndexedFasta requires either {fasta, gzi} or {path, gziPath}");
+		super({
+			fasta: s,
+			fai: r,
+			faiPath: i,
+			path: t
+		});
+	}
+};
+//#endregion
+export { w as BgzipIndexedFasta, v as FetchableSmallFasta, C as IndexedFasta, _ as parseSmallFasta };

package/dist/index.es.js

@@ -1,6 +1,6 @@
 import { n as e, t } from "./rolldown-runtime-DF993M8W.js";
 import { $t as n, B as r, Bt as i, C as a, G as o, H as s, I as c, It as l, Jt as u, K as d, Kt as f, L as p, M as m, P as h, Qt as g, R as _, S as v, Sn as y, Wt as b, et as x, fn as S, i as C, j as w, k as T, o as E, pn as D, pt as O, tn as k, tt as A, y as ee, yt as j, z as M } from "./clipOptions-B5PibDq3.js";
-import { $ as te, $t as N, A as P, An as ne, At as re, B as ie, Bt as ae, C as oe, Cn as F, Ct as se, D as ce, Dn as le, Dt as ue, E as de, En as I, Et as fe, F as pe, Ft as me, G as he, Gt as ge, H as _e, Ht as ve, I as ye, It as be, J as xe, Jt as Se, K as Ce, Kt as we, L as Te, Lt as Ee, M as De, Mn as Oe, Mt as ke, N as Ae, Nn as je, Nt as Me, O as Ne, On as L, Ot as Pe, P as Fe, Pn as Ie, Pt as Le, Q as Re, Qt as ze, R as Be, Rt as Ve, S as He, Sn as R, St as Ue, T as We, Tn as Ge, Tt as Ke, U as qe, Ut as Je, V as Ye, Vt as Xe, W as Ze, Wt as Qe, X as $e, Xt as et, Y as tt, Yt as nt, Z as rt, Zt as it, _ as at, _n as ot, _t as st, a as ct, an as lt, at as ut, b as dt, bn as ft, bt as pt, c as mt, cn as ht, ct as gt, d as _t, dn as vt, dt as yt, en as bt, et as xt, f as St, fn as Ct, ft as wt, g as Tt, gn as Et, gt as Dt, h as Ot, hn as kt, ht as At, i as jt, in as Mt, it as Nt, j as Pt, jn as Ft, jt as It, k as Lt, kn as Rt, kt as zt, l as Bt, ln as Vt, lt as Ht, m as Ut, mn as Wt, mt as Gt, n as Kt, nn as qt, nt as Jt, o as Yt, on as Xt, ot as Zt, p as Qt, pn as $t, pt as en, q as tn, qt as nn, r as rn, rn as an, rt as on, s as sn, sn as cn, st as ln, tn as un, tt as dn, u as fn, un as pn, ut as mn, v as hn, vn as gn, vt as _n, w as vn, wn as yn, wt as bn, x as xn, xn as Sn, xt as Cn, y as wn, yn as Tn, yt as En, z as Dn, zt as On } from "./agentApi-Z65dw-sD.js";
+import { $ as te, $t as N, A as P, An as ne, At as re, B as ie, Bt as ae, C as oe, Cn as F, Ct as se, D as ce, Dn as le, Dt as ue, E as de, En as I, Et as fe, F as pe, Ft as me, G as he, Gt as ge, H as _e, Ht as ve, I as ye, It as be, J as xe, Jt as Se, K as Ce, Kt as we, L as Te, Lt as Ee, M as De, Mn as Oe, Mt as ke, N as Ae, Nn as je, Nt as Me, O as Ne, On as L, Ot as Pe, P as Fe, Pn as Ie, Pt as Le, Q as Re, Qt as ze, R as Be, Rt as Ve, S as He, Sn as R, St as Ue, T as We, Tn as Ge, Tt as Ke, U as qe, Ut as Je, V as Ye, Vt as Xe, W as Ze, Wt as Qe, X as $e, Xt as et, Y as tt, Yt as nt, Z as rt, Zt as it, _ as at, _n as ot, _t as st, a as ct, an as lt, at as ut, b as dt, bn as ft, bt as pt, c as mt, cn as ht, ct as gt, d as _t, dn as vt, dt as yt, en as bt, et as xt, f as St, fn as Ct, ft as wt, g as Tt, gn as Et, gt as Dt, h as Ot, hn as kt, ht as At, i as jt, in as Mt, it as Nt, j as Pt, jn as Ft, jt as It, k as Lt, kn as Rt, kt as zt, l as Bt, ln as Vt, lt as Ht, m as Ut, mn as Wt, mt as Gt, n as Kt, nn as qt, nt as Jt, o as Yt, on as Xt, ot as Zt, p as Qt, pn as $t, pt as en, q as tn, qt as nn, r as rn, rn as an, rt as on, s as sn, sn as cn, st as ln, tn as un, tt as dn, u as fn, un as pn, ut as mn, v as hn, vn as gn, vt as _n, w as vn, wn as yn, wt as bn, x as xn, xn as Sn, xt as Cn, y as wn, yn as Tn, yt as En, z as Dn, zt as On } from "./agentApi-BgZUOeB-.js";
 import { D as kn, T as An, b as jn, nt as Mn, v as Nn, y as Pn } from "./vega-scale-Ctz_wa3z.js";
 import { h as Fn } from "./indexer-En7gpvLN.js";
 import { A as In, E as Ln, G as Rn, I as zn, O as Bn, T as Vn, W as Hn, a as Un, c as Wn, f as Gn, h as Kn, i as qn, m as Jn, n as Yn, p as Xn, r as Zn, s as Qn, t as $n, v as er, w as tr } from "./viewSelectors-KtD-QSN0.js";
@@ -13253,7 +13253,7 @@ var Q_ = {
 	contributors: [],
 	license: "MIT",
 	homepage: "https://genomespy.app/",
-	version: "1.0.0",
+	version: "1.1.0",
 	main: "dist/index.js",
 	module: "dist/index.es.js",
 	type: "module",
@@ -13293,7 +13293,7 @@ var Q_ = {
 	files: ["dist/", "src/**/*.d.ts"],
 	repository: {
 		type: "git",
-		url: "github:genome-spy/genome-spy",
+		url: "git+https://github.com/genome-spy/genome-spy.git",
 		directory: "packages/app"
 	},
 	scripts: {
@@ -13305,15 +13305,14 @@ var Q_ = {
 		"test:tsc:tests": "tsc -p tsconfig.tests.json --noEmit",
 		"smoke:examples:webgpu": "node ../core/scripts/runWebGpuExamples.mjs --scope app --all --compare-webgl",
 		storybook: "storybook dev -p 6006",
-		"build-storybook": "storybook build",
-		prepublishOnly: "npm run build"
+		"build-storybook": "storybook build"
 	},
 	dependencies: {
 		"@floating-ui/dom": "^1.6.1",
 		"@fortawesome/fontawesome-free": "^6.4.2",
 		"@fortawesome/fontawesome-svg-core": "^6.4.2",
 		"@fortawesome/free-solid-svg-icons": "^6.4.2",
-		"@genome-spy/core": "^1.0.0",
+		"@genome-spy/core": "^1.1.0",
 		"@reduxjs/toolkit": "^2.11.0",
 		"d3-color": "^3.1.0",
 		idb: "^7.1.1",
@@ -13326,10 +13325,9 @@ var Q_ = {
 		zarrita: "^0.6.1"
 	},
 	devDependencies: {
-		"@genome-spy/app-agent": "^1.0.0",
-		"@genome-spy/inspector": "^1.0.0"
-	},
-	gitHead: "adb70d2246e3407282e3704e0e5cef214aa73a54"
+		"@genome-spy/app-agent": "^1.1.0",
+		"@genome-spy/inspector": "^1.1.0"
+	}
 };
 //#endregion
 //#region src/utils/version.js
@@ -22555,7 +22553,7 @@ var wC = class {
 		}, this.genomeSpy.viewFactory.addViewType(Km, ((e, t, n, r, i) => new t_(e, t, n, r, i, this.provenance, this.intentExecutor, Lx(this)))), this.#o();
 	}
 	getAgentApi() {
-		return this.#e ||= import("./agentApi-Z65dw-sD.js").then((e) => e.t).then((e) => e.createAgentApi(this)), this.#e;
+		return this.#e ||= import("./agentApi-BgZUOeB-.js").then((e) => e.t).then((e) => e.createAgentApi(this)), this.#e;
 	}
 	async getDebugModules() {
 		return import("./debug-DP4WzTNo.js");