@genome-spy/app 1.2.0 → 1.3.0

package/dist/{esm-Bv7Frz7C.js → esm-DzQDfrsZ.js}

@@ -18,17 +18,14 @@ function t(t, n, r, i, a = 0, o = n.length) {
 	}
 	let l = e(t);
 	if (l !== -1) {
-		if (l === 0) {
-			for (let e = 0; e < r; e++) {
-				let t = c;
-				for (; c < s && n.charCodeAt(c) !== 58 && n.charCodeAt(c) !== 9;) c++;
-				i(n, t, c, e);
-				let r = n.indexOf("	", c);
-				c = (r === -1 || r > s ? s : r) + 1;
-			}
-			return;
+		if (l === 0) for (let e = 0; e < r; e++) {
+			let t = c;
+			for (; c < s && n.charCodeAt(c) !== 58 && n.charCodeAt(c) !== 9;) c++;
+			i(n, t, c, e);
+			let r = n.indexOf("	", c);
+			c = (r === -1 || r > s ? s : r) + 1;
 		}
-		for (let e = 0; e < r; e++) {
+		else for (let e = 0; e < r; e++) {
 			let t = 0, r = c, a = -1, o = -1;
 			for (; c < s;) {
 				let e = n.charCodeAt(c);

package/dist/esm-aGLCvYRP.js

@@ -0,0 +1,238 @@
+import { n as e } from "./esm-C6erfjPM.js";
+import { t } from "./SharedReadCache-9sT2aIxW.js";
+import { i as n, n as r } from "./esm-BUkWqSr2.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(e, t) {
+		let { compressed: i, uncompressed: a, nextCompressedPosition: o } = await this.gzi.getRelevantBlocksForRead(e, t);
+		if (i.length === 0) return /* @__PURE__ */ new Uint8Array();
+		let s = t + e, 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 r(n), e.uncompressedStart, t, s);
+		})));
+		return n(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: t, path: n }) {
+		let r;
+		if (t) r = t;
+		else if (n) r = new e(n);
+		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 t({});
+	constructor({ fasta: t, fai: n, path: r, faiPath: i }) {
+		if (t) this.fasta = t;
+		else if (r) this.fasta = new e(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 e(i);
+		else if (r) this.fai = new e(`${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: t, path: n, fai: r, faiPath: i, gzi: a, gziPath: o }) {
+		let s;
+		if (t && a) s = new h({
+			filehandle: t,
+			gziFilehandle: a
+		});
+		else if (n && o) s = new h({
+			filehandle: new e(n),
+			gziFilehandle: new e(o)
+		});
+		else throw Error("BgzipIndexedFasta requires either {fasta, gzi} or {path, gziPath}");
+		super({
+			fasta: s,
+			fai: r,
+			faiPath: i,
+			path: n
+		});
+	}
+};
+//#endregion
+export { w as BgzipIndexedFasta, v as FetchableSmallFasta, C as IndexedFasta, _ as parseSmallFasta };

package/dist/{esm-VFJeyk9i.js → esm-nzwgJFGz.js}

@@ -1,4 +1,4 @@
-import { n as e, t } from "./rolldown-runtime-DF993M8W.js";
+import { n as e, t } from "./rolldown-runtime-DeIk2rA4.js";
 //#region ../../node_modules/generic-filehandle2/esm/util.js
 async function n(e) {
 	return e.bytes ? e.bytes() : new Uint8Array(await e.arrayBuffer());
@@ -74,20 +74,25 @@ var l = class {
 };
 //#endregion
 //#region ../../node_modules/generic-filehandle2/esm/remoteFile.js
-function u(e, t = {}) {
-	let n = new Set(Object.keys(t).map((e) => e.toLowerCase())), r = Object.entries(e).filter(([e]) => !n.has(e.toLowerCase()));
-	return {
-		...Object.fromEntries(r),
-		...t
-	};
+function u(...e) {
+	let t = /* @__PURE__ */ new Map();
+	for (let n of e) for (let [e, r] of Object.entries(n ?? {})) t.set(e.toLowerCase(), [e, r]);
+	return Object.fromEntries(t.values());
 }
 function d(e) {
-	return Number.isSafeInteger(e) && e >= 0;
+	let t = e.body;
+	typeof t?.cancel == "function" && t.cancel().catch(() => void 0);
 }
 function f(e) {
+	return Number.isSafeInteger(e) && e >= 0;
+}
+function p(e) {
+	return typeof e == "object" && !!e && "name" in e && e.name === "TypeError";
+}
+function m(e) {
 	return (typeof e == "object" && e && "message" in e && typeof e.message == "string" ? e.message : `${e}`).replace(/\.$/, "");
 }
-var p = class {
+var h = class {
 	url;
 	get source() {
 		return this.url;
@@ -109,15 +114,12 @@ var p = class {
 			mode: "cors",
 			...this.baseOverrides,
 			...e.overrides,
-			headers: u({
-				...this.baseHeaders,
-				...e.headers
-			}, t),
+			headers: u(this.baseHeaders, e.headers, t),
 			...n ? { signal: n } : {}
 		};
 	}
 	async fetch(e, t) {
-		let n = (t) => Error(`${f(t)} fetching ${e}`, { cause: t }), r;
+		let n = (n) => p(n) && !t?.signal?.aborted ? Error(`${m(n)} fetching ${e}`, { cause: n }) : n, r;
 		try {
 			r = await this.fetchImplementation(e, t);
 		} catch (i) {
@@ -136,29 +138,31 @@ var p = class {
 		return r;
 	}
 	async read(e, t, n = {}) {
-		if (e === 0) return /* @__PURE__ */ new Uint8Array();
-		if (!d(e) || !d(t)) throw TypeError(`read() called with an invalid length or position (length=${e}, position=${t}). The index file may be corrupt.`);
-		return this.fetchBytes(e, t, n);
+		if (!f(e) || !f(t)) throw TypeError(`read() called with an invalid length or position (length=${e}, position=${t}). The index file may be corrupt.`);
+		return e === 0 ? /* @__PURE__ */ new Uint8Array() : this.fetchBytes(e, t, n);
 	}
 	async fetchBytes(e, t, r) {
 		let i = await this.fetch(this.url, this.buildRequest(r, { range: `bytes=${t}-${t + e - 1}` }));
-		if (i.status === 416) return /* @__PURE__ */ new Uint8Array();
+		if (i.status === 416) return d(i), /* @__PURE__ */ new Uint8Array();
 		if (this.checkOk(i), i.status === 200 && t === 0 || i.status === 206) {
 			let t = a(i.headers.get("content-range"));
 			t !== void 0 && (this._stat = { size: t });
 			let o = r.onProgress ? await c(i, r.onProgress) : await n(i);
 			return !this._stat && i.status === 200 && (this._stat = { size: o.byteLength }), o.byteLength <= e ? o : o.slice(0, e);
 		}
-		throw Error(i.status === 200 ? `${this.url} fetch returned status 200, expected 206` : `HTTP ${i.status} fetching ${this.url}`);
+		throw d(i), Error(i.status === 200 ? `${this.url} fetch returned status 200, expected 206` : `HTTP ${i.status} fetching ${this.url}`);
 	}
 	checkOk(e) {
-		if (!e.ok) throw Error(`HTTP ${e.status} fetching ${this.url}`);
+		if (!e.ok) throw d(e), Error(`HTTP ${e.status} fetching ${this.url}`);
 	}
 	async readFile(e) {
-		let { encoding: t, opts: n } = i(e), a = await this.fetch(this.url, this.buildRequest(n));
-		this.checkOk(a);
-		let o = await r(a, t, n.onProgress);
-		return a.status === 200 && typeof o != "string" && (this._stat = { size: o.byteLength }), o;
+		let { encoding: t, opts: n } = i(e), r = await this.fetch(this.url, this.buildRequest(n));
+		this.checkOk(r);
+		let a = await this.readFileBody(r, t, n.onProgress);
+		return r.status === 200 && typeof a != "string" && (this._stat = { size: a.byteLength }), a;
+	}
+	readFileBody(e, t, n) {
+		return r(e, t, n);
 	}
 	async stat() {
 		return this._stat || (this.statProbe ??= this.read(10, 0).finally(() => {
@@ -168,13 +172,13 @@ var p = class {
 	close() {
 		return Promise.resolve();
 	}
-}, m = (/* @__PURE__ */ t(((e, t) => {
+}, g = (/* @__PURE__ */ t(((e, t) => {
 	t.exports = {};
 })))();
-function h(e) {
+function _(e) {
 	return typeof e == "object" && !!e && "unref" in e && typeof e.unref == "function";
 }
-var g = class {
+var v = class {
 	filename;
 	get source() {
 		return this.filename;
@@ -190,10 +194,10 @@ var g = class {
 	touch() {
 		this.fdIdleTimeoutMs <= 0 || (this.idleTimer !== void 0 && clearTimeout(this.idleTimer), this.idleTimer = setTimeout(() => {
 			this.idleTimer = void 0, this.dropHandle();
-		}, this.fdIdleTimeoutMs), h(this.idleTimer) && this.idleTimer.unref());
+		}, this.fdIdleTimeoutMs), _(this.idleTimer) && this.idleTimer.unref());
 	}
 	async handle() {
-		return this.fh ? this.fh : (this.opening ??= (0, m.open)(this.filename, "r").then((e) => (this.fh = e, this.opening = void 0, e), (e) => {
+		return this.fh ? this.fh : (this.opening ??= (0, g.open)(this.filename, "r").then((e) => (this.fh = e, this.opening = void 0, e), (e) => {
 			throw this.opening = void 0, e;
 		}), this.opening);
 	}
@@ -224,7 +228,7 @@ var g = class {
 	async readWithOwnHandle(e, t, n) {
 		let r;
 		try {
-			return r = await (0, m.open)(this.filename, "r"), await this.readFrom(r, e, t, n);
+			return r = await (0, g.open)(this.filename, "r"), await this.readFrom(r, e, t, n);
 		} finally {
 			if (r) try {
 				await r.close();
@@ -232,18 +236,18 @@ var g = class {
 		}
 	}
 	async readFile(e) {
-		return (0, m.readFile)(this.filename, e);
+		return (0, g.readFile)(this.filename, e);
 	}
 	async stat() {
-		return (0, m.stat)(this.filename);
+		return (0, g.stat)(this.filename);
 	}
 	async close() {
 		await this.dropHandle();
 	}
-}, _ = /* @__PURE__ */ e({
+}, y = /* @__PURE__ */ e({
 	BlobFile: () => l,
-	LocalFile: () => g,
-	RemoteFile: () => p
+	LocalFile: () => v,
+	RemoteFile: () => h
 });
 //#endregion
-export { g as n, p as r, _ as t };
+export { v as n, h as r, y as t };

package/dist/figWigMetadataSourceAdapter-8Kf_vZRf.js

@@ -0,0 +1,36 @@
+import { t as e } from "./tableMetadataSourceAdapter-DQrEXCo6.js";
+import { r as t } from "./url-DeOdSRrv.js";
+import { FigWig as n } from "./dist-D6xbz5Ks.js";
+//#region src/sampleView/metadata/adapters/figWigMetadataSourceAdapter.js
+var r = class extends e {
+	#e;
+	constructor(e, n = {}) {
+		super(e, {
+			...n,
+			sampleIdField: "name",
+			excludedColumns: [
+				"dtype",
+				"group",
+				"sample"
+			]
+		});
+		let r = e.backend;
+		this.#e = t(n.baseUrl, r.url);
+	}
+	async loadRows(e) {
+		let t = new n({ url: this.#e });
+		try {
+			return (await t.getTracks({ signal: e })).map((e) => {
+				let t = {
+					...e.metadata,
+					name: e.name
+				};
+				return delete t.dtype, delete t.group, t;
+			});
+		} finally {
+			await t.close();
+		}
+	}
+};
+//#endregion
+export { r as default };

package/dist/figWigMetadataSourceAdapter-DdDMZpYO.js

@@ -0,0 +1,36 @@
+import { u as e } from "./flowOutput-D5qpxWe0.js";
+import { t } from "./tableMetadataSourceAdapter-CUNwLsdi.js";
+import { FigWig as n } from "./dist-CmY6iewb.js";
+//#region src/sampleView/metadata/adapters/figWigMetadataSourceAdapter.js
+var r = class extends t {
+	#e;
+	constructor(t, n = {}) {
+		super(t, {
+			...n,
+			sampleIdField: "name",
+			excludedColumns: [
+				"dtype",
+				"group",
+				"sample"
+			]
+		});
+		let r = t.backend;
+		this.#e = e(n.baseUrl, r.url);
+	}
+	async loadRows(e) {
+		let t = new n({ url: this.#e });
+		try {
+			return (await t.getTracks({ signal: e })).map((e) => {
+				let t = {
+					...e.metadata,
+					name: e.name
+				};
+				return delete t.dtype, delete t.group, t;
+			});
+		} finally {
+			await t.close();
+		}
+	}
+};
+//#endregion
+export { r as default };