@genome-spy/app 1.1.1 → 1.3.0

package/dist/esm-C6erfjPM.js

@@ -0,0 +1,252 @@
+import { n as e } from "./rolldown-runtime-DeIk2rA4.js";
+import { t } from "./__vite-browser-external-Dgu_Ldik.js";
+//#region ../../node_modules/generic-filehandle2/esm/util.js
+async function n(e) {
+	return e.bytes ? e.bytes() : new Uint8Array(await e.arrayBuffer());
+}
+async function r(e, t, r) {
+	if (t === "utf8" || t === "utf-8") return e.text();
+	if (t) throw Error(`unsupported encoding: ${t}`);
+	return r && "body" in e ? c(e, r) : n(e);
+}
+function i(e) {
+	return typeof e == "string" ? {
+		encoding: e,
+		opts: {}
+	} : {
+		encoding: e?.encoding,
+		opts: e ?? {}
+	};
+}
+function a(e) {
+	let t = /\/(\d+)$/.exec(e ?? "")?.[1];
+	return t === void 0 ? void 0 : parseInt(t, 10);
+}
+function o(e) {
+	let t = e.headers.get("content-length"), n = t === null ? NaN : Number(t);
+	return Number.isSafeInteger(n) && n >= 0 ? n : void 0;
+}
+var s = 50;
+async function c(e, t) {
+	let r = o(e), i = e.body;
+	if (!i || r === void 0) {
+		let i = await n(e);
+		return t(i.byteLength, r ?? i.byteLength), i;
+	}
+	let a = i.getReader(), c = new Uint8Array(r), l = 0, u = Date.now();
+	t(0, r);
+	for (let e = await a.read(); !e.done; e = await a.read()) {
+		if (l + e.value.byteLength > c.length) {
+			let t = new Uint8Array(Math.max(l + e.value.byteLength, c.length * 2));
+			t.set(c.subarray(0, l)), c = t;
+		}
+		c.set(e.value, l), l += e.value.byteLength;
+		let n = Date.now();
+		n - u >= s && (u = n, t(l, r));
+	}
+	return t(l, r), l === c.length ? c : c.slice(0, l);
+}
+//#endregion
+//#region ../../node_modules/generic-filehandle2/esm/blobFile.js
+var l = class {
+	source;
+	blob;
+	constructor(e) {
+		this.blob = e;
+	}
+	async read(e, t = 0, r = {}) {
+		if (e === 0) return /* @__PURE__ */ new Uint8Array();
+		r.signal?.throwIfAborted();
+		let i = await n(this.blob.slice(t, t + e));
+		return r.signal?.throwIfAborted(), i;
+	}
+	async readFile(e) {
+		let { encoding: t, opts: n } = i(e);
+		n.signal?.throwIfAborted();
+		let a = await r(this.blob, t);
+		return n.signal?.throwIfAborted(), a;
+	}
+	stat() {
+		return Promise.resolve({ size: this.blob.size });
+	}
+	close() {
+		return Promise.resolve();
+	}
+};
+//#endregion
+//#region ../../node_modules/generic-filehandle2/esm/remoteFile.js
+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) {
+	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 h = class {
+	url;
+	get source() {
+		return this.url;
+	}
+	_stat;
+	statProbe;
+	fetchImplementation;
+	baseHeaders;
+	baseOverrides;
+	baseSignal;
+	constructor(e, t = {}) {
+		this.url = e, this.baseHeaders = t.headers ?? {}, this.baseOverrides = t.overrides ?? {}, this.baseSignal = t.signal, this.fetchImplementation = t.fetch ?? globalThis.fetch.bind(globalThis);
+	}
+	buildRequest(e, t) {
+		let n = e.signal ?? this.baseSignal;
+		return {
+			method: "GET",
+			redirect: "follow",
+			mode: "cors",
+			...this.baseOverrides,
+			...e.overrides,
+			headers: u(this.baseHeaders, e.headers, t),
+			...n ? { signal: n } : {}
+		};
+	}
+	async fetch(e, t) {
+		let n = (n) => p(n) && !t?.signal?.aborted ? Error(`${m(n)} fetching ${e}`, { cause: n }) : n, r;
+		try {
+			r = await this.fetchImplementation(e, t);
+		} catch (i) {
+			if (`${i}`.includes("Failed to fetch")) {
+				console.warn(`generic-filehandle: refetching ${e} to attempt to work around chrome CORS header caching bug`);
+				try {
+					r = await this.fetchImplementation(e, {
+						...t,
+						cache: "reload"
+					});
+				} catch (e) {
+					throw n(e);
+				}
+			} else throw n(i);
+		}
+		return r;
+	}
+	async read(e, t, n = {}) {
+		if (!f(e) || !f(t)) throw TypeError(`read() called with an invalid length or position (length=${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}-${t + e - 1}` }));
+		if (i.status === 416) return d(i), /* @__PURE__ */ new Uint8Array();
+		if (this.checkOk(i), i.status === 200 && t === 0 || i.status === 206) {
+			let t = a(i.headers.get("content-range"));
+			t !== void 0 && (this._stat = { size: t });
+			let o = r.onProgress ? await c(i, r.onProgress) : await n(i);
+			return !this._stat && i.status === 200 && (this._stat = { size: o.byteLength }), o.byteLength <= e ? o : o.slice(0, e);
+		}
+		throw d(i), Error(i.status === 200 ? `${this.url} fetch returned status 200, expected 206` : `HTTP ${i.status} fetching ${this.url}`);
+	}
+	checkOk(e) {
+		if (!e.ok) throw d(e), Error(`HTTP ${e.status} fetching ${this.url}`);
+	}
+	async readFile(e) {
+		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(() => {
+			this.statProbe = void 0;
+		}), await this.statProbe), this._stat ?? { size: 0 };
+	}
+	close() {
+		return Promise.resolve();
+	}
+}, g = t();
+function _(e) {
+	return typeof e == "object" && !!e && "unref" in e && typeof e.unref == "function";
+}
+var v = class {
+	filename;
+	get source() {
+		return this.filename;
+	}
+	cacheFd;
+	fdIdleTimeoutMs;
+	fh;
+	opening;
+	idleTimer;
+	constructor(e, t = {}) {
+		this.filename = e, this.cacheFd = t.cacheFd ?? !0, this.fdIdleTimeoutMs = t.fdIdleTimeoutMs ?? 3e4;
+	}
+	touch() {
+		this.fdIdleTimeoutMs <= 0 || (this.idleTimer !== void 0 && clearTimeout(this.idleTimer), this.idleTimer = setTimeout(() => {
+			this.idleTimer = void 0, this.dropHandle();
+		}, this.fdIdleTimeoutMs), _(this.idleTimer) && this.idleTimer.unref());
+	}
+	async handle() {
+		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);
+	}
+	async dropHandle() {
+		this.idleTimer !== void 0 && (clearTimeout(this.idleTimer), this.idleTimer = void 0);
+		let e = this.fh ?? await this.opening?.catch(() => void 0);
+		if (this.fh = void 0, e) try {
+			await e.close();
+		} catch {}
+	}
+	async read(e, t = 0, n = {}) {
+		if (e === 0) return /* @__PURE__ */ new Uint8Array();
+		if (n.signal?.throwIfAborted(), !this.cacheFd) return this.readWithOwnHandle(e, t, n);
+		for (let r = 0;; r++) {
+			let i = await this.handle();
+			try {
+				let r = await this.readFrom(i, e, t, n);
+				return this.touch(), r;
+			} catch (e) {
+				if (await this.dropHandle(), r > 0 || n.signal?.aborted) throw e;
+			}
+		}
+	}
+	async readFrom(e, t, n, r) {
+		let i = new Uint8Array(t), a = await e.read(i, 0, t, n);
+		return r.signal?.throwIfAborted(), a.buffer.subarray(0, a.bytesRead);
+	}
+	async readWithOwnHandle(e, t, n) {
+		let r;
+		try {
+			return r = await (0, g.open)(this.filename, "r"), await this.readFrom(r, e, t, n);
+		} finally {
+			if (r) try {
+				await r.close();
+			} catch {}
+		}
+	}
+	async readFile(e) {
+		return (0, g.readFile)(this.filename, e);
+	}
+	async stat() {
+		return (0, g.stat)(this.filename);
+	}
+	async close() {
+		await this.dropHandle();
+	}
+}, y = /* @__PURE__ */ e({
+	BlobFile: () => l,
+	LocalFile: () => v,
+	RemoteFile: () => h
+});
+//#endregion
+export { v as n, h as r, y as t };

package/dist/{esm-DFHFX1sH.js → esm-CVjC7qA4.js}

@@ -1,6 +1,6 @@
-import { t as e } from "./esm-C3A-AuRi.js";
-import { n as t, r as n } from "./esm-Dndm-NaA.js";
-import { n as r, r as i } from "./esm-VFJeyk9i.js";
+import { n as e, r as t } from "./esm-nzwgJFGz.js";
+import { t as n } from "./esm-C3A-AuRi.js";
+import { n as r, r as i } from "./esm-BUkWqSr2.js";
 //#region ../../node_modules/@gmod/bam/esm/chunk.js
 var a = class {
 	minv;
@@ -68,11 +68,7 @@ function u(e) {
 	let t = [e[0]];
 	for (let n = 1; n < e.length; n++) {
 		let r = e[n], i = t[t.length - 1].maxv;
-		if ((r.minv.blockPosition - i.blockPosition || r.minv.dataPosition - i.dataPosition) >= 0) {
-			t.push(r);
-			continue;
-		}
-		(r.maxv.blockPosition - i.blockPosition || r.maxv.dataPosition - i.dataPosition) > 0 && t.push(new a(i, r.maxv, r.bin, r.endPosition));
+		(r.minv.blockPosition - i.blockPosition || r.minv.dataPosition - i.dataPosition) >= 0 ? t.push(r) : (r.maxv.blockPosition - i.blockPosition || r.maxv.dataPosition - i.dataPosition) > 0 && t.push(new a(i, r.maxv, r.bin, r.endPosition));
 	}
 	return t;
 }
@@ -158,13 +154,13 @@ function v(e, t, n, r, i = []) {
 }
 //#endregion
 //#region ../../node_modules/@gmod/bam/esm/indexFile.js
-function y(t, n = 5) {
-	let r = new e({ maxSize: n });
-	return (e) => {
-		let n = r.get(e);
+function y(e, t = 5) {
+	let r = new n({ maxSize: t });
+	return (t) => {
+		let n = r.get(t);
 		if (n !== void 0) return n;
-		let i = t(e);
-		return i && r.set(e, i), i;
+		let i = e(t);
+		return i && r.set(t, i), i;
 	};
 }
 var b = class {
@@ -628,10 +624,10 @@ var k = class extends b {
 		};
 	}
 	async _parse(e) {
-		let n = await this.filehandle.readFile(e), r = await t(n), i = new DataView(r.buffer, r.byteOffset, r.byteLength), o = i.getUint32(0, !0);
+		let t = await this.filehandle.readFile(e), n = await r(t), i = new DataView(n.buffer, n.byteOffset, n.byteLength), o = i.getUint32(0, !0);
 		if (o !== ae && o !== oe) throw Error(`Not a CSI file ${o}`);
 		this.minShift = i.getInt32(4, !0), this.depth = i.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-		let c = this.maxBinNumber, l = i.getInt32(12, !0), u = l >= 30 ? this.parseAuxData(r, 16) : void 0, p = i.getInt32(16 + l, !0), h = 16 + l + 4, g, _ = [];
+		let c = this.maxBinNumber, l = i.getInt32(12, !0), u = l >= 30 ? this.parseAuxData(n, 16) : void 0, p = i.getInt32(16 + l, !0), h = 16 + l + 4, g, _ = [];
 		for (let e = 0; e < p; e++) {
 			_.push(h);
 			let e = i.getInt32(h, !0);
@@ -640,7 +636,7 @@ var k = class extends b {
 				let e = i.getUint32(h, !0);
 				if (h += 4, e > this.maxBinNumber) h += 44;
 				else {
-					g = m(r, h, 1, g), h += 8;
+					g = m(n, h, 1, g), h += 8;
 					let e = i.getInt32(h, !0);
 					h += 4 + 16 * e;
 				}
@@ -649,22 +645,22 @@ var k = class extends b {
 		function v(e) {
 			let t = _[e];
 			if (t === void 0) return;
-			let n = i.getInt32(t, !0);
+			let r = i.getInt32(t, !0);
 			t += 4;
 			let o = {}, l;
-			for (let e = 0; e < n; e++) {
+			for (let e = 0; e < r; e++) {
 				let e = i.getUint32(t, !0);
-				if (t += 4, e > c) l = d(r, t + 28), t += 44;
+				if (t += 4, e > c) l = d(n, t + 28), t += 44;
 				else {
 					t += 8;
-					let n = i.getInt32(t, !0);
+					let r = i.getInt32(t, !0);
 					t += 4;
-					let c = Array(n);
-					for (let i = 0; i < n; i += 1) {
-						let n = s(r, t);
+					let c = Array(r);
+					for (let i = 0; i < r; i += 1) {
+						let r = s(n, t);
 						t += 8;
-						let o = s(r, t);
-						t += 8, c[i] = new a(n, o, e);
+						let o = s(n, t);
+						t += 8, c[i] = new a(r, o, e);
 					}
 					o[e] = c;
 				}
@@ -1190,8 +1186,8 @@ function ye(e) {
 	return n;
 }
 var K = 65536, be = 33554432;
-function q(e, t, n) {
-	return e ?? (t ? new r(t) : n ? new i(n) : void 0);
+function q(n, r, i) {
+	return n ?? (r ? new e(r) : i ? new t(i) : void 0);
 }
 function J(e, t, n) {
 	let r = e?.[0];
@@ -1266,11 +1262,11 @@ var X = 104857600, Z = 6, xe = class {
 	}
 	async getHeaderPre(e = {}) {
 		if (!this.index) throw Error("no index to read a header from: use HtsgetFile for htsget sources");
-		let n = await this.index.parse(e), r = n.firstDataLine === void 0 ? K : n.firstDataLine.blockPosition + K, i, a;
+		let t = await this.index.parse(e), n = t.firstDataLine === void 0 ? K : t.firstDataLine.blockPosition + K, i, a;
 		do {
-			let n = await this.bam.read(r, 0, { signal: e.signal });
-			a = n.length < r, i = this.applyHeader(await t(n)), r *= 2;
-		} while (i === void 0 && !a && r <= be);
+			let t = await this.bam.read(n, 0, { signal: e.signal });
+			a = t.length < n, i = this.applyHeader(await r(t)), n *= 2;
+		} while (i === void 0 && !a && n <= be);
 		if (i === void 0) throw Error("Insufficient data for reference sequences");
 		return i;
 	}
@@ -1406,12 +1402,12 @@ var X = 104857600, Z = 6, xe = class {
 		return await Promise.all(Array.from({ length: m }, () => p())), d.flat();
 	}
 	async _readChunkFeatures(e, t) {
-		let r = await this.bam.read(e.fetchedSize(), e.minv.blockPosition, { signal: t.signal });
+		let n = await this.bam.read(e.fetchedSize(), e.minv.blockPosition, { signal: t.signal });
 		c(t.signal);
-		let { buffer: i, cpositions: a, dpositions: o } = await n(r, e);
+		let { buffer: r, cpositions: a, dpositions: o } = await i(n, e);
 		return {
-			features: this.readBamFeatures(i, a, o, e),
-			bytes: i.byteLength
+			features: this.readBamFeatures(r, a, o, e),
+			bytes: r.byteLength
 		};
 	}
 	readBamFeatures(e, t, n, r) {
@@ -1492,8 +1488,8 @@ async function we(e, { url: t, headers: n }, r) {
 	});
 	return new Uint8Array(await o.arrayBuffer());
 }
-async function Te(e, n, r) {
-	return g(await Promise.all(n.map(async (n) => t(await we(e, n, r)))));
+async function Te(e, t, n) {
+	return g(await Promise.all(t.map(async (t) => r(await we(e, t, n)))));
 }
 var Ee = class extends Q {
 	baseUrl;