@genome-spy/core 0.75.0 → 0.77.0

package/dist/bundle/browser-KWU9rWZT.js

@@ -0,0 +1,123 @@
+import { t as e } from "./chunk-DmhlhrBa.js";
+//#region ../../node_modules/generic-filehandle2/esm/util.js
+async function t(e) {
+	return e.bytes ? e.bytes() : new Uint8Array(await e.arrayBuffer());
+}
+//#endregion
+//#region ../../node_modules/generic-filehandle2/esm/blobFile.js
+var n = class {
+	blob;
+	constructor(e) {
+		this.blob = e;
+	}
+	async read(e, n = 0) {
+		return e === 0 ? new Uint8Array() : t(this.blob.slice(n, n + e));
+	}
+	async readFile(e) {
+		let n = typeof e == "string" ? e : e?.encoding;
+		if (n === "utf8") return this.blob.text();
+		if (n) throw Error(`unsupported encoding: ${n}`);
+		return t(this.blob);
+	}
+	stat() {
+		return Promise.resolve({ size: this.blob.size });
+	}
+	close() {
+		return Promise.resolve();
+	}
+};
+//#endregion
+//#region ../../node_modules/generic-filehandle2/esm/remoteFile.js
+function r(e) {
+	return (typeof e == "object" && e && "message" in e && typeof e.message == "string" ? e.message : `${e}`).replace(/\.$/, "");
+}
+var i = class {
+	url;
+	_stat;
+	fetchImplementation;
+	baseHeaders;
+	baseOverrides;
+	constructor(e, t = {}) {
+		this.url = e, this.baseHeaders = t.headers ?? {}, this.baseOverrides = t.overrides ?? {}, this.fetchImplementation = t.fetch ?? globalThis.fetch.bind(globalThis);
+	}
+	buildRequest(e, t) {
+		return {
+			...this.baseOverrides,
+			...e.overrides,
+			headers: {
+				...this.baseHeaders,
+				...e.headers,
+				...t
+			},
+			method: "GET",
+			redirect: "follow",
+			mode: "cors",
+			signal: e.signal
+		};
+	}
+	async fetch(e, t) {
+		let n = (t) => Error(`${r(t)} fetching ${e}`, { cause: t }), i;
+		try {
+			i = await this.fetchImplementation(e, t);
+		} catch (r) {
+			if (`${r}`.includes("Failed to fetch")) {
+				console.warn(`generic-filehandle: refetching ${e} to attempt to work around chrome CORS header caching bug`);
+				try {
+					i = await this.fetchImplementation(e, {
+						...t,
+						cache: "reload"
+					});
+				} catch (e) {
+					throw n(e);
+				}
+			} else throw n(r);
+		}
+		return i;
+	}
+	async read(e, n, r = {}) {
+		if (e === 0) return new Uint8Array();
+		if (Number.isNaN(e) || Number.isNaN(n)) throw TypeError(`read() called with NaN length or position (length=${e}, position=${n}). The index file may be corrupt.`);
+		let i = await this.fetch(this.url, this.buildRequest(r, { range: `bytes=${n}-${n + e - 1}` }));
+		if (i.status === 416) return new Uint8Array();
+		if (!i.ok) throw Error(`HTTP ${i.status} fetching ${this.url}`);
+		if (i.status === 200 && n === 0 || i.status === 206) {
+			let n = i.headers.get("content-range"), r = /\/(\d+)$/.exec(n ?? "");
+			r?.[1] && (this._stat = { size: parseInt(r[1], 10) });
+			let a = await t(i);
+			return !this._stat && i.status === 200 && (this._stat = { size: a.byteLength }), a.byteLength <= e ? a : a.subarray(0, e);
+		}
+		throw Error(i.status === 200 ? `${this.url} fetch returned status 200, expected 206` : `HTTP ${i.status} fetching ${this.url}`);
+	}
+	async readFile(e = {}) {
+		let n = typeof e == "string" ? e : e.encoding, r = typeof e == "string" ? {} : e, i = await this.fetch(this.url, this.buildRequest(r));
+		if (!i.ok) throw Error(`HTTP ${i.status} fetching ${this.url}`);
+		if (n === "utf8") return i.text();
+		if (n) throw Error(`unsupported encoding: ${n}`);
+		return t(i);
+	}
+	async stat() {
+		return this._stat || await this.read(10, 0), this._stat ?? { size: 0 };
+	}
+	close() {
+		return Promise.resolve();
+	}
+}, a = /* @__PURE__ */ e({
+	BlobFile: () => n,
+	LocalFile: () => o,
+	RemoteFile: () => i
+}), o = class {
+	readFile() {
+		return Promise.reject(/* @__PURE__ */ Error("unimplemented"));
+	}
+	read() {
+		return Promise.reject(/* @__PURE__ */ Error("unimplemented"));
+	}
+	stat() {
+		return Promise.reject(/* @__PURE__ */ Error("unimplemented"));
+	}
+	close() {
+		return Promise.reject(/* @__PURE__ */ Error("unimplemented"));
+	}
+};
+//#endregion
+export { a as n, i as r, o as t };

package/dist/bundle/{esm-CgfVIRJ-.js → esm-0dYHNV_D.js}

@@ -1,5 +1,5 @@
-import { t as e } from "./esm-BDFRLEuD.js";
-import { t } from "./browser-BTgw5ieH.js";
+import { t as e } from "./esm-C49STiCR.js";
+import { t } from "./browser-KWU9rWZT.js";
 //#region node_modules/@gmod/indexedfasta/esm/indexedFasta.js
 function n(e, t, n, r) {
 	return e + t * Math.floor(r / n) + r % n;

package/dist/bundle/{esm-sIoQYZ21.js → esm-CRMf_I9V.js}

@@ -1,6 +1,6 @@
-import { t as e } from "./esm-CGX-qz1d.js";
-import { n as t, r as n } from "./esm-BDFRLEuD.js";
-import { r, t as i } from "./browser-BTgw5ieH.js";
+import { n as e, r as t } from "./esm-C49STiCR.js";
+import { t as n } from "./esm-CuVa5T98.js";
+import { r, t as i } from "./browser-KWU9rWZT.js";
 import { t as a } from "./AbortablePromiseCache-3gHJdF3E.js";
 //#region ../../node_modules/@gmod/tabix/esm/chunk.js
 var o = class {
@@ -132,8 +132,8 @@ var b = class extends s {
 			coordinateType: i
 		};
 	}
-	async _parse(e = {}) {
-		let n = await t(await this.filehandle.readFile(e)), r = new DataView(n.buffer), 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");
@@ -226,8 +226,8 @@ var w = class extends s {
 		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(e = {}) {
-		let n = await t(await this.filehandle.readFile(e)), r = new DataView(n.buffer);
+	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",
@@ -305,11 +305,11 @@ var w = class extends s {
 		return f(l, d);
 	}
 }, T = class {
-	constructor({ path: t, filehandle: n, url: o, tbiPath: s, tbiUrl: c, tbiFilehandle: l, csiPath: u, csiUrl: d, csiFilehandle: f, renameRefSeqs: p, chunkCacheSize: m = 5 * 2 ** 20 }) {
-		this.cache = new e({ maxSize: 1e3 });
+	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 (n) this.filehandle = n;
-		else if (t) this.filehandle = new i(t);
+		if (t) this.filehandle = t;
+		else if (e) this.filehandle = new i(e);
 		else if (o) this.filehandle = new r(o);
 		else throw TypeError("must provide either filehandle or path");
 		if (l) this.index = new w({
@@ -328,8 +328,8 @@ var w = class extends s {
 			filehandle: new i(u),
 			renameRefSeqs: h
 		});
-		else if (t) this.index = new w({
-			filehandle: new i(`${t}.tbi`),
+		else if (e) this.index = new w({
+			filehandle: new i(`${e}.tbi`),
 			renameRefSeqs: h
 		});
 		else if (d) this.index = new b({ filehandle: new r(d) });
@@ -337,7 +337,7 @@ var w = class extends s {
 		else if (o) this.index = new w({ filehandle: new r(`${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 e({ maxSize: Math.floor(m / 65536) }),
+			cache: new n({ maxSize: Math.floor(m / 65536) }),
 			fill: (e, t) => this.readChunk(e, { signal: t })
 		});
 	}
@@ -386,8 +386,8 @@ var w = class extends s {
 	async getMetadata(e = {}) {
 		return this.index.getMetadata(e);
 	}
-	async getHeaderBuffer(e = {}) {
-		let { firstDataLine: n, metaChar: r, maxBlockSize: i } = await this.getMetadata(e), a = (n?.blockPosition || 0) + i, o = await t(await this.filehandle.read(a, 0, 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++) {
@@ -453,8 +453,8 @@ var w = class extends s {
 	async lineCount(e, t = {}) {
 		return this.index.lineCount(e, t);
 	}
-	async readChunk(e, t = {}) {
-		return n(await this.filehandle.read(e.fetchedSize(), e.minv.blockPosition, t), e, this.cache);
+	async readChunk(e, n = {}) {
+		return t(await this.filehandle.read(e.fetchedSize(), e.minv.blockPosition, n), e, this.cache);
 	}
 };
 //#endregion