@genome-spy/app 0.88.1 → 0.90.0

package/dist/{esm-CcDLRSvC.js → esm-DtNElqRr.js}

@@ -1,8 +1,8 @@
-import { t as e } from "./esm-VvpZ9hsq.js";
-import { i as t, r as n } from "./esm-BA6yMcc-.js";
-import { n as r, r as i } from "./esm-BdT7qUL-.js";
+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 { t as a } from "./AbortablePromiseCache-BTmAcN-t.js";
-//#region ../core/node_modules/@gmod/tabix/esm/chunk.js
+//#region ../../node_modules/@gmod/tabix/esm/chunk.js
 var o = class {
 	constructor(e, t, n, r) {
 		this.minv = e, this.maxv = t, this.bin = n, this._fetchedSize = r;
@@ -58,7 +58,7 @@ function u(e, t = 0) {
 	return ((e[t + 4] | e[t + 5] << 8 | e[t + 6] << 16 | e[t + 7] << 24) >>> 0) * l + (n >>> 0);
 }
 //#endregion
-//#region ../core/node_modules/@gmod/tabix/esm/util.js
+//#region ../../node_modules/@gmod/tabix/esm/util.js
 function d(e, t) {
 	return t.minv.blockPosition - e.maxv.blockPosition < 65e3 && t.maxv.blockPosition - e.minv.blockPosition < 5e6;
 }
@@ -73,7 +73,7 @@ function f(e, t) {
 	return n;
 }
 //#endregion
-//#region ../core/node_modules/@gmod/tabix/esm/virtualOffset.js
+//#region ../../node_modules/@gmod/tabix/esm/virtualOffset.js
 var p = class {
 	constructor(e, t) {
 		this.blockPosition = e, this.dataPosition = t;
@@ -89,7 +89,7 @@ function m(e, t = 0) {
 	return new p(e[t + 7] * 1099511627776 + e[t + 6] * 4294967296 + e[t + 5] * 16777216 + e[t + 4] * 65536 + e[t + 3] * 256 + e[t + 2], e[t + 1] << 8 | e[t]);
 }
 //#endregion
-//#region ../core/node_modules/@gmod/tabix/esm/csi.js
+//#region ../../node_modules/@gmod/tabix/esm/csi.js
 var h = 21582659, g = 38359875, _ = {
 	0: "generic",
 	1: "SAM",
@@ -133,12 +133,12 @@ var b = class extends s {
 		};
 	}
 	async _parse(e = {}) {
-		let t = await n(await this.filehandle.readFile(e)), r = new DataView(t.buffer), i;
+		let n = await t(await this.filehandle.readFile(e)), 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");
 		this.minShift = r.getInt32(4, !0), this.depth = r.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-		let a = 2 ** (this.minShift + this.depth * 3), s = r.getInt32(12, !0), c = s && s >= 30 ? this.parseAuxData(t, 16) : {
+		let a = 2 ** (this.minShift + this.depth * 3), s = r.getInt32(12, !0), c = s && s >= 30 ? this.parseAuxData(n, 16) : {
 			refIdToName: [],
 			refNameToId: {},
 			metaChar: void 0,
@@ -152,25 +152,25 @@ var b = class extends s {
 		}, l = r.getInt32(16 + s, !0), u, d = 16 + s + 4, f = Array(l).fill(0).map(() => {
 			let e = r.getInt32(d, !0);
 			d += 4;
-			let n = {}, i;
+			let t = {}, i;
 			for (let a = 0; a < e; a += 1) {
 				let e = r.getUint32(d, !0);
-				if (e > this.maxBinNumber) i = this.parsePseudoBin(t, d + 4), d += 48;
+				if (e > this.maxBinNumber) i = this.parsePseudoBin(n, d + 4), d += 48;
 				else {
-					let i = m(t, d + 4);
+					let i = m(n, d + 4);
 					u = this._findFirstData(u, i);
 					let a = r.getInt32(d + 12, !0);
 					d += 16;
 					let s = Array(a);
-					for (let n = 0; n < a; n += 1) {
-						let r = m(t, d), i = m(t, d + 8);
-						d += 16, s[n] = new o(r, i, e);
+					for (let t = 0; t < a; t += 1) {
+						let r = m(n, d), i = m(n, d + 8);
+						d += 16, s[t] = new o(r, i, e);
 					}
-					n[e] = s;
+					t[e] = s;
 				}
 			}
 			return {
-				binIndex: n,
+				binIndex: t,
 				stats: i
 			};
 		});
@@ -227,61 +227,61 @@ var w = class extends s {
 		return r === void 0 || !n.indices[r] ? -1 : n.indices[r].stats?.lineCount ?? -1;
 	}
 	async _parse(e = {}) {
-		let t = await n(await this.filehandle.readFile(e)), r = new DataView(t.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 = {
+		let n = await this.filehandle.readFile(e), r = await t(n), i = new DataView(r.buffer);
+		if (i.getUint32(0, !0) !== x) throw Error("Not a TBI file");
+		let a = i.getUint32(4, !0), s = i.getUint32(8, !0), c = s & 65536 ? "zero-based-half-open" : "1-based-closed", l = {
 			0: "generic",
 			1: "SAM",
 			2: "VCF"
-		}[a & 15];
-		if (!c) throw Error(`invalid Tabix preset format flags ${a}`);
-		let l = {
-			ref: r.getInt32(12, !0),
-			start: r.getInt32(16, !0),
-			end: r.getInt32(20, !0)
-		}, u = r.getInt32(24, !0), d = 2 ** 29, f = u ? String.fromCharCode(u) : void 0, p = r.getInt32(28, !0), h = r.getInt32(32, !0), { refNameToId: g, refIdToName: _ } = this._parseNameBytes(t.slice(36, 36 + h)), v = 36 + h, y;
+		}[s & 15];
+		if (!l) throw Error(`invalid Tabix preset format flags ${s}`);
+		let u = {
+			ref: i.getInt32(12, !0),
+			start: i.getInt32(16, !0),
+			end: i.getInt32(20, !0)
+		}, d = i.getInt32(24, !0), f = 2 ** 29, p = d ? String.fromCharCode(d) : void 0, h = i.getInt32(28, !0), g = i.getInt32(32, !0), { refNameToId: _, refIdToName: v } = this._parseNameBytes(r.slice(36, 36 + g)), y = 36 + g, b;
 		return {
-			indices: Array(i).fill(0).map(() => {
-				let e = r.getInt32(v, !0);
-				v += 4;
-				let n = {}, i;
+			indices: Array(a).fill(0).map(() => {
+				let e = i.getInt32(y, !0);
+				y += 4;
+				let t = {}, n;
 				for (let a = 0; a < e; a += 1) {
-					let e = r.getUint32(v, !0);
-					if (v += 4, e > 37450) throw Error("tabix index contains too many bins, please use a CSI index");
+					let e = i.getUint32(y, !0);
+					if (y += 4, e > 37450) throw Error("tabix index contains too many bins, please use a CSI index");
 					if (e === 37450) {
-						let e = r.getInt32(v, !0);
-						v += 4, e === 2 && (i = this.parsePseudoBin(t, v)), v += 16 * e;
+						let e = i.getInt32(y, !0);
+						y += 4, e === 2 && (n = this.parsePseudoBin(r, y)), y += 16 * e;
 					} else {
-						let i = r.getInt32(v, !0);
-						v += 4;
-						let a = Array(i);
-						for (let n = 0; n < i; n += 1) {
-							let r = m(t, v), i = m(t, v + 8);
-							v += 16, y = this._findFirstData(y, r), a[n] = new o(r, i, e);
+						let n = i.getInt32(y, !0);
+						y += 4;
+						let a = Array(n);
+						for (let t = 0; t < n; t += 1) {
+							let n = m(r, y), i = m(r, y + 8);
+							y += 16, b = this._findFirstData(b, n), a[t] = new o(n, i, e);
 						}
-						n[e] = a;
+						t[e] = a;
 					}
 				}
-				let a = r.getInt32(v, !0);
-				v += 4;
+				let a = i.getInt32(y, !0);
+				y += 4;
 				let s = Array(a);
-				for (let e = 0; e < a; e += 1) s[e] = m(t, v), v += 8, y = this._findFirstData(y, s[e]);
+				for (let e = 0; e < a; e += 1) s[e] = m(r, y), y += 8, b = this._findFirstData(b, s[e]);
 				return {
-					binIndex: n,
+					binIndex: t,
 					linearIndex: s,
-					stats: i
+					stats: n
 				};
 			}),
-			metaChar: f,
+			metaChar: p,
 			maxBinNumber: 37449,
-			maxRefLength: d,
-			skipLines: p,
-			firstDataLine: y,
-			columnNumbers: l,
-			coordinateType: s,
-			format: c,
-			refIdToName: _,
-			refNameToId: g,
+			maxRefLength: f,
+			skipLines: h,
+			firstDataLine: b,
+			columnNumbers: u,
+			coordinateType: c,
+			format: l,
+			refIdToName: v,
+			refNameToId: _,
 			maxBlockSize: 65536
 		};
 	}
@@ -387,17 +387,17 @@ var w = class extends s {
 		return this.index.getMetadata(e);
 	}
 	async getHeaderBuffer(e = {}) {
-		let { firstDataLine: t, metaChar: r, maxBlockSize: i } = await this.getMetadata(e), a = (t?.blockPosition || 0) + i, o = await n(await this.filehandle.read(a, 0, e));
+		let { firstDataLine: n, metaChar: r, maxBlockSize: i } = await this.getMetadata(e), a = (n?.blockPosition || 0) + i, o = await this.filehandle.read(a, 0, e), s = await t(o);
 		if (r) {
 			let e = -1, t = r.charCodeAt(0);
-			for (let n = 0, r = o.length; n < r; n++) {
-				let r = o[n];
+			for (let n = 0, r = s.length; n < r; n++) {
+				let r = s[n];
 				if (n === e + 1 && r !== t) break;
 				r === 10 && (e = n);
 			}
-			return o.subarray(0, e + 1);
+			return s.subarray(0, e + 1);
 		}
-		return o;
+		return s;
 	}
 	async getHeader(e = {}) {
 		let t = new TextDecoder("utf8"), n = await this.getHeaderBuffer(e);
@@ -453,8 +453,9 @@ var w = class extends s {
 	async lineCount(e, t = {}) {
 		return this.index.lineCount(e, t);
 	}
-	async readChunk(e, n = {}) {
-		return t(await this.filehandle.read(e.fetchedSize(), e.minv.blockPosition, n), e, this.cache);
+	async readChunk(e, t = {}) {
+		let r = await this.filehandle.read(e.fetchedSize(), e.minv.blockPosition, t);
+		return n(r, e, this.cache);
 	}
 };
 //#endregion