@genome-spy/app 0.56.1 → 0.57.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/_commonjsHelpers-DjF3Plf2.js +26 -0
- package/dist/{index-BpoXW6_f.js → index-Bg62fPK7.js} +367 -388
- package/dist/index-C159nEYc.js +212 -0
- package/dist/index-CfEH2hsw.js +626 -0
- package/dist/{index-_ftu0t0z.js → index-CubKalvr.js} +1 -1
- package/dist/{index-WACuLhO6.js → index-DNzxWHJt.js} +2 -2
- package/dist/{index-HGQZ77IK.js → index-DhPRJZz0.js} +2 -2
- package/dist/{index-B6haPltu.js → index-DluFz_0j.js} +1 -1
- package/dist/{index-COovE1Oo.js → index-Dpv0n-cZ.js} +288 -287
- package/dist/{index-CjesiOz_.js → index-DutovjI-.js} +24 -24
- package/dist/index.es.js +9329 -8978
- package/dist/index.js +598 -793
- package/dist/{long-BXK3UEks.js → long-DM5IWGqg.js} +2 -2
- package/dist/remoteFile-DwSeXAZ0.js +94 -0
- package/dist/style.css +1 -1
- package/package.json +3 -3
- package/dist/_commonjsHelpers-DSebQMb9.js +0 -28
- package/dist/index-BhtH2nrr.js +0 -513
- package/dist/index-nCZhu2o-.js +0 -613
- package/dist/remoteFile-DuIsnepi.js +0 -90
@@ -1,7 +1,7 @@
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import { b as J } from "./index-
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import {
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import { b as J } from "./index-DluFz_0j.js";
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import { A as Gn, L as Yn } from "./index-C159nEYc.js";
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import { L as nr } from "./__vite-browser-external-C--ziKoh.js";
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import { R as ir } from "./remoteFile-
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import { R as ir } from "./remoteFile-DwSeXAZ0.js";
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const st = BigInt(32);
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function rr(e, n, t) {
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const i = +!!t, a = +!t;
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@@ -152,12 +152,12 @@ const x = /* @__PURE__ */ new Map(), re = "___parser_", M = {
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doublele: !0,
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doublebe: !1
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};
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class
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class S {
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constructor() {
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this.varName = "", this.type = "", this.options = {}, this.endian = "be", this.useContextVariables = !1;
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}
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static start() {
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return new
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return new S();
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}
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primitiveGenerateN(n, t) {
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const i = Ye[n], a = Ke[n];
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@@ -404,9 +404,9 @@ class N {
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nest(n, t) {
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if (typeof t != "object" && typeof n == "object" && (t = n, n = ""), !t || !t.type)
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throw new Error("type is required for nest.");
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if (!(t.type instanceof
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if (!(t.type instanceof S) && !x.has(t.type))
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throw new Error("type must be a known parser name or a Parser object.");
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if (!(t.type instanceof
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if (!(t.type instanceof S) && !n)
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throw new Error("type must be a Parser object if the variable name is omitted.");
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return this.setNextParser("nest", n, t);
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}
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@@ -480,7 +480,7 @@ class N {
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n = this.options.length;
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else if (this.type === "array" && typeof this.options.length == "number") {
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let t = NaN;
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typeof this.options.type == "string" ? t = M[this.options.type] : this.options.type instanceof
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typeof this.options.type == "string" ? t = M[this.options.type] : this.options.type instanceof S && (t = this.options.type.sizeOf()), n = this.options.length * t;
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} else this.type === "seek" ? n = this.options.length : this.type === "nest" ? n = this.options.type.sizeOf() : this.type || (n = 0);
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return this.next && (n += this.next.sizeOf()), n;
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}
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@@ -489,7 +489,7 @@ class N {
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return this.compiled || this.compile(), this.compiled(n, this.constructorFn);
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}
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setNextParser(n, t, i) {
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const a = new
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const a = new S();
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return a.type = n, a.varName = t, a.options = i, a.endian = this.endian, this.head ? this.head.next = a : this.next = a, this.head = a, this;
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}
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// Call code generator for this parser
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@@ -584,29 +584,29 @@ class N {
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const i = n.generateTmpVariable();
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n.pushCode(`var ${i} = 0;`);
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const a = (f = 0) => {
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let
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let _ = 0;
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for (let c = f; c < n.bitFields.length; c++) {
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const h = n.bitFields[c].options.length;
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if (
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if (_ + h > 32)
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break;
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-
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_ += h;
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}
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return
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return _;
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}, r = (f) => (f <= 8 ? (n.pushCode(`${i} = dataView.getUint8(offset);`), f = 8) : f <= 16 ? (n.pushCode(`${i} = dataView.getUint16(offset);`), f = 16) : f <= 24 ? (n.pushCode(`${i} = (dataView.getUint16(offset) << 8) | dataView.getUint8(offset + 2);`), f = 24) : (n.pushCode(`${i} = dataView.getUint32(offset);`), f = 32), n.pushCode(`offset += ${f / 8};`), f);
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let o = 0;
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const l = this.endian === "be";
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let u = 0, s = 0;
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n.bitFields.forEach((f,
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n.bitFields.forEach((f, _) => {
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let c = f.options.length;
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if (c > s) {
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if (s) {
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const g = -1 >>> 32 - s;
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n.pushCode(`${f.varName} = (${i} & 0x${g.toString(16)}) << ${c - s};`), c -= s;
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}
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o = 0, s = u = r(a(
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o = 0, s = u = r(a(_) - s);
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}
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const h = l ? u - o - c : o,
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n.pushCode(`${f.varName} ${c < f.options.length ? "|=" : "="} ${i} >> ${h} & 0x${
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const h = l ? u - o - c : o, d = -1 >>> 32 - c;
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n.pushCode(`${f.varName} ${c < f.options.length ? "|=" : "="} ${i} >> ${h} & 0x${d.toString(16)};`), f.options.length === 32 && n.pushCode(`${f.varName} >>>= 0`), f.options.assert && f.generateAssert(n), f.options.formatter && f.generateFormatter(n, f.varName, f.options.formatter), o += c, s -= c;
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}), n.bitFields = [];
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}
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}
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@@ -648,22 +648,22 @@ class N {
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if (x.get(a)) {
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const f = n.generateTmpVariable();
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if (n.pushCode(`var ${f} = ${re + a}(offset, {`), n.useContextVariables) {
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const
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n.pushCode(`$parent: ${
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const _ = n.generateVariable();
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n.pushCode(`$parent: ${_},`), n.pushCode(`$root: ${_}.$root,`), !this.options.readUntil && i === void 0 && n.pushCode(`$index: ${t} - ${r},`);
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}
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n.pushCode("});"), n.pushCode(`var ${l} = ${f}.result; offset = ${f}.offset;`), a !== this.alias && n.addReference(a);
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} else {
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const f = Ye[a],
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n.pushCode(`var ${l} = dataView.get${f}(offset, ${
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const f = Ye[a], _ = Ke[a];
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n.pushCode(`var ${l} = dataView.get${f}(offset, ${_});`), n.pushCode(`offset += ${M[a]};`);
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}
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else if (a instanceof
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else if (a instanceof S) {
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n.pushCode(`var ${l} = {};`);
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const f = n.generateVariable();
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n.pushScope(l), n.useContextVariables && (n.pushCode(`${l}.$parent = ${f};`), n.pushCode(`${l}.$root = ${f}.$root;`), !this.options.readUntil && i === void 0 && n.pushCode(`${l}.$index = ${t} - ${r};`)), a.generate(n), n.useContextVariables && (n.pushCode(`delete ${l}.$parent;`), n.pushCode(`delete ${l}.$root;`), n.pushCode(`delete ${l}.$index;`)), n.popScope();
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}
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if (s ? n.pushCode(`${o}[${l}.${u}] = ${l};`) : n.pushCode(`${o}.push(${l});`), n.pushCode("}"), typeof this.options.readUntil == "function") {
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const f = this.options.readUntil,
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n.pushCode(`while (!${
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const f = this.options.readUntil, _ = n.addImport(f);
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n.pushCode(`while (!${_}.call(${n.generateVariable()}, ${l}, buffer.subarray(offset)));`);
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}
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}
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generateChoiceCase(n, t, i) {
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const r = Ye[i], o = Ke[i];
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n.pushCode(`${a} = dataView.get${r}(offset, ${o});`), n.pushCode(`offset += ${M[i]}`);
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}
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} else i instanceof
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} else i instanceof S && (n.pushPath(t), i.generate(n), n.popPath(t));
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}
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generateChoice(n) {
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const t = n.generateOption(this.options.tag), i = n.generateVariable(this.varName);
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}
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generateNest(n) {
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const t = n.generateVariable(this.varName);
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if (this.options.type instanceof
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if (this.options.type instanceof S) {
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if (this.varName && (n.pushCode(`${t} = {};`), n.useContextVariables)) {
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n.pushCode(`${t}.$parent = ${i};`), n.pushCode(`${t}.$root = ${i}.$root;`);
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const u = this.options.readUntil, s = n.generateTmpVariable(), f = n.generateTmpVariable();
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n.pushCode(`var ${s} = offset;`), n.pushCode(`var ${f} = 0;`), n.pushCode("while (offset < buffer.length) {"), n.pushCode(`${f} = dataView.getUint8(offset);`);
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const
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n.pushCode(`if (${
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const _ = n.addImport(u);
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n.pushCode(`if (${_}.call(${n.generateVariable()}, ${f}, buffer.subarray(offset))) break;`), n.pushCode("offset += 1;"), n.pushCode("}"), n.pushCode(`${i} = buffer.subarray(${s}, offset);`);
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const a = n.generateTmpVariable(), r = n.generateTmpVariable(), o = n.generateTmpVariable(), l = n.addImport(this.options.wrapper);
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if (n.pushCode(`${i} = ${l}.call(this, ${i}).subarray(0);`), n.pushCode(`var ${a} = buffer;`), n.pushCode(`var ${r} = offset;`), n.pushCode(`var ${o} = dataView;`), n.pushCode(`buffer = ${i};`), n.pushCode("offset = 0;"), n.pushCode("dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);"), this.options.type instanceof
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if (n.pushCode(`${i} = ${l}.call(this, ${i}).subarray(0);`), n.pushCode(`var ${a} = buffer;`), n.pushCode(`var ${r} = offset;`), n.pushCode(`var ${o} = dataView;`), n.pushCode(`buffer = ${i};`), n.pushCode("offset = 0;"), n.pushCode("dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);"), this.options.type instanceof S)
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this.varName && n.pushCode(`${t} = {};`), n.pushPath(this.varName), this.options.type.generate(n), n.popPath(this.varName);
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const t = this.options.type, i = n.generateOption(this.options.offset), a = n.generateTmpVariable(), r = n.generateVariable(this.varName);
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if (n.pushCode(`var ${a} = offset;`), n.pushCode(`offset = ${i};`), this.options.type instanceof S) {
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const t = [...this.getRanges(), ...n.getRanges()].sort((r, o) => r.min < o.min ? -1 : r.min > o.min ? 1 : r.max < o.max ? -1 : o.max > r.max ? 1 : 0), i = [];
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for (
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o.min > a.max + 1 ? (i.push(a), a = o) : o.max > a.max && (a = new pe([{ min: a.min, max: o.max }]));
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}
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e.bi_valid === 16 ? (Be(e, e.bi_buf), e.bi_buf = 0, e.bi_valid = 0) : e.bi_valid >= 8 && (e.pending_buf[e.pending++] = e.bi_buf & 255, e.bi_buf >>= 8, e.bi_valid -= 8);
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const t = n.dyn_tree, i = n.max_code, a = n.stat_desc.static_tree, r = n.stat_desc.has_stree, o = n.stat_desc.extra_bits, l = n.stat_desc.extra_base, u = n.stat_desc.max_length;
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let s, f, _, c, h, d, g = 0;
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f = e.heap[s], c = t[t[f * 2 + 1] * 2 + 1] + 1, c > u && (c = u, g++), t[f * 2 + 1] = c, !(f > i) && (e.bl_count[c]++, h = 0, f >= l && (h = o[f - l]),
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f = e.heap[s], c = t[t[f * 2 + 1] * 2 + 1] + 1, c > u && (c = u, g++), t[f * 2 + 1] = c, !(f > i) && (e.bl_count[c]++, h = 0, f >= l && (h = o[f - l]), d = t[f * 2], e.opt_len += d * (c + h), r && (e.static_len += d * (a[f * 2 + 1] + h)));
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_ = e.heap[--s], !(_ > i) && (t[_ * 2 + 1] !== c && (e.opt_len += (c - t[_ * 2 + 1]) * t[_ * 2], t[_ * 2 + 1] = c), f--);
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return a > i && (a = i), a === 0 ? 0 : (e.avail_in -= a, n.set(e.input.subarray(e.next_in, e.next_in + a), t), e.state.wrap === 1 ? e.adler = Ue(e.adler, n, a, t) : e.state.wrap === 2 && (e.adler = R(e.adler, n, a, t)), e.next_in += a, e.total_in += a, a);
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let t = e.max_chain_length, i = e.strstart, a, r, o = e.prev_length, l = e.nice_match;
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const u = e.strstart > e.w_size - Y ? e.strstart - (e.w_size - Y) : 0, s = e.window, f = e.w_mask,
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let h = s[i + o - 1],
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const u = e.strstart > e.w_size - Y ? e.strstart - (e.w_size - Y) : 0, s = e.window, f = e.w_mask, _ = e.prev, c = e.strstart + Q;
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let h = s[i + o - 1], d = s[i + o];
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if (a = n, !(s[a + o] !==
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if (a = n, !(s[a + o] !== d || s[a + o - 1] !== h || s[a] !== s[i] || s[++a] !== s[i + 1])) {
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if (e.match_start = n, o = r, r >= l)
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break;
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h = s[i + o - 1],
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|
+
h = s[i + o - 1], d = s[i + o];
|
1177
1175
|
}
|
1178
1176
|
}
|
1179
|
-
while ((n =
|
1177
|
+
while ((n = _[n & f]) > u && --t !== 0);
|
1180
1178
|
return o <= e.lookahead ? o : e.lookahead;
|
1181
1179
|
}, me = (e) => {
|
1182
1180
|
const n = e.w_size;
|
@@ -1631,80 +1629,80 @@ Gt.prototype.onEnd = function(e) {
|
|
1631
1629
|
};
|
1632
1630
|
const Xe = 16209, Ma = 16191;
|
1633
1631
|
var Ha = function(n, t) {
|
1634
|
-
let i, a, r, o, l, u, s, f,
|
1632
|
+
let i, a, r, o, l, u, s, f, _, c, h, d, g, k, y, E, C, p, $, N, b, m, w, v;
|
1635
1633
|
const I = n.state;
|
1636
|
-
i = n.next_in,
|
1634
|
+
i = n.next_in, w = n.input, a = i + (n.avail_in - 5), r = n.next_out, v = n.output, o = r - (t - n.avail_out), l = r + (n.avail_out - 257), u = I.dmax, s = I.wsize, f = I.whave, _ = I.wnext, c = I.window, h = I.hold, d = I.bits, g = I.lencode, k = I.distcode, y = (1 << I.lenbits) - 1, E = (1 << I.distbits) - 1;
|
1637
1635
|
e:
|
1638
1636
|
do {
|
1639
|
-
|
1637
|
+
d < 15 && (h += w[i++] << d, d += 8, h += w[i++] << d, d += 8), C = g[h & y];
|
1640
1638
|
t:
|
1641
1639
|
for (; ; ) {
|
1642
|
-
if (
|
1643
|
-
|
1644
|
-
else if (
|
1645
|
-
$ = C & 65535,
|
1640
|
+
if (p = C >>> 24, h >>>= p, d -= p, p = C >>> 16 & 255, p === 0)
|
1641
|
+
v[r++] = C & 65535;
|
1642
|
+
else if (p & 16) {
|
1643
|
+
$ = C & 65535, p &= 15, p && (d < p && (h += w[i++] << d, d += 8), $ += h & (1 << p) - 1, h >>>= p, d -= p), d < 15 && (h += w[i++] << d, d += 8, h += w[i++] << d, d += 8), C = k[h & E];
|
1646
1644
|
n:
|
1647
1645
|
for (; ; ) {
|
1648
|
-
if (
|
1649
|
-
if (
|
1646
|
+
if (p = C >>> 24, h >>>= p, d -= p, p = C >>> 16 & 255, p & 16) {
|
1647
|
+
if (N = C & 65535, p &= 15, d < p && (h += w[i++] << d, d += 8, d < p && (h += w[i++] << d, d += 8)), N += h & (1 << p) - 1, N > u) {
|
1650
1648
|
n.msg = "invalid distance too far back", I.mode = Xe;
|
1651
1649
|
break e;
|
1652
1650
|
}
|
1653
|
-
if (h >>>=
|
1654
|
-
if (
|
1651
|
+
if (h >>>= p, d -= p, p = r - o, N > p) {
|
1652
|
+
if (p = N - p, p > f && I.sane) {
|
1655
1653
|
n.msg = "invalid distance too far back", I.mode = Xe;
|
1656
1654
|
break e;
|
1657
1655
|
}
|
1658
|
-
if (b = 0,
|
1659
|
-
if (b += s -
|
1660
|
-
$ -=
|
1656
|
+
if (b = 0, m = c, _ === 0) {
|
1657
|
+
if (b += s - p, p < $) {
|
1658
|
+
$ -= p;
|
1661
1659
|
do
|
1662
|
-
|
1663
|
-
while (--
|
1664
|
-
b = r -
|
1660
|
+
v[r++] = c[b++];
|
1661
|
+
while (--p);
|
1662
|
+
b = r - N, m = v;
|
1665
1663
|
}
|
1666
|
-
} else if (
|
1667
|
-
if (b += s +
|
1668
|
-
$ -=
|
1664
|
+
} else if (_ < p) {
|
1665
|
+
if (b += s + _ - p, p -= _, p < $) {
|
1666
|
+
$ -= p;
|
1669
1667
|
do
|
1670
|
-
|
1671
|
-
while (--
|
1672
|
-
if (b = 0,
|
1673
|
-
|
1668
|
+
v[r++] = c[b++];
|
1669
|
+
while (--p);
|
1670
|
+
if (b = 0, _ < $) {
|
1671
|
+
p = _, $ -= p;
|
1674
1672
|
do
|
1675
|
-
|
1676
|
-
while (--
|
1677
|
-
b = r -
|
1673
|
+
v[r++] = c[b++];
|
1674
|
+
while (--p);
|
1675
|
+
b = r - N, m = v;
|
1678
1676
|
}
|
1679
1677
|
}
|
1680
|
-
} else if (b +=
|
1681
|
-
$ -=
|
1678
|
+
} else if (b += _ - p, p < $) {
|
1679
|
+
$ -= p;
|
1682
1680
|
do
|
1683
|
-
|
1684
|
-
while (--
|
1685
|
-
b = r -
|
1681
|
+
v[r++] = c[b++];
|
1682
|
+
while (--p);
|
1683
|
+
b = r - N, m = v;
|
1686
1684
|
}
|
1687
1685
|
for (; $ > 2; )
|
1688
|
-
|
1689
|
-
$ && (
|
1686
|
+
v[r++] = m[b++], v[r++] = m[b++], v[r++] = m[b++], $ -= 3;
|
1687
|
+
$ && (v[r++] = m[b++], $ > 1 && (v[r++] = m[b++]));
|
1690
1688
|
} else {
|
1691
|
-
b = r -
|
1689
|
+
b = r - N;
|
1692
1690
|
do
|
1693
|
-
|
1691
|
+
v[r++] = v[b++], v[r++] = v[b++], v[r++] = v[b++], $ -= 3;
|
1694
1692
|
while ($ > 2);
|
1695
|
-
$ && (
|
1693
|
+
$ && (v[r++] = v[b++], $ > 1 && (v[r++] = v[b++]));
|
1696
1694
|
}
|
1697
|
-
} else if (
|
1695
|
+
} else if (p & 64) {
|
1698
1696
|
n.msg = "invalid distance code", I.mode = Xe;
|
1699
1697
|
break e;
|
1700
1698
|
} else {
|
1701
|
-
C = k[(C & 65535) + (h & (1 <<
|
1699
|
+
C = k[(C & 65535) + (h & (1 << p) - 1)];
|
1702
1700
|
continue n;
|
1703
1701
|
}
|
1704
1702
|
break;
|
1705
1703
|
}
|
1706
|
-
} else if (
|
1707
|
-
if (
|
1704
|
+
} else if (p & 64)
|
1705
|
+
if (p & 32) {
|
1708
1706
|
I.mode = Ma;
|
1709
1707
|
break e;
|
1710
1708
|
} else {
|
@@ -1712,13 +1710,13 @@ var Ha = function(n, t) {
|
|
1712
1710
|
break e;
|
1713
1711
|
}
|
1714
1712
|
else {
|
1715
|
-
C = g[(C & 65535) + (h & (1 <<
|
1713
|
+
C = g[(C & 65535) + (h & (1 << p) - 1)];
|
1716
1714
|
continue t;
|
1717
1715
|
}
|
1718
1716
|
break;
|
1719
1717
|
}
|
1720
1718
|
} while (i < a && r < l);
|
1721
|
-
$ =
|
1719
|
+
$ = d >> 3, i -= $, d -= $ << 3, h &= (1 << d) - 1, n.next_in = i, n.next_out = r, n.avail_in = i < a ? 5 + (a - i) : 5 - (i - a), n.avail_out = r < l ? 257 + (l - r) : 257 - (r - l), I.hold = h, I.bits = d;
|
1722
1720
|
};
|
1723
1721
|
const de = 15, un = 852, hn = 592, cn = 0, gt = 1, dn = 2, ja = new Uint16Array([
|
1724
1722
|
/* Length codes 257..285 base */
|
@@ -1856,48 +1854,48 @@ const de = 15, un = 852, hn = 592, cn = 0, gt = 1, dn = 2, ja = new Uint16Array(
|
|
1856
1854
|
64
|
1857
1855
|
]), Wa = (e, n, t, i, a, r, o, l) => {
|
1858
1856
|
const u = l.bits;
|
1859
|
-
let s = 0, f = 0,
|
1860
|
-
const
|
1857
|
+
let s = 0, f = 0, _ = 0, c = 0, h = 0, d = 0, g = 0, k = 0, y = 0, E = 0, C, p, $, N, b, m = null, w;
|
1858
|
+
const v = new Uint16Array(de + 1), I = new Uint16Array(de + 1);
|
1861
1859
|
let ie = null, Jt, je, Ge;
|
1862
1860
|
for (s = 0; s <= de; s++)
|
1863
|
-
|
1861
|
+
v[s] = 0;
|
1864
1862
|
for (f = 0; f < i; f++)
|
1865
|
-
|
1866
|
-
for (h = u, c = de; c >= 1 &&
|
1863
|
+
v[n[t + f]]++;
|
1864
|
+
for (h = u, c = de; c >= 1 && v[c] === 0; c--)
|
1867
1865
|
;
|
1868
1866
|
if (h > c && (h = c), c === 0)
|
1869
1867
|
return a[r++] = 1 << 24 | 64 << 16 | 0, a[r++] = 1 << 24 | 64 << 16 | 0, l.bits = 1, 0;
|
1870
|
-
for (
|
1868
|
+
for (_ = 1; _ < c && v[_] === 0; _++)
|
1871
1869
|
;
|
1872
|
-
for (h <
|
1873
|
-
if (k <<= 1, k -=
|
1870
|
+
for (h < _ && (h = _), k = 1, s = 1; s <= de; s++)
|
1871
|
+
if (k <<= 1, k -= v[s], k < 0)
|
1874
1872
|
return -1;
|
1875
1873
|
if (k > 0 && (e === cn || c !== 1))
|
1876
1874
|
return -1;
|
1877
1875
|
for (I[1] = 0, s = 1; s < de; s++)
|
1878
|
-
I[s + 1] = I[s] +
|
1876
|
+
I[s + 1] = I[s] + v[s];
|
1879
1877
|
for (f = 0; f < i; f++)
|
1880
1878
|
n[t + f] !== 0 && (o[I[n[t + f]]++] = f);
|
1881
|
-
if (e === cn ? (
|
1879
|
+
if (e === cn ? (m = ie = o, w = 20) : e === gt ? (m = ja, ie = Ga, w = 257) : (m = Ya, ie = Ka, w = 0), E = 0, f = 0, s = _, b = r, d = h, g = 0, $ = -1, y = 1 << h, N = y - 1, e === gt && y > un || e === dn && y > hn)
|
1882
1880
|
return 1;
|
1883
1881
|
for (; ; ) {
|
1884
|
-
Jt = s - g, o[f] + 1 <
|
1882
|
+
Jt = s - g, o[f] + 1 < w ? (je = 0, Ge = o[f]) : o[f] >= w ? (je = ie[o[f] - w], Ge = m[o[f] - w]) : (je = 96, Ge = 0), C = 1 << s - g, p = 1 << d, _ = p;
|
1885
1883
|
do
|
1886
|
-
|
1887
|
-
while (
|
1884
|
+
p -= C, a[b + (E >> g) + p] = Jt << 24 | je << 16 | Ge | 0;
|
1885
|
+
while (p !== 0);
|
1888
1886
|
for (C = 1 << s - 1; E & C; )
|
1889
1887
|
C >>= 1;
|
1890
|
-
if (C !== 0 ? (E &= C - 1, E += C) : E = 0, f++, --
|
1888
|
+
if (C !== 0 ? (E &= C - 1, E += C) : E = 0, f++, --v[s] === 0) {
|
1891
1889
|
if (s === c)
|
1892
1890
|
break;
|
1893
1891
|
s = n[t + o[f]];
|
1894
1892
|
}
|
1895
|
-
if (s > h && (E &
|
1896
|
-
for (g === 0 && (g = h), b +=
|
1897
|
-
|
1898
|
-
if (
|
1893
|
+
if (s > h && (E & N) !== $) {
|
1894
|
+
for (g === 0 && (g = h), b += _, d = s - g, k = 1 << d; d + g < c && (k -= v[d + g], !(k <= 0)); )
|
1895
|
+
d++, k <<= 1;
|
1896
|
+
if (y += 1 << d, e === gt && y > un || e === dn && y > hn)
|
1899
1897
|
return 1;
|
1900
|
-
$ = E &
|
1898
|
+
$ = E & N, a[$] = h << 24 | d << 16 | b - r | 0;
|
1901
1899
|
}
|
1902
1900
|
}
|
1903
1901
|
return E !== 0 && (a[b + E] = s - g << 24 | 64 << 16 | 0), l.bits = h, 0;
|
@@ -1971,16 +1969,16 @@ const so = (e) => {
|
|
1971
1969
|
const r = e.state;
|
1972
1970
|
return r.window === null && (r.wsize = 1 << r.wbits, r.wnext = 0, r.whave = 0, r.window = new Uint8Array(r.wsize)), i >= r.wsize ? (r.window.set(n.subarray(t - r.wsize, t), 0), r.wnext = 0, r.whave = r.wsize) : (a = r.wsize - r.wnext, a > i && (a = i), r.window.set(n.subarray(t - i, t - i + a), r.wnext), i -= a, i ? (r.window.set(n.subarray(t - i, t), 0), r.wnext = i, r.whave = r.wsize) : (r.wnext += a, r.wnext === r.wsize && (r.wnext = 0), r.whave < r.wsize && (r.whave += a))), 0;
|
1973
1971
|
}, lo = (e, n) => {
|
1974
|
-
let t, i, a, r, o, l, u, s, f,
|
1975
|
-
const
|
1976
|
-
let
|
1972
|
+
let t, i, a, r, o, l, u, s, f, _, c, h, d, g, k = 0, y, E, C, p, $, N, b, m;
|
1973
|
+
const w = new Uint8Array(4);
|
1974
|
+
let v, I;
|
1977
1975
|
const ie = (
|
1978
1976
|
/* permutation of code lengths */
|
1979
1977
|
new Uint8Array([16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15])
|
1980
1978
|
);
|
1981
1979
|
if (he(e) || !e.output || !e.input && e.avail_in !== 0)
|
1982
1980
|
return P;
|
1983
|
-
t = e.state, t.mode === K && (t.mode = wt), o = e.next_out, a = e.output, u = e.avail_out, r = e.next_in, i = e.input, l = e.avail_in, s = t.hold, f = t.bits,
|
1981
|
+
t = e.state, t.mode === K && (t.mode = wt), o = e.next_out, a = e.output, u = e.avail_out, r = e.next_in, i = e.input, l = e.avail_in, s = t.hold, f = t.bits, _ = l, c = u, m = ue;
|
1984
1982
|
e:
|
1985
1983
|
for (; ; )
|
1986
1984
|
switch (t.mode) {
|
@@ -1995,7 +1993,7 @@ const so = (e) => {
|
|
1995
1993
|
l--, s += i[r++] << f, f += 8;
|
1996
1994
|
}
|
1997
1995
|
if (t.wrap & 2 && s === 35615) {
|
1998
|
-
t.wbits === 0 && (t.wbits = 15), t.check = 0,
|
1996
|
+
t.wbits === 0 && (t.wbits = 15), t.check = 0, w[0] = s & 255, w[1] = s >>> 8 & 255, t.check = R(t.check, w, 2, 0), s = 0, f = 0, t.mode = bn;
|
1999
1997
|
break;
|
2000
1998
|
}
|
2001
1999
|
if (t.head && (t.head.done = !1), !(t.wrap & 1) || /* check if zlib header allowed */
|
@@ -2027,21 +2025,21 @@ const so = (e) => {
|
|
2027
2025
|
e.msg = "unknown header flags set", t.mode = O;
|
2028
2026
|
break;
|
2029
2027
|
}
|
2030
|
-
t.head && (t.head.text = s >> 8 & 1), t.flags & 512 && t.wrap & 4 && (
|
2028
|
+
t.head && (t.head.text = s >> 8 & 1), t.flags & 512 && t.wrap & 4 && (w[0] = s & 255, w[1] = s >>> 8 & 255, t.check = R(t.check, w, 2, 0)), s = 0, f = 0, t.mode = gn;
|
2031
2029
|
case gn:
|
2032
2030
|
for (; f < 32; ) {
|
2033
2031
|
if (l === 0)
|
2034
2032
|
break e;
|
2035
2033
|
l--, s += i[r++] << f, f += 8;
|
2036
2034
|
}
|
2037
|
-
t.head && (t.head.time = s), t.flags & 512 && t.wrap & 4 && (
|
2035
|
+
t.head && (t.head.time = s), t.flags & 512 && t.wrap & 4 && (w[0] = s & 255, w[1] = s >>> 8 & 255, w[2] = s >>> 16 & 255, w[3] = s >>> 24 & 255, t.check = R(t.check, w, 4, 0)), s = 0, f = 0, t.mode = wn;
|
2038
2036
|
case wn:
|
2039
2037
|
for (; f < 16; ) {
|
2040
2038
|
if (l === 0)
|
2041
2039
|
break e;
|
2042
2040
|
l--, s += i[r++] << f, f += 8;
|
2043
2041
|
}
|
2044
|
-
t.head && (t.head.xflags = s & 255, t.head.os = s >> 8), t.flags & 512 && t.wrap & 4 && (
|
2042
|
+
t.head && (t.head.xflags = s & 255, t.head.os = s >> 8), t.flags & 512 && t.wrap & 4 && (w[0] = s & 255, w[1] = s >>> 8 & 255, t.check = R(t.check, w, 2, 0)), s = 0, f = 0, t.mode = mn;
|
2045
2043
|
case mn:
|
2046
2044
|
if (t.flags & 1024) {
|
2047
2045
|
for (; f < 16; ) {
|
@@ -2049,7 +2047,7 @@ const so = (e) => {
|
|
2049
2047
|
break e;
|
2050
2048
|
l--, s += i[r++] << f, f += 8;
|
2051
2049
|
}
|
2052
|
-
t.length = s, t.head && (t.head.extra_len = s), t.flags & 512 && t.wrap & 4 && (
|
2050
|
+
t.length = s, t.head && (t.head.extra_len = s), t.flags & 512 && t.wrap & 4 && (w[0] = s & 255, w[1] = s >>> 8 & 255, t.check = R(t.check, w, 2, 0)), s = 0, f = 0;
|
2053
2051
|
} else t.head && (t.head.extra = null);
|
2054
2052
|
t.mode = yn;
|
2055
2053
|
case yn:
|
@@ -2191,46 +2189,46 @@ const so = (e) => {
|
|
2191
2189
|
}
|
2192
2190
|
for (; t.have < 19; )
|
2193
2191
|
t.lens[ie[t.have++]] = 0;
|
2194
|
-
if (t.lencode = t.lendyn, t.lenbits = 7,
|
2192
|
+
if (t.lencode = t.lendyn, t.lenbits = 7, v = { bits: t.lenbits }, m = Ae(Xa, t.lens, 0, 19, t.lencode, 0, t.work, v), t.lenbits = v.bits, m) {
|
2195
2193
|
e.msg = "invalid code lengths set", t.mode = O;
|
2196
2194
|
break;
|
2197
2195
|
}
|
2198
2196
|
t.have = 0, t.mode = Tn;
|
2199
2197
|
case Tn:
|
2200
2198
|
for (; t.have < t.nlen + t.ndist; ) {
|
2201
|
-
for (; k = t.lencode[s & (1 << t.lenbits) - 1],
|
2199
|
+
for (; k = t.lencode[s & (1 << t.lenbits) - 1], y = k >>> 24, E = k >>> 16 & 255, C = k & 65535, !(y <= f); ) {
|
2202
2200
|
if (l === 0)
|
2203
2201
|
break e;
|
2204
2202
|
l--, s += i[r++] << f, f += 8;
|
2205
2203
|
}
|
2206
2204
|
if (C < 16)
|
2207
|
-
s >>>=
|
2205
|
+
s >>>= y, f -= y, t.lens[t.have++] = C;
|
2208
2206
|
else {
|
2209
2207
|
if (C === 16) {
|
2210
|
-
for (I =
|
2208
|
+
for (I = y + 2; f < I; ) {
|
2211
2209
|
if (l === 0)
|
2212
2210
|
break e;
|
2213
2211
|
l--, s += i[r++] << f, f += 8;
|
2214
2212
|
}
|
2215
|
-
if (s >>>=
|
2213
|
+
if (s >>>= y, f -= y, t.have === 0) {
|
2216
2214
|
e.msg = "invalid bit length repeat", t.mode = O;
|
2217
2215
|
break;
|
2218
2216
|
}
|
2219
2217
|
b = t.lens[t.have - 1], h = 3 + (s & 3), s >>>= 2, f -= 2;
|
2220
2218
|
} else if (C === 17) {
|
2221
|
-
for (I =
|
2219
|
+
for (I = y + 3; f < I; ) {
|
2222
2220
|
if (l === 0)
|
2223
2221
|
break e;
|
2224
2222
|
l--, s += i[r++] << f, f += 8;
|
2225
2223
|
}
|
2226
|
-
s >>>=
|
2224
|
+
s >>>= y, f -= y, b = 0, h = 3 + (s & 7), s >>>= 3, f -= 3;
|
2227
2225
|
} else {
|
2228
|
-
for (I =
|
2226
|
+
for (I = y + 7; f < I; ) {
|
2229
2227
|
if (l === 0)
|
2230
2228
|
break e;
|
2231
2229
|
l--, s += i[r++] << f, f += 8;
|
2232
2230
|
}
|
2233
|
-
s >>>=
|
2231
|
+
s >>>= y, f -= y, b = 0, h = 11 + (s & 127), s >>>= 7, f -= 7;
|
2234
2232
|
}
|
2235
2233
|
if (t.have + h > t.nlen + t.ndist) {
|
2236
2234
|
e.msg = "invalid bit length repeat", t.mode = O;
|
@@ -2246,11 +2244,11 @@ const so = (e) => {
|
|
2246
2244
|
e.msg = "invalid code -- missing end-of-block", t.mode = O;
|
2247
2245
|
break;
|
2248
2246
|
}
|
2249
|
-
if (t.lenbits = 9,
|
2247
|
+
if (t.lenbits = 9, v = { bits: t.lenbits }, m = Ae(gi, t.lens, 0, t.nlen, t.lencode, 0, t.work, v), t.lenbits = v.bits, m) {
|
2250
2248
|
e.msg = "invalid literal/lengths set", t.mode = O;
|
2251
2249
|
break;
|
2252
2250
|
}
|
2253
|
-
if (t.distbits = 6, t.distcode = t.distdyn,
|
2251
|
+
if (t.distbits = 6, t.distcode = t.distdyn, v = { bits: t.distbits }, m = Ae(wi, t.lens, t.nlen, t.ndist, t.distcode, 0, t.work, v), t.distbits = v.bits, m) {
|
2254
2252
|
e.msg = "invalid distances set", t.mode = O;
|
2255
2253
|
break;
|
2256
2254
|
}
|
@@ -2263,20 +2261,20 @@ const so = (e) => {
|
|
2263
2261
|
e.next_out = o, e.avail_out = u, e.next_in = r, e.avail_in = l, t.hold = s, t.bits = f, Ha(e, c), o = e.next_out, a = e.output, u = e.avail_out, r = e.next_in, i = e.input, l = e.avail_in, s = t.hold, f = t.bits, t.mode === K && (t.back = -1);
|
2264
2262
|
break;
|
2265
2263
|
}
|
2266
|
-
for (t.back = 0; k = t.lencode[s & (1 << t.lenbits) - 1],
|
2264
|
+
for (t.back = 0; k = t.lencode[s & (1 << t.lenbits) - 1], y = k >>> 24, E = k >>> 16 & 255, C = k & 65535, !(y <= f); ) {
|
2267
2265
|
if (l === 0)
|
2268
2266
|
break e;
|
2269
2267
|
l--, s += i[r++] << f, f += 8;
|
2270
2268
|
}
|
2271
2269
|
if (E && !(E & 240)) {
|
2272
|
-
for (
|
2270
|
+
for (p = y, $ = E, N = C; k = t.lencode[N + ((s & (1 << p + $) - 1) >> p)], y = k >>> 24, E = k >>> 16 & 255, C = k & 65535, !(p + y <= f); ) {
|
2273
2271
|
if (l === 0)
|
2274
2272
|
break e;
|
2275
2273
|
l--, s += i[r++] << f, f += 8;
|
2276
2274
|
}
|
2277
|
-
s >>>=
|
2275
|
+
s >>>= p, f -= p, t.back += p;
|
2278
2276
|
}
|
2279
|
-
if (s >>>=
|
2277
|
+
if (s >>>= y, f -= y, t.back += y, t.length = C, E === 0) {
|
2280
2278
|
t.mode = Bn;
|
2281
2279
|
break;
|
2282
2280
|
}
|
@@ -2300,20 +2298,20 @@ const so = (e) => {
|
|
2300
2298
|
}
|
2301
2299
|
t.was = t.length, t.mode = On;
|
2302
2300
|
case On:
|
2303
|
-
for (; k = t.distcode[s & (1 << t.distbits) - 1],
|
2301
|
+
for (; k = t.distcode[s & (1 << t.distbits) - 1], y = k >>> 24, E = k >>> 16 & 255, C = k & 65535, !(y <= f); ) {
|
2304
2302
|
if (l === 0)
|
2305
2303
|
break e;
|
2306
2304
|
l--, s += i[r++] << f, f += 8;
|
2307
2305
|
}
|
2308
2306
|
if (!(E & 240)) {
|
2309
|
-
for (
|
2307
|
+
for (p = y, $ = E, N = C; k = t.distcode[N + ((s & (1 << p + $) - 1) >> p)], y = k >>> 24, E = k >>> 16 & 255, C = k & 65535, !(p + y <= f); ) {
|
2310
2308
|
if (l === 0)
|
2311
2309
|
break e;
|
2312
2310
|
l--, s += i[r++] << f, f += 8;
|
2313
2311
|
}
|
2314
|
-
s >>>=
|
2312
|
+
s >>>= p, f -= p, t.back += p;
|
2315
2313
|
}
|
2316
|
-
if (s >>>=
|
2314
|
+
if (s >>>= y, f -= y, t.back += y, E & 64) {
|
2317
2315
|
e.msg = "invalid distance code", t.mode = O;
|
2318
2316
|
break;
|
2319
2317
|
}
|
@@ -2340,12 +2338,12 @@ const so = (e) => {
|
|
2340
2338
|
e.msg = "invalid distance too far back", t.mode = O;
|
2341
2339
|
break;
|
2342
2340
|
}
|
2343
|
-
h > t.wnext ? (h -= t.wnext,
|
2341
|
+
h > t.wnext ? (h -= t.wnext, d = t.wsize - h) : d = t.wnext - h, h > t.length && (h = t.length), g = t.window;
|
2344
2342
|
} else
|
2345
|
-
g = a,
|
2343
|
+
g = a, d = o - t.offset, h = t.length;
|
2346
2344
|
h > u && (h = u), u -= h, t.length -= h;
|
2347
2345
|
do
|
2348
|
-
a[o++] = g[
|
2346
|
+
a[o++] = g[d++];
|
2349
2347
|
while (--h);
|
2350
2348
|
t.length === 0 && (t.mode = Qe);
|
2351
2349
|
break;
|
@@ -2384,10 +2382,10 @@ const so = (e) => {
|
|
2384
2382
|
}
|
2385
2383
|
t.mode = Dn;
|
2386
2384
|
case Dn:
|
2387
|
-
|
2385
|
+
m = Ja;
|
2388
2386
|
break e;
|
2389
2387
|
case O:
|
2390
|
-
|
2388
|
+
m = mi;
|
2391
2389
|
break e;
|
2392
2390
|
case vi:
|
2393
2391
|
return yi;
|
@@ -2395,8 +2393,8 @@ const so = (e) => {
|
|
2395
2393
|
default:
|
2396
2394
|
return P;
|
2397
2395
|
}
|
2398
|
-
return e.next_out = o, e.avail_out = u, e.next_in = r, e.avail_in = l, t.hold = s, t.bits = f, (t.wsize || c !== e.avail_out && t.mode < O && (t.mode < yt || n !== pn)) && Ni(e, e.output, e.next_out, c - e.avail_out),
|
2399
|
-
t.flags ? R(t.check, a, c, e.next_out - c) : Ue(t.check, a, c, e.next_out - c)), e.data_type = t.bits + (t.last ? 64 : 0) + (t.mode === K ? 128 : 0) + (t.mode === Je || t.mode === mt ? 256 : 0), (
|
2396
|
+
return e.next_out = o, e.avail_out = u, e.next_in = r, e.avail_in = l, t.hold = s, t.bits = f, (t.wsize || c !== e.avail_out && t.mode < O && (t.mode < yt || n !== pn)) && Ni(e, e.output, e.next_out, c - e.avail_out), _ -= e.avail_in, c -= e.avail_out, e.total_in += _, e.total_out += c, t.total += c, t.wrap & 4 && c && (e.adler = t.check = /*UPDATE_CHECK(state.check, strm.next_out - _out, _out);*/
|
2397
|
+
t.flags ? R(t.check, a, c, e.next_out - c) : Ue(t.check, a, c, e.next_out - c)), e.data_type = t.bits + (t.last ? 64 : 0) + (t.mode === K ? 128 : 0) + (t.mode === Je || t.mode === mt ? 256 : 0), (_ === 0 && c === 0 || n === pn) && m === ue && (m = eo), m;
|
2400
2398
|
}, fo = (e) => {
|
2401
2399
|
if (he(e))
|
2402
2400
|
return P;
|
@@ -2539,36 +2537,36 @@ function Ct(e, n, t, i) {
|
|
2539
2537
|
return e < i && n >= t;
|
2540
2538
|
}
|
2541
2539
|
function Ho(e) {
|
2542
|
-
const n = e ? "big" : "little", t = new
|
2540
|
+
const n = e ? "big" : "little", t = new S().endianess(n).uint32("chromId").uint32("start").uint32("end").uint32("validCnt").floatle("minScore").floatle("maxScore").floatle("sumData").floatle("sumSqData").saveOffset("offset"), i = new S().endianess(n).uint8("isLeaf").skip(1).uint16("cnt").choice({
|
2543
2541
|
tag: "isLeaf",
|
2544
2542
|
choices: {
|
2545
|
-
1: new
|
2543
|
+
1: new S().endianess(n).array("blocksToFetch", {
|
2546
2544
|
length: "cnt",
|
2547
|
-
type: new
|
2545
|
+
type: new S().endianess(n).uint32("startChrom").uint32("startBase").uint32("endChrom").uint32("endBase").uint64("blockOffset").uint64("blockSize").saveOffset("offset")
|
2548
2546
|
}),
|
2549
|
-
0: new
|
2547
|
+
0: new S().array("recurOffsets", {
|
2550
2548
|
length: "cnt",
|
2551
|
-
type: new
|
2549
|
+
type: new S().endianess(n).uint32("startChrom").uint32("startBase").uint32("endChrom").uint32("endBase").uint64("blockOffset").saveOffset("offset")
|
2552
2550
|
})
|
2553
2551
|
}
|
2554
|
-
}), a = new
|
2552
|
+
}), a = new S().endianess(n).uint32("chromId").int32("start").int32("end").string("rest", {
|
2555
2553
|
zeroTerminated: !0
|
2556
2554
|
}).saveOffset("offset");
|
2557
2555
|
return {
|
2558
|
-
bigWigParser: new
|
2556
|
+
bigWigParser: new S().endianess(n).skip(4).int32("blockStart").skip(4).uint32("itemStep").uint32("itemSpan").uint8("blockType").skip(1).uint16("itemCount").choice({
|
2559
2557
|
tag: "blockType",
|
2560
2558
|
choices: {
|
2561
|
-
[Mo]: new
|
2559
|
+
[Mo]: new S().array("items", {
|
2562
2560
|
length: "itemCount",
|
2563
|
-
type: new
|
2561
|
+
type: new S().floatle("score")
|
2564
2562
|
}),
|
2565
|
-
[xo]: new
|
2563
|
+
[xo]: new S().array("items", {
|
2566
2564
|
length: "itemCount",
|
2567
|
-
type: new
|
2565
|
+
type: new S().endianess(n).int32("start").floatle("score")
|
2568
2566
|
}),
|
2569
|
-
[Zo]: new
|
2567
|
+
[Zo]: new S().array("items", {
|
2570
2568
|
length: "itemCount",
|
2571
|
-
type: new
|
2569
|
+
type: new S().endianess(n).int32("start").int32("end").floatle("score")
|
2572
2570
|
})
|
2573
2571
|
}
|
2574
2572
|
}),
|
@@ -2582,7 +2580,7 @@ class Ti {
|
|
2582
2580
|
if (this.bbi = n, this.refsByName = t, this.cirTreeOffset = i, this.isBigEndian = a, this.isCompressed = r, this.blockType = o, this.featureCache = new Gn({
|
2583
2581
|
cache: new Yn({ maxSize: 1e3 }),
|
2584
2582
|
fill: async (u, s) => {
|
2585
|
-
const f = Number(u.length),
|
2583
|
+
const f = Number(u.length), _ = Number(u.offset), { buffer: c } = await this.bbi.read(J.Buffer.alloc(f), 0, f, _, {
|
2586
2584
|
signal: s
|
2587
2585
|
});
|
2588
2586
|
return c;
|
@@ -2596,53 +2594,53 @@ class Ti {
|
|
2596
2594
|
try {
|
2597
2595
|
const { refsByName: o, bbi: l, cirTreeOffset: u, isBigEndian: s } = this, f = o[n];
|
2598
2596
|
f === void 0 && a.complete();
|
2599
|
-
const
|
2597
|
+
const _ = { chrId: f, start: t, end: i };
|
2600
2598
|
this.cirTreePromise || (this.cirTreePromise = l.read(J.Buffer.alloc(48), 0, 48, Number(u), r));
|
2601
2599
|
const { buffer: c } = await this.cirTreePromise, h = s ? c.readUInt32BE(4) : c.readUInt32LE(4);
|
2602
|
-
let
|
2603
|
-
const k = (
|
2600
|
+
let d = [], g = 0;
|
2601
|
+
const k = (p, $, N) => {
|
2604
2602
|
try {
|
2605
|
-
const b =
|
2606
|
-
if (
|
2607
|
-
offset:
|
2608
|
-
length:
|
2609
|
-
})))),
|
2610
|
-
const
|
2611
|
-
|
2603
|
+
const b = p.subarray($), m = this.leafParser.parse(b);
|
2604
|
+
if (m.blocksToFetch && (d = d.concat(m.blocksToFetch.filter((w) => y(w)).map((w) => ({
|
2605
|
+
offset: w.blockOffset,
|
2606
|
+
length: w.blockSize
|
2607
|
+
})))), m.recurOffsets) {
|
2608
|
+
const w = m.recurOffsets.filter((v) => y(v)).map((v) => Number(v.blockOffset));
|
2609
|
+
w.length > 0 && C(w, N + 1);
|
2612
2610
|
}
|
2613
2611
|
} catch (b) {
|
2614
2612
|
a.error(b);
|
2615
2613
|
}
|
2616
|
-
},
|
2617
|
-
const { startChrom: $, startBase:
|
2618
|
-
return ($ < f || $ === f &&
|
2619
|
-
}, E = async (
|
2614
|
+
}, y = (p) => {
|
2615
|
+
const { startChrom: $, startBase: N, endChrom: b, endBase: m } = p;
|
2616
|
+
return ($ < f || $ === f && N <= i) && (b > f || b === f && m >= t);
|
2617
|
+
}, E = async (p, $, N) => {
|
2620
2618
|
try {
|
2621
|
-
const b = $.max - $.min,
|
2622
|
-
for (const
|
2623
|
-
$.contains(
|
2619
|
+
const b = $.max - $.min, m = $.min, w = await this.featureCache.get(`${b}_${m}`, { length: b, offset: m }, r == null ? void 0 : r.signal);
|
2620
|
+
for (const v of p)
|
2621
|
+
$.contains(v) && (k(w, v - m, N), g -= 1, g === 0 && this.readFeatures(a, d, {
|
2624
2622
|
...r,
|
2625
|
-
request:
|
2623
|
+
request: _
|
2626
2624
|
}).catch((I) => a.error(I)));
|
2627
2625
|
} catch (b) {
|
2628
2626
|
a.error(b);
|
2629
2627
|
}
|
2630
|
-
}, C = (
|
2628
|
+
}, C = (p, $) => {
|
2631
2629
|
try {
|
2632
|
-
g +=
|
2633
|
-
const
|
2630
|
+
g += p.length;
|
2631
|
+
const N = 4 + Number(h) * 32;
|
2634
2632
|
let b = new pe([
|
2635
|
-
{ min:
|
2633
|
+
{ min: p[0], max: p[0] + N }
|
2636
2634
|
]);
|
2637
|
-
for (let
|
2638
|
-
const
|
2639
|
-
{ min:
|
2635
|
+
for (let m = 1; m < p.length; m += 1) {
|
2636
|
+
const w = new pe([
|
2637
|
+
{ min: p[m], max: p[m] + N }
|
2640
2638
|
]);
|
2641
|
-
b = b.union(
|
2639
|
+
b = b.union(w);
|
2642
2640
|
}
|
2643
|
-
b.getRanges().map((
|
2644
|
-
} catch (
|
2645
|
-
a.error(
|
2641
|
+
b.getRanges().map((m) => E(p, m, $));
|
2642
|
+
} catch (N) {
|
2643
|
+
a.error(N);
|
2646
2644
|
}
|
2647
2645
|
};
|
2648
2646
|
return C([Number(u) + 48], 1);
|
@@ -2663,7 +2661,7 @@ class Ti {
|
|
2663
2661
|
r += 4;
|
2664
2662
|
const f = o.getUint32(r, !0);
|
2665
2663
|
r += 4;
|
2666
|
-
const
|
2664
|
+
const _ = o.getFloat32(r, !0);
|
2667
2665
|
r += 4;
|
2668
2666
|
const c = o.getFloat32(r, !0);
|
2669
2667
|
r += 4;
|
@@ -2672,7 +2670,7 @@ class Ti {
|
|
2672
2670
|
start: u,
|
2673
2671
|
end: s,
|
2674
2672
|
maxScore: c,
|
2675
|
-
minScore:
|
2673
|
+
minScore: _,
|
2676
2674
|
summary: !0,
|
2677
2675
|
score: h / (f || 1)
|
2678
2676
|
});
|
@@ -2700,36 +2698,36 @@ class Ti {
|
|
2700
2698
|
o += 4;
|
2701
2699
|
const f = r.getUint8(o);
|
2702
2700
|
o += 2;
|
2703
|
-
const
|
2701
|
+
const _ = r.getUint16(o, !0);
|
2704
2702
|
o += 2;
|
2705
|
-
const c = new Array(
|
2703
|
+
const c = new Array(_);
|
2706
2704
|
switch (f) {
|
2707
2705
|
case 1: {
|
2708
|
-
for (let h = 0; h <
|
2709
|
-
const
|
2706
|
+
for (let h = 0; h < _; h++) {
|
2707
|
+
const d = r.getInt32(o, !0);
|
2710
2708
|
o += 4;
|
2711
2709
|
const g = r.getInt32(o, !0);
|
2712
2710
|
o += 4;
|
2713
2711
|
const k = r.getFloat32(o, !0);
|
2714
|
-
o += 4, c[h] = { start:
|
2712
|
+
o += 4, c[h] = { start: d, end: g, score: k };
|
2715
2713
|
}
|
2716
2714
|
break;
|
2717
2715
|
}
|
2718
2716
|
case 2: {
|
2719
|
-
for (let h = 0; h <
|
2720
|
-
const
|
2717
|
+
for (let h = 0; h < _; h++) {
|
2718
|
+
const d = r.getInt32(o, !0);
|
2721
2719
|
o += 4;
|
2722
2720
|
const g = r.getFloat32(o, !0);
|
2723
|
-
o += 4, c[h] = { score: g, start:
|
2721
|
+
o += 4, c[h] = { score: g, start: d, end: d + s };
|
2724
2722
|
}
|
2725
2723
|
break;
|
2726
2724
|
}
|
2727
2725
|
case 3: {
|
2728
|
-
for (let h = 0; h <
|
2729
|
-
const
|
2726
|
+
for (let h = 0; h < _; h++) {
|
2727
|
+
const d = r.getFloat32(o, !0);
|
2730
2728
|
o += 4;
|
2731
2729
|
const g = l + h * u;
|
2732
|
-
c[h] = { score:
|
2730
|
+
c[h] = { score: d, start: g, end: g + s };
|
2733
2731
|
}
|
2734
2732
|
break;
|
2735
2733
|
}
|
@@ -2741,21 +2739,21 @@ class Ti {
|
|
2741
2739
|
const { blockType: a, isCompressed: r } = this, { signal: o, request: l } = i, u = Po(t);
|
2742
2740
|
et(o), await Promise.all(u.map(async (s) => {
|
2743
2741
|
et(o);
|
2744
|
-
const { length: f, offset:
|
2742
|
+
const { length: f, offset: _ } = s, c = await this.featureCache.get(`${f}_${_}`, s, o);
|
2745
2743
|
for (const h of s.blocks) {
|
2746
2744
|
et(o);
|
2747
|
-
let
|
2748
|
-
switch (r && (g = Fo(c.subarray(
|
2745
|
+
let d = Number(h.offset) - Number(s.offset), g = c;
|
2746
|
+
switch (r && (g = Fo(c.subarray(d)), d = 0), et(o), a) {
|
2749
2747
|
case "summary": {
|
2750
|
-
n.next(this.parseSummaryBlock(g,
|
2748
|
+
n.next(this.parseSummaryBlock(g, d, l));
|
2751
2749
|
break;
|
2752
2750
|
}
|
2753
2751
|
case "bigwig": {
|
2754
|
-
n.next(this.parseBigWigBlock(g,
|
2752
|
+
n.next(this.parseBigWigBlock(g, d, l));
|
2755
2753
|
break;
|
2756
2754
|
}
|
2757
2755
|
case "bigbed": {
|
2758
|
-
n.next(this.parseBigBedBlock(g,
|
2756
|
+
n.next(this.parseBigBedBlock(g, d, Number(h.offset) * 256, l));
|
2759
2757
|
break;
|
2760
2758
|
}
|
2761
2759
|
default:
|
@@ -2794,15 +2792,15 @@ function jo(e, n, t, i) {
|
|
2794
2792
|
function l(f) {
|
2795
2793
|
try {
|
2796
2794
|
s(i.next(f));
|
2797
|
-
} catch (
|
2798
|
-
o(
|
2795
|
+
} catch (_) {
|
2796
|
+
o(_);
|
2799
2797
|
}
|
2800
2798
|
}
|
2801
2799
|
function u(f) {
|
2802
2800
|
try {
|
2803
2801
|
s(i.throw(f));
|
2804
|
-
} catch (
|
2805
|
-
o(
|
2802
|
+
} catch (_) {
|
2803
|
+
o(_);
|
2806
2804
|
}
|
2807
2805
|
}
|
2808
2806
|
function s(f) {
|
@@ -2815,8 +2813,8 @@ function Ai(e, n) {
|
|
2815
2813
|
var t = { label: 0, sent: function() {
|
2816
2814
|
if (r[0] & 1) throw r[1];
|
2817
2815
|
return r[1];
|
2818
|
-
}, trys: [], ops: [] }, i, a, r, o;
|
2819
|
-
return o =
|
2816
|
+
}, trys: [], ops: [] }, i, a, r, o = Object.create((typeof Iterator == "function" ? Iterator : Object).prototype);
|
2817
|
+
return o.next = l(0), o.throw = l(1), o.return = l(2), typeof Symbol == "function" && (o[Symbol.iterator] = function() {
|
2820
2818
|
return this;
|
2821
2819
|
}), o;
|
2822
2820
|
function l(s) {
|
@@ -2909,34 +2907,39 @@ function be(e) {
|
|
2909
2907
|
function Go(e, n, t) {
|
2910
2908
|
if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
|
2911
2909
|
var i = t.apply(e, n || []), a, r = [];
|
2912
|
-
return a =
|
2910
|
+
return a = Object.create((typeof AsyncIterator == "function" ? AsyncIterator : Object).prototype), l("next"), l("throw"), l("return", o), a[Symbol.asyncIterator] = function() {
|
2913
2911
|
return this;
|
2914
2912
|
}, a;
|
2915
|
-
function o(
|
2916
|
-
|
2917
|
-
return
|
2918
|
-
|
2913
|
+
function o(h) {
|
2914
|
+
return function(d) {
|
2915
|
+
return Promise.resolve(d).then(h, _);
|
2916
|
+
};
|
2917
|
+
}
|
2918
|
+
function l(h, d) {
|
2919
|
+
i[h] && (a[h] = function(g) {
|
2920
|
+
return new Promise(function(k, y) {
|
2921
|
+
r.push([h, g, k, y]) > 1 || u(h, g);
|
2919
2922
|
});
|
2920
|
-
});
|
2923
|
+
}, d && (a[h] = d(a[h])));
|
2921
2924
|
}
|
2922
|
-
function
|
2925
|
+
function u(h, d) {
|
2923
2926
|
try {
|
2924
|
-
|
2925
|
-
} catch (
|
2926
|
-
|
2927
|
+
s(i[h](d));
|
2928
|
+
} catch (g) {
|
2929
|
+
c(r[0][3], g);
|
2927
2930
|
}
|
2928
2931
|
}
|
2929
|
-
function
|
2930
|
-
|
2932
|
+
function s(h) {
|
2933
|
+
h.value instanceof be ? Promise.resolve(h.value.v).then(f, _) : c(r[0][2], h);
|
2931
2934
|
}
|
2932
|
-
function
|
2933
|
-
|
2935
|
+
function f(h) {
|
2936
|
+
u("next", h);
|
2934
2937
|
}
|
2935
|
-
function
|
2936
|
-
|
2938
|
+
function _(h) {
|
2939
|
+
u("throw", h);
|
2937
2940
|
}
|
2938
|
-
function
|
2939
|
-
|
2941
|
+
function c(h, d) {
|
2942
|
+
h(d), r.shift(), r.length && u(r[0][0], r[0][1]);
|
2940
2943
|
}
|
2941
2944
|
}
|
2942
2945
|
function Yo(e) {
|
@@ -3016,14 +3019,14 @@ var Wt = function() {
|
|
3016
3019
|
} catch (g) {
|
3017
3020
|
r = g instanceof St ? g.errors : [g];
|
3018
3021
|
}
|
3019
|
-
var
|
3020
|
-
if (
|
3022
|
+
var _ = this._finalizers;
|
3023
|
+
if (_) {
|
3021
3024
|
this._finalizers = null;
|
3022
3025
|
try {
|
3023
|
-
for (var c = Le(
|
3024
|
-
var
|
3026
|
+
for (var c = Le(_), h = c.next(); !h.done; h = c.next()) {
|
3027
|
+
var d = h.value;
|
3025
3028
|
try {
|
3026
|
-
Zn(
|
3029
|
+
Zn(d);
|
3027
3030
|
} catch (g) {
|
3028
3031
|
r = r ?? [], g instanceof St ? r = Pt(Pt([], Lt(r)), Lt(g.errors)) : r.push(g);
|
3029
3032
|
}
|
@@ -3657,26 +3660,26 @@ function Ji(e, n) {
|
|
3657
3660
|
});
|
3658
3661
|
}
|
3659
3662
|
function $s(e, n, t, i, a, r, o, l) {
|
3660
|
-
var u = [], s = 0, f = 0,
|
3661
|
-
|
3663
|
+
var u = [], s = 0, f = 0, _ = !1, c = function() {
|
3664
|
+
_ && !u.length && !s && n.complete();
|
3662
3665
|
}, h = function(g) {
|
3663
|
-
return s < i ?
|
3664
|
-
},
|
3666
|
+
return s < i ? d(g) : u.push(g);
|
3667
|
+
}, d = function(g) {
|
3665
3668
|
s++;
|
3666
3669
|
var k = !1;
|
3667
|
-
Ee(t(g, f++)).subscribe(Pe(n, function(
|
3668
|
-
n.next(
|
3670
|
+
Ee(t(g, f++)).subscribe(Pe(n, function(y) {
|
3671
|
+
n.next(y);
|
3669
3672
|
}, function() {
|
3670
3673
|
k = !0;
|
3671
3674
|
}, void 0, function() {
|
3672
3675
|
if (k)
|
3673
3676
|
try {
|
3674
3677
|
s--;
|
3675
|
-
for (var
|
3678
|
+
for (var y = function() {
|
3676
3679
|
var E = u.shift();
|
3677
|
-
o ||
|
3680
|
+
o || d(E);
|
3678
3681
|
}; u.length && s < i; )
|
3679
|
-
|
3682
|
+
y();
|
3680
3683
|
c();
|
3681
3684
|
} catch (E) {
|
3682
3685
|
n.error(E);
|
@@ -3684,7 +3687,7 @@ function $s(e, n, t, i, a, r, o, l) {
|
|
3684
3687
|
}));
|
3685
3688
|
};
|
3686
3689
|
return e.subscribe(Pe(n, h, function() {
|
3687
|
-
|
3690
|
+
_ = !0, c();
|
3688
3691
|
})), function() {
|
3689
3692
|
};
|
3690
3693
|
}
|
@@ -3710,8 +3713,8 @@ function Ss(e, n, t, i, a) {
|
|
3710
3713
|
return function(r, o) {
|
3711
3714
|
var l = t, u = n, s = 0;
|
3712
3715
|
r.subscribe(Pe(o, function(f) {
|
3713
|
-
var
|
3714
|
-
u = l ? e(u, f,
|
3716
|
+
var _ = s++;
|
3717
|
+
u = l ? e(u, f, _) : (l = !0, f);
|
3715
3718
|
}, function() {
|
3716
3719
|
l && o.next(u), o.complete();
|
3717
3720
|
}));
|
@@ -3733,10 +3736,10 @@ function Ts(e) {
|
|
3733
3736
|
return new TextDecoder().decode(e);
|
3734
3737
|
}
|
3735
3738
|
function jn(e) {
|
3736
|
-
const n = e ? "big" : "little", t = new
|
3739
|
+
const n = e ? "big" : "little", t = new S().endianess(n).int32("magic").uint16("version").uint16("numZoomLevels").uint64("chromTreeOffset").uint64("unzoomedDataOffset").uint64("unzoomedIndexOffset").uint16("fieldCount").uint16("definedFieldCount").uint64("asOffset").uint64("totalSummaryOffset").uint32("uncompressBufSize").uint64("extHeaderOffset").array("zoomLevels", {
|
3737
3740
|
length: "numZoomLevels",
|
3738
|
-
type: new
|
3739
|
-
}), i = new
|
3741
|
+
type: new S().endianess(n).uint32("reductionLevel").uint32("reserved").uint64("dataOffset").uint64("indexOffset")
|
3742
|
+
}), i = new S().endianess(n).uint64("basesCovered").doublele("scoreMin").doublele("scoreMax").doublele("scoreSum").doublele("scoreSumSquares"), a = new S().endianess(n).uint32("magic").uint32("blockSize").uint32("keySize").uint32("valSize").uint64("itemCount"), r = new S().endianess(n).uint8("isLeafNode").skip(1).uint16("cnt").saveOffset("offset");
|
3740
3743
|
return {
|
3741
3744
|
chromTreeParser: a,
|
3742
3745
|
totalSummaryParser: i,
|
@@ -3745,10 +3748,6 @@ function jn(e) {
|
|
3745
3748
|
};
|
3746
3749
|
}
|
3747
3750
|
class tr {
|
3748
|
-
/* fetch and parse header information from a bigwig or bigbed file
|
3749
|
-
* @param abortSignal - abort the operation, can be null
|
3750
|
-
* @return a Header object
|
3751
|
-
*/
|
3752
3751
|
getHeader(n) {
|
3753
3752
|
return this.headerP || (this.headerP = this._getHeader(n).catch((t) => {
|
3754
3753
|
throw this.headerP = void 0, t;
|
@@ -3790,8 +3789,8 @@ class tr {
|
|
3790
3789
|
if (o.totalSummaryOffset > t - 8 * 5)
|
3791
3790
|
return this._getMainHeader(n, t * 2);
|
3792
3791
|
if (o.totalSummaryOffset) {
|
3793
|
-
const f = i.subarray(Number(o.totalSummaryOffset)),
|
3794
|
-
o.totalSummary = { ...
|
3792
|
+
const f = i.subarray(Number(o.totalSummaryOffset)), _ = r.totalSummaryParser.parse(f);
|
3793
|
+
o.totalSummary = { ..._, basesCovered: Number(_.basesCovered) };
|
3795
3794
|
}
|
3796
3795
|
return { ...o, isBigEndian: a };
|
3797
3796
|
}
|
@@ -3810,25 +3809,25 @@ class tr {
|
|
3810
3809
|
const u = Number(n.chromTreeOffset);
|
3811
3810
|
for (; l % 4 !== 0; )
|
3812
3811
|
l += 1;
|
3813
|
-
const s = l - u, { buffer: f } = await this.bbi.read(J.Buffer.alloc(s), 0, s, Number(u), t),
|
3814
|
-
let E =
|
3812
|
+
const s = l - u, { buffer: f } = await this.bbi.read(J.Buffer.alloc(s), 0, s, Number(u), t), _ = jn(i), { keySize: c } = _.chromTreeParser.parse(f), h = new S().endianess(a).string("key", { stripNull: !0, length: c }).uint32("refId").uint32("refSize").saveOffset("offset"), d = new S().endianess(a).skip(c).uint64("childOffset").saveOffset("offset"), g = 32, k = async (y) => {
|
3813
|
+
let E = y;
|
3815
3814
|
if (E >= f.length)
|
3816
3815
|
throw new Error("reading beyond end of buffer");
|
3817
|
-
const C =
|
3818
|
-
if (E += C.offset,
|
3819
|
-
for (let
|
3816
|
+
const C = _.isLeafNode.parse(f.subarray(E)), { isLeafNode: p, cnt: $ } = C;
|
3817
|
+
if (E += C.offset, p)
|
3818
|
+
for (let N = 0; N < $; N += 1) {
|
3820
3819
|
const b = h.parse(f.subarray(E));
|
3821
3820
|
E += b.offset;
|
3822
|
-
const { key:
|
3823
|
-
o[this.renameRefSeqs(
|
3821
|
+
const { key: m, refId: w, refSize: v } = b, I = { name: m, id: w, length: v };
|
3822
|
+
o[this.renameRefSeqs(m)] = w, r[w] = I;
|
3824
3823
|
}
|
3825
3824
|
else {
|
3826
|
-
const
|
3825
|
+
const N = [];
|
3827
3826
|
for (let b = 0; b < $; b += 1) {
|
3828
|
-
const
|
3829
|
-
E +=
|
3827
|
+
const m = d.parse(f.subarray(E)), { childOffset: w } = m;
|
3828
|
+
E += m.offset, N.push(k(Number(w) - Number(u)));
|
3830
3829
|
}
|
3831
|
-
await Promise.all(
|
3830
|
+
await Promise.all(N);
|
3832
3831
|
}
|
3833
3832
|
};
|
3834
3833
|
return await k(g), {
|
@@ -3858,7 +3857,7 @@ class tr {
|
|
3858
3857
|
let o;
|
3859
3858
|
const { basesPerSpan: l, scale: u } = a || {};
|
3860
3859
|
return l ? o = await this.getView(1 / l, a) : u ? o = await this.getView(u, a) : o = await this.getView(1, a), new Z((s) => {
|
3861
|
-
o.readWigData(r, t, i, s, a);
|
3860
|
+
o.readWigData(r, t, i, s, a).catch((f) => s.error(f));
|
3862
3861
|
});
|
3863
3862
|
}
|
3864
3863
|
async getFeatures(n, t, i, a) {
|
@@ -3871,16 +3870,18 @@ class Fs extends tr {
|
|
3871
3870
|
* Retrieves a BlockView of a specific zoomLevel
|
3872
3871
|
*
|
3873
3872
|
* @param scale - number
|
3874
|
-
*
|
3873
|
+
*
|
3874
|
+
* @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
|
3875
|
+
* or scale used to infer the zoomLevel to use
|
3875
3876
|
*/
|
3876
3877
|
async getView(n, t) {
|
3877
3878
|
const { zoomLevels: i, refsByName: a, fileSize: r, isBigEndian: o, uncompressBufSize: l } = await this.getHeader(t), u = 1 / n;
|
3878
3879
|
let s = i.length;
|
3879
3880
|
r || (s -= 1);
|
3880
3881
|
for (let f = s; f >= 0; f -= 1) {
|
3881
|
-
const
|
3882
|
-
if (
|
3883
|
-
const c = Number(
|
3882
|
+
const _ = i[f];
|
3883
|
+
if (_ && _.reductionLevel <= 2 * u) {
|
3884
|
+
const c = Number(_.indexOffset);
|
3884
3885
|
return new Ti(this.bbi, a, c, o, l > 0, "summary");
|
3885
3886
|
}
|
3886
3887
|
}
|
@@ -3913,12 +3914,12 @@ class Ls extends tr {
|
|
3913
3914
|
* @return a Promise for an array of Index data structure since there can be multiple extraIndexes in a bigbed, see bedToBigBed documentation
|
3914
3915
|
*/
|
3915
3916
|
async _readIndices(n) {
|
3916
|
-
const { extHeaderOffset: t, isBigEndian: i } = await this.getHeader(n), { buffer: a } = await this.bbi.read(J.Buffer.alloc(64), 0, 64, Number(t)), r = i ? "big" : "little", o = new
|
3917
|
+
const { extHeaderOffset: t, isBigEndian: i } = await this.getHeader(n), { buffer: a } = await this.bbi.read(J.Buffer.alloc(64), 0, 64, Number(t)), r = i ? "big" : "little", o = new S().endianess(r).uint16("size").uint16("count").uint64("offset").parse(a), { count: l, offset: u } = o;
|
3917
3918
|
if (l === 0)
|
3918
3919
|
return [];
|
3919
|
-
const s = 20, f = s * l, { buffer:
|
3920
|
-
for (let
|
3921
|
-
h.push(c.parse(
|
3920
|
+
const s = 20, f = s * l, { buffer: _ } = await this.bbi.read(J.Buffer.alloc(f), 0, f, Number(u)), c = new S().endianess(r).int16("type").int16("fieldcount").uint64("offset").skip(4).int16("field"), h = [];
|
3921
|
+
for (let d = 0; d < l; d += 1)
|
3922
|
+
h.push(c.parse(_.subarray(d * s)));
|
3922
3923
|
return h;
|
3923
3924
|
}
|
3924
3925
|
/*
|
@@ -3934,41 +3935,41 @@ class Ls extends tr {
|
|
3934
3935
|
if (a.length === 0)
|
3935
3936
|
return [];
|
3936
3937
|
const r = a.map(async (o) => {
|
3937
|
-
const { offset: l, field: u } = o, { buffer: s } = await this.bbi.read(J.Buffer.alloc(32), 0, 32, Number(l), t), f = i ? "big" : "little",
|
3938
|
+
const { offset: l, field: u } = o, { buffer: s } = await this.bbi.read(J.Buffer.alloc(32), 0, 32, Number(l), t), f = i ? "big" : "little", _ = new S().endianess(f).int32("magic").int32("blockSize").int32("keySize").int32("valSize").uint64("itemCount"), { blockSize: c, keySize: h, valSize: d } = _.parse(s), g = new S().endianess(f).int8("nodeType").skip(1).int16("cnt").choice({
|
3938
3939
|
tag: "nodeType",
|
3939
3940
|
choices: {
|
3940
|
-
0: new
|
3941
|
+
0: new S().array("leafkeys", {
|
3941
3942
|
length: "cnt",
|
3942
|
-
type: new
|
3943
|
+
type: new S().endianess(f).string("key", { length: h, stripNull: !0 }).uint64("offset")
|
3943
3944
|
}),
|
3944
|
-
1: new
|
3945
|
+
1: new S().array("keys", {
|
3945
3946
|
length: "cnt",
|
3946
|
-
type: new
|
3947
|
+
type: new S().endianess(f).string("key", { length: h, stripNull: !0 }).uint64("offset").uint32("length").uint32("reserved")
|
3947
3948
|
})
|
3948
3949
|
}
|
3949
3950
|
}), k = async (E) => {
|
3950
|
-
const C = Number(E),
|
3951
|
-
if (
|
3951
|
+
const C = Number(E), p = 4 + c * (h + d), { buffer: $ } = await this.bbi.read(J.Buffer.alloc(p), 0, p, C, t), N = g.parse($);
|
3952
|
+
if (N.leafkeys) {
|
3952
3953
|
let b;
|
3953
|
-
for (
|
3954
|
-
const { key: m } = S.leafkeys[w];
|
3954
|
+
for (const { key: m, offset: w } of N.leafkeys) {
|
3955
3955
|
if (n.localeCompare(m) < 0 && b)
|
3956
3956
|
return k(b);
|
3957
|
-
b =
|
3957
|
+
b = w;
|
3958
3958
|
}
|
3959
3959
|
return k(b);
|
3960
3960
|
}
|
3961
|
-
for (
|
3962
|
-
if (
|
3963
|
-
return { ...
|
3961
|
+
for (const b of N.keys)
|
3962
|
+
if (b.key === n)
|
3963
|
+
return { ...b, field: u };
|
3964
3964
|
};
|
3965
3965
|
return k(Number(l) + 32);
|
3966
3966
|
});
|
3967
3967
|
return As(await Promise.all(r));
|
3968
3968
|
}
|
3969
3969
|
/*
|
3970
|
-
* retrieve the features from the bigbed data that were found through the
|
3971
|
-
* note that there can be multiple extraIndex, see
|
3970
|
+
* retrieve the features from the bigbed data that were found through the
|
3971
|
+
* lookup of the extraIndex note that there can be multiple extraIndex, see
|
3972
|
+
* the BigBed specification and the -extraIndex argument to bedToBigBed
|
3972
3973
|
*
|
3973
3974
|
* @param name - the name to search for
|
3974
3975
|
* @param opts - a SearchOptions argument with optional signal
|
@@ -3979,7 +3980,7 @@ class Ls extends tr {
|
|
3979
3980
|
if (i.length === 0)
|
3980
3981
|
return [];
|
3981
3982
|
const a = await this.getUnzoomedView(t), r = i.map((l) => new Z((u) => {
|
3982
|
-
a.readFeatures(u, [l], t);
|
3983
|
+
a.readFeatures(u, [l], t).catch((s) => u.error(s));
|
3983
3984
|
}).pipe(er((u, s) => u.concat(s)), Ji((u) => {
|
3984
3985
|
for (const s of u)
|
3985
3986
|
s.field = l.field;
|