@gmod/tabix 3.0.5 → 3.1.0
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/CHANGELOG.md +3 -11
- package/README.md +0 -1
- package/dist/chunk.d.ts +1 -1
- package/dist/chunk.js +1 -1
- package/dist/chunk.js.map +1 -1
- package/dist/csi.d.ts +3 -3
- package/dist/csi.js +3 -4
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +2 -2
- package/dist/indexFile.js +2 -2
- package/dist/indexFile.js.map +1 -1
- package/dist/tabixIndexedFile.d.ts +6 -1
- package/dist/tabixIndexedFile.js +16 -14
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.d.ts +1 -1
- package/dist/tbi.js +6 -8
- package/dist/tbi.js.map +1 -1
- package/dist/util.js +9 -9
- package/dist/util.js.map +1 -1
- package/esm/chunk.d.ts +1 -1
- package/esm/chunk.js +1 -1
- package/esm/chunk.js.map +1 -1
- package/esm/csi.d.ts +3 -3
- package/esm/csi.js +3 -4
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +2 -2
- package/esm/indexFile.js +2 -2
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +6 -1
- package/esm/tabixIndexedFile.js +16 -14
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/tbi.d.ts +1 -1
- package/esm/tbi.js +6 -8
- package/esm/tbi.js.map +1 -1
- package/esm/util.js +9 -9
- package/esm/util.js.map +1 -1
- package/package.json +2 -2
- package/src/chunk.ts +1 -1
- package/src/csi.ts +3 -5
- package/src/indexFile.ts +3 -3
- package/src/tabixIndexedFile.ts +21 -13
- package/src/tbi.ts +13 -14
- package/src/util.ts +8 -8
- package/dist/package.json +0 -1
- package/dist/tabix-bundle.js +0 -1
package/CHANGELOG.md
CHANGED
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@@ -1,27 +1,19 @@
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# [3.1.0](https://github.com/GMOD/tabix-js/compare/v3.0.5...v3.1.0) (2025-10-01)
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## [3.0.4](https://github.com/GMOD/tabix-js/compare/v3.0.3...v3.0.4) (2025-05-13)
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## [3.0.5](https://github.com/GMOD/tabix-js/compare/v3.0.4...v3.0.5) (2025-05-26)
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## [3.0.4](https://github.com/GMOD/tabix-js/compare/v3.0.3...v3.0.4) (2025-05-13)
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## [3.0.3](https://github.com/GMOD/tabix-js/compare/v3.0.2...v3.0.3) (2025-05-13)
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## [3.0.2](https://github.com/GMOD/tabix-js/compare/v3.0.1...v3.0.2) (2025-04-30)
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## [3.0.1](https://github.com/GMOD/tabix-js/compare/v3.0.0...v3.0.1) (2025-04-30)
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# [3.0.0](https://github.com/GMOD/tabix-js/compare/v2.0.5...v3.0.0) (2025-04-30)
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## [2.0.5](https://github.com/GMOD/tabix-js/compare/v2.0.4...v2.0.5) (2025-03-18)
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## [2.0.4](https://github.com/GMOD/tabix-js/compare/v2.0.3...v2.0.4) (2024-12-18)
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package/README.md
CHANGED
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@@ -179,7 +179,6 @@ console.log(lines)
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- `args`
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
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- `args.path`
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**[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** 
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- `args.filehandle` **filehandle?** 
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package/dist/chunk.d.ts
CHANGED
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@@ -4,7 +4,7 @@ export default class Chunk {
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maxv: VirtualOffset;
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bin: number;
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_fetchedSize?: number;
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constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?:
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constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: number);
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toUniqueString(): string;
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toString(): string;
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compareTo(b: Chunk): number;
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package/dist/chunk.js
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Object.defineProperty(exports, "__esModule", { value: true });
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// little class representing a chunk in the index
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class Chunk {
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constructor(minv, maxv, bin, fetchedSize
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constructor(minv, maxv, bin, fetchedSize) {
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this.minv = minv;
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this.maxv = maxv;
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this.bin = bin;
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package/dist/chunk.js.map
CHANGED
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{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,
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{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAoB;QAEpB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AA1CD,wBA0CC"}
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package/dist/csi.d.ts
CHANGED
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@@ -12,7 +12,7 @@ export default class CSI extends IndexFile {
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refIdToName: string[];
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refNameToId: Record<string, number>;
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skipLines: number;
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metaChar: string |
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metaChar: string | undefined;
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columnNumbers: {
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ref: number;
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start: number;
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refIdToName: string[];
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refNameToId: Record<string, number>;
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skipLines: number;
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metaChar: string |
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metaChar: string | undefined;
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columnNumbers: {
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ref: number;
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start: number;
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maxRefLength: number;
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refIdToName: never[];
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refNameToId: {};
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metaChar:
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metaChar: undefined;
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columnNumbers: {
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ref: number;
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start: number;
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package/dist/csi.js
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const dataView = new DataView(bytes.buffer);
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const formatFlags = dataView.getInt32(offset, true);
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const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
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const format = formats[(formatFlags &
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const format = formats[(formatFlags & 0xF)];
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if (!format) {
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throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
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}
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end: dataView.getInt32(offset + 12, true),
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};
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const metaValue = dataView.getInt32(offset + 16, true);
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const metaChar = metaValue ? String.fromCharCode(metaValue) :
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const metaChar = metaValue ? String.fromCharCode(metaValue) : undefined;
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const skipLines = dataView.getInt32(offset + 20, true);
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const nameSectionLength = dataView.getInt32(offset + 24, true);
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const { refIdToName, refNameToId } = this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength));
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};
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}
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// fetch and parse the index
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async _parse(opts = {}) {
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const bytes = await (0, bgzf_filehandle_1.unzip)(await this.filehandle.readFile(opts));
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const dataView = new DataView(bytes.buffer);
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: {
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refIdToName: [],
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refNameToId: {},
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metaChar:
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metaChar: undefined,
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columnNumbers: { ref: 0, start: 1, end: 2 },
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coordinateType: 'zero-based-half-open',
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format: 'generic',
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package/dist/csi.js.map
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{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAmD;AACnD,uCAAmD;AACnD,uCAA0C;AAC1C,uEAA6D;AAE7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,OAAO,GAAG;IACd,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,KAAK;IACR,CAAC,EAAE,KAAK;CACT,CAAA;AAED,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE,CAAC;YACV,OAAO,KAAK,CAAC,SAAS,CAAA;QACxB,CAAC;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACnD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,WAAW,GAAG,GAAG,CAAc,CAAC,CAAA;QACxD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,
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+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAmD;AACnD,uCAAmD;AACnD,uCAA0C;AAC1C,uEAA6D;AAE7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,OAAO,GAAG;IACd,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,KAAK;IACR,CAAC,EAAE,KAAK;CACT,CAAA;AAED,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE,CAAC;YACV,OAAO,KAAK,CAAC,SAAS,CAAA;QACxB,CAAC;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACnD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,WAAW,GAAG,GAAG,CAAc,CAAC,CAAA;QACxD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CAAA;QAED,OAAO;YACL,WAAW;YACX,WAAW;YACX,SAAS;YACT,QAAQ;YACR,aAAa;YACb,MAAM;YACN,cAAc;SACf,CAAA;IACH,CAAC;IAED,eAAe,CAAC,UAAsB;QACpC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,MAAM,WAAW,GAA2B,EAAE,CAAA;QAC9C,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;QACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;gBACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;oBACtB,MAAM,OAAO,GAAG,IAAI,CAAC,YAAY,CAC/B,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,CAAC,CAAC,CAAC,CACtD,CAAA;oBACD,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;gBAClC,CAAC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QACD,OAAO;YACL,WAAW;YACX,WAAW;SACZ,CAAA;IACH,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAA;QAC/D,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,0BAA0B;QAC1B,IAAI,UAAU,CAAA;QACd,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,UAAU,EAAE,CAAC;YAC/C,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,UAAU,EAAE,CAAC;YACtD,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1D,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GACP,SAAS,IAAI,SAAS,IAAI,EAAE;YAC1B,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC;YAC9B,CAAC,CAAC;gBACE,WAAW,EAAE,EAAE;gBACf,WAAW,EAAE,EAAE;gBACf,QAAQ,EAAE,SAAS;gBACnB,aAAa,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE;gBAC3C,cAAc,EAAE,sBAAsB;gBACtC,MAAM,EAAE,SAAS;aAClB,CAAA;QACP,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,aAAwC,CAAA;QAC5C,IAAI,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QACnC,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;YACnD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACpD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;gBAChD,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,mEAAmE;oBACnE,2BAA2B;oBAC3B,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oBAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;gBACnC,CAAC;qBAAM,CAAC;oBACN,MAAM,OAAO,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oBAChD,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,OAAO,CAAC,CAAA;oBAC3D,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;oBAC3D,UAAU,IAAI,EAAE,CAAA;oBAChB,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QAC5B,CAAC,CAAC,CAAA;QAEF,OAAO;YACL,GAAG,GAAG;YACN,GAAG,EAAE,IAAI;YACT,QAAQ;YACR,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,aAAa;YACb,UAAU;YACV,OAAO;YACP,KAAK,EAAE,IAAI,CAAC,KAAK;YACjB,YAAY,EAAE,IAAI,CAAC,YAAY;YAC/B,YAAY;SACb,CAAA;IACH,CAAC;IAED,cAAc,CAAC,KAAiB,EAAE,MAAc;QAC9C,OAAO;YACL,SAAS,EAAE,IAAA,iCAAuB,EAAC,KAAK,EAAE,MAAM,GAAG,EAAE,CAAC;SACvD,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,GAAW,EACX,GAAW,EACX,OAAgB,EAAE;QAElB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QAED,uCAAuC;QACvC,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC/C,MAAM,MAAM,GAAY,EAAE,CAAA;QAE1B,sEAAsE;QACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACrB,KAAK,MAAM,CAAC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;wBACjC,MAAM,CAAC,IAAI,CAAC,IAAI,kBAAK,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;oBAC7C,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,IAAI,0BAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxD,CAAC;IAED;;OAEG;IACH,QAAQ,CAAC,GAAW,EAAE,GAAW;QAC/B,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;QACvC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC;YAClB,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;QACf,CAAC,CAAC,wCAAwC;QAC1C,GAAG,IAAI,CAAC,CAAA;QACR,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,OAAO,CAAC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC5C,MAAM,IAAI,KAAK,CACb,SAAS,GAAG,IAAI,GAAG,mDAAmD,IAAI,CAAC,QAAQ,WAAW,IAAI,CAAC,KAAK,0DAA0D,CACnK,CAAA;YACH,CAAC;YACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAU,CAAC,CAAA;QAC5B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF;AAlPD,sBAkPC"}
|
package/dist/indexFile.d.ts
CHANGED
|
@@ -7,7 +7,7 @@ export interface Options {
|
|
|
7
7
|
export interface IndexData {
|
|
8
8
|
refNameToId: Record<string, number>;
|
|
9
9
|
refIdToName: string[];
|
|
10
|
-
metaChar: string |
|
|
10
|
+
metaChar: string | undefined;
|
|
11
11
|
columnNumbers: {
|
|
12
12
|
ref: number;
|
|
13
13
|
start: number;
|
|
@@ -31,7 +31,7 @@ export default abstract class IndexFile {
|
|
|
31
31
|
[key: string]: any;
|
|
32
32
|
refNameToId: Record<string, number>;
|
|
33
33
|
refIdToName: string[];
|
|
34
|
-
metaChar: string |
|
|
34
|
+
metaChar: string | undefined;
|
|
35
35
|
columnNumbers: {
|
|
36
36
|
ref: number;
|
|
37
37
|
start: number;
|
package/dist/indexFile.js
CHANGED
|
@@ -21,9 +21,9 @@ class IndexFile {
|
|
|
21
21
|
}
|
|
22
22
|
async parse(opts = {}) {
|
|
23
23
|
if (!this.parseP) {
|
|
24
|
-
this.parseP = this._parse(opts).catch((
|
|
24
|
+
this.parseP = this._parse(opts).catch((error) => {
|
|
25
25
|
this.parseP = undefined;
|
|
26
|
-
throw
|
|
26
|
+
throw error;
|
|
27
27
|
});
|
|
28
28
|
}
|
|
29
29
|
return this.parseP;
|
package/dist/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAmBA,MAA8B,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAmBA,MAA8B,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;gBACvD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,KAAK,CAAA;YACb,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IACvC,CAAC;CACF;AA3DD,4BA2DC"}
|
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
import LRU from 'quick-lru';
|
|
1
2
|
import Chunk from './chunk.ts';
|
|
2
3
|
import { IndexData, Options } from './indexFile.ts';
|
|
3
4
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
@@ -12,6 +13,10 @@ export default class TabixIndexedFile {
|
|
|
12
13
|
private index;
|
|
13
14
|
private renameRefSeq;
|
|
14
15
|
private chunkCache;
|
|
16
|
+
cache: LRU<string, {
|
|
17
|
+
buffer: Uint8Array;
|
|
18
|
+
nextIn: number;
|
|
19
|
+
}>;
|
|
15
20
|
/**
|
|
16
21
|
* @param {object} args
|
|
17
22
|
*
|
|
@@ -69,7 +74,7 @@ export default class TabixIndexedFile {
|
|
|
69
74
|
[key: string]: any;
|
|
70
75
|
refNameToId: Record<string, number>;
|
|
71
76
|
refIdToName: string[];
|
|
72
|
-
metaChar: string |
|
|
77
|
+
metaChar: string | undefined;
|
|
73
78
|
columnNumbers: {
|
|
74
79
|
ref: number;
|
|
75
80
|
start: number;
|
package/dist/tabixIndexedFile.js
CHANGED
|
@@ -42,6 +42,9 @@ class TabixIndexedFile {
|
|
|
42
42
|
* just the names of the reference sequences that are used for querying.
|
|
43
43
|
*/
|
|
44
44
|
constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, renameRefSeqs = n => n, chunkCacheSize = 5 * 2 ** 20, }) {
|
|
45
|
+
this.cache = new quick_lru_1.default({
|
|
46
|
+
maxSize: 1000,
|
|
47
|
+
});
|
|
45
48
|
if (filehandle) {
|
|
46
49
|
this.filehandle = filehandle;
|
|
47
50
|
}
|
|
@@ -231,11 +234,12 @@ class TabixIndexedFile {
|
|
|
231
234
|
let lastNewline = -1;
|
|
232
235
|
const newlineByte = '\n'.charCodeAt(0);
|
|
233
236
|
const metaByte = metaChar.charCodeAt(0);
|
|
234
|
-
for (let i = 0
|
|
235
|
-
|
|
237
|
+
for (let i = 0, l = bytes.length; i < l; i++) {
|
|
238
|
+
const byte = bytes[i];
|
|
239
|
+
if (i === lastNewline + 1 && byte !== metaByte) {
|
|
236
240
|
break;
|
|
237
241
|
}
|
|
238
|
-
if (
|
|
242
|
+
if (byte === newlineByte) {
|
|
239
243
|
lastNewline = i;
|
|
240
244
|
}
|
|
241
245
|
}
|
|
@@ -317,7 +321,7 @@ class TabixIndexedFile {
|
|
|
317
321
|
}
|
|
318
322
|
}
|
|
319
323
|
else if (currentColumnNumber === start) {
|
|
320
|
-
startCoordinate = parseInt(line.slice(currentColumnStart, i), 10);
|
|
324
|
+
startCoordinate = Number.parseInt(line.slice(currentColumnStart, i), 10);
|
|
321
325
|
// we convert to 0-based-half-open
|
|
322
326
|
if (coordinateType === '1-based-closed') {
|
|
323
327
|
startCoordinate -= 1;
|
|
@@ -328,14 +332,12 @@ class TabixIndexedFile {
|
|
|
328
332
|
overlaps: false,
|
|
329
333
|
};
|
|
330
334
|
}
|
|
331
|
-
if (end === 0 || end === start)
|
|
332
|
-
|
|
333
|
-
|
|
334
|
-
|
|
335
|
-
|
|
336
|
-
|
|
337
|
-
};
|
|
338
|
-
}
|
|
335
|
+
if ((end === 0 || end === start) && // if we have no end, we assume the feature is 1 bp long
|
|
336
|
+
startCoordinate + 1 <= regionStart) {
|
|
337
|
+
return {
|
|
338
|
+
startCoordinate,
|
|
339
|
+
overlaps: false,
|
|
340
|
+
};
|
|
339
341
|
}
|
|
340
342
|
}
|
|
341
343
|
else if (format === 'VCF' && currentColumnNumber === 4) {
|
|
@@ -380,7 +382,7 @@ class TabixIndexedFile {
|
|
|
380
382
|
if (valueEnd === -1) {
|
|
381
383
|
valueEnd = info.length;
|
|
382
384
|
}
|
|
383
|
-
endCoordinate = parseInt(info.slice(j + 4, valueEnd), 10);
|
|
385
|
+
endCoordinate = Number.parseInt(info.slice(j + 4, valueEnd), 10);
|
|
384
386
|
break;
|
|
385
387
|
}
|
|
386
388
|
prevChar = info[j];
|
|
@@ -408,7 +410,7 @@ class TabixIndexedFile {
|
|
|
408
410
|
*/
|
|
409
411
|
async readChunk(c, opts = {}) {
|
|
410
412
|
const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
|
|
411
|
-
return (0, bgzf_filehandle_1.unzipChunkSlice)(ret, c);
|
|
413
|
+
return (0, bgzf_filehandle_1.unzipChunkSlice)(ret, c, this.cache);
|
|
412
414
|
}
|
|
413
415
|
}
|
|
414
416
|
exports.default = TabixIndexedFile;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
{"version":3,"file":"tabixIndexedFile.js","sourceRoot":"","sources":["../src/tabixIndexedFile.ts"],"names":[],"mappings":";;;;;AAAA,4FAAiE;AACjE,2DAA8D;AAC9D,6DAA2D;AAC3D,0DAA2B;AAG3B,sDAA0B;AAE1B,sDAA0B;AAC1B,uCAA4C;AAI5C,SAAS,OAAO,CAAC,GAAW;IAC1B,4CAA4C;IAC5C,OAAO,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;AACvC,CAAC;AAgBD,MAAqB,gBAAgB;IASnC;;;;;;;;;;;;;;;;;;;;;;;;;OAyBG;IACH,YAAY,EACV,IAAI,EACJ,UAAU,EACV,GAAG,EACH,OAAO,EACP,MAAM,EACN,aAAa,EACb,OAAO,EACP,MAAM,EACN,aAAa,EACb,aAAa,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EACtB,cAAc,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,GAa7B;QAtDM,UAAK,GAAG,IAAI,mBAAG,CAAiD;YACrE,OAAO,EAAE,IAAI;SACd,CAAC,CAAA;QAqDA,IAAI,UAAU,EAAE,CAAC;YACf,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC9B,CAAC;aAAM,IAAI,IAAI,EAAE,CAAC;YAChB,IAAI,CAAC,UAAU,GAAG,IAAI,+BAAS,CAAC,IAAI,CAAC,CAAA;QACvC,CAAC;aAAM,IAAI,GAAG,EAAE,CAAC;YACf,IAAI,CAAC,UAAU,GAAG,IAAI,gCAAU,CAAC,GAAG,CAAC,CAAA;QACvC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,SAAS,CAAC,wCAAwC,CAAC,CAAA;QAC/D,CAAC;QAED,IAAI,aAAa,EAAE,CAAC;YAClB,IAAI,CAAC,KAAK,GAAG,IAAI,gBAAG,CAAC;gBACnB,UAAU,EAAE,aAAa;gBACzB,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,aAAa,EAAE,CAAC;YACzB,IAAI,CAAC,KAAK,GAAG,IAAI,gBAAG,CAAC;gBACnB,UAAU,EAAE,aAAa;gBACzB,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,IAAI,CAAC,KAAK,GAAG,IAAI,gBAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,+BAAS,CAAC,OAAO,CAAC;gBAClC,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,IAAI,CAAC,KAAK,GAAG,IAAI,gBAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,+BAAS,CAAC,OAAO,CAAC;gBAClC,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,IAAI,EAAE,CAAC;YAChB,IAAI,CAAC,KAAK,GAAG,IAAI,gBAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,+BAAS,CAAC,GAAG,IAAI,MAAM,CAAC;gBACxC,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,MAAM,EAAE,CAAC;YAClB,IAAI,CAAC,KAAK,GAAG,IAAI,gBAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,gCAAU,CAAC,MAAM,CAAC;aACnC,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,MAAM,EAAE,CAAC;YAClB,IAAI,CAAC,KAAK,GAAG,IAAI,gBAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,gCAAU,CAAC,MAAM,CAAC;aACnC,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,GAAG,EAAE,CAAC;YACf,IAAI,CAAC,KAAK,GAAG,IAAI,gBAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,gCAAU,CAAC,GAAG,GAAG,MAAM,CAAC;aACzC,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,SAAS,CACjB,oFAAoF,CACrF,CAAA;QACH,CAAC;QAED,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;QACjC,IAAI,CAAC,UAAU,GAAG,IAAI,iCAAqB,CAAmB;YAC5D,KAAK,EAAE,IAAI,mBAAG,CAAC,EAAE,OAAO,EAAE,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC;YACnE,IAAI,EAAE,CAAC,IAAW,EAAE,MAAoB,EAAE,EAAE,CAC1C,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,MAAM,EAAE,CAAC;SACnC,CAAC,CAAA;IACJ,CAAC;IAED;;;;;;;;;;;;OAYG;IACH,KAAK,CAAC,QAAQ,CACZ,OAAe,EACf,CAAqB,EACrB,CAAqB,EACrB,IAAqC;QAErC,IAAI,MAA+B,CAAA;QACnC,IAAI,OAAO,GAAY,EAAE,CAAA;QACzB,IAAI,QAAoD,CAAA;QAExD,IAAI,OAAO,IAAI,KAAK,UAAU,EAAE,CAAC;YAC/B,QAAQ,GAAG,IAAI,CAAA;QACjB,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,IAAI,CAAA;YACd,QAAQ,GAAG,IAAI,CAAC,YAAY,CAAA;YAC5B,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACtB,CAAC;QAED,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACtD,IAAA,0BAAgB,EAAC,MAAM,CAAC,CAAA;QACxB,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;QACpB,MAAM,GAAG,GAAG,CAAC,IAAI,QAAQ,CAAC,YAAY,CAAA;QACtC,IAAI,CAAC,CAAC,KAAK,IAAI,GAAG,CAAC,EAAE,CAAC;YACpB,MAAM,IAAI,SAAS,CACjB,4EAA4E,CAC7E,CAAA;QACH,CAAC;QACD,IAAI,KAAK,KAAK,GAAG,EAAE,CAAC;YAClB,OAAM;QACR,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,CAAC,CAAA;QAC5E,IAAA,0BAAgB,EAAC,MAAM,CAAC,CAAA;QACxB,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;QAEvC,qEAAqE;QACrE,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;YACvB,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,GAAG,CAClE,CAAC,CAAC,QAAQ,EAAE,EACZ,CAAC,EACD,MAAM,CACP,CAAA;YAED,IAAA,0BAAgB,EAAC,MAAM,CAAC,CAAA;YACxB,IAAI,UAAU,GAAG,CAAC,CAAA;YAClB,IAAI,GAAG,GAAG,CAAC,CAAA;YAEX,iEAAiE;YACjE,oEAAoE;YACpE,yEAAyE;YACzE,MAAM,GAAG,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAClC,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;YAC/B,OAAO,UAAU,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;gBAC/B,IAAI,IAAY,CAAA;gBAChB,IAAI,CAAS,CAAA;gBACb,IAAI,UAAU,EAAE,CAAC;oBACf,CAAC,GAAG,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,UAAU,CAAC,CAAA;oBACjC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;wBACb,MAAK;oBACP,CAAC;oBACD,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;gBACjC,CAAC;qBAAM,CAAC;oBACN,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,UAAU,CAAC,CAAA;oBAClD,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;wBACb,MAAK;oBACP,CAAC;oBACD,MAAM,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;oBACrC,IAAI,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;gBAC1B,CAAC;gBAED,uEAAuE;gBACvE,IAAI,UAAU,EAAE,CAAC;oBACf,OAAO,UAAU,GAAG,CAAC,CAAC,IAAI,CAAC,YAAY,IAAI,UAAU,CAAC,GAAG,EAAE,CAAE,EAAE,CAAC,CAAA,CAAC;oBACjE,GAAG,EAAE,CAAA;gBACP,CAAC;gBAED,+DAA+D;gBAC/D,MAAM,EAAE,eAAe,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,SAAS,CAClD,QAAQ,EACR,OAAO,EACP,KAAK,EACL,GAAG,EACH,IAAI,CACL,CAAA;gBAED,IAAI,QAAQ,EAAE,CAAC;oBACb,QAAQ,CACN,IAAI;oBACJ,gEAAgE;oBAChE,aAAa;oBACb,EAAE;oBACF,gEAAgE;oBAChE,gEAAgE;oBAChE,UAAU;oBACV,EAAE;oBACF,gEAAgE;oBAChE,+DAA+D;oBAC/D,iEAAiE;oBACjE,QAAQ;oBACR,UAAU,CAAC,GAAG,CAAE,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;wBACzB,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAE,CAAC;wBAC/B,CAAC,CA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|
package/dist/tbi.d.ts
CHANGED
package/dist/tbi.js
CHANGED
|
@@ -92,7 +92,7 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
92
92
|
1: 'SAM',
|
|
93
93
|
2: 'VCF',
|
|
94
94
|
};
|
|
95
|
-
const format = formatOpts[formatFlags &
|
|
95
|
+
const format = formatOpts[formatFlags & 0xF];
|
|
96
96
|
if (!format) {
|
|
97
97
|
throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
|
|
98
98
|
}
|
|
@@ -105,7 +105,7 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
105
105
|
const depth = 5;
|
|
106
106
|
const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
|
|
107
107
|
const maxRefLength = 2 ** (14 + depth * 3);
|
|
108
|
-
const metaChar = metaValue ? String.fromCharCode(metaValue) :
|
|
108
|
+
const metaChar = metaValue ? String.fromCharCode(metaValue) : undefined;
|
|
109
109
|
const skipLines = dataView.getInt32(28, true);
|
|
110
110
|
// read sequence dictionary
|
|
111
111
|
const nameSectionLength = dataView.getInt32(32, true);
|
|
@@ -217,7 +217,7 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
217
217
|
if (!ba) {
|
|
218
218
|
return [];
|
|
219
219
|
}
|
|
220
|
-
const minOffset = ba.linearIndex.length
|
|
220
|
+
const minOffset = ba.linearIndex.length > 0
|
|
221
221
|
? ba.linearIndex[min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
|
|
222
222
|
? ba.linearIndex.length - 1
|
|
223
223
|
: min >> TAD_LIDX_SHIFT]
|
|
@@ -241,15 +241,13 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
241
241
|
// Use the linear index to find minimum file position of chunks that could
|
|
242
242
|
// contain alignments in the region
|
|
243
243
|
const nintv = ba.linearIndex.length;
|
|
244
|
-
let lowest
|
|
244
|
+
let lowest;
|
|
245
245
|
const minLin = Math.min(min >> 14, nintv - 1);
|
|
246
246
|
const maxLin = Math.min(max >> 14, nintv - 1);
|
|
247
247
|
for (let i = minLin; i <= maxLin; ++i) {
|
|
248
248
|
const vp = ba.linearIndex[i];
|
|
249
|
-
if (vp) {
|
|
250
|
-
|
|
251
|
-
lowest = vp;
|
|
252
|
-
}
|
|
249
|
+
if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
|
|
250
|
+
lowest = vp;
|
|
253
251
|
}
|
|
254
252
|
}
|
|
255
253
|
return (0, util_ts_1.optimizeChunks)(chunks, lowest);
|
package/dist/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAmD;AACnD,uCAAmD;AACnD,uCAA4D;AAC5D,uEAA6D;AAE7D,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAS;IAC/C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAA;IACxD,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAA;QAC9B,IAAA,0BAAgB,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAC7B,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,KAAK,KAAK,SAAS,CAAC,aAAa,EAAE,CAAC;YACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,6CAA6C;QAC7C,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC/C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,UAAU,GAA2B;YACzC,CAAC,EAAE,SAAS;YACZ,CAAC,EAAE,KAAK;YACR,CAAC,EAAE,KAAK;SACT,CAAA;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC5C,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;YAChC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;YAClC,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;SACjC,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAmD;AACnD,uCAAmD;AACnD,uCAA4D;AAC5D,uEAA6D;AAE7D,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAS;IAC/C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAA;IACxD,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAA;QAC9B,IAAA,0BAAgB,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAC7B,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,KAAK,KAAK,SAAS,CAAC,aAAa,EAAE,CAAC;YACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,6CAA6C;QAC7C,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC/C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,UAAU,GAA2B;YACzC,CAAC,EAAE,SAAS;YACZ,CAAC,EAAE,KAAK;YACR,CAAC,EAAE,KAAK;SACT,CAAA;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC5C,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;YAChC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;YAClC,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;SACjC,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAE7C,2BAA2B;QAC3B,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QACrD,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CACxC,CAAA;QAED,+CAA+C;QAC/C,IAAI,UAAU,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACvC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;YACnD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACpD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;gBAChD,UAAU,IAAI,CAAC,CAAA;gBACf,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;oBACtD,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;wBACrB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAChD,CAAC;oBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;gBAC/B,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;oBACtD,UAAU,IAAI,CAAC,CAAA;oBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBACrD,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,mBAAmB;YACnB,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACvD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;YAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACxC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gBAC7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|
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|
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|
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|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAkBA,4CAcC;AAQD,0CAGC;AAED,wCAKC;AAED,wCAgCC;AAjFD,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;;GAWG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,IAAI,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAkBA,4CAcC;AAQD,0CAGC;AAED,wCAKC;AAED,wCAgCC;AAjFD,MAAM,UAAW,SAAQ,KAAK;CAE7B;AACD;;;;;;;;;;;GAWG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACI,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAA4B,CAAA;IAEhC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,EAAE,EAAE;QAC1B,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC"}
|
package/esm/chunk.d.ts
CHANGED
|
@@ -4,7 +4,7 @@ export default class Chunk {
|
|
|
4
4
|
maxv: VirtualOffset;
|
|
5
5
|
bin: number;
|
|
6
6
|
_fetchedSize?: number;
|
|
7
|
-
constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?:
|
|
7
|
+
constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: number);
|
|
8
8
|
toUniqueString(): string;
|
|
9
9
|
toString(): string;
|
|
10
10
|
compareTo(b: Chunk): number;
|
package/esm/chunk.js
CHANGED
package/esm/chunk.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAoB;QAEpB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
|
package/esm/csi.d.ts
CHANGED
|
@@ -12,7 +12,7 @@ export default class CSI extends IndexFile {
|
|
|
12
12
|
refIdToName: string[];
|
|
13
13
|
refNameToId: Record<string, number>;
|
|
14
14
|
skipLines: number;
|
|
15
|
-
metaChar: string |
|
|
15
|
+
metaChar: string | undefined;
|
|
16
16
|
columnNumbers: {
|
|
17
17
|
ref: number;
|
|
18
18
|
start: number;
|
|
@@ -43,7 +43,7 @@ export default class CSI extends IndexFile {
|
|
|
43
43
|
refIdToName: string[];
|
|
44
44
|
refNameToId: Record<string, number>;
|
|
45
45
|
skipLines: number;
|
|
46
|
-
metaChar: string |
|
|
46
|
+
metaChar: string | undefined;
|
|
47
47
|
columnNumbers: {
|
|
48
48
|
ref: number;
|
|
49
49
|
start: number;
|
|
@@ -68,7 +68,7 @@ export default class CSI extends IndexFile {
|
|
|
68
68
|
maxRefLength: number;
|
|
69
69
|
refIdToName: never[];
|
|
70
70
|
refNameToId: {};
|
|
71
|
-
metaChar:
|
|
71
|
+
metaChar: undefined;
|
|
72
72
|
columnNumbers: {
|
|
73
73
|
ref: number;
|
|
74
74
|
start: number;
|
package/esm/csi.js
CHANGED
|
@@ -47,7 +47,7 @@ export default class CSI extends IndexFile {
|
|
|
47
47
|
const dataView = new DataView(bytes.buffer);
|
|
48
48
|
const formatFlags = dataView.getInt32(offset, true);
|
|
49
49
|
const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
|
|
50
|
-
const format = formats[(formatFlags &
|
|
50
|
+
const format = formats[(formatFlags & 0xF)];
|
|
51
51
|
if (!format) {
|
|
52
52
|
throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
|
|
53
53
|
}
|
|
@@ -57,7 +57,7 @@ export default class CSI extends IndexFile {
|
|
|
57
57
|
end: dataView.getInt32(offset + 12, true),
|
|
58
58
|
};
|
|
59
59
|
const metaValue = dataView.getInt32(offset + 16, true);
|
|
60
|
-
const metaChar = metaValue ? String.fromCharCode(metaValue) :
|
|
60
|
+
const metaChar = metaValue ? String.fromCharCode(metaValue) : undefined;
|
|
61
61
|
const skipLines = dataView.getInt32(offset + 20, true);
|
|
62
62
|
const nameSectionLength = dataView.getInt32(offset + 24, true);
|
|
63
63
|
const { refIdToName, refNameToId } = this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength));
|
|
@@ -93,7 +93,6 @@ export default class CSI extends IndexFile {
|
|
|
93
93
|
refIdToName,
|
|
94
94
|
};
|
|
95
95
|
}
|
|
96
|
-
// fetch and parse the index
|
|
97
96
|
async _parse(opts = {}) {
|
|
98
97
|
const bytes = await unzip(await this.filehandle.readFile(opts));
|
|
99
98
|
const dataView = new DataView(bytes.buffer);
|
|
@@ -118,7 +117,7 @@ export default class CSI extends IndexFile {
|
|
|
118
117
|
: {
|
|
119
118
|
refIdToName: [],
|
|
120
119
|
refNameToId: {},
|
|
121
|
-
metaChar:
|
|
120
|
+
metaChar: undefined,
|
|
122
121
|
columnNumbers: { ref: 0, start: 1, end: 2 },
|
|
123
122
|
coordinateType: 'zero-based-half-open',
|
|
124
123
|
format: 'generic',
|