@gmod/tabix 2.0.5 → 3.0.1
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 +5 -7
- package/dist/chunk.d.ts +1 -1
- package/dist/csi.d.ts +3 -3
- package/dist/csi.js +13 -13
- package/dist/csi.js.map +1 -1
- package/dist/index.d.ts +3 -3
- package/dist/index.js +6 -6
- package/dist/index.js.map +1 -1
- package/dist/indexFile.d.ts +3 -3
- package/dist/indexFile.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tabixIndexedFile.d.ts +3 -3
- package/dist/tabixIndexedFile.js +17 -17
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.d.ts +3 -3
- package/dist/tbi.js +15 -15
- package/dist/tbi.js.map +1 -1
- package/dist/util.d.ts +2 -2
- package/esm/chunk.d.ts +1 -1
- package/esm/csi.d.ts +3 -3
- package/esm/csi.js +5 -5
- package/esm/csi.js.map +1 -1
- package/esm/index.d.ts +3 -3
- package/esm/index.js +3 -3
- package/esm/index.js.map +1 -1
- package/esm/indexFile.d.ts +3 -3
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +3 -3
- package/esm/tabixIndexedFile.js +5 -5
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/tbi.d.ts +3 -3
- package/esm/tbi.js +5 -5
- package/esm/tbi.js.map +1 -1
- package/esm/util.d.ts +2 -2
- package/package.json +17 -10
- package/src/chunk.ts +1 -1
- package/src/csi.ts +5 -6
- package/src/index.ts +3 -3
- package/src/indexFile.ts +4 -3
- package/src/tabixIndexedFile.ts +9 -7
- package/src/tbi.ts +6 -5
- package/src/util.ts +2 -2
package/CHANGELOG.md
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## [
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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.
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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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## [2.0.3](https://github.com/GMOD/tabix-js/compare/v2.0.2...v2.0.3) (2024-12-18)
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## [2.0.2](https://github.com/GMOD/tabix-js/compare/v2.0.0...v2.0.2) (2024-12-12)
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# [2.0.0](https://github.com/GMOD/tabix-js/compare/v1.6.1...v2.0.0) (2024-12-12)
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## [1.6.1](https://github.com/GMOD/tabix-js/compare/v1.6.0...v1.6.1) (2024-12-07)
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# [1.6.0](https://github.com/GMOD/tabix-js/compare/v1.5.15...v1.6.0) (2024-11-30)
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package/dist/chunk.d.ts
CHANGED
package/dist/csi.d.ts
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import
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import
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import
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import Chunk from './chunk.ts';
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import IndexFile, { Options } from './indexFile.ts';
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import VirtualOffset from './virtualOffset.ts';
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export default class CSI extends IndexFile {
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private maxBinNumber;
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private depth;
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package/dist/csi.js
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@@ -37,11 +37,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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const
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const
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const
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const
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const
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const chunk_ts_1 = __importDefault(require("./chunk.js"));
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const indexFile_ts_1 = __importDefault(require("./indexFile.js"));
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const long_ts_1 = require("./long.js");
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const util_ts_1 = require("./util.js");
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const virtualOffset_ts_1 = __importStar(require("./virtualOffset.js"));
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const CSI1_MAGIC = 21582659; // CSI\1
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const CSI2_MAGIC = 38359875; // CSI\2
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const formats = {
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function rshift(num, bits) {
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return Math.floor(num / 2 ** bits);
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}
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class CSI extends
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class CSI extends indexFile_ts_1.default {
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constructor(args) {
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super(args);
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this.maxBinNumber = 0;
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@@ -179,16 +179,16 @@ class CSI extends indexFile_1.default {
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currOffset += 4 + 8 + 4 + 16 + 16;
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}
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else {
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const loffset = (0,
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const loffset = (0, virtualOffset_ts_1.fromBytes)(bytes, currOffset + 4);
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firstDataLine = this._findFirstData(firstDataLine, loffset);
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const chunkCount = dataView.getInt32(currOffset + 12, true);
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currOffset += 16;
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const chunks = new Array(chunkCount);
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for (let k = 0; k < chunkCount; k += 1) {
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const u = (0,
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const v = (0,
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const u = (0, virtualOffset_ts_1.fromBytes)(bytes, currOffset);
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const v = (0, virtualOffset_ts_1.fromBytes)(bytes, currOffset + 8);
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currOffset += 16;
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chunks[k] = new
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chunks[k] = new chunk_ts_1.default(u, v, bin);
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}
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binIndex[bin] = chunks;
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}
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}
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parsePseudoBin(bytes, offset) {
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return {
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lineCount: (0,
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lineCount: (0, long_ts_1.longFromBytesToUnsigned)(bytes, offset + 28),
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};
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}
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async blocksForRange(refName, min, max, opts = {}) {
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for (let bin = start; bin <= end; bin++) {
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if (ba.binIndex[bin]) {
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for (const c of ba.binIndex[bin]) {
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chunks.push(new
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chunks.push(new chunk_ts_1.default(c.minv, c.maxv, bin));
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}
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}
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}
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}
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return (0,
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return (0, util_ts_1.optimizeChunks)(chunks, new virtualOffset_ts_1.default(0, 0));
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}
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/**
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* calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
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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,
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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,IAAI,CAAA;QAClE,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,4BAA4B;IAE5B,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,IAAI;gBACd,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,Q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|
package/dist/index.d.ts
CHANGED
|
@@ -1,3 +1,3 @@
|
|
|
1
|
-
export { default as TabixIndexedFile } from './tabixIndexedFile';
|
|
2
|
-
export { default as CSI } from './csi';
|
|
3
|
-
export { default as TBI } from './tbi';
|
|
1
|
+
export { default as TabixIndexedFile } from './tabixIndexedFile.ts';
|
|
2
|
+
export { default as CSI } from './csi.ts';
|
|
3
|
+
export { default as TBI } from './tbi.ts';
|
package/dist/index.js
CHANGED
|
@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
exports.TBI = exports.CSI = exports.TabixIndexedFile = void 0;
|
|
7
|
-
var
|
|
8
|
-
Object.defineProperty(exports, "TabixIndexedFile", { enumerable: true, get: function () { return __importDefault(
|
|
9
|
-
var
|
|
10
|
-
Object.defineProperty(exports, "CSI", { enumerable: true, get: function () { return __importDefault(
|
|
11
|
-
var
|
|
12
|
-
Object.defineProperty(exports, "TBI", { enumerable: true, get: function () { return __importDefault(
|
|
7
|
+
var tabixIndexedFile_ts_1 = require("./tabixIndexedFile.js");
|
|
8
|
+
Object.defineProperty(exports, "TabixIndexedFile", { enumerable: true, get: function () { return __importDefault(tabixIndexedFile_ts_1).default; } });
|
|
9
|
+
var csi_ts_1 = require("./csi.js");
|
|
10
|
+
Object.defineProperty(exports, "CSI", { enumerable: true, get: function () { return __importDefault(csi_ts_1).default; } });
|
|
11
|
+
var tbi_ts_1 = require("./tbi.js");
|
|
12
|
+
Object.defineProperty(exports, "TBI", { enumerable: true, get: function () { return __importDefault(tbi_ts_1).default; } });
|
|
13
13
|
//# sourceMappingURL=index.js.map
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,6DAAmE;AAA1D,wIAAA,OAAO,OAAoB;AACpC,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO"}
|
package/dist/indexFile.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import
|
|
2
|
-
import VirtualOffset from './virtualOffset';
|
|
3
|
-
import
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import VirtualOffset from './virtualOffset.ts';
|
|
3
|
+
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
4
4
|
export interface Options {
|
|
5
5
|
signal?: AbortSignal;
|
|
6
6
|
}
|
package/dist/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;
|
|
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,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,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"}
|
package/dist/tabix-bundle.js
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
(()=>{var e={83:(e,t,i)=>{"use strict";var n=i(447),a=i(805),r=i(996),s=i(681),o=i(674),l=i(442),h=i(414),d=Object.prototype.toString;function c(e){if(!(this instanceof c))return new c(e);this.options=a.assign({chunkSize:16384,windowBits:0,to:""},e||{});var t=this.options;t.raw&&t.windowBits>=0&&t.windowBits<16&&(t.windowBits=-t.windowBits,0===t.windowBits&&(t.windowBits=-15)),!(t.windowBits>=0&&t.windowBits<16)||e&&e.windowBits||(t.windowBits+=32),t.windowBits>15&&t.windowBits<48&&(15&t.windowBits||(t.windowBits|=15)),this.err=0,this.msg="",this.ended=!1,this.chunks=[],this.strm=new l,this.strm.avail_out=0;var i=n.inflateInit2(this.strm,t.windowBits);if(i!==s.Z_OK)throw new Error(o[i]);if(this.header=new h,n.inflateGetHeader(this.strm,this.header),t.dictionary&&("string"==typeof t.dictionary?t.dictionary=r.string2buf(t.dictionary):"[object ArrayBuffer]"===d.call(t.dictionary)&&(t.dictionary=new 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c(e){return/^[\u0000-\u007F]*$/.test(e)}t.default=class{constructor({path:e,filehandle:t,url:i,tbiPath:n,tbiUrl:o,tbiFilehandle:l,csiPath:c,csiUrl:f,csiFilehandle:u,renameRefSeqs:_=e=>e,chunkCacheSize:g=5242880}){if(t)this.filehandle=t;else if(e)this.filehandle=new s.LocalFile(e);else{if(!i)throw new TypeError("must provide either filehandle or path");this.filehandle=new s.RemoteFile(i)}if(l)this.index=new h.default({filehandle:l,renameRefSeqs:_});else if(u)this.index=new d.default({filehandle:u,renameRefSeqs:_});else if(n)this.index=new h.default({filehandle:new s.LocalFile(n),renameRefSeqs:_});else if(c)this.index=new d.default({filehandle:new s.LocalFile(c),renameRefSeqs:_});else if(e)this.index=new h.default({filehandle:new s.LocalFile(`${e}.tbi`),renameRefSeqs:_});else if(f)this.index=new d.default({filehandle:new s.RemoteFile(f)});else if(o)this.index=new h.default({filehandle:new s.RemoteFile(o)});else{if(!i)throw new TypeError("must provide one of tbiFilehandle, tbiPath, 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t}for(k=65535&p,(v&=15)&&(_<v&&(u+=S[n++]<<_,_+=8),k+=u&(1<<v)-1,u>>>=v,_-=v),_<15&&(u+=S[n++]<<_,_+=8,u+=S[n++]<<_,_+=8),p=b[u&m];;){if(u>>>=v=p>>>24,_-=v,16&(v=p>>>16&255)){if(y=65535&p,_<(v&=15)&&(u+=S[n++]<<_,(_+=8)<v&&(u+=S[n++]<<_,_+=8)),(y+=u&(1<<v)-1)>l){e.msg="invalid distance too far back",i.mode=30;break e}if(u>>>=v,_-=v,y>(v=r-s)){if((v=y-v)>d&&i.sane){e.msg="invalid distance too far back",i.mode=30;break e}if(x=0,z=f,0===c){if(x+=h-v,v<k){k-=v;do{B[r++]=f[x++]}while(--v);x=r-y,z=B}}else if(c<v){if(x+=h+c-v,(v-=c)<k){k-=v;do{B[r++]=f[x++]}while(--v);if(x=0,c<k){k-=v=c;do{B[r++]=f[x++]}while(--v);x=r-y,z=B}}}else if(x+=c-v,v<k){k-=v;do{B[r++]=f[x++]}while(--v);x=r-y,z=B}for(;k>2;)B[r++]=z[x++],B[r++]=z[x++],B[r++]=z[x++],k-=3;k&&(B[r++]=z[x++],k>1&&(B[r++]=z[x++]))}else{x=r-y;do{B[r++]=B[x++],B[r++]=B[x++],B[r++]=B[x++],k-=3}while(k>2);k&&(B[r++]=B[x++],k>1&&(B[r++]=B[x++]))}break}if(64&v){e.msg="invalid distance code",i.mode=30;break e}p=b[(65535&p)+(u&(1<<v)-1)]}}break}}while(n<a&&r<o);n-=k=_>>3,u&=(1<<(_-=k<<3))-1,e.next_in=n,e.next_out=r,e.avail_in=n<a?a-n+5:5-(n-a),e.avail_out=r<o?o-r+257:257-(r-o),i.hold=u,i.bits=_}},303:(e,t,i)=>{"use strict";var n=i(411),a=i(805),r=i(996),s=i(674),o=i(442),l=Object.prototype.toString;function h(e){if(!(this instanceof h))return new h(e);this.options=a.assign({level:-1,method:8,chunkSize:16384,windowBits:15,memLevel:8,strategy:0,to:""},e||{});var t=this.options;t.raw&&t.windowBits>0?t.windowBits=-t.windowBits:t.gzip&&t.windowBits>0&&t.windowBits<16&&(t.windowBits+=16),this.err=0,this.msg="",this.ended=!1,this.chunks=[],this.strm=new o,this.strm.avail_out=0;var i=n.deflateInit2(this.strm,t.level,t.method,t.windowBits,t.memLevel,t.strategy);if(0!==i)throw new Error(s[i]);if(t.header&&n.deflateSetHeader(this.strm,t.header),t.dictionary){var d;if(d="string"==typeof t.dictionary?r.string2buf(t.dictionary):"[object ArrayBuffer]"===l.call(t.dictionary)?new 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4===s?(i=n.deflateEnd(this.strm),this.onEnd(i),this.ended=!0,0===i):2!==s||(this.onEnd(0),o.avail_out=0,!0)},h.prototype.onData=function(e){this.chunks.push(e)},h.prototype.onEnd=function(e){0===e&&("string"===this.options.to?this.result=this.chunks.join(""):this.result=a.flattenChunks(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg},t.Deflate=h,t.deflate=d,t.deflateRaw=function(e,t){return(t=t||{}).raw=!0,d(e,t)},t.gzip=function(e,t){return(t=t||{}).gzip=!0,d(e,t)}},392:e=>{"use strict";class t{constructor(e={}){if(!(e.maxSize&&e.maxSize>0))throw new TypeError("`maxSize` must be a number greater than 0");this.maxSize=e.maxSize,this.cache=new Map,this.oldCache=new Map,this._size=0}_set(e,t){this.cache.set(e,t),this._size++,this._size>=this.maxSize&&(this._size=0,this.oldCache=this.cache,this.cache=new Map)}get(e){if(this.cache.has(e))return this.cache.get(e);if(this.oldCache.has(e)){const t=this.oldCache.get(e);return 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t=e.state,i=t.pending;i>e.avail_out&&(i=e.avail_out),0!==i&&(a.arraySet(e.output,t.pending_buf,t.pending_out,i,e.next_out),e.next_out+=i,t.pending_out+=i,e.total_out+=i,e.avail_out-=i,t.pending-=i,0===t.pending&&(t.pending_out=0))}function p(e,t){r._tr_flush_block(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,m(e.strm)}function v(e,t){e.pending_buf[e.pending++]=t}function k(e,t){e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=255&t}function y(e,t){var 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t,i,n,r,l,h,d,f,u,_,g=e.w_size;do{if(r=e.window_size-e.lookahead-e.strstart,e.strstart>=g+(g-c)){a.arraySet(e.window,e.window,g,g,0),e.match_start-=g,e.strstart-=g,e.block_start-=g,t=i=e.hash_size;do{n=e.head[--t],e.head[t]=n>=g?n-g:0}while(--i);t=i=g;do{n=e.prev[--t],e.prev[t]=n>=g?n-g:0}while(--i);r+=g}if(0===e.strm.avail_in)break;if(h=e.strm,d=e.window,f=e.strstart+e.lookahead,u=r,_=void 0,(_=h.avail_in)>u&&(_=u),i=0===_?0:(h.avail_in-=_,a.arraySet(d,h.input,h.next_in,_,f),1===h.state.wrap?h.adler=s(h.adler,d,_,f):2===h.state.wrap&&(h.adler=o(h.adler,d,_,f)),h.next_in+=_,h.total_in+=_,_),e.lookahead+=i,e.lookahead+e.insert>=3)for(l=e.strstart-e.insert,e.ins_h=e.window[l],e.ins_h=(e.ins_h<<e.hash_shift^e.window[l+1])&e.hash_mask;e.insert&&(e.ins_h=(e.ins_h<<e.hash_shift^e.window[l+3-1])&e.hash_mask,e.prev[l&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=l,l++,e.insert--,!(e.lookahead+e.insert<3)););}while(e.lookahead<c&&0!==e.strm.avail_in)}function z(e,t){for(var i,n;;){if(e.lookahead<c){if(x(e),e.lookahead<c&&0===t)return 1;if(0===e.lookahead)break}if(i=0,e.lookahead>=3&&(e.ins_h=(e.ins_h<<e.hash_shift^e.window[e.strstart+3-1])&e.hash_mask,i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),0!==i&&e.strstart-i<=e.w_size-c&&(e.match_length=y(e,i)),e.match_length>=3)if(n=r._tr_tally(e,e.strstart-e.match_start,e.match_length-3),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=3){e.match_length--;do{e.strstart++,e.ins_h=(e.ins_h<<e.hash_shift^e.window[e.strstart+3-1])&e.hash_mask,i=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart}while(0!=--e.match_length);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=(e.ins_h<<e.hash_shift^e.window[e.strstart+1])&e.hash_mask;else n=r._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(p(e,!1),0===e.strm.avail_out))return 1}return e.insert=e.strstart<2?e.strstart:2,4===t?(p(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(p(e,!1),0===e.strm.avail_out)?1:2}function S(e,t){for(var i,n,a;;){if(e.lookahead<c){if(x(e),e.lookahead<c&&0===t)return 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a.Buf16(573),w(this.depth),this.l_buf=0,this.lit_bufsize=0,this.last_lit=0,this.d_buf=0,this.opt_len=0,this.static_len=0,this.matches=0,this.insert=0,this.bi_buf=0,this.bi_valid=0}function I(e){var t;return e&&e.state?(e.total_in=e.total_out=0,e.data_type=2,(t=e.state).pending=0,t.pending_out=0,t.wrap<0&&(t.wrap=-t.wrap),t.status=t.wrap?42:u,e.adler=2===t.wrap?0:1,t.last_flush=0,r._tr_init(t),0):g(e,h)}function T(e){var t,i=I(e);return 0===i&&((t=e.state).window_size=2*t.w_size,w(t.head),t.max_lazy_match=n[t.level].max_lazy,t.good_match=n[t.level].good_length,t.nice_match=n[t.level].nice_length,t.max_chain_length=n[t.level].max_chain,t.strstart=0,t.block_start=0,t.lookahead=0,t.insert=0,t.match_length=t.prev_length=2,t.match_available=0,t.ins_h=0),i}function C(e,t,i,n,r,s){if(!e)return h;var o=1;if(-1===t&&(t=6),n<0?(o=0,n=-n):n>15&&(o=2,n-=16),r<1||r>9||8!==i||n<8||n>15||t<0||t>9||s<0||s>4)return g(e,h);8===n&&(n=9);var l=new E;return 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e.insert=0,4===t?(p(e,!0),0===e.strm.avail_out?3:4):(e.strstart>e.block_start&&(p(e,!1),e.strm.avail_out),1)})),new B(4,4,8,4,z),new B(4,5,16,8,z),new B(4,6,32,32,z),new B(4,4,16,16,S),new B(8,16,32,32,S),new B(8,16,128,128,S),new B(8,32,128,256,S),new B(32,128,258,1024,S),new B(32,258,258,4096,S)],t.deflateInit=function(e,t){return C(e,t,8,15,8,0)},t.deflateInit2=C,t.deflateReset=T,t.deflateResetKeep=I,t.deflateSetHeader=function(e,t){return e&&e.state?2!==e.state.wrap?h:(e.state.gzhead=t,0):h},t.deflate=function(e,t){var i,a,s,l;if(!e||!e.state||t>5||t<0)return e?g(e,h):h;if(a=e.state,!e.output||!e.input&&0!==e.avail_in||a.status===_&&4!==t)return g(e,0===e.avail_out?-5:h);if(a.strm=e,i=a.last_flush,a.last_flush=t,42===a.status)if(2===a.wrap)e.adler=0,v(a,31),v(a,139),v(a,8),a.gzhead?(v(a,(a.gzhead.text?1:0)+(a.gzhead.hcrc?2:0)+(a.gzhead.extra?4:0)+(a.gzhead.name?8:0)+(a.gzhead.comment?16:0)),v(a,255&a.gzhead.time),v(a,a.gzhead.time>>8&255),v(a,a.gzhead.time>>16&255),v(a,a.gzhead.time>>24&255),v(a,9===a.level?2:a.strategy>=2||a.level<2?4:0),v(a,255&a.gzhead.os),a.gzhead.extra&&a.gzhead.extra.length&&(v(a,255&a.gzhead.extra.length),v(a,a.gzhead.extra.length>>8&255)),a.gzhead.hcrc&&(e.adler=o(e.adler,a.pending_buf,a.pending,0)),a.gzindex=0,a.status=69):(v(a,0),v(a,0),v(a,0),v(a,0),v(a,0),v(a,9===a.level?2:a.strategy>=2||a.level<2?4:0),v(a,3),a.status=u);else{var 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a.status=73;if(73===a.status)if(a.gzhead.name){s=a.pending;do{if(a.pending===a.pending_buf_size&&(a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),m(e),s=a.pending,a.pending===a.pending_buf_size)){l=1;break}l=a.gzindex<a.gzhead.name.length?255&a.gzhead.name.charCodeAt(a.gzindex++):0,v(a,l)}while(0!==l);a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),0===l&&(a.gzindex=0,a.status=91)}else a.status=91;if(91===a.status)if(a.gzhead.comment){s=a.pending;do{if(a.pending===a.pending_buf_size&&(a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),m(e),s=a.pending,a.pending===a.pending_buf_size)){l=1;break}l=a.gzindex<a.gzhead.comment.length?255&a.gzhead.comment.charCodeAt(a.gzindex++):0,v(a,l)}while(0!==l);a.gzhead.hcrc&&a.pending>s&&(e.adler=o(e.adler,a.pending_buf,a.pending-s,s)),0===l&&(a.status=f)}else a.status=f;if(a.status===f&&(a.gzhead.hcrc?(a.pending+2>a.pending_buf_size&&m(e),a.pending+2<=a.pending_buf_size&&(v(a,255&e.adler),v(a,e.adler>>8&255),e.adler=0,a.status=u)):a.status=u),0!==a.pending){if(m(e),0===e.avail_out)return a.last_flush=-1,0}else if(0===e.avail_in&&b(t)<=b(i)&&4!==t)return g(e,-5);if(a.status===_&&0!==e.avail_in)return g(e,-5);if(0!==e.avail_in||0!==a.lookahead||0!==t&&a.status!==_){var y=2===a.strategy?function(e,t){for(var i;;){if(0===e.lookahead&&(x(e),0===e.lookahead)){if(0===t)return 1;break}if(e.match_length=0,i=r._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++,i&&(p(e,!1),0===e.strm.avail_out))return 1}return e.insert=0,4===t?(p(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(p(e,!1),0===e.strm.avail_out)?1:2}(a,t):3===a.strategy?function(e,t){for(var i,n,a,s,o=e.window;;){if(e.lookahead<=d){if(x(e),e.lookahead<=d&&0===t)return 1;if(0===e.lookahead)break}if(e.match_length=0,e.lookahead>=3&&e.strstart>0&&(n=o[a=e.strstart-1])===o[++a]&&n===o[++a]&&n===o[++a]){s=e.strstart+d;do{}while(n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&n===o[++a]&&a<s);e.match_length=d-(s-a),e.match_length>e.lookahead&&(e.match_length=e.lookahead)}if(e.match_length>=3?(i=r._tr_tally(e,1,e.match_length-3),e.lookahead-=e.match_length,e.strstart+=e.match_length,e.match_length=0):(i=r._tr_tally(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++),i&&(p(e,!1),0===e.strm.avail_out))return 1}return e.insert=0,4===t?(p(e,!0),0===e.strm.avail_out?3:4):e.last_lit&&(p(e,!1),0===e.strm.avail_out)?1:2}(a,t):n[a.level].func(a,t);if(3!==y&&4!==y||(a.status=_),1===y||3===y)return 0===e.avail_out&&(a.last_flush=-1),0;if(2===y&&(1===t?r._tr_align(a):5!==t&&(r._tr_stored_block(a,0,0,!1),3===t&&(w(a.head),0===a.lookahead&&(a.strstart=0,a.block_start=0,a.insert=0))),m(e),0===e.avail_out))return a.last_flush=-1,0}return 4!==t?0:a.wrap<=0?1:(2===a.wrap?(v(a,255&e.adler),v(a,e.adler>>8&255),v(a,e.adler>>16&255),v(a,e.adler>>24&255),v(a,255&e.total_in),v(a,e.total_in>>8&255),v(a,e.total_in>>16&255),v(a,e.total_in>>24&255)):(k(a,e.adler>>>16),k(a,65535&e.adler)),m(e),a.wrap>0&&(a.wrap=-a.wrap),0!==a.pending?0:1)},t.deflateEnd=function(e){var t;return e&&e.state?42!==(t=e.state.status)&&69!==t&&73!==t&&91!==t&&t!==f&&t!==u&&t!==_?g(e,h):(e.state=null,t===u?g(e,-3):0):h},t.deflateSetDictionary=function(e,t){var i,n,r,o,l,d,c,f,u=t.length;if(!e||!e.state)return h;if(2===(o=(i=e.state).wrap)||1===o&&42!==i.status||i.lookahead)return h;for(1===o&&(e.adler=s(e.adler,t,u,0)),i.wrap=0,u>=i.w_size&&(0===o&&(w(i.head),i.strstart=0,i.block_start=0,i.insert=0),f=new 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n=i(805),a=i(269),r=i(823),s=i(293),o=i(998),l=-2,h=12,d=30;function c(e){return(e>>>24&255)+(e>>>8&65280)+((65280&e)<<8)+((255&e)<<24)}function f(){this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new n.Buf16(320),this.work=new n.Buf16(288),this.lendyn=null,this.distdyn=null,this.sane=0,this.back=0,this.was=0}function u(e){var t;return e&&e.state?(t=e.state,e.total_in=e.total_out=t.total=0,e.msg="",t.wrap&&(e.adler=1&t.wrap),t.mode=1,t.last=0,t.havedict=0,t.dmax=32768,t.head=null,t.hold=0,t.bits=0,t.lencode=t.lendyn=new n.Buf32(852),t.distcode=t.distdyn=new n.Buf32(592),t.sane=1,t.back=-1,0):l}function _(e){var t;return 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e;b--,m+=f[_++]<<p,p+=8}i.head&&(i.head.time=m),512&i.flags&&(M[0]=255&m,M[1]=m>>>8&255,M[2]=m>>>16&255,M[3]=m>>>24&255,i.check=r(i.check,M,4,0)),m=0,p=0,i.mode=4;case 4:for(;p<16;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}i.head&&(i.head.xflags=255&m,i.head.os=m>>8),512&i.flags&&(M[0]=255&m,M[1]=m>>>8&255,i.check=r(i.check,M,2,0)),m=0,p=0,i.mode=5;case 5:if(1024&i.flags){for(;p<16;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}i.length=m,i.head&&(i.head.extra_len=m),512&i.flags&&(M[0]=255&m,M[1]=m>>>8&255,i.check=r(i.check,M,2,0)),m=0,p=0}else i.head&&(i.head.extra=null);i.mode=6;case 6:if(1024&i.flags&&((z=i.length)>b&&(z=b),z&&(i.head&&(O=i.head.extra_len-i.length,i.head.extra||(i.head.extra=new Array(i.head.extra_len)),n.arraySet(i.head.extra,f,_,z,O)),512&i.flags&&(i.check=r(i.check,f,z,_)),b-=z,_+=z,i.length-=z),i.length))break e;i.length=0,i.mode=7;case 7:if(2048&i.flags){if(0===b)break e;z=0;do{O=f[_+z++],i.head&&O&&i.length<65536&&(i.head.name+=String.fromCharCode(O))}while(O&&z<b);if(512&i.flags&&(i.check=r(i.check,f,z,_)),b-=z,_+=z,O)break e}else i.head&&(i.head.name=null);i.length=0,i.mode=8;case 8:if(4096&i.flags){if(0===b)break e;z=0;do{O=f[_+z++],i.head&&O&&i.length<65536&&(i.head.comment+=String.fromCharCode(O))}while(O&&z<b);if(512&i.flags&&(i.check=r(i.check,f,z,_)),b-=z,_+=z,O)break e}else i.head&&(i.head.comment=null);i.mode=9;case 9:if(512&i.flags){for(;p<16;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(m!==(65535&i.check)){e.msg="header crc mismatch",i.mode=d;break}m=0,p=0}i.head&&(i.head.hcrc=i.flags>>9&1,i.head.done=!0),e.adler=i.check=0,i.mode=h;break;case 10:for(;p<32;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}e.adler=i.check=c(m),m=0,p=0,i.mode=11;case 11:if(0===i.havedict)return e.next_out=g,e.avail_out=w,e.next_in=_,e.avail_in=b,i.hold=m,i.bits=p,2;e.adler=i.check=1,i.mode=h;case h:if(5===t||6===t)break e;case 13:if(i.last){m>>>=7&p,p-=7&p,i.mode=27;break}for(;p<3;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}switch(i.last=1&m,p-=1,3&(m>>>=1)){case 0:i.mode=14;break;case 1:if(v(i),i.mode=20,6===t){m>>>=2,p-=2;break e}break;case 2:i.mode=17;break;case 3:e.msg="invalid block type",i.mode=d}m>>>=2,p-=2;break;case 14:for(m>>>=7&p,p-=7&p;p<32;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if((65535&m)!=(m>>>16^65535)){e.msg="invalid stored block lengths",i.mode=d;break}if(i.length=65535&m,m=0,p=0,i.mode=15,6===t)break e;case 15:i.mode=16;case 16:if(z=i.length){if(z>b&&(z=b),z>w&&(z=w),0===z)break e;n.arraySet(u,f,_,z,g),b-=z,_+=z,w-=z,g+=z,i.length-=z;break}i.mode=h;break;case 17:for(;p<14;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(i.nlen=257+(31&m),m>>>=5,p-=5,i.ndist=1+(31&m),m>>>=5,p-=5,i.ncode=4+(15&m),m>>>=4,p-=4,i.nlen>286||i.ndist>30){e.msg="too many length or distance symbols",i.mode=d;break}i.have=0,i.mode=18;case 18:for(;i.have<i.ncode;){for(;p<3;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}i.lens[U[i.have++]]=7&m,m>>>=3,p-=3}for(;i.have<19;)i.lens[U[i.have++]]=0;if(i.lencode=i.lendyn,i.lenbits=7,N={bits:i.lenbits},R=o(0,i.lens,0,19,i.lencode,0,i.work,N),i.lenbits=N.bits,R){e.msg="invalid code lengths set",i.mode=d;break}i.have=0,i.mode=19;case 19:for(;i.have<i.nlen+i.ndist;){for(;I=(D=i.lencode[m&(1<<i.lenbits)-1])>>>16&255,T=65535&D,!((E=D>>>24)<=p);){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(T<16)m>>>=E,p-=E,i.lens[i.have++]=T;else{if(16===T){for(F=E+2;p<F;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(m>>>=E,p-=E,0===i.have){e.msg="invalid bit length repeat",i.mode=d;break}O=i.lens[i.have-1],z=3+(3&m),m>>>=2,p-=2}else if(17===T){for(F=E+3;p<F;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}p-=E,O=0,z=3+(7&(m>>>=E)),m>>>=3,p-=3}else{for(F=E+7;p<F;){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}p-=E,O=0,z=11+(127&(m>>>=E)),m>>>=7,p-=7}if(i.have+z>i.nlen+i.ndist){e.msg="invalid bit length repeat",i.mode=d;break}for(;z--;)i.lens[i.have++]=O}}if(i.mode===d)break;if(0===i.lens[256]){e.msg="invalid code -- missing end-of-block",i.mode=d;break}if(i.lenbits=9,N={bits:i.lenbits},R=o(1,i.lens,0,i.nlen,i.lencode,0,i.work,N),i.lenbits=N.bits,R){e.msg="invalid literal/lengths set",i.mode=d;break}if(i.distbits=6,i.distcode=i.distdyn,N={bits:i.distbits},R=o(2,i.lens,i.nlen,i.ndist,i.distcode,0,i.work,N),i.distbits=N.bits,R){e.msg="invalid distances set",i.mode=d;break}if(i.mode=20,6===t)break e;case 20:i.mode=21;case 21:if(b>=6&&w>=258){e.next_out=g,e.avail_out=w,e.next_in=_,e.avail_in=b,i.hold=m,i.bits=p,s(e,x),g=e.next_out,u=e.output,w=e.avail_out,_=e.next_in,f=e.input,b=e.avail_in,m=i.hold,p=i.bits,i.mode===h&&(i.back=-1);break}for(i.back=0;I=(D=i.lencode[m&(1<<i.lenbits)-1])>>>16&255,T=65535&D,!((E=D>>>24)<=p);){if(0===b)break e;b--,m+=f[_++]<<p,p+=8}if(I&&!(240&I)){for(C=E,A=I,P=T;I=(D=i.lencode[P+((m&(1<<C+A)-1)>>C)])>>>16&255,T=65535&D,!(C+(E=D>>>24)<=p);){if(0===b)break 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+
(()=>{"use strict";var e={};(e=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(e,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(e,"__esModule",{value:!0})})(e);var r=function(e){return e&&e.__esModule?e:{default:e}};Object.defineProperty(exports,"__esModule",{value:!0}),exports.TBI=exports.CSI=exports.TabixIndexedFile=void 0;var t=require("./tabixIndexedFile.js");Object.defineProperty(exports,"TabixIndexedFile",{enumerable:!0,get:function(){return r(t).default}});var o=require("./csi.js");Object.defineProperty(exports,"CSI",{enumerable:!0,get:function(){return r(o).default}});var n=require("./tbi.js");Object.defineProperty(exports,"TBI",{enumerable:!0,get:function(){return r(n).default}}),window.gmodTABIX=e})();
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@@ -1,6 +1,6 @@
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1
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-
import
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2
|
-
import {
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|
3
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-
import
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import { IndexData, Options } from './indexFile.ts';
|
|
3
|
+
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
4
4
|
type GetLinesCallback = (line: string, fileOffset: number) => void;
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|
5
5
|
interface GetLinesOpts {
|
|
6
6
|
[key: string]: unknown;
|
package/dist/tabixIndexedFile.js
CHANGED
|
@@ -4,12 +4,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
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|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
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|
6
6
|
const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
|
|
7
|
-
const quick_lru_1 = __importDefault(require("quick-lru"));
|
|
8
|
-
const generic_filehandle2_1 = require("generic-filehandle2");
|
|
9
7
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
10
|
-
const
|
|
11
|
-
const
|
|
12
|
-
const
|
|
8
|
+
const generic_filehandle2_1 = require("generic-filehandle2");
|
|
9
|
+
const quick_lru_1 = __importDefault(require("quick-lru"));
|
|
10
|
+
const csi_ts_1 = __importDefault(require("./csi.js"));
|
|
11
|
+
const tbi_ts_1 = __importDefault(require("./tbi.js"));
|
|
12
|
+
const util_ts_1 = require("./util.js");
|
|
13
13
|
function isASCII(str) {
|
|
14
14
|
// eslint-disable-next-line no-control-regex
|
|
15
15
|
return /^[\u0000-\u007F]*$/.test(str);
|
|
@@ -55,47 +55,47 @@ class TabixIndexedFile {
|
|
|
55
55
|
throw new TypeError('must provide either filehandle or path');
|
|
56
56
|
}
|
|
57
57
|
if (tbiFilehandle) {
|
|
58
|
-
this.index = new
|
|
58
|
+
this.index = new tbi_ts_1.default({
|
|
59
59
|
filehandle: tbiFilehandle,
|
|
60
60
|
renameRefSeqs,
|
|
61
61
|
});
|
|
62
62
|
}
|
|
63
63
|
else if (csiFilehandle) {
|
|
64
|
-
this.index = new
|
|
64
|
+
this.index = new csi_ts_1.default({
|
|
65
65
|
filehandle: csiFilehandle,
|
|
66
66
|
renameRefSeqs,
|
|
67
67
|
});
|
|
68
68
|
}
|
|
69
69
|
else if (tbiPath) {
|
|
70
|
-
this.index = new
|
|
70
|
+
this.index = new tbi_ts_1.default({
|
|
71
71
|
filehandle: new generic_filehandle2_1.LocalFile(tbiPath),
|
|
72
72
|
renameRefSeqs,
|
|
73
73
|
});
|
|
74
74
|
}
|
|
75
75
|
else if (csiPath) {
|
|
76
|
-
this.index = new
|
|
76
|
+
this.index = new csi_ts_1.default({
|
|
77
77
|
filehandle: new generic_filehandle2_1.LocalFile(csiPath),
|
|
78
78
|
renameRefSeqs,
|
|
79
79
|
});
|
|
80
80
|
}
|
|
81
81
|
else if (path) {
|
|
82
|
-
this.index = new
|
|
82
|
+
this.index = new tbi_ts_1.default({
|
|
83
83
|
filehandle: new generic_filehandle2_1.LocalFile(`${path}.tbi`),
|
|
84
84
|
renameRefSeqs,
|
|
85
85
|
});
|
|
86
86
|
}
|
|
87
87
|
else if (csiUrl) {
|
|
88
|
-
this.index = new
|
|
88
|
+
this.index = new csi_ts_1.default({
|
|
89
89
|
filehandle: new generic_filehandle2_1.RemoteFile(csiUrl),
|
|
90
90
|
});
|
|
91
91
|
}
|
|
92
92
|
else if (tbiUrl) {
|
|
93
|
-
this.index = new
|
|
93
|
+
this.index = new tbi_ts_1.default({
|
|
94
94
|
filehandle: new generic_filehandle2_1.RemoteFile(tbiUrl),
|
|
95
95
|
});
|
|
96
96
|
}
|
|
97
97
|
else if (url) {
|
|
98
|
-
this.index = new
|
|
98
|
+
this.index = new tbi_ts_1.default({
|
|
99
99
|
filehandle: new generic_filehandle2_1.RemoteFile(`${url}.tbi`),
|
|
100
100
|
});
|
|
101
101
|
}
|
|
@@ -134,7 +134,7 @@ class TabixIndexedFile {
|
|
|
134
134
|
signal = opts.signal;
|
|
135
135
|
}
|
|
136
136
|
const metadata = await this.index.getMetadata(options);
|
|
137
|
-
(0,
|
|
137
|
+
(0, util_ts_1.checkAbortSignal)(signal);
|
|
138
138
|
const start = s ?? 0;
|
|
139
139
|
const end = e ?? metadata.maxRefLength;
|
|
140
140
|
if (!(start <= end)) {
|
|
@@ -144,12 +144,12 @@ class TabixIndexedFile {
|
|
|
144
144
|
return;
|
|
145
145
|
}
|
|
146
146
|
const chunks = await this.index.blocksForRange(refName, start, end, options);
|
|
147
|
-
(0,
|
|
147
|
+
(0, util_ts_1.checkAbortSignal)(signal);
|
|
148
148
|
const decoder = new TextDecoder('utf8');
|
|
149
149
|
// now go through each chunk and parse and filter the lines out of it
|
|
150
150
|
for (const c of chunks) {
|
|
151
151
|
const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
|
|
152
|
-
(0,
|
|
152
|
+
(0, util_ts_1.checkAbortSignal)(signal);
|
|
153
153
|
let blockStart = 0;
|
|
154
154
|
let pos = 0;
|
|
155
155
|
// fast path, Buffer is just ASCII chars and not gigantor, can be
|
|
@@ -219,7 +219,7 @@ class TabixIndexedFile {
|
|
|
219
219
|
*/
|
|
220
220
|
async getHeaderBuffer(opts = {}) {
|
|
221
221
|
const { firstDataLine, metaChar, maxBlockSize } = await this.getMetadata(opts);
|
|
222
|
-
(0,
|
|
222
|
+
(0, util_ts_1.checkAbortSignal)(opts.signal);
|
|
223
223
|
const maxFetch = (firstDataLine?.blockPosition || 0) + maxBlockSize;
|
|
224
224
|
// TODO: what if we don't have a firstDataLine, and the header actually
|
|
225
225
|
// takes up more than one block? this case is not covered here
|
|
@@ -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;IAMnC;;;;;;;;;;;;;;;;;;;;;;;;;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;QACC,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,CAAC,IAAI,CAAC,YAAY;wBACnB,CAAC,CACJ,CAAA;gBACH,CAAC;qBAAM,IAAI,eAAe,KAA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|
package/dist/tbi.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import
|
|
2
|
-
import
|
|
3
|
-
import
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import IndexFile, { Options } from './indexFile.ts';
|
|
3
|
+
import VirtualOffset from './virtualOffset.ts';
|
|
4
4
|
export default class TabixIndex extends IndexFile {
|
|
5
5
|
lineCount(refName: string, opts?: Options): Promise<any>;
|
|
6
6
|
_parse(opts?: Options): Promise<{
|
package/dist/tbi.js
CHANGED
|
@@ -36,12 +36,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
36
36
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
37
37
|
};
|
|
38
38
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
39
|
-
const virtualOffset_1 = __importStar(require("./virtualOffset"));
|
|
40
|
-
const chunk_1 = __importDefault(require("./chunk"));
|
|
41
39
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
42
|
-
const
|
|
43
|
-
const
|
|
44
|
-
const
|
|
40
|
+
const chunk_ts_1 = __importDefault(require("./chunk.js"));
|
|
41
|
+
const indexFile_ts_1 = __importDefault(require("./indexFile.js"));
|
|
42
|
+
const long_ts_1 = require("./long.js");
|
|
43
|
+
const util_ts_1 = require("./util.js");
|
|
44
|
+
const virtualOffset_ts_1 = __importStar(require("./virtualOffset.js"));
|
|
45
45
|
const TBI_MAGIC = 21578324; // TBI\1
|
|
46
46
|
const TAD_LIDX_SHIFT = 14;
|
|
47
47
|
/**
|
|
@@ -60,7 +60,7 @@ function reg2bins(beg, end) {
|
|
|
60
60
|
[4681 + (beg >> 14), 4681 + (end >> 14)],
|
|
61
61
|
];
|
|
62
62
|
}
|
|
63
|
-
class TabixIndex extends
|
|
63
|
+
class TabixIndex extends indexFile_ts_1.default {
|
|
64
64
|
async lineCount(refName, opts = {}) {
|
|
65
65
|
const indexData = await this.parse(opts);
|
|
66
66
|
const refId = indexData.refNameToId[refName];
|
|
@@ -77,7 +77,7 @@ class TabixIndex extends indexFile_1.default {
|
|
|
77
77
|
async _parse(opts = {}) {
|
|
78
78
|
const buf = await this.filehandle.readFile(opts);
|
|
79
79
|
const bytes = await (0, bgzf_filehandle_1.unzip)(buf);
|
|
80
|
-
(0,
|
|
80
|
+
(0, util_ts_1.checkAbortSignal)(opts.signal);
|
|
81
81
|
const dataView = new DataView(bytes.buffer);
|
|
82
82
|
const magic = dataView.getUint32(0, true);
|
|
83
83
|
if (magic !== TBI_MAGIC /* "TBI\1" */) {
|
|
@@ -138,11 +138,11 @@ class TabixIndex extends indexFile_1.default {
|
|
|
138
138
|
currOffset += 4;
|
|
139
139
|
const chunks = new Array(chunkCount);
|
|
140
140
|
for (let k = 0; k < chunkCount; k += 1) {
|
|
141
|
-
const u = (0,
|
|
142
|
-
const v = (0,
|
|
141
|
+
const u = (0, virtualOffset_ts_1.fromBytes)(bytes, currOffset);
|
|
142
|
+
const v = (0, virtualOffset_ts_1.fromBytes)(bytes, currOffset + 8);
|
|
143
143
|
currOffset += 16;
|
|
144
144
|
firstDataLine = this._findFirstData(firstDataLine, u);
|
|
145
|
-
chunks[k] = new
|
|
145
|
+
chunks[k] = new chunk_ts_1.default(u, v, bin);
|
|
146
146
|
}
|
|
147
147
|
binIndex[bin] = chunks;
|
|
148
148
|
}
|
|
@@ -152,7 +152,7 @@ class TabixIndex extends indexFile_1.default {
|
|
|
152
152
|
currOffset += 4;
|
|
153
153
|
const linearIndex = new Array(linearCount);
|
|
154
154
|
for (let k = 0; k < linearCount; k += 1) {
|
|
155
|
-
linearIndex[k] = (0,
|
|
155
|
+
linearIndex[k] = (0, virtualOffset_ts_1.fromBytes)(bytes, currOffset);
|
|
156
156
|
currOffset += 8;
|
|
157
157
|
firstDataLine = this._findFirstData(firstDataLine, linearIndex[k]);
|
|
158
158
|
}
|
|
@@ -179,7 +179,7 @@ class TabixIndex extends indexFile_1.default {
|
|
|
179
179
|
}
|
|
180
180
|
parsePseudoBin(bytes, offset) {
|
|
181
181
|
return {
|
|
182
|
-
lineCount: (0,
|
|
182
|
+
lineCount: (0, long_ts_1.longFromBytesToUnsigned)(bytes, offset + 16),
|
|
183
183
|
};
|
|
184
184
|
}
|
|
185
185
|
_parseNameBytes(namesBytes) {
|
|
@@ -221,7 +221,7 @@ class TabixIndex extends indexFile_1.default {
|
|
|
221
221
|
? ba.linearIndex[min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
|
|
222
222
|
? ba.linearIndex.length - 1
|
|
223
223
|
: min >> TAD_LIDX_SHIFT]
|
|
224
|
-
: new
|
|
224
|
+
: new virtualOffset_ts_1.default(0, 0);
|
|
225
225
|
if (!minOffset) {
|
|
226
226
|
console.warn('querying outside of possible tabix range');
|
|
227
227
|
}
|
|
@@ -233,7 +233,7 @@ class TabixIndex extends indexFile_1.default {
|
|
|
233
233
|
for (let bin = start; bin <= end; bin++) {
|
|
234
234
|
if (ba.binIndex[bin]) {
|
|
235
235
|
for (const c of ba.binIndex[bin]) {
|
|
236
|
-
chunks.push(new
|
|
236
|
+
chunks.push(new chunk_ts_1.default(c.minv, c.maxv, bin));
|
|
237
237
|
}
|
|
238
238
|
}
|
|
239
239
|
}
|
|
@@ -252,7 +252,7 @@ class TabixIndex extends indexFile_1.default {
|
|
|
252
252
|
}
|
|
253
253
|
}
|
|
254
254
|
}
|
|
255
|
-
return (0,
|
|
255
|
+
return (0, util_ts_1.optimizeChunks)(chunks, lowest);
|
|
256
256
|
}
|
|
257
257
|
}
|
|
258
258
|
exports.default = TabixIndex;
|
package/dist/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,
|
|
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,IAAI,CAAA;QAClE,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;gBAC7C,UAAU,IAAI,CAAC,CAAA;gBACf,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;YACpE,CAAC;YACD,OAAO;gBACL,QAAQ;gBACR,WAAW;gBACX,KAAK;aACN,CAAA;QACH,CAAC,CAAC,CAAA;QAEF,OAAO;YACL,OAAO;YACP,QAAQ;YACR,YAAY;YACZ,YAAY;YACZ,SAAS;YACT,aAAa;YACb,aAAa;YACb,cAAc;YACd,MAAM;YACN,WAAW;YACX,WAAW;YACX,YAAY,EAAE,CAAC,IAAI,EAAE;SACtB,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,eAAe,CAAC,UAAsB;QACpC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAa,EAAE,CAAA;QAChC,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,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,MAAM,SAAS,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM;YACrC,CAAC,CAAC,EAAE,CAAC,WAAW,CACZ,GAAG,IAAI,cAAc,IAAI,EAAE,CAAC,WAAW,CAAC,MAAM;gBAC5C,CAAC,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC;gBAC3B,CAAC,CAAC,GAAG,IAAI,cAAc,CAC1B;YACH,CAAC,CAAC,IAAI,0BAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QAC3B,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,OAAO,CAAC,IAAI,CAAC,0CAA0C,CAAC,CAAA;QAC1D,CAAC;QAED,4CAA4C;QAE5C,MAAM,eAAe,GAAG,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA,CAAC,uCAAuC;QAClF,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,0EAA0E;QAC1E,mCAAmC;QACnC,MAAM,KAAK,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM,CAAA;QACnC,IAAI,MAAM,GAAG,IAAI,CAAA;QACjB,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7C,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,IAAI,MAAM,EAAE,EAAE,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YAC5B,IAAI,EAAE,EAAE,CAAC;gBACP,IAAI,CAAC,MAAM,IAAI,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxC,MAAM,GAAG,EAAE,CAAA;gBACb,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,MAAM,CAAC,CAAA;IACvC,CAAC;CACF;AA/ND,6BA+NC"}
|
package/dist/util.d.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import Chunk from './chunk';
|
|
2
|
-
import VirtualOffset from './virtualOffset';
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import VirtualOffset from './virtualOffset.ts';
|
|
3
3
|
/**
|
|
4
4
|
* Properly check if the given AbortSignal is aborted. Per the standard, if the
|
|
5
5
|
* signal reads as aborted, this function throws either a DOMException
|
package/esm/chunk.d.ts
CHANGED
package/esm/csi.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import
|
|
2
|
-
import
|
|
3
|
-
import
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import IndexFile, { Options } from './indexFile.ts';
|
|
3
|
+
import VirtualOffset from './virtualOffset.ts';
|
|
4
4
|
export default class CSI extends IndexFile {
|
|
5
5
|
private maxBinNumber;
|
|
6
6
|
private depth;
|
package/esm/csi.js
CHANGED
|
@@ -1,9 +1,9 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
|
-
import
|
|
3
|
-
import
|
|
4
|
-
import {
|
|
5
|
-
import
|
|
6
|
-
import {
|
|
2
|
+
import Chunk from "./chunk.js";
|
|
3
|
+
import IndexFile from "./indexFile.js";
|
|
4
|
+
import { longFromBytesToUnsigned } from "./long.js";
|
|
5
|
+
import { optimizeChunks } from "./util.js";
|
|
6
|
+
import VirtualOffset, { fromBytes } from "./virtualOffset.js";
|
|
7
7
|
const CSI1_MAGIC = 21582659; // CSI\1
|
|
8
8
|
const CSI2_MAGIC = 38359875; // CSI\2
|
|
9
9
|
const formats = {
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAsB,MAAM,gBAAgB,CAAA;AACnD,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AACnD,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC1C,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;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,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;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,IAAI,CAAA;QAClE,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,4BAA4B;IAE5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,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,IAAI;gBACd,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,SAAS,CAAC,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,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,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,uBAAuB,CAAC,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,KAAK,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;oBAC7C,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,cAAc,CAAC,MAAM,EAAE,IAAI,aAAa,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"}
|
package/esm/index.d.ts
CHANGED
|
@@ -1,3 +1,3 @@
|
|
|
1
|
-
export { default as TabixIndexedFile } from './tabixIndexedFile';
|
|
2
|
-
export { default as CSI } from './csi';
|
|
3
|
-
export { default as TBI } from './tbi';
|
|
1
|
+
export { default as TabixIndexedFile } from './tabixIndexedFile.ts';
|
|
2
|
+
export { default as CSI } from './csi.ts';
|
|
3
|
+
export { default as TBI } from './tbi.ts';
|
package/esm/index.js
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
export { default as TabixIndexedFile } from
|
|
2
|
-
export { default as CSI } from
|
|
3
|
-
export { default as TBI } from
|
|
1
|
+
export { default as TabixIndexedFile } from "./tabixIndexedFile.js";
|
|
2
|
+
export { default as CSI } from "./csi.js";
|
|
3
|
+
export { default as TBI } from "./tbi.js";
|
|
4
4
|
//# sourceMappingURL=index.js.map
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,gBAAgB,EAAE,MAAM,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACnE,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA"}
|
package/esm/indexFile.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import
|
|
2
|
-
import VirtualOffset from './virtualOffset';
|
|
3
|
-
import
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import VirtualOffset from './virtualOffset.ts';
|
|
3
|
+
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
4
4
|
export interface Options {
|
|
5
5
|
signal?: AbortSignal;
|
|
6
6
|
}
|
package/esm/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAmBA,MAAM,CAAC,OAAO,OAAgB,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,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,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"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import
|
|
2
|
-
import {
|
|
3
|
-
import
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import { IndexData, Options } from './indexFile.ts';
|
|
3
|
+
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
4
4
|
type GetLinesCallback = (line: string, fileOffset: number) => void;
|
|
5
5
|
interface GetLinesOpts {
|
|
6
6
|
[key: string]: unknown;
|
package/esm/tabixIndexedFile.js
CHANGED
|
@@ -1,10 +1,10 @@
|
|
|
1
1
|
import AbortablePromiseCache from '@gmod/abortable-promise-cache';
|
|
2
|
-
import LRU from 'quick-lru';
|
|
3
|
-
import { RemoteFile, LocalFile } from 'generic-filehandle2';
|
|
4
2
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
|
|
5
|
-
import {
|
|
6
|
-
import
|
|
7
|
-
import CSI from
|
|
3
|
+
import { LocalFile, RemoteFile } from 'generic-filehandle2';
|
|
4
|
+
import LRU from 'quick-lru';
|
|
5
|
+
import CSI from "./csi.js";
|
|
6
|
+
import TBI from "./tbi.js";
|
|
7
|
+
import { checkAbortSignal } from "./util.js";
|
|
8
8
|
function isASCII(str) {
|
|
9
9
|
// eslint-disable-next-line no-control-regex
|
|
10
10
|
return /^[\u0000-\u007F]*$/.test(str);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
{"version":3,"file":"tabixIndexedFile.js","sourceRoot":"","sources":["../src/tabixIndexedFile.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,+BAA+B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAA;AAC9D,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AAC3D,OAAO,GAAG,MAAM,WAAW,CAAA;AAG3B,OAAO,GAAG,MAAM,UAAU,CAAA;AAE1B,OAAO,GAAG,MAAM,UAAU,CAAA;AAC1B,OAAO,EAAE,gBAAgB,EAAE,MAAM,WAAW,CAAA;AAI5C,SAAS,OAAO,CAAC,GAAW;IAC1B,4CAA4C;IAC5C,OAAO,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;AACvC,CAAC;AAgBD,MAAM,CAAC,OAAO,OAAO,gBAAgB;IAMnC;;;;;;;;;;;;;;;;;;;;;;;;;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;QACC,IAAI,UAAU,EAAE,CAAC;YACf,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC9B,CAAC;aAAM,IAAI,IAAI,EAAE,CAAC;YAChB,IAAI,CAAC,UAAU,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,CAAA;QACvC,CAAC;aAAM,IAAI,GAAG,EAAE,CAAC;YACf,IAAI,CAAC,UAAU,GAAG,IAAI,UAAU,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,GAAG,CAAC;gBACnB,UAAU,EAAE,aAAa;gBACzB,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,aAAa,EAAE,CAAC;YACzB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,aAAa;gBACzB,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,SAAS,CAAC,OAAO,CAAC;gBAClC,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,SAAS,CAAC,OAAO,CAAC;gBAClC,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,IAAI,EAAE,CAAC;YAChB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,SAAS,CAAC,GAAG,IAAI,MAAM,CAAC;gBACxC,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,MAAM,EAAE,CAAC;YAClB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,UAAU,CAAC,MAAM,CAAC;aACnC,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,MAAM,EAAE,CAAC;YAClB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,UAAU,CAAC,MAAM,CAAC;aACnC,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,GAAG,EAAE,CAAC;YACf,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,UAAU,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,qBAAqB,CAAmB;YAC5D,KAAK,EAAE,IAAI,GAAG,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,gBAAgB,CAAC,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,gBAAgB,CAAC,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,gBAAgB,CAAC,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,CAA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|
package/esm/tbi.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import
|
|
2
|
-
import
|
|
3
|
-
import
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import IndexFile, { Options } from './indexFile.ts';
|
|
3
|
+
import VirtualOffset from './virtualOffset.ts';
|
|
4
4
|
export default class TabixIndex extends IndexFile {
|
|
5
5
|
lineCount(refName: string, opts?: Options): Promise<any>;
|
|
6
6
|
_parse(opts?: Options): Promise<{
|
package/esm/tbi.js
CHANGED
|
@@ -1,9 +1,9 @@
|
|
|
1
|
-
import VirtualOffset, { fromBytes } from './virtualOffset';
|
|
2
|
-
import Chunk from './chunk';
|
|
3
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
4
|
-
import
|
|
5
|
-
import IndexFile from
|
|
6
|
-
import { longFromBytesToUnsigned } from
|
|
2
|
+
import Chunk from "./chunk.js";
|
|
3
|
+
import IndexFile from "./indexFile.js";
|
|
4
|
+
import { longFromBytesToUnsigned } from "./long.js";
|
|
5
|
+
import { checkAbortSignal, optimizeChunks } from "./util.js";
|
|
6
|
+
import VirtualOffset, { fromBytes } from "./virtualOffset.js";
|
|
7
7
|
const TBI_MAGIC = 21578324; // TBI\1
|
|
8
8
|
const TAD_LIDX_SHIFT = 14;
|
|
9
9
|
/**
|
package/esm/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAsB,MAAM,gBAAgB,CAAA;AACnD,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AACnD,OAAO,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC5D,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;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,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAAS;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,KAAK,CAAC,GAAG,CAAC,CAAA;QAC9B,gBAAgB,CAAC,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,IAAI,CAAA;QAClE,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,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,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,KAAK,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,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gBAC7C,UAAU,IAAI,CAAC,CAAA;gBACf,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;YACpE,CAAC;YACD,OAAO;gBACL,QAAQ;gBACR,WAAW;gBACX,KAAK;aACN,CAAA;QACH,CAAC,CAAC,CAAA;QAEF,OAAO;YACL,OAAO;YACP,QAAQ;YACR,YAAY;YACZ,YAAY;YACZ,SAAS;YACT,aAAa;YACb,aAAa;YACb,cAAc;YACd,MAAM;YACN,WAAW;YACX,WAAW;YACX,YAAY,EAAE,CAAC,IAAI,EAAE;SACtB,CAAA;IACH,CAAC;IAED,cAAc,CAAC,KAAiB,EAAE,MAAc;QAC9C,OAAO;YACL,SAAS,EAAE,uBAAuB,CAAC,KAAK,EAAE,MAAM,GAAG,EAAE,CAAC;SACvD,CAAA;IACH,CAAC;IAED,eAAe,CAAC,UAAsB;QACpC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAa,EAAE,CAAA;QAChC,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,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,MAAM,SAAS,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM;YACrC,CAAC,CAAC,EAAE,CAAC,WAAW,CACZ,GAAG,IAAI,cAAc,IAAI,EAAE,CAAC,WAAW,CAAC,MAAM;gBAC5C,CAAC,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC;gBAC3B,CAAC,CAAC,GAAG,IAAI,cAAc,CAC1B;YACH,CAAC,CAAC,IAAI,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QAC3B,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,OAAO,CAAC,IAAI,CAAC,0CAA0C,CAAC,CAAA;QAC1D,CAAC;QAED,4CAA4C;QAE5C,MAAM,eAAe,GAAG,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA,CAAC,uCAAuC;QAClF,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,KAAK,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;oBAC7C,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,0EAA0E;QAC1E,mCAAmC;QACnC,MAAM,KAAK,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM,CAAA;QACnC,IAAI,MAAM,GAAG,IAAI,CAAA;QACjB,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;QAC7C,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,IAAI,MAAM,EAAE,EAAE,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YAC5B,IAAI,EAAE,EAAE,CAAC;gBACP,IAAI,CAAC,MAAM,IAAI,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxC,MAAM,GAAG,EAAE,CAAA;gBACb,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;IACvC,CAAC;CACF"}
|
package/esm/util.d.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import Chunk from './chunk';
|
|
2
|
-
import VirtualOffset from './virtualOffset';
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import VirtualOffset from './virtualOffset.ts';
|
|
3
3
|
/**
|
|
4
4
|
* Properly check if the given AbortSignal is aborted. Per the standard, if the
|
|
5
5
|
* signal reads as aborted, this function throws either a DOMException
|
package/package.json
CHANGED
|
@@ -1,7 +1,17 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/tabix",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "3.0.1",
|
|
4
4
|
"description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
|
|
5
|
+
"type": "module",
|
|
6
|
+
"types": "./dist/index.d.ts",
|
|
7
|
+
"exports": {
|
|
8
|
+
"import": {
|
|
9
|
+
"import": "./esm/index.js"
|
|
10
|
+
},
|
|
11
|
+
"require": {
|
|
12
|
+
"require": "./dist/index.js"
|
|
13
|
+
}
|
|
14
|
+
},
|
|
5
15
|
"license": "MIT",
|
|
6
16
|
"repository": "GMOD/tabix-js",
|
|
7
17
|
"main": "dist/index.js",
|
|
@@ -26,8 +36,8 @@
|
|
|
26
36
|
"docs": "documentation readme --shallow src/tabixIndexedFile.ts --section TabixIndexedFile",
|
|
27
37
|
"clean": "rimraf dist esm",
|
|
28
38
|
"prebuild": "npm run clean && npm run lint",
|
|
29
|
-
"build:esm": "tsc --outDir esm",
|
|
30
|
-
"build:es5": "tsc --module commonjs --outDir dist",
|
|
39
|
+
"build:esm": "tsc --target es2020 --outDir esm",
|
|
40
|
+
"build:es5": "tsc --target es2020 --module commonjs --outDir dist",
|
|
31
41
|
"build": "npm run build:esm && npm run build:es5",
|
|
32
42
|
"postbuild": "webpack",
|
|
33
43
|
"preversion": "npm run lint && npm test run && npm run build",
|
|
@@ -43,19 +53,16 @@
|
|
|
43
53
|
"dependencies": {
|
|
44
54
|
"@gmod/abortable-promise-cache": "^2.0.0",
|
|
45
55
|
"@gmod/bgzf-filehandle": "^2.0.1",
|
|
46
|
-
"generic-filehandle2": "^
|
|
56
|
+
"generic-filehandle2": "^2.0.1",
|
|
47
57
|
"quick-lru": "^4.0.0"
|
|
48
58
|
},
|
|
49
59
|
"devDependencies": {
|
|
50
|
-
"@
|
|
51
|
-
"@eslint/js": "^9.9.0",
|
|
52
|
-
"@types/node": "^20.11.16",
|
|
53
|
-
"@typescript-eslint/eslint-plugin": "^8.0.1",
|
|
54
|
-
"@typescript-eslint/parser": "^8.0.1",
|
|
60
|
+
"@types/node": "^22.15.3",
|
|
55
61
|
"@vitest/coverage-v8": "^3.0.1",
|
|
56
62
|
"documentation": "^14.0.3",
|
|
57
63
|
"eslint": "^9.9.0",
|
|
58
|
-
"eslint-plugin-
|
|
64
|
+
"eslint-plugin-import": "^2.31.0",
|
|
65
|
+
"eslint-plugin-unicorn": "^59.0.0",
|
|
59
66
|
"prettier": "^3.3.3",
|
|
60
67
|
"rimraf": "^6.0.1",
|
|
61
68
|
"standard-changelog": "^6.0.0",
|
package/src/chunk.ts
CHANGED
package/src/csi.ts
CHANGED
|
@@ -1,11 +1,10 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle'
|
|
2
2
|
|
|
3
|
-
import
|
|
4
|
-
import
|
|
5
|
-
import {
|
|
6
|
-
|
|
7
|
-
import
|
|
8
|
-
import { longFromBytesToUnsigned } from './long'
|
|
3
|
+
import Chunk from './chunk.ts'
|
|
4
|
+
import IndexFile, { Options } from './indexFile.ts'
|
|
5
|
+
import { longFromBytesToUnsigned } from './long.ts'
|
|
6
|
+
import { optimizeChunks } from './util.ts'
|
|
7
|
+
import VirtualOffset, { fromBytes } from './virtualOffset.ts'
|
|
9
8
|
|
|
10
9
|
const CSI1_MAGIC = 21582659 // CSI\1
|
|
11
10
|
const CSI2_MAGIC = 38359875 // CSI\2
|
package/src/index.ts
CHANGED
|
@@ -1,3 +1,3 @@
|
|
|
1
|
-
export { default as TabixIndexedFile } from './tabixIndexedFile'
|
|
2
|
-
export { default as CSI } from './csi'
|
|
3
|
-
export { default as TBI } from './tbi'
|
|
1
|
+
export { default as TabixIndexedFile } from './tabixIndexedFile.ts'
|
|
2
|
+
export { default as CSI } from './csi.ts'
|
|
3
|
+
export { default as TBI } from './tbi.ts'
|
package/src/indexFile.ts
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
|
-
import
|
|
2
|
-
import VirtualOffset from './virtualOffset'
|
|
3
|
-
|
|
1
|
+
import Chunk from './chunk.ts'
|
|
2
|
+
import VirtualOffset from './virtualOffset.ts'
|
|
3
|
+
|
|
4
|
+
import type { GenericFilehandle } from 'generic-filehandle2'
|
|
4
5
|
|
|
5
6
|
export interface Options {
|
|
6
7
|
signal?: AbortSignal
|
package/src/tabixIndexedFile.ts
CHANGED
|
@@ -1,13 +1,15 @@
|
|
|
1
1
|
import AbortablePromiseCache from '@gmod/abortable-promise-cache'
|
|
2
|
-
import LRU from 'quick-lru'
|
|
3
|
-
import { GenericFilehandle, RemoteFile, LocalFile } from 'generic-filehandle2'
|
|
4
2
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
|
|
5
|
-
import {
|
|
6
|
-
import
|
|
3
|
+
import { LocalFile, RemoteFile } from 'generic-filehandle2'
|
|
4
|
+
import LRU from 'quick-lru'
|
|
5
|
+
|
|
6
|
+
import Chunk from './chunk.ts'
|
|
7
|
+
import CSI from './csi.ts'
|
|
8
|
+
import IndexFile, { IndexData, Options } from './indexFile.ts'
|
|
9
|
+
import TBI from './tbi.ts'
|
|
10
|
+
import { checkAbortSignal } from './util.ts'
|
|
7
11
|
|
|
8
|
-
import
|
|
9
|
-
import TBI from './tbi'
|
|
10
|
-
import CSI from './csi'
|
|
12
|
+
import type { GenericFilehandle } from 'generic-filehandle2'
|
|
11
13
|
|
|
12
14
|
function isASCII(str: string) {
|
|
13
15
|
// eslint-disable-next-line no-control-regex
|
package/src/tbi.ts
CHANGED
|
@@ -1,9 +1,10 @@
|
|
|
1
|
-
import VirtualOffset, { fromBytes } from './virtualOffset'
|
|
2
|
-
import Chunk from './chunk'
|
|
3
1
|
import { unzip } from '@gmod/bgzf-filehandle'
|
|
4
|
-
|
|
5
|
-
import
|
|
6
|
-
import {
|
|
2
|
+
|
|
3
|
+
import Chunk from './chunk.ts'
|
|
4
|
+
import IndexFile, { Options } from './indexFile.ts'
|
|
5
|
+
import { longFromBytesToUnsigned } from './long.ts'
|
|
6
|
+
import { checkAbortSignal, optimizeChunks } from './util.ts'
|
|
7
|
+
import VirtualOffset, { fromBytes } from './virtualOffset.ts'
|
|
7
8
|
|
|
8
9
|
const TBI_MAGIC = 21578324 // TBI\1
|
|
9
10
|
const TAD_LIDX_SHIFT = 14
|
package/src/util.ts
CHANGED