@gmod/tabix 2.0.4 → 3.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +4 -6
- package/README.md +3 -3
- 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 -4
- 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 -4
- 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 +19 -12
- package/src/chunk.ts +1 -1
- package/src/csi.ts +5 -6
- package/src/index.ts +3 -3
- package/src/indexFile.ts +4 -5
- package/src/tabixIndexedFile.ts +9 -7
- package/src/tbi.ts +6 -5
- package/src/util.ts +2 -2
package/dist/tbi.js
CHANGED
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@@ -36,12 +36,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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-
const virtualOffset_1 = __importStar(require("./virtualOffset"));
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-
const chunk_1 = __importDefault(require("./chunk"));
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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 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 TBI_MAGIC = 21578324; // TBI\1
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const TAD_LIDX_SHIFT = 14;
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/**
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@@ -60,7 +60,7 @@ function reg2bins(beg, end) {
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[4681 + (beg >> 14), 4681 + (end >> 14)],
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];
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}
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-
class TabixIndex extends
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+
class TabixIndex extends indexFile_ts_1.default {
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async lineCount(refName, opts = {}) {
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const indexData = await this.parse(opts);
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const refId = indexData.refNameToId[refName];
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@@ -77,7 +77,7 @@ class TabixIndex extends indexFile_1.default {
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async _parse(opts = {}) {
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const buf = await this.filehandle.readFile(opts);
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const bytes = await (0, bgzf_filehandle_1.unzip)(buf);
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(0,
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(0, util_ts_1.checkAbortSignal)(opts.signal);
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const dataView = new DataView(bytes.buffer);
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const magic = dataView.getUint32(0, true);
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if (magic !== TBI_MAGIC /* "TBI\1" */) {
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@@ -138,11 +138,11 @@ class TabixIndex extends indexFile_1.default {
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currOffset += 4;
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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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firstDataLine = this._findFirstData(firstDataLine, u);
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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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@@ -152,7 +152,7 @@ class TabixIndex extends indexFile_1.default {
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currOffset += 4;
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const linearIndex = new Array(linearCount);
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for (let k = 0; k < linearCount; k += 1) {
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linearIndex[k] = (0,
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linearIndex[k] = (0, virtualOffset_ts_1.fromBytes)(bytes, currOffset);
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currOffset += 8;
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firstDataLine = this._findFirstData(firstDataLine, linearIndex[k]);
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}
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@@ -179,7 +179,7 @@ class TabixIndex extends indexFile_1.default {
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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 + 16),
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};
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}
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_parseNameBytes(namesBytes) {
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@@ -221,7 +221,7 @@ class TabixIndex extends indexFile_1.default {
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? ba.linearIndex[min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
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? ba.linearIndex.length - 1
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: min >> TAD_LIDX_SHIFT]
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-
: new
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: new virtualOffset_ts_1.default(0, 0);
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if (!minOffset) {
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console.warn('querying outside of possible tabix range');
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}
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@@ -233,7 +233,7 @@ class TabixIndex extends indexFile_1.default {
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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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@@ -252,7 +252,7 @@ class TabixIndex extends indexFile_1.default {
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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, lowest);
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}
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}
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exports.default = TabixIndex;
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package/dist/tbi.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,
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1
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+
{"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;gBAC7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|
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,IAA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|
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
|
@@ -1,8 +1,7 @@
|
|
|
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
|
-
[key: string]: unknown;
|
|
6
5
|
signal?: AbortSignal;
|
|
7
6
|
}
|
|
8
7
|
export interface IndexData {
|
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
|
-
{"version":3,"file":"tabixIndexedFile.js","sourceRoot":"","sources":["../src/tabixIndexedFile.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,+BAA+B,CAAA;AACjE,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EAAqB,UAAU,EAAE,SAAS,EAAE,MAAM,qBAAqB,CAAA;AAC9E,OAAO,EAAE,KAAK,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAA;AAC9D,OAAO,EAAE,gBAAgB,EAAE,MAAM,QAAQ,CAAA;AAIzC,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AAEvB,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,CA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|
|
1
|
+
{"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": "3.0.0",
|
|
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",
|
|
@@ -47,23 +57,20 @@
|
|
|
47
57
|
"quick-lru": "^4.0.0"
|
|
48
58
|
},
|
|
49
59
|
"devDependencies": {
|
|
50
|
-
"@
|
|
51
|
-
"@
|
|
52
|
-
"@types/node": "^20.11.16",
|
|
53
|
-
"@typescript-eslint/eslint-plugin": "^8.0.1",
|
|
54
|
-
"@typescript-eslint/parser": "^8.0.1",
|
|
55
|
-
"@vitest/coverage-v8": "^2.0.5",
|
|
60
|
+
"@types/node": "^22.15.3",
|
|
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",
|
|
62
69
|
"typescript": "^5.7.0",
|
|
63
70
|
"typescript-eslint": "^8.0.1",
|
|
64
|
-
"vitest": "^
|
|
71
|
+
"vitest": "^3.0.1",
|
|
65
72
|
"webpack": "^5.93.0",
|
|
66
|
-
"webpack-cli": "^
|
|
73
|
+
"webpack-cli": "^6.0.1"
|
|
67
74
|
},
|
|
68
75
|
"publishConfig": {
|
|
69
76
|
"access": "public"
|
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
|
@@ -1,10 +1,9 @@
|
|
|
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
|
-
// support having some unknown parts of the options
|
|
7
|
-
[key: string]: unknown
|
|
8
7
|
signal?: AbortSignal
|
|
9
8
|
}
|
|
10
9
|
|
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