@gmod/bam 1.1.11 → 1.1.14
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 +21 -9
- package/dist/bai.d.ts +1 -1
- package/dist/bai.js +38 -51
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +1 -0
- package/dist/bamFile.js +21 -7
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +6 -7
- package/dist/csi.js.map +1 -1
- package/dist/htsget.js +5 -1
- package/dist/htsget.js.map +1 -1
- package/dist/indexFile.d.ts +1 -1
- package/dist/record.d.ts +8 -8
- package/dist/record.js +18 -28
- package/dist/record.js.map +1 -1
- package/esm/bai.d.ts +1 -1
- package/esm/bai.js +6 -5
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +1 -0
- package/esm/bamFile.js +12 -7
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +1 -6
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +1 -1
- package/esm/record.d.ts +8 -8
- package/esm/record.js +18 -28
- package/esm/record.js.map +1 -1
- package/package.json +13 -18
package/CHANGELOG.md
CHANGED
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@@ -1,30 +1,42 @@
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## [1.1.14](https://github.com/GMOD/bam-js/compare/v1.1.13...v1.1.14) (2022-03-14)
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- Fix seq function for corner case
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## [1.1.13](https://github.com/GMOD/bam-js/compare/v1.1.12...v1.1.13) (2022-02-25)
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- Optimize qual and sequence string record functions for less GC pressure
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<a name="1.1.12"></a>
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## [1.1.12](https://github.com/GMOD/bam-js/compare/v1.1.11...v1.1.12) (2022-02-17)
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- Add blocksForRange method to BamFile class to help stats estimation in JBrowse 2
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<a name="1.1.11"></a>
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## [1.1.11](https://github.com/GMOD/bam-js/compare/v1.1.10...v1.1.11) (2022-01-26)
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- Cache setup of index file parsing
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<a name="1.1.10"></a>
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## [1.1.10](https://github.com/GMOD/bam-js/compare/v1.1.9...v1.1.10) (2022-01-18)
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## [1.1.10](https://github.com/GMOD/bam-js/compare/v1.1.9...v1.1.10) (2022-01-18)
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- Make _refID and flags public fields
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- Make \_refID and flags public fields
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- Small internal changes to the handling of opts
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<a name="1.1.9"></a>
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## [1.1.9](https://github.com/GMOD/bam-js/compare/v1.1.8...v1.1.9) (2021-12-14)
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## [1.1.9](https://github.com/GMOD/bam-js/compare/v1.1.8...v1.1.9) (2021-12-14)
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- Add ESM module export in package.json (smaller bundle size for consumers)
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- Cache BAI readFile result for compatibility with node.js native filehandles (which otherwise fail if re-reading the filehandle twice)
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<a name="1.1.8"></a>
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## [1.1.8](https://github.com/GMOD/bam-js/compare/v1.1.7...v1.1.8) (2021-05-21)
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## [1.1.8](https://github.com/GMOD/bam-js/compare/v1.1.7...v1.1.8) (2021-05-21)
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- Fix types for yieldThreadTime
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package/dist/bai.d.ts
CHANGED
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@@ -9,7 +9,7 @@ export default class BAI extends IndexFile {
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};
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lineCount(refId: number, opts?: BaseOpts): Promise<any>;
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fetchBai(opts?: BaseOpts): Promise<Buffer>;
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_parse(
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_parse(): Promise<{
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[key: string]: any;
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}>;
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indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<{
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package/dist/bai.js
CHANGED
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@@ -117,8 +117,7 @@ var BAI = /** @class */ (function (_super) {
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return this.baiP;
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};
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// fetch and parse the index
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BAI.prototype._parse = function (
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if (opts === void 0) { opts = {}; }
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BAI.prototype._parse = function () {
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return __awaiter(this, void 0, void 0, function () {
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var data, bytes, depth, binLimit, currOffset, i, binCount, stats, binIndex, j, bin, chunkCount, chunks, k, u, v, linearCount, linearIndex, k;
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return __generator(this, function (_a) {
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// read the indexes for each reference sequence
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data.indices = new Array(data.refCount);
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currOffset = 8;
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i = 0;
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if (!(i < data.refCount)) return [3 /*break*/, 5];
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return [4 /*yield*/, (0, util_1.abortBreakPoint)(opts.signal)
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// the binning index
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];
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case 3:
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_a.sent();
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binCount = bytes.readInt32LE(currOffset);
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stats = void 0;
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currOffset += 4;
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binIndex = {};
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for (j = 0; j < binCount; j += 1) {
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bin = bytes.readUInt32LE(currOffset);
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for (i = 0; i < data.refCount; i += 1) {
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binCount = bytes.readInt32LE(currOffset);
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stats = void 0;
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currOffset += 4;
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currOffset += 32;
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}
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else if (bin > binLimit + 1) {
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throw new Error('bai index contains too many bins, please use CSI');
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}
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else {
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chunkCount = bytes.readInt32LE(currOffset);
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binIndex = {};
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for (j = 0; j < binCount; j += 1) {
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bin = bytes.readUInt32LE(currOffset);
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currOffset += 4;
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if (bin === binLimit + 1) {
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currOffset += 4;
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stats = this.parsePseudoBin(bytes, currOffset);
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currOffset += 32;
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}
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else if (bin > binLimit + 1) {
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throw new Error('bai index contains too many bins, please use CSI');
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}
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else {
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chunkCount = bytes.readInt32LE(currOffset);
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currOffset += 4;
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chunks = new Array(chunkCount);
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for (k = 0; k < chunkCount; k += 1) {
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u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
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v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
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currOffset += 16;
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this._findFirstData(data, u);
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chunks[k] = new chunk_1.default(u, v, bin);
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}
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binIndex[bin] = chunks;
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}
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binIndex[bin] = chunks;
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}
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linearCount = bytes.readInt32LE(currOffset);
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currOffset += 4;
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linearIndex = new Array(linearCount);
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for (k = 0; k < linearCount; k += 1) {
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linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
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currOffset += 8;
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this._findFirstData(data, linearIndex[k]);
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}
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data.indices[i] = { binIndex: binIndex, linearIndex: linearIndex, stats: stats };
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}
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currOffset += 4;
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linearIndex = new Array(linearCount);
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for (k = 0; k < linearCount; k += 1) {
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linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
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currOffset += 8;
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this._findFirstData(data, linearIndex[k]);
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}
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data.indices[i] = { binIndex: binIndex, linearIndex: linearIndex, stats: stats };
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_a.label = 4;
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case 4:
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i += 1;
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return [3 /*break*/, 2];
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case 5: return [2 /*return*/, data];
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return [2 /*return*/, data];
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}
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});
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});
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if (!ba) {
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return [2 /*return*/, []];
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}
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overlappingBins = this.reg2bins(min, max)
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;
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overlappingBins = this.reg2bins(min, max);
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chunks = [];
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// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
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for (_i = 0, overlappingBins_1 = overlappingBins; _i < overlappingBins_1.length; _i++) {
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package/dist/bai.js.map
CHANGED
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{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,iDAA2C;AAC3C,kDAA2B;AAE3B,0DAAmC;AACnC,+
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|
+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,iDAA2C;AAC3C,kDAA2B;AAE3B,0DAAmC;AACnC,+BAA+D;AAE/D,IAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAED;IAAiC,uBAAS;IAA1C;;IAkNA,CAAC;IA/MC,4BAAc,GAAd,UAAe,KAAa,EAAE,MAAc;QAC1C,IAAM,SAAS,GAAG,IAAA,mBAAY,EAC5B,cAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,CAAC,EAC3D,IAAI,CACL,CACF,CAAA;QACD,OAAO,EAAE,SAAS,WAAA,EAAE,CAAA;IACtB,CAAC;IAEK,uBAAS,GAAf,UAAgB,KAAa,EAAE,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;4BACnC,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAA7B,IAAI,GAAG,SAAsB;wBAC7B,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACjC,IAAI,CAAC,KAAK,EAAE;4BACV,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACK,GAAG,GAAG,KAAK,CAAC,KAAK,IAAI,EAAE,CAAA;wBAC7B,sBAAO,GAAG,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,EAAA;;;;KACxD;IAED,sBAAQ,GAAR,UAAS,IAAmB;QAA5B,iBAQC;QARQ,qBAAA,EAAA,SAAmB;QAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE;YACd,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,UAAA,CAAC;gBAChD,KAAI,CAAC,IAAI,GAAG,SAAS,CAAA;gBACrB,MAAM,CAAC,CAAA;YACT,CAAC,CAAoB,CAAA;SACtB;QACD,OAAO,IAAI,CAAC,IAAI,CAAA;IAClB,CAAC;IAED,4BAA4B;IACtB,oBAAM,GAAZ;;;;;;wBACQ,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;wBAC3D,qBAAM,IAAI,CAAC,QAAQ,EAAE;4BAEnC,0BAA0B;0BAFS;;wBAA7B,KAAK,GAAG,SAAqB;wBAEnC,0BAA0B;wBAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;4BACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;yBAClC;wBAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBAC9B,KAAK,GAAG,CAAC,CAAA;wBACT,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;wBAEnD,+CAA+C;wBAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;wBACnC,UAAU,GAAG,CAAC,CAAA;wBAClB,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;4BAEnC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;4BAC1C,KAAK,SAAA,CAAA;4BAET,UAAU,IAAI,CAAC,CAAA;4BACT,QAAQ,GAA+B,EAAE,CAAA;4BAC/C,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gCAC9B,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gCAC1C,UAAU,IAAI,CAAC,CAAA;gCACf,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE;oCACxB,UAAU,IAAI,CAAC,CAAA;oCACf,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oCAC9C,UAAU,IAAI,EAAE,CAAA;iCACjB;qCAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE;oCAC7B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;iCACpE;qCAAM;oCACC,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;oCAChD,UAAU,IAAI,CAAC,CAAA;oCACT,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oCACpC,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;wCAChC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wCAChC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wCAC1C,UAAU,IAAI,EAAE,CAAA;wCAChB,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;wCAC5B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;qCACjC;oCACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;iCACvB;6BACF;4BAEK,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;4BACjD,UAAU,IAAI,CAAC,CAAA;4BAIT,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;4BAC1C,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE;gCACvC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gCAC7C,UAAU,IAAI,CAAC,CAAA;gCACf,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;6BAC1C;4BAED,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,UAAA,EAAE,WAAW,aAAA,EAAE,KAAK,OAAA,EAAE,CAAA;yBACnD;wBAED,sBAAO,IAAI,EAAA;;;;KACZ;IAEK,sBAAQ,GAAd,UACE,KAAa,EACb,KAAc,EACd,GAAY,EACZ,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;;wBAEb,CAAC,GAAG,KAAK,CAAA;wBACT,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;wBACf,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAAlC,SAAS,GAAG,SAAsB;wBAClC,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACvC,IAAI,CAAC,MAAM,EAAE;4BACX,sBAAO,EAAE,EAAA;yBACV;wBACO,KAA4B,MAAM,YAAlB,EAAhB,WAAW,mBAAG,EAAE,KAAA,EAAE,KAAK,GAAK,MAAM,MAAX,CAAW;wBAC1C,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;4BACvB,sBAAO,EAAE,EAAA;yBACV;wBACK,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;wBACtE,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;wBAEvD,IAAI,KAAK,EAAE;4BACT,MAAM,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;yBAChC;6BAAM;4BACL,MAAM,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;yBAC3C;wBACK,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;wBACnE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE;4BACpC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;yBAC1D;wBACG,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;wBACjD,KAAS,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE;4BAC9C,MAAM,CAAC,CAAC,CAAC,GAAG;gCACV,KAAK,EAAE,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,GAAG,UAAU;gCACpD,KAAK,EAAE,CAAC,GAAG,CAAC;gCACZ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC;6BACf,CAAA;4BACD,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;yBAC9C;wBACD,sBAAO,MAAM,CAAC,GAAG,CAAC,UAAA,CAAC;gCACjB,6BAAY,CAAC,KAAE,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,KAAK,CAAC,SAAS,CAAC,GAAG,SAAS,IAAE;4BACjE,CAAC,CAAC,EAAA;;;;KACH;IAED;;;OAGG;IACH,sBAAQ,GAAR,UAAS,GAAW,EAAE,GAAW;QAC/B,GAAG,IAAI,CAAC,CAAA;QACR,OAAO;YACL,CAAC,CAAC,EAAE,CAAC,CAAC;YACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;SACzC,CAAA;IACH,CAAC;IAEK,4BAAc,GAApB,UACE,KAAa,EACb,GAAW,EACX,GAAW,EACX,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;;wBAEnB,IAAI,GAAG,GAAG,CAAC,EAAE;4BACX,GAAG,GAAG,CAAC,CAAA;yBACR;wBAEiB,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAAlC,SAAS,GAAG,SAAsB;wBACxC,IAAI,CAAC,SAAS,EAAE;4BACd,sBAAO,EAAE,EAAA;yBACV;wBACK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACnC,IAAI,CAAC,EAAE,EAAE;4BACP,sBAAO,EAAE,EAAA;yBACV;wBAGK,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;wBACzC,MAAM,GAAY,EAAE,CAAA;wBAE1B,sEAAsE;wBACtE,WAA0C,EAAf,mCAAe,EAAf,6BAAe,EAAf,IAAe,EAAE;4BAAjC,0BAAY,EAAX,KAAK,QAAA,EAAE,GAAG,QAAA;4BACpB,KAAS,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE;gCACvC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;oCACd,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;oCAClC,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;wCACzC,MAAM,CAAC,IAAI,CAAC,IAAI,eAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;qCAClE;iCACF;6BACF;yBACF;wBAIK,KAAK,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM,CAAA;wBAC/B,MAAM,GAAG,IAAI,CAAA;wBACX,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;wBACvC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;wBAC7C,KAAS,CAAC,GAAG,MAAM,EAAE,CAAC,IAAI,MAAM,EAAE,EAAE,CAAC,EAAE;4BAC/B,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;4BAC5B,IAAI,EAAE,EAAE;gCACN,IAAI,CAAC,MAAM,IAAI,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE;oCACvC,MAAM,GAAG,EAAE,CAAA;iCACZ;6BACF;yBACF;wBAED,sBAAO,IAAA,qBAAc,EAAC,MAAM,EAAE,MAAM,CAAC,EAAA;;;;KACtC;IACH,UAAC;AAAD,CAAC,AAlND,CAAiC,mBAAS,GAkNzC"}
|
package/dist/bamFile.d.ts
CHANGED
package/dist/bamFile.js
CHANGED
|
@@ -164,10 +164,10 @@ var BamFile = /** @class */ (function () {
|
|
|
164
164
|
throw new Error('Error reading header');
|
|
165
165
|
}
|
|
166
166
|
if (bytesRead < ret) {
|
|
167
|
-
buffer = buffer.
|
|
167
|
+
buffer = buffer.subarray(0, bytesRead);
|
|
168
168
|
}
|
|
169
169
|
else {
|
|
170
|
-
buffer = buffer.
|
|
170
|
+
buffer = buffer.subarray(0, ret);
|
|
171
171
|
}
|
|
172
172
|
return [3 /*break*/, 5];
|
|
173
173
|
case 3: return [4 /*yield*/, this.bam.readFile(opts)];
|
|
@@ -226,10 +226,10 @@ var BamFile = /** @class */ (function () {
|
|
|
226
226
|
throw new Error('Error reading refseqs from header');
|
|
227
227
|
}
|
|
228
228
|
if (bytesRead < refSeqBytes) {
|
|
229
|
-
buffer = buffer.
|
|
229
|
+
buffer = buffer.subarray(0, bytesRead);
|
|
230
230
|
}
|
|
231
231
|
else {
|
|
232
|
-
buffer = buffer.
|
|
232
|
+
buffer = buffer.subarray(0, refSeqBytes);
|
|
233
233
|
}
|
|
234
234
|
return [4 /*yield*/, (0, bgzf_filehandle_1.unzip)(buffer)];
|
|
235
235
|
case 2:
|
|
@@ -573,10 +573,10 @@ var BamFile = /** @class */ (function () {
|
|
|
573
573
|
buffer = res.buffer;
|
|
574
574
|
(0, util_1.checkAbortSignal)(signal);
|
|
575
575
|
if (bytesRead < bufsize) {
|
|
576
|
-
buffer = buffer.
|
|
576
|
+
buffer = buffer.subarray(0, bytesRead);
|
|
577
577
|
}
|
|
578
578
|
else {
|
|
579
|
-
buffer = buffer.
|
|
579
|
+
buffer = buffer.subarray(0, bufsize);
|
|
580
580
|
}
|
|
581
581
|
return [4 /*yield*/, (0, bgzf_filehandle_1.unzipChunkSlice)(buffer, chunk)];
|
|
582
582
|
case 2:
|
|
@@ -635,7 +635,7 @@ var BamFile = /** @class */ (function () {
|
|
|
635
635
|
(blockStart - dpositions[pos]) +
|
|
636
636
|
chunk.minv.dataPosition +
|
|
637
637
|
1
|
|
638
|
-
: buffer_crc32_1.default.signed(ba.
|
|
638
|
+
: buffer_crc32_1.default.signed(ba.subarray(blockStart, blockEnd)),
|
|
639
639
|
});
|
|
640
640
|
sink.push(feature);
|
|
641
641
|
if (!(this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime)) return [3 /*break*/, 3];
|
|
@@ -684,6 +684,20 @@ var BamFile = /** @class */ (function () {
|
|
|
684
684
|
});
|
|
685
685
|
});
|
|
686
686
|
};
|
|
687
|
+
BamFile.prototype.blocksForRange = function (seqName, start, end, opts) {
|
|
688
|
+
return __awaiter(this, void 0, void 0, function () {
|
|
689
|
+
var seqId;
|
|
690
|
+
return __generator(this, function (_a) {
|
|
691
|
+
switch (_a.label) {
|
|
692
|
+
case 0: return [4 /*yield*/, this.index.parse()];
|
|
693
|
+
case 1:
|
|
694
|
+
_a.sent();
|
|
695
|
+
seqId = this.chrToIndex && this.chrToIndex[seqName];
|
|
696
|
+
return [2 /*return*/, this.index.blocksForRange(seqId, start, end, opts)];
|
|
697
|
+
}
|
|
698
|
+
});
|
|
699
|
+
});
|
|
700
|
+
};
|
|
687
701
|
return BamFile;
|
|
688
702
|
}());
|
|
689
703
|
exports.default = BamFile;
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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package/dist/csi.js
CHANGED
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@@ -16,7 +16,11 @@ var __extends = (this && this.__extends) || (function () {
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16
16
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})();
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17
17
|
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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18
18
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if (k2 === undefined) k2 = k;
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|
19
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-
Object.
|
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19
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+
var desc = Object.getOwnPropertyDescriptor(m, k);
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|
20
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+
if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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21
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+
desc = { enumerable: true, get: function() { return m[k]; } };
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22
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+
}
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23
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+
Object.defineProperty(o, k2, desc);
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20
24
|
}) : (function(o, m, k, k2) {
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21
25
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if (k2 === undefined) k2 = k;
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|
22
26
|
o[k2] = m[k];
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@@ -148,7 +152,7 @@ var CSI = /** @class */ (function (_super) {
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148
152
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data.metaChar = data.metaValue ? String.fromCharCode(data.metaValue) : '';
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149
153
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data.skipLines = bytes.readInt32LE(offset + 20);
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150
154
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var nameSectionLength = bytes.readInt32LE(offset + 24);
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151
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-
Object.assign(data, this._parseNameBytes(bytes.
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155
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+
Object.assign(data, this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength)));
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152
156
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return data;
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153
157
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};
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|
154
158
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CSI.prototype._parseNameBytes = function (namesBytes) {
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|
@@ -257,11 +261,6 @@ var CSI = /** @class */ (function (_super) {
|
|
|
257
261
|
});
|
|
258
262
|
};
|
|
259
263
|
CSI.prototype.parsePseudoBin = function (bytes, offset) {
|
|
260
|
-
// const one = Long.fromBytesLE(bytes.slice(offset + 4, offset + 12), true)
|
|
261
|
-
// const two = Long.fromBytesLE(bytes.slice(offset + 12, offset + 20), true)
|
|
262
|
-
// const three = longToNumber(
|
|
263
|
-
// Long.fromBytesLE(bytes.slice(offset + 20, offset + 28), true),
|
|
264
|
-
// )
|
|
265
264
|
var lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
|
|
266
265
|
return { lineCount: lineCount };
|
|
267
266
|
};
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,yDAA6C;AAC7C,+DAA0D;AAC1D,kDAA2B;AAC3B,+BAAgF;AAEhF,0DAAmC;AAEnC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED;IAAiC,uBAAS;IAIxC,aAAY,IAAS;QAArB,YACE,kBAAM,IAAI,CAAC,SAIZ;QAHC,KAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,KAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,KAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;;IACnB,CAAC;IACK,uBAAS,GAAf,UAAgB,KAAa;;;;;4BACT,qBAAM,IAAI,CAAC,KAAK,EAAE,EAAA;;wBAA9B,SAAS,GAAG,SAAkB;wBACpC,IAAI,CAAC,SAAS,EAAE;4BACd,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACK,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACpC,IAAI,CAAC,GAAG,EAAE;4BACR,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACO,KAAK,GAAK,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,MAA7B,CAA6B;wBAC1C,IAAI,KAAK,EAAE;4BACT,sBAAO,KAAK,CAAC,SAAS,EAAA;yBACvB;wBACD,sBAAO,CAAC,CAAC,EAAA;;;;KACV;IAEK,sBAAQ,GAAd;;;gBACE,sBAAO,EAAE,EAAA;;;KACV;IAED,0BAAY,GAAZ,UAAa,KAAa,EAAE,MAAc,EAAE,SAAiB;QAC3D,IAAI,SAAS,GAAG,EAAE,EAAE;YAClB,OAAO,EAAE,CAAA;SACV;QAED,IAAM,IAAI,GAA2B,EAAE,CAAA;QACvC,IAAI,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC5C,IAAI,CAAC,cAAc;YACjB,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACxE,IAAI,CAAC,MAAM,GACT,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,IAAI,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACzB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,4CAAqC,IAAI,CAAC,WAAW,CAAE,CAAC,CAAA;SACzE;QACD,IAAI,CAAC,aAAa,GAAG;YACnB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QACzE,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,CAAC,MAAM,CACX,IAAI,EACJ,IAAI,CAAC,eAAe,CAClB,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CACF,CAAA;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,6BAAe,GAAf,UAAgB,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,IAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,aAAA,EAAE,WAAW,aAAA,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IACtB,oBAAM,GAAZ,UAAa,IAA8B;;;;;;;wBACnC,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;wBACzD,qBAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAA;;wBAA9C,MAAM,GAAG,CAAC,SAAoC,CAAW;wBACjD,qBAAM,IAAA,uBAAK,EAAC,MAAM,CAAC;4BAEjC,0BAA0B;0BAFO;;wBAA3B,KAAK,GAAG,SAAmB;wBAEjC,0BAA0B;wBAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BACxC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BAC/C,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM;4BACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;4BACjC,oDAAoD;yBACrD;wBAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACjC,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;wBACrD,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;wBACvC,IAAI,SAAS,EAAE;4BACb,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,EAAE,SAAS,CAAC,CAAC,CAAA;yBAC7D;wBACD,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;wBAEjD,+CAA+C;wBAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;wBACnC,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;wBAC1B,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAA;wBAC/B,qBAAM,IAAA,sBAAe,EAAC,IAAI,CAAC,MAAM,CAAC;4BAClC,oBAAoB;0BADc;;wBAAlC,SAAkC,CAAA;wBAE5B,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAC9C,UAAU,IAAI,CAAC,CAAA;wBACT,QAAQ,GAA+B,EAAE,CAAA;wBAC3C,KAAK,SAAA,CAAA;wBACT,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;4BAC9B,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;4BAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;gCAC3B,yDAAyD;gCACzD,qCAAqC;gCACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;gCAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;6BAClC;iCAAM;gCACC,OAAO,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;gCAChD,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;gCAC5B,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,GAAG,EAAE,CAAC,CAAA;gCACrD,UAAU,IAAI,EAAE,CAAA;gCACV,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;gCACpC,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;oCAChC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oCAChC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oCAC1C,UAAU,IAAI,EAAE,CAAA;oCAChB,+BAA+B;oCAC/B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;iCACjC;gCACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;6BACvB;yBACF;wBAED,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,UAAA,EAAE,KAAK,OAAA,EAAE,CAAA;;;wBA/BJ,CAAC,IAAI,CAAC,CAAA;;4BAkCzC,sBAAO,IAAI,EAAA;;;;KACZ;IAED,4BAAc,GAAd,UAAe,KAAa,EAAE,MAAc;QAC1C,IAAM,SAAS,GAAG,IAAA,mBAAY,EAC5B,cAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,CAAC,EAC3D,IAAI,CACL,CACF,CAAA;QACD,OAAO,EAAE,SAAS,WAAA,EAAE,CAAA;IACtB,CAAC;IAEK,4BAAc,GAApB,UACE,KAAa,EACb,GAAW,EACX,GAAW,EACX,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;;wBAEnB,IAAI,GAAG,GAAG,CAAC,EAAE;4BACX,GAAG,GAAG,CAAC,CAAA;yBACR;wBAEiB,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAAlC,SAAS,GAAG,SAAsB;wBACxC,IAAI,CAAC,SAAS,EAAE;4BACd,sBAAO,EAAE,EAAA;yBACV;wBACK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACnC,IAAI,CAAC,EAAE,EAAE;4BACP,sBAAO,EAAE,EAAA;yBACV;wBAEK,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,uCAAuC;wBAAxC,CAAA;wBACzC,MAAM,GAAY,EAAE,CAAA;wBAE1B,sEAAsE;wBACtE,WAA0C,EAAf,mCAAe,EAAf,6BAAe,EAAf,IAAe,EAAE;4BAAjC,0BAAY,EAAX,KAAK,QAAA,EAAE,GAAG,QAAA;4BACpB,KAAS,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE;gCACvC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;oCACd,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;oCAClC,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,EAAE,CAAC,EAAE;wCACzC,MAAM,CAAC,IAAI,CAAC,IAAI,eAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;qCAClE;iCACF;6BACF;yBACF;wBAED,sBAAO,IAAA,qBAAc,EAAC,MAAM,EAAE,IAAI,uBAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAA;;;;KACvD;IAED;;;OAGG;IACH,sBAAQ,GAAR,UAAS,GAAW,EAAE,GAAW;QAC/B,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;QACvC,IAAI,GAAG,GAAG,CAAC,EAAE;YACX,GAAG,GAAG,CAAC,CAAA;SACR;QACD,IAAI,GAAG,GAAG,SAAA,CAAC,EAAI,EAAE,CAAA,EAAE;YACjB,GAAG,GAAG,SAAA,CAAC,EAAI,EAAE,CAAA,CAAA;SACd,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,IAAM,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;YAC7D,IAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,IAAM,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;gBAC3C,MAAM,IAAI,KAAK,CACb,gBAAS,GAAG,cAAI,GAAG,6DAAmD,IAAI,CAAC,QAAQ,qBAAW,IAAI,CAAC,KAAK,6DAA0D,CACnK,CAAA;aACF;YACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;SAClB;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IACH,UAAC;AAAD,CAAC,AAnOD,CAAiC,mBAAS,GAmOzC"}
|
package/dist/htsget.js
CHANGED
|
@@ -27,7 +27,11 @@ var __assign = (this && this.__assign) || function () {
|
|
|
27
27
|
};
|
|
28
28
|
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
|
|
29
29
|
if (k2 === undefined) k2 = k;
|
|
30
|
-
Object.
|
|
30
|
+
var desc = Object.getOwnPropertyDescriptor(m, k);
|
|
31
|
+
if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
|
|
32
|
+
desc = { enumerable: true, get: function() { return m[k]; } };
|
|
33
|
+
}
|
|
34
|
+
Object.defineProperty(o, k2, desc);
|
|
31
35
|
}) : (function(o, m, k, k2) {
|
|
32
36
|
if (k2 === undefined) k2 = k;
|
|
33
37
|
o[k2] = m[k];
|
package/dist/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,mDAA8C;AAC9C,gCAA6B;AAE7B,yDAA6C;AAC7C,6BAAuC;AAWvC,SAAe,MAAM,CAAC,GAAsB,EAAE,IAAyB;;;;;;wBACzD,qBAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,UAAO,KAAkB;;;;;oCACvB,GAAG,GAAc,KAAK,IAAnB,EAAE,OAAO,GAAK,KAAK,QAAV,CAAU;yCAC1B,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAvB,wBAAuB;oCACzB,sBAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,EAAA;;oCAKvC,OAAO,GAAc,OAAO,QAArB,EAAK,IAAI,UAAK,OAAO,EAA9B,WAAoB,CAAF,CAAY;oCACxB,qBAAM,KAAK,CAAC,GAAG,wBACtB,IAAI,KACP,OAAO,wBAAO,IAAI,CAAC,OAAO,GAAK,IAAI,KACnC,EAAA;;oCAHI,QAAM,SAGV;oCACF,IAAI,CAAC,KAAG,CAAC,EAAE,EAAE;wCACX,MAAM,IAAI,KAAK,CAAC,0BAAmB,KAAG,CAAC,UAAU,CAAE,CAAC,CAAA;qCACrD;oCACM,KAAA,CAAA,KAAA,MAAM,CAAA,CAAC,IAAI,CAAA;oCAAC,qBAAM,KAAG,CAAC,WAAW,EAAE,EAAA;wCAA1C,sBAAO,cAAY,SAAuB,EAAC,EAAA;;;yBAE9C,CAAC,CACH,EAAA;;oBApBK,GAAG,GAAG,SAoBX;oBAEM,KAAA,CAAA,KAAA,MAAM,CAAA,CAAC,MAAM,CAAA;oBAAC,qBAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,UAAA,GAAG,IAAI,OAAA,IAAA,uBAAK,EAAC,GAAG,CAAC,EAAV,CAAU,CAAC,CAAC,EAAA;wBAAlE,sBAAO,cAAc,SAA6C,EAAC,EAAA;;;;CACpE;AAED;IAAwC,8BAAO;IAK7C,oBAAY,IAA0C;QAAtD;QACE,mCAAmC;QACnC,kBAAM,EAAE,aAAa,EAAE,GAAG,EAAE,aAAa,EAAE,GAAG,EAAE,CAAC,SAGlD;QAFC,KAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,KAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;;IAC7B,CAAC;IAEM,0CAAqB,GAA5B,UACE,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAIC;QAJD,qBAAA,EAAA;YACE,WAAW,EAAE,KAAK;YAClB,aAAa,EAAE,KAAK;YACpB,aAAa,EAAE,MAAM;SACtB;;;;;;wBAEK,IAAI,GAAG,UAAG,IAAI,CAAC,OAAO,cAAI,IAAI,CAAC,OAAO,CAAE,CAAA;wBACxC,GAAG,GAAG,UAAG,IAAI,4BAAkB,GAAG,oBAAU,GAAG,kBAAQ,GAAG,gBAAa,CAAA;wBACvE,KAAK,GAAG,IAAI,CAAC,UAAU,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;wBACtC,6BAAM,KAAK,CAAC,GAAG,eAAO,IAAI,EAAG,GAAA;;wBAAtC,MAAM,GAAG,SAA6B;wBAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;4BACd,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;yBACnC;wBACY,6BAAM,MAAM,CAAC,IAAI,EAAE,GAAA;;wBAA1B,IAAI,GAAG,SAAmB;wBAClB,6BAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAA;;wBAArD,KAAK,GAAG,SAA6C;wBACrD,KAAK,GAAG;4BACZ,MAAM,EAAE,KAAK;4BACb,KAAK,EAAE,EAAE,IAAI,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,EAAE;4BACpC,QAAQ;gCACN,OAAO,UAAG,GAAG,cAAI,GAAG,cAAI,GAAG,CAAE,CAAA;4BAC/B,CAAC;yBACF,CAAA;wBAED,sBAAA,SAAO,iBAAA,cAAA,IAAI,CAAC,mBAAmB;4BAC7B,aAAa;4BACb,CAAC,KAAK,CAAC,EACP,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA,CAAA,CAAA,EAAA;4BAPD,4CAAA,SAOC,IAAA;;wBAPD,SAOC,CAAA;;;;;KACF;IAED,YAAY;IACN,+BAAU,GAAhB,UAAiB,MAGhB;;;;gBACS,KAAK,GAAK,MAAM,MAAX,CAAW;gBAChB,MAAM,GAAgB,KAAK,OAArB,EAAS,EAAE,GAAK,KAAK,MAAV,CAAU;gBACnC,sBAAO,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,EAAA;;;KACvE;IAEK,8BAAS,GAAf,UAAgB,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;;wBAC3B,GAAG,GAAG,UAAG,IAAI,CAAC,OAAO,cAAI,IAAI,CAAC,OAAO,mCAAgC,CAAA;wBAC5D,qBAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,EAAA;;wBAA/B,MAAM,GAAG,SAAsB;wBACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;4BACd,MAAM,IAAI,KAAK,CAAC,0BAAmB,MAAM,CAAC,UAAU,CAAE,CAAC,CAAA;yBACxD;wBACY,qBAAM,MAAM,CAAC,IAAI,EAAE,EAAA;;wBAA1B,IAAI,GAAG,SAAmB;wBAClB,qBAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,EAAA;;wBAA5C,KAAK,GAAG,SAAoC;wBAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,mBAAS,EAAE;4BACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;yBAClC;wBACK,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBAE9B,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;wBACnD,SAAS,GAAG,IAAA,qBAAe,EAAC,UAAU,CAAC,CAAA;wBAIvC,QAAQ,GAAa,EAAE,CAAA;wBACvB,QAAQ,GAA2B,EAAE,CAAA;wBACrC,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,UAAC,CAAkB,IAAK,OAAA,CAAC,CAAC,GAAG,KAAK,IAAI,EAAd,CAAc,CAAC,CAAA;wBACxE,OAAO,CAAC,OAAO,CAAC,UAAC,MAA8B,EAAE,KAAa;4BAC5D,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,UAAC,IAAgB;gCACnC,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oCACrB,uBAAuB;oCACvB,IAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oCAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;oCACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;iCAC1B;4BACH,CAAC,CAAC,CAAA;wBACJ,CAAC,CAAC,CAAA;wBACF,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;wBAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;wBAC1B,sBAAO,SAAS,EAAA;;;;KACjB;IACH,iBAAC;AAAD,CAAC,AA/FD,CAAwC,iBAAO,GA+F9C"}
|
package/dist/indexFile.d.ts
CHANGED
|
@@ -21,7 +21,7 @@ export default abstract class IndexFile {
|
|
|
21
21
|
end: number;
|
|
22
22
|
score: number;
|
|
23
23
|
}[]>;
|
|
24
|
-
abstract blocksForRange(chrId: number, start: number, end: number, opts
|
|
24
|
+
abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
|
|
25
25
|
_findFirstData(data: any, virtualOffset: VirtualOffset): void;
|
|
26
26
|
parse(opts?: BaseOpts): Promise<any>;
|
|
27
27
|
hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
|
package/dist/record.d.ts
CHANGED
|
@@ -30,12 +30,12 @@ export default class BamRecord {
|
|
|
30
30
|
strand(): 1 | -1;
|
|
31
31
|
multi_segment_next_segment_strand(): 1 | -1 | undefined;
|
|
32
32
|
name(): any;
|
|
33
|
-
_read_name():
|
|
33
|
+
_read_name(): string;
|
|
34
34
|
/**
|
|
35
35
|
* Get the value of a tag, parsing the tags as far as necessary.
|
|
36
36
|
* Only called if we have not already parsed that field.
|
|
37
37
|
*/
|
|
38
|
-
_parseTag(tagName?: string):
|
|
38
|
+
_parseTag(tagName?: string): string | number | undefined;
|
|
39
39
|
_parseAllTags(): void;
|
|
40
40
|
_parseCigar(cigar: string): (string | number)[][];
|
|
41
41
|
/**
|
|
@@ -76,12 +76,12 @@ export default class BamRecord {
|
|
|
76
76
|
getReadBases(): string;
|
|
77
77
|
seq(): string;
|
|
78
78
|
getPairOrientation(): string | null;
|
|
79
|
-
_bin_mq_nl():
|
|
80
|
-
_flag_nc():
|
|
81
|
-
seq_length():
|
|
82
|
-
_next_refid():
|
|
83
|
-
_next_pos():
|
|
84
|
-
template_length():
|
|
79
|
+
_bin_mq_nl(): number;
|
|
80
|
+
_flag_nc(): number;
|
|
81
|
+
seq_length(): number;
|
|
82
|
+
_next_refid(): number;
|
|
83
|
+
_next_pos(): number;
|
|
84
|
+
template_length(): number;
|
|
85
85
|
toJSON(): {
|
|
86
86
|
[key: string]: any;
|
|
87
87
|
};
|