@gmod/bam 2.0.2 → 2.0.3
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 +10 -2
- package/dist/bai.d.ts +1 -1
- package/dist/bai.js +10 -10
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +0 -1
- package/dist/bamFile.js +16 -16
- package/dist/bamFile.js.map +1 -1
- package/dist/chunk.d.ts +0 -1
- package/dist/csi.d.ts +1 -2
- package/dist/csi.js +8 -8
- package/dist/csi.js.map +1 -1
- package/dist/htsget.d.ts +0 -1
- package/dist/htsget.js +5 -5
- package/dist/htsget.js.map +1 -1
- package/dist/record.d.ts +0 -1
- package/dist/sam.js +1 -2
- package/dist/sam.js.map +1 -1
- package/dist/util.d.ts +0 -1
- package/dist/util.js +10 -11
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.d.ts +0 -1
- package/dist/virtualOffset.js +1 -2
- package/dist/virtualOffset.js.map +1 -1
- package/esm/bai.d.ts +1 -1
- package/esm/bamFile.d.ts +0 -1
- package/esm/bamFile.js +1 -1
- package/esm/bamFile.js.map +1 -1
- package/esm/chunk.d.ts +0 -1
- package/esm/csi.d.ts +1 -2
- package/esm/htsget.d.ts +0 -1
- package/esm/record.d.ts +0 -1
- package/esm/util.d.ts +0 -1
- package/esm/virtualOffset.d.ts +0 -1
- package/package.json +7 -8
- package/src/bamFile.ts +1 -1
package/CHANGELOG.md
CHANGED
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@@ -1,11 +1,19 @@
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## [2.0.
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## [2.0.3](https://github.com/GMOD/bam-js/compare/v2.0.2...v2.0.3) (2024-07-23)
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### Reverts
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-
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* Revert "Migrate to eslint9" ([65adcbb](https://github.com/GMOD/bam-js/commit/65adcbb2793243659682d30694f8604d241a5337))
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* Revert "Run format" ([2a02535](https://github.com/GMOD/bam-js/commit/2a02535db4df80f245232522cdba771cbf5ea214))
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## [2.0.2](https://github.com/GMOD/bam-js/compare/v2.0.1...v2.0.2) (2024-02-21)
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- Update typescript-eslint config and related fixes
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## [2.0.1](https://github.com/GMOD/bam-js/compare/v2.0.0...v2.0.1) (2024-2-20)
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- Update to buffer-crc32 1.0.0
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- Fix BAM header parsing of refNames containing a :
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package/dist/bai.d.ts
CHANGED
package/dist/bai.js
CHANGED
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@@ -36,8 +36,8 @@ function reg2bins(beg, end) {
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}
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class BAI extends indexFile_1.default {
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lineCount(refId, opts) {
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var _a, _b;
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return __awaiter(this, void 0, void 0, function* () {
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var _a, _b;
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const indexData = yield this.parse(opts);
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return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
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});
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};
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});
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}
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indexCov(
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return __awaiter(this,
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indexCov(seqId_1, start_1, end_1) {
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return __awaiter(this, arguments, void 0, function* (seqId, start, end, opts = {}) {
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const v = 16384;
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const range = start !== undefined;
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const indexData = yield this.parse(opts);
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return depths.map(d => (Object.assign(Object.assign({}, d), { score: (d.score * ((stats === null || stats === void 0 ? void 0 : stats.lineCount) || 0)) / totalSize })));
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});
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}
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blocksForRange(
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return __awaiter(this,
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blocksForRange(refId_1, min_1, max_1) {
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return __awaiter(this, arguments, void 0, function* (refId, min, max, opts = {}) {
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if (min < 0) {
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min = 0;
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}
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return (0, util_1.optimizeChunks)(chunks, lowest);
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});
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}
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parse(
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return __awaiter(this,
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parse() {
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return __awaiter(this, arguments, void 0, function* (opts = {}) {
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if (!this.setupP) {
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this.setupP = this._parse(opts).catch(e => {
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this.setupP = undefined;
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return this.setupP;
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});
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}
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hasRefSeq(
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hasRefSeq(seqId_1) {
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return __awaiter(this, arguments, void 0, function* (seqId, opts = {}) {
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var _a;
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const header = yield this.parse(opts);
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return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
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});
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package/dist/bai.js.map
CHANGED
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@@ -1 +1 @@
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+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,mDAA0D;AAC1D,oDAA2B;AAE3B,iCAAgF;AAChF,4DAAmC;AAEnC,MAAM,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,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,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;KACzC,CAAA;AACH,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAGlC,SAAS,CAAC,KAAa,EAAE,IAAe;;;YAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,OAAO,CAAA,MAAA,MAAA,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,KAAK,0CAAE,SAAS,KAAI,CAAC,CAAA;QACxD,CAAC;KAAA;IAED,4BAA4B;IACtB,MAAM,CAAC,IAAe;;YAC1B,MAAM,KAAK,GAAG,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAA;YAE9D,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE,CAAC;gBACxC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;YAED,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACrC,MAAM,KAAK,GAAG,CAAC,CAAA;YACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YAEnD,+CAA+C;YAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;YACZ,IAAI,aAAwC,CAAA;YAI5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAItB,QAAQ,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACxC,IAAI,KAAK,CAAA;gBAET,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;gBAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;oBACrC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,CAAA;oBACpC,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;wBACzB,IAAI,IAAI,CAAC,CAAA;wBACT,KAAK,GAAG,IAAA,qBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;wBACxC,IAAI,IAAI,EAAE,CAAA;oBACZ,CAAC;yBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;wBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;oBACrE,CAAC;yBAAM,CAAC;wBACN,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;wBAC1C,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;wBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;4BACpC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;4BAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;wBAClC,CAAC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;oBACxB,CAAC;gBACH,CAAC;gBAED,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBAC3C,IAAI,IAAI,CAAC,CAAA;gBACT,mEAAmE;gBACnE,qEAAqE;gBACrE,OAAO;gBACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;gBACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;oBACrC,MAAM,MAAM,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;oBACrC,IAAI,IAAI,CAAC,CAAA;oBACT,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;oBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;gBACzB,CAAC;gBAED,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;YAC/C,CAAC;YAED,OAAO;gBACL,GAAG,EAAE,IAAI;gBACT,aAAa;gBACb,YAAY,EAAE,CAAC,IAAI,EAAE;gBACrB,OAAO;gBACP,QAAQ;aACT,CAAA;QACH,CAAC;KAAA;IAEK,QAAQ;6DACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,OAAiB,EAAE;YAEnB,MAAM,CAAC,GAAG,KAAK,CAAA;YACf,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;YACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACvC,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,OAAO,EAAE,CAAA;YACX,CAAC;YACD,MAAM,EAAE,WAAW,GAAG,EAAE,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;YAC1C,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC7B,OAAO,EAAE,CAAA;YACX,CAAC;YACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;YACvD,MAAM,MAAM,GAAG,KAAK;gBAClB,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;gBACxB,CAAC,CAAC,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;YACrC,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;YACnE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBACrC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;YAC3D,CAAC;YACD,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;YACjD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC/C,MAAM,CAAC,CAAC,CAAC,GAAG;oBACV,KAAK,EAAE,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,GAAG,UAAU;oBACpD,KAAK,EAAE,CAAC,GAAG,CAAC;oBACZ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC;iBACf,CAAA;gBACD,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;YAC/C,CAAC;YACD,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,iCAClB,CAAC,KACJ,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAA,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,SAAS,KAAI,CAAC,CAAC,CAAC,GAAG,SAAS,IACtD,CAAC,CAAA;QACL,CAAC;KAAA;IAEK,cAAc;6DAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;YAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,GAAG,GAAG,CAAC,CAAA;YACT,CAAC;YAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,OAAO,EAAE,CAAA;YACX,CAAC;YACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACnC,IAAI,CAAC,EAAE,EAAE,CAAC;gBACR,OAAO,EAAE,CAAA;YACX,CAAC;YAED,uCAAuC;YACvC,MAAM,eAAe,GAAG,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;YAC1C,MAAM,MAAM,GAAY,EAAE,CAAA;YAE1B,sEAAsE;YACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;gBAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;oBACxC,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;wBACrB,MAAM,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;wBAClC,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE,CAAC;4BACjC,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;wBACvB,CAAC;oBACH,CAAC;gBACH,CAAC;YACH,CAAC;YAED,0EAA0E;YAC1E,mCAAmC;YACnC,MAAM,KAAK,GAAG,EAAE,CAAC,WAAW,CAAC,MAAM,CAAA;YACnC,IAAI,MAAiC,CAAA;YACrC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;YAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;YAC7C,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,IAAI,MAAM,EAAE,EAAE,CAAC,EAAE,CAAC;gBACtC,MAAM,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;gBAC5B,IAAI,EAAE,IAAI,CAAC,CAAC,MAAM,IAAI,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;oBAChD,MAAM,GAAG,EAAE,CAAA;gBACb,CAAC;YACH,CAAC;YAED,OAAO,IAAA,qBAAc,EAAC,MAAM,EAAE,MAAM,CAAC,CAAA;QACvC,CAAC;KAAA;IAEK,KAAK;6DAAC,OAAiB,EAAE;YAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;gBACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;oBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;oBACvB,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAEK,SAAS;6DAAC,KAAa,EAAE,OAAiB,EAAE;;YAChD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACrC,OAAO,CAAC,CAAC,CAAA,MAAA,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;QAC1C,CAAC;KAAA;CACF;AApMD,sBAoMC"}
|
package/dist/bamFile.d.ts
CHANGED
package/dist/bamFile.js
CHANGED
|
@@ -42,7 +42,7 @@ const buffer_1 = require("buffer");
|
|
|
42
42
|
const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
|
|
43
43
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
44
44
|
const generic_filehandle_1 = require("generic-filehandle");
|
|
45
|
-
const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
|
|
45
|
+
const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
|
|
46
46
|
const quick_lru_1 = __importDefault(require("quick-lru"));
|
|
47
47
|
// locals
|
|
48
48
|
const bai_1 = __importDefault(require("./bai"));
|
|
@@ -53,9 +53,9 @@ const util_1 = require("./util");
|
|
|
53
53
|
exports.BAM_MAGIC = 21840194;
|
|
54
54
|
const blockLen = 1 << 16;
|
|
55
55
|
function gen2array(gen) {
|
|
56
|
-
var _a, gen_1, gen_1_1;
|
|
57
|
-
var _b, e_1, _c, _d;
|
|
58
56
|
return __awaiter(this, void 0, void 0, function* () {
|
|
57
|
+
var _a, gen_1, gen_1_1;
|
|
58
|
+
var _b, e_1, _c, _d;
|
|
59
59
|
let out = [];
|
|
60
60
|
try {
|
|
61
61
|
for (_a = true, gen_1 = __asyncValues(gen); gen_1_1 = yield gen_1.next(), _b = gen_1_1.done, !_b; _a = true) {
|
|
@@ -197,8 +197,8 @@ class BamFile {
|
|
|
197
197
|
}
|
|
198
198
|
return this.headerP;
|
|
199
199
|
}
|
|
200
|
-
getHeaderText(
|
|
201
|
-
return __awaiter(this,
|
|
200
|
+
getHeaderText() {
|
|
201
|
+
return __awaiter(this, arguments, void 0, function* (opts = {}) {
|
|
202
202
|
yield this.getHeader(opts);
|
|
203
203
|
return this.header;
|
|
204
204
|
});
|
|
@@ -241,8 +241,8 @@ class BamFile {
|
|
|
241
241
|
});
|
|
242
242
|
}
|
|
243
243
|
streamRecordsForRange(chr, min, max, opts) {
|
|
244
|
-
var _a;
|
|
245
244
|
return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
|
|
245
|
+
var _a;
|
|
246
246
|
yield __await(this.getHeader(opts));
|
|
247
247
|
const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
|
|
248
248
|
if (chrId === undefined || !this.index) {
|
|
@@ -254,8 +254,8 @@ class BamFile {
|
|
|
254
254
|
}
|
|
255
255
|
});
|
|
256
256
|
}
|
|
257
|
-
_fetchChunkFeatures(
|
|
258
|
-
return __asyncGenerator(this, arguments, function* _fetchChunkFeatures_1() {
|
|
257
|
+
_fetchChunkFeatures(chunks_1, chrId_1, min_1, max_1) {
|
|
258
|
+
return __asyncGenerator(this, arguments, function* _fetchChunkFeatures_1(chunks, chrId, min, max, opts = {}) {
|
|
259
259
|
const { viewAsPairs } = opts;
|
|
260
260
|
const feats = [];
|
|
261
261
|
let done = false;
|
|
@@ -349,14 +349,14 @@ class BamFile {
|
|
|
349
349
|
return mateFeatPromises.flat();
|
|
350
350
|
});
|
|
351
351
|
}
|
|
352
|
-
_readRegion(
|
|
353
|
-
return __awaiter(this,
|
|
352
|
+
_readRegion(position_1, size_1) {
|
|
353
|
+
return __awaiter(this, arguments, void 0, function* (position, size, opts = {}) {
|
|
354
354
|
const { bytesRead, buffer } = yield this.bam.read(buffer_1.Buffer.alloc(size), 0, size, position, opts);
|
|
355
355
|
return buffer.subarray(0, Math.min(bytesRead, size));
|
|
356
356
|
});
|
|
357
357
|
}
|
|
358
|
-
_readChunk(
|
|
359
|
-
return __awaiter(this,
|
|
358
|
+
_readChunk(_a) {
|
|
359
|
+
return __awaiter(this, arguments, void 0, function* ({ chunk, opts }) {
|
|
360
360
|
const buffer = yield this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
|
|
361
361
|
const { buffer: data, cpositions, dpositions, } = yield (0, bgzf_filehandle_1.unzipChunkSlice)(buffer, chunk);
|
|
362
362
|
return { data, cpositions, dpositions, chunk };
|
|
@@ -424,22 +424,22 @@ class BamFile {
|
|
|
424
424
|
});
|
|
425
425
|
}
|
|
426
426
|
hasRefSeq(seqName) {
|
|
427
|
-
var _a, _b;
|
|
428
427
|
return __awaiter(this, void 0, void 0, function* () {
|
|
428
|
+
var _a, _b;
|
|
429
429
|
const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
|
|
430
430
|
return seqId === undefined ? false : (_b = this.index) === null || _b === void 0 ? void 0 : _b.hasRefSeq(seqId);
|
|
431
431
|
});
|
|
432
432
|
}
|
|
433
433
|
lineCount(seqName) {
|
|
434
|
-
var _a;
|
|
435
434
|
return __awaiter(this, void 0, void 0, function* () {
|
|
435
|
+
var _a;
|
|
436
436
|
const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
|
|
437
437
|
return seqId === undefined || !this.index ? 0 : this.index.lineCount(seqId);
|
|
438
438
|
});
|
|
439
439
|
}
|
|
440
440
|
indexCov(seqName, start, end) {
|
|
441
|
-
var _a;
|
|
442
441
|
return __awaiter(this, void 0, void 0, function* () {
|
|
442
|
+
var _a;
|
|
443
443
|
if (!this.index) {
|
|
444
444
|
return [];
|
|
445
445
|
}
|
|
@@ -449,8 +449,8 @@ class BamFile {
|
|
|
449
449
|
});
|
|
450
450
|
}
|
|
451
451
|
blocksForRange(seqName, start, end, opts) {
|
|
452
|
-
var _a;
|
|
453
452
|
return __awaiter(this, void 0, void 0, function* () {
|
|
453
|
+
var _a;
|
|
454
454
|
if (!this.index) {
|
|
455
455
|
return [];
|
|
456
456
|
}
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
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1
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|
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1
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+
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AI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,EAAE,CAAC;oBAC3B,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAA;gBAC1B,CAAC;YACH,CAAC;YAED,MAAM,gBAAgB,GAAG,MAAM,OAAO,CAAC,GAAG,CACxC,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,CAAM,CAAC,EAAC,EAAE;gBAC9B,MAAM,EAAE,IAAI,EAAE,UAAU,EAAE,UAAU,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC;oBACpE,KAAK,EAAE,CAAC;oBACR,IAAI;iBACL,CAAC,CAAA;gBACF,MAAM,QAAQ,GAAG,EAAkB,CAAA;gBACnC,KAAK,MAAM,OAAO,IAAI,MAAM,IAAI,CAAC,eAAe,CAC9C,IAAI,EACJ,UAAU,EACV,UAAU,EACV,KAAK,CACN,EAAE,CAAC;oBACF,IAAI,YAAY,CAAC,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC;wBAChE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBACxB,CAAC;gBACH,CAAC;gBACD,OAAO,QAAQ,CAAA;YACjB,CAAC,CAAA,CAAC,CACH,CAAA;YACD,OAAO,gBAAgB,CAAC,IAAI,EAAE,CAAA;QAChC,CAAC;KAAA;IAEK,WAAW;6DAAC,QAAgB,EAAE,IAAY,EAAE,OAAiB,EAAE;YACnE,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC/C,eAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAClB,CAAC,EACD,IAAI,EACJ,QAAQ,EACR,IAAI,CACL,CAAA;YAED,OAAO,MAAM,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC,CAAA;QACtD,CAAC;KAAA;IAEK,UAAU;6DAAC,EAAE,KAAK,EAAE,IAAI,EAAoC;YAChE,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,WAAW,CACnC,KAAK,CAAC,IAAI,CAAC,aAAa,EACxB,KAAK,CAAC,WAAW,EAAE,EACnB,IAAI,CACL,CAAA;YAED,MAAM,EACJ,MAAM,EAAE,IAAI,EACZ,UAAU,EACV,UAAU,GACX,GAAG,MAAM,IAAA,iCAAe,EAAC,MAAM,EAAE,KAAK,CAAC,CAAA;YACxC,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,UAAU,EAAE,KAAK,EAAE,CAAA;QAChD,CAAC;KAAA;IAEK,eAAe,CACnB,EAAU,EACV,UAAoB,EACpB,UAAoB,EACpB,KAAY;;YAEZ,IAAI,UAAU,GAAG,CAAC,CAAA;YAClB,MAAM,IAAI,GAAG,EAAkB,CAAA;YAC/B,IAAI,GAAG,GAAG,CAAC,CAAA;YACX,IAAI,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;YAEtB,OAAO,UAAU,GAAG,CAAC,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;gBAClC,MAAM,SAAS,GAAG,EAAE,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBAC5C,MAAM,QAAQ,GAAG,UAAU,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,CAAA;gBAE/C,wDAAwD;gBACxD,IAAI,UAAU,EAAE,CAAC;oBACf,OAAO,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,YAAY,IAAI,UAAU,CAAC,GAAG,EAAE,CAAC,EAAE,CAAC,CAAA,CAAC;oBACpE,GAAG,EAAE,CAAA;gBACP,CAAC;gBAED,+DAA+D;gBAC/D,IAAI,QAAQ,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;oBACzB,MAAM,OAAO,GAAG,IAAI,gBAAU,CAAC;wBAC7B,KAAK,EAAE;4BACL,SAAS,EAAE,EAAE;4BACb,KAAK,EAAE,UAAU;4BACjB,GAAG,EAAE,QAAQ;yBACd;wBACD,qEAAqE;wBACrE,+DAA+D;wBAC/D,WAAW;wBACX,EAAE;wBACF,gEAAgE;wBAChE,aAAa;wBACb,EAAE;wBACF,gEAAgE;wBAChE,gEAAgE;wBAChE,UAAU;wBACV,EAAE;wBACF,qEAAqE;wBACrE,qEAAqE;wBACrE,4DAA4D;wBAC5D,EAAE;wBACF,gEAAgE;wBAChE,4DAA4D;wBAC5D,EAAE;wBACF,oEAAoE;wBACpE,uBAAuB;wBACvB,UAAU,EACR,UAAU,CAAC,MAAM,GAAG,CAAC;4BACnB,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gCAC1B,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC;gCAC9B,KAAK,CAAC,IAAI,CAAC,YAAY;gCACvB,CAAC;4BACH,CAAC,CAAC,yDAAyD;gCACzD,sBAAK,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC;qBACnD,CAAC,CAAA;oBAEF,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBAClB,IAAI,IAAI,CAAC,eAAe,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,IAAI,GAAG,IAAI,CAAC,eAAe,EAAE,CAAC;wBACtE,MAAM,IAAA,cAAO,EAAC,CAAC,CAAC,CAAA;wBAChB,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;oBACpB,CAAC;gBACH,CAAC;gBAED,UAAU,GAAG,QAAQ,GAAG,CAAC,CAAA;YAC3B,CAAC;YACD,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;IAEK,SAAS,CAAC,OAAe;;;YAC7B,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,OAAO,CAAC,CAAA;YACxC,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAA,IAAI,CAAC,KAAK,0CAAE,SAAS,CAAC,KAAK,CAAC,CAAA;QACnE,CAAC;KAAA;IAEK,SAAS,CAAC,OAAe;;;YAC7B,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,OAAO,CAAC,CAAA;YACxC,OAAO,KAAK,KAAK,SAAS,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;QAC7E,CAAC;KAAA;IAEK,QAAQ,CAAC,OAAe,EAAE,KAAc,EAAE,GAAY;;;YAC1D,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;gBAChB,OAAO,EAAE,CAAA;YACX,CAAC;YACD,MAAM,IAAI,CAAC,KAAK,CAAC,KAAK,EAAE,CAAA;YACxB,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,OAAO,CAAC,CAAA;YACxC,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;QAC1E,CAAC;KAAA;IAEK,cAAc,CAClB,OAAe,EACf,KAAa,EACb,GAAW,EACX,IAAe;;;YAEf,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;gBAChB,OAAO,EAAE,CAAA;YACX,CAAC;YACD,MAAM,IAAI,CAAC,KAAK,CAAC,KAAK,EAAE,CAAA;YACxB,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,OAAO,CAAC,CAAA;YACxC,OAAO,KAAK,KAAK,SAAS;gBACxB,CAAC,CAAC,EAAE;gBACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;QACxD,CAAC;KAAA;CACF;AAzdD,0BAydC"}
|
package/dist/chunk.d.ts
CHANGED
package/dist/csi.d.ts
CHANGED
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
/// <reference types="node" />
|
|
2
1
|
import VirtualOffset from './virtualOffset';
|
|
3
2
|
import Chunk from './chunk';
|
|
4
3
|
import { BaseOpts } from './util';
|
|
@@ -47,7 +46,7 @@ export default class CSI extends IndexFile {
|
|
|
47
46
|
binIndex: Record<string, Chunk[]>;
|
|
48
47
|
stats?: {
|
|
49
48
|
lineCount: number;
|
|
50
|
-
}
|
|
49
|
+
};
|
|
51
50
|
}[];
|
|
52
51
|
refCount: number;
|
|
53
52
|
csi: boolean;
|
package/dist/csi.js
CHANGED
|
@@ -56,8 +56,8 @@ class CSI extends indexFile_1.default {
|
|
|
56
56
|
this.minShift = 0;
|
|
57
57
|
}
|
|
58
58
|
lineCount(refId, opts) {
|
|
59
|
-
var _a, _b;
|
|
60
59
|
return __awaiter(this, void 0, void 0, function* () {
|
|
60
|
+
var _a, _b;
|
|
61
61
|
const indexData = yield this.parse(opts);
|
|
62
62
|
return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
|
|
63
63
|
});
|
|
@@ -156,8 +156,8 @@ class CSI extends indexFile_1.default {
|
|
|
156
156
|
refCount, csi: true, maxBlockSize: 1 << 16 }, aux);
|
|
157
157
|
});
|
|
158
158
|
}
|
|
159
|
-
blocksForRange(
|
|
160
|
-
return __awaiter(this,
|
|
159
|
+
blocksForRange(refId_1, min_1, max_1) {
|
|
160
|
+
return __awaiter(this, arguments, void 0, function* (refId, min, max, opts = {}) {
|
|
161
161
|
if (min < 0) {
|
|
162
162
|
min = 0;
|
|
163
163
|
}
|
|
@@ -212,8 +212,8 @@ class CSI extends indexFile_1.default {
|
|
|
212
212
|
}
|
|
213
213
|
return bins;
|
|
214
214
|
}
|
|
215
|
-
parse(
|
|
216
|
-
return __awaiter(this,
|
|
215
|
+
parse() {
|
|
216
|
+
return __awaiter(this, arguments, void 0, function* (opts = {}) {
|
|
217
217
|
if (!this.setupP) {
|
|
218
218
|
this.setupP = this._parse(opts).catch(e => {
|
|
219
219
|
this.setupP = undefined;
|
|
@@ -223,9 +223,9 @@ class CSI extends indexFile_1.default {
|
|
|
223
223
|
return this.setupP;
|
|
224
224
|
});
|
|
225
225
|
}
|
|
226
|
-
hasRefSeq(
|
|
227
|
-
|
|
228
|
-
|
|
226
|
+
hasRefSeq(seqId_1) {
|
|
227
|
+
return __awaiter(this, arguments, void 0, function* (seqId, opts = {}) {
|
|
228
|
+
var _a;
|
|
229
229
|
const header = yield this.parse(opts);
|
|
230
230
|
return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
|
|
231
231
|
});
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAC7C,iEAA0D;AAC1D,oDAA2B;AAC3B,iCAMe;AAEf,4DAAmC;AAEnC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,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,MAAqB,GAAI,SAAQ,mBAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;IA6MtB,CAAC;IAzMO,SAAS,CAAC,KAAa,EAAE,IAAe;;;YAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,OAAO,CAAA,MAAA,MAAA,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,KAAK,0CAAE,SAAS,KAAI,CAAC,CAAA
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAC7C,iEAA0D;AAC1D,oDAA2B;AAC3B,iCAMe;AAEf,4DAAmC;AAEnC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,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,MAAqB,GAAI,SAAQ,mBAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;IA6MtB,CAAC;IAzMO,SAAS,CAAC,KAAa,EAAE,IAAe;;;YAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,OAAO,CAAA,MAAA,MAAA,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,KAAK,0CAAE,SAAS,KAAI,CAAC,CAAA;QACxD,CAAC;KAAA;IAEK,QAAQ;;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;KAAA;IAED,YAAY,CAAC,KAAa,EAAE,MAAc;QACxC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GACV,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EACnC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,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,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,uBACE,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW,IACR,IAAA,qBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB,EACF;IACH,CAAC;IAED,4BAA4B;IACtB,MAAM,CAAC,IAA8B;;YACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;YAEjC,IAAI,UAAU,CAAA;YACd,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC;gBACzC,UAAU,GAAG,CAAC,CAAA;YAChB,CAAC;iBAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE,CAAC;gBAChD,UAAU,GAAG,CAAC,CAAA;YAChB,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;YACtD,CAAC;YAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACjC,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;YAC3D,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;YACtE,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;YAIlD,+CAA+C;YAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;YAC7B,IAAI,aAAwC,CAAA;YAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAGtB,QAAQ,CAAC,CAAA;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACxC,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;gBAC5C,IAAI,KAAK,CAAA,CAAC,iDAAiD;gBAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;oBAClC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,CAAA;oBACpC,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;wBAC5B,KAAK,GAAG,IAAA,qBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;wBACxC,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;oBACjB,CAAC;yBAAM,CAAC;wBACN,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;wBACpE,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;wBAC1C,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;wBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;4BACvC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,CAAA;4BACT,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;4BAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;wBAClC,CAAC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;oBACxB,CAAC;gBACH,CAAC;gBAED,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;YAClC,CAAC;YAED,uBACE,UAAU;gBACV,aAAa;gBACb,OAAO;gBACP,QAAQ,EACR,GAAG,EAAE,IAAI,EACT,YAAY,EAAE,CAAC,IAAI,EAAE,IAClB,GAAG,EACP;QACH,CAAC;KAAA;IAEK,cAAc;6DAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;YAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,GAAG,GAAG,CAAC,CAAA;YACT,CAAC;YAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,MAAM,EAAE,GAAG,SAAS,aAAT,SAAS,uBAAT,SAAS,CAAE,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,EAAE,EAAE,CAAC;gBACR,OAAO,EAAE,CAAA;YACX,CAAC;YACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;YAE/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,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|
package/dist/htsget.d.ts
CHANGED
package/dist/htsget.js
CHANGED
|
@@ -100,8 +100,8 @@ class HtsgetFile extends bamFile_1.default {
|
|
|
100
100
|
this.trackId = args.trackId;
|
|
101
101
|
}
|
|
102
102
|
streamRecordsForRange(chr, min, max, opts) {
|
|
103
|
-
var _a;
|
|
104
103
|
return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
|
|
104
|
+
var _a;
|
|
105
105
|
const base = `${this.baseUrl}/${this.trackId}`;
|
|
106
106
|
const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
|
|
107
107
|
const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
|
|
@@ -148,16 +148,16 @@ class HtsgetFile extends bamFile_1.default {
|
|
|
148
148
|
}
|
|
149
149
|
});
|
|
150
150
|
}
|
|
151
|
-
_readChunk(
|
|
152
|
-
return __awaiter(this,
|
|
151
|
+
_readChunk(_a) {
|
|
152
|
+
return __awaiter(this, arguments, void 0, function* ({ chunk }) {
|
|
153
153
|
if (!chunk.buffer) {
|
|
154
154
|
throw new Error('expected chunk.buffer in htsget');
|
|
155
155
|
}
|
|
156
156
|
return { data: chunk.buffer, cpositions: [], dpositions: [], chunk };
|
|
157
157
|
});
|
|
158
158
|
}
|
|
159
|
-
getHeader(
|
|
160
|
-
return __awaiter(this,
|
|
159
|
+
getHeader() {
|
|
160
|
+
return __awaiter(this, arguments, void 0, function* (opts = {}) {
|
|
161
161
|
const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
|
|
162
162
|
const result = yield fetch(url, opts);
|
|
163
163
|
if (!result.ok) {
|
package/dist/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAC7C,mCAA+B;AAE/B,qDAA8C;AAE9C,+BAAuC;AAMvC,SAAe,MAAM,CAAC,GAAkB,EAAE,IAA0B;;QAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,CAAM,KAAK,EAAC,EAAE;YACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,OAAO,eAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjD,CAAC;iBAAM,CAAC;gBACN,+DAA+D;gBAC/D,mBAAmB;gBAEnB,MAAM,EAAE,OAAO,KAAc,OAAO,EAAhB,IAAI,UAAK,OAAO,EAA9B,WAAoB,CAAU,CAAA;gBACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,kCACtB,IAAI,KACP,OAAO,kCAAO,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,GAAK,IAAI,KACpC,CAAA;gBACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;oBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;gBACH,CAAC;gBACD,OAAO,eAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;YAC7C,CAAC;QACH,CAAC,CAAA,CAAC,CACH,CAAA;QAED,OAAO,eAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,CAAC;CAAA;AAED,MAAqB,UAAW,SAAQ,iBAAO;IAK7C,YAAY,IAA0C;QACpD,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QACvB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAEM,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;;;YAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;YAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;YAC7E,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,GAAG,CAAC,CAAA;YACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,oBAAM,EAAE,CAAA,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,MAAM,MAAM,GAAG,cAAM,KAAK,CAAC,GAAG,oBAAO,IAAI,EAAG,CAAA,CAAA;gBAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;oBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,cAAM,MAAM,CAAC,IAAI,EAAE,CAAA,EAAE,CAChE,CAAA;gBACH,CAAC;gBACD,MAAM,IAAI,GAAG,cAAM,MAAM,CAAC,IAAI,EAAE,CAAA,CAAA;gBAChC,MAAM,KAAK,GAAG,cAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA,CAAA;gBAE3D,cAAA,KAAK,CAAC,CAAC,iBAAA,cAAA,IAAI,CAAC,mBAAmB,CAC7B;oBACE,sCAAsC;oBACtC;wBACE,MAAM,EAAE,KAAK;wBACb,YAAY,EAAE,SAAS;wBACvB,GAAG,EAAE,CAAC;wBACN,SAAS;4BACP,OAAO,CAAC,CAAA;wBACV,CAAC;wBACD,cAAc;4BACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;wBAC/B,CAAC;wBACD,WAAW;4BACT,OAAO,CAAC,CAAA;wBACV,CAAC;wBACD,IAAI,EAAE;4BACJ,YAAY,EAAE,CAAC;4BACf,aAAa,EAAE,CAAC;4BAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;yBACnB;wBACD,IAAI,EAAE;4BACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;4BACrC,aAAa,EAAE,CAAC;4BAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;yBACnB;wBACD,QAAQ;4BACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;wBAC/B,CAAC;qBACF;iBACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA,CAAA,CAAA,CAAA;YACH,CAAC
|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAC7C,mCAA+B;AAE/B,qDAA8C;AAE9C,+BAAuC;AAMvC,SAAe,MAAM,CAAC,GAAkB,EAAE,IAA0B;;QAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,CAAM,KAAK,EAAC,EAAE;YACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,OAAO,eAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjD,CAAC;iBAAM,CAAC;gBACN,+DAA+D;gBAC/D,mBAAmB;gBAEnB,MAAM,EAAE,OAAO,KAAc,OAAO,EAAhB,IAAI,UAAK,OAAO,EAA9B,WAAoB,CAAU,CAAA;gBACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,kCACtB,IAAI,KACP,OAAO,kCAAO,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,GAAK,IAAI,KACpC,CAAA;gBACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;oBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;gBACH,CAAC;gBACD,OAAO,eAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;YAC7C,CAAC;QACH,CAAC,CAAA,CAAC,CACH,CAAA;QAED,OAAO,eAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,CAAC;CAAA;AAED,MAAqB,UAAW,SAAQ,iBAAO;IAK7C,YAAY,IAA0C;QACpD,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QACvB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAEM,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;;;YAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;YAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;YAC7E,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,GAAG,CAAC,CAAA;YACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,oBAAM,EAAE,CAAA,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,MAAM,MAAM,GAAG,cAAM,KAAK,CAAC,GAAG,oBAAO,IAAI,EAAG,CAAA,CAAA;gBAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;oBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,cAAM,MAAM,CAAC,IAAI,EAAE,CAAA,EAAE,CAChE,CAAA;gBACH,CAAC;gBACD,MAAM,IAAI,GAAG,cAAM,MAAM,CAAC,IAAI,EAAE,CAAA,CAAA;gBAChC,MAAM,KAAK,GAAG,cAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA,CAAA;gBAE3D,cAAA,KAAK,CAAC,CAAC,iBAAA,cAAA,IAAI,CAAC,mBAAmB,CAC7B;oBACE,sCAAsC;oBACtC;wBACE,MAAM,EAAE,KAAK;wBACb,YAAY,EAAE,SAAS;wBACvB,GAAG,EAAE,CAAC;wBACN,SAAS;4BACP,OAAO,CAAC,CAAA;wBACV,CAAC;wBACD,cAAc;4BACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;wBAC/B,CAAC;wBACD,WAAW;4BACT,OAAO,CAAC,CAAA;wBACV,CAAC;wBACD,IAAI,EAAE;4BACJ,YAAY,EAAE,CAAC;4BACf,aAAa,EAAE,CAAC;4BAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;yBACnB;wBACD,IAAI,EAAE;4BACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;4BACrC,aAAa,EAAE,CAAC;4BAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;yBACnB;wBACD,QAAQ;4BACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;wBAC/B,CAAC;qBACF;iBACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA,CAAA,CAAA,CAAA;YACH,CAAC;QACH,CAAC;KAAA;IAEK,UAAU;6DAAC,EAAE,KAAK,EAAoC;YAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;gBAClB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;YACpD,CAAC;YACD,OAAO,EAAE,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,UAAU,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,KAAK,EAAE,CAAA;QACtE,CAAC;KAAA;IAEK,SAAS;6DAAC,OAAiB,EAAE;YACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;YAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;YACH,CAAC;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,mBAAS,EAAE,CAAC;gBACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACpC,MAAM,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;YACzD,MAAM,SAAS,GAAG,IAAA,qBAAe,EAAC,UAAU,CAAC,CAAA;YAE7C,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;YAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;YACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;gBAChD,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,IAAI,MAAM,GAAG,CAAC,CAAA;gBACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;oBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;wBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oBACtB,CAAC;yBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;wBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;oBACtB,CAAC;gBACH,CAAC;gBACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;gBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;YACvC,CAAC;YACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;YAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;YAC1B,OAAO,SAAS,CAAA;QAClB,CAAC;KAAA;CACF;AAtHD,6BAsHC"}
|
package/dist/record.d.ts
CHANGED
package/dist/sam.js
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.parseHeaderText =
|
|
3
|
+
exports.parseHeaderText = parseHeaderText;
|
|
4
4
|
function parseHeaderText(text) {
|
|
5
5
|
const lines = text.split(/\r?\n/);
|
|
6
6
|
const data = [];
|
|
@@ -20,5 +20,4 @@ function parseHeaderText(text) {
|
|
|
20
20
|
}
|
|
21
21
|
return data;
|
|
22
22
|
}
|
|
23
|
-
exports.parseHeaderText = parseHeaderText;
|
|
24
23
|
//# sourceMappingURL=sam.js.map
|
package/dist/sam.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;AAAA,0CAkBC;AAlBD,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,MAAM,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBAC5B,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;gBACjC,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
|
package/dist/util.d.ts
CHANGED
package/dist/util.js
CHANGED
|
@@ -12,12 +12,20 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
12
12
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
13
13
|
};
|
|
14
14
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
15
|
-
exports.
|
|
15
|
+
exports.timeout = timeout;
|
|
16
|
+
exports.longToNumber = longToNumber;
|
|
17
|
+
exports.checkAbortSignal = checkAbortSignal;
|
|
18
|
+
exports.abortBreakPoint = abortBreakPoint;
|
|
19
|
+
exports.canMergeBlocks = canMergeBlocks;
|
|
20
|
+
exports.makeOpts = makeOpts;
|
|
21
|
+
exports.optimizeChunks = optimizeChunks;
|
|
22
|
+
exports.parsePseudoBin = parsePseudoBin;
|
|
23
|
+
exports.findFirstData = findFirstData;
|
|
24
|
+
exports.parseNameBytes = parseNameBytes;
|
|
16
25
|
const long_1 = __importDefault(require("long"));
|
|
17
26
|
function timeout(ms) {
|
|
18
27
|
return new Promise(resolve => setTimeout(resolve, ms));
|
|
19
28
|
}
|
|
20
|
-
exports.timeout = timeout;
|
|
21
29
|
function longToNumber(long) {
|
|
22
30
|
if (long.greaterThan(Number.MAX_SAFE_INTEGER) ||
|
|
23
31
|
long.lessThan(Number.MIN_SAFE_INTEGER)) {
|
|
@@ -25,7 +33,6 @@ function longToNumber(long) {
|
|
|
25
33
|
}
|
|
26
34
|
return long.toNumber();
|
|
27
35
|
}
|
|
28
|
-
exports.longToNumber = longToNumber;
|
|
29
36
|
/**
|
|
30
37
|
* Properly check if the given AbortSignal is aborted.
|
|
31
38
|
* Per the standard, if the signal reads as aborted,
|
|
@@ -54,7 +61,6 @@ function checkAbortSignal(signal) {
|
|
|
54
61
|
}
|
|
55
62
|
}
|
|
56
63
|
}
|
|
57
|
-
exports.checkAbortSignal = checkAbortSignal;
|
|
58
64
|
/**
|
|
59
65
|
* Skips to the next tick, then runs `checkAbortSignal`.
|
|
60
66
|
* Await this to inside an otherwise synchronous loop to
|
|
@@ -67,16 +73,13 @@ function abortBreakPoint(signal) {
|
|
|
67
73
|
checkAbortSignal(signal);
|
|
68
74
|
});
|
|
69
75
|
}
|
|
70
|
-
exports.abortBreakPoint = abortBreakPoint;
|
|
71
76
|
function canMergeBlocks(chunk1, chunk2) {
|
|
72
77
|
return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
|
|
73
78
|
chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);
|
|
74
79
|
}
|
|
75
|
-
exports.canMergeBlocks = canMergeBlocks;
|
|
76
80
|
function makeOpts(obj = {}) {
|
|
77
81
|
return 'aborted' in obj ? { signal: obj } : obj;
|
|
78
82
|
}
|
|
79
|
-
exports.makeOpts = makeOpts;
|
|
80
83
|
function optimizeChunks(chunks, lowest) {
|
|
81
84
|
const mergedChunks = [];
|
|
82
85
|
let lastChunk;
|
|
@@ -108,12 +111,10 @@ function optimizeChunks(chunks, lowest) {
|
|
|
108
111
|
}
|
|
109
112
|
return mergedChunks;
|
|
110
113
|
}
|
|
111
|
-
exports.optimizeChunks = optimizeChunks;
|
|
112
114
|
function parsePseudoBin(bytes, offset) {
|
|
113
115
|
const lineCount = longToNumber(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true));
|
|
114
116
|
return { lineCount };
|
|
115
117
|
}
|
|
116
|
-
exports.parsePseudoBin = parsePseudoBin;
|
|
117
118
|
function findFirstData(firstDataLine, virtualOffset) {
|
|
118
119
|
return firstDataLine
|
|
119
120
|
? firstDataLine.compareTo(virtualOffset) > 0
|
|
@@ -121,7 +122,6 @@ function findFirstData(firstDataLine, virtualOffset) {
|
|
|
121
122
|
: firstDataLine
|
|
122
123
|
: virtualOffset;
|
|
123
124
|
}
|
|
124
|
-
exports.findFirstData = findFirstData;
|
|
125
125
|
function parseNameBytes(namesBytes, renameRefSeq = s => s) {
|
|
126
126
|
let currRefId = 0;
|
|
127
127
|
let currNameStart = 0;
|
|
@@ -141,5 +141,4 @@ function parseNameBytes(namesBytes, renameRefSeq = s => s) {
|
|
|
141
141
|
}
|
|
142
142
|
return { refNameToId, refIdToName };
|
|
143
143
|
}
|
|
144
|
-
exports.parseNameBytes = parseNameBytes;
|
|
145
144
|
//# sourceMappingURL=util.js.map
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAIA,0BAEC;AAED,oCAQC;AAaD,4CAgBC;AAQD,0CAGC;AAED,wCAKC;AAaD,4BAEC;AAED,wCAgCC;AAED,wCAQC;AAED,sCASC;AAED,wCAqBC;AA5JD,gDAAuB;AAIvB,SAAgB,OAAO,CAAC,EAAU;IAChC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAED,SAAgB,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;YAC9B,YAAY;YACZ,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAaD,SAAgB,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAC,GAAG,CAAA;AAC/D,CAAC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAA4B,CAAA;IAEhC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACrB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,SAAgB,cAAc,CAAC,KAAa,EAAE,MAAc;IAC1D,MAAM,SAAS,GAAG,YAAY,CAC5B,cAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,GAAG,CAAC,CAAC,EACrD,IAAI,CACL,CACF,CAAA;IACD,OAAO,EAAE,SAAS,EAAE,CAAA;AACtB,CAAC;AAED,SAAgB,aAAa,CAC3B,aAAwC,EACxC,aAA4B;IAE5B,OAAO,aAAa;QAClB,CAAC,CAAC,aAAa,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;YAC1C,CAAC,CAAC,aAAa;YACf,CAAC,CAAC,aAAa;QACjB,CAAC,CAAC,aAAa,CAAA;AACnB,CAAC;AAED,SAAgB,cAAc,CAC5B,UAAkB,EAClB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;gBAC3D,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;gBAC/B,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;YAClC,CAAC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC"}
|
package/dist/virtualOffset.d.ts
CHANGED
package/dist/virtualOffset.js
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.fromBytes =
|
|
3
|
+
exports.fromBytes = fromBytes;
|
|
4
4
|
class VirtualOffset {
|
|
5
5
|
constructor(blockPosition, dataPosition) {
|
|
6
6
|
this.blockPosition = blockPosition; // < offset of the compressed data block
|
|
@@ -38,5 +38,4 @@ function fromBytes(bytes, offset = 0, bigendian = false) {
|
|
|
38
38
|
bytes[offset + 3] * 0x100 +
|
|
39
39
|
bytes[offset + 2], (bytes[offset + 1] << 8) | bytes[offset]);
|
|
40
40
|
}
|
|
41
|
-
exports.fromBytes = fromBytes;
|
|
42
41
|
//# sourceMappingURL=virtualOffset.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;AAgCA,8BAcC;AA9CD,MAAqB,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AA/BD,gCA+BC;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC"}
|
package/esm/bai.d.ts
CHANGED
package/esm/bamFile.d.ts
CHANGED
package/esm/bamFile.js
CHANGED
|
@@ -2,7 +2,7 @@ import { Buffer } from 'buffer';
|
|
|
2
2
|
import crc32 from 'buffer-crc32';
|
|
3
3
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
|
|
4
4
|
import { LocalFile, RemoteFile } from 'generic-filehandle';
|
|
5
|
-
import AbortablePromiseCache from 'abortable-promise-cache';
|
|
5
|
+
import AbortablePromiseCache from '@gmod/abortable-promise-cache';
|
|
6
6
|
import QuickLRU from 'quick-lru';
|
|
7
7
|
// locals
|
|
8
8
|
import BAI from './bai';
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
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1
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+
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,EAAiB,CAAA;QACpC,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;QAC3C,KAAK,MAAM,CAAC,IAAI,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC;YAC3B,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,EAAE,CAAC;gBAC3B,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAA;YAC1B,CAAC;QACH,CAAC;QAED,MAAM,gBAAgB,GAAG,MAAM,OAAO,CAAC,GAAG,CACxC,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE;YAC9B,MAAM,EAAE,IAAI,EAAE,UAAU,EAAE,UAAU,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC;gBACpE,KAAK,EAAE,CAAC;gBACR,IAAI;aACL,CAAC,CAAA;YACF,MAAM,QAAQ,GAAG,EAAkB,CAAA;YACnC,KAAK,MAAM,OAAO,IAAI,MAAM,IAAI,CAAC,eAAe,CAC9C,IAAI,EACJ,UAAU,EACV,UAAU,EACV,KAAK,CACN,EAAE,CAAC;gBACF,IAAI,YAAY,CAAC,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC;oBAChE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACxB,CAAC;YACH,CAAC;YACD,OAAO,QAAQ,CAAA;QACjB,CAAC,CAAC,CACH,CAAA;QACD,OAAO,gBAAgB,CAAC,IAAI,EAAE,CAAA;IAChC,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,QAAgB,EAAE,IAAY,EAAE,OAAiB,EAAE;QACnE,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC/C,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAClB,CAAC,EACD,IAAI,EACJ,QAAQ,EACR,IAAI,CACL,CAAA;QAED,OAAO,MAAM,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,EAAE,KAAK,EAAE,IAAI,EAAoC;QAChE,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,WAAW,CACnC,KAAK,CAAC,IAAI,CAAC,aAAa,EACxB,KAAK,CAAC,WAAW,EAAE,EACnB,IAAI,CACL,CAAA;QAED,MAAM,EACJ,MAAM,EAAE,IAAI,EACZ,UAAU,EACV,UAAU,GACX,GAAG,MAAM,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,CAAA;QACxC,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,UAAU,EAAE,KAAK,EAAE,CAAA;IAChD,CAAC;IAED,KAAK,CAAC,eAAe,CACnB,EAAU,EACV,UAAoB,EACpB,UAAoB,EACpB,KAAY;QAEZ,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,MAAM,IAAI,GAAG,EAAkB,CAAA;QAC/B,IAAI,GAAG,GAAG,CAAC,CAAA;QACX,IAAI,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;QAEtB,OAAO,UAAU,GAAG,CAAC,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;YAClC,MAAM,SAAS,GAAG,EAAE,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC5C,MAAM,QAAQ,GAAG,UAAU,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,CAAA;YAE/C,wDAAwD;YACxD,IAAI,UAAU,EAAE,CAAC;gBACf,OAAO,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,YAAY,IAAI,UAAU,CAAC,GAAG,EAAE,CAAC,EAAE,CAAC,CAAA,CAAC;gBACpE,GAAG,EAAE,CAAA;YACP,CAAC;YAED,+DAA+D;YAC/D,IAAI,QAAQ,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;gBACzB,MAAM,OAAO,GAAG,IAAI,UAAU,CAAC;oBAC7B,KAAK,EAAE;wBACL,SAAS,EAAE,EAAE;wBACb,KAAK,EAAE,UAAU;wBACjB,GAAG,EAAE,QAAQ;qBACd;oBACD,qEAAqE;oBACrE,+DAA+D;oBAC/D,WAAW;oBACX,EAAE;oBACF,gEAAgE;oBAChE,aAAa;oBACb,EAAE;oBACF,gEAAgE;oBAChE,gEAAgE;oBAChE,UAAU;oBACV,EAAE;oBACF,qEAAqE;oBACrE,qEAAqE;oBACrE,4DAA4D;oBAC5D,EAAE;oBACF,gEAAgE;oBAChE,4DAA4D;oBAC5D,EAAE;oBACF,oEAAoE;oBACpE,uBAAuB;oBACvB,UAAU,EACR,UAAU,CAAC,MAAM,GAAG,CAAC;wBACnB,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;4BAC1B,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC;4BAC9B,KAAK,CAAC,IAAI,CAAC,YAAY;4BACvB,CAAC;wBACH,CAAC,CAAC,yDAAyD;4BACzD,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC;iBACnD,CAAC,CAAA;gBAEF,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBAClB,IAAI,IAAI,CAAC,eAAe,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,IAAI,GAAG,IAAI,CAAC,eAAe,EAAE,CAAC;oBACtE,MAAM,OAAO,CAAC,CAAC,CAAC,CAAA;oBAChB,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;gBACpB,CAAC;YACH,CAAC;YAED,UAAU,GAAG,QAAQ,GAAG,CAAC,CAAA;QAC3B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe;;QAC7B,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,OAAO,CAAC,CAAA;QACxC,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAA,IAAI,CAAC,KAAK,0CAAE,SAAS,CAAC,KAAK,CAAC,CAAA;IACnE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe;;QAC7B,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,OAAO,CAAC,CAAA;QACxC,OAAO,KAAK,KAAK,SAAS,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IAC7E,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,OAAe,EAAE,KAAc,EAAE,GAAY;;QAC1D,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,IAAI,CAAC,KAAK,CAAC,KAAK,EAAE,CAAA;QACxB,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,OAAO,CAAC,CAAA;QACxC,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;IAC1E,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,KAAa,EACb,GAAW,EACX,IAAe;;QAEf,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,IAAI,CAAC,KAAK,CAAC,KAAK,EAAE,CAAA;QACxB,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,OAAO,CAAC,CAAA;QACxC,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;CACF"}
|
package/esm/chunk.d.ts
CHANGED
package/esm/csi.d.ts
CHANGED
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
/// <reference types="node" />
|
|
2
1
|
import VirtualOffset from './virtualOffset';
|
|
3
2
|
import Chunk from './chunk';
|
|
4
3
|
import { BaseOpts } from './util';
|
|
@@ -47,7 +46,7 @@ export default class CSI extends IndexFile {
|
|
|
47
46
|
binIndex: Record<string, Chunk[]>;
|
|
48
47
|
stats?: {
|
|
49
48
|
lineCount: number;
|
|
50
|
-
}
|
|
49
|
+
};
|
|
51
50
|
}[];
|
|
52
51
|
refCount: number;
|
|
53
52
|
csi: boolean;
|
package/esm/htsget.d.ts
CHANGED
package/esm/record.d.ts
CHANGED
package/esm/util.d.ts
CHANGED
package/esm/virtualOffset.d.ts
CHANGED
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bam",
|
|
3
|
-
"version": "2.0.
|
|
3
|
+
"version": "2.0.3",
|
|
4
4
|
"description": "Parser for BAM and BAM index (bai) files",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/bam-js",
|
|
@@ -22,7 +22,7 @@
|
|
|
22
22
|
"scripts": {
|
|
23
23
|
"test": "jest",
|
|
24
24
|
"coverage": "npm test -- --coverage",
|
|
25
|
-
"lint": "eslint --report-unused-disable-directives --max-warnings 0
|
|
25
|
+
"lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
|
|
26
26
|
"clean": "rimraf dist esm",
|
|
27
27
|
"build:esm": "tsc --target es2018 --outDir esm",
|
|
28
28
|
"build:es5": "tsc --target es2015 --module commonjs --outDir dist",
|
|
@@ -39,8 +39,8 @@
|
|
|
39
39
|
"genomics"
|
|
40
40
|
],
|
|
41
41
|
"dependencies": {
|
|
42
|
+
"@gmod/abortable-promise-cache": "^2.0.0",
|
|
42
43
|
"@gmod/bgzf-filehandle": "^1.4.4",
|
|
43
|
-
"abortable-promise-cache": "^1.5.0",
|
|
44
44
|
"buffer-crc32": "^1.0.0",
|
|
45
45
|
"generic-filehandle": "^3.0.0",
|
|
46
46
|
"long": "^4.0.0",
|
|
@@ -52,16 +52,15 @@
|
|
|
52
52
|
"@types/node": "^20.11.19",
|
|
53
53
|
"@typescript-eslint/eslint-plugin": "^7.0.2",
|
|
54
54
|
"@typescript-eslint/parser": "^7.0.2",
|
|
55
|
-
"eslint": "^
|
|
55
|
+
"eslint": "^9.0.0",
|
|
56
56
|
"eslint-config-prettier": "^9.1.0",
|
|
57
|
-
"eslint-plugin-import": "^2.27.5",
|
|
58
57
|
"eslint-plugin-prettier": "^5.1.3",
|
|
59
|
-
"eslint-plugin-unicorn": "^
|
|
58
|
+
"eslint-plugin-unicorn": "^54.0.0",
|
|
60
59
|
"jest": "^29.5.0",
|
|
61
60
|
"jest-fetch-mock": "^3.0.3",
|
|
62
61
|
"prettier": "^3.2.5",
|
|
63
|
-
"rimraf": "^
|
|
64
|
-
"standard-changelog": "^
|
|
62
|
+
"rimraf": "^6.0.1",
|
|
63
|
+
"standard-changelog": "^6.0.0",
|
|
65
64
|
"ts-jest": "^29.1.0",
|
|
66
65
|
"typescript": "^5.0.4"
|
|
67
66
|
},
|
package/src/bamFile.ts
CHANGED
|
@@ -2,7 +2,7 @@ import { Buffer } from 'buffer'
|
|
|
2
2
|
import crc32 from 'buffer-crc32'
|
|
3
3
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
|
|
4
4
|
import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
|
|
5
|
-
import AbortablePromiseCache from 'abortable-promise-cache'
|
|
5
|
+
import AbortablePromiseCache from '@gmod/abortable-promise-cache'
|
|
6
6
|
import QuickLRU from 'quick-lru'
|
|
7
7
|
|
|
8
8
|
// locals
|