@gmod/bam 5.0.5 → 5.0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +3 -11
- package/dist/bai.d.ts +17 -16
- package/dist/bai.js +67 -16
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +3 -8
- package/dist/bamFile.js +7 -31
- package/dist/bamFile.js.map +1 -1
- package/dist/chunk.d.ts +4 -4
- package/dist/chunk.js.map +1 -1
- package/dist/csi.d.ts +9 -9
- package/dist/csi.js +52 -45
- package/dist/csi.js.map +1 -1
- package/dist/htsget.d.ts +1 -1
- package/dist/htsget.js +2 -2
- package/dist/htsget.js.map +1 -1
- package/dist/indexFile.d.ts +2 -2
- package/dist/indexFile.js +1 -1
- package/dist/indexFile.js.map +1 -1
- package/dist/long.js.map +1 -1
- package/dist/nullFilehandle.d.ts +6 -0
- package/dist/nullFilehandle.js +18 -0
- package/dist/nullFilehandle.js.map +1 -0
- package/dist/record.js +2 -3
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +3 -2
- package/dist/util.js +9 -1
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.d.ts +7 -2
- package/dist/virtualOffset.js +2 -14
- package/dist/virtualOffset.js.map +1 -1
- package/esm/bai.d.ts +17 -16
- package/esm/bai.js +67 -16
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +3 -8
- package/esm/bamFile.js +6 -30
- package/esm/bamFile.js.map +1 -1
- package/esm/chunk.d.ts +4 -4
- package/esm/chunk.js.map +1 -1
- package/esm/csi.d.ts +9 -9
- package/esm/csi.js +51 -11
- package/esm/csi.js.map +1 -1
- package/esm/htsget.d.ts +1 -1
- package/esm/htsget.js +2 -2
- package/esm/htsget.js.map +1 -1
- package/esm/indexFile.d.ts +2 -2
- package/esm/indexFile.js +1 -1
- package/esm/indexFile.js.map +1 -1
- package/esm/long.js.map +1 -1
- package/esm/nullFilehandle.d.ts +6 -0
- package/esm/nullFilehandle.js +15 -0
- package/esm/nullFilehandle.js.map +1 -0
- package/esm/record.js +2 -3
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +3 -2
- package/esm/util.js +8 -1
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.d.ts +7 -2
- package/esm/virtualOffset.js +1 -14
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +4 -3
- package/src/bai.ts +83 -30
- package/src/bamFile.ts +21 -41
- package/src/chunk.ts +3 -3
- package/src/csi.ts +58 -21
- package/src/htsget.ts +3 -2
- package/src/indexFile.ts +3 -2
- package/src/long.ts +8 -8
- package/src/nullFilehandle.ts +16 -0
- package/src/record.ts +14 -12
- package/src/util.ts +12 -4
- package/src/virtualOffset.ts +15 -22
- package/dist/errors.d.ts +0 -23
- package/dist/errors.js +0 -33
- package/dist/errors.js.map +0 -1
- package/esm/errors.d.ts +0 -23
- package/esm/errors.js +0 -24
- package/esm/errors.js.map +0 -1
- package/src/errors.ts +0 -22
package/dist/csi.js
CHANGED
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@@ -1,46 +1,14 @@
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"use strict";
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var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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Object.defineProperty(o, "default", { enumerable: true, value: v });
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o["default"] = v;
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var __importStar = (this && this.__importStar) || (function () {
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var ownKeys = function(o) {
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ownKeys = Object.getOwnPropertyNames || function (o) {
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for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
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if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
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__setModuleDefault(result, mod);
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return result;
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})();
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var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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const
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const quick_lru_1 = __importDefault(require("quick-lru"));
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const chunk_1 = __importDefault(require("./chunk"));
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const util_1 = require("./util");
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const indexFile_1 = __importDefault(require("./indexFile"));
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const util_1 = require("./util");
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const virtualOffset_1 = require("./virtualOffset");
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const CSI1_MAGIC = 21582659; // CSI\1
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const CSI2_MAGIC = 38359875; // CSI\2
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function lshift(num, bits) {
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@@ -56,7 +24,7 @@ class CSI extends indexFile_1.default {
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setupP;
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async lineCount(refId, opts) {
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const indexData = await this.parse(opts);
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return indexData.indices
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return indexData.indices(refId)?.stats?.lineCount || 0;
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}
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async indexCov() {
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return [];
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@@ -109,14 +77,43 @@ class CSI extends indexFile_1.default {
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this.minShift = dataView.getInt32(4, true);
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this.depth = dataView.getInt32(8, true);
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this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
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const maxBinNumber = this.maxBinNumber;
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const auxLength = dataView.getInt32(12, true);
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const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
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const refCount = dataView.getInt32(16 + auxLength, true);
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// read the indexes for each reference sequence
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let curr = 16 + auxLength + 4;
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let firstDataLine;
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const
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const offsets = [];
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for (let i = 0; i < refCount; i++) {
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offsets.push(curr);
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const binCount = dataView.getInt32(curr, true);
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curr += 4;
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for (let j = 0; j < binCount; j++) {
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const bin = dataView.getUint32(curr, true);
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curr += 4;
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if (bin > this.maxBinNumber) {
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curr += 28 + 16;
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}
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else {
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curr += 8;
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const chunkCount = dataView.getInt32(curr, true);
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curr += 4;
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for (let k = 0; k < chunkCount; k += 1) {
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curr += 8;
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curr += 8;
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}
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}
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}
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}
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const indicesCache = new quick_lru_1.default({
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maxSize: 5,
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});
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function getIndices(refId) {
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let curr = offsets[refId];
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if (curr === undefined) {
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return undefined;
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}
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// the binning index
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const binCount = dataView.getInt32(curr, true);
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curr += 4;
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for (let j = 0; j < binCount; j++) {
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const bin = dataView.getUint32(curr, true);
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curr += 4;
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if (bin >
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if (bin > maxBinNumber) {
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stats = (0, util_1.parsePseudoBin)(bytes, curr + 28);
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curr += 28 + 16;
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}
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binIndex[bin] = chunks;
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}
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}
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return {
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binIndex,
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stats,
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};
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}
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return {
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csiVersion,
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firstDataLine,
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indices
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indices: (refId) => {
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if (!indicesCache.has(refId)) {
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const result = getIndices(refId);
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if (result) {
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indicesCache.set(refId, result);
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}
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return result;
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}
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return indicesCache.get(refId);
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},
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csi: true,
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maxBlockSize: 1 << 16,
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min = 0;
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}
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const indexData = await this.parse(opts);
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const ba = indexData.indices
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const ba = indexData.indices(refId);
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if (!ba) {
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return [];
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}
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// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
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for (const [start, end] of overlappingBins) {
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for (let bin = start; bin <= end; bin++) {
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// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
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if (ba.binIndex[bin]) {
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const binChunks = ba.binIndex[bin];
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for (const c of binChunks) {
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}
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}
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}
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return (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.
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return (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.VirtualOffset(0, 0));
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}
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/**
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* calculate the list of bins that may overlap with region [beg,end)
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}
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async hasRefSeq(seqId, opts = {}) {
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const header = await this.parse(opts);
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return !!header.indices
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return !!header.indices(seqId)?.binIndex;
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}
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}
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exports.default = CSI;
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package/dist/csi.js.map
CHANGED
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{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"
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+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,0DAAgC;AAEhC,oDAA2B;AAC3B,4DAAmC;AACnC,iCAMe;AACf,mDAA0D;AAE1D,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,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAChC,YAAY,GAAG,CAAC,CAAA;IAChB,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEb,MAAM,CAA4B;IAEzC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,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,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,IAAA,qBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;oBACX,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,mBAAQ,CAAwC;YACvE,OAAO,EAAE,CAAC;SACX,CAAC,CAAA;QAEF,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA,CAAC,iDAAiD;YAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,KAAK,GAAG,IAAA,qBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACpE,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBA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|
package/dist/htsget.d.ts
CHANGED
package/dist/htsget.js
CHANGED
|
@@ -34,9 +34,9 @@ var __importStar = (this && this.__importStar) || (function () {
|
|
|
34
34
|
})();
|
|
35
35
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
36
36
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
37
|
-
const util_1 = require("./util");
|
|
38
37
|
const bamFile_1 = __importStar(require("./bamFile"));
|
|
39
38
|
const sam_1 = require("./sam");
|
|
39
|
+
const util_1 = require("./util");
|
|
40
40
|
async function concat(arr, opts) {
|
|
41
41
|
const res = await Promise.all(arr.map(async (chunk) => {
|
|
42
42
|
const { url, headers } = chunk;
|
|
@@ -51,7 +51,7 @@ async function concat(arr, opts) {
|
|
|
51
51
|
return new Uint8Array(ret);
|
|
52
52
|
}
|
|
53
53
|
else {
|
|
54
|
-
//remove referer header, it is not even allowed to be specified
|
|
54
|
+
// remove referer header, it is not even allowed to be specified
|
|
55
55
|
// @ts-expect-error
|
|
56
56
|
const { referer, ...rest } = headers;
|
|
57
57
|
const res = await fetch(url, {
|
package/dist/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;
|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,qDAA8C;AAE9C,+BAAuC;AACvC,iCAA4D;AAM5D,KAAK,UAAU,MAAM,CAAC,GAAkB,EAAE,IAA0B;IAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;YAC5B,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;YAC5C,CAAC;YACD,MAAM,GAAG,GAAG,MAAM,GAAG,CAAC,WAAW,EAAE,CAAA;YACnC,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;QAC5B,CAAC;aAAM,CAAC;YACN,gEAAgE;YAChE,mBAAmB;YAEnB,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,CAAA;YACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;gBAC3B,GAAG,IAAI;gBACP,OAAO,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE;aACvC,CAAC,CAAA;YACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;YACH,CAAC;YACD,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;QAChD,CAAC;IACH,CAAC,CAAC,CACH,CAAA;IAED,OAAO,IAAA,uBAAgB,EAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;AACxE,CAAC;AAED,MAAqB,UAAW,SAAQ,iBAAO;IACrC,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEvB,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;IAED,KAAK,CAAC,CAAC,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,MAAM,EAAE,CAAA;QACV,CAAC;aAAM,CAAC;YACN,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,CAAC,CAAA;YAC5C,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,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;YAE3D,KAAK,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAC7B;gBACE,sCAAsC;gBACtC;oBACE,MAAM,EAAE,KAAK;oBACb,YAAY,EAAE,SAAS;oBACvB,GAAG,EAAE,CAAC;oBACN,SAAS;wBACP,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,cAAc;wBACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;oBACD,WAAW;wBACT,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,CAAC;wBACf,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;wBACrC,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,QAAQ;wBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;iBACF;aACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;QACH,CAAC;IACH,CAAC;IAED,mBAAmB;IACnB,KAAK,CAAC,UAAU,CAAC,EAAE,KAAK,EAAoC;QAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YAClB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;QACpD,CAAC;QACD,OAAO;YACL,IAAI,EAAE,KAAK,CAAC,MAAM;YAClB,UAAU,EAAE,EAAE;YACd,UAAU,EAAE,EAAE;YACd,KAAK;SACN,CAAA;IACH,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAiB,EAAE;QACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;QACH,CAAC;QACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,mBAAS,EAAE,CAAC;YAC7C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAE1C,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;QACvC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAC,CAAA;QACjE,MAAM,SAAS,GAAG,IAAA,qBAAe,EAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF;AA/HD,6BA+HC"}
|
package/dist/indexFile.d.ts
CHANGED
|
@@ -1,12 +1,12 @@
|
|
|
1
|
-
import { GenericFilehandle } from 'generic-filehandle2';
|
|
2
1
|
import Chunk from './chunk';
|
|
3
2
|
import { BaseOpts } from './util';
|
|
3
|
+
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
4
4
|
export default abstract class IndexFile {
|
|
5
5
|
filehandle: GenericFilehandle;
|
|
6
6
|
renameRefSeq: (s: string) => string;
|
|
7
7
|
/**
|
|
8
8
|
* @param {filehandle} filehandle
|
|
9
|
-
* @param {function}
|
|
9
|
+
* @param {function} renameRefSeqs
|
|
10
10
|
*/
|
|
11
11
|
constructor({ filehandle, renameRefSeq, }: {
|
|
12
12
|
filehandle: GenericFilehandle;
|
package/dist/indexFile.js
CHANGED
package/dist/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAKA,MAA8B,SAAS;IAC9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAE1C;;;OAGG;IACH,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;CAcF;AA/BD,4BA+BC"}
|
package/dist/long.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":";;;AAGA,0DAYC;AAfY,QAAA,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AACxB,QAAA,cAAc,GAAG,sBAAc,GAAG,sBAAc,CAAA;AAE7D,SAAgB,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":";;;AAGA,0DAYC;AAfY,QAAA,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AACxB,QAAA,cAAc,GAAG,sBAAc,GAAG,sBAAc,CAAA;AAE7D,SAAgB,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,sBAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
"use strict";
|
|
2
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
class NullFilehandle {
|
|
4
|
+
read() {
|
|
5
|
+
throw new Error('never called');
|
|
6
|
+
}
|
|
7
|
+
stat() {
|
|
8
|
+
throw new Error('never called');
|
|
9
|
+
}
|
|
10
|
+
readFile() {
|
|
11
|
+
throw new Error('never called');
|
|
12
|
+
}
|
|
13
|
+
close() {
|
|
14
|
+
throw new Error('never called');
|
|
15
|
+
}
|
|
16
|
+
}
|
|
17
|
+
exports.default = NullFilehandle;
|
|
18
|
+
//# sourceMappingURL=nullFilehandle.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"nullFilehandle.js","sourceRoot":"","sources":["../src/nullFilehandle.ts"],"names":[],"mappings":";;AAAA,MAAqB,cAAc;IAC1B,IAAI;QACT,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IACM,IAAI;QACT,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,QAAQ;QACb,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,KAAK;QACV,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;CACF;AAfD,iCAeC"}
|
package/dist/record.js
CHANGED
|
@@ -332,14 +332,13 @@ class BamRecord {
|
|
|
332
332
|
return (this.seq_length + 1) >> 1;
|
|
333
333
|
}
|
|
334
334
|
get seq() {
|
|
335
|
-
const { byteArray } = this.bytes;
|
|
336
335
|
const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
|
|
337
336
|
const seqBytes = this.num_seq_bytes;
|
|
338
337
|
const len = this.seq_length;
|
|
339
338
|
const buf = [];
|
|
340
339
|
let i = 0;
|
|
341
340
|
for (let j = 0; j < seqBytes; ++j) {
|
|
342
|
-
const sb = byteArray[p + j];
|
|
341
|
+
const sb = this.byteArray[p + j];
|
|
343
342
|
buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
|
|
344
343
|
i++;
|
|
345
344
|
if (i < len) {
|
|
@@ -408,7 +407,7 @@ class BamRecord {
|
|
|
408
407
|
if (k.startsWith('_') || k === 'bytes') {
|
|
409
408
|
continue;
|
|
410
409
|
}
|
|
411
|
-
|
|
410
|
+
// @ts-ignore
|
|
412
411
|
data[k] = this[k];
|
|
413
412
|
}
|
|
414
413
|
return data;
|
package/dist/record.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/util.d.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import Chunk from './chunk';
|
|
2
|
-
import VirtualOffset from './virtualOffset';
|
|
2
|
+
import { Offset, VirtualOffset } from './virtualOffset';
|
|
3
3
|
export declare function timeout(ms: number): Promise<unknown>;
|
|
4
4
|
/**
|
|
5
5
|
* Properly check if the given AbortSignal is aborted.
|
|
@@ -32,7 +32,7 @@ export interface BaseOpts {
|
|
|
32
32
|
signal?: AbortSignal;
|
|
33
33
|
}
|
|
34
34
|
export declare function makeOpts(obj?: AbortSignal | BaseOpts): BaseOpts;
|
|
35
|
-
export declare function optimizeChunks(chunks: Chunk[], lowest?:
|
|
35
|
+
export declare function optimizeChunks(chunks: Chunk[], lowest?: Offset): Chunk[];
|
|
36
36
|
export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
|
|
37
37
|
lineCount: number;
|
|
38
38
|
};
|
|
@@ -43,3 +43,4 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
|
|
|
43
43
|
};
|
|
44
44
|
export declare function sum(array: Uint8Array[]): number;
|
|
45
45
|
export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
|
|
46
|
+
export declare function gen2array<T>(gen: AsyncIterable<T[]>): Promise<T[]>;
|
package/dist/util.js
CHANGED
|
@@ -11,6 +11,7 @@ exports.findFirstData = findFirstData;
|
|
|
11
11
|
exports.parseNameBytes = parseNameBytes;
|
|
12
12
|
exports.sum = sum;
|
|
13
13
|
exports.concatUint8Array = concatUint8Array;
|
|
14
|
+
exports.gen2array = gen2array;
|
|
14
15
|
const long_1 = require("./long");
|
|
15
16
|
function timeout(ms) {
|
|
16
17
|
return new Promise(resolve => setTimeout(resolve, ms));
|
|
@@ -35,7 +36,7 @@ function checkAbortSignal(signal) {
|
|
|
35
36
|
// console.log('bam aborted!')
|
|
36
37
|
if (typeof DOMException === 'undefined') {
|
|
37
38
|
const e = new Error('aborted');
|
|
38
|
-
|
|
39
|
+
// @ts-ignore
|
|
39
40
|
e.code = 'ERR_ABORTED';
|
|
40
41
|
throw e;
|
|
41
42
|
}
|
|
@@ -142,4 +143,11 @@ function concatUint8Array(args) {
|
|
|
142
143
|
}
|
|
143
144
|
return mergedArray;
|
|
144
145
|
}
|
|
146
|
+
async function gen2array(gen) {
|
|
147
|
+
let out = [];
|
|
148
|
+
for await (const x of gen) {
|
|
149
|
+
out = out.concat(x);
|
|
150
|
+
}
|
|
151
|
+
return out;
|
|
152
|
+
}
|
|
145
153
|
//# sourceMappingURL=util.js.map
|
package/dist/util.js.map
CHANGED
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@@ -1 +1 @@
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|
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1
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-
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1
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+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAIA,0BAEC;AAcD,4CAgBC;AAQD,0CAGC;AAED,wCAKC;AAaD,4BAEC;AAED,wCAgCC;AAED,wCAIC;AAED,sCASC;AAED,wCAwBC;AAED,kBAMC;AACD,4CAQC;AAED,8BAMC;AA1KD,iCAAgD;AAGhD,SAAgB,OAAO,CAAC,EAAU;IAChC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAED;;;;;;;;;;;GAWG;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,aAAa;YACb,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACI,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;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,MAAe;IAC7D,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,KAAiB,EAAE,MAAc;IAC9D,OAAO;QACL,SAAS,EAAE,IAAA,8BAAuB,EAAC,KAAK,EAAE,MAAM,CAAC;KAClD,CAAA;AACH,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,UAAsB,EACtB,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,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;oBACvC,OAAO,IAAI,MAAM,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAE,CAAC,CAAA;gBAChD,CAAC;gBACD,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;AAED,SAAgB,GAAG,CAAC,KAAmB;IACrC,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE,CAAC;QAC1B,GAAG,IAAI,KAAK,CAAC,MAAM,CAAA;IACrB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AACD,SAAgB,gBAAgB,CAAC,IAAkB;IACjD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAA;IAC7C,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAEM,KAAK,UAAU,SAAS,CAAI,GAAuB;IACxD,IAAI,GAAG,GAAQ,EAAE,CAAA;IACjB,IAAI,KAAK,EAAE,MAAM,CAAC,IAAI,GAAG,EAAE,CAAC;QAC1B,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;IACrB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
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package/dist/virtualOffset.d.ts
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@@ -1,9 +1,14 @@
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1
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export
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export interface Offset {
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blockPosition: number;
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dataPosition: number;
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4
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toString(): string;
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compareTo(arg: Offset): number;
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}
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export declare class VirtualOffset {
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blockPosition: number;
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9
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dataPosition: number;
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10
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constructor(blockPosition: number, dataPosition: number);
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toString(): string;
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6
12
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compareTo(b: VirtualOffset): number;
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-
static min(...args: VirtualOffset[]): VirtualOffset;
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8
13
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}
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9
14
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export declare function fromBytes(bytes: Uint8Array, offset?: number, bigendian?: boolean): VirtualOffset;
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package/dist/virtualOffset.js
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@@ -1,5 +1,6 @@
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1
1
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"use strict";
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2
2
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.VirtualOffset = void 0;
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4
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exports.fromBytes = fromBytes;
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5
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class VirtualOffset {
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blockPosition;
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@@ -14,21 +15,8 @@ class VirtualOffset {
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compareTo(b) {
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15
16
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return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
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}
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static min(...args) {
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let min;
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let i = 0;
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for (; !min; i += 1) {
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min = args[i];
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}
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-
for (; i < args.length; i += 1) {
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-
if (min.compareTo(args[i]) > 0) {
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min = args[i];
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}
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-
}
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-
return min;
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29
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-
}
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30
18
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}
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31
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-
exports.
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19
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+
exports.VirtualOffset = VirtualOffset;
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32
20
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function fromBytes(bytes, offset = 0, bigendian = false) {
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33
21
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if (bigendian) {
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34
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throw new Error('big-endian virtual file offsets not implemented');
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"
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1
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+
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AAyBA,8BAcC;AAhCD,MAAa,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,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;CACF;AAjBD,sCAiBC;AACD,SAAgB,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACxE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}
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package/esm/bai.d.ts
CHANGED
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@@ -1,7 +1,12 @@
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1
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-
import VirtualOffset from './virtualOffset';
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2
1
|
import Chunk from './chunk';
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3
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-
import { BaseOpts } from './util';
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4
2
|
import IndexFile from './indexFile';
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3
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+
import { BaseOpts } from './util';
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|
4
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+
import { VirtualOffset } from './virtualOffset';
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|
5
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+
export interface IndexCovEntry {
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6
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+
start: number;
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7
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+
end: number;
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8
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+
score: number;
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9
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+
}
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5
10
|
export default class BAI extends IndexFile {
|
|
6
11
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setupP?: ReturnType<BAI['_parse']>;
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|
7
12
|
lineCount(refId: number, opts?: BaseOpts): Promise<number>;
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@@ -9,32 +14,28 @@ export default class BAI extends IndexFile {
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9
14
|
bai: boolean;
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10
15
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firstDataLine: VirtualOffset | undefined;
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11
16
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maxBlockSize: number;
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|
12
|
-
indices: {
|
|
13
|
-
binIndex: Record<
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|
17
|
+
indices: (refId: number) => {
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|
18
|
+
binIndex: Record<number, Chunk[]>;
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|
14
19
|
linearIndex: VirtualOffset[];
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15
|
-
stats
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20
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+
stats: {
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16
21
|
lineCount: number;
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|
17
|
-
};
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|
18
|
-
}
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|
22
|
+
} | undefined;
|
|
23
|
+
} | undefined;
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19
24
|
refCount: number;
|
|
20
25
|
}>;
|
|
21
|
-
indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<
|
|
22
|
-
start: number;
|
|
23
|
-
end: number;
|
|
24
|
-
score: number;
|
|
25
|
-
}[]>;
|
|
26
|
+
indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<IndexCovEntry[]>;
|
|
26
27
|
blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
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|
27
28
|
parse(opts?: BaseOpts): Promise<{
|
|
28
29
|
bai: boolean;
|
|
29
30
|
firstDataLine: VirtualOffset | undefined;
|
|
30
31
|
maxBlockSize: number;
|
|
31
|
-
indices: {
|
|
32
|
-
binIndex: Record<
|
|
32
|
+
indices: (refId: number) => {
|
|
33
|
+
binIndex: Record<number, Chunk[]>;
|
|
33
34
|
linearIndex: VirtualOffset[];
|
|
34
|
-
stats
|
|
35
|
+
stats: {
|
|
35
36
|
lineCount: number;
|
|
36
37
|
} | undefined;
|
|
37
|
-
}
|
|
38
|
+
} | undefined;
|
|
38
39
|
refCount: number;
|
|
39
40
|
}>;
|
|
40
41
|
hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
|