@gmod/bam 1.1.18 → 2.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +61 -25
- package/README.md +95 -57
- package/dist/bai.d.ts +34 -15
- package/dist/bai.js +87 -91
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +33 -27
- package/dist/bamFile.js +127 -121
- package/dist/bamFile.js.map +1 -1
- package/dist/chunk.d.ts +4 -8
- package/dist/chunk.js +2 -8
- package/dist/chunk.js.map +1 -1
- package/dist/csi.d.ts +74 -10
- package/dist/csi.js +78 -90
- package/dist/csi.js.map +1 -1
- package/dist/htsget.d.ts +5 -8
- package/dist/htsget.js +72 -47
- package/dist/htsget.js.map +1 -1
- package/dist/index.d.ts +5 -6
- package/dist/index.js +11 -11
- package/dist/index.js.map +1 -1
- package/dist/indexFile.d.ts +0 -6
- package/dist/indexFile.js +0 -35
- package/dist/indexFile.js.map +1 -1
- package/dist/nullIndex.d.ts +7 -0
- package/dist/nullIndex.js +33 -0
- package/dist/nullIndex.js.map +1 -0
- package/dist/record.d.ts +2 -2
- package/dist/record.js +34 -24
- package/dist/record.js.map +1 -1
- package/dist/sam.js +9 -7
- package/dist/sam.js.map +1 -1
- package/dist/util.d.ts +13 -1
- package/dist/util.js +47 -15
- package/dist/util.js.map +1 -1
- package/esm/bai.d.ts +34 -15
- package/esm/bai.js +86 -91
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +33 -27
- package/esm/bamFile.js +124 -120
- package/esm/bamFile.js.map +1 -1
- package/esm/chunk.d.ts +4 -8
- package/esm/chunk.js +2 -8
- package/esm/chunk.js.map +1 -1
- package/esm/csi.d.ts +74 -10
- package/esm/csi.js +85 -93
- package/esm/csi.js.map +1 -1
- package/esm/htsget.d.ts +5 -8
- package/esm/htsget.js +68 -43
- package/esm/htsget.js.map +1 -1
- package/esm/index.d.ts +5 -6
- package/esm/index.js +5 -6
- package/esm/index.js.map +1 -1
- package/esm/indexFile.d.ts +0 -6
- package/esm/indexFile.js +0 -22
- package/esm/indexFile.js.map +1 -1
- package/esm/nullIndex.d.ts +7 -0
- package/esm/nullIndex.js +16 -0
- package/esm/nullIndex.js.map +1 -0
- package/esm/record.d.ts +2 -2
- package/esm/record.js +34 -24
- package/esm/record.js.map +1 -1
- package/esm/sam.js +9 -7
- package/esm/sam.js.map +1 -1
- package/esm/util.d.ts +13 -1
- package/esm/util.js +40 -14
- package/esm/util.js.map +1 -1
- package/package.json +16 -17
- package/src/bai.ts +99 -102
- package/src/bamFile.ts +174 -198
- package/src/chunk.ts +6 -20
- package/src/csi.ts +102 -111
- package/src/htsget.ts +81 -61
- package/src/index.ts +5 -7
- package/src/indexFile.ts +0 -27
- package/src/nullIndex.ts +18 -0
- package/src/record.ts +34 -24
- package/src/sam.ts +9 -7
- package/src/util.ts +54 -13
- package/src/declare.d.ts +0 -2
package/dist/bamFile.js
CHANGED
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@@ -19,7 +19,7 @@ var __await = (this && this.__await) || function (v) { return this instanceof __
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var __asyncDelegator = (this && this.__asyncDelegator) || function (o) {
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var i, p;
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return i = {}, verb("next"), verb("throw", function (e) { throw e; }), verb("return"), i[Symbol.iterator] = function () { return this; }, i;
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function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done:
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function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }
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};
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var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
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if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
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@@ -37,13 +37,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.BAM_MAGIC = void 0;
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const buffer_1 = require("buffer");
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const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
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const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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const object_entries_ponyfill_1 = __importDefault(require("object.entries-ponyfill"));
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const generic_filehandle_1 = require("generic-filehandle");
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const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
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const quick_lru_1 = __importDefault(require("quick-lru"));
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-
//locals
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+
// locals
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const bai_1 = __importDefault(require("./bai"));
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const csi_1 = __importDefault(require("./csi"));
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const record_1 = __importDefault(require("./record"));
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@@ -51,21 +51,18 @@ const sam_1 = require("./sam");
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const util_1 = require("./util");
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exports.BAM_MAGIC = 21840194;
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const blockLen = 1 << 16;
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function flat(arr) {
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return [].concat(...arr);
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}
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function gen2array(gen) {
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var _a, gen_1, gen_1_1;
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var _b, e_1, _c, _d;
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return __awaiter(this, void 0, void 0, function* () {
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-
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let out = [];
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try {
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for (_a = true, gen_1 = __asyncValues(gen); gen_1_1 = yield gen_1.next(), _b = gen_1_1.done, !_b;) {
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_d = gen_1_1.value;
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_a = false;
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try {
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const x = _d;
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out.
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out = out.concat(x);
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}
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finally {
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_a = true;
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@@ -82,28 +79,34 @@ function gen2array(gen) {
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return out;
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});
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}
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class NullFilehandle {
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read() {
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throw new Error('never called');
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}
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stat() {
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throw new Error('never called');
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}
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readFile() {
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throw new Error('never called');
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}
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close() {
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throw new Error('never called');
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}
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}
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class BamFile {
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-
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* @param {string} [args.bamPath]
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* @param {FileHandle} [args.bamFilehandle]
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* @param {string} [args.baiPath]
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* @param {FileHandle} [args.baiFilehandle]
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*/
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constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, fetchSizeLimit, chunkSizeLimit, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
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constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
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this.htsget = false;
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this.featureCache = new abortable_promise_cache_1.default({
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-
//@ts-ignore
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cache: new quick_lru_1.default({
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maxSize: 50,
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}),
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-
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-
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fill: (args, signal) => __awaiter(this, void 0, void 0, function* () {
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const { chunk, opts } = args;
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const { data, cpositions, dpositions } = yield this._readChunk({
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chunk,
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opts: Object.assign(Object.assign({}, opts), { signal }),
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});
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-
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return feats;
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return this.readBamFeatures(data, cpositions, dpositions, chunk);
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}),
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});
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this.renameRefSeq = renameRefSeqs;
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@@ -116,6 +119,10 @@ class BamFile {
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else if (bamUrl) {
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this.bam = new generic_filehandle_1.RemoteFile(bamUrl);
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}
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else if (htsget) {
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this.htsget = true;
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this.bam = new NullFilehandle();
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}
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else {
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throw new Error('unable to initialize bam');
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}
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@@ -143,34 +150,32 @@ class BamFile {
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else if (bamUrl) {
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this.index = new bai_1.default({ filehandle: new generic_filehandle_1.RemoteFile(`${bamUrl}.bai`) });
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}
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else if (htsget) {
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this.htsget = true;
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}
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else {
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throw new Error('unable to infer index format');
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}
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this.fetchSizeLimit = fetchSizeLimit || 500000000; // 500MB
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this.chunkSizeLimit = chunkSizeLimit || 300000000; // 300MB
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this.yieldThreadTime = yieldThreadTime;
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}
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-
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getHeaderPre(origOpts) {
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return __awaiter(this, void 0, void 0, function* () {
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const opts = (0, util_1.makeOpts)(origOpts);
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if (!this.index) {
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return;
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}
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const indexData = yield this.index.parse(opts);
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const ret = indexData.firstDataLine
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? indexData.firstDataLine.blockPosition + 65535
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: undefined;
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let buffer;
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if (ret) {
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const
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const
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(
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if (!bytesRead) {
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const s = ret + blockLen;
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const res = yield this.bam.read(buffer_1.Buffer.alloc(s), 0, s, 0, opts);
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if (!res.bytesRead) {
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throw new Error('Error reading header');
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}
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buffer = buffer.subarray(0, bytesRead);
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}
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else {
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buffer = buffer.subarray(0, ret);
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}
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buffer = res.buffer.subarray(0, Math.min(res.bytesRead, ret));
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}
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else {
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buffer = (yield this.bam.readFile(opts));
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@@ -187,6 +192,15 @@ class BamFile {
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return (0, sam_1.parseHeaderText)(this.header);
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});
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}
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getHeader(opts) {
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if (!this.headerP) {
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this.headerP = this.getHeaderPre(opts).catch(e => {
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this.headerP = undefined;
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throw e;
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});
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}
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return this.headerP;
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}
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getHeaderText(opts = {}) {
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return __awaiter(this, void 0, void 0, function* () {
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yield this.getHeader(opts);
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@@ -195,13 +209,13 @@ class BamFile {
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}
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// the full length of the refseq block is not given in advance so this grabs
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// a chunk and doubles it if all refseqs haven't been processed
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_readRefSeqs(start, refSeqBytes, opts
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_readRefSeqs(start, refSeqBytes, opts) {
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return __awaiter(this, void 0, void 0, function* () {
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if (start > refSeqBytes) {
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return this._readRefSeqs(start, refSeqBytes * 2, opts);
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}
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const size = refSeqBytes + blockLen;
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const { bytesRead, buffer } = yield this.bam.read(Buffer.alloc(size), 0, refSeqBytes, 0, opts);
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const { bytesRead, buffer } = yield this.bam.read(buffer_1.Buffer.alloc(size), 0, refSeqBytes, 0, opts);
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if (!bytesRead) {
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throw new Error('Error reading refseqs from header');
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}
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@@ -225,59 +239,34 @@ class BamFile {
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return { chrToIndex, indexToChr };
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});
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}
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getRecordsForRange(chr, min, max, opts
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viewAsPairs: false,
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pairAcrossChr: false,
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maxInsertSize: 200000,
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}) {
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getRecordsForRange(chr, min, max, opts) {
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return __awaiter(this, void 0, void 0, function* () {
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return
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return gen2array(this.streamRecordsForRange(chr, min, max, opts));
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});
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}
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streamRecordsForRange(chr, min, max, opts
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streamRecordsForRange(chr, min, max, opts) {
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var _a;
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return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
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const chrId = this.chrToIndex
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-
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chunks = [];
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yield __await(this.getHeader(opts));
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const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
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if (chrId === undefined || !this.index) {
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yield yield __await([]);
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}
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else {
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chunks = yield __await(this.index.blocksForRange(chrId, min - 1, max, opts));
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throw new Error('Error in index fetch');
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}
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}
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for (let i = 0; i < chunks.length; i += 1) {
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yield __await((0, util_1.abortBreakPoint)(signal));
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const size = chunks[i].fetchedSize();
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if (size > this.chunkSizeLimit) {
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throw new Error(`Too many BAM features. BAM chunk size ${size} bytes exceeds chunkSizeLimit of ${this.chunkSizeLimit}`);
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}
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}
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const totalSize = chunks
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.map(s => s.fetchedSize())
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.reduce((a, b) => a + b, 0);
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if (totalSize > this.fetchSizeLimit) {
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throw new Error(`data size of ${totalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
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const chunks = yield __await(this.index.blocksForRange(chrId, min - 1, max, opts));
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yield __await(yield* __asyncDelegator(__asyncValues(this._fetchChunkFeatures(chunks, chrId, min, max, opts))));
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}
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yield __await(yield* __asyncDelegator(__asyncValues(this._fetchChunkFeatures(chunks, chrId, min, max, opts))));
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});
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}
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_fetchChunkFeatures(chunks, chrId, min, max, opts) {
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_fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
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return __asyncGenerator(this, arguments, function* _fetchChunkFeatures_1() {
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-
const { viewAsPairs
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const { viewAsPairs } = opts;
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const feats = [];
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let done = false;
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|
-
for (
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273
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const
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-
const records = (yield __await(this.featureCache.get(c.toString(), {
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chunk: c,
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opts,
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-
}, opts.signal)));
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+
for (const chunk of chunks) {
|
|
267
|
+
const records = yield __await(this.featureCache.get(chunk.toString(), { chunk, opts }, opts.signal));
|
|
278
268
|
const recs = [];
|
|
279
|
-
for (
|
|
280
|
-
const feature = records[i];
|
|
269
|
+
for (const feature of records) {
|
|
281
270
|
if (feature.seq_id() === chrId) {
|
|
282
271
|
if (feature.get('start') >= max) {
|
|
283
272
|
// past end of range, can stop iterating
|
|
@@ -304,35 +293,35 @@ class BamFile {
|
|
|
304
293
|
}
|
|
305
294
|
fetchPairs(chrId, feats, opts) {
|
|
306
295
|
return __awaiter(this, void 0, void 0, function* () {
|
|
307
|
-
const { pairAcrossChr
|
|
296
|
+
const { pairAcrossChr, maxInsertSize = 200000 } = opts;
|
|
308
297
|
const unmatedPairs = {};
|
|
309
298
|
const readIds = {};
|
|
310
299
|
feats.map(ret => {
|
|
311
300
|
const readNames = {};
|
|
312
|
-
for (
|
|
313
|
-
const name =
|
|
314
|
-
const id =
|
|
301
|
+
for (const element of ret) {
|
|
302
|
+
const name = element.name();
|
|
303
|
+
const id = element.id();
|
|
315
304
|
if (!readNames[name]) {
|
|
316
305
|
readNames[name] = 0;
|
|
317
306
|
}
|
|
318
307
|
readNames[name]++;
|
|
319
308
|
readIds[id] = 1;
|
|
320
309
|
}
|
|
321
|
-
(
|
|
310
|
+
for (const [k, v] of Object.entries(readNames)) {
|
|
322
311
|
if (v === 1) {
|
|
323
312
|
unmatedPairs[k] = true;
|
|
324
313
|
}
|
|
325
|
-
}
|
|
314
|
+
}
|
|
326
315
|
});
|
|
327
316
|
const matePromises = [];
|
|
328
317
|
feats.map(ret => {
|
|
329
|
-
for (
|
|
330
|
-
const f = ret[i];
|
|
318
|
+
for (const f of ret) {
|
|
331
319
|
const name = f.name();
|
|
332
320
|
const start = f.get('start');
|
|
333
321
|
const pnext = f._next_pos();
|
|
334
322
|
const rnext = f._next_refid();
|
|
335
|
-
if (
|
|
323
|
+
if (this.index &&
|
|
324
|
+
unmatedPairs[name] &&
|
|
336
325
|
(pairAcrossChr ||
|
|
337
326
|
(rnext === chrId && Math.abs(start - pnext) < maxInsertSize))) {
|
|
338
327
|
matePromises.push(this.index.blocksForRange(rnext, pnext, pnext + 1, opts));
|
|
@@ -341,38 +330,39 @@ class BamFile {
|
|
|
341
330
|
});
|
|
342
331
|
// filter out duplicate chunks (the blocks are lists of chunks, blocks are
|
|
343
332
|
// concatenated, then filter dup chunks)
|
|
344
|
-
const
|
|
345
|
-
|
|
346
|
-
|
|
347
|
-
|
|
348
|
-
|
|
349
|
-
|
|
350
|
-
if (mateTotalSize > this.fetchSizeLimit) {
|
|
351
|
-
throw new Error(`data size of ${mateTotalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
|
|
333
|
+
const map = new Map();
|
|
334
|
+
const res = yield Promise.all(matePromises);
|
|
335
|
+
for (const m of res.flat()) {
|
|
336
|
+
if (!map.has(m.toString())) {
|
|
337
|
+
map.set(m.toString(), m);
|
|
338
|
+
}
|
|
352
339
|
}
|
|
353
|
-
const mateFeatPromises =
|
|
340
|
+
const mateFeatPromises = yield Promise.all([...map.values()].map((c) => __awaiter(this, void 0, void 0, function* () {
|
|
354
341
|
const { data, cpositions, dpositions, chunk } = yield this._readChunk({
|
|
355
342
|
chunk: c,
|
|
356
343
|
opts,
|
|
357
344
|
});
|
|
358
|
-
const feats = yield this.readBamFeatures(data, cpositions, dpositions, chunk);
|
|
359
345
|
const mateRecs = [];
|
|
360
|
-
for (
|
|
361
|
-
const feature = feats[i];
|
|
346
|
+
for (const feature of yield this.readBamFeatures(data, cpositions, dpositions, chunk)) {
|
|
362
347
|
if (unmatedPairs[feature.get('name')] && !readIds[feature.id()]) {
|
|
363
348
|
mateRecs.push(feature);
|
|
364
349
|
}
|
|
365
350
|
}
|
|
366
351
|
return mateRecs;
|
|
367
|
-
}));
|
|
368
|
-
return flat(
|
|
352
|
+
})));
|
|
353
|
+
return mateFeatPromises.flat();
|
|
354
|
+
});
|
|
355
|
+
}
|
|
356
|
+
_readRegion(position, size, opts = {}) {
|
|
357
|
+
return __awaiter(this, void 0, void 0, function* () {
|
|
358
|
+
const { bytesRead, buffer } = yield this.bam.read(buffer_1.Buffer.alloc(size), 0, size, position, opts);
|
|
359
|
+
return buffer.subarray(0, Math.min(bytesRead, size));
|
|
369
360
|
});
|
|
370
361
|
}
|
|
371
362
|
_readChunk({ chunk, opts }) {
|
|
372
363
|
return __awaiter(this, void 0, void 0, function* () {
|
|
373
|
-
const
|
|
374
|
-
const { buffer,
|
|
375
|
-
const { buffer: data, cpositions, dpositions, } = yield (0, bgzf_filehandle_1.unzipChunkSlice)(buffer.subarray(0, Math.min(bytesRead, size)), chunk);
|
|
364
|
+
const buffer = yield this._readRegion(chunk.minv.blockPosition, chunk.fetchedSize(), opts);
|
|
365
|
+
const { buffer: data, cpositions, dpositions, } = yield (0, bgzf_filehandle_1.unzipChunkSlice)(buffer, chunk);
|
|
376
366
|
return { data, cpositions, dpositions, chunk };
|
|
377
367
|
});
|
|
378
368
|
}
|
|
@@ -398,23 +388,27 @@ class BamFile {
|
|
|
398
388
|
start: blockStart,
|
|
399
389
|
end: blockEnd,
|
|
400
390
|
},
|
|
401
|
-
// the below results in an automatically calculated file-offset based
|
|
402
|
-
// if the info for that is available, otherwise crc32 of the
|
|
391
|
+
// the below results in an automatically calculated file-offset based
|
|
392
|
+
// ID if the info for that is available, otherwise crc32 of the
|
|
393
|
+
// features
|
|
403
394
|
//
|
|
404
|
-
// cpositions[pos] refers to actual file offset of a bgzip block
|
|
395
|
+
// cpositions[pos] refers to actual file offset of a bgzip block
|
|
396
|
+
// boundaries
|
|
405
397
|
//
|
|
406
|
-
// we multiply by (1 <<8) in order to make sure each block has a
|
|
407
|
-
// address space so that data in that block could never
|
|
398
|
+
// we multiply by (1 <<8) in order to make sure each block has a
|
|
399
|
+
// "unique" address space so that data in that block could never
|
|
400
|
+
// overlap
|
|
408
401
|
//
|
|
409
402
|
// then the blockStart-dpositions is an uncompressed file offset from
|
|
410
|
-
// that bgzip block boundary, and since the cpositions are multiplied
|
|
411
|
-
// (1 << 8) these uncompressed offsets get a unique space
|
|
403
|
+
// that bgzip block boundary, and since the cpositions are multiplied
|
|
404
|
+
// by (1 << 8) these uncompressed offsets get a unique space
|
|
412
405
|
//
|
|
413
|
-
// this has an extra chunk.minv.dataPosition added on because it
|
|
414
|
-
// starts at 0 instead of chunk.minv.dataPosition
|
|
406
|
+
// this has an extra chunk.minv.dataPosition added on because it
|
|
407
|
+
// blockStart starts at 0 instead of chunk.minv.dataPosition
|
|
415
408
|
//
|
|
416
|
-
// the +1 is just to avoid any possible uniqueId 0 but this does not
|
|
417
|
-
|
|
409
|
+
// the +1 is just to avoid any possible uniqueId 0 but this does not
|
|
410
|
+
// realistically happen
|
|
411
|
+
fileOffset: cpositions.length > 0
|
|
418
412
|
? cpositions[pos] * (1 << 8) +
|
|
419
413
|
(blockStart - dpositions[pos]) +
|
|
420
414
|
chunk.minv.dataPosition +
|
|
@@ -434,29 +428,41 @@ class BamFile {
|
|
|
434
428
|
});
|
|
435
429
|
}
|
|
436
430
|
hasRefSeq(seqName) {
|
|
431
|
+
var _a, _b;
|
|
437
432
|
return __awaiter(this, void 0, void 0, function* () {
|
|
438
|
-
const
|
|
439
|
-
return this.index.hasRefSeq(
|
|
433
|
+
const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
|
|
434
|
+
return seqId === undefined ? false : (_b = this.index) === null || _b === void 0 ? void 0 : _b.hasRefSeq(seqId);
|
|
440
435
|
});
|
|
441
436
|
}
|
|
442
437
|
lineCount(seqName) {
|
|
438
|
+
var _a;
|
|
443
439
|
return __awaiter(this, void 0, void 0, function* () {
|
|
444
|
-
const
|
|
445
|
-
return this.index.lineCount(
|
|
440
|
+
const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
|
|
441
|
+
return seqId === undefined || !this.index ? 0 : this.index.lineCount(seqId);
|
|
446
442
|
});
|
|
447
443
|
}
|
|
448
444
|
indexCov(seqName, start, end) {
|
|
445
|
+
var _a;
|
|
449
446
|
return __awaiter(this, void 0, void 0, function* () {
|
|
447
|
+
if (!this.index) {
|
|
448
|
+
return [];
|
|
449
|
+
}
|
|
450
450
|
yield this.index.parse();
|
|
451
|
-
const seqId = this.chrToIndex
|
|
452
|
-
return this.index.indexCov(seqId, start, end);
|
|
451
|
+
const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
|
|
452
|
+
return seqId === undefined ? [] : this.index.indexCov(seqId, start, end);
|
|
453
453
|
});
|
|
454
454
|
}
|
|
455
455
|
blocksForRange(seqName, start, end, opts) {
|
|
456
|
+
var _a;
|
|
456
457
|
return __awaiter(this, void 0, void 0, function* () {
|
|
458
|
+
if (!this.index) {
|
|
459
|
+
return [];
|
|
460
|
+
}
|
|
457
461
|
yield this.index.parse();
|
|
458
|
-
const seqId = this.chrToIndex
|
|
459
|
-
return
|
|
462
|
+
const seqId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[seqName];
|
|
463
|
+
return seqId === undefined
|
|
464
|
+
? []
|
|
465
|
+
: this.index.blocksForRange(seqId, start, end, opts);
|
|
460
466
|
});
|
|
461
467
|
}
|
|
462
468
|
}
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/chunk.d.ts
CHANGED
|
@@ -1,16 +1,12 @@
|
|
|
1
|
+
/// <reference types="node" />
|
|
1
2
|
import VirtualOffset from './virtualOffset';
|
|
2
3
|
export default class Chunk {
|
|
3
4
|
minv: VirtualOffset;
|
|
4
5
|
maxv: VirtualOffset;
|
|
5
6
|
bin: number;
|
|
6
|
-
_fetchedSize?: number;
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
* @param {VirtualOffset} maxv
|
|
10
|
-
* @param {number} bin
|
|
11
|
-
* @param {number} [fetchedSize]
|
|
12
|
-
*/
|
|
13
|
-
constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: undefined);
|
|
7
|
+
_fetchedSize?: number | undefined;
|
|
8
|
+
buffer?: Buffer;
|
|
9
|
+
constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, _fetchedSize?: number | undefined);
|
|
14
10
|
toUniqueString(): string;
|
|
15
11
|
toString(): string;
|
|
16
12
|
compareTo(b: Chunk): number;
|
package/dist/chunk.js
CHANGED
|
@@ -2,17 +2,11 @@
|
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
// little class representing a chunk in the index
|
|
4
4
|
class Chunk {
|
|
5
|
-
|
|
6
|
-
* @param {VirtualOffset} minv
|
|
7
|
-
* @param {VirtualOffset} maxv
|
|
8
|
-
* @param {number} bin
|
|
9
|
-
* @param {number} [fetchedSize]
|
|
10
|
-
*/
|
|
11
|
-
constructor(minv, maxv, bin, fetchedSize = undefined) {
|
|
5
|
+
constructor(minv, maxv, bin, _fetchedSize) {
|
|
12
6
|
this.minv = minv;
|
|
13
7
|
this.maxv = maxv;
|
|
14
8
|
this.bin = bin;
|
|
15
|
-
this._fetchedSize =
|
|
9
|
+
this._fetchedSize = _fetchedSize;
|
|
16
10
|
}
|
|
17
11
|
toUniqueString() {
|
|
18
12
|
return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
|
package/dist/chunk.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAGxB,YACS,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAe;QACnB,SAAI,GAAJ,IAAI,CAAe;QACnB,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE;YACnC,OAAO,IAAI,CAAC,YAAY,CAAA;SACzB;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AAlCD,wBAkCC"}
|