@gmod/bbi 3.0.1 → 4.0.0
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 +9 -4
- package/dist/bbi.d.ts +5 -5
- package/dist/bbi.js +14 -21
- package/dist/bbi.js.map +1 -1
- package/dist/bigbed.d.ts +11 -4
- package/dist/bigbed.js +18 -12
- package/dist/bigbed.js.map +1 -1
- package/dist/bigwig.d.ts +1 -1
- package/dist/bigwig.js +2 -2
- package/dist/bigwig.js.map +1 -1
- package/dist/{blockView.d.ts → block-view.d.ts} +1 -1
- package/dist/{blockView.js → block-view.js} +25 -17
- package/dist/block-view.js.map +1 -0
- package/dist/range.js +3 -4
- package/dist/range.js.map +1 -1
- package/dist/unzip.d.ts +1 -2
- package/dist/unzip.js +1 -1
- package/dist/unzip.js.map +1 -1
- package/dist/util.js +12 -12
- package/dist/util.js.map +1 -1
- package/esm/bbi.d.ts +5 -5
- package/esm/bbi.js +13 -20
- package/esm/bbi.js.map +1 -1
- package/esm/bigbed.d.ts +11 -4
- package/esm/bigbed.js +7 -12
- package/esm/bigbed.js.map +1 -1
- package/esm/bigwig.d.ts +1 -1
- package/esm/bigwig.js +1 -1
- package/esm/bigwig.js.map +1 -1
- package/esm/{blockView.d.ts → block-view.d.ts} +1 -1
- package/esm/{blockView.js → block-view.js} +25 -17
- package/esm/block-view.js.map +1 -0
- package/esm/range.js +3 -4
- package/esm/range.js.map +1 -1
- package/esm/unzip.d.ts +1 -2
- package/esm/unzip.js +1 -2
- package/esm/unzip.js.map +1 -1
- package/esm/util.js +12 -12
- package/esm/util.js.map +1 -1
- package/package.json +15 -15
- package/src/bbi.ts +29 -35
- package/src/bigbed.ts +11 -23
- package/src/bigwig.ts +1 -1
- package/src/{blockView.ts → block-view.ts} +30 -21
- package/src/range.ts +3 -4
- package/src/unzip.ts +1 -2
- package/src/util.ts +11 -11
- package/dist/blockView.js.map +0 -1
- package/esm/blockView.js.map +0 -1
- package/src/declare.d.ts +0 -2
package/CHANGELOG.md
CHANGED
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@@ -1,13 +1,18 @@
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-
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+
# [4.0.0](https://github.com/GMOD/bbi-js/compare/v3.0.1...v4.0.0) (2023-05-05)
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### Features
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-
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- Improve typescripting, refactoring
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- Options argument only accepts {signal}, not just signal now
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## [3.0.1](https://github.com/GMOD/bbi-js/compare/v3.0.0...v3.0.1) (2023-04-21)
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### Features
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- explicit buffer import ([#53](https://github.com/GMOD/bbi-js/issues/53))
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([2699c98](https://github.com/GMOD/bbi-js/commit/2699c983dea380bbb56773058ba3f233c833d9c8))
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-
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* Add explicit Buffer import
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# [3.0.0](https://github.com/GMOD/bbi-js/compare/v2.0.5...v3.0.0) (2023-01-11)
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package/dist/bbi.d.ts
CHANGED
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@@ -1,6 +1,6 @@
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import { GenericFilehandle } from 'generic-filehandle';
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import { Observable } from 'rxjs';
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import { BlockView } from './
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import { BlockView } from './block-view';
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export interface Feature {
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start: number;
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end: number;
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@@ -51,8 +51,8 @@ export declare abstract class BBI {
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protected bbi: GenericFilehandle;
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private headerP?;
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protected renameRefSeqs: (a: string) => string;
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getHeader(opts?: RequestOptions
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constructor(
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getHeader(opts?: RequestOptions): Promise<Header>;
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constructor(args: {
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filehandle?: GenericFilehandle;
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path?: string;
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url?: string;
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@@ -62,8 +62,8 @@ export declare abstract class BBI {
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private _getMainHeader;
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private _isBigEndian;
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private _readChromTree;
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protected getUnzoomedView(opts
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protected abstract getView(scale: number, opts
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protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
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protected abstract getView(scale: number, opts?: RequestOptions): Promise<BlockView>;
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/**
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* Gets features from a BigWig file
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*
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package/dist/bbi.js
CHANGED
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@@ -15,7 +15,7 @@ const binary_parser_1 = require("binary-parser");
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const generic_filehandle_1 = require("generic-filehandle");
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const rxjs_1 = require("rxjs");
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const operators_1 = require("rxjs/operators");
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const
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const block_view_1 = require("./block-view");
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const BIG_WIG_MAGIC = -2003829722;
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const BIG_BED_MAGIC = -2021002517;
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function toString(arr) {
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@@ -83,10 +83,9 @@ class BBI {
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* @param abortSignal - abort the operation, can be null
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* @return a Header object
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*/
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getHeader(opts
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const options = 'aborted' in opts ? { signal: opts } : opts;
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getHeader(opts) {
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if (!this.headerP) {
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this.headerP = this._getHeader(
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this.headerP = this._getHeader(opts).catch(e => {
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this.headerP = undefined;
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throw e;
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});
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@@ -99,8 +98,8 @@ class BBI {
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* @param url - a URL string
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* @param renameRefSeqs - an optional method to rename the internal reference sequences using a mapping function
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*/
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constructor(
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const { filehandle, renameRefSeqs = s => s, path, url } =
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constructor(args) {
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const { filehandle, renameRefSeqs = s => s, path, url } = args;
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this.renameRefSeqs = renameRefSeqs;
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if (filehandle) {
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this.bbi = filehandle;
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@@ -231,7 +230,7 @@ class BBI {
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getUnzoomedView(opts) {
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return __awaiter(this, void 0, void 0, function* () {
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const { unzoomedIndexOffset, refsByName, uncompressBufSize, isBigEndian, fileType, } = yield this.getHeader(opts);
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return new
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return new block_view_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType);
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});
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}
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/**
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* @param end - The end of a region
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* @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
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*/
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getFeatureStream(refName, start, end, opts
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scale: 1,
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}) {
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getFeatureStream(refName, start, end, 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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const chrName = this.renameRefSeqs(refName);
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let view;
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const { basesPerSpan, scale } = opts || {};
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if (basesPerSpan) {
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view = yield this.getView(1 / basesPerSpan, opts);
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}
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else if (
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view = yield this.getView(
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else if (scale) {
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view = yield this.getView(scale, opts);
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}
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else {
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view = yield this.getView(1, opts);
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}
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throw new Error('unable to get block view for data');
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}
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return new rxjs_1.Observable((observer) => {
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return new rxjs_1.Observable(observer => {
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view.readWigData(chrName, start, end, observer, opts);
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});
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});
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}
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getFeatures(refName, start, end, opts
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scale: 1,
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}) {
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getFeatures(refName, start, end, opts) {
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return __awaiter(this, void 0, void 0, function* () {
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const ob = yield this.getFeatureStream(refName, start, end, opts);
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const ret = yield (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
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package/dist/bbi.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,mCAA+B;AAC/B,iDAAsC;AACtC,2DAA6E;AAC7E,+
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+
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,mCAA+B;AAC/B,iDAAsC;AACtC,2DAA6E;AAC7E,+BAAiD;AACjD,8CAAwC;AACxC,6CAAwC;AAExC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AACjC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AAEjC,SAAS,QAAQ,CAAC,GAAe;IAC/B,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;AACtC,CAAC;AAyCD;;;;GAIG;AACH,SAAS,UAAU,CAAC,IAAa;IAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;IAClC,MAAM,YAAY,GAAG,IAAI,sBAAM,EAAE;SAC9B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,eAAe,CAAC;SACvB,MAAM,CAAC,iBAAiB,CAAC;SACzB,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,qBAAqB,CAAC;SAC7B,MAAM,CAAC,YAAY,CAAC;SACpB,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,UAAU,CAAC,CAAC,iCAAiC;SACpD,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,iBAAiB,CAAC,CAAC,oCAAoC;SAC9D,KAAK,CAAC,YAAY,EAAE;QACnB,MAAM,EAAE,eAAe;QACvB,IAAI,EAAE,IAAI,sBAAM,EAAE;aACf,SAAS,CAAC,EAAE,CAAC;aACb,MAAM,CAAC,gBAAgB,CAAC;aACxB,MAAM,CAAC,UAAU,CAAC;aAClB,MAAM,CAAC,YAAY,CAAC;aACpB,MAAM,CAAC,aAAa,CAAC;KACzB,CAAC,CAAA;IAEJ,MAAM,kBAAkB,GAAG,IAAI,sBAAM,EAAE;SACpC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,cAAc,CAAC;SACtB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,iBAAiB,CAAC,CAAA;IAE9B,MAAM,eAAe,GAAG,IAAI,sBAAM,EAAE;SACjC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,OAAO,CAAC;SACf,MAAM,CAAC,WAAW,CAAC;SACnB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,WAAW,CAAC,CAAA;IAEtB,MAAM,UAAU,GAAG,IAAI,sBAAM,EAAE;SAC5B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,YAAY,CAAC;SACnB,IAAI,CAAC,CAAC,CAAC;SACP,MAAM,CAAC,KAAK,CAAC;SACb,UAAU,CAAC,QAAQ,CAAC,CAAA;IAEvB,OAAO;QACL,eAAe;QACf,kBAAkB;QAClB,YAAY;QACZ,UAAU;KACX,CAAA;AACH,CAAC;AAQD,MAAsB,GAAG;IAOvB;;;OAGG;IACI,SAAS,CAAC,IAAqB;QACpC,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE;YACjB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC7C,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;gBACxB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IAED;;;;;OAKG;IACH,YAAmB,IAKlB;QACC,MAAM,EAAE,UAAU,EAAE,aAAa,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,IAAI,CAAA;QAC9D,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;QAClC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,UAAU,CAAA;SACtB;aAAM,IAAI,GAAG,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,IAAI,+BAAU,CAAC,GAAG,CAAC,CAAA;SAC/B;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,GAAG,GAAG,IAAI,8BAAS,CAAC,IAAI,CAAC,CAAA;SAC/B;aAAM;YACL,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;SACjC;IACH,CAAC;IAEa,UAAU,CAAC,IAAqB;;YAC5C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;YAC9C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;YACtD,uCAAY,MAAM,GAAK,MAAM,EAAE;QACjC,CAAC;KAAA;IAEa,cAAc,CAC1B,IAAqB,EACrB,WAAW,GAAG,IAAI;;YAElB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,eAAM,CAAC,KAAK,CAAC,WAAW,CAAC,EACzB,CAAC,EACD,WAAW,EACX,CAAC,EACD,IAAI,CACL,CAAA;YACD,MAAM,WAAW,GAAG,IAAI,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;YAC7C,MAAM,GAAG,GAAG,UAAU,CAAC,WAAW,CAAC,CAAA;YACnC,MAAM,MAAM,GAAG,GAAG,CAAC,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;YAC7C,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,kBAAkB,EAAE,GAAG,MAAM,CAAA;YACtD,MAAM,CAAC,QAAQ,GAAG,KAAK,KAAK,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAA;YAC/D,IAAI,QAAQ,GAAG,WAAW,IAAI,kBAAkB,GAAG,WAAW,EAAE;gBAC9D,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;aAClD;YACD,IAAI,QAAQ,EAAE;gBACZ,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;gBACnC,MAAM,CAAC,OAAO,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAA;aACxE;YACD,IAAI,MAAM,CAAC,kBAAkB,GAAG,WAAW,EAAE;gBAC3C,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;aAClD;YACD,IAAI,MAAM,CAAC,kBAAkB,EAAE;gBAC7B,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAC,CAAA;gBAC/D,MAAM,GAAG,GAAG,GAAG,CAAC,kBAAkB,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBAC9C,MAAM,CAAC,YAAY,mCAAQ,GAAG,KAAE,YAAY,EAAE,MAAM,CAAC,GAAG,CAAC,YAAY,CAAC,GAAE,CAAA;aACzE;YACD,uCAAY,MAAM,KAAE,WAAW,IAAE;QACnC,CAAC;KAAA;IAEO,YAAY,CAAC,MAAc;QACjC,IAAI,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC/B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,KAAK,CAAA;SACb;QACD,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,IAAI,CAAA;SACZ;QACD,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;IAC7C,CAAC;IAED,qCAAqC;IACvB,cAAc,CAC1B,MAAc,EACd,IAA+B;;YAE/B,MAAM,IAAI,GAAG,MAAM,CAAC,WAAW,CAAA;YAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;YAClC,MAAM,YAAY,GAEd,EAAE,CAAA;YACN,MAAM,UAAU,GAA8B,EAAE,CAAA;YAEhD,IAAI,kBAAkB,GAAG,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAA;YAC1D,MAAM,eAAe,GAAG,MAAM,CAAC,MAAM,CAAC,eAAe,CAAC,CAAA;YACtD,OAAO,kBAAkB,GAAG,CAAC,KAAK,CAAC,EAAE;gBACnC,kBAAkB,IAAI,CAAC,CAAA;aACxB;YACD,MAAM,GAAG,GAAG,kBAAkB,GAAG,eAAe,CAAA;YAChD,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,eAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,MAAM,CAAC,eAAe,CAAC,EACvB,IAAI,CACL,CAAA;YAED,MAAM,CAAC,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAC1B,MAAM,EAAE,OAAO,EAAE,GAAG,CAAC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|
package/dist/bigbed.d.ts
CHANGED
|
@@ -1,11 +1,18 @@
|
|
|
1
|
+
import AbortablePromiseCache from 'abortable-promise-cache';
|
|
1
2
|
import { BBI, Feature, RequestOptions } from './bbi';
|
|
2
|
-
|
|
3
|
+
interface Index {
|
|
4
|
+
type: number;
|
|
5
|
+
fieldcount: number;
|
|
6
|
+
offset: number;
|
|
7
|
+
field: number;
|
|
8
|
+
}
|
|
3
9
|
export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
|
|
4
10
|
export declare class BigBed extends BBI {
|
|
5
|
-
readIndicesCache:
|
|
6
|
-
readIndices(opts?:
|
|
7
|
-
protected getView(_scale: number, opts
|
|
11
|
+
readIndicesCache: AbortablePromiseCache<RequestOptions, Index[]>;
|
|
12
|
+
readIndices(opts?: RequestOptions): Promise<Index[]>;
|
|
13
|
+
protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view").BlockView>;
|
|
8
14
|
private _readIndices;
|
|
9
15
|
private searchExtraIndexBlocks;
|
|
10
16
|
searchExtraIndex(name: string, opts?: RequestOptions): Promise<Feature[]>;
|
|
11
17
|
}
|
|
18
|
+
export {};
|
package/dist/bigbed.js
CHANGED
|
@@ -8,6 +8,17 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
|
|
|
8
8
|
step((generator = generator.apply(thisArg, _arguments || [])).next());
|
|
9
9
|
});
|
|
10
10
|
};
|
|
11
|
+
var __rest = (this && this.__rest) || function (s, e) {
|
|
12
|
+
var t = {};
|
|
13
|
+
for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
|
|
14
|
+
t[p] = s[p];
|
|
15
|
+
if (s != null && typeof Object.getOwnPropertySymbols === "function")
|
|
16
|
+
for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
|
|
17
|
+
if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
|
|
18
|
+
t[p[i]] = s[p[i]];
|
|
19
|
+
}
|
|
20
|
+
return t;
|
|
21
|
+
};
|
|
11
22
|
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
12
23
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
13
24
|
};
|
|
@@ -29,20 +40,15 @@ class BigBed extends bbi_1.BBI {
|
|
|
29
40
|
super(...arguments);
|
|
30
41
|
this.readIndicesCache = new abortable_promise_cache_1.default({
|
|
31
42
|
cache: new quick_lru_1.default({ maxSize: 1 }),
|
|
32
|
-
fill: (args, signal) =>
|
|
33
|
-
return this._readIndices(Object.assign(Object.assign({}, args), { signal }));
|
|
34
|
-
}),
|
|
43
|
+
fill: (args, signal) => this._readIndices(Object.assign(Object.assign({}, args), { signal })),
|
|
35
44
|
});
|
|
36
45
|
}
|
|
37
46
|
readIndices(opts = {}) {
|
|
38
|
-
const
|
|
39
|
-
return this.readIndicesCache.get(JSON.stringify(
|
|
47
|
+
const { signal } = opts, rest = __rest(opts, ["signal"]);
|
|
48
|
+
return this.readIndicesCache.get(JSON.stringify(rest), opts, signal);
|
|
40
49
|
}
|
|
41
50
|
/*
|
|
42
51
|
* retrieve unzoomed view for any scale
|
|
43
|
-
* @param scale - unused
|
|
44
|
-
* @param abortSignal - an optional AbortSignal to kill operation
|
|
45
|
-
* @return promise for a BlockView
|
|
46
52
|
*/
|
|
47
53
|
getView(_scale, opts) {
|
|
48
54
|
return __awaiter(this, void 0, void 0, function* () {
|
|
@@ -99,7 +105,7 @@ class BigBed extends bbi_1.BBI {
|
|
|
99
105
|
return __awaiter(this, void 0, void 0, function* () {
|
|
100
106
|
const { isBigEndian } = yield this.getHeader(opts);
|
|
101
107
|
const indices = yield this.readIndices(opts);
|
|
102
|
-
if (
|
|
108
|
+
if (indices.length === 0) {
|
|
103
109
|
return [];
|
|
104
110
|
}
|
|
105
111
|
const locs = indices.map((index) => __awaiter(this, void 0, void 0, function* () {
|
|
@@ -181,7 +187,7 @@ class BigBed extends bbi_1.BBI {
|
|
|
181
187
|
searchExtraIndex(name, opts = {}) {
|
|
182
188
|
return __awaiter(this, void 0, void 0, function* () {
|
|
183
189
|
const blocks = yield this.searchExtraIndexBlocks(name, opts);
|
|
184
|
-
if (
|
|
190
|
+
if (blocks.length === 0) {
|
|
185
191
|
return [];
|
|
186
192
|
}
|
|
187
193
|
const view = yield this.getUnzoomedView(opts);
|
|
@@ -189,8 +195,8 @@ class BigBed extends bbi_1.BBI {
|
|
|
189
195
|
return new rxjs_1.Observable(observer => {
|
|
190
196
|
view.readFeatures(observer, [block], opts);
|
|
191
197
|
}).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
|
|
192
|
-
for (
|
|
193
|
-
|
|
198
|
+
for (const element of x) {
|
|
199
|
+
element.field = block.field;
|
|
194
200
|
}
|
|
195
201
|
return x;
|
|
196
202
|
}));
|
package/dist/bigbed.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,mCAA+B;AAC/B,iDAAsC;AACtC,+BAAwD;AACxD,8CAA4C;AAC5C,sFAA2D;AAC3D,0DAAgC;AAEhC,+BAAoD;AAgBpD,SAAgB,WAAW,CAAI,EAAqB;IAClD,OAAO,EAAE,CAAC,MAAM,CAAC,CAAC,CAAgB,EAAU,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrD,CAAC;AAFD,kCAEC;AAED,MAAa,MAAO,SAAQ,SAAG;IAA/B;;QACS,qBAAgB,GAAG,IAAI,iCAAqB,CAA0B;YAC3E,KAAK,EAAE,IAAI,mBAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;YACnC,IAAI,EAAE,CAAC,IAAoB,EAAE,MAAoB,EAAE,EAAE,CACnD,IAAI,CAAC,YAAY,iCAAM,IAAI,KAAE,MAAM,IAAG;SACzC,CAAC,CAAA;IAqMJ,CAAC;IAnMQ,WAAW,CAAC,OAAuB,EAAE;QAC1C,MAAM,EAAE,MAAM,KAAc,IAAI,EAAb,IAAI,UAAK,IAAI,EAA1B,UAAmB,CAAO,CAAA;QAChC,OAAO,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,MAAM,CAAC,CAAA;IACtE,CAAC;IAED;;OAEG;IACa,OAAO,CAAC,MAAc,EAAE,IAAqB;;YAC3D,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QACnC,CAAC;KAAA;IAED;;;;OAIG;IACW,YAAY,CAAC,IAAoB;;YAC7C,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YACnE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,eAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,eAAe,CAAC,CACxB,CAAA;YACD,MAAM,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;YACzC,MAAM,GAAG,GAAG,IAAI,sBAAM,EAAE;iBACrB,SAAS,CAAC,EAAE,CAAC;iBACb,MAAM,CAAC,MAAM,CAAC;iBACd,MAAM,CAAC,OAAO,CAAC;iBACf,MAAM,CAAC,QAAQ,CAAC;iBAChB,KAAK,CAAC,IAAI,CAAC,CAAA;YAEd,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,GAAG,CAAA;YAE7B,wCAAwC;YACxC,IAAI,KAAK,KAAK,CAAC,EAAE;gBACf,OAAO,EAAE,CAAA;aACV;YAED,MAAM,QAAQ,GAAG,EAAE,CAAA;YACnB,MAAM,GAAG,GAAG,QAAQ,GAAG,KAAK,CAAA;YAC5B,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,eAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,MAAM,CAAC,MAAM,CAAC,CACf,CAAA;YACD,MAAM,SAAS,GAAG,IAAI,sBAAM,EAAE;iBAC3B,SAAS,CAAC,EAAE,CAAC;iBACb,KAAK,CAAC,MAAM,CAAC;iBACb,KAAK,CAAC,YAAY,CAAC;iBACnB,MAAM,CAAC,QAAQ,CAAC;iBAChB,IAAI,CAAC,CAAC,CAAC;iBACP,KAAK,CAAC,OAAO,CAAC,CAAA;YACjB,MAAM,OAAO,GAAG,EAAa,CAAA;YAE7B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE;gBACjC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;aAC7D;YACD,OAAO,OAAO,CAAA;QAChB,CAAC;KAAA;IAED;;;;;;;OAOG;IACW,sBAAsB,CAClC,IAAY,EACZ,OAAuB,EAAE;;YAEzB,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAClD,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;YAC5C,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE;gBACxB,OAAO,EAAE,CAAA;aACV;YACD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,CAAO,KAAU,EAA4B,EAAE;gBACtE,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;gBAC/B,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,eAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,MAAM,CAAC,EACd,IAAI,CACL,CAAA;gBACD,MAAM,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;gBACzC,MAAM,CAAC,GAAG,IAAI,sBAAM,EAAE;qBACnB,SAAS,CAAC,EAAE,CAAC;qBACb,KAAK,CAAC,OAAO,CAAC;qBACd,KAAK,CAAC,WAAW,CAAC;qBAClB,KAAK,CAAC,SAAS,CAAC;qBAChB,KAAK,CAAC,SAAS,CAAC;qBAChB,MAAM,CAAC,WAAW,CAAC,CAAA;gBAEtB,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACrD,2CAA2C;gBAC3C,MAAM,GAAG,GAAG,IAAI,sBAAM,EAAE;qBACrB,SAAS,CAAC,EAAE,CAAC;qBACb,IAAI,CAAC,UAAU,CAAC;qBAChB,IAAI,CAAC,CAAC,CAAC;qBACP,KAAK,CAAC,KAAK,CAAC;qBACZ,MAAM,CAAC;oBACN,GAAG,EAAE,UAAU;oBACf,OAAO,EAAE;wBACP,CAAC,EAAE,IAAI,sBAAM,EAAE,CAAC,KAAK,CAAC,UAAU,EAAE;4BAChC,MAAM,EAAE,KAAK;4BACb,IAAI,EAAE,IAAI,sBAAM,EAAE;iCACf,SAAS,CAAC,EAAE,CAAC;iCACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;iCACnD,MAAM,CAAC,QAAQ,CAAC;yBACpB,CAAC;wBACF,CAAC,EAAE,IAAI,sBAAM,EAAE,CAAC,KAAK,CAAC,MAAM,EAAE;4BAC5B,MAAM,EAAE,KAAK;4BACb,IAAI,EAAE,IAAI,sBAAM,EAAE;iCACf,SAAS,CAAC,EAAE,CAAC;iCACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;iCACnD,MAAM,CAAC,QAAQ,CAAC;iCAChB,MAAM,CAAC,QAAQ,CAAC;iCAChB,MAAM,CAAC,UAAU,CAAC;yBACtB,CAAC;qBACH;iBACF,CAAC,CAAA;gBAEJ,MAAM,WAAW,GAAG,CAClB,UAAkB,EACQ,EAAE;oBAC5B,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,CAAA;oBAC9B,MAAM,GAAG,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,OAAO,GAAG,OAAO,CAAC,CAAA;oBAC/C,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,eAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;oBACD,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;oBAC9B,IAAI,IAAI,CAAC,QAAQ,EAAE;wBACjB,IAAI,UAAU,CAAA;wBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;4BAChD,MAAM,EAAE,GAAG,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,EAAE;gCAC7C,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;6BAC/B;4BACD,UAAU,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;yBACrC;wBACD,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;qBAC/B;oBACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;wBAC5C,IAAI,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,EAAE;4BAC7B,uCAAY,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,KAAE,KAAK,IAAE;yBAClC;qBACF;oBAED,OAAO,SAAS,CAAA;gBAClB,CAAC,CAAA,CAAA;gBACD,MAAM,cAAc,GAAG,EAAE,CAAA;gBACzB,OAAO,WAAW,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,cAAc,CAAC,CAAA;YACrD,CAAC,CAAA,CAAC,CAAA;YACF,OAAO,WAAW,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAA;QAC7C,CAAC;KAAA;IAED;;;;;;;OAOG;IACU,gBAAgB,CAAC,IAAY,EAAE,OAAuB,EAAE;;YACnE,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,sBAAsB,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC5D,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;gBACvB,OAAO,EAAE,CAAA;aACV;YACD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;YAC7C,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE;gBAC7B,OAAO,IAAI,iBAAU,CAAY,QAAQ,CAAC,EAAE;oBAC1C,IAAI,CAAC,YAAY,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,EAAE,IAAI,CAAC,CAAA;gBAC5C,CAAC,CAAC,CAAC,IAAI,CACL,IAAA,kBAAM,EAAC,CAAC,GAAG,EAAE,IAAI,EAAE,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,EACvC,IAAA,eAAG,EAAC,CAAC,CAAC,EAAE;oBACN,KAAK,MAAM,OAAO,IAAI,CAAC,EAAE;wBACvB,OAAO,CAAC,KAAK,GAAG,KAAK,CAAC,KAAK,CAAA;qBAC5B;oBACD,OAAO,CAAC,CAAA;gBACV,CAAC,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YACF,MAAM,GAAG,GAAG,MAAM,IAAA,qBAAc,EAAC,IAAA,YAAK,EAAC,GAAG,GAAG,CAAC,CAAC,CAAA;YAC/C,OAAO,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,CAAA,MAAA,CAAC,CAAC,IAAI,0CAAE,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,MAAK,IAAI,CAAA,EAAA,CAAC,CAAA;QAC1E,CAAC;KAAA;CACF;AA1MD,wBA0MC"}
|
package/dist/bigwig.d.ts
CHANGED
package/dist/bigwig.js
CHANGED
|
@@ -10,7 +10,7 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
|
|
|
10
10
|
};
|
|
11
11
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
12
12
|
exports.BigWig = void 0;
|
|
13
|
-
const
|
|
13
|
+
const block_view_1 = require("./block-view");
|
|
14
14
|
const bbi_1 = require("./bbi");
|
|
15
15
|
class BigWig extends bbi_1.BBI {
|
|
16
16
|
/**
|
|
@@ -32,7 +32,7 @@ class BigWig extends bbi_1.BBI {
|
|
|
32
32
|
const zh = zoomLevels[i];
|
|
33
33
|
if (zh && zh.reductionLevel <= 2 * basesPerPx) {
|
|
34
34
|
const indexOffset = Number(zh.indexOffset);
|
|
35
|
-
return new
|
|
35
|
+
return new block_view_1.BlockView(this.bbi, refsByName, indexOffset, isBigEndian, uncompressBufSize > 0, 'summary');
|
|
36
36
|
}
|
|
37
37
|
}
|
|
38
38
|
return this.getUnzoomedView(opts);
|
package/dist/bigwig.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,
|
|
1
|
+
{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,6CAAwC;AACxC,+BAA2C;AAE3C,MAAa,MAAO,SAAQ,SAAG;IAC7B;;;;;OAKG;IACa,OAAO,CAAC,KAAa,EAAE,IAAoB;;YACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;YAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;YAChC,IAAI,CAAC,QAAQ,EAAE;gBACb,4EAA4E;gBAC5E,QAAQ,IAAI,CAAC,CAAA;aACd;YAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;gBACrC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;gBACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE;oBAC7C,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;oBAE1C,OAAO,IAAI,sBAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;iBACF;aACF;YACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QACnC,CAAC;KAAA;CACF;AAlCD,wBAkCC"}
|
|
@@ -29,7 +29,7 @@ export declare class BlockView {
|
|
|
29
29
|
private leafParser;
|
|
30
30
|
private bigBedParser;
|
|
31
31
|
constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
|
|
32
|
-
readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts
|
|
32
|
+
readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts?: Options): Promise<void>;
|
|
33
33
|
private parseSummaryBlock;
|
|
34
34
|
private parseBigBedBlock;
|
|
35
35
|
private parseBigWigBlock;
|
|
@@ -177,7 +177,7 @@ class BlockView {
|
|
|
177
177
|
const p = this.leafParser.parse(data);
|
|
178
178
|
if (p.blocksToFetch) {
|
|
179
179
|
blocksToFetch = blocksToFetch.concat(p.blocksToFetch
|
|
180
|
-
.filter(filterFeats)
|
|
180
|
+
.filter(f => filterFeats(f))
|
|
181
181
|
.map((l) => ({
|
|
182
182
|
offset: l.blockOffset,
|
|
183
183
|
length: l.blockSize,
|
|
@@ -185,7 +185,7 @@ class BlockView {
|
|
|
185
185
|
}
|
|
186
186
|
if (p.recurOffsets) {
|
|
187
187
|
const recurOffsets = p.recurOffsets
|
|
188
|
-
.filter(filterFeats)
|
|
188
|
+
.filter(f => filterFeats(f))
|
|
189
189
|
.map(l => Number(l.blockOffset));
|
|
190
190
|
if (recurOffsets.length > 0) {
|
|
191
191
|
cirFobRecur(recurOffsets, level + 1);
|
|
@@ -205,10 +205,10 @@ class BlockView {
|
|
|
205
205
|
try {
|
|
206
206
|
const length = fr.max() - fr.min();
|
|
207
207
|
const offset = fr.min();
|
|
208
|
-
const resultBuffer = yield this.featureCache.get(`${length}_${offset}`, { length, offset }, opts.signal);
|
|
209
|
-
for (
|
|
210
|
-
if (fr.contains(
|
|
211
|
-
cirFobRecur2(resultBuffer,
|
|
208
|
+
const resultBuffer = yield this.featureCache.get(`${length}_${offset}`, { length, offset }, opts === null || opts === void 0 ? void 0 : opts.signal);
|
|
209
|
+
for (const element of off) {
|
|
210
|
+
if (fr.contains(element)) {
|
|
211
|
+
cirFobRecur2(resultBuffer, element - offset, level);
|
|
212
212
|
outstanding -= 1;
|
|
213
213
|
if (outstanding === 0) {
|
|
214
214
|
this.readFeatures(observer, blocksToFetch, Object.assign(Object.assign({}, opts), { request }));
|
|
@@ -223,7 +223,8 @@ class BlockView {
|
|
|
223
223
|
const cirFobRecur = (offset, level) => {
|
|
224
224
|
try {
|
|
225
225
|
outstanding += offset.length;
|
|
226
|
-
|
|
226
|
+
// Upper bound on size, based on a completely full leaf node.
|
|
227
|
+
const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32;
|
|
227
228
|
let spans = new range_1.default(offset[0], offset[0] + maxCirBlockSpan);
|
|
228
229
|
for (let i = 1; i < offset.length; i += 1) {
|
|
229
230
|
const blockSpan = new range_1.default(offset[i], offset[i] + maxCirBlockSpan);
|
|
@@ -311,7 +312,7 @@ class BlockView {
|
|
|
311
312
|
offset += 2;
|
|
312
313
|
const items = new Array(itemCount);
|
|
313
314
|
switch (blockType) {
|
|
314
|
-
case 1:
|
|
315
|
+
case 1: {
|
|
315
316
|
for (let i = 0; i < itemCount; i++) {
|
|
316
317
|
const start = dataView.getInt32(offset, true);
|
|
317
318
|
offset += 4;
|
|
@@ -322,7 +323,8 @@ class BlockView {
|
|
|
322
323
|
items[i] = { start, end, score };
|
|
323
324
|
}
|
|
324
325
|
break;
|
|
325
|
-
|
|
326
|
+
}
|
|
327
|
+
case 2: {
|
|
326
328
|
for (let i = 0; i < itemCount; i++) {
|
|
327
329
|
const start = dataView.getInt32(offset, true);
|
|
328
330
|
offset += 4;
|
|
@@ -331,7 +333,8 @@ class BlockView {
|
|
|
331
333
|
items[i] = { score, start, end: start + itemSpan };
|
|
332
334
|
}
|
|
333
335
|
break;
|
|
334
|
-
|
|
336
|
+
}
|
|
337
|
+
case 3: {
|
|
335
338
|
for (let i = 0; i < itemCount; i++) {
|
|
336
339
|
const score = dataView.getFloat32(offset, true);
|
|
337
340
|
offset += 4;
|
|
@@ -339,6 +342,7 @@ class BlockView {
|
|
|
339
342
|
items[i] = { score, start, end: start + itemSpan };
|
|
340
343
|
}
|
|
341
344
|
break;
|
|
345
|
+
}
|
|
342
346
|
}
|
|
343
347
|
return request
|
|
344
348
|
? items.filter((f) => coordFilter(f.start, f.end, request.start, request.end))
|
|
@@ -355,7 +359,7 @@ class BlockView {
|
|
|
355
359
|
(0, util_1.checkAbortSignal)(signal);
|
|
356
360
|
const { length, offset } = blockGroup;
|
|
357
361
|
const data = yield this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
|
|
358
|
-
blockGroup.blocks
|
|
362
|
+
for (const block of blockGroup.blocks) {
|
|
359
363
|
(0, util_1.checkAbortSignal)(signal);
|
|
360
364
|
let blockOffset = Number(block.offset) - Number(blockGroup.offset);
|
|
361
365
|
let resultData = data;
|
|
@@ -365,19 +369,23 @@ class BlockView {
|
|
|
365
369
|
}
|
|
366
370
|
(0, util_1.checkAbortSignal)(signal);
|
|
367
371
|
switch (blockType) {
|
|
368
|
-
case 'summary':
|
|
372
|
+
case 'summary': {
|
|
369
373
|
observer.next(this.parseSummaryBlock(resultData, blockOffset, request));
|
|
370
374
|
break;
|
|
371
|
-
|
|
375
|
+
}
|
|
376
|
+
case 'bigwig': {
|
|
372
377
|
observer.next(this.parseBigWigBlock(resultData, blockOffset, request));
|
|
373
378
|
break;
|
|
374
|
-
|
|
379
|
+
}
|
|
380
|
+
case 'bigbed': {
|
|
375
381
|
observer.next(this.parseBigBedBlock(resultData, blockOffset, Number(block.offset) * (1 << 8), request));
|
|
376
382
|
break;
|
|
377
|
-
|
|
383
|
+
}
|
|
384
|
+
default: {
|
|
378
385
|
console.warn(`Don't know what to do with ${blockType}`);
|
|
386
|
+
}
|
|
379
387
|
}
|
|
380
|
-
}
|
|
388
|
+
}
|
|
381
389
|
})));
|
|
382
390
|
observer.complete();
|
|
383
391
|
}
|
|
@@ -388,4 +396,4 @@ class BlockView {
|
|
|
388
396
|
}
|
|
389
397
|
}
|
|
390
398
|
exports.BlockView = BlockView;
|
|
391
|
-
//# sourceMappingURL=
|
|
399
|
+
//# sourceMappingURL=block-view.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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|
package/dist/range.js
CHANGED
|
@@ -59,7 +59,7 @@ class Range {
|
|
|
59
59
|
return new Range(oranges);
|
|
60
60
|
}
|
|
61
61
|
intersection(arg) {
|
|
62
|
-
// eslint-disable-next-line @typescript-eslint/no-this-alias
|
|
62
|
+
// eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
|
|
63
63
|
let s0 = this;
|
|
64
64
|
let s1 = arg;
|
|
65
65
|
const r0 = this.ranges();
|
|
@@ -95,8 +95,7 @@ class Range {
|
|
|
95
95
|
coverage() {
|
|
96
96
|
let tot = 0;
|
|
97
97
|
const rl = this.ranges();
|
|
98
|
-
for (
|
|
99
|
-
const r = rl[ri];
|
|
98
|
+
for (const r of rl) {
|
|
100
99
|
tot += r.max() - r.min() + 1;
|
|
101
100
|
}
|
|
102
101
|
return tot;
|
|
@@ -106,7 +105,7 @@ class Range {
|
|
|
106
105
|
let b = tmpb;
|
|
107
106
|
if (arguments.length < 2) {
|
|
108
107
|
b = a;
|
|
109
|
-
// eslint-disable-next-line @typescript-eslint/no-this-alias
|
|
108
|
+
// eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
|
|
110
109
|
a = this;
|
|
111
110
|
}
|
|
112
111
|
if (a.min() < b.min()) {
|
package/dist/range.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"range.js","sourceRoot":"","sources":["../src/range.ts"],"names":[],"mappings":";AAAA,sDAAsD;;AAEtD;;;GAGG;AACH,MAAqB,KAAK;IAGxB,YAAmB,IAAS,EAAE,IAAU;QACtC,IAAI,CAAC,MAAM;YACT,SAAS,CAAC,MAAM,KAAK,CAAC;gBACpB,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,CAAC;gBAC5B,CAAC,CAAC,CAAC,IAAI,IAAI;oBACX,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,IAAI,CAAC;oBACzB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IACd,CAAC;IAEM,GAAG;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC3B,CAAC;IAEM,GAAG;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,CAAA;IAChD,CAAC;IAEM,QAAQ,CAAC,GAAW;QACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC9C,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE;gBAChC,OAAO,IAAI,CAAA;aACZ;SACF;QACD,OAAO,KAAK,CAAA;IACd,CAAC;IAEM,YAAY;QACjB,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAA;IAC/B,CAAC;IAEM,SAAS;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAQ,EAAE,EAAE,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IAC/D,CAAC;IAEM,QAAQ;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAQ,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACvE,CAAC;IAEM,KAAK,CAAC,EAAS;QACpB,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,EAAE,CAAC,MAAM,CAAC,EAAE,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;QAC5E,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,IAAI,OAAO,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAEvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YACzC,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;YACrB,IAAI,GAAG,CAAC,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE;gBACjC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,OAAO,GAAG,GAAG,CAAA;aACd;iBAAM,IAAI,GAAG,CAAC,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,EAAE,EAAE;gBACpC,OAAO,GAAG,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,GAAG,CAAC,GAAG,EAAE,CAAC,CAAA;aAC9C;SACF;QACD,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAErB,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE;YACxB,OAAO,OAAO,CAAC,CAAC,CAAC,CAAA;SAClB;QACD,OAAO,IAAI,KAAK,CAAC,OAAO,CAAC,CAAA;IAC3B,CAAC;IAEM,YAAY,CAAC,GAAU;QAC5B,
|
|
1
|
+
{"version":3,"file":"range.js","sourceRoot":"","sources":["../src/range.ts"],"names":[],"mappings":";AAAA,sDAAsD;;AAEtD;;;GAGG;AACH,MAAqB,KAAK;IAGxB,YAAmB,IAAS,EAAE,IAAU;QACtC,IAAI,CAAC,MAAM;YACT,SAAS,CAAC,MAAM,KAAK,CAAC;gBACpB,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,CAAC;gBAC5B,CAAC,CAAC,CAAC,IAAI,IAAI;oBACX,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,IAAI,CAAC;oBACzB,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IACd,CAAC;IAEM,GAAG;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC3B,CAAC;IAEM,GAAG;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,CAAA;IAChD,CAAC;IAEM,QAAQ,CAAC,GAAW;QACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC9C,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE;gBAChC,OAAO,IAAI,CAAA;aACZ;SACF;QACD,OAAO,KAAK,CAAA;IACd,CAAC;IAEM,YAAY;QACjB,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAA;IAC/B,CAAC;IAEM,SAAS;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAQ,EAAE,EAAE,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IAC/D,CAAC;IAEM,QAAQ;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAQ,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACvE,CAAC;IAEM,KAAK,CAAC,EAAS;QACpB,MAAM,MAAM,GAAG,IAAI,CAAC,SAAS,EAAE,CAAC,MAAM,CAAC,EAAE,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;QAC5E,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,IAAI,OAAO,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAEvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YACzC,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;YACrB,IAAI,GAAG,CAAC,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE;gBACjC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,OAAO,GAAG,GAAG,CAAA;aACd;iBAAM,IAAI,GAAG,CAAC,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,EAAE,EAAE;gBACpC,OAAO,GAAG,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,GAAG,CAAC,GAAG,EAAE,CAAC,CAAA;aAC9C;SACF;QACD,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAErB,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE;YACxB,OAAO,OAAO,CAAC,CAAC,CAAC,CAAA;SAClB;QACD,OAAO,IAAI,KAAK,CAAC,OAAO,CAAC,CAAA;IAC3B,CAAC;IAEM,YAAY,CAAC,GAAU;QAC5B,uFAAuF;QACvF,IAAI,EAAE,GAAG,IAAI,CAAA;QACb,IAAI,EAAE,GAAG,GAAG,CAAA;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,EAAE,CAAA;QACxB,MAAM,EAAE,GAAG,EAAE,CAAC,MAAM,EAAE,CAAA;QACtB,MAAM,EAAE,GAAG,EAAE,CAAC,MAAM,CAAA;QAEpB,MAAM,EAAE,GAAG,EAAE,CAAC,MAAM,CAAA;QACpB,IAAI,EAAE,GAAG,CAAC,CAAA;QAEV,IAAI,EAAE,GAAG,CAAC,CAAA;QACV,MAAM,EAAE,GAAG,EAAE,CAAA;QAEb,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE;YACzB,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAA;YACX,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAA;YACX,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;YAC3C,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;YAC3C,IAAI,MAAM,IAAI,MAAM,EAAE;gBACpB,EAAE,CAAC,IAAI,CAAC,IAAI,KAAK,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;aACnC;YACD,IAAI,EAAE,CAAC,GAAG,EAAE,GAAG,EAAE,CAAC,GAAG,EAAE,EAAE;gBACvB,EAAE,IAAI,CAAC,CAAA;aACR;iBAAM;gBACL,EAAE,IAAI,CAAC,CAAA;aACR;SACF;QAED,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;SAC3C;QACD,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE;YACnB,OAAO,EAAE,CAAC,CAAC,CAAC,CAAA;SACb;QACD,OAAO,IAAI,KAAK,CAAC,EAAE,CAAC,CAAA;IACtB,CAAC;IAEM,QAAQ;QACb,IAAI,GAAG,GAAG,CAAC,CAAA;QACX,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,EAAE,CAAA;QACxB,KAAK,MAAM,CAAC,IAAI,EAAE,EAAE;YAClB,GAAG,IAAI,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;SAC7B;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAEM,UAAU,CAAC,IAAW,EAAE,IAAW;QACxC,IAAI,CAAC,GAAG,IAAI,CAAA;QACZ,IAAI,CAAC,GAAG,IAAI,CAAA;QACZ,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE;YACxB,CAAC,GAAG,CAAC,CAAA;YACL,uFAAuF;YACvF,CAAC,GAAG,IAAI,CAAA;SACT;QAED,IAAI,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;YACrB,OAAO,CAAC,CAAC,CAAA;SACV;QACD,IAAI,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;YACrB,OAAO,CAAC,CAAA;SACT;QACD,IAAI,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;YACrB,OAAO,CAAC,CAAC,CAAA;SACV;QACD,IAAI,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;YACrB,OAAO,CAAC,CAAA;SACT;QACD,OAAO,CAAC,CAAA;IACV,CAAC;CACF;AAtID,wBAsIC"}
|
package/dist/unzip.d.ts
CHANGED
|
@@ -1,2 +1 @@
|
|
|
1
|
-
|
|
2
|
-
export { inflateSync as unzip };
|
|
1
|
+
export { inflateSync as unzip } from 'zlib';
|
package/dist/unzip.js
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.unzip = void 0;
|
|
4
|
-
|
|
4
|
+
var zlib_1 = require("zlib");
|
|
5
5
|
Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.inflateSync; } });
|
|
6
6
|
//# sourceMappingURL=unzip.js.map
|
package/dist/unzip.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA
|
|
1
|
+
{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,6BAA2C;AAAlC,6FAAA,WAAW,OAAS"}
|
package/dist/util.js
CHANGED
|
@@ -25,21 +25,21 @@ function groupBlocks(blocks) {
|
|
|
25
25
|
const blockGroups = [];
|
|
26
26
|
let lastBlock;
|
|
27
27
|
let lastBlockEnd;
|
|
28
|
-
for (
|
|
28
|
+
for (const block of blocks) {
|
|
29
29
|
if (lastBlock &&
|
|
30
30
|
lastBlockEnd &&
|
|
31
|
-
Number(
|
|
31
|
+
Number(block.offset) - lastBlockEnd <= 2000) {
|
|
32
32
|
lastBlock.length = BigInt(Number(lastBlock.length) +
|
|
33
|
-
Number(
|
|
33
|
+
Number(block.length) -
|
|
34
34
|
lastBlockEnd +
|
|
35
|
-
Number(
|
|
36
|
-
lastBlock.blocks.push(
|
|
35
|
+
Number(block.offset));
|
|
36
|
+
lastBlock.blocks.push(block);
|
|
37
37
|
}
|
|
38
38
|
else {
|
|
39
39
|
blockGroups.push((lastBlock = {
|
|
40
|
-
blocks: [
|
|
41
|
-
length:
|
|
42
|
-
offset:
|
|
40
|
+
blocks: [block],
|
|
41
|
+
length: block.length,
|
|
42
|
+
offset: block.offset,
|
|
43
43
|
}));
|
|
44
44
|
}
|
|
45
45
|
lastBlockEnd = Number(lastBlock.offset) + Number(lastBlock.length);
|
|
@@ -64,14 +64,14 @@ function checkAbortSignal(signal) {
|
|
|
64
64
|
}
|
|
65
65
|
if (signal.aborted) {
|
|
66
66
|
// console.log('bam aborted!')
|
|
67
|
-
if (typeof DOMException
|
|
68
|
-
throw new DOMException('aborted', 'AbortError');
|
|
69
|
-
}
|
|
70
|
-
else {
|
|
67
|
+
if (typeof DOMException === 'undefined') {
|
|
71
68
|
const e = new AbortError('aborted');
|
|
72
69
|
e.code = 'ERR_ABORTED';
|
|
73
70
|
throw e;
|
|
74
71
|
}
|
|
72
|
+
else {
|
|
73
|
+
throw new DOMException('aborted', 'AbortError');
|
|
74
|
+
}
|
|
75
75
|
}
|
|
76
76
|
}
|
|
77
77
|
exports.checkAbortSignal = checkAbortSignal;
|