@gmod/bbi 4.0.4 → 4.0.6
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 +8 -0
- package/dist/bbi.d.ts +3 -6
- package/dist/bbi.js +7 -8
- package/dist/bbi.js.map +1 -1
- package/dist/bigbed.d.ts +1 -1
- package/dist/bigbed.js +16 -16
- package/dist/bigbed.js.map +1 -1
- package/dist/bigint-polyfill/pure.js +4 -5
- package/dist/bigint-polyfill/pure.js.map +1 -1
- package/dist/bigwig.d.ts +3 -1
- package/dist/bigwig.js +3 -1
- package/dist/bigwig.js.map +1 -1
- package/dist/block-view.js +5 -4
- package/dist/block-view.js.map +1 -1
- package/dist/range.js +5 -3
- package/dist/range.js.map +1 -1
- package/dist/unzip-pako.d.ts +0 -1
- package/dist/unzip-pako.js +1 -2
- package/dist/unzip-pako.js.map +1 -1
- package/dist/unzip.d.ts +0 -1
- package/dist/util.js +4 -4
- package/dist/util.js.map +1 -1
- package/esm/bbi.d.ts +3 -6
- package/esm/bbi.js +5 -6
- package/esm/bbi.js.map +1 -1
- package/esm/bigbed.d.ts +1 -1
- package/esm/bigbed.js +10 -10
- package/esm/bigbed.js.map +1 -1
- package/esm/bigwig.d.ts +3 -1
- package/esm/bigwig.js +3 -1
- package/esm/bigwig.js.map +1 -1
- package/esm/block-view.js +3 -2
- package/esm/block-view.js.map +1 -1
- package/esm/range.js +5 -3
- package/esm/range.js.map +1 -1
- package/esm/unzip-pako.d.ts +0 -1
- package/esm/unzip.d.ts +0 -1
- package/package.json +9 -9
- package/src/bbi.ts +13 -12
- package/src/bigbed.ts +10 -10
- package/src/bigwig.ts +3 -1
- package/src/block-view.ts +3 -2
- package/src/range.ts +3 -6
package/CHANGELOG.md
CHANGED
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@@ -1,3 +1,11 @@
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1
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## [4.0.6](https://github.com/GMOD/bbi-js/compare/v4.0.5...v4.0.6) (2024-07-23)
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## [4.0.5](https://github.com/GMOD/bbi-js/compare/v4.0.4...v4.0.5) (2024-06-19)
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## [4.0.4](https://github.com/GMOD/bbi-js/compare/v4.0.3...v4.0.4) (2024-3-5)
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package/dist/bbi.d.ts
CHANGED
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@@ -23,6 +23,7 @@ interface RefInfo {
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length: number;
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}
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export interface Header {
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version: number;
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autoSql: string;
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totalSummary: Statistics;
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zoomLevels: any;
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@@ -35,12 +36,8 @@ export interface Header {
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extHeaderOffset: number;
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isBigEndian: boolean;
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fileType: string;
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refsByName:
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};
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refsByNumber: {
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[key: number]: RefInfo;
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};
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refsByName: Record<string, number>;
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refsByNumber: Record<number, RefInfo>;
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}
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export interface RequestOptions {
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signal?: AbortSignal;
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package/dist/bbi.js
CHANGED
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@@ -21,7 +21,8 @@ const BIG_BED_MAGIC = -2021002517;
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function toString(arr) {
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return new TextDecoder().decode(arr);
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}
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/**
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* get the compiled parsers for different sections of the bigwig file
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*
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* @param isBE - is big endian, typically false
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* @return an object with compiled parsers
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@@ -79,10 +80,6 @@ function getParsers(isBE) {
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};
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}
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class BBI {
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/* fetch and parse header information from a bigwig or bigbed file
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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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if (!this.headerP) {
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this.headerP = this._getHeader(opts).catch(e => {
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@@ -125,8 +122,8 @@ class BBI {
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return Object.assign(Object.assign({}, header), chroms);
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});
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}
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_getMainHeader(
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return __awaiter(this,
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_getMainHeader(opts_1) {
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return __awaiter(this, arguments, void 0, function* (opts, requestSize = 2000) {
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const { buffer } = yield this.bbi.read(buffer_1.Buffer.alloc(requestSize), 0, requestSize, 0, opts);
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const isBigEndian = this._isBigEndian(buffer);
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const ret = getParsers(isBigEndian);
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@@ -263,7 +260,9 @@ class BBI {
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view = yield this.getView(1, opts);
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}
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return new rxjs_1.Observable(observer => {
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view
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view
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.readWigData(chrName, start, end, observer, opts)
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.catch(e => observer.error(e));
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});
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});
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}
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package/dist/bbi.js.map
CHANGED
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@@ -1 +1 @@
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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,+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;
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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;AA0CD;;;;;GAKG;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;IAOhB,SAAS,CAAC,IAAqB;QACpC,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC;YAClB,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;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IAED;;;;;;;;;OASG;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,CAAC;YACf,IAAI,CAAC,GAAG,GAAG,UAAU,CAAA;QACvB,CAAC;aAAM,IAAI,GAAG,EAAE,CAAC;YACf,IAAI,CAAC,GAAG,GAAG,IAAI,+BAAU,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC;aAAM,IAAI,IAAI,EAAE,CAAC;YAChB,IAAI,CAAC,GAAG,GAAG,IAAI,8BAAS,CAAC,IAAI,CAAC,CAAA;QAChC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;QAClC,CAAC;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;6DAC1B,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,CAAC;gBAC/D,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;YACnD,CAAC;YACD,IAAI,QAAQ,EAAE,CAAC;gBACb,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;YACzE,CAAC;YAED,mDAAmD;YACnD,4CAA4C;YAC5C,IAAI,MAAM,CAAC,kBAAkB,GAAG,WAAW,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gBACpD,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;YACnD,CAAC;YAED,IAAI,MAAM,CAAC,kBAAkB,EAAE,CAAC;gBAC9B,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;YAC1E,CAAC;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,CAAC;YACnD,OAAO,KAAK,CAAA;QACd,CAAC;QACD,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE,CAAC;YACnD,OAAO,IAAI,CAAA;QACb,CAAC;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,GAGd,EAAE,CAAA;YACN,MAAM,UAAU,GAA2B,EAAE,CAAA;YAE7C,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,CAAC;gBACpC,kBAAkB,IAAI,CAAC,CAAA;YACzB,CAAC;YACD,MAAM,GAAG,GAAG,kBAAkB,GAAG,eAAe,CAAA;YAChD,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,eAAM,CAAC,KAAK,CA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|
package/dist/bigbed.d.ts
CHANGED
package/dist/bigbed.js
CHANGED
|
@@ -23,18 +23,18 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
23
23
|
return (mod && mod.__esModule) ? mod : { "default": mod };
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24
24
|
};
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|
25
25
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
26
|
-
exports.BigBed =
|
|
26
|
+
exports.BigBed = void 0;
|
|
27
|
+
exports.filterUndef = filterUndef;
|
|
27
28
|
const buffer_1 = require("buffer");
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|
28
29
|
const binary_parser_1 = require("binary-parser");
|
|
29
30
|
const rxjs_1 = require("rxjs");
|
|
30
31
|
const operators_1 = require("rxjs/operators");
|
|
31
|
-
const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
|
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32
|
+
const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
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|
32
33
|
const quick_lru_1 = __importDefault(require("quick-lru"));
|
|
33
34
|
const bbi_1 = require("./bbi");
|
|
34
35
|
function filterUndef(ts) {
|
|
35
36
|
return ts.filter((t) => !!t);
|
|
36
37
|
}
|
|
37
|
-
exports.filterUndef = filterUndef;
|
|
38
38
|
class BigBed extends bbi_1.BBI {
|
|
39
39
|
constructor() {
|
|
40
40
|
super(...arguments);
|
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@@ -101,8 +101,8 @@ class BigBed extends bbi_1.BBI {
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|
101
101
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* @param opts - a SearchOptions argument with optional signal
|
|
102
102
|
* @return a Promise for an array of bigbed block Loc entries
|
|
103
103
|
*/
|
|
104
|
-
searchExtraIndexBlocks(
|
|
105
|
-
return __awaiter(this,
|
|
104
|
+
searchExtraIndexBlocks(name_1) {
|
|
105
|
+
return __awaiter(this, arguments, void 0, function* (name, opts = {}) {
|
|
106
106
|
const { isBigEndian } = yield this.getHeader(opts);
|
|
107
107
|
const indices = yield this.readIndices(opts);
|
|
108
108
|
if (indices.length === 0) {
|
|
@@ -154,18 +154,17 @@ class BigBed extends bbi_1.BBI {
|
|
|
154
154
|
const node = bpt.parse(buffer);
|
|
155
155
|
if (node.leafkeys) {
|
|
156
156
|
let lastOffset;
|
|
157
|
-
for (
|
|
158
|
-
const { key } = node.leafkeys[i];
|
|
157
|
+
for (const { key, offset } of node.leafkeys) {
|
|
159
158
|
if (name.localeCompare(key) < 0 && lastOffset) {
|
|
160
159
|
return bptReadNode(lastOffset);
|
|
161
160
|
}
|
|
162
|
-
lastOffset =
|
|
161
|
+
lastOffset = offset;
|
|
163
162
|
}
|
|
164
163
|
return bptReadNode(lastOffset);
|
|
165
164
|
}
|
|
166
|
-
for (
|
|
167
|
-
if (
|
|
168
|
-
return Object.assign(Object.assign({},
|
|
165
|
+
for (const n of node.keys) {
|
|
166
|
+
if (n.key === name) {
|
|
167
|
+
return Object.assign(Object.assign({}, n), { field });
|
|
169
168
|
}
|
|
170
169
|
}
|
|
171
170
|
return undefined;
|
|
@@ -177,15 +176,16 @@ class BigBed extends bbi_1.BBI {
|
|
|
177
176
|
});
|
|
178
177
|
}
|
|
179
178
|
/*
|
|
180
|
-
* retrieve the features from the bigbed data that were found through the
|
|
181
|
-
* note that there can be multiple extraIndex, see
|
|
179
|
+
* retrieve the features from the bigbed data that were found through the
|
|
180
|
+
* lookup of the extraIndex note that there can be multiple extraIndex, see
|
|
181
|
+
* the BigBed specification and the -extraIndex argument to bedToBigBed
|
|
182
182
|
*
|
|
183
183
|
* @param name - the name to search for
|
|
184
184
|
* @param opts - a SearchOptions argument with optional signal
|
|
185
185
|
* @return a Promise for an array of Feature
|
|
186
186
|
*/
|
|
187
|
-
searchExtraIndex(
|
|
188
|
-
return __awaiter(this,
|
|
187
|
+
searchExtraIndex(name_1) {
|
|
188
|
+
return __awaiter(this, arguments, void 0, function* (name, opts = {}) {
|
|
189
189
|
const blocks = yield this.searchExtraIndexBlocks(name, opts);
|
|
190
190
|
if (blocks.length === 0) {
|
|
191
191
|
return [];
|
|
@@ -193,7 +193,7 @@ class BigBed extends bbi_1.BBI {
|
|
|
193
193
|
const view = yield this.getUnzoomedView(opts);
|
|
194
194
|
const res = blocks.map(block => {
|
|
195
195
|
return new rxjs_1.Observable(observer => {
|
|
196
|
-
view.readFeatures(observer, [block], opts);
|
|
196
|
+
view.readFeatures(observer, [block], opts).catch(e => observer.error(e));
|
|
197
197
|
}).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
|
|
198
198
|
for (const element of x) {
|
|
199
199
|
element.field = block.field;
|
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":";;;;;;;;;;;;;;;;;;;;;;;;;;AAuBA,kCAEC;AAzBD,mCAA+B;AAC/B,iDAAsC;AACtC,+BAAwD;AACxD,8CAA4C;AAC5C,4FAAiE;AACjE,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;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,CAAC;gBAChB,OAAO,EAAE,CAAA;YACX,CAAC;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,CAAC;gBAClC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC9D,CAAC;YACD,OAAO,OAAO,CAAA;QAChB,CAAC;KAAA;IAED;;;;;;;OAOG;IACW,sBAAsB;6DAClC,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,CAAC;gBACzB,OAAO,EAAE,CAAA;YACX,CAAC;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,CAAC;wBAClB,IAAI,UAAU,CAAA;wBACd,KAAK,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;4BAC5C,IAAI,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,EAAE,CAAC;gCAC9C,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;4BAChC,CAAC;4BACD,UAAU,GAAG,MAAM,CAAA;wBACrB,CAAC;wBACD,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;oBAChC,CAAC;oBACD,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;wBAC1B,IAAI,CAAC,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;4BACnB,uCAAY,CAAC,KAAE,KAAK,IAAE;wBACxB,CAAC;oBACH,CAAC;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;;;;;;;;OAQG;IACU,gBAAgB;6DAAC,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,CAAC;gBACxB,OAAO,EAAE,CAAA;YACX,CAAC;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,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;gBAC1E,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,CAAC;wBACxB,OAAO,CAAC,KAAK,GAAG,KAAK,CAAC,KAAK,CAAA;oBAC7B,CAAC;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"}
|
|
@@ -1,6 +1,9 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.
|
|
3
|
+
exports.getBigInt64 = getBigInt64;
|
|
4
|
+
exports.getBigUint64 = getBigUint64;
|
|
5
|
+
exports.setBigInt64 = setBigInt64;
|
|
6
|
+
exports.setBigUint64 = setBigUint64;
|
|
4
7
|
const BigInt32 = BigInt(32);
|
|
5
8
|
function getBigInt64(dataView, byteOffset, littleEndian) {
|
|
6
9
|
const littleEndianMask = Number(!!littleEndian);
|
|
@@ -11,7 +14,6 @@ function getBigInt64(dataView, byteOffset, littleEndian) {
|
|
|
11
14
|
BigInt(dataView.getUint32(byteOffset, littleEndian) * littleEndianMask +
|
|
12
15
|
dataView.getUint32(byteOffset + 4, littleEndian) * bigEndianMask));
|
|
13
16
|
}
|
|
14
|
-
exports.getBigInt64 = getBigInt64;
|
|
15
17
|
function getBigUint64(dataView, byteOffset, littleEndian) {
|
|
16
18
|
const a = dataView.getUint32(byteOffset, littleEndian);
|
|
17
19
|
const b = dataView.getUint32(byteOffset + 4, littleEndian);
|
|
@@ -23,7 +25,6 @@ function getBigUint64(dataView, byteOffset, littleEndian) {
|
|
|
23
25
|
return ((BigInt(a * bigEndianMask + b * littleEndianMask) << BigInt32) |
|
|
24
26
|
BigInt(a * littleEndianMask + b * bigEndianMask));
|
|
25
27
|
}
|
|
26
|
-
exports.getBigUint64 = getBigUint64;
|
|
27
28
|
function setBigInt64(dataView, byteOffset, value, littleEndian) {
|
|
28
29
|
const hi = Number(value >> BigInt32);
|
|
29
30
|
const lo = Number(value & BigInt(0xffffffff));
|
|
@@ -36,7 +37,6 @@ function setBigInt64(dataView, byteOffset, value, littleEndian) {
|
|
|
36
37
|
dataView.setUint32(byteOffset + 4, lo, littleEndian);
|
|
37
38
|
}
|
|
38
39
|
}
|
|
39
|
-
exports.setBigInt64 = setBigInt64;
|
|
40
40
|
function setBigUint64(dataView, byteOffset, value, littleEndian) {
|
|
41
41
|
const hi = Number(value >> BigInt32);
|
|
42
42
|
const lo = Number(value & BigInt(0xffffffff));
|
|
@@ -49,5 +49,4 @@ function setBigUint64(dataView, byteOffset, value, littleEndian) {
|
|
|
49
49
|
dataView.setUint32(byteOffset + 4, lo, littleEndian);
|
|
50
50
|
}
|
|
51
51
|
}
|
|
52
|
-
exports.setBigUint64 = setBigUint64;
|
|
53
52
|
//# sourceMappingURL=pure.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"pure.js","sourceRoot":"","sources":["../../src/bigint-polyfill/pure.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"pure.js","sourceRoot":"","sources":["../../src/bigint-polyfill/pure.ts"],"names":[],"mappings":";;AAEA,kCAmBC;AAED,oCAkBC;AAED,kCAgBC;AAED,oCAgBC;AA7ED,MAAM,QAAQ,GAAG,MAAM,CAAC,EAAE,CAAC,CAAA;AAE3B,SAAgB,WAAW,CACzB,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,MAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,OAAO,CACL,CAAC,MAAM,CACL,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,aAAa;QACzD,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,gBAAgB,CACrE;QACC,QAAQ,CAAC;QACX,MAAM,CACJ,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,gBAAgB;YAC7D,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,aAAa,CACnE,CACF,CAAA;AACH,CAAC;AAED,SAAgB,YAAY,CAC1B,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,MAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,CAAA;IACtD,MAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,CAAA;IAE1D,MAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,4EAA4E;IAC5E,gDAAgD;IAChD,kCAAkC;IAClC,OAAO,CACL,CAAC,MAAM,CAAC,CAAC,GAAG,aAAa,GAAG,CAAC,GAAG,gBAAgB,CAAC,IAAI,QAAQ,CAAC;QAC9D,MAAM,CAAC,CAAC,GAAG,gBAAgB,GAAG,CAAC,GAAG,aAAa,CAAC,CACjD,CAAA;AACH,CAAC;AAED,SAAgB,WAAW,CACzB,QAAkB,EAClB,UAAkB,EAClB,KAAa,EACb,YAAiC;IAEjC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,IAAI,QAAQ,CAAC,CAAA;IACpC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,CAAA;IAE7C,IAAI,YAAY,EAAE,CAAC;QACjB,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QACnD,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;IAClD,CAAC;SAAM,CAAC;QACN,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QAC/C,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;IACtD,CAAC;AACH,CAAC;AAED,SAAgB,YAAY,CAC1B,QAAkB,EAClB,UAAkB,EAClB,KAAa,EACb,YAAiC;IAEjC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,IAAI,QAAQ,CAAC,CAAA;IACpC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,CAAA;IAE7C,IAAI,YAAY,EAAE,CAAC;QACjB,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QACpD,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;IAClD,CAAC;SAAM,CAAC;QACN,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QAChD,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;IACtD,CAAC;AACH,CAAC"}
|
package/dist/bigwig.d.ts
CHANGED
|
@@ -5,7 +5,9 @@ export declare class BigWig extends BBI {
|
|
|
5
5
|
* Retrieves a BlockView of a specific zoomLevel
|
|
6
6
|
*
|
|
7
7
|
* @param scale - number
|
|
8
|
-
*
|
|
8
|
+
*
|
|
9
|
+
* @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
|
|
10
|
+
* or scale used to infer the zoomLevel to use
|
|
9
11
|
*/
|
|
10
12
|
protected getView(scale: number, opts: RequestOptions): Promise<BlockView>;
|
|
11
13
|
}
|
package/dist/bigwig.js
CHANGED
|
@@ -17,7 +17,9 @@ class BigWig extends bbi_1.BBI {
|
|
|
17
17
|
* Retrieves a BlockView of a specific zoomLevel
|
|
18
18
|
*
|
|
19
19
|
* @param scale - number
|
|
20
|
-
*
|
|
20
|
+
*
|
|
21
|
+
* @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
|
|
22
|
+
* or scale used to infer the zoomLevel to use
|
|
21
23
|
*/
|
|
22
24
|
getView(scale, opts) {
|
|
23
25
|
return __awaiter(this, void 0, void 0, function* () {
|
package/dist/bigwig.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,6CAAwC;AACxC,+BAA2C;AAE3C,MAAa,MAAO,SAAQ,SAAG;IAC7B
|
|
1
|
+
{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,6CAAwC;AACxC,+BAA2C;AAE3C,MAAa,MAAO,SAAQ,SAAG;IAC7B;;;;;;;OAOG;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,CAAC;gBACd,4EAA4E;gBAC5E,QAAQ,IAAI,CAAC,CAAA;YACf,CAAC;YAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;gBACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;oBAC9C,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;gBACH,CAAC;YACH,CAAC;YACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QACnC,CAAC;KAAA;CACF;AApCD,wBAoCC"}
|
package/dist/block-view.js
CHANGED
|
@@ -15,7 +15,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
15
15
|
exports.BlockView = void 0;
|
|
16
16
|
const buffer_1 = require("buffer");
|
|
17
17
|
const binary_parser_1 = require("binary-parser");
|
|
18
|
-
const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
|
|
18
|
+
const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
|
|
19
19
|
const quick_lru_1 = __importDefault(require("quick-lru"));
|
|
20
20
|
// locals
|
|
21
21
|
const range_1 = __importDefault(require("./range"));
|
|
@@ -178,7 +178,7 @@ class BlockView {
|
|
|
178
178
|
if (p.blocksToFetch) {
|
|
179
179
|
blocksToFetch = blocksToFetch.concat(p.blocksToFetch
|
|
180
180
|
.filter(f => filterFeats(f))
|
|
181
|
-
.map(
|
|
181
|
+
.map(l => ({
|
|
182
182
|
offset: l.blockOffset,
|
|
183
183
|
length: l.blockSize,
|
|
184
184
|
})));
|
|
@@ -234,6 +234,7 @@ class BlockView {
|
|
|
234
234
|
]);
|
|
235
235
|
spans = spans.union(blockSpan);
|
|
236
236
|
}
|
|
237
|
+
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
|
237
238
|
spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));
|
|
238
239
|
}
|
|
239
240
|
catch (e) {
|
|
@@ -353,8 +354,8 @@ class BlockView {
|
|
|
353
354
|
? items.filter((f) => coordFilter(f.start, f.end, request.start, request.end))
|
|
354
355
|
: items;
|
|
355
356
|
}
|
|
356
|
-
readFeatures(
|
|
357
|
-
return __awaiter(this,
|
|
357
|
+
readFeatures(observer_1, blocks_1) {
|
|
358
|
+
return __awaiter(this, arguments, void 0, function* (observer, blocks, opts = {}) {
|
|
358
359
|
try {
|
|
359
360
|
const { blockType, isCompressed } = this;
|
|
360
361
|
const { signal, request } = opts;
|
package/dist/block-view.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/range.js
CHANGED
|
@@ -1,5 +1,8 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
|
|
2
|
+
/**
|
|
3
|
+
* Adapted from a combination of Range and _Compound in the
|
|
4
|
+
* Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
|
|
5
|
+
*/
|
|
3
6
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
4
7
|
class Range {
|
|
5
8
|
constructor(arg1) {
|
|
@@ -48,8 +51,7 @@ class Range {
|
|
|
48
51
|
});
|
|
49
52
|
const oranges = [];
|
|
50
53
|
let current = ranges[0];
|
|
51
|
-
for (
|
|
52
|
-
const nxt = ranges[i];
|
|
54
|
+
for (const nxt of ranges) {
|
|
53
55
|
if (nxt.min > current.max + 1) {
|
|
54
56
|
oranges.push(current);
|
|
55
57
|
current = nxt;
|
package/dist/range.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"range.js","sourceRoot":"","sources":["../src/range.ts"],"names":[],"mappings":";AAAA
|
|
1
|
+
{"version":3,"file":"range.js","sourceRoot":"","sources":["../src/range.ts"],"names":[],"mappings":";AAAA;;;GAGG;;AAMH,MAAqB,KAAK;IAGxB,YAAmB,IAAc;QAC/B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;IACpB,CAAC;IAED,IAAI,GAAG;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC3B,CAAC;IAED,IAAI,GAAG;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,CAAA;IAChD,CAAC;IAEM,QAAQ,CAAC,GAAW;QACzB,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;YAC5B,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC;gBACjC,OAAO,IAAI,CAAA;YACb,CAAC;QACH,CAAC;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,CAAC,EAAE,CAAC,IAAI,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAA;IACtE,CAAC;IAEM,QAAQ;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IAC9D,CAAC;IAEM,KAAK,CAAC,EAAS;QACpB,MAAM,MAAM,GAAG,CAAC,GAAG,IAAI,CAAC,SAAS,EAAE,EAAE,GAAG,EAAE,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACpE,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBAClB,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,OAAO,CAAC,CAAA;YACV,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,OAAO,CAAC,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,OAAO,CAAC,CAAA;YACV,CAAC;QACH,CAAC,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,EAAa,CAAA;QAC7B,IAAI,OAAO,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAEvB,KAAK,MAAM,GAAG,IAAI,MAAM,EAAE,CAAC;YACzB,IAAI,GAAG,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,CAAC,EAAE,CAAC;gBAC9B,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,OAAO,GAAG,GAAG,CAAA;YACf,CAAC;iBAAM,IAAI,GAAG,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;gBACjC,OAAO,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,OAAO,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC3D,CAAC;QACH,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAErB,OAAO,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,OAAO,CAAC,CAAA;IAC/D,CAAC;CACF;AAjED,wBAiEC"}
|
package/dist/unzip-pako.d.ts
CHANGED
package/dist/unzip-pako.js
CHANGED
|
@@ -1,9 +1,8 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.unzip =
|
|
3
|
+
exports.unzip = unzip;
|
|
4
4
|
const pako_1 = require("pako");
|
|
5
5
|
function unzip(input) {
|
|
6
6
|
return (0, pako_1.inflateRaw)(input.subarray(2));
|
|
7
7
|
}
|
|
8
|
-
exports.unzip = unzip;
|
|
9
8
|
//# sourceMappingURL=unzip-pako.js.map
|
package/dist/unzip-pako.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;AAGA,sBAEC;AAJD,+BAAiC;AAEjC,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,IAAA,iBAAU,EAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}
|
package/dist/unzip.d.ts
CHANGED
package/dist/util.js
CHANGED
|
@@ -9,7 +9,10 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
|
|
|
9
9
|
});
|
|
10
10
|
};
|
|
11
11
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
12
|
-
exports.
|
|
12
|
+
exports.AbortError = void 0;
|
|
13
|
+
exports.groupBlocks = groupBlocks;
|
|
14
|
+
exports.checkAbortSignal = checkAbortSignal;
|
|
15
|
+
exports.abortBreakPoint = abortBreakPoint;
|
|
13
16
|
class AbortError extends Error {
|
|
14
17
|
constructor(message) {
|
|
15
18
|
super(message);
|
|
@@ -45,7 +48,6 @@ function groupBlocks(blocks) {
|
|
|
45
48
|
}
|
|
46
49
|
return blockGroups;
|
|
47
50
|
}
|
|
48
|
-
exports.groupBlocks = groupBlocks;
|
|
49
51
|
/**
|
|
50
52
|
* Properly check if the given AbortSignal is aborted.
|
|
51
53
|
* Per the standard, if the signal reads as aborted,
|
|
@@ -73,7 +75,6 @@ function checkAbortSignal(signal) {
|
|
|
73
75
|
}
|
|
74
76
|
}
|
|
75
77
|
}
|
|
76
|
-
exports.checkAbortSignal = checkAbortSignal;
|
|
77
78
|
/**
|
|
78
79
|
* Skips to the next tick, then runs `checkAbortSignal`.
|
|
79
80
|
* Await this to inside an otherwise synchronous loop to
|
|
@@ -86,5 +87,4 @@ function abortBreakPoint(signal) {
|
|
|
86
87
|
checkAbortSignal(signal);
|
|
87
88
|
});
|
|
88
89
|
}
|
|
89
|
-
exports.abortBreakPoint = abortBreakPoint;
|
|
90
90
|
//# sourceMappingURL=util.js.map
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;AAUA,kCAgCC;AAaD,4CAeC;AAQD,0CAGC;AAjFD,MAAa,UAAW,SAAQ,KAAK;IAGnC,YAAmB,OAAe;QAChC,KAAK,CAAC,OAAO,CAAC,CAAA;QACd,IAAI,CAAC,IAAI,GAAG,aAAa,CAAA;IAC3B,CAAC;CACF;AAPD,gCAOC;AACD,iCAAiC;AACjC,gDAAgD;AAChD,SAAgB,WAAW,CAAC,MAA4C;IACtE,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;IAE9D,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,IAAI,SAAS,CAAA;IACb,IAAI,YAAY,CAAA;IAChB,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IACE,SAAS;YACT,YAAY;YACZ,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,YAAY,IAAI,IAAI,EAC3C,CAAC;YACD,SAAS,CAAC,MAAM,GAAG,MAAM,CACvB,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC;gBACtB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC;gBACpB,YAAY;gBACZ,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CACvB,CAAA;YACD,SAAS,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC9B,CAAC;aAAM,CAAC;YACN,WAAW,CAAC,IAAI,CACd,CAAC,SAAS,GAAG;gBACX,MAAM,EAAE,CAAC,KAAK,CAAC;gBACf,MAAM,EAAE,KAAK,CAAC,MAAM;gBACpB,MAAM,EAAE,KAAK,CAAC,MAAM;aACrB,CAAC,CACH,CAAA;QACH,CAAC;QACD,YAAY,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,WAAW,CAAA;AACpB,CAAC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA"}
|
package/esm/bbi.d.ts
CHANGED
|
@@ -23,6 +23,7 @@ interface RefInfo {
|
|
|
23
23
|
length: number;
|
|
24
24
|
}
|
|
25
25
|
export interface Header {
|
|
26
|
+
version: number;
|
|
26
27
|
autoSql: string;
|
|
27
28
|
totalSummary: Statistics;
|
|
28
29
|
zoomLevels: any;
|
|
@@ -35,12 +36,8 @@ export interface Header {
|
|
|
35
36
|
extHeaderOffset: number;
|
|
36
37
|
isBigEndian: boolean;
|
|
37
38
|
fileType: string;
|
|
38
|
-
refsByName:
|
|
39
|
-
|
|
40
|
-
};
|
|
41
|
-
refsByNumber: {
|
|
42
|
-
[key: number]: RefInfo;
|
|
43
|
-
};
|
|
39
|
+
refsByName: Record<string, number>;
|
|
40
|
+
refsByNumber: Record<number, RefInfo>;
|
|
44
41
|
}
|
|
45
42
|
export interface RequestOptions {
|
|
46
43
|
signal?: AbortSignal;
|
package/esm/bbi.js
CHANGED
|
@@ -9,7 +9,8 @@ const BIG_BED_MAGIC = -2021002517;
|
|
|
9
9
|
function toString(arr) {
|
|
10
10
|
return new TextDecoder().decode(arr);
|
|
11
11
|
}
|
|
12
|
-
|
|
12
|
+
/**
|
|
13
|
+
* get the compiled parsers for different sections of the bigwig file
|
|
13
14
|
*
|
|
14
15
|
* @param isBE - is big endian, typically false
|
|
15
16
|
* @return an object with compiled parsers
|
|
@@ -67,10 +68,6 @@ function getParsers(isBE) {
|
|
|
67
68
|
};
|
|
68
69
|
}
|
|
69
70
|
export class BBI {
|
|
70
|
-
/* fetch and parse header information from a bigwig or bigbed file
|
|
71
|
-
* @param abortSignal - abort the operation, can be null
|
|
72
|
-
* @return a Header object
|
|
73
|
-
*/
|
|
74
71
|
getHeader(opts) {
|
|
75
72
|
if (!this.headerP) {
|
|
76
73
|
this.headerP = this._getHeader(opts).catch(e => {
|
|
@@ -242,7 +239,9 @@ export class BBI {
|
|
|
242
239
|
view = await this.getView(1, opts);
|
|
243
240
|
}
|
|
244
241
|
return new Observable(observer => {
|
|
245
|
-
view
|
|
242
|
+
view
|
|
243
|
+
.readWigData(chrName, start, end, observer, opts)
|
|
244
|
+
.catch(e => observer.error(e));
|
|
246
245
|
});
|
|
247
246
|
}
|
|
248
247
|
async getFeatures(refName, start, end, opts) {
|
package/esm/bbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAC/B,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAqB,MAAM,oBAAoB,CAAA;AAC7E,OAAO,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjD,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;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;
|
|
1
|
+
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAC/B,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAqB,MAAM,oBAAoB,CAAA;AAC7E,OAAO,EAAE,cAAc,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjD,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;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;AA0CD;;;;;GAKG;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,MAAM,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,MAAM,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,MAAM,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,MAAM,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,MAAM,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,MAAM,OAAgB,GAAG;IAOhB,SAAS,CAAC,IAAqB;QACpC,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC;YAClB,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;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IAED;;;;;;;;;OASG;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,CAAC;YACf,IAAI,CAAC,GAAG,GAAG,UAAU,CAAA;QACvB,CAAC;aAAM,IAAI,GAAG,EAAE,CAAC;YACf,IAAI,CAAC,GAAG,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;QAChC,CAAC;aAAM,IAAI,IAAI,EAAE,CAAC;YAChB,IAAI,CAAC,GAAG,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,CAAA;QAChC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;QAClC,CAAC;IACH,CAAC;IAEO,KAAK,CAAC,UAAU,CAAC,IAAqB;QAC5C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;QAC9C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACtD,OAAO,EAAE,GAAG,MAAM,EAAE,GAAG,MAAM,EAAE,CAAA;IACjC,CAAC;IAEO,KAAK,CAAC,cAAc,CAC1B,IAAqB,EACrB,WAAW,GAAG,IAAI;QAElB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,EACzB,CAAC,EACD,WAAW,EACX,CAAC,EACD,IAAI,CACL,CAAA;QACD,MAAM,WAAW,GAAG,IAAI,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,UAAU,CAAC,WAAW,CAAC,CAAA;QACnC,MAAM,MAAM,GAAG,GAAG,CAAC,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,kBAAkB,EAAE,GAAG,MAAM,CAAA;QACtD,MAAM,CAAC,QAAQ,GAAG,KAAK,KAAK,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAA;QAC/D,IAAI,QAAQ,GAAG,WAAW,IAAI,kBAAkB,GAAG,WAAW,EAAE,CAAC;YAC/D,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;QACnD,CAAC;QACD,IAAI,QAAQ,EAAE,CAAC;YACb,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;YACnC,MAAM,CAAC,OAAO,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAA;QACzE,CAAC;QAED,mDAAmD;QACnD,4CAA4C;QAC5C,IAAI,MAAM,CAAC,kBAAkB,GAAG,WAAW,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACpD,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;QACnD,CAAC;QAED,IAAI,MAAM,CAAC,kBAAkB,EAAE,CAAC;YAC9B,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAC,CAAA;YAC/D,MAAM,GAAG,GAAG,GAAG,CAAC,kBAAkB,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC9C,MAAM,CAAC,YAAY,GAAG,EAAE,GAAG,GAAG,EAAE,YAAY,EAAE,MAAM,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,CAAA;QAC1E,CAAC;QACD,OAAO,EAAE,GAAG,MAAM,EAAE,WAAW,EAAE,CAAA;IACnC,CAAC;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,CAAC;YACnD,OAAO,KAAK,CAAA;QACd,CAAC;QACD,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE,CAAC;YACnD,OAAO,IAAI,CAAA;QACb,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;IAC7C,CAAC;IAED,qCAAqC;IAC7B,KAAK,CAAC,cAAc,CAC1B,MAAc,EACd,IAA+B;QAE/B,MAAM,IAAI,GAAG,MAAM,CAAC,WAAW,CAAA;QAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;QAClC,MAAM,YAAY,GAGd,EAAE,CAAA;QACN,MAAM,UAAU,GAA2B,EAAE,CAAA;QAE7C,IAAI,kBAAkB,GAAG,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAA;QAC1D,MAAM,eAAe,GAAG,MAAM,CAAC,MAAM,CAA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|
package/esm/bigbed.d.ts
CHANGED
package/esm/bigbed.js
CHANGED
|
@@ -2,7 +2,7 @@ import { Buffer } from 'buffer';
|
|
|
2
2
|
import { Parser } from 'binary-parser';
|
|
3
3
|
import { Observable, merge, firstValueFrom } from 'rxjs';
|
|
4
4
|
import { map, reduce } from 'rxjs/operators';
|
|
5
|
-
import AbortablePromiseCache from 'abortable-promise-cache';
|
|
5
|
+
import AbortablePromiseCache from '@gmod/abortable-promise-cache';
|
|
6
6
|
import QuickLRU from 'quick-lru';
|
|
7
7
|
import { BBI } from './bbi';
|
|
8
8
|
export function filterUndef(ts) {
|
|
@@ -122,18 +122,17 @@ export class BigBed extends BBI {
|
|
|
122
122
|
const node = bpt.parse(buffer);
|
|
123
123
|
if (node.leafkeys) {
|
|
124
124
|
let lastOffset;
|
|
125
|
-
for (
|
|
126
|
-
const { key } = node.leafkeys[i];
|
|
125
|
+
for (const { key, offset } of node.leafkeys) {
|
|
127
126
|
if (name.localeCompare(key) < 0 && lastOffset) {
|
|
128
127
|
return bptReadNode(lastOffset);
|
|
129
128
|
}
|
|
130
|
-
lastOffset =
|
|
129
|
+
lastOffset = offset;
|
|
131
130
|
}
|
|
132
131
|
return bptReadNode(lastOffset);
|
|
133
132
|
}
|
|
134
|
-
for (
|
|
135
|
-
if (
|
|
136
|
-
return { ...
|
|
133
|
+
for (const n of node.keys) {
|
|
134
|
+
if (n.key === name) {
|
|
135
|
+
return { ...n, field };
|
|
137
136
|
}
|
|
138
137
|
}
|
|
139
138
|
return undefined;
|
|
@@ -144,8 +143,9 @@ export class BigBed extends BBI {
|
|
|
144
143
|
return filterUndef(await Promise.all(locs));
|
|
145
144
|
}
|
|
146
145
|
/*
|
|
147
|
-
* retrieve the features from the bigbed data that were found through the
|
|
148
|
-
* note that there can be multiple extraIndex, see
|
|
146
|
+
* retrieve the features from the bigbed data that were found through the
|
|
147
|
+
* lookup of the extraIndex note that there can be multiple extraIndex, see
|
|
148
|
+
* the BigBed specification and the -extraIndex argument to bedToBigBed
|
|
149
149
|
*
|
|
150
150
|
* @param name - the name to search for
|
|
151
151
|
* @param opts - a SearchOptions argument with optional signal
|
|
@@ -159,7 +159,7 @@ export class BigBed extends BBI {
|
|
|
159
159
|
const view = await this.getUnzoomedView(opts);
|
|
160
160
|
const res = blocks.map(block => {
|
|
161
161
|
return new Observable(observer => {
|
|
162
|
-
view.readFeatures(observer, [block], opts);
|
|
162
|
+
view.readFeatures(observer, [block], opts).catch(e => observer.error(e));
|
|
163
163
|
}).pipe(reduce((acc, curr) => acc.concat(curr)), map(x => {
|
|
164
164
|
for (const element of x) {
|
|
165
165
|
element.field = block.field;
|
package/esm/bigbed.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAC/B,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AACxD,OAAO,EAAE,GAAG,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAA;AAC5C,OAAO,qBAAqB,MAAM,
|
|
1
|
+
{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAC/B,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AACxD,OAAO,EAAE,GAAG,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAA;AAC5C,OAAO,qBAAqB,MAAM,+BAA+B,CAAA;AACjE,OAAO,QAAQ,MAAM,WAAW,CAAA;AAEhC,OAAO,EAAE,GAAG,EAA2B,MAAM,OAAO,CAAA;AAgBpD,MAAM,UAAU,WAAW,CAAI,EAAqB;IAClD,OAAO,EAAE,CAAC,MAAM,CAAC,CAAC,CAAgB,EAAU,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,MAAM,OAAO,MAAO,SAAQ,GAAG;IAA/B;;QACS,qBAAgB,GAAG,IAAI,qBAAqB,CAA0B;YAC3E,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;YACnC,IAAI,EAAE,CAAC,IAAoB,EAAE,MAAoB,EAAE,EAAE,CACnD,IAAI,CAAC,YAAY,CAAC,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC;SACzC,CAAC,CAAA;IAqMJ,CAAC;IAnMQ,WAAW,CAAC,OAAuB,EAAE;QAC1C,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,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;IACO,KAAK,CAAC,OAAO,CAAC,MAAc,EAAE,IAAqB;QAC3D,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;IAED;;;;OAIG;IACK,KAAK,CAAC,YAAY,CAAC,IAAoB;QAC7C,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QACnE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,eAAe,CAAC,CACxB,CAAA;QACD,MAAM,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;QACzC,MAAM,GAAG,GAAG,IAAI,MAAM,EAAE;aACrB,SAAS,CAAC,EAAE,CAAC;aACb,MAAM,CAAC,MAAM,CAAC;aACd,MAAM,CAAC,OAAO,CAAC;aACf,MAAM,CAAC,QAAQ,CAAC;aAChB,KAAK,CAAC,IAAI,CAAC,CAAA;QAEd,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,GAAG,CAAA;QAE7B,wCAAwC;QACxC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,QAAQ,GAAG,EAAE,CAAA;QACnB,MAAM,GAAG,GAAG,QAAQ,GAAG,KAAK,CAAA;QAC5B,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,MAAM,CAAC,MAAM,CAAC,CACf,CAAA;QACD,MAAM,SAAS,GAAG,IAAI,MAAM,EAAE;aAC3B,SAAS,CAAC,EAAE,CAAC;aACb,KAAK,CAAC,MAAM,CAAC;aACb,KAAK,CAAC,YAAY,CAAC;aACnB,MAAM,CAAC,QAAQ,CAAC;aAChB,IAAI,CAAC,CAAC,CAAC;aACP,KAAK,CAAC,OAAO,CAAC,CAAA;QACjB,MAAM,OAAO,GAAG,EAAa,CAAA;QAE7B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;QAC9D,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;IAED;;;;;;;OAOG;IACK,KAAK,CAAC,sBAAsB,CAClC,IAAY,EACZ,OAAuB,EAAE;QAEzB,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAClD,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAC5C,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,EAAE,KAAU,EAA4B,EAAE;YACtE,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;YAC/B,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,MAAM,CAAC,EACd,IAAI,CACL,CAAA;YACD,MAAM,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;YACzC,MAAM,CAAC,GAAG,IAAI,MAAM,EAAE;iBACnB,SAAS,CAAC,EAAE,CAAC;iBACb,KAAK,CAAC,OAAO,CAAC;iBACd,KAAK,CAAC,WAAW,CAAC;iBAClB,KAAK,CAAC,SAAS,CAAC;iBAChB,KAAK,CAAC,SAAS,CAAC;iBAChB,MAAM,CAAC,WAAW,CAAC,CAAA;YAEtB,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACrD,2CAA2C;YAC3C,MAAM,GAAG,GAAG,IAAI,MAAM,EAAE;iBACrB,SAAS,CAAC,EAAE,CAAC;iBACb,IAAI,CAAC,UAAU,CAAC;iBAChB,IAAI,CAAC,CAAC,CAAC;iBACP,KAAK,CAAC,KAAK,CAAC;iBACZ,MAAM,CAAC;gBACN,GAAG,EAAE,UAAU;gBACf,OAAO,EAAE;oBACP,CAAC,EAAE,IAAI,MAAM,EAAE,CAAC,KAAK,CAAC,UAAU,EAAE;wBAChC,MAAM,EAAE,KAAK;wBACb,IAAI,EAAE,IAAI,MAAM,EAAE;6BACf,SAAS,CAAC,EAAE,CAAC;6BACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;6BACnD,MAAM,CAAC,QAAQ,CAAC;qBACpB,CAAC;oBACF,CAAC,EAAE,IAAI,MAAM,EAAE,CAAC,KAAK,CAAC,MAAM,EAAE;wBAC5B,MAAM,EAAE,KAAK;wBACb,IAAI,EAAE,IAAI,MAAM,EAAE;6BACf,SAAS,CAAC,EAAE,CAAC;6BACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;6BACnD,MAAM,CAAC,QAAQ,CAAC;6BAChB,MAAM,CAAC,QAAQ,CAAC;6BAChB,MAAM,CAAC,UAAU,CAAC;qBACtB,CAAC;iBACH;aACF,CAAC,CAAA;YAEJ,MAAM,WAAW,GAAG,KAAK,EACvB,UAAkB,EACQ,EAAE;gBAC5B,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,CAAA;gBAC9B,MAAM,GAAG,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,OAAO,GAAG,OAAO,CAAC,CAAA;gBAC/C,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;gBACD,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;gBAC9B,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;oBAClB,IAAI,UAAU,CAAA;oBACd,KAAK,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;wBAC5C,IAAI,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,EAAE,CAAC;4BAC9C,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;wBAChC,CAAC;wBACD,UAAU,GAAG,MAAM,CAAA;oBACrB,CAAC;oBACD,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;gBAChC,CAAC;gBACD,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;oBAC1B,IAAI,CAAC,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;wBACnB,OAAO,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,CAAA;oBACxB,CAAC;gBACH,CAAC;gBAED,OAAO,SAAS,CAAA;YAClB,CAAC,CAAA;YACD,MAAM,cAAc,GAAG,EAAE,CAAA;YACzB,OAAO,WAAW,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,cAAc,CAAC,CAAA;QACrD,CAAC,CAAC,CAAA;QACF,OAAO,WAAW,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAA;IAC7C,CAAC;IAED;;;;;;;;OAQG;IACI,KAAK,CAAC,gBAAgB,CAAC,IAAY,EAAE,OAAuB,EAAE;QACnE,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,sBAAsB,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAC5D,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE;YAC7B,OAAO,IAAI,UAAU,CAAY,QAAQ,CAAC,EAAE;gBAC1C,IAAI,CAAC,YAAY,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;YAC1E,CAAC,CAAC,CAAC,IAAI,CACL,MAAM,CAAC,CAAC,GAAG,EAAE,IAAI,EAAE,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,EACvC,GAAG,CAAC,CAAC,CAAC,EAAE;gBACN,KAAK,MAAM,OAAO,IAAI,CAAC,EAAE,CAAC;oBACxB,OAAO,CAAC,KAAK,GAAG,KAAK,CAAC,KAAK,CAAA;gBAC7B,CAAC;gBACD,OAAO,CAAC,CAAA;YACV,CAAC,CAAC,CACH,CAAA;QACH,CAAC,CAAC,CAAA;QACF,MAAM,GAAG,GAAG,MAAM,cAAc,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,CAAC,CAAA;QAC/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;IAC1E,CAAC;CACF"}
|
package/esm/bigwig.d.ts
CHANGED
|
@@ -5,7 +5,9 @@ export declare class BigWig extends BBI {
|
|
|
5
5
|
* Retrieves a BlockView of a specific zoomLevel
|
|
6
6
|
*
|
|
7
7
|
* @param scale - number
|
|
8
|
-
*
|
|
8
|
+
*
|
|
9
|
+
* @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
|
|
10
|
+
* or scale used to infer the zoomLevel to use
|
|
9
11
|
*/
|
|
10
12
|
protected getView(scale: number, opts: RequestOptions): Promise<BlockView>;
|
|
11
13
|
}
|
package/esm/bigwig.js
CHANGED
|
@@ -5,7 +5,9 @@ export class BigWig extends BBI {
|
|
|
5
5
|
* Retrieves a BlockView of a specific zoomLevel
|
|
6
6
|
*
|
|
7
7
|
* @param scale - number
|
|
8
|
-
*
|
|
8
|
+
*
|
|
9
|
+
* @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
|
|
10
|
+
* or scale used to infer the zoomLevel to use
|
|
9
11
|
*/
|
|
10
12
|
async getView(scale, opts) {
|
|
11
13
|
const { zoomLevels, refsByName, fileSize, isBigEndian, uncompressBufSize } = await this.getHeader(opts);
|
package/esm/bigwig.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B
|
|
1
|
+
{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;QAChC,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,4EAA4E;YAC5E,QAAQ,IAAI,CAAC,CAAA;QACf,CAAC;QAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;gBAE1C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}
|
package/esm/block-view.js
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import { Buffer } from 'buffer';
|
|
2
2
|
import { Parser } from 'binary-parser';
|
|
3
|
-
import AbortablePromiseCache from 'abortable-promise-cache';
|
|
3
|
+
import AbortablePromiseCache from '@gmod/abortable-promise-cache';
|
|
4
4
|
import QuickLRU from 'quick-lru';
|
|
5
5
|
// locals
|
|
6
6
|
import Range from './range';
|
|
@@ -162,7 +162,7 @@ export class BlockView {
|
|
|
162
162
|
if (p.blocksToFetch) {
|
|
163
163
|
blocksToFetch = blocksToFetch.concat(p.blocksToFetch
|
|
164
164
|
.filter(f => filterFeats(f))
|
|
165
|
-
.map(
|
|
165
|
+
.map(l => ({
|
|
166
166
|
offset: l.blockOffset,
|
|
167
167
|
length: l.blockSize,
|
|
168
168
|
})));
|
|
@@ -221,6 +221,7 @@ export class BlockView {
|
|
|
221
221
|
]);
|
|
222
222
|
spans = spans.union(blockSpan);
|
|
223
223
|
}
|
|
224
|
+
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
|
224
225
|
spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));
|
|
225
226
|
}
|
|
226
227
|
catch (e) {
|
package/esm/block-view.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/esm/range.js
CHANGED
|
@@ -1,4 +1,7 @@
|
|
|
1
|
-
|
|
1
|
+
/**
|
|
2
|
+
* Adapted from a combination of Range and _Compound in the
|
|
3
|
+
* Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
|
|
4
|
+
*/
|
|
2
5
|
export default class Range {
|
|
3
6
|
constructor(arg1) {
|
|
4
7
|
this.ranges = arg1;
|
|
@@ -46,8 +49,7 @@ export default class Range {
|
|
|
46
49
|
});
|
|
47
50
|
const oranges = [];
|
|
48
51
|
let current = ranges[0];
|
|
49
|
-
for (
|
|
50
|
-
const nxt = ranges[i];
|
|
52
|
+
for (const nxt of ranges) {
|
|
51
53
|
if (nxt.min > current.max + 1) {
|
|
52
54
|
oranges.push(current);
|
|
53
55
|
current = nxt;
|
package/esm/range.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"range.js","sourceRoot":"","sources":["../src/range.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"range.js","sourceRoot":"","sources":["../src/range.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAMH,MAAM,CAAC,OAAO,OAAO,KAAK;IAGxB,YAAmB,IAAc;QAC/B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;IACpB,CAAC;IAED,IAAI,GAAG;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC3B,CAAC;IAED,IAAI,GAAG;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,CAAA;IAChD,CAAC;IAEM,QAAQ,CAAC,GAAW;QACzB,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;YAC5B,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC;gBACjC,OAAO,IAAI,CAAA;YACb,CAAC;QACH,CAAC;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,CAAC,EAAE,CAAC,IAAI,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAA;IACtE,CAAC;IAEM,QAAQ;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IAC9D,CAAC;IAEM,KAAK,CAAC,EAAS;QACpB,MAAM,MAAM,GAAG,CAAC,GAAG,IAAI,CAAC,SAAS,EAAE,EAAE,GAAG,EAAE,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACpE,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBAClB,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,OAAO,CAAC,CAAA;YACV,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,OAAO,CAAC,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,OAAO,CAAC,CAAA;YACV,CAAC;QACH,CAAC,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,EAAa,CAAA;QAC7B,IAAI,OAAO,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAEvB,KAAK,MAAM,GAAG,IAAI,MAAM,EAAE,CAAC;YACzB,IAAI,GAAG,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,CAAC,EAAE,CAAC;gBAC9B,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,OAAO,GAAG,GAAG,CAAA;YACf,CAAC;iBAAM,IAAI,GAAG,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;gBACjC,OAAO,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,OAAO,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC3D,CAAC;QACH,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAErB,OAAO,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,OAAO,CAAC,CAAA;IAC/D,CAAC;CACF"}
|
package/esm/unzip-pako.d.ts
CHANGED
package/esm/unzip.d.ts
CHANGED
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bbi",
|
|
3
|
-
"version": "4.0.
|
|
3
|
+
"version": "4.0.6",
|
|
4
4
|
"description": "Parser for BigWig/BigBed files",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/bbi-js",
|
|
@@ -22,7 +22,7 @@
|
|
|
22
22
|
"scripts": {
|
|
23
23
|
"test": "jest",
|
|
24
24
|
"coverage": "npm test -- --coverage",
|
|
25
|
-
"lint": "eslint --report-unused-disable-directives --max-warnings 0
|
|
25
|
+
"lint": "eslint --report-unused-disable-directives --max-warnings 0 src",
|
|
26
26
|
"format": "prettier",
|
|
27
27
|
"clean": "rimraf dist esm",
|
|
28
28
|
"prebuild": "npm run clean",
|
|
@@ -42,7 +42,7 @@
|
|
|
42
42
|
"genomics"
|
|
43
43
|
],
|
|
44
44
|
"dependencies": {
|
|
45
|
-
"abortable-promise-cache": "^
|
|
45
|
+
"@gmod/abortable-promise-cache": "^2.0.0",
|
|
46
46
|
"binary-parser": "^2.1.0",
|
|
47
47
|
"generic-filehandle": "^3.0.0",
|
|
48
48
|
"pako": "^2.0.0",
|
|
@@ -54,17 +54,17 @@
|
|
|
54
54
|
"@types/jest": "^29.5.12",
|
|
55
55
|
"@types/node": "^20.11.16",
|
|
56
56
|
"@types/pako": "^2.0.0",
|
|
57
|
-
"@typescript-eslint/eslint-plugin": "^
|
|
58
|
-
"@typescript-eslint/parser": "^
|
|
59
|
-
"eslint": "^
|
|
57
|
+
"@typescript-eslint/eslint-plugin": "^7.3.1",
|
|
58
|
+
"@typescript-eslint/parser": "^7.3.1",
|
|
59
|
+
"eslint": "^9.0.0",
|
|
60
60
|
"eslint-config-prettier": "^9.1.0",
|
|
61
61
|
"eslint-plugin-prettier": "^5.1.3",
|
|
62
|
-
"eslint-plugin-unicorn": "^
|
|
62
|
+
"eslint-plugin-unicorn": "^54.0.0",
|
|
63
63
|
"jest": "^29.6.2",
|
|
64
64
|
"jest-environment-jsdom": "^29.6.2",
|
|
65
65
|
"prettier": "^3.2.5",
|
|
66
|
-
"rimraf": "^
|
|
67
|
-
"standard-changelog": "^
|
|
66
|
+
"rimraf": "^6.0.1",
|
|
67
|
+
"standard-changelog": "^6.0.0",
|
|
68
68
|
"ts-jest": "^29.1.2",
|
|
69
69
|
"typescript": "^5.1.6"
|
|
70
70
|
},
|
package/src/bbi.ts
CHANGED
|
@@ -35,6 +35,7 @@ interface RefInfo {
|
|
|
35
35
|
length: number
|
|
36
36
|
}
|
|
37
37
|
export interface Header {
|
|
38
|
+
version: number
|
|
38
39
|
autoSql: string
|
|
39
40
|
totalSummary: Statistics
|
|
40
41
|
zoomLevels: any
|
|
@@ -47,11 +48,12 @@ export interface Header {
|
|
|
47
48
|
extHeaderOffset: number
|
|
48
49
|
isBigEndian: boolean
|
|
49
50
|
fileType: string
|
|
50
|
-
refsByName:
|
|
51
|
-
refsByNumber:
|
|
51
|
+
refsByName: Record<string, number>
|
|
52
|
+
refsByNumber: Record<number, RefInfo>
|
|
52
53
|
}
|
|
53
54
|
|
|
54
|
-
|
|
55
|
+
/**
|
|
56
|
+
* get the compiled parsers for different sections of the bigwig file
|
|
55
57
|
*
|
|
56
58
|
* @param isBE - is big endian, typically false
|
|
57
59
|
* @return an object with compiled parsers
|
|
@@ -126,10 +128,6 @@ export abstract class BBI {
|
|
|
126
128
|
|
|
127
129
|
protected renameRefSeqs: (a: string) => string
|
|
128
130
|
|
|
129
|
-
/* fetch and parse header information from a bigwig or bigbed file
|
|
130
|
-
* @param abortSignal - abort the operation, can be null
|
|
131
|
-
* @return a Header object
|
|
132
|
-
*/
|
|
133
131
|
public getHeader(opts?: RequestOptions) {
|
|
134
132
|
if (!this.headerP) {
|
|
135
133
|
this.headerP = this._getHeader(opts).catch(e => {
|
|
@@ -232,10 +230,11 @@ export abstract class BBI {
|
|
|
232
230
|
) {
|
|
233
231
|
const isBE = header.isBigEndian
|
|
234
232
|
const le = isBE ? 'big' : 'little'
|
|
235
|
-
const refsByNumber:
|
|
236
|
-
|
|
237
|
-
|
|
238
|
-
|
|
233
|
+
const refsByNumber: Record<
|
|
234
|
+
number,
|
|
235
|
+
{ name: string; id: number; length: number }
|
|
236
|
+
> = []
|
|
237
|
+
const refsByName: Record<string, number> = {}
|
|
239
238
|
|
|
240
239
|
let unzoomedDataOffset = Number(header.unzoomedDataOffset)
|
|
241
240
|
const chromTreeOffset = Number(header.chromTreeOffset)
|
|
@@ -361,7 +360,9 @@ export abstract class BBI {
|
|
|
361
360
|
}
|
|
362
361
|
|
|
363
362
|
return new Observable<Feature[]>(observer => {
|
|
364
|
-
view
|
|
363
|
+
view
|
|
364
|
+
.readWigData(chrName, start, end, observer, opts)
|
|
365
|
+
.catch(e => observer.error(e))
|
|
365
366
|
})
|
|
366
367
|
}
|
|
367
368
|
|
package/src/bigbed.ts
CHANGED
|
@@ -2,7 +2,7 @@ import { Buffer } from 'buffer'
|
|
|
2
2
|
import { Parser } from 'binary-parser'
|
|
3
3
|
import { Observable, merge, firstValueFrom } from 'rxjs'
|
|
4
4
|
import { map, reduce } from 'rxjs/operators'
|
|
5
|
-
import AbortablePromiseCache from 'abortable-promise-cache'
|
|
5
|
+
import AbortablePromiseCache from '@gmod/abortable-promise-cache'
|
|
6
6
|
import QuickLRU from 'quick-lru'
|
|
7
7
|
|
|
8
8
|
import { BBI, Feature, RequestOptions } from './bbi'
|
|
@@ -174,18 +174,17 @@ export class BigBed extends BBI {
|
|
|
174
174
|
const node = bpt.parse(buffer)
|
|
175
175
|
if (node.leafkeys) {
|
|
176
176
|
let lastOffset
|
|
177
|
-
for (
|
|
178
|
-
const { key } = node.leafkeys[i]
|
|
177
|
+
for (const { key, offset } of node.leafkeys) {
|
|
179
178
|
if (name.localeCompare(key) < 0 && lastOffset) {
|
|
180
179
|
return bptReadNode(lastOffset)
|
|
181
180
|
}
|
|
182
|
-
lastOffset =
|
|
181
|
+
lastOffset = offset
|
|
183
182
|
}
|
|
184
183
|
return bptReadNode(lastOffset)
|
|
185
184
|
}
|
|
186
|
-
for (
|
|
187
|
-
if (
|
|
188
|
-
return { ...
|
|
185
|
+
for (const n of node.keys) {
|
|
186
|
+
if (n.key === name) {
|
|
187
|
+
return { ...n, field }
|
|
189
188
|
}
|
|
190
189
|
}
|
|
191
190
|
|
|
@@ -198,8 +197,9 @@ export class BigBed extends BBI {
|
|
|
198
197
|
}
|
|
199
198
|
|
|
200
199
|
/*
|
|
201
|
-
* retrieve the features from the bigbed data that were found through the
|
|
202
|
-
* note that there can be multiple extraIndex, see
|
|
200
|
+
* retrieve the features from the bigbed data that were found through the
|
|
201
|
+
* lookup of the extraIndex note that there can be multiple extraIndex, see
|
|
202
|
+
* the BigBed specification and the -extraIndex argument to bedToBigBed
|
|
203
203
|
*
|
|
204
204
|
* @param name - the name to search for
|
|
205
205
|
* @param opts - a SearchOptions argument with optional signal
|
|
@@ -213,7 +213,7 @@ export class BigBed extends BBI {
|
|
|
213
213
|
const view = await this.getUnzoomedView(opts)
|
|
214
214
|
const res = blocks.map(block => {
|
|
215
215
|
return new Observable<Feature[]>(observer => {
|
|
216
|
-
view.readFeatures(observer, [block], opts)
|
|
216
|
+
view.readFeatures(observer, [block], opts).catch(e => observer.error(e))
|
|
217
217
|
}).pipe(
|
|
218
218
|
reduce((acc, curr) => acc.concat(curr)),
|
|
219
219
|
map(x => {
|
package/src/bigwig.ts
CHANGED
|
@@ -6,7 +6,9 @@ export class BigWig extends BBI {
|
|
|
6
6
|
* Retrieves a BlockView of a specific zoomLevel
|
|
7
7
|
*
|
|
8
8
|
* @param scale - number
|
|
9
|
-
*
|
|
9
|
+
*
|
|
10
|
+
* @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
|
|
11
|
+
* or scale used to infer the zoomLevel to use
|
|
10
12
|
*/
|
|
11
13
|
protected async getView(scale: number, opts: RequestOptions) {
|
|
12
14
|
const { zoomLevels, refsByName, fileSize, isBigEndian, uncompressBufSize } =
|
package/src/block-view.ts
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { Buffer } from 'buffer'
|
|
2
2
|
import { Observer } from 'rxjs'
|
|
3
3
|
import { Parser } from 'binary-parser'
|
|
4
|
-
import AbortablePromiseCache from 'abortable-promise-cache'
|
|
4
|
+
import AbortablePromiseCache from '@gmod/abortable-promise-cache'
|
|
5
5
|
import { GenericFilehandle } from 'generic-filehandle'
|
|
6
6
|
import QuickLRU from 'quick-lru'
|
|
7
7
|
|
|
@@ -235,7 +235,7 @@ export class BlockView {
|
|
|
235
235
|
blocksToFetch = blocksToFetch.concat(
|
|
236
236
|
p.blocksToFetch
|
|
237
237
|
.filter(f => filterFeats(f))
|
|
238
|
-
.map(
|
|
238
|
+
.map(l => ({
|
|
239
239
|
offset: l.blockOffset,
|
|
240
240
|
length: l.blockSize,
|
|
241
241
|
})),
|
|
@@ -306,6 +306,7 @@ export class BlockView {
|
|
|
306
306
|
])
|
|
307
307
|
spans = spans.union(blockSpan)
|
|
308
308
|
}
|
|
309
|
+
// eslint-disable-next-line @typescript-eslint/no-floating-promises
|
|
309
310
|
spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level))
|
|
310
311
|
} catch (e) {
|
|
311
312
|
observer.error(e)
|
package/src/range.ts
CHANGED
|
@@ -1,5 +1,3 @@
|
|
|
1
|
-
/* eslint prefer-rest-params:0, no-nested-ternary:0 */
|
|
2
|
-
|
|
3
1
|
/**
|
|
4
2
|
* Adapted from a combination of Range and _Compound in the
|
|
5
3
|
* Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
|
|
@@ -45,7 +43,7 @@ export default class Range {
|
|
|
45
43
|
return this.ranges.map(r => `[${r.min}-${r.max}]`).join(',')
|
|
46
44
|
}
|
|
47
45
|
|
|
48
|
-
public union(s1: Range)
|
|
46
|
+
public union(s1: Range) {
|
|
49
47
|
const ranges = [...this.getRanges(), ...s1.getRanges()].sort((a, b) => {
|
|
50
48
|
if (a.min < b.min) {
|
|
51
49
|
return -1
|
|
@@ -59,11 +57,10 @@ export default class Range {
|
|
|
59
57
|
return 0
|
|
60
58
|
}
|
|
61
59
|
})
|
|
62
|
-
const oranges = []
|
|
60
|
+
const oranges = [] as Range[]
|
|
63
61
|
let current = ranges[0]
|
|
64
62
|
|
|
65
|
-
for (
|
|
66
|
-
const nxt = ranges[i]
|
|
63
|
+
for (const nxt of ranges) {
|
|
67
64
|
if (nxt.min > current.max + 1) {
|
|
68
65
|
oranges.push(current)
|
|
69
66
|
current = nxt
|