@gmod/bbi 3.0.0 → 4.0.0

package/CHANGELOG.md

@@ -1,6 +1,20 @@
-# [3.0.0](https://github.com/GMOD/bbi-js/compare/v2.0.5...v3.0.0) (2023-01-11)
+# [4.0.0](https://github.com/GMOD/bbi-js/compare/v3.0.1...v4.0.0) (2023-05-05)
+
+
+
+- Improve typescripting, refactoring
+- Options argument only accepts {signal}, not just signal now
 
+## [3.0.1](https://github.com/GMOD/bbi-js/compare/v3.0.0...v3.0.1) (2023-04-21)
 
+### Features
+
+- explicit buffer import ([#53](https://github.com/GMOD/bbi-js/issues/53))
+  ([2699c98](https://github.com/GMOD/bbi-js/commit/2699c983dea380bbb56773058ba3f233c833d9c8))
+
+* Add explicit Buffer import
+
+# [3.0.0](https://github.com/GMOD/bbi-js/compare/v2.0.5...v3.0.0) (2023-01-11)
 
 - Update to rxjs 7
 
@@ -38,7 +52,9 @@
 
 ### Reverts
 
-- Revert "Use subarray instead of slice since slice is deprecated under node xref 'https://nodejs.org/api/buffer.html#bufslicestart-end'" ([44116cc](https://github.com/GMOD/bbi-js/commit/44116cce54601727d37f1c449bfcc60c1b4e602d))
+- Revert "Use subarray instead of slice since slice is deprecated under node
+  xref 'https://nodejs.org/api/buffer.html#bufslicestart-end'"
+  ([44116cc](https://github.com/GMOD/bbi-js/commit/44116cce54601727d37f1c449bfcc60c1b4e602d))
 
 * Back to slice instead of subarray, as subarray returned a UInt8Array instead
   of a true Buffer
@@ -64,11 +80,13 @@
 
 ## [1.0.29](https://github.com/GMOD/bbi-js/compare/v1.0.28...v1.0.29) (2020-01-28)
 
-- Accidentally made the package include itself as dependency in 1.0.28, republish
+- Accidentally made the package include itself as dependency in 1.0.28,
+  republish
 
 ## [1.0.28](https://github.com/GMOD/bbi-js/compare/v1.0.27...v1.0.28) (2020-01-28)
 
-- Change typescript interface to use object keys instead of Map type for refsByName, refsById
+- Change typescript interface to use object keys instead of Map type for
+  refsByName, refsById
 - Typescript only release change
 
 ## [1.0.27](https://github.com/GMOD/bbi-js/compare/v1.0.26...v1.0.27) (2020-01-10)
@@ -80,11 +98,13 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.26](https://github.com/GMOD/bbi-js/compare/v1.0.25...v1.0.26) (2019-11-10)
 
-- Fix important bug with fixed step bigwig files not using the proper start coordinate
+- Fix important bug with fixed step bigwig files not using the proper start
+  coordinate
 
 ## [1.0.25](https://github.com/GMOD/bbi-js/compare/v1.0.24...v1.0.25) (2019-11-03)
 
-- Add fix for files with a large header, if autoSql is large in a bigbed file would be likely scenario
+- Add fix for files with a large header, if autoSql is large in a bigbed file
+  would be likely scenario
 
 ## [1.0.24](https://github.com/GMOD/bbi-js/compare/v1.0.23...v1.0.24) (2019-10-29)
 
@@ -109,22 +129,26 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.19](https://github.com/GMOD/bbi-js/compare/v1.0.18...v1.0.19) (2019-05-02)
 
-- Add regression fix since 1.0.16 for uncompressed files. Thanks to @lidaof for reporting!
+- Add regression fix since 1.0.16 for uncompressed files. Thanks to @lidaof for
+  reporting!
 
 ## [1.0.18](https://github.com/GMOD/bbi-js/compare/v1.0.17...v1.0.18) (2019-05-02)
 
 - Improve error handling of the observables (issue #20, pull #21)
-- Bump generic-filehandle to 1.0.9 to fix compatibility with native browser fetch
+- Bump generic-filehandle to 1.0.9 to fix compatibility with native browser
+  fetch
 
 ## [1.0.17](https://github.com/GMOD/bbi-js/compare/v1.0.16...v1.0.17) (2019-04-30)
 
 - Use some standard rxjs notions for combining operator results
-- Add parsing of the extraIndex data in BigBed, allowing you to call bigbed.searchExtraIndex(name[,opts])
+- Add parsing of the extraIndex data in BigBed, allowing you to call
+  bigbed.searchExtraIndex(name[,opts])
 
 ## [1.0.16](https://github.com/GMOD/bbi-js/compare/v1.0.15...v1.0.16) (2019-04-23)
 
 - Pre-compile binary-parser instances for faster
-- Important: fixed bug that caused bigwig summary blocks to not be returned in output
+- Important: fixed bug that caused bigwig summary blocks to not be returned in
+  output
 
 ## [1.0.15](https://github.com/GMOD/bbi-js/compare/v1.0.14...v1.0.15) (2019-04-18)
 
@@ -149,12 +173,15 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.10](https://github.com/GMOD/bbi-js/compare/v1.0.9...v1.0.10) (2019-04-09)
 
-- Fix misinterpretation of variable step wig files in this module (the span is not variable in variable step files, only the step, use bedGraphToBigWig for variable span)
+- Fix misinterpretation of variable step wig files in this module (the span is
+  not variable in variable step files, only the step, use bedGraphToBigWig for
+  variable span)
 - Improved docs
 
 ## [1.0.9](https://github.com/GMOD/bbi-js/compare/v1.0.8...v1.0.9) (2019-04-05)
 
-- Added caching of networking requests (thanks @rbuels for the abortable-promise-cache module!)
+- Added caching of networking requests (thanks @rbuels for the
+  abortable-promise-cache module!)
 - Fix some type errors on the range class
 - Correct using span on fixed size wiggle types
 
@@ -166,7 +193,8 @@ Thanks to @skinner for both of these contributions!
 ## [1.0.7](https://github.com/GMOD/bbi-js/compare/v1.0.6...v1.0.7) (2019-04-01)
 
 - Added getFeatureStream which returns an Observable from rxjs
-- Added url option to BigWig and BigBed constructors to allow usage of RemoteFile filehandle
+- Added url option to BigWig and BigBed constructors to allow usage of
+  RemoteFile filehandle
 - Added typescript backend for better processing
 
 ## [1.0.6](https://github.com/GMOD/bbi-js/compare/v1.0.5...v1.0.6) (2019-03-15)
@@ -179,7 +207,8 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.4](https://github.com/GMOD/bbi-js/compare/v1.0.3...v1.0.4) (2019-01-28)
 
-- Add renameRefSeqs functionality where you can apply a callback to the refseq names
+- Add renameRefSeqs functionality where you can apply a callback to the refseq
+  names
 - Consistently apply start/end coordinate filters at different zoom levels
 
 ## [1.0.3](https://github.com/GMOD/bbi-js/compare/v1.0.2...v1.0.3) (2019-01-27)
@@ -192,7 +221,8 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.1](https://github.com/GMOD/bbi-js/compare/v1.0.0...v1.0.1) (2019-01-24)
 
-- Added exports for BigWig and BigBed. const {BigWig, BigBed} = require('@gmod/bbi')
+- Added exports for BigWig and BigBed. const {BigWig, BigBed} =
+  require('@gmod/bbi')
 
 # 1.0.0 (2019-01-23)
 

package/README.md

@@ -10,7 +10,7 @@ A parser for bigwig and bigbed file formats
 
 If using locally
 
-```ts
+```typescript
 const { BigWig } = require('@gmod/bbi')
 const file = new BigWig({
   path: 'volvox.bw',
@@ -21,10 +21,11 @@ const file = new BigWig({
 })()
 ```
 
-If using remotely, you can use it in combination with generic-filehandle or your own implementation of something like generic-filehandle
+If using remotely, you can use it in combination with generic-filehandle or your
+own implementation of something like generic-filehandle
 https://github.com/GMOD/generic-filehandle/
 
-```ts
+```typescript
 const { BigWig } = require('@gmod/bbi')
 const { RemoteFile } = require('generic-filehandle')
 
@@ -53,7 +54,11 @@ Accepts an object containing either
 
 - path - path to a local file
 - url - path to a url
-- filehandle - a filehandle instance that you can implement as a custom class yourself. path and url are based on https://www.npmjs.com/package/generic-filehandle but by implementing a class containing the Filehandle interface specified therein, you can pass it to this module
+- filehandle - a filehandle instance that you can implement as a custom class
+  yourself. path and url are based on
+  https://www.npmjs.com/package/generic-filehandle but by implementing a class
+  containing the Filehandle interface specified therein, you can pass it to this
+  module
 
 ### BigWig
 
@@ -62,15 +67,20 @@ Accepts an object containing either
 - refName - a name of a chromosome in the file
 - start - a 0-based half open start coordinate
 - end - a 0-based half open end coordinate
-- opts.scale - indicates zoom level to use, specified as pxPerBp, e.g. being zoomed out, you might have 100bp per pixel so opts.scale would be 1/100. the zoom level that is returned is the one which has reductionLevel<=2/opts.scale (reductionLevel is a property of the zoom level structure in the bigwig file data)
+- opts.scale - indicates zoom level to use, specified as pxPerBp, e.g. being
+  zoomed out, you might have 100bp per pixel so opts.scale would be 1/100. the
+  zoom level that is returned is the one which has reductionLevel<=2/opts.scale
+  (reductionLevel is a property of the zoom level structure in the bigwig file
+  data)
 - opts.basesPerScale - optional, inverse of opts.scale e.g. bpPerPx
 - opts.signal - optional, an AbortSignal to halt processing
 
-Returns a promise to an array of features. If an incorrect refName or no features are found the result is an empty array.
+Returns a promise to an array of features. If an incorrect refName or no
+features are found the result is an empty array.
 
 Example:
 
-```ts
+```typescript
 const feats = await bigwig.getFeatures('chr1', 0, 100)
 // returns array of features with start, end, score
 // coordinates on returned data are are 0-based half open
@@ -80,7 +90,9 @@ const feats = await bigwig.getFeatures('chr1', 0, 100)
 
 ### Understanding scale and reductionLevel
 
-Here is what the reductionLevel structure looks like in a file. The zoomLevel that is chosen is the first reductionLevel<2\*opts.basesPerScale (or reductionLevel<2/opts.scale) when scanning backwards through this list
+Here is what the reductionLevel structure looks like in a file. The zoomLevel
+that is chosen is the first reductionLevel<2\*opts.basesPerScale (or
+reductionLevel<2/opts.scale) when scanning backwards through this list
 
       [ { reductionLevel: 40, ... },
         { reductionLevel: 160, ... },
@@ -92,9 +104,10 @@ Here is what the reductionLevel structure looks like in a file. The zoomLevel th
 
 #### getFeatureStream(refName, start, end, opts)
 
-Same as getFeatures but returns an RxJS observable stream, useful for very large queries
+Same as getFeatures but returns an RxJS observable stream, useful for very large
+queries
 
-```ts
+```typescript
 const observer = await bigwig.getFeatureStream('chr1', 0, 100)
 observer.subscribe(
   chunk => {
@@ -118,7 +131,8 @@ observer.subscribe(
 - end - a 0-based half open end coordinate
 - opts.signal - optional, an AbortSignal to halt processing
 
-returns a promise to an array of features. no concept of zoom levels is used with bigwig data
+returns a promise to an array of features. no concept of zoom levels is used
+with bigwig data
 
 #### getFeatureStream(refName, start, end, opts)
 
@@ -126,20 +140,30 @@ Similar to BigWig, returns an RxJS observable for a observable stream
 
 #### searchExtraIndex(name, opts)
 
-Specific, to bigbed files, this method searches the bigBed "extra indexes", there can be multiple indexes e.g. for the gene ID and gene name columns. See the usage of -extraIndex in bedToBigBed here https://genome.ucsc.edu/goldenpath/help/bigBed.html
+Specific, to bigbed files, this method searches the bigBed "extra indexes",
+there can be multiple indexes e.g. for the gene ID and gene name columns. See
+the usage of -extraIndex in bedToBigBed here
+https://genome.ucsc.edu/goldenpath/help/bigBed.html
 
 This function accepts two arguments
 
 - name: a string to search for in the BigBed extra indices
 - opts: an opject that can optionally contain opts.signal, an abort signal
 
-Returns a Promise to an array of Features, with an extra field indicating the field that was matched
+Returns a Promise to an array of Features, with an extra field indicating the
+field that was matched
 
 ### How to parse BigBed results
 
-The BigBed line contents are returned as a raw text line e.g. {start: 0, end:100, rest: "ENST00000456328.2\t1000\t..."} where "rest" contains tab delimited text for the fields from 4 and on in the BED format. Since BED files from BigBed format often come with autoSql (a description of all the columns) it can be useful to parse it with BED parser that can handle autoSql. The rest line can be parsed by the @gmod/bed module, which is not by default integrated with this module, but can be combined with it as follows
+The BigBed line contents are returned as a raw text line e.g. {start: 0,
+end:100, rest: "ENST00000456328.2\t1000\t..."} where "rest" contains tab
+delimited text for the fields from 4 and on in the BED format. Since BED files
+from BigBed format often come with autoSql (a description of all the columns) it
+can be useful to parse it with BED parser that can handle autoSql. The rest line
+can be parsed by the @gmod/bed module, which is not by default integrated with
+this module, but can be combined with it as follows
 
-```ts
+```typescript
 import {BigBed} from '@gmod/bbi'
 import BED from '@gmod/bed'
 
@@ -190,7 +214,10 @@ Features after parsing with @gmod/bed:
 
 ## Academic Use
 
-This package was written with funding from the [NHGRI](http://genome.gov) as part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic project that you publish, please cite the most recent JBrowse paper, which will be linked from [jbrowse.org](http://jbrowse.org).
+This package was written with funding from the [NHGRI](http://genome.gov) as
+part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
+project that you publish, please cite the most recent JBrowse paper, which will
+be linked from [jbrowse.org](http://jbrowse.org).
 
 ## License
 

package/dist/bbi.d.ts

@@ -1,6 +1,6 @@
 import { GenericFilehandle } from 'generic-filehandle';
 import { Observable } from 'rxjs';
-import { BlockView } from './blockView';
+import { BlockView } from './block-view';
 export interface Feature {
     start: number;
     end: number;
@@ -51,8 +51,8 @@ export declare abstract class BBI {
     protected bbi: GenericFilehandle;
     private headerP?;
     protected renameRefSeqs: (a: string) => string;
-    getHeader(opts?: RequestOptions | AbortSignal): Promise<Header>;
-    constructor(options?: {
+    getHeader(opts?: RequestOptions): Promise<Header>;
+    constructor(args: {
         filehandle?: GenericFilehandle;
         path?: string;
         url?: string;
@@ -62,8 +62,8 @@ export declare abstract class BBI {
     private _getMainHeader;
     private _isBigEndian;
     private _readChromTree;
-    protected getUnzoomedView(opts: RequestOptions): Promise<BlockView>;
-    protected abstract getView(scale: number, opts: RequestOptions): Promise<BlockView>;
+    protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
+    protected abstract getView(scale: number, opts?: RequestOptions): Promise<BlockView>;
     /**
      * Gets features from a BigWig file
      *

package/dist/bbi.js

@@ -10,11 +10,12 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BBI = void 0;
+const buffer_1 = require("buffer");
 const binary_parser_1 = require("binary-parser");
 const generic_filehandle_1 = require("generic-filehandle");
 const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
-const blockView_1 = require("./blockView");
+const block_view_1 = require("./block-view");
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
 function toString(arr) {
@@ -82,10 +83,9 @@ class BBI {
      * @param abortSignal - abort the operation, can be null
      * @return a Header object
      */
-    getHeader(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
+    getHeader(opts) {
         if (!this.headerP) {
-            this.headerP = this._getHeader(options).catch(e => {
+            this.headerP = this._getHeader(opts).catch(e => {
                 this.headerP = undefined;
                 throw e;
             });
@@ -98,8 +98,8 @@ class BBI {
      * @param url - a URL string
      * @param renameRefSeqs - an optional method to rename the internal reference sequences using a mapping function
      */
-    constructor(options = {}) {
-        const { filehandle, renameRefSeqs = s => s, path, url } = options;
+    constructor(args) {
+        const { filehandle, renameRefSeqs = s => s, path, url } = args;
         this.renameRefSeqs = renameRefSeqs;
         if (filehandle) {
             this.bbi = filehandle;
@@ -123,7 +123,7 @@ class BBI {
     }
     _getMainHeader(opts, requestSize = 2000) {
         return __awaiter(this, void 0, void 0, function* () {
-            const { buffer } = yield this.bbi.read(Buffer.alloc(requestSize), 0, requestSize, 0, opts);
+            const { buffer } = yield this.bbi.read(buffer_1.Buffer.alloc(requestSize), 0, requestSize, 0, opts);
             const isBigEndian = this._isBigEndian(buffer);
             const ret = getParsers(isBigEndian);
             const header = ret.headerParser.parse(buffer);
@@ -171,7 +171,7 @@ class BBI {
                 unzoomedDataOffset += 1;
             }
             const off = unzoomedDataOffset - chromTreeOffset;
-            const { buffer } = yield this.bbi.read(Buffer.alloc(off), 0, off, Number(chromTreeOffset), opts);
+            const { buffer } = yield this.bbi.read(buffer_1.Buffer.alloc(off), 0, off, Number(chromTreeOffset), opts);
             const p = getParsers(isBE);
             const { keySize } = p.chromTreeParser.parse(buffer);
             const leafNodeParser = new binary_parser_1.Parser()
@@ -230,7 +230,7 @@ class BBI {
     getUnzoomedView(opts) {
         return __awaiter(this, void 0, void 0, function* () {
             const { unzoomedIndexOffset, refsByName, uncompressBufSize, isBigEndian, fileType, } = yield this.getHeader(opts);
-            return new blockView_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType);
+            return new block_view_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType);
         });
     }
     /**
@@ -241,33 +241,27 @@ class BBI {
      * @param end - The end of a region
      * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
      */
-    getFeatureStream(refName, start, end, opts = {
-        scale: 1,
-    }) {
+    getFeatureStream(refName, start, end, opts) {
         return __awaiter(this, void 0, void 0, function* () {
             yield this.getHeader(opts);
             const chrName = this.renameRefSeqs(refName);
             let view;
-            if (opts.basesPerSpan) {
-                view = yield this.getView(1 / opts.basesPerSpan, opts);
+            const { basesPerSpan, scale } = opts || {};
+            if (basesPerSpan) {
+                view = yield this.getView(1 / basesPerSpan, opts);
             }
-            else if (opts.scale) {
-                view = yield this.getView(opts.scale, opts);
+            else if (scale) {
+                view = yield this.getView(scale, opts);
             }
             else {
                 view = yield this.getView(1, opts);
             }
-            if (!view) {
-                throw new Error('unable to get block view for data');
-            }
-            return new rxjs_1.Observable((observer) => {
+            return new rxjs_1.Observable(observer => {
                 view.readWigData(chrName, start, end, observer, opts);
             });
         });
     }
-    getFeatures(refName, start, end, opts = {
-        scale: 1,
-    }) {
+    getFeatures(refName, start, end, opts) {
         return __awaiter(this, void 0, void 0, function* () {
             const ob = yield this.getFeatureStream(refName, start, end, opts);
             const ret = yield (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));

package/dist/bbi.js.map

@@ -1 +1 @@
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package/dist/bigbed.d.ts

@@ -1,11 +1,18 @@
+import AbortablePromiseCache from 'abortable-promise-cache';
 import { BBI, Feature, RequestOptions } from './bbi';
-import { BlockView } from './blockView';
+interface Index {
+    type: number;
+    fieldcount: number;
+    offset: number;
+    field: number;
+}
 export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
 export declare class BigBed extends BBI {
-    readIndicesCache: any;
-    readIndices(opts?: AbortSignal | RequestOptions): any;
-    protected getView(_scale: number, opts: RequestOptions): Promise<BlockView>;
+    readIndicesCache: AbortablePromiseCache<RequestOptions, Index[]>;
+    readIndices(opts?: RequestOptions): Promise<Index[]>;
+    protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view").BlockView>;
     private _readIndices;
     private searchExtraIndexBlocks;
     searchExtraIndex(name: string, opts?: RequestOptions): Promise<Feature[]>;
 }
+export {};

package/dist/bigbed.js

@@ -8,11 +8,23 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
+var __rest = (this && this.__rest) || function (s, e) {
+    var t = {};
+    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
+        t[p] = s[p];
+    if (s != null && typeof Object.getOwnPropertySymbols === "function")
+        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
+            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
+                t[p[i]] = s[p[i]];
+        }
+    return t;
+};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BigBed = exports.filterUndef = void 0;
+const buffer_1 = require("buffer");
 const binary_parser_1 = require("binary-parser");
 const rxjs_1 = require("rxjs");
 const operators_1 = require("rxjs/operators");
@@ -28,20 +40,15 @@ class BigBed extends bbi_1.BBI {
         super(...arguments);
         this.readIndicesCache = new abortable_promise_cache_1.default({
             cache: new quick_lru_1.default({ maxSize: 1 }),
-            fill: (args, signal) => __awaiter(this, void 0, void 0, function* () {
-                return this._readIndices(Object.assign(Object.assign({}, args), { signal }));
-            }),
+            fill: (args, signal) => this._readIndices(Object.assign(Object.assign({}, args), { signal })),
         });
     }
     readIndices(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
-        return this.readIndicesCache.get(JSON.stringify(options), options, options.signal);
+        const { signal } = opts, rest = __rest(opts, ["signal"]);
+        return this.readIndicesCache.get(JSON.stringify(rest), opts, signal);
     }
     /*
      * retrieve unzoomed view for any scale
-     * @param scale - unused
-     * @param abortSignal - an optional AbortSignal to kill operation
-     * @return promise for a BlockView
      */
     getView(_scale, opts) {
         return __awaiter(this, void 0, void 0, function* () {
@@ -56,7 +63,7 @@ class BigBed extends bbi_1.BBI {
     _readIndices(opts) {
         return __awaiter(this, void 0, void 0, function* () {
             const { extHeaderOffset, isBigEndian } = yield this.getHeader(opts);
-            const { buffer: data } = yield this.bbi.read(Buffer.alloc(64), 0, 64, Number(extHeaderOffset));
+            const { buffer: data } = yield this.bbi.read(buffer_1.Buffer.alloc(64), 0, 64, Number(extHeaderOffset));
             const le = isBigEndian ? 'big' : 'little';
             const ret = new binary_parser_1.Parser()
                 .endianess(le)
@@ -71,7 +78,7 @@ class BigBed extends bbi_1.BBI {
             }
             const blocklen = 20;
             const len = blocklen * count;
-            const { buffer } = yield this.bbi.read(Buffer.alloc(len), 0, len, Number(offset));
+            const { buffer } = yield this.bbi.read(buffer_1.Buffer.alloc(len), 0, len, Number(offset));
             const extParser = new binary_parser_1.Parser()
                 .endianess(le)
                 .int16('type')
@@ -98,12 +105,12 @@ class BigBed extends bbi_1.BBI {
         return __awaiter(this, void 0, void 0, function* () {
             const { isBigEndian } = yield this.getHeader(opts);
             const indices = yield this.readIndices(opts);
-            if (!indices.length) {
+            if (indices.length === 0) {
                 return [];
             }
             const locs = indices.map((index) => __awaiter(this, void 0, void 0, function* () {
                 const { offset, field } = index;
-                const { buffer: data } = yield this.bbi.read(Buffer.alloc(32), 0, 32, Number(offset), opts);
+                const { buffer: data } = yield this.bbi.read(buffer_1.Buffer.alloc(32), 0, 32, Number(offset), opts);
                 const le = isBigEndian ? 'big' : 'little';
                 const p = new binary_parser_1.Parser()
                     .endianess(le)
@@ -143,7 +150,7 @@ class BigBed extends bbi_1.BBI {
                 const bptReadNode = (nodeOffset) => __awaiter(this, void 0, void 0, function* () {
                     const val = Number(nodeOffset);
                     const len = 4 + blockSize * (keySize + valSize);
-                    const { buffer } = yield this.bbi.read(Buffer.alloc(len), 0, len, val, opts);
+                    const { buffer } = yield this.bbi.read(buffer_1.Buffer.alloc(len), 0, len, val, opts);
                     const node = bpt.parse(buffer);
                     if (node.leafkeys) {
                         let lastOffset;
@@ -180,7 +187,7 @@ class BigBed extends bbi_1.BBI {
     searchExtraIndex(name, opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
             const blocks = yield this.searchExtraIndexBlocks(name, opts);
-            if (!blocks.length) {
+            if (blocks.length === 0) {
                 return [];
             }
             const view = yield this.getUnzoomedView(opts);
@@ -188,8 +195,8 @@ class BigBed extends bbi_1.BBI {
                 return new rxjs_1.Observable(observer => {
                     view.readFeatures(observer, [block], opts);
                 }).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
-                    for (let i = 0; i < x.length; i += 1) {
-                        x[i].field = block.field;
+                    for (const element of x) {
+                        element.field = block.field;
                     }
                     return x;
                 }));

package/dist/bigbed.js.map

@@ -1 +1 @@
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package/dist/bigwig.d.ts

@@ -1,4 +1,4 @@
-import { BlockView } from './blockView';
+import { BlockView } from './block-view';
 import { BBI, RequestOptions } from './bbi';
 export declare class BigWig extends BBI {
     /**