@gmod/bbi 1.0.28 → 1.0.32

package/CHANGELOG.md

@@ -1,14 +1,30 @@
-## [1.0.28](https://github.com/GMOD/bbi-js/compare/v1.0.27...v1.0.28) (2020-01-28)
+## [1.0.32](https://github.com/GMOD/bbi-js/compare/v1.0.31...v1.0.32) (2022-02-16)
+
+
+
+- Use pako to decode on command line instead of using zlib to avoid need to
+  manually polyfill zlib
+
+## [1.0.31](https://github.com/GMOD/bbi-js/compare/v1.0.30...v1.0.31) (2021-12-14)
+
+- Add esm module builds with less babelification for smaller bundle sizes
+
+## [1.0.30](https://github.com/GMOD/bbi-js/compare/v1.0.29...v1.0.30) (2020-06-25)
+
+- Use abortable-promise-cache instead of abortable-memoize
+- Allow opts parameter to getHeader instead of just abortsignal
 
+## [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
+
+## [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
 - Typescript only release change
 
 ## [1.0.27](https://github.com/GMOD/bbi-js/compare/v1.0.26...v1.0.27) (2020-01-10)
 
-
-
 - Reduce number of requests needed on initial header
 - Add definedFieldCount to the returned Header
 
@@ -16,8 +32,6 @@ 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
 
 ## [1.0.25](https://github.com/GMOD/bbi-js/compare/v1.0.24...v1.0.25) (2019-11-03)
@@ -26,138 +40,97 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.24](https://github.com/GMOD/bbi-js/compare/v1.0.23...v1.0.24) (2019-10-29)
 
-
-
 - Fix the uniqueIds generated via the bigbed features
 
 ## [1.0.23](https://github.com/GMOD/bbi-js/compare/v1.0.22...v1.0.23) (2019-10-06)
 
-
 - Small refactor of `filehandle.read()` to make it more robust
 
-
 ## [1.0.22](https://github.com/GMOD/bbi-js/compare/v1.0.21...v1.0.22) (2019-06-13)
 
-
-
 - Bump generic-filehandle
 - Add more checks for abort signal to allow early bailing
 
 ## [1.0.21](https://github.com/GMOD/bbi-js/compare/v1.0.20...v1.0.21) (2019-05-09)
 
-
-
 - Add fix for reading files with greater than 256 contigs
 
 ## [1.0.20](https://github.com/GMOD/bbi-js/compare/v1.0.19...v1.0.20) (2019-05-06)
 
-
-
 - Add fix that prevented accessing the lowest zoom/reduction level
 
 ## [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!
 
 ## [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
 
 ## [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])
 
 ## [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
 
 ## [1.0.15](https://github.com/GMOD/bbi-js/compare/v1.0.14...v1.0.15) (2019-04-18)
 
-
-
 - Make important performance improvement for BigWig data
 
 ## [1.0.14](https://github.com/GMOD/bbi-js/compare/v1.0.12...v1.0.14) (2019-04-17)
 
-
-
 - Improve documentation for integration with @gmod/bed@2
 - Fix some cases where abortSignal was passed incorrectly to filehandle
 
 ## [1.0.13](https://github.com/GMOD/bbi-js/compare/v1.0.12...v1.0.13) (2019-04-14)
 
-
-
 - Added uniqueId to objects returned from BigBed to avoid issue with duplicates
 
 ## [1.0.12](https://github.com/GMOD/bbi-js/compare/v1.0.11...v1.0.12) (2019-04-12)
 
 - Fix returning bigbed objects on empty regions
 
-
 ## [1.0.11](https://github.com/GMOD/bbi-js/compare/v1.0.10...v1.0.11) (2019-04-10)
 
-
-
 - Removed polyfill of Array.prototype.flat which modifies global scope
 
 ## [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)
 - 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!)
 - Fix some type errors on the range class
 - Correct using span on fixed size wiggle types
 
 ## [1.0.8](https://github.com/GMOD/bbi-js/compare/v1.0.7...v1.0.8) (2019-04-01)
 
-
-
 - Fix @babel/runtime in deployed package
 - Bugfix to the url argument to the BigWig/BigBed
 
 ## [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 typescript backend for better processing
 
 ## [1.0.6](https://github.com/GMOD/bbi-js/compare/v1.0.5...v1.0.6) (2019-03-15)
 
-
-
 - Fix issue with fixed step and variable step bigwig files not working at all
 
 ## [1.0.5](https://github.com/GMOD/bbi-js/compare/v1.0.4...v1.0.5) (2019-03-07)
 
-
-
 - Fix issue with jest being in deps instead of devDeps
 
 ## [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
 - Consistently apply start/end coordinate filters at different zoom levels
 
@@ -167,19 +140,13 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.2](https://github.com/GMOD/bbi-js/compare/v1.0.1...v1.0.2) (2019-01-24)
 
-
-
 - Added regenerator-runtime to babel dist compilation
 
 ## [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')
 
 # 1.0.0 (2019-01-23)
 
-
-
 - Initial version
 - Has support for bigwig and bigbed files

package/README.md

@@ -1,8 +1,8 @@
 # bbi-js
 
 [![NPM version](https://img.shields.io/npm/v/@gmod/bbi.svg?style=flat-square)](https://npmjs.org/package/@gmod/bbi)
-[![Build Status](https://img.shields.io/travis/GMOD/bbi-js/master.svg?style=flat-square)](https://travis-ci.org/GMOD/bbi-js) [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/bbi-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/bbi-js/branch/master)
-
+[![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/bbi-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/bbi-js/branch/master)
+[![Build Status](https://img.shields.io/github/workflow/status/GMOD/bbi-js/Push/master?logo=github&style=flat-query)](https://github.com/GMOD/bbi-js/actions?query=branch%3Amaster+workflow%3APush+)
 
 A parser for bigwig and bigbed file formats
 
@@ -11,14 +11,36 @@ A parser for bigwig and bigbed file formats
 If using locally
 
     const {BigWig} = require('@gmod/bbi');
-    const ti = new BigWig({
+    const file = new BigWig({
       path: 'volvox.bw'
     });
     (async () => {
-      await ti.getHeader();
-      const feats = await ti.getFeatures('chr1', 0, 100, { scale: 1 });
+      await file.getHeader();
+      const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 });
     })();
 
+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/
+
+    const {BigWig} = require('@gmod/bbi');
+    const {RemoteFile} = require('generic-filehandle')
+
+    // if running in the browser, RemoteFile will use the the global fetch
+    const file = new BigWig({
+      filehandle: new RemoteFile('volvox.bw')
+    });
+
+
+    // if running under node.js you must supply the fetch function to RemoteFile
+    const fetch = require('node-fetch')
+    const file = new BigWig({
+      filehandle: new RemoteFile('volvox.bw', {fetch})
+    });
+
+    (async () => {
+      await file.getHeader();
+      const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 });
+    })();
 
 ## Documentation
 
@@ -26,22 +48,20 @@ If using locally
 
 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
-
+- 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
 
 ### BigWig
 
 #### getFeatures(refName, start, end, opts)
 
-* 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.basesPerScale - optional, inverse of opts.scale e.g. bpPerPx
-* opts.signal - optional, an AbortSignal to halt processing
-
+- 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.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.
 
@@ -53,10 +73,9 @@ Example:
     // no conversion to 1-based as in wig is done)
     // note refseq is not returned on the object, it is clearly chr1 from the query though
 
-
 ### 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, ... },
@@ -66,7 +85,6 @@ Here is what the reductionLevel structure looks like in a file. The zoomLevel th
         { reductionLevel: 40960, ... },
         { reductionLevel: 163840, ... } ]
 
-
 #### getFeatureStream(refName, start, end, opts)
 
 Same as getFeatures but returns an RxJS observable stream, useful for very large queries
@@ -84,10 +102,10 @@ Same as getFeatures but returns an RxJS observable stream, useful for very large
 
 #### getFeatures(refName, start, end, opts)
 
-* 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.signal - optional, an AbortSignal to halt processing
+- 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.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
 
@@ -108,8 +126,7 @@ Returns a Promise to an array of Features, with an extra field indicating the fi
 
 ### 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
 
 ```js
     import {BigBed} from '@gmod/bbi'
@@ -156,7 +173,6 @@ Features after parsing with @gmod/bed:
         spID: 'AL137655' }
 ```
 
-
 ## 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).
@@ -164,4 +180,3 @@ This package was written with funding from the [NHGRI](http://genome.gov) as par
 ## License
 
 MIT © [Colin Diesh](https://github.com/cmdcolin)
-

package/dist/bbi.d.ts

@@ -42,15 +42,16 @@ export interface Header {
         [key: number]: RefInfo;
     };
 }
-declare class AbortAwareCache {
-    private cache;
-    abortableMemoize(fn: (signal?: AbortSignal) => Promise<any>): (signal?: AbortSignal) => Promise<any>;
+export interface RequestOptions {
+    signal?: AbortSignal;
+    headers?: Record<string, string>;
+    [key: string]: unknown;
 }
 export declare abstract class BBI {
     protected bbi: GenericFilehandle;
-    protected headerCache: AbortAwareCache;
+    protected headerCache: any;
     protected renameRefSeqs: (a: string) => string;
-    getHeader: (abortSignal?: AbortSignal) => Promise<Header>;
+    getHeader(opts?: RequestOptions | AbortSignal): any;
     constructor(options?: {
         filehandle?: GenericFilehandle;
         path?: string;
@@ -61,8 +62,8 @@ export declare abstract class BBI {
     private _getMainHeader;
     private _isBigEndian;
     private _readChromTree;
-    protected getUnzoomedView(abortSignal?: AbortSignal): Promise<BlockView>;
-    protected abstract getView(scale: number, abortSignal?: AbortSignal): Promise<BlockView>;
+    protected getUnzoomedView(opts: RequestOptions): Promise<BlockView>;
+    protected abstract getView(scale: number, opts: RequestOptions): Promise<BlockView>;
     /**
      * Gets features from a BigWig file
      *
@@ -71,15 +72,13 @@ export declare abstract 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: string, start: number, end: number, opts?: {
-        basesPerSpan?: number;
+    getFeatureStream(refName: string, start: number, end: number, opts?: RequestOptions & {
         scale?: number;
-        signal?: AbortSignal;
-    }): Promise<Observable<Feature[]>>;
-    getFeatures(refName: string, start: number, end: number, opts?: {
         basesPerSpan?: number;
+    }): Promise<Observable<Feature[]>>;
+    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions & {
         scale?: number;
-        signal?: AbortSignal;
+        basesPerSpan?: number;
     }): Promise<Feature[]>;
 }
 export {};