@gmod/bbi 2.0.5 → 3.0.1

package/CHANGELOG.md

@@ -1,12 +1,23 @@
-## [2.0.5](https://github.com/GMOD/bbi-js/compare/v2.0.4...v2.0.5) (2022-12-17)
+## [3.0.1](https://github.com/GMOD/bbi-js/compare/v3.0.0...v3.0.1) (2023-04-21)
 
 
+### Features
 
-- Cleanup package.json and README
+* explicit buffer import ([#53](https://github.com/GMOD/bbi-js/issues/53)) ([2699c98](https://github.com/GMOD/bbi-js/commit/2699c983dea380bbb56773058ba3f233c833d9c8))
 
-## [2.0.4](https://github.com/GMOD/bbi-js/compare/v2.0.3...v2.0.4) (2022-10-15)
 
 
+- 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
+
+## [2.0.5](https://github.com/GMOD/bbi-js/compare/v2.0.4...v2.0.5) (2022-12-17)
+
+- Cleanup package.json and README
+
+## [2.0.4](https://github.com/GMOD/bbi-js/compare/v2.0.3...v2.0.4) (2022-10-15)
 
 - Use plain TextDecoder for decoding autoSql
 
@@ -36,7 +47,9 @@
 
 ### 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
@@ -62,11 +75,13 @@
 
 ## [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)
@@ -78,11 +93,13 @@ 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)
 
@@ -107,22 +124,26 @@ 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)
 
@@ -147,12 +168,15 @@ 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
 
@@ -164,7 +188,8 @@ 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)
@@ -177,7 +202,8 @@ 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)
@@ -190,7 +216,8 @@ 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

@@ -10,37 +10,41 @@ A parser for bigwig and bigbed file formats
 
 If using locally
 
-    const {BigWig} = require('@gmod/bbi');
-    const file = new BigWig({
-      path: 'volvox.bw'
-    });
-    (async () => {
-      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')
-    });
-
+```typescript
+const { BigWig } = require('@gmod/bbi')
+const file = new BigWig({
+  path: 'volvox.bw',
+})
+;(async () => {
+  await file.getHeader()
+  const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 })
+})()
+```
 
-    // 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})
-    });
+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/
 
-    (async () => {
-      await file.getHeader();
-      const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 });
-    })();
+```typescript
+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
 
@@ -50,7 +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
 
@@ -59,23 +67,32 @@ 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:
 
-    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
-    // 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
+```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
+// 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, ... },
@@ -87,16 +104,23 @@ 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
-
-    const observer = await bigwig.getFeatureStream('chr1', 0, 100)
-    observer.subscribe(chunk => {
-       /* chunk contains array of features with start, end, score */
-    }, error => {
-       /* process error */
-    }, () => {
-       /* completed */
-    })
+Same as getFeatures but returns an RxJS observable stream, useful for very large
+queries
+
+```typescript
+const observer = await bigwig.getFeatureStream('chr1', 0, 100)
+observer.subscribe(
+  chunk => {
+    /* chunk contains array of features with start, end, score */
+  },
+  error => {
+    /* process error */
+  },
+  () => {
+    /* completed */
+  },
+)
+```
 
 ### BigBed
 
@@ -107,7 +131,8 @@ Same as getFeatures but returns an RxJS observable stream, useful for very large
 - 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)
 
@@ -115,67 +140,84 @@ 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
-
-```js
-    import {BigBed} from '@gmod/bbi'
-    import BED from '@gmod/bed'
-
-    const ti = new BigBed({
-      filehandle: new LocalFile(require.resolve('./data/hg18.bb')),
-    })
-    const {autoSql} = await ti.getHeader()
-    const feats = await ti.getFeatures('chr7', 0, 100000)
-    const parser = new BED({autoSql})
-    const lines = feats.map(f => {
-        const { start, end, rest, uniqueId } = f
-        return parser.parseLine(`chr7\t${start}\t${end}\t${rest}, { uniqueId })\
-    })
-    // @gmod/bbi returns features with {uniqueId, start, end, rest}
-    // we reconstitute this as a line for @gmod/bed with a template string
-    // note: the uniqueId is based on file offsets and helps to deduplicate exact feature copies if they exist
+The BigBed line contents are returned as a raw text line e.g. {start: 0,
+end:100, rest: "ENST00000456328.2\t1000\t..."} where "rest" contains tab
+delimited text for the fields from 4 and on in the BED format. Since BED files
+from BigBed format often come with autoSql (a description of all the columns) it
+can be useful to parse it with BED parser that can handle autoSql. The rest line
+can be parsed by the @gmod/bed module, which is not by default integrated with
+this module, but can be combined with it as follows
+
+```typescript
+import {BigBed} from '@gmod/bbi'
+import BED from '@gmod/bed'
+
+const ti = new BigBed({
+  filehandle: new LocalFile(require.resolve('./data/hg18.bb')),
+})
+const {autoSql} = await ti.getHeader()
+const feats = await ti.getFeatures('chr7', 0, 100000)
+const parser = new BED({autoSql})
+const lines = feats.map(f => {
+    const { start, end, rest, uniqueId } = f
+    return parser.parseLine(`chr7\t${start}\t${end}\t${rest}, { uniqueId })\
+})
+// @gmod/bbi returns features with {uniqueId, start, end, rest}
+// we reconstitute this as a line for @gmod/bed with a template string
+// note: the uniqueId is based on file offsets and helps to deduplicate exact feature copies if they exist
 ```
 
 Features before parsing with @gmod/bed:
 
-```
-      { chromId: 0,
-        start: 64068,
-        end: 64107,
-        rest: 'uc003sil.1\t0\t-\t64068\t64068\t255,0,0\t.\tDQ584609',
-        uniqueId: 'bb-171' }
+```json
+{
+  "chromId": 0,
+  "start": 64068,
+  "end": 64107,
+  "rest": "uc003sil.1\t0\t-\t64068\t64068\t255,0,0\t.\tDQ584609",
+  "uniqueId": "bb-171"
+}
 ```
 
 Features after parsing with @gmod/bed:
 
-```
-      { uniqueId: 'bb-0',
-        chrom: 'chr7',
-        chromStart: 54028,
-        chromEnd: 73584,
-        name: 'uc003sii.2',
-        score: 0,
-        strand: -1,
-        thickStart: 54028,
-        thickEnd: 54028,
-        reserved: '255,0,0',
-        spID: 'AL137655' }
+```json
+{
+  "uniqueId": "bb-0",
+  "chrom": "chr7",
+  "chromStart": 54028,
+  "chromEnd": 73584,
+  "name": "uc003sii.2",
+  "score": 0,
+  "strand": -1,
+  "thickStart": 54028,
+  "thickEnd": 54028,
+  "reserved": "255,0,0",
+  "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).
+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.js

@@ -10,6 +10,7 @@ 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");
@@ -78,6 +79,20 @@ function getParsers(isBE) {
     };
 }
 class BBI {
+    /* fetch and parse header information from a bigwig or bigbed file
+     * @param abortSignal - abort the operation, can be null
+     * @return a Header object
+     */
+    getHeader(opts = {}) {
+        const options = 'aborted' in opts ? { signal: opts } : opts;
+        if (!this.headerP) {
+            this.headerP = this._getHeader(options).catch(e => {
+                this.headerP = undefined;
+                throw e;
+            });
+        }
+        return this.headerP;
+    }
     /*
      * @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
      * @param path - a Local file path as a string
@@ -100,20 +115,6 @@ class BBI {
             throw new Error('no file given');
         }
     }
-    /* fetch and parse header information from a bigwig or bigbed file
-     * @param abortSignal - abort the operation, can be null
-     * @return a Header object
-     */
-    getHeader(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
-        if (!this.headerP) {
-            this.headerP = this._getHeader(options).catch(e => {
-                this.headerP = undefined;
-                throw e;
-            });
-        }
-        return this.headerP;
-    }
     _getHeader(opts) {
         return __awaiter(this, void 0, void 0, function* () {
             const header = yield this._getMainHeader(opts);
@@ -123,7 +124,7 @@ 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 +172,7 @@ 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()
@@ -270,10 +271,8 @@ class BBI {
     }) {
         return __awaiter(this, void 0, void 0, function* () {
             const ob = yield this.getFeatureStream(refName, start, end, opts);
-            const ret = yield ob
-                .pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)))
-                .toPromise();
-            return ret || [];
+            const ret = yield (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
+            return ret.flat();
         });
     }
 }

package/dist/bbi.js.map

@@ -1 +1 @@
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package/dist/bigbed.js

@@ -13,6 +13,7 @@ var __importDefault = (this && this.__importDefault) || function (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");
@@ -56,7 +57,7 @@ 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 +72,7 @@ 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')
@@ -103,7 +104,7 @@ class BigBed extends bbi_1.BBI {
             }
             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 +144,7 @@ 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;
@@ -194,7 +195,7 @@ class BigBed extends bbi_1.BBI {
                     return x;
                 }));
             });
-            const ret = yield (0, rxjs_1.merge)(...res).toPromise();
+            const ret = yield (0, rxjs_1.firstValueFrom)((0, rxjs_1.merge)(...res));
             return ret.filter(f => { var _a; return ((_a = f.rest) === null || _a === void 0 ? void 0 : _a.split('\t')[(f.field || 0) - 3]) === name; });
         });
     }

package/dist/bigbed.js.map

@@ -1 +1 @@
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package/dist/blockView.js

@@ -13,6 +13,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BlockView = void 0;
+const buffer_1 = require("buffer");
 const binary_parser_1 = require("binary-parser");
 const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
@@ -139,7 +140,7 @@ class BlockView {
             fill: (requestData, signal) => __awaiter(this, void 0, void 0, function* () {
                 const len = Number(requestData.length);
                 const off = Number(requestData.offset);
-                const { buffer } = yield this.bbi.read(Buffer.alloc(len), 0, len, off, {
+                const { buffer } = yield this.bbi.read(buffer_1.Buffer.alloc(len), 0, len, off, {
                     signal,
                 });
                 return buffer;
@@ -162,7 +163,7 @@ class BlockView {
                 }
                 const request = { chrId, start, end };
                 if (!this.cirTreePromise) {
-                    this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, Number(cirTreeOffset), opts);
+                    this.cirTreePromise = bbi.read(buffer_1.Buffer.alloc(48), 0, 48, Number(cirTreeOffset), opts);
                 }
                 const { buffer } = yield this.cirTreePromise;
                 const cirBlockSize = isBigEndian

package/dist/blockView.js.map

@@ -1 +1 @@
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package/dist/unzip-pako.d.ts

@@ -1,2 +1,3 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 export declare function unzip(input: Buffer): Uint8Array;

package/dist/unzip-pako.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;;AAAA,+BAAiC;AAEjC,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,IAAA,iBAAU,EAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC;AAFD,sBAEC"}
+{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;;AACA,+BAAiC;AAEjC,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,IAAA,iBAAU,EAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC;AAFD,sBAEC"}

package/esm/bbi.js

@@ -1,7 +1,8 @@
+import { Buffer } from 'buffer';
 import { Parser } from 'binary-parser';
 import { LocalFile, RemoteFile } from 'generic-filehandle';
-import { Observable } from 'rxjs';
-import { reduce } from 'rxjs/operators';
+import { firstValueFrom, Observable } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 import { BlockView } from './blockView';
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
@@ -66,6 +67,20 @@ function getParsers(isBE) {
     };
 }
 export class BBI {
+    /* fetch and parse header information from a bigwig or bigbed file
+     * @param abortSignal - abort the operation, can be null
+     * @return a Header object
+     */
+    getHeader(opts = {}) {
+        const options = 'aborted' in opts ? { signal: opts } : opts;
+        if (!this.headerP) {
+            this.headerP = this._getHeader(options).catch(e => {
+                this.headerP = undefined;
+                throw e;
+            });
+        }
+        return this.headerP;
+    }
     /*
      * @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
      * @param path - a Local file path as a string
@@ -88,20 +103,6 @@ export class BBI {
             throw new Error('no file given');
         }
     }
-    /* fetch and parse header information from a bigwig or bigbed file
-     * @param abortSignal - abort the operation, can be null
-     * @return a Header object
-     */
-    getHeader(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
-        if (!this.headerP) {
-            this.headerP = this._getHeader(options).catch(e => {
-                this.headerP = undefined;
-                throw e;
-            });
-        }
-        return this.headerP;
-    }
     async _getHeader(opts) {
         const header = await this._getMainHeader(opts);
         const chroms = await this._readChromTree(header, opts);
@@ -247,10 +248,8 @@ export class BBI {
         scale: 1,
     }) {
         const ob = await this.getFeatureStream(refName, start, end, opts);
-        const ret = await ob
-            .pipe(reduce((acc, curr) => acc.concat(curr)))
-            .toPromise();
-        return ret || [];
+        const ret = await firstValueFrom(ob.pipe(toArray()));
+        return ret.flat();
     }
 }
 //# sourceMappingURL=bbi.js.map

package/esm/bbi.js.map

@@ -1 +1 @@
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package/esm/bigbed.js

@@ -1,5 +1,6 @@
+import { Buffer } from 'buffer';
 import { Parser } from 'binary-parser';
-import { Observable, merge } from 'rxjs';
+import { Observable, merge, firstValueFrom } from 'rxjs';
 import { map, reduce } from 'rxjs/operators';
 import AbortablePromiseCache from 'abortable-promise-cache';
 import QuickLRU from 'quick-lru';
@@ -171,7 +172,7 @@ export class BigBed extends BBI {
                 return x;
             }));
         });
-        const ret = await merge(...res).toPromise();
+        const ret = await firstValueFrom(merge(...res));
         return ret.filter(f => { var _a; return ((_a = f.rest) === null || _a === void 0 ? void 0 : _a.split('\t')[(f.field || 0) - 3]) === name; });
     }
 }

package/esm/bigbed.js.map

@@ -1 +1 @@
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package/esm/blockView.js

@@ -1,3 +1,4 @@
+import { Buffer } from 'buffer';
 import { Parser } from 'binary-parser';
 import AbortablePromiseCache from 'abortable-promise-cache';
 import QuickLRU from 'quick-lru';

package/esm/blockView.js.map

@@ -1 +1 @@
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package/esm/unzip-pako.d.ts

@@ -1,2 +1,3 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 export declare function unzip(input: Buffer): Uint8Array;

package/esm/unzip-pako.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AAEjC,MAAM,UAAU,KAAK,CAAC,KAAa;IACjC,OAAO,UAAU,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}
+{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AAEjC,MAAM,UAAU,KAAK,CAAC,KAAa;IACjC,OAAO,UAAU,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;AACtC,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "2.0.5",
+  "version": "3.0.1",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -46,28 +46,28 @@
     "generic-filehandle": "^3.0.0",
     "pako": "^2.0.0",
     "quick-lru": "^4.0.0",
-    "rxjs": "^6.5.2"
+    "rxjs": "^7.8.0"
   },
   "devDependencies": {
     "@gmod/bed": "^2.1.2",
-    "@types/jest": "^29.1.2",
+    "@types/jest": "^29.2.4",
     "@types/long": "^5.0.0",
-    "@types/node": "^18.11.0",
+    "@types/node": "^18.11.15",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.40.0",
-    "@typescript-eslint/parser": "^5.40.0",
+    "@typescript-eslint/eslint-plugin": "^5.46.1",
+    "@typescript-eslint/parser": "^5.46.1",
     "cross-fetch": "^3.0.2",
-    "eslint": "^8.25.0",
+    "eslint": "^8.29.0",
     "eslint-config-prettier": "^8.3.0",
     "eslint-plugin-import": "^2.25.3",
     "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^29.2.0",
-    "jest-environment-jsdom": "^29.2.0",
-    "prettier": "^2.5.1",
+    "jest": "^29.3.1",
+    "jest-environment-jsdom": "^29.3.1",
+    "prettier": "^2.8.1",
     "rimraf": "^3.0.2",
     "standard-changelog": "^2.0.11",
     "ts-jest": "^29.0.3",
-    "typescript": "^4.8.4"
+    "typescript": "^4.9.4"
   },
   "publishConfig": {
     "access": "public"

package/src/bbi.ts

@@ -1,7 +1,8 @@
+import { Buffer } from 'buffer'
 import { Parser } from 'binary-parser'
 import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
-import { Observable, Observer } from 'rxjs'
-import { reduce } from 'rxjs/operators'
+import { firstValueFrom, Observable, Observer } from 'rxjs'
+import { toArray } from 'rxjs/operators'
 import { BlockView } from './blockView'
 
 const BIG_WIG_MAGIC = -2003829722
@@ -367,12 +368,10 @@ export abstract class BBI {
     opts: RequestOptions & { scale?: number; basesPerSpan?: number } = {
       scale: 1,
     },
-  ): Promise<Feature[]> {
+  ) {
     const ob = await this.getFeatureStream(refName, start, end, opts)
 
-    const ret = await ob
-      .pipe(reduce((acc, curr) => acc.concat(curr)))
-      .toPromise()
-    return ret || []
+    const ret = await firstValueFrom(ob.pipe(toArray()))
+    return ret.flat()
   }
 }

package/src/bigbed.ts

@@ -1,5 +1,6 @@
+import { Buffer } from 'buffer'
 import { Parser } from 'binary-parser'
-import { Observable, merge } from 'rxjs'
+import { Observable, merge, firstValueFrom } from 'rxjs'
 import { map, reduce } from 'rxjs/operators'
 import AbortablePromiseCache from 'abortable-promise-cache'
 import QuickLRU from 'quick-lru'
@@ -216,10 +217,7 @@ export class BigBed extends BBI {
    * @param opts - a SearchOptions argument with optional signal
    * @return a Promise for an array of Feature
    */
-  public async searchExtraIndex(
-    name: string,
-    opts: RequestOptions = {},
-  ): Promise<Feature[]> {
+  public async searchExtraIndex(name: string, opts: RequestOptions = {}) {
     const blocks = await this.searchExtraIndexBlocks(name, opts)
     if (!blocks.length) {
       return []
@@ -238,7 +236,7 @@ export class BigBed extends BBI {
         }),
       )
     })
-    const ret = await merge(...res).toPromise()
+    const ret = await firstValueFrom(merge(...res))
     return ret.filter(f => f.rest?.split('\t')[(f.field || 0) - 3] === name)
   }
 }

package/src/blockView.ts

@@ -1,3 +1,4 @@
+import { Buffer } from 'buffer'
 import { Observer } from 'rxjs'
 import { Parser } from 'binary-parser'
 import AbortablePromiseCache from 'abortable-promise-cache'

package/src/unzip-pako.ts

@@ -1,3 +1,4 @@
+import { Buffer } from 'buffer'
 import { inflateRaw } from 'pako'
 
 export function unzip(input: Buffer) {