@gmod/bbi 8.1.1 → 9.0.0

package/CHANGELOG.md

@@ -1,3 +1,7 @@
+# [9.0.0](https://github.com/GMOD/bbi-js/compare/v8.1.2...v9.0.0) (2026-03-20)
+
+## [8.1.2](https://github.com/GMOD/bbi-js/compare/v8.1.1...v8.1.2) (2026-03-20)
+
 ## [8.1.1](https://github.com/GMOD/bbi-js/compare/v8.1.0...v8.1.1) (2026-01-06)
 
 

package/README.md

@@ -6,47 +6,69 @@
 
 A parser for bigwig and bigbed file formats
 
+## Installation
+
+```bash
+npm install @gmod/bbi
+```
+
 ## Usage
 
-If using locally
+### Local files
 
 ```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 })
-})()
+import { BigWig } from '@gmod/bbi'
+
+const file = new BigWig({ path: 'volvox.bw' })
+const header = await file.getHeader()
+const features = await file.getFeatures('chr1', 0, 100, { scale: 1 })
 ```
 
-If using remotely, you can use it in combination with generic-filehandle2 or
-your own implementation of something like generic-filehandle2
-https://github.com/GMOD/generic-filehandle2/
+### Remote files
+
+You can use the `url` option or provide a custom filehandle from
+[generic-filehandle2](https://github.com/GMOD/generic-filehandle2/):
 
 ```typescript
-const { BigWig } = require('@gmod/bbi')
-const { RemoteFile } = require('generic-filehandle2')
+import { BigWig } from '@gmod/bbi'
 
-// if running in the browser or newer versions of node.js, RemoteFile will use
-// the the global fetch
+// Using url directly
 const file = new BigWig({
-  filehandle: new RemoteFile('volvox.bw'),
+  url: 'https://example.com/file.bw',
 })
 
-// old versions of node.js without a global fetch, supply custom fetch function
-const fetch = require('node-fetch')
+// Or with a custom RemoteFile instance
+import { RemoteFile } from 'generic-filehandle2'
+
 const file = new BigWig({
-  filehandle: new RemoteFile('volvox.bw', { fetch }),
+  filehandle: new RemoteFile('https://example.com/file.bw'),
 })
 
-;(async () => {
-  await file.getHeader()
-  const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 })
-})()
+const header = await file.getHeader()
+const features = await file.getFeatures('chr1', 0, 100, { scale: 1 })
 ```
 
+### Using without npm (CDN)
+
+You can use this library directly in the browser without npm by importing from
+an ESM CDN like [esm.sh](https://esm.sh) (note that we don't necessarily
+recommend CDN usage, it is just a way to test things easily):
+
+```html
+<script type="module">
+  import { BigWig } from 'https://esm.sh/@gmod/bbi'
+
+  const file = new BigWig({
+    url: 'https://example.com/file.bw',
+  })
+  const header = await file.getHeader()
+  const features = await file.getFeatures('chr1', 0, 100)
+  console.log(features)
+</script>
+```
+
+See the [example](./example/) folder for a complete working demo.
+
 ## Documentation
 
 ### BigWig/BigBed constructors
@@ -103,26 +125,6 @@ reductionLevel<2/opts.scale) when scanning backwards through this list
         { reductionLevel: 40960, ... },
         { reductionLevel: 163840, ... } ]
 
-#### getFeatureStream(refName, start, end, opts)
-
-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 */
-  },
-)
-```
-
 #### getFeaturesAsArrays(refName, start, end, opts)
 
 Same parameters as getFeatures, but returns typed arrays instead of an array of
@@ -200,10 +202,6 @@ they exist.
 returns a promise to an array of features. no concept of zoom levels is used
 with bigwig data
 
-#### getFeatureStream(refName, start, end, opts)
-
-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",
@@ -233,11 +231,9 @@ this module, but can be combined with it as follows
 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 file = new BigBed({ path: './data/hg18.bb' })
+const { autoSql } = await file.getHeader()
+const feats = await file.getFeatures('chr7', 0, 100000)
 const parser = new BED({ autoSql })
 const lines = feats.map(f => {
   const { start, end, rest, uniqueId } = f

package/dist/array-feature-view.d.ts

@@ -18,5 +18,8 @@ export declare class ArrayFeatureView {
     minScore(i: number): number | undefined;
     maxScore(i: number): number | undefined;
     id(i: number): string;
-    get(i: number, key: string): string | number | boolean | undefined;
+    get(i: number, key: 'refName' | 'source'): string;
+    get(i: number, key: 'start' | 'end' | 'score' | 'minScore' | 'maxScore'): number | undefined;
+    get(i: number, key: 'summary'): boolean;
+    get(i: number, key: string): any;
 }

package/dist/array-feature-view.js.map

@@ -1 +1 @@
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+{"version":3,"file":"array-feature-view.js","sourceRoot":"","sources":["../src/array-feature-view.ts"],"names":[],"mappings":";;;AAEA,MAAa,gBAAgB;IACX,MAAM,CAAY;IAClB,IAAI,CAAY;IAChB,MAAM,CAAc;IACpB,SAAS,CAA0B;IACnC,SAAS,CAA0B;IACnC,SAAS,CAAS;IAC1B,OAAO,CAAQ;IACf,QAAQ,CAAQ;IAExB,YACE,MAAkD,EAClD,MAAc,EACd,OAAe;QAEf,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,MAAM,CAAA;QAC3B,IAAI,CAAC,IAAI,GAAG,MAAM,CAAC,IAAI,CAAA;QACvB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,MAAM,CAAA;QAC3B,IAAI,CAAC,SAAS,GAAG,MAAM,CAAC,SAAS,CAAA;QACjC,IAAI,CAAC,SAAS,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;QAChE,IAAI,CAAC,SAAS,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;QAChE,IAAI,CAAC,OAAO,GAAG,MAAM,CAAA;QACrB,IAAI,CAAC,QAAQ,GAAG,OAAO,CAAA;IACzB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,CAAA;IAC3B,CAAC;IAED,IAAI,MAAM;QACR,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IAED,IAAI,OAAO;QACT,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,KAAK,CAAC,CAAS;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAE,CAAA;IACxB,CAAC;IAED,GAAG,CAAC,CAAS;QACX,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,CAAE,CAAA;IACtB,CAAC;IAED,KAAK,CAAC,CAAS;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAE,CAAA;IACxB,CAAC;IAED,QAAQ,CAAC,CAAS;QAChB,OAAO,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,CAAA;IAC5B,CAAC;IAED,QAAQ,CAAC,CAAS;QAChB,OAAO,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,CAAA;IAC5B,CAAC;IAED,EAAE,CAAC,CAAS;QACV,OAAO,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,QAAQ,IAAI,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAA;IAC7E,CAAC;IAUD,GAAG,CAAC,CAAS,EAAE,GAAW;QACxB,QAAQ,GAAG,EAAE,CAAC;YACZ,KAAK,OAAO;gBACV,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;YACvB,KAAK,KAAK;gBACR,OAAO,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACrB,KAAK,OAAO;gBACV,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;YACvB,KAAK,SAAS;gBACZ,OAAO,IAAI,CAAC,QAAQ,CAAA;YACtB,KAAK,QAAQ;gBACX,OAAO,IAAI,CAAC,OAAO,CAAA;YACrB,KAAK,UAAU;gBACb,OAAO,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,CAAA;YAC5B,KAAK,UAAU;gBACb,OAAO,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,CAAA;YAC5B,KAAK,SAAS;gBACZ,OAAO,IAAI,CAAC,SAAS,CAAA;YACvB;gBACE,OAAO,SAAS,CAAA;QACpB,CAAC;IACH,CAAC;CACF;AA3FD,4CA2FC"}

package/dist/bbi.d.ts

@@ -1,6 +1,5 @@
-import { Observable } from 'rxjs';
 import { BlockView } from './block-view.ts';
-import type { BigWigFeatureArrays, BigWigHeaderWithRefNames, Feature, RequestOptions2, RequestOptions, SummaryFeatureArrays } from './types.ts';
+import type { BigWigFeatureArrays, BigWigHeaderWithRefNames, RequestOptions2, RequestOptions, SummaryFeatureArrays } from './types.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export declare abstract class BBI {
     protected bbi: GenericFilehandle;
@@ -16,30 +15,11 @@ export declare abstract class BBI {
     private _getHeader;
     private _getMainHeader;
     private _readChromosomeTree;
+    private viewCache;
+    protected getOrCreateBlockView(refsByName: Record<string, number>, rTreeOffset: number, uncompressBufSize: number, blockType: string): BlockView;
     protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
     protected abstract getView(scale: number, opts?: RequestOptions): Promise<BlockView>;
-    /**
-     * Gets features from a BigWig file
-     *
-     * @param refName - The chromosome name
-     *
-     * @param start - The start of a region
-     *
-     * @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?: RequestOptions2): Promise<Observable<Feature[]>>;
-    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<any[]>;
-    /**
-     * Gets features from a BigWig file as typed arrays (more efficient than getFeatures)
-     *
-     * @param refName - The chromosome name
-     * @param start - The start of a region
-     * @param end - The end of a region
-     * @param opts - Options including basesPerSpan or scale
-     * @returns Promise with typed arrays: starts, ends, scores (and minScores/maxScores for summary data)
-     */
+    private _getView;
+    getFeatures(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<import("./types.ts").Feature[]>;
     getFeaturesAsArrays(refName: string, start: number, end: number, opts?: RequestOptions2): Promise<BigWigFeatureArrays | SummaryFeatureArrays>;
 }

package/dist/bbi.js

@@ -2,8 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BBI = void 0;
 const generic_filehandle2_1 = require("generic-filehandle2");
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
 const block_view_ts_1 = require("./block-view.js");
 const BIG_WIG_MAGIC = -2003829722;
 const BIG_BED_MAGIC = -2021002517;
@@ -61,13 +59,12 @@ class BBI {
     async _getMainHeader(opts, requestSize = 2000) {
         const b = await this.bbi.read(requestSize, 0, opts);
         const dataView = getDataView(b);
-        const r1 = dataView.getInt32(0, true);
-        if (r1 !== BIG_WIG_MAGIC && r1 !== BIG_BED_MAGIC) {
-            throw new Error('not a BigWig/BigBed file');
-        }
         let offset = 0;
         const magic = dataView.getInt32(offset, true);
         offset += 4;
+        if (magic !== BIG_WIG_MAGIC && magic !== BIG_BED_MAGIC) {
+            throw new Error('not a BigWig/BigBed file');
+        }
         const version = dataView.getUint16(offset, true);
         offset += 2;
         const numZoomLevels = dataView.getUint16(offset, true);
@@ -128,7 +125,6 @@ class BBI {
             const scoreSum = dataView.getFloat64(offset, true);
             offset += 8;
             const scoreSumSquares = dataView.getFloat64(offset, true);
-            offset += 8;
             totalSummary = {
                 scoreMin,
                 scoreMax,
@@ -169,33 +165,18 @@ class BBI {
         const refsByName = {};
         const chromosomeTreeOffset = header.chromosomeTreeOffset;
         const dataView = getDataView(await this.bbi.read(32, chromosomeTreeOffset, opts));
-        let offset = 0;
-        // const magic = dataView.getUint32(offset, true) // unused
-        offset += 4;
-        // const blockSize = dataView.getUint32(offset, true) // unused
-        offset += 4;
-        const keySize = dataView.getUint32(offset, true);
-        offset += 4;
-        const valSize = dataView.getUint32(offset, true);
-        offset += 4;
-        // const itemCount = dataView.getBigUint64(offset, true) // unused
-        offset += 8;
+        const keySize = dataView.getUint32(8, true);
+        const valSize = dataView.getUint32(12, true);
         // Recursively traverses the B+ tree to populate chromosome name-to-ID mappings
         const readBPlusTreeNode = async (currentOffset) => {
-            const b = await this.bbi.read(4, currentOffset);
-            const dataView = getDataView(b);
-            let offset = 0;
-            const isLeafNode = dataView.getUint8(offset);
-            offset += 1;
-            // const reserved = dataView.getUint8(offset) // unused
-            offset += 1;
-            const count = dataView.getUint16(offset, true);
-            offset += 2;
+            const header = getDataView(await this.bbi.read(4, currentOffset));
+            const isLeafNode = header.getUint8(0);
+            const count = header.getUint16(2, true);
             // Leaf nodes contain the actual chromosome name-to-ID mappings
             if (isLeafNode) {
-                const b = await this.bbi.read(count * (keySize + valSize), currentOffset + offset);
+                const b = await this.bbi.read(count * (keySize + valSize), currentOffset + 4);
                 const dataView = getDataView(b);
-                offset = 0;
+                let offset = 0;
                 for (let n = 0; n < count; n++) {
                     const keyEnd = b.indexOf(0, offset);
                     const effectiveKeyEnd = keyEnd !== -1 && keyEnd < offset + keySize
@@ -208,18 +189,14 @@ class BBI {
                     const refSize = dataView.getUint32(offset, true);
                     offset += 4;
                     refsByName[this.renameRefSeqs(key)] = refId;
-                    refsByNumber[refId] = {
-                        name: key,
-                        id: refId,
-                        length: refSize,
-                    };
+                    refsByNumber[refId] = { name: key, id: refId, length: refSize };
                 }
             }
             else {
                 // Non-leaf nodes contain pointers to child nodes
+                const dataView = getDataView(await this.bbi.read(count * (keySize + 8), currentOffset + 4));
                 const nextNodes = [];
-                const dataView = getDataView(await this.bbi.read(count * (keySize + 8), currentOffset + offset));
-                offset = 0;
+                let offset = 0;
                 for (let n = 0; n < count; n++) {
                     offset += keySize;
                     const childOffset = Number(dataView.getBigUint64(offset, true));
@@ -235,115 +212,36 @@ class BBI {
             refsByNumber,
         };
     }
+    viewCache = new Map();
+    getOrCreateBlockView(refsByName, rTreeOffset, uncompressBufSize, blockType) {
+        const key = `${rTreeOffset}_${blockType}`;
+        let view = this.viewCache.get(key);
+        if (!view) {
+            view = new block_view_ts_1.BlockView(this.bbi, refsByName, rTreeOffset, uncompressBufSize, blockType);
+            this.viewCache.set(key, view);
+        }
+        return view;
+    }
     /*
      * fetches the "unzoomed" view of the bigwig data. this is the default for bigbed
      * @param abortSignal - a signal to optionally abort this operation
      */
     async getUnzoomedView(opts) {
         const { unzoomedIndexOffset, refsByName, uncompressBufSize, fileType } = await this.getHeader(opts);
-        return new block_view_ts_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, uncompressBufSize, fileType);
+        return this.getOrCreateBlockView(refsByName, unzoomedIndexOffset, uncompressBufSize, fileType);
     }
-    /**
-     * Gets features from a BigWig file
-     *
-     * @param refName - The chromosome name
-     *
-     * @param start - The start of a region
-     *
-     * @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
-     */
-    async getFeatureStream(refName, start, end, opts) {
-        await this.getHeader(opts);
-        const chrName = this.renameRefSeqs(refName);
-        let view;
+    async _getView(opts) {
         const { basesPerSpan, scale } = opts || {};
-        if (basesPerSpan) {
-            view = await this.getView(1 / basesPerSpan, opts);
-        }
-        else if (scale) {
-            view = await this.getView(scale, opts);
-        }
-        else {
-            view = await this.getView(1, opts);
-        }
-        return new rxjs_1.Observable(observer => {
-            view
-                .readWigData(chrName, start, end, observer, opts)
-                .catch((e) => {
-                observer.error(e);
-            });
-        });
+        const viewScale = basesPerSpan ? 1 / basesPerSpan : (scale ?? 1);
+        return this.getView(viewScale, opts);
     }
     async getFeatures(refName, start, end, opts) {
-        const ob = await this.getFeatureStream(refName, start, end, opts);
-        const arrays = await (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
-        const totalLength = arrays.reduce((sum, arr) => sum + arr.length, 0);
-        const result = new Array(totalLength);
-        let index = 0;
-        for (const arr of arrays) {
-            for (const item of arr) {
-                result[index++] = item;
-            }
-        }
-        return result;
+        const view = await this._getView(opts);
+        return view.readWigData(this.renameRefSeqs(refName), start, end, opts);
     }
-    /**
-     * Gets features from a BigWig file as typed arrays (more efficient than getFeatures)
-     *
-     * @param refName - The chromosome name
-     * @param start - The start of a region
-     * @param end - The end of a region
-     * @param opts - Options including basesPerSpan or scale
-     * @returns Promise with typed arrays: starts, ends, scores (and minScores/maxScores for summary data)
-     */
     async getFeaturesAsArrays(refName, start, end, opts) {
-        const features = await this.getFeatures(refName, start, end, opts);
-        const count = features.length;
-        if (count === 0) {
-            return {
-                starts: new Int32Array(0),
-                ends: new Int32Array(0),
-                scores: new Float32Array(0),
-                isSummary: false,
-            };
-        }
-        const hasSummary = features[0]?.summary === true;
-        if (hasSummary) {
-            const starts = new Int32Array(count);
-            const ends = new Int32Array(count);
-            const scores = new Float32Array(count);
-            const minScores = new Float32Array(count);
-            const maxScores = new Float32Array(count);
-            for (let i = 0; i < count; i++) {
-                const f = features[i];
-                starts[i] = f.start;
-                ends[i] = f.end;
-                scores[i] = f.score ?? 0;
-                minScores[i] = f.minScore ?? 0;
-                maxScores[i] = f.maxScore ?? 0;
-            }
-            return {
-                starts,
-                ends,
-                scores,
-                minScores,
-                maxScores,
-                isSummary: true,
-            };
-        }
-        const starts = new Int32Array(count);
-        const ends = new Int32Array(count);
-        const scores = new Float32Array(count);
-        for (let i = 0; i < count; i++) {
-            const f = features[i];
-            starts[i] = f.start;
-            ends[i] = f.end;
-            scores[i] = f.score ?? 0;
-        }
-        return { starts, ends, scores, isSummary: false };
+        const view = await this._getView(opts);
+        return view.readWigDataAsArrays(this.renameRefSeqs(refName), start, end, opts);
     }
 }
 exports.BBI = BBI;

package/dist/bbi.js.map

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

@@ -7,7 +7,6 @@ interface Index {
     offset: number;
     field: number;
 }
-export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
 export declare class BigBed extends BBI {
     readIndicesCache: AbortablePromiseCache<RequestOptions, Index[], string>;
     readIndices(opts?: RequestOptions): Promise<Index[]>;

package/dist/bigbed.js

@@ -4,16 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BigBed = void 0;
-exports.filterUndef = filterUndef;
 const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
 const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
 const bbi_ts_1 = require("./bbi.js");
 const decoder = new TextDecoder('utf8');
-function filterUndef(ts) {
-    return ts.filter((t) => !!t);
-}
 function getTabField(str, fieldIndex) {
     if (fieldIndex < 0) {
         return undefined;
@@ -41,11 +35,9 @@ async function readBPlusTreeNode(bbi, nodeOffset, blockSize, keySize, valSize, n
     const len = 4 + blockSize * (keySize + valSize);
     const buffer = await bbi.read(len, nodeOffset, opts);
     const dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
-    let offset = 0;
-    const nodeType = dataView.getInt8(offset);
-    offset += 2; // skip nodeType byte + 1 reserved byte
-    const cnt = dataView.getInt16(offset, true);
-    offset += 2;
+    const nodeType = dataView.getInt8(0);
+    const cnt = dataView.getInt16(2, true);
+    let offset = 4;
     // Non-leaf node (nodeType === 0): contains keys and child node pointers for navigation
     if (nodeType === 0) {
         const leafkeys = [];
@@ -139,13 +131,8 @@ class BigBed extends bbi_ts_1.BBI {
         const { extHeaderOffset } = await this.getHeader(opts);
         const b = await this.bbi.read(64, extHeaderOffset);
         const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-        let offset = 0;
-        // const _size = dataView.getUint16(offset, true)
-        offset += 2;
-        const count = dataView.getUint16(offset, true);
-        offset += 2;
-        const dataOffset = Number(dataView.getBigUint64(offset, true));
-        offset += 8;
+        const count = dataView.getUint16(2, true);
+        const dataOffset = Number(dataView.getBigUint64(4, true));
         // no extra index is defined if count==0
         if (count === 0) {
             return [];
@@ -157,14 +144,10 @@ class BigBed extends bbi_ts_1.BBI {
         for (let i = 0; i < count; i += 1) {
             const b = buffer.subarray(i * blocklen);
             const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-            let offset = 0;
-            const type = dataView.getInt16(offset, true);
-            offset += 2;
-            const fieldcount = dataView.getInt16(offset, true);
-            offset += 2;
-            const dataOffset = Number(dataView.getBigUint64(offset, true));
-            offset += 8 + 4; // skip 8-byte offset + 4 reserved bytes
-            const field = dataView.getInt16(offset, true);
+            const type = dataView.getInt16(0, true);
+            const fieldcount = dataView.getInt16(2, true);
+            const dataOffset = Number(dataView.getBigUint64(4, true));
+            const field = dataView.getInt16(16, true);
             indices.push({
                 type,
                 fieldcount,
@@ -193,20 +176,13 @@ class BigBed extends bbi_ts_1.BBI {
             const { offset: offset2, field } = index;
             const b = await this.bbi.read(32, offset2, opts);
             const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-            let offset = 0;
-            // const _magic = dataView.getInt32(offset, true)
-            offset += 4;
-            const blockSize = dataView.getInt32(offset, true);
-            offset += 4;
-            const keySize = dataView.getInt32(offset, true);
-            offset += 4;
-            const valSize = dataView.getInt32(offset, true);
-            offset += 4;
-            // const _itemCount = Number(dataView.getBigUint64(offset, true))
-            offset += 8;
+            const blockSize = dataView.getInt32(4, true);
+            const keySize = dataView.getInt32(8, true);
+            const valSize = dataView.getInt32(12, true);
             return readBPlusTreeNode(this.bbi, offset2 + 32, blockSize, keySize, valSize, name, field, opts);
         });
-        return filterUndef(await Promise.all(locs));
+        const results = await Promise.all(locs);
+        return results.filter((l) => l !== undefined);
     }
     /*
      * retrieve the features from the bigbed data that were found through the
@@ -225,20 +201,12 @@ class BigBed extends bbi_ts_1.BBI {
             return [];
         }
         const view = await this.getUnzoomedView(opts);
-        const res = blocks.map(block => {
-            return new rxjs_1.Observable(observer => {
-                view.readFeatures(observer, [block], opts).catch((e) => {
-                    observer.error(e);
-                });
-            }).pipe((0, operators_1.reduce)((acc, curr) => {
-                acc.push(...curr);
-                return acc;
-            }, []), (0, operators_1.map)(features => features.map(f => ({ ...f, field: block.field }))));
-        });
-        const ret = await (0, rxjs_1.firstValueFrom)((0, rxjs_1.merge)(...res));
-        // Filter to features where the indexed field matches the search name
+        const results = await Promise.all(blocks.map(async (block) => {
+            const features = await view.readFeatures([block], opts);
+            return features.map(f => ({ ...f, field: block.field }));
+        }));
         // field offset is adjusted by -3 to account for chrom, chromStart, chromEnd columns
-        return ret.filter(f => {
+        return results.flat().filter(f => {
             if (!f.rest) {
                 return false;
             }