@gmod/bbi 3.0.0 → 4.0.0

package/esm/bigwig.js

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

package/esm/bigwig.js.map

@@ -1 +1 @@
-{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAA;AACvC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;OAKG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;QAChC,IAAI,CAAC,QAAQ,EAAE;YACb,4EAA4E;YAC5E,QAAQ,IAAI,CAAC,CAAA;SACd;QAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;YACrC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE;gBAC7C,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;gBAE1C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;aACF;SACF;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}
+{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;OAKG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;QAChC,IAAI,CAAC,QAAQ,EAAE;YACb,4EAA4E;YAC5E,QAAQ,IAAI,CAAC,CAAA;SACd;QAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;YACrC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE;gBAC7C,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;gBAE1C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;aACF;SACF;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}

package/{dist/blockView.d.ts → esm/block-view.d.ts}

@@ -29,7 +29,7 @@ export declare class BlockView {
     private leafParser;
     private bigBedParser;
     constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isBigEndian: boolean, isCompressed: boolean, blockType: string);
-    readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts: Options): Promise<void>;
+    readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts?: Options): Promise<void>;
     private parseSummaryBlock;
     private parseBigBedBlock;
     private parseBigWigBlock;

package/esm/{blockView.js → block-view.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';
@@ -160,7 +161,7 @@ export class BlockView {
                     const p = this.leafParser.parse(data);
                     if (p.blocksToFetch) {
                         blocksToFetch = blocksToFetch.concat(p.blocksToFetch
-                            .filter(filterFeats)
+                            .filter(f => filterFeats(f))
                             .map((l) => ({
                             offset: l.blockOffset,
                             length: l.blockSize,
@@ -168,7 +169,7 @@ export class BlockView {
                     }
                     if (p.recurOffsets) {
                         const recurOffsets = p.recurOffsets
-                            .filter(filterFeats)
+                            .filter(f => filterFeats(f))
                             .map(l => Number(l.blockOffset));
                         if (recurOffsets.length > 0) {
                             cirFobRecur(recurOffsets, level + 1);
@@ -188,10 +189,10 @@ export class BlockView {
                 try {
                     const length = fr.max() - fr.min();
                     const offset = fr.min();
-                    const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts.signal);
-                    for (let i = 0; i < off.length; i += 1) {
-                        if (fr.contains(off[i])) {
-                            cirFobRecur2(resultBuffer, off[i] - offset, level);
+                    const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts === null || opts === void 0 ? void 0 : opts.signal);
+                    for (const element of off) {
+                        if (fr.contains(element)) {
+                            cirFobRecur2(resultBuffer, element - offset, level);
                             outstanding -= 1;
                             if (outstanding === 0) {
                                 this.readFeatures(observer, blocksToFetch, { ...opts, request });
@@ -206,7 +207,8 @@ export class BlockView {
             const cirFobRecur = (offset, level) => {
                 try {
                     outstanding += offset.length;
-                    const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32; // Upper bound on size, based on a completely full leaf node.
+                    // Upper bound on size, based on a completely full leaf node.
+                    const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32;
                     let spans = new Range(offset[0], offset[0] + maxCirBlockSpan);
                     for (let i = 1; i < offset.length; i += 1) {
                         const blockSpan = new Range(offset[i], offset[i] + maxCirBlockSpan);
@@ -293,7 +295,7 @@ export class BlockView {
         offset += 2;
         const items = new Array(itemCount);
         switch (blockType) {
-            case 1:
+            case 1: {
                 for (let i = 0; i < itemCount; i++) {
                     const start = dataView.getInt32(offset, true);
                     offset += 4;
@@ -304,7 +306,8 @@ export class BlockView {
                     items[i] = { start, end, score };
                 }
                 break;
-            case 2:
+            }
+            case 2: {
                 for (let i = 0; i < itemCount; i++) {
                     const start = dataView.getInt32(offset, true);
                     offset += 4;
@@ -313,7 +316,8 @@ export class BlockView {
                     items[i] = { score, start, end: start + itemSpan };
                 }
                 break;
-            case 3:
+            }
+            case 3: {
                 for (let i = 0; i < itemCount; i++) {
                     const score = dataView.getFloat32(offset, true);
                     offset += 4;
@@ -321,6 +325,7 @@ export class BlockView {
                     items[i] = { score, start, end: start + itemSpan };
                 }
                 break;
+            }
         }
         return request
             ? items.filter((f) => coordFilter(f.start, f.end, request.start, request.end))
@@ -336,7 +341,7 @@ export class BlockView {
                 checkAbortSignal(signal);
                 const { length, offset } = blockGroup;
                 const data = await this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
-                blockGroup.blocks.forEach(block => {
+                for (const block of blockGroup.blocks) {
                     checkAbortSignal(signal);
                     let blockOffset = Number(block.offset) - Number(blockGroup.offset);
                     let resultData = data;
@@ -346,19 +351,23 @@ export class BlockView {
                     }
                     checkAbortSignal(signal);
                     switch (blockType) {
-                        case 'summary':
+                        case 'summary': {
                             observer.next(this.parseSummaryBlock(resultData, blockOffset, request));
                             break;
-                        case 'bigwig':
+                        }
+                        case 'bigwig': {
                             observer.next(this.parseBigWigBlock(resultData, blockOffset, request));
                             break;
-                        case 'bigbed':
+                        }
+                        case 'bigbed': {
                             observer.next(this.parseBigBedBlock(resultData, blockOffset, Number(block.offset) * (1 << 8), request));
                             break;
-                        default:
+                        }
+                        default: {
                             console.warn(`Don't know what to do with ${blockType}`);
+                        }
                     }
-                });
+                }
             }));
             observer.complete();
         }
@@ -367,4 +376,4 @@ export class BlockView {
         }
     }
 }
-//# sourceMappingURL=blockView.js.map
+//# sourceMappingURL=block-view.js.map

package/esm/block-view.js.map

@@ -0,0 +1 @@
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package/esm/range.js

@@ -57,7 +57,7 @@ export default class Range {
         return new Range(oranges);
     }
     intersection(arg) {
-        // eslint-disable-next-line @typescript-eslint/no-this-alias
+        // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
         let s0 = this;
         let s1 = arg;
         const r0 = this.ranges();
@@ -93,8 +93,7 @@ export default class Range {
     coverage() {
         let tot = 0;
         const rl = this.ranges();
-        for (let ri = 0; ri < rl.length; ri += 1) {
-            const r = rl[ri];
+        for (const r of rl) {
             tot += r.max() - r.min() + 1;
         }
         return tot;
@@ -104,7 +103,7 @@ export default class Range {
         let b = tmpb;
         if (arguments.length < 2) {
             b = a;
-            // eslint-disable-next-line @typescript-eslint/no-this-alias
+            // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
             a = this;
         }
         if (a.min() < b.min()) {

package/esm/range.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/esm/unzip.d.ts

@@ -1,2 +1 @@
-import { inflateSync } from 'zlib';
-export { inflateSync as unzip };
+export { inflateSync as unzip } from 'zlib';

package/esm/unzip.js

@@ -1,3 +1,2 @@
-import { inflateSync } from 'zlib';
-export { inflateSync as unzip };
+export { inflateSync as unzip } from 'zlib';
 //# sourceMappingURL=unzip.js.map

package/esm/unzip.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,MAAM,CAAA;AAClC,OAAO,EAAE,WAAW,IAAI,KAAK,EAAE,CAAA"}
+{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,IAAI,KAAK,EAAE,MAAM,MAAM,CAAA"}

package/esm/util.js

@@ -12,21 +12,21 @@ export function groupBlocks(blocks) {
     const blockGroups = [];
     let lastBlock;
     let lastBlockEnd;
-    for (let i = 0; i < blocks.length; i += 1) {
+    for (const block of blocks) {
         if (lastBlock &&
             lastBlockEnd &&
-            Number(blocks[i].offset) - lastBlockEnd <= 2000) {
+            Number(block.offset) - lastBlockEnd <= 2000) {
             lastBlock.length = BigInt(Number(lastBlock.length) +
-                Number(blocks[i].length) -
+                Number(block.length) -
                 lastBlockEnd +
-                Number(blocks[i].offset));
-            lastBlock.blocks.push(blocks[i]);
+                Number(block.offset));
+            lastBlock.blocks.push(block);
         }
         else {
             blockGroups.push((lastBlock = {
-                blocks: [blocks[i]],
-                length: blocks[i].length,
-                offset: blocks[i].offset,
+                blocks: [block],
+                length: block.length,
+                offset: block.offset,
             }));
         }
         lastBlockEnd = Number(lastBlock.offset) + Number(lastBlock.length);
@@ -50,14 +50,14 @@ export function checkAbortSignal(signal) {
     }
     if (signal.aborted) {
         // console.log('bam aborted!')
-        if (typeof DOMException !== 'undefined') {
-            throw new DOMException('aborted', 'AbortError');
-        }
-        else {
+        if (typeof DOMException === 'undefined') {
             const e = new AbortError('aborted');
             e.code = 'ERR_ABORTED';
             throw e;
         }
+        else {
+            throw new DOMException('aborted', 'AbortError');
+        }
     }
 }
 /**

package/esm/util.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "3.0.0",
+  "version": "4.0.0",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -43,6 +43,7 @@
   "dependencies": {
     "abortable-promise-cache": "^1.4.1",
     "binary-parser": "^2.1.0",
+    "eslint-plugin-unicorn": "^46.0.0",
     "generic-filehandle": "^3.0.0",
     "pako": "^2.0.0",
     "quick-lru": "^4.0.0",
@@ -50,24 +51,23 @@
   },
   "devDependencies": {
     "@gmod/bed": "^2.1.2",
-    "@types/jest": "^29.2.4",
+    "@types/jest": "^29.5.0",
     "@types/long": "^5.0.0",
-    "@types/node": "^18.11.15",
+    "@types/node": "^18.15.7",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.46.1",
-    "@typescript-eslint/parser": "^5.46.1",
-    "cross-fetch": "^3.0.2",
-    "eslint": "^8.29.0",
-    "eslint-config-prettier": "^8.3.0",
-    "eslint-plugin-import": "^2.25.3",
+    "@typescript-eslint/eslint-plugin": "^5.56.0",
+    "@typescript-eslint/parser": "^5.56.0",
+    "eslint": "^8.36.0",
+    "eslint-config-prettier": "^8.8.0",
+    "eslint-plugin-import": "^2.27.5",
     "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^29.3.1",
-    "jest-environment-jsdom": "^29.3.1",
-    "prettier": "^2.8.1",
-    "rimraf": "^3.0.2",
+    "jest": "^29.5.0",
+    "jest-environment-jsdom": "^29.5.0",
+    "prettier": "^2.8.7",
+    "rimraf": "^5.0.0",
     "standard-changelog": "^2.0.11",
-    "ts-jest": "^29.0.3",
-    "typescript": "^4.9.4"
+    "ts-jest": "^29.0.5",
+    "typescript": "^5.0.2"
   },
   "publishConfig": {
     "access": "public"

package/src/bbi.ts

@@ -1,8 +1,9 @@
+import { Buffer } from 'buffer'
 import { Parser } from 'binary-parser'
 import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
-import { firstValueFrom, Observable, Observer } from 'rxjs'
+import { firstValueFrom, Observable } from 'rxjs'
 import { toArray } from 'rxjs/operators'
-import { BlockView } from './blockView'
+import { BlockView } from './block-view'
 
 const BIG_WIG_MAGIC = -2003829722
 const BIG_BED_MAGIC = -2021002517
@@ -129,10 +130,9 @@ export abstract class BBI {
    * @param abortSignal - abort the operation, can be null
    * @return a Header object
    */
-  public getHeader(opts: RequestOptions | AbortSignal = {}) {
-    const options = 'aborted' in opts ? { signal: opts as AbortSignal } : opts
+  public getHeader(opts?: RequestOptions) {
     if (!this.headerP) {
-      this.headerP = this._getHeader(options).catch(e => {
+      this.headerP = this._getHeader(opts).catch(e => {
         this.headerP = undefined
         throw e
       })
@@ -146,15 +146,13 @@ export abstract class BBI {
    * @param url - a URL string
    * @param renameRefSeqs - an optional method to rename the internal reference sequences using a mapping function
    */
-  public constructor(
-    options: {
-      filehandle?: GenericFilehandle
-      path?: string
-      url?: string
-      renameRefSeqs?: (a: string) => string
-    } = {},
-  ) {
-    const { filehandle, renameRefSeqs = s => s, path, url } = options
+  public constructor(args: {
+    filehandle?: GenericFilehandle
+    path?: string
+    url?: string
+    renameRefSeqs?: (a: string) => string
+  }) {
+    const { filehandle, renameRefSeqs = s => s, path, url } = args
     this.renameRefSeqs = renameRefSeqs
     if (filehandle) {
       this.bbi = filehandle
@@ -167,14 +165,14 @@ export abstract class BBI {
     }
   }
 
-  private async _getHeader(opts: RequestOptions) {
+  private async _getHeader(opts?: RequestOptions) {
     const header = await this._getMainHeader(opts)
     const chroms = await this._readChromTree(header, opts)
     return { ...header, ...chroms }
   }
 
   private async _getMainHeader(
-    opts: RequestOptions,
+    opts?: RequestOptions,
     requestSize = 2000,
   ): Promise<Header> {
     const { buffer } = await this.bbi.read(
@@ -207,7 +205,7 @@ export abstract class BBI {
     return { ...header, isBigEndian }
   }
 
-  private _isBigEndian(buffer: Buffer): boolean {
+  private _isBigEndian(buffer: Buffer) {
     let ret = buffer.readInt32LE(0)
     if (ret === BIG_WIG_MAGIC || ret === BIG_BED_MAGIC) {
       return false
@@ -220,7 +218,10 @@ export abstract class BBI {
   }
 
   // todo: add progress if long running
-  private async _readChromTree(header: Header, opts: { signal?: AbortSignal }) {
+  private async _readChromTree(
+    header: Header,
+    opts?: { signal?: AbortSignal },
+  ) {
     const isBE = header.isBigEndian
     const le = isBE ? 'big' : 'little'
     const refsByNumber: {
@@ -298,7 +299,7 @@ export abstract class BBI {
    * fetches the "unzoomed" view of the bigwig data. this is the default for bigbed
    * @param abortSignal - a signal to optionally abort this operation
    */
-  protected async getUnzoomedView(opts: RequestOptions): Promise<BlockView> {
+  protected async getUnzoomedView(opts?: RequestOptions) {
     const {
       unzoomedIndexOffset,
       refsByName,
@@ -321,7 +322,7 @@ export abstract class BBI {
    */
   protected abstract getView(
     scale: number,
-    opts: RequestOptions,
+    opts?: RequestOptions,
   ): Promise<BlockView>
 
   /**
@@ -336,26 +337,22 @@ export abstract class BBI {
     refName: string,
     start: number,
     end: number,
-    opts: RequestOptions & { scale?: number; basesPerSpan?: number } = {
-      scale: 1,
-    },
-  ): Promise<Observable<Feature[]>> {
+    opts?: RequestOptions & { scale?: number; basesPerSpan?: number },
+  ) {
     await this.getHeader(opts)
     const chrName = this.renameRefSeqs(refName)
     let view: BlockView
+    const { basesPerSpan, scale } = opts || {}
 
-    if (opts.basesPerSpan) {
-      view = await this.getView(1 / opts.basesPerSpan, opts)
-    } else if (opts.scale) {
-      view = await this.getView(opts.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)
     }
 
-    if (!view) {
-      throw new Error('unable to get block view for data')
-    }
-    return new Observable((observer: Observer<Feature[]>): void => {
+    return new Observable<Feature[]>(observer => {
       view.readWigData(chrName, start, end, observer, opts)
     })
   }
@@ -364,9 +361,7 @@ export abstract class BBI {
     refName: string,
     start: number,
     end: number,
-    opts: RequestOptions & { scale?: number; basesPerSpan?: number } = {
-      scale: 1,
-    },
+    opts?: RequestOptions & { scale?: number; basesPerSpan?: number },
   ) {
     const ob = await this.getFeatureStream(refName, start, end, opts)
 

package/src/bigbed.ts

@@ -1,3 +1,4 @@
+import { Buffer } from 'buffer'
 import { Parser } from 'binary-parser'
 import { Observable, merge, firstValueFrom } from 'rxjs'
 import { map, reduce } from 'rxjs/operators'
@@ -5,7 +6,6 @@ import AbortablePromiseCache from 'abortable-promise-cache'
 import QuickLRU from 'quick-lru'
 
 import { BBI, Feature, RequestOptions } from './bbi'
-import { BlockView } from './blockView'
 
 interface Loc {
   key: string
@@ -26,32 +26,21 @@ export function filterUndef<T>(ts: (T | undefined)[]): T[] {
 }
 
 export class BigBed extends BBI {
-  public readIndicesCache = new AbortablePromiseCache({
+  public readIndicesCache = new AbortablePromiseCache<RequestOptions, Index[]>({
     cache: new QuickLRU({ maxSize: 1 }),
-    fill: async (args: any, signal?: AbortSignal) => {
-      return this._readIndices({ ...args, signal })
-    },
+    fill: (args: RequestOptions, signal?: AbortSignal) =>
+      this._readIndices({ ...args, signal }),
   })
 
-  public readIndices(opts: AbortSignal | RequestOptions = {}) {
-    const options = 'aborted' in opts ? { signal: opts } : opts
-    return this.readIndicesCache.get(
-      JSON.stringify(options),
-      options,
-      options.signal,
-    )
+  public readIndices(opts: RequestOptions = {}) {
+    const { signal, ...rest } = opts
+    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
    */
-  protected async getView(
-    _scale: number,
-    opts: RequestOptions,
-  ): Promise<BlockView> {
+  protected async getView(_scale: number, opts?: RequestOptions) {
     return this.getUnzoomedView(opts)
   }
 
@@ -120,7 +109,7 @@ export class BigBed extends BBI {
   ): Promise<Loc[]> {
     const { isBigEndian } = await this.getHeader(opts)
     const indices = await this.readIndices(opts)
-    if (!indices.length) {
+    if (indices.length === 0) {
       return []
     }
     const locs = indices.map(async (index: any): Promise<Loc | undefined> => {
@@ -218,7 +207,7 @@ export class BigBed extends BBI {
    */
   public async searchExtraIndex(name: string, opts: RequestOptions = {}) {
     const blocks = await this.searchExtraIndexBlocks(name, opts)
-    if (!blocks.length) {
+    if (blocks.length === 0) {
       return []
     }
     const view = await this.getUnzoomedView(opts)
@@ -228,8 +217,8 @@ export class BigBed extends BBI {
       }).pipe(
         reduce((acc, curr) => acc.concat(curr)),
         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/src/bigwig.ts

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