@gmod/bbi - npm Package Compare versions

Comparing version 3.0.1 to 4.0.0

CHANGELOG.md

@@ -1,12 +0,17 @@
-## [3.0.1](https://github.com/GMOD/bbi-js/compare/v3.0.0...v3.0.1) (2023-04-21)
+# [4.0.0](https://github.com/GMOD/bbi-js/compare/v3.0.1...v4.0.0) (2023-05-05)
 
 
-### Features
 
-* explicit buffer import ([#53](https://github.com/GMOD/bbi-js/issues/53)) ([2699c98](https://github.com/GMOD/bbi-js/commit/2699c983dea380bbb56773058ba3f233c833d9c8))
+- Improve typescripting, refactoring
+- Options argument only accepts {signal}, not just signal now
 
+## [3.0.1](https://github.com/GMOD/bbi-js/compare/v3.0.0...v3.0.1) (2023-04-21)
 
+### Features
 
-- Add explicit Buffer import
+- explicit buffer import ([#53](https://github.com/GMOD/bbi-js/issues/53))
+  ([2699c98](https://github.com/GMOD/bbi-js/commit/2699c983dea380bbb56773058ba3f233c833d9c8))
 
+* Add explicit Buffer import
+
 # [3.0.0](https://github.com/GMOD/bbi-js/compare/v2.0.5...v3.0.0) (2023-01-11)
@@ -13,0 +18,0 @@

dist/bbi.d.ts

 import { GenericFilehandle } from 'generic-filehandle';
 import { Observable } from 'rxjs';
-import { BlockView } from './blockView';
+import { BlockView } from './block-view';
 export interface Feature {
@@ -54,4 +54,4 @@ start: number;
     protected renameRefSeqs: (a: string) => string;
-    getHeader(opts?: RequestOptions | AbortSignal): Promise<Header>;
-    constructor(options?: {
+    getHeader(opts?: RequestOptions): Promise<Header>;
+    constructor(args: {
         filehandle?: GenericFilehandle;
@@ -66,4 +66,4 @@ path?: string;
     private _readChromTree;
-    protected getUnzoomedView(opts: RequestOptions): Promise<BlockView>;
-    protected abstract getView(scale: number, opts: RequestOptions): Promise<BlockView>;
+    protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
+    protected abstract getView(scale: number, opts?: RequestOptions): Promise<BlockView>;
     /**
@@ -70,0 +70,0 @@ * Gets features from a BigWig file

dist/bbi.js

@@ -18,3 +18,3 @@ "use strict";
 const operators_1 = require("rxjs/operators");
-const blockView_1 = require("./blockView");
+const block_view_1 = require("./block-view");
 const BIG_WIG_MAGIC = -2003829722;
@@ -87,6 +87,5 @@ const BIG_BED_MAGIC = -2021002517;
      */
-    getHeader(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
+    getHeader(opts) {
         if (!this.headerP) {
-            this.headerP = this._getHeader(options).catch(e => {
+            this.headerP = this._getHeader(opts).catch(e => {
                 this.headerP = undefined;
@@ -104,4 +103,4 @@ throw e;
      */
-    constructor(options = {}) {
-        const { filehandle, renameRefSeqs = s => s, path, url } = options;
+    constructor(args) {
+        const { filehandle, renameRefSeqs = s => s, path, url } = args;
         this.renameRefSeqs = renameRefSeqs;
@@ -237,3 +236,3 @@ if (filehandle) {
             const { unzoomedIndexOffset, refsByName, uncompressBufSize, isBigEndian, fileType, } = yield this.getHeader(opts);
-            return new blockView_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType);
+            return new block_view_1.BlockView(this.bbi, refsByName, unzoomedIndexOffset, isBigEndian, uncompressBufSize > 0, fileType);
         });
@@ -249,5 +248,3 @@ }
      */
-    getFeatureStream(refName, start, end, opts = {
-        scale: 1,
-    }) {
+    getFeatureStream(refName, start, end, opts) {
         return __awaiter(this, void 0, void 0, function* () {
@@ -257,7 +254,8 @@ yield this.getHeader(opts);
             let view;
-            if (opts.basesPerSpan) {
-                view = yield this.getView(1 / opts.basesPerSpan, opts);
+            const { basesPerSpan, scale } = opts || {};
+            if (basesPerSpan) {
+                view = yield this.getView(1 / basesPerSpan, opts);
             }
-            else if (opts.scale) {
-                view = yield this.getView(opts.scale, opts);
+            else if (scale) {
+                view = yield this.getView(scale, opts);
             }
@@ -267,6 +265,3 @@ else {
             }
-            if (!view) {
-                throw new Error('unable to get block view for data');
-            }
-            return new rxjs_1.Observable((observer) => {
+            return new rxjs_1.Observable(observer => {
                 view.readWigData(chrName, start, end, observer, opts);
@@ -276,5 +271,3 @@ });
     }
-    getFeatures(refName, start, end, opts = {
-        scale: 1,
-    }) {
+    getFeatures(refName, start, end, opts) {
         return __awaiter(this, void 0, void 0, function* () {
@@ -281,0 +274,0 @@ const ob = yield this.getFeatureStream(refName, start, end, opts);

dist/bigbed.d.ts

@@ -0,8 +1,14 @@
+import AbortablePromiseCache from 'abortable-promise-cache';
 import { BBI, Feature, RequestOptions } from './bbi';
-import { BlockView } from './blockView';
+interface Index {
+    type: number;
+    fieldcount: number;
+    offset: number;
+    field: number;
+}
 export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
 export declare class BigBed extends BBI {
-    readIndicesCache: any;
-    readIndices(opts?: AbortSignal | RequestOptions): any;
-    protected getView(_scale: number, opts: RequestOptions): Promise<BlockView>;
+    readIndicesCache: AbortablePromiseCache<RequestOptions, Index[]>;
+    readIndices(opts?: RequestOptions): Promise<Index[]>;
+    protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view").BlockView>;
     private _readIndices;
@@ -12,1 +18,2 @@ private searchExtraIndexBlocks;
 }
+export {};

dist/bigbed.js

@@ -11,2 +11,13 @@ "use strict";
 };
+var __rest = (this && this.__rest) || function (s, e) {
+    var t = {};
+    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
+        t[p] = s[p];
+    if (s != null && typeof Object.getOwnPropertySymbols === "function")
+        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
+            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
+                t[p[i]] = s[p[i]];
+        }
+    return t;
+};
 var __importDefault = (this && this.__importDefault) || function (mod) {
@@ -33,16 +44,11 @@ return (mod && mod.__esModule) ? mod : { "default": mod };
             cache: new quick_lru_1.default({ maxSize: 1 }),
-            fill: (args, signal) => __awaiter(this, void 0, void 0, function* () {
-                return this._readIndices(Object.assign(Object.assign({}, args), { signal }));
-            }),
+            fill: (args, signal) => this._readIndices(Object.assign(Object.assign({}, args), { signal })),
         });
     }
     readIndices(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
-        return this.readIndicesCache.get(JSON.stringify(options), options, options.signal);
+        const { signal } = opts, rest = __rest(opts, ["signal"]);
+        return this.readIndicesCache.get(JSON.stringify(rest), opts, signal);
     }
     /*
      * retrieve unzoomed view for any scale
-     * @param scale - unused
-     * @param abortSignal - an optional AbortSignal to kill operation
-     * @return promise for a BlockView
      */
@@ -104,3 +110,3 @@ getView(_scale, opts) {
             const indices = yield this.readIndices(opts);
-            if (!indices.length) {
+            if (indices.length === 0) {
                 return [];
@@ -187,3 +193,3 @@ }
             const blocks = yield this.searchExtraIndexBlocks(name, opts);
-            if (!blocks.length) {
+            if (blocks.length === 0) {
                 return [];
@@ -196,4 +202,4 @@ }
                 }).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
-                    for (let i = 0; i < x.length; i += 1) {
-                        x[i].field = block.field;
+                    for (const element of x) {
+                        element.field = block.field;
                     }
@@ -200,0 +206,0 @@ return x;

dist/bigwig.d.ts

@@ -1,2 +0,2 @@
-import { BlockView } from './blockView';
+import { BlockView } from './block-view';
 import { BBI, RequestOptions } from './bbi';
@@ -3,0 +3,0 @@ export declare class BigWig extends BBI {

dist/bigwig.js

@@ -13,3 +13,3 @@ "use strict";
 exports.BigWig = void 0;
-const blockView_1 = require("./blockView");
+const block_view_1 = require("./block-view");
 const bbi_1 = require("./bbi");
@@ -36,3 +36,3 @@ class BigWig extends bbi_1.BBI {
                     const indexOffset = Number(zh.indexOffset);
-                    return new blockView_1.BlockView(this.bbi, refsByName, indexOffset, isBigEndian, uncompressBufSize > 0, 'summary');
+                    return new block_view_1.BlockView(this.bbi, refsByName, indexOffset, isBigEndian, uncompressBufSize > 0, 'summary');
                 }
@@ -39,0 +39,0 @@ }

dist/range.js

@@ -62,3 +62,3 @@ "use strict";
     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;
@@ -99,4 +99,3 @@ let s1 = arg;
         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;
@@ -111,3 +110,3 @@ }
             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;
@@ -114,0 +113,0 @@ }

dist/unzip.d.ts

@@ -1,2 +0,1 @@
-import { inflateSync } from 'zlib';
-export { inflateSync as unzip };
+export { inflateSync as unzip } from 'zlib';

dist/unzip.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.unzip = void 0;
-const zlib_1 = require("zlib");
+var zlib_1 = require("zlib");
 Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.inflateSync; } });
 //# sourceMappingURL=unzip.js.map

dist/util.js

@@ -28,17 +28,17 @@ "use strict";
     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,
             }));
@@ -68,6 +68,3 @@ }
         // console.log('bam aborted!')
-        if (typeof DOMException !== 'undefined') {
-            throw new DOMException('aborted', 'AbortError');
-        }
-        else {
+        if (typeof DOMException === 'undefined') {
             const e = new AbortError('aborted');
@@ -77,2 +74,5 @@ e.code = 'ERR_ABORTED';
         }
+        else {
+            throw new DOMException('aborted', 'AbortError');
+        }
     }
@@ -79,0 +79,0 @@ }

esm/bbi.d.ts

 import { GenericFilehandle } from 'generic-filehandle';
 import { Observable } from 'rxjs';
-import { BlockView } from './blockView';
+import { BlockView } from './block-view';
 export interface Feature {
@@ -54,4 +54,4 @@ start: number;
     protected renameRefSeqs: (a: string) => string;
-    getHeader(opts?: RequestOptions | AbortSignal): Promise<Header>;
-    constructor(options?: {
+    getHeader(opts?: RequestOptions): Promise<Header>;
+    constructor(args: {
         filehandle?: GenericFilehandle;
@@ -66,4 +66,4 @@ path?: string;
     private _readChromTree;
-    protected getUnzoomedView(opts: RequestOptions): Promise<BlockView>;
-    protected abstract getView(scale: number, opts: RequestOptions): Promise<BlockView>;
+    protected getUnzoomedView(opts?: RequestOptions): Promise<BlockView>;
+    protected abstract getView(scale: number, opts?: RequestOptions): Promise<BlockView>;
     /**
@@ -70,0 +70,0 @@ * Gets features from a BigWig file

esm/bbi.js

@@ -6,3 +6,3 @@ import { Buffer } from 'buffer';
 import { toArray } from 'rxjs/operators';
-import { BlockView } from './blockView';
+import { BlockView } from './block-view';
 const BIG_WIG_MAGIC = -2003829722;
@@ -75,6 +75,5 @@ const BIG_BED_MAGIC = -2021002517;
      */
-    getHeader(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
+    getHeader(opts) {
         if (!this.headerP) {
-            this.headerP = this._getHeader(options).catch(e => {
+            this.headerP = this._getHeader(opts).catch(e => {
                 this.headerP = undefined;
@@ -92,4 +91,4 @@ throw e;
      */
-    constructor(options = {}) {
-        const { filehandle, renameRefSeqs = s => s, path, url } = options;
+    constructor(args) {
+        const { filehandle, renameRefSeqs = s => s, path, url } = args;
         this.renameRefSeqs = renameRefSeqs;
@@ -228,13 +227,12 @@ if (filehandle) {
      */
-    async getFeatureStream(refName, start, end, opts = {
-        scale: 1,
-    }) {
+    async getFeatureStream(refName, start, end, opts) {
         await this.getHeader(opts);
         const chrName = this.renameRefSeqs(refName);
         let view;
-        if (opts.basesPerSpan) {
-            view = await this.getView(1 / opts.basesPerSpan, opts);
+        const { basesPerSpan, scale } = opts || {};
+        if (basesPerSpan) {
+            view = await this.getView(1 / basesPerSpan, opts);
         }
-        else if (opts.scale) {
-            view = await this.getView(opts.scale, opts);
+        else if (scale) {
+            view = await this.getView(scale, opts);
         }
@@ -244,12 +242,7 @@ else {
         }
-        if (!view) {
-            throw new Error('unable to get block view for data');
-        }
-        return new Observable((observer) => {
+        return new Observable(observer => {
             view.readWigData(chrName, start, end, observer, opts);
         });
     }
-    async getFeatures(refName, start, end, opts = {
-        scale: 1,
-    }) {
+    async getFeatures(refName, start, end, opts) {
         const ob = await this.getFeatureStream(refName, start, end, opts);
@@ -256,0 +249,0 @@ const ret = await firstValueFrom(ob.pipe(toArray()));

esm/bigbed.d.ts

@@ -0,8 +1,14 @@
+import AbortablePromiseCache from 'abortable-promise-cache';
 import { BBI, Feature, RequestOptions } from './bbi';
-import { BlockView } from './blockView';
+interface Index {
+    type: number;
+    fieldcount: number;
+    offset: number;
+    field: number;
+}
 export declare function filterUndef<T>(ts: (T | undefined)[]): T[];
 export declare class BigBed extends BBI {
-    readIndicesCache: any;
-    readIndices(opts?: AbortSignal | RequestOptions): any;
-    protected getView(_scale: number, opts: RequestOptions): Promise<BlockView>;
+    readIndicesCache: AbortablePromiseCache<RequestOptions, Index[]>;
+    readIndices(opts?: RequestOptions): Promise<Index[]>;
+    protected getView(_scale: number, opts?: RequestOptions): Promise<import("./block-view").BlockView>;
     private _readIndices;
@@ -12,1 +18,2 @@ private searchExtraIndexBlocks;
 }
+export {};

esm/bigbed.js

@@ -16,16 +16,11 @@ import { Buffer } from 'buffer';
             cache: new QuickLRU({ maxSize: 1 }),
-            fill: async (args, signal) => {
-                return this._readIndices({ ...args, signal });
-            },
+            fill: (args, signal) => this._readIndices({ ...args, signal }),
         });
     }
     readIndices(opts = {}) {
-        const options = 'aborted' in opts ? { signal: opts } : opts;
-        return this.readIndicesCache.get(JSON.stringify(options), options, options.signal);
+        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
      */
@@ -82,3 +77,3 @@ async getView(_scale, opts) {
         const indices = await this.readIndices(opts);
-        if (!indices.length) {
+        if (indices.length === 0) {
             return [];
@@ -163,3 +158,3 @@ }
         const blocks = await this.searchExtraIndexBlocks(name, opts);
-        if (!blocks.length) {
+        if (blocks.length === 0) {
             return [];
@@ -172,4 +167,4 @@ }
             }).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;
                 }
@@ -176,0 +171,0 @@ return x;

esm/bigwig.d.ts

@@ -1,2 +0,2 @@
-import { BlockView } from './blockView';
+import { BlockView } from './block-view';
 import { BBI, RequestOptions } from './bbi';
@@ -3,0 +3,0 @@ export declare class BigWig extends BBI {

esm/bigwig.js

@@ -1,2 +0,2 @@
-import { BlockView } from './blockView';
+import { BlockView } from './block-view';
 import { BBI } from './bbi';
@@ -3,0 +3,0 @@ export class BigWig extends BBI {

esm/range.js

@@ -60,3 +60,3 @@ /* eslint prefer-rest-params:0, no-nested-ternary:0 */
     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;
@@ -97,4 +97,3 @@ let s1 = arg;
         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;
@@ -109,3 +108,3 @@ }
             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;
@@ -112,0 +111,0 @@ }

esm/unzip.d.ts

@@ -1,2 +0,1 @@
-import { inflateSync } from 'zlib';
-export { inflateSync as unzip };
+export { inflateSync as unzip } from 'zlib';

esm/unzip.js

@@ -1,3 +0,2 @@
-import { inflateSync } from 'zlib';
-export { inflateSync as unzip };
+export { inflateSync as unzip } from 'zlib';
 //# sourceMappingURL=unzip.js.map

esm/util.js

@@ -15,17 +15,17 @@ /* eslint no-bitwise: ["error", { "allow": ["|"] }] */
     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,
             }));
@@ -54,6 +54,3 @@ }
         // console.log('bam aborted!')
-        if (typeof DOMException !== 'undefined') {
-            throw new DOMException('aborted', 'AbortError');
-        }
-        else {
+        if (typeof DOMException === 'undefined') {
             const e = new AbortError('aborted');
@@ -63,2 +60,5 @@ e.code = 'ERR_ABORTED';
         }
+        else {
+            throw new DOMException('aborted', 'AbortError');
+        }
     }
@@ -65,0 +65,0 @@ }

package.json

 {
   "name": "@gmod/bbi",
-  "version": "3.0.1",
+  "version": "4.0.0",
   "description": "Parser for BigWig/BigBed files",
@@ -46,2 +46,3 @@ "license": "MIT",
     "binary-parser": "^2.1.0",
+    "eslint-plugin-unicorn": "^46.0.0",
     "generic-filehandle": "^3.0.0",
@@ -54,20 +55,19 @@ "pako": "^2.0.0",
     "@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"
   },
@@ -74,0 +74,0 @@ "publishConfig": {

src/bbi.ts

 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'
 
@@ -133,6 +133,5 @@ const BIG_WIG_MAGIC = -2003829722
    */
-  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
@@ -151,11 +150,9 @@ throw e
    */
-  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
@@ -173,3 +170,3 @@ if (filehandle) {
 
-  private async _getHeader(opts: RequestOptions) {
+  private async _getHeader(opts?: RequestOptions) {
     const header = await this._getMainHeader(opts)
@@ -181,3 +178,3 @@ const chroms = await this._readChromTree(header, opts)
   private async _getMainHeader(
-    opts: RequestOptions,
+    opts?: RequestOptions,
     requestSize = 2000,
@@ -215,3 +212,3 @@ ): Promise<Header> {
 
-  private _isBigEndian(buffer: Buffer): boolean {
+  private _isBigEndian(buffer: Buffer) {
     let ret = buffer.readInt32LE(0)
@@ -229,3 +226,6 @@ if (ret === BIG_WIG_MAGIC || ret === BIG_BED_MAGIC) {
   // 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
@@ -308,3 +308,3 @@ const le = isBE ? 'big' : 'little'
    */
-  protected async getUnzoomedView(opts: RequestOptions): Promise<BlockView> {
+  protected async getUnzoomedView(opts?: RequestOptions) {
     const {
@@ -332,3 +332,3 @@ unzoomedIndexOffset,
     scale: number,
-    opts: RequestOptions,
+    opts?: RequestOptions,
   ): Promise<BlockView>
@@ -348,14 +348,13 @@
     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 {
@@ -365,6 +364,3 @@ 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)
@@ -378,5 +374,3 @@ })
     end: number,
-    opts: RequestOptions & { scale?: number; basesPerSpan?: number } = {
-      scale: 1,
-    },
+    opts?: RequestOptions & { scale?: number; basesPerSpan?: number },
   ) {
@@ -383,0 +377,0 @@ const ob = await this.getFeatureStream(refName, start, end, opts)

src/bigbed.ts

@@ -9,3 +9,2 @@ import { Buffer } from 'buffer'
 import { BBI, Feature, RequestOptions } from './bbi'
-import { BlockView } from './blockView'
 
@@ -31,16 +30,11 @@ interface Loc {
 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)
   }
@@ -50,10 +44,4 @@
    * 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)
@@ -127,3 +115,3 @@ }
     const indices = await this.readIndices(opts)
-    if (!indices.length) {
+    if (indices.length === 0) {
       return []
@@ -226,3 +214,3 @@ }
     const blocks = await this.searchExtraIndexBlocks(name, opts)
-    if (!blocks.length) {
+    if (blocks.length === 0) {
       return []
@@ -237,4 +225,4 @@ }
         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
           }
@@ -241,0 +229,0 @@ return x

src/bigwig.ts

@@ -1,2 +0,2 @@
-import { BlockView } from './blockView'
+import { BlockView } from './block-view'
 import { BBI, RequestOptions } from './bbi'
@@ -3,0 +3,0 @@

src/range.ts

@@ -72,3 +72,3 @@ /* eslint prefer-rest-params:0, no-nested-ternary:0 */
   public intersection(arg: Range): Range {
-    // 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
@@ -113,4 +113,3 @@ let s1 = arg
     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
@@ -126,3 +125,3 @@ }
       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
@@ -129,0 +128,0 @@ }

src/unzip.ts

@@ -1,2 +0,1 @@
-import { inflateSync } from 'zlib'
-export { inflateSync as unzip }
+export { inflateSync as unzip } from 'zlib'

src/util.ts

@@ -18,21 +18,21 @@ /* eslint no-bitwise: ["error", { "allow": ["|"] }] */
   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),
+          Number(block.offset),
       )
-      lastBlock.blocks.push(blocks[i])
+      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,
         }),
@@ -65,8 +65,8 @@ )
     // 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')
     }
@@ -73,0 +73,0 @@ }

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Dev dependency count

18

decreased by-5.26%

Worsened metrics

Total package byte prevSize

244983

decreased by-0.44%

Dependency count

7

increased by16.67%

Number of package files

81

decreased by-1.22%

Lines of code

4145

decreased by-0.05%

Dependency changes

• + Addedeslint-plugin-unicorn@^46.0.0

• + Added@babel/code-frame@7.26.2(transitive)

• + Added@babel/helper-validator-identifier@7.25.9(transitive)

• + Added@eslint-community/eslint-utils@4.4.1(transitive)

• + Added@eslint-community/regexpp@4.12.1(transitive)

• + Added@eslint/config-array@0.19.0(transitive)

• + Added@eslint/core@0.9.0(transitive)

• + Added@eslint/eslintrc@3.2.0(transitive)

• + Added@eslint/js@9.15.0(transitive)

• + Added@eslint/object-schema@2.1.4(transitive)

• + Added@eslint/plugin-kit@0.2.3(transitive)

• + Added@humanfs/core@0.19.1(transitive)

• + Added@humanfs/node@0.16.6(transitive)

• + Added@humanwhocodes/module-importer@1.0.1(transitive)

• + Added@humanwhocodes/retry@0.3.10.4.1(transitive)

• + Added@types/estree@1.0.6(transitive)

• + Added@types/json-schema@7.0.15(transitive)

• + Added@types/normalize-package-data@2.4.4(transitive)

• + Addedacorn@8.14.0(transitive)

• + Addedacorn-jsx@5.3.2(transitive)

• + Addedajv@6.12.6(transitive)

• + Addedansi-styles@4.3.0(transitive)

• + Addedargparse@2.0.1(transitive)

• + Addedbalanced-match@1.0.2(transitive)

• + Addedbrace-expansion@1.1.11(transitive)

• + Addedbuiltin-modules@3.3.0(transitive)

• + Addedcallsites@3.1.0(transitive)

• + Addedchalk@4.1.2(transitive)

• + Addedci-info@3.9.0(transitive)

• + Addedclean-regexp@1.0.0(transitive)

• + Addedcolor-convert@2.0.1(transitive)

• + Addedcolor-name@1.1.4(transitive)

• + Addedconcat-map@0.0.1(transitive)

• + Addedcross-spawn@7.0.6(transitive)

• + Addeddebug@4.3.7(transitive)

• + Addeddeep-is@0.1.4(transitive)

• + Addederror-ex@1.3.2(transitive)

• + Addedescape-string-regexp@1.0.54.0.0(transitive)

• + Addedeslint@9.15.0(transitive)

• + Addedeslint-plugin-unicorn@46.0.1(transitive)

• + Addedeslint-scope@8.2.0(transitive)

• + Addedeslint-visitor-keys@3.4.34.2.0(transitive)

• + Addedespree@10.3.0(transitive)

• + Addedesquery@1.6.0(transitive)

• + Addedesrecurse@4.3.0(transitive)

• + Addedestraverse@5.3.0(transitive)

• + Addedesutils@2.0.3(transitive)

• + Addedfast-deep-equal@3.1.3(transitive)

• + Addedfast-json-stable-stringify@2.1.0(transitive)

• + Addedfast-levenshtein@2.0.6(transitive)

• + Addedfile-entry-cache@8.0.0(transitive)

• + Addedfind-up@4.1.05.0.0(transitive)

• + Addedflat-cache@4.0.1(transitive)

• + Addedflatted@3.3.2(transitive)

• + Addedfunction-bind@1.1.2(transitive)

• + Addedglob-parent@6.0.2(transitive)

• + Addedglobals@14.0.0(transitive)

• + Addedhas-flag@4.0.0(transitive)

• + Addedhasown@2.0.2(transitive)

• + Addedhosted-git-info@2.8.9(transitive)

• + Addedignore@5.3.2(transitive)

• + Addedimport-fresh@3.3.0(transitive)

• + Addedimurmurhash@0.1.4(transitive)

• + Addedindent-string@4.0.0(transitive)

• + Addedis-arrayish@0.2.1(transitive)

• + Addedis-builtin-module@3.2.1(transitive)

• + Addedis-core-module@2.15.1(transitive)

• + Addedis-extglob@2.1.1(transitive)

• + Addedis-glob@4.0.3(transitive)

• + Addedisexe@2.0.0(transitive)

• + Addedjs-tokens@4.0.0(transitive)

• + Addedjs-yaml@4.1.0(transitive)

• + Addedjsesc@0.5.03.0.2(transitive)

• + Addedjson-buffer@3.0.1(transitive)

• + Addedjson-parse-even-better-errors@2.3.1(transitive)

• + Addedjson-schema-traverse@0.4.1(transitive)

• + Addedjson-stable-stringify-without-jsonify@1.0.1(transitive)

• + Addedkeyv@4.5.4(transitive)

• + Addedlevn@0.4.1(transitive)

• + Addedlines-and-columns@1.2.4(transitive)

• + Addedlocate-path@5.0.06.0.0(transitive)

• + Addedlodash@4.17.21(transitive)

• + Addedlodash.merge@4.6.2(transitive)

• + Addedmin-indent@1.0.1(transitive)

• + Addedminimatch@3.1.2(transitive)

• + Addedms@2.1.3(transitive)

• + Addednatural-compare@1.4.0(transitive)

• + Addednormalize-package-data@2.5.0(transitive)

• + Addedoptionator@0.9.4(transitive)

• + Addedp-limit@2.3.03.1.0(transitive)

• + Addedp-locate@4.1.05.0.0(transitive)

• + Addedp-try@2.2.0(transitive)

• + Addedparent-module@1.0.1(transitive)

• + Addedparse-json@5.2.0(transitive)

• + Addedpath-exists@4.0.0(transitive)

• + Addedpath-key@3.1.1(transitive)

• + Addedpath-parse@1.0.7(transitive)

• + Addedpicocolors@1.1.1(transitive)

• + Addedpluralize@8.0.0(transitive)

• + Addedprelude-ls@1.2.1(transitive)

• + Addedpunycode@2.3.1(transitive)

• + Addedread-pkg@5.2.0(transitive)

• + Addedread-pkg-up@7.0.1(transitive)

• + Addedregexp-tree@0.1.27(transitive)

• + Addedregjsparser@0.9.1(transitive)

• + Addedresolve@1.22.8(transitive)

• + Addedresolve-from@4.0.0(transitive)

• + Addedsafe-regex@2.1.1(transitive)

• + Addedsemver@5.7.27.6.3(transitive)

• + Addedshebang-command@2.0.0(transitive)

• + Addedshebang-regex@3.0.0(transitive)

• + Addedspdx-correct@3.2.0(transitive)

• + Addedspdx-exceptions@2.5.0(transitive)

• + Addedspdx-expression-parse@3.0.1(transitive)

• + Addedspdx-license-ids@3.0.20(transitive)

• + Addedstrip-indent@3.0.0(transitive)

• + Addedstrip-json-comments@3.1.1(transitive)

• + Addedsupports-color@7.2.0(transitive)

• + Addedsupports-preserve-symlinks-flag@1.0.0(transitive)

• + Addedtype-check@0.4.0(transitive)

• + Addedtype-fest@0.6.00.8.1(transitive)

• + Addeduri-js@4.4.1(transitive)

• + Addedvalidate-npm-package-license@3.0.4(transitive)

• + Addedwhich@2.0.2(transitive)

• + Addedword-wrap@1.2.5(transitive)

• + Addedyocto-queue@0.1.0(transitive)