@gmod/bbi - npm Package Compare versions

Comparing version 4.0.4 to 4.0.5

CHANGELOG.md

@@ -0,1 +1,5 @@
+## [4.0.5](https://github.com/GMOD/bbi-js/compare/v4.0.4...v4.0.5) (2024-06-19)
+
+
+
 ## [4.0.4](https://github.com/GMOD/bbi-js/compare/v4.0.3...v4.0.4) (2024-3-5)
@@ -2,0 +6,0 @@

dist/bbi.d.ts

@@ -26,2 +26,3 @@ import { GenericFilehandle } from 'generic-filehandle';
 export interface Header {
+    version: number;
     autoSql: string;
@@ -39,8 +40,4 @@ totalSummary: Statistics;
     fileType: string;
-    refsByName: {
-        [key: string]: number;
-    };
-    refsByNumber: {
-        [key: number]: RefInfo;
-    };
+    refsByName: Record<string, number>;
+    refsByNumber: Record<number, RefInfo>;
 }
@@ -47,0 +44,0 @@ export interface RequestOptions {

dist/bbi.js

@@ -24,3 +24,4 @@ "use strict";
 }
-/* get the compiled parsers for different sections of the bigwig file
+/**
+ * get the compiled parsers for different sections of the bigwig file
  *
@@ -83,6 +84,2 @@ * @param isBE - is big endian, typically false
 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) {
@@ -130,4 +127,4 @@ if (!this.headerP) {
     }
-    _getMainHeader(opts, requestSize = 2000) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _getMainHeader(opts_1) {
+        return __awaiter(this, arguments, void 0, function* (opts, requestSize = 2000) {
             const { buffer } = yield this.bbi.read(buffer_1.Buffer.alloc(requestSize), 0, requestSize, 0, opts);
@@ -269,3 +266,5 @@ const isBigEndian = this._isBigEndian(buffer);
             return new rxjs_1.Observable(observer => {
-                view.readWigData(chrName, start, end, observer, opts);
+                view
+                    .readWigData(chrName, start, end, observer, opts)
+                    .catch(e => observer.error(e));
             });
@@ -272,0 +271,0 @@ });

dist/bigbed.js

@@ -104,4 +104,4 @@ "use strict";
      */
-    searchExtraIndexBlocks(name, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    searchExtraIndexBlocks(name_1) {
+        return __awaiter(this, arguments, void 0, function* (name, opts = {}) {
             const { isBigEndian } = yield this.getHeader(opts);
@@ -158,14 +158,13 @@ const indices = yield this.readIndices(opts);
                         let lastOffset;
-                        for (let i = 0; i < node.leafkeys.length; i += 1) {
-                            const { key } = node.leafkeys[i];
+                        for (const { key, offset } of node.leafkeys) {
                             if (name.localeCompare(key) < 0 && lastOffset) {
                                 return bptReadNode(lastOffset);
                             }
-                            lastOffset = node.leafkeys[i].offset;
+                            lastOffset = offset;
                         }
                         return bptReadNode(lastOffset);
                     }
-                    for (let i = 0; i < node.keys.length; i += 1) {
-                        if (node.keys[i].key === name) {
-                            return Object.assign(Object.assign({}, node.keys[i]), { field });
+                    for (const n of node.keys) {
+                        if (n.key === name) {
+                            return Object.assign(Object.assign({}, n), { field });
                         }
@@ -182,4 +181,5 @@ }
     /*
-     * retrieve the features from the bigbed data that were found through the lookup of the extraIndex
-     * note that there can be multiple extraIndex, see the BigBed specification and the -extraIndex argument to bedToBigBed
+     * retrieve the features from the bigbed data that were found through the
+     * lookup of the extraIndex note that there can be multiple extraIndex, see
+     * the BigBed specification and the -extraIndex argument to bedToBigBed
      *
@@ -190,4 +190,4 @@ * @param name - the name to search for
      */
-    searchExtraIndex(name, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    searchExtraIndex(name_1) {
+        return __awaiter(this, arguments, void 0, function* (name, opts = {}) {
             const blocks = yield this.searchExtraIndexBlocks(name, opts);
@@ -200,3 +200,3 @@ if (blocks.length === 0) {
                 return new rxjs_1.Observable(observer => {
-                    view.readFeatures(observer, [block], opts);
+                    view.readFeatures(observer, [block], opts).catch(e => observer.error(e));
                 }).pipe((0, operators_1.reduce)((acc, curr) => acc.concat(curr)), (0, operators_1.map)(x => {
@@ -203,0 +203,0 @@ for (const element of x) {

dist/bigwig.d.ts

@@ -8,5 +8,7 @@ import { BlockView } from './block-view';
      * @param scale - number
-     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
+     *
+     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
+     * or scale used to infer the zoomLevel to use
      */
     protected getView(scale: number, opts: RequestOptions): Promise<BlockView>;
 }

dist/bigwig.js

@@ -20,3 +20,5 @@ "use strict";
      * @param scale - number
-     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
+     *
+     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
+     * or scale used to infer the zoomLevel to use
      */
@@ -23,0 +25,0 @@ getView(scale, opts) {

dist/block-view.js

@@ -181,3 +181,3 @@ "use strict";
                                 .filter(f => filterFeats(f))
-                                .map((l) => ({
+                                .map(l => ({
                                 offset: l.blockOffset,
@@ -238,2 +238,3 @@ length: l.blockSize,
                         }
+                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
                         spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));
@@ -358,4 +359,4 @@ }
     }
-    readFeatures(observer, blocks, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
+    readFeatures(observer_1, blocks_1) {
+        return __awaiter(this, arguments, void 0, function* (observer, blocks, opts = {}) {
             try {
@@ -362,0 +363,0 @@ const { blockType, isCompressed } = this;

dist/range.js

 "use strict";
-/* eslint prefer-rest-params:0, no-nested-ternary:0 */
+/**
+ * Adapted from a combination of Range and _Compound in the
+ * Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
+ */
 Object.defineProperty(exports, "__esModule", { value: true });
@@ -51,4 +54,3 @@ class Range {
         let current = ranges[0];
-        for (let i = 1; i < ranges.length; i += 1) {
-            const nxt = ranges[i];
+        for (const nxt of ranges) {
             if (nxt.min > current.max + 1) {
@@ -55,0 +57,0 @@ oranges.push(current);

esm/bbi.d.ts

@@ -26,2 +26,3 @@ import { GenericFilehandle } from 'generic-filehandle';
 export interface Header {
+    version: number;
     autoSql: string;
@@ -39,8 +40,4 @@ totalSummary: Statistics;
     fileType: string;
-    refsByName: {
-        [key: string]: number;
-    };
-    refsByNumber: {
-        [key: number]: RefInfo;
-    };
+    refsByName: Record<string, number>;
+    refsByNumber: Record<number, RefInfo>;
 }
@@ -47,0 +44,0 @@ export interface RequestOptions {

esm/bbi.js

@@ -12,3 +12,4 @@ import { Buffer } from 'buffer';
 }
-/* get the compiled parsers for different sections of the bigwig file
+/**
+ * get the compiled parsers for different sections of the bigwig file
  *
@@ -71,6 +72,2 @@ * @param isBE - is big endian, typically false
 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) {
@@ -247,3 +244,5 @@ if (!this.headerP) {
         return new Observable(observer => {
-            view.readWigData(chrName, start, end, observer, opts);
+            view
+                .readWigData(chrName, start, end, observer, opts)
+                .catch(e => observer.error(e));
         });
@@ -250,0 +249,0 @@ }

esm/bigbed.js

@@ -125,14 +125,13 @@ import { Buffer } from 'buffer';
                     let lastOffset;
-                    for (let i = 0; i < node.leafkeys.length; i += 1) {
-                        const { key } = node.leafkeys[i];
+                    for (const { key, offset } of node.leafkeys) {
                         if (name.localeCompare(key) < 0 && lastOffset) {
                             return bptReadNode(lastOffset);
                         }
-                        lastOffset = node.leafkeys[i].offset;
+                        lastOffset = offset;
                     }
                     return bptReadNode(lastOffset);
                 }
-                for (let i = 0; i < node.keys.length; i += 1) {
-                    if (node.keys[i].key === name) {
-                        return { ...node.keys[i], field };
+                for (const n of node.keys) {
+                    if (n.key === name) {
+                        return { ...n, field };
                     }
@@ -148,4 +147,5 @@ }
     /*
-     * retrieve the features from the bigbed data that were found through the lookup of the extraIndex
-     * note that there can be multiple extraIndex, see the BigBed specification and the -extraIndex argument to bedToBigBed
+     * retrieve the features from the bigbed data that were found through the
+     * lookup of the extraIndex note that there can be multiple extraIndex, see
+     * the BigBed specification and the -extraIndex argument to bedToBigBed
      *
@@ -164,3 +164,3 @@ * @param name - the name to search for
             return new Observable(observer => {
-                view.readFeatures(observer, [block], opts);
+                view.readFeatures(observer, [block], opts).catch(e => observer.error(e));
             }).pipe(reduce((acc, curr) => acc.concat(curr)), map(x => {
@@ -167,0 +167,0 @@ for (const element of x) {

esm/bigwig.d.ts

@@ -8,5 +8,7 @@ import { BlockView } from './block-view';
      * @param scale - number
-     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
+     *
+     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
+     * or scale used to infer the zoomLevel to use
      */
     protected getView(scale: number, opts: RequestOptions): Promise<BlockView>;
 }

esm/bigwig.js

@@ -8,3 +8,5 @@ import { BlockView } from './block-view';
      * @param scale - number
-     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
+     *
+     * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
+     * or scale used to infer the zoomLevel to use
      */
@@ -11,0 +13,0 @@ async getView(scale, opts) {

esm/block-view.js

@@ -165,3 +165,3 @@ import { Buffer } from 'buffer';
                             .filter(f => filterFeats(f))
-                            .map((l) => ({
+                            .map(l => ({
                             offset: l.blockOffset,
@@ -225,2 +225,3 @@ length: l.blockSize,
                     }
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
                     spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));
@@ -227,0 +228,0 @@ }

esm/range.js

@@ -1,2 +0,5 @@
-/* eslint prefer-rest-params:0, no-nested-ternary:0 */
+/**
+ * Adapted from a combination of Range and _Compound in the
+ * Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
+ */
 export default class Range {
@@ -49,4 +52,3 @@ constructor(arg1) {
         let current = ranges[0];
-        for (let i = 1; i < ranges.length; i += 1) {
-            const nxt = ranges[i];
+        for (const nxt of ranges) {
             if (nxt.min > current.max + 1) {
@@ -53,0 +55,0 @@ oranges.push(current);

package.json

 {
   "name": "@gmod/bbi",
-  "version": "4.0.4",
+  "version": "4.0.5",
   "description": "Parser for BigWig/BigBed files",
@@ -25,3 +25,3 @@ "license": "MIT",
     "coverage": "npm test -- --coverage",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts src",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src",
     "format": "prettier",
@@ -58,8 +58,8 @@ "clean": "rimraf dist esm",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^6.21.0",
-    "@typescript-eslint/parser": "^6.21.0",
-    "eslint": "^8.46.0",
+    "@typescript-eslint/eslint-plugin": "^7.3.1",
+    "@typescript-eslint/parser": "^7.3.1",
+    "eslint": "^9.0.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^51.0.0",
+    "eslint-plugin-unicorn": "^54.0.0",
     "jest": "^29.6.2",
@@ -69,3 +69,3 @@ "jest-environment-jsdom": "^29.6.2",
     "rimraf": "^5.0.1",
-    "standard-changelog": "^5.0.0",
+    "standard-changelog": "^6.0.0",
     "ts-jest": "^29.1.2",
@@ -72,0 +72,0 @@ "typescript": "^5.1.6"

src/bbi.ts

@@ -38,2 +38,3 @@ import { Buffer } from 'buffer'
 export interface Header {
+  version: number
   autoSql: string
@@ -51,7 +52,8 @@ totalSummary: Statistics
   fileType: string
-  refsByName: { [key: string]: number }
-  refsByNumber: { [key: number]: RefInfo }
+  refsByName: Record<string, number>
+  refsByNumber: Record<number, RefInfo>
 }
 
-/* get the compiled parsers for different sections of the bigwig file
+/**
+ * get the compiled parsers for different sections of the bigwig file
  *
@@ -131,6 +133,2 @@ * @param isBE - is big endian, typically false
 
-  /* fetch and parse header information from a bigwig or bigbed file
-   * @param abortSignal - abort the operation, can be null
-   * @return a Header object
-   */
   public getHeader(opts?: RequestOptions) {
@@ -238,6 +236,7 @@ if (!this.headerP) {
     const le = isBE ? 'big' : 'little'
-    const refsByNumber: {
-      [key: number]: { name: string; id: number; length: number }
-    } = []
-    const refsByName: { [key: string]: number } = {}
+    const refsByNumber: Record<
+      number,
+      { name: string; id: number; length: number }
+    > = []
+    const refsByName: Record<string, number> = {}
 
@@ -368,3 +367,5 @@ let unzoomedDataOffset = Number(header.unzoomedDataOffset)
     return new Observable<Feature[]>(observer => {
-      view.readWigData(chrName, start, end, observer, opts)
+      view
+        .readWigData(chrName, start, end, observer, opts)
+        .catch(e => observer.error(e))
     })
@@ -371,0 +372,0 @@ }

src/bigbed.ts

@@ -177,14 +177,13 @@ import { Buffer } from 'buffer'
           let lastOffset
-          for (let i = 0; i < node.leafkeys.length; i += 1) {
-            const { key } = node.leafkeys[i]
+          for (const { key, offset } of node.leafkeys) {
             if (name.localeCompare(key) < 0 && lastOffset) {
               return bptReadNode(lastOffset)
             }
-            lastOffset = node.leafkeys[i].offset
+            lastOffset = offset
           }
           return bptReadNode(lastOffset)
         }
-        for (let i = 0; i < node.keys.length; i += 1) {
-          if (node.keys[i].key === name) {
-            return { ...node.keys[i], field }
+        for (const n of node.keys) {
+          if (n.key === name) {
+            return { ...n, field }
           }
@@ -202,4 +201,5 @@ }
   /*
-   * retrieve the features from the bigbed data that were found through the lookup of the extraIndex
-   * note that there can be multiple extraIndex, see the BigBed specification and the -extraIndex argument to bedToBigBed
+   * retrieve the features from the bigbed data that were found through the
+   * lookup of the extraIndex note that there can be multiple extraIndex, see
+   * the BigBed specification and the -extraIndex argument to bedToBigBed
    *
@@ -218,3 +218,3 @@ * @param name - the name to search for
       return new Observable<Feature[]>(observer => {
-        view.readFeatures(observer, [block], opts)
+        view.readFeatures(observer, [block], opts).catch(e => observer.error(e))
       }).pipe(
@@ -221,0 +221,0 @@ reduce((acc, curr) => acc.concat(curr)),

src/bigwig.ts

@@ -9,3 +9,5 @@ import { BlockView } from './block-view'
    * @param scale - number
-   * @param opts - An object containing basesPerSpan (e.g. pixels per basepair) or scale used to infer the zoomLevel to use
+   *
+   * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
+   * or scale used to infer the zoomLevel to use
    */
@@ -12,0 +14,0 @@ protected async getView(scale: number, opts: RequestOptions) {

src/block-view.ts

@@ -238,3 +238,3 @@ import { Buffer } from 'buffer'
                 .filter(f => filterFeats(f))
-                .map((l: { blockOffset: bigint; blockSize: bigint }) => ({
+                .map(l => ({
                   offset: l.blockOffset,
@@ -310,2 +310,3 @@ length: l.blockSize,
           }
+          // eslint-disable-next-line @typescript-eslint/no-floating-promises
           spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level))
@@ -312,0 +313,0 @@ } catch (e) {

src/range.ts

@@ -1,3 +0,1 @@
-/* eslint prefer-rest-params:0, no-nested-ternary:0 */
-
 /**
@@ -48,3 +46,3 @@ * Adapted from a combination of Range and _Compound in the
 
-  public union(s1: Range): Range {
+  public union(s1: Range) {
     const ranges = [...this.getRanges(), ...s1.getRanges()].sort((a, b) => {
@@ -63,7 +61,6 @@ if (a.min < b.min) {
     })
-    const oranges = []
+    const oranges = [] as Range[]
     let current = ranges[0]
 
-    for (let i = 1; i < ranges.length; i += 1) {
-      const nxt = ranges[i]
+    for (const nxt of ranges) {
       if (nxt.min > current.max + 1) {
@@ -70,0 +67,0 @@ oranges.push(current)

No alert changes

Improved metrics

Lines of code

4015

increased by0.2%

Worsened metrics

Total package byte prevSize

239611

decreased by-0.25%

No dependency changes