@gmod/bbi - npm Package Compare versions

Comparing version 4.0.3 to 4.0.4

CHANGELOG.md

@@ -1,12 +0,16 @@
-## [4.0.3](https://github.com/GMOD/bbi-js/compare/v4.0.2...v4.0.3) (2024-01-16)
+## [4.0.4](https://github.com/GMOD/bbi-js/compare/v4.0.3...v4.0.4) (2024-3-5)
 
 
-### Performance Improvements
 
-* optimize `parseBigBedBlock` ([#58](https://github.com/GMOD/bbi-js/issues/58)) ([eb3f7a4](https://github.com/GMOD/bbi-js/commit/eb3f7a4885c4e8262c6e3e63696b533e53072463))
+- Fix issue fetching data from file where refNames are not sorted (#59)
 
+## [4.0.3](https://github.com/GMOD/bbi-js/compare/v4.0.2...v4.0.3) (2024-01-16)
 
+### Performance Improvements
 
-- Small perf improvement (#58)
+- optimize `parseBigBedBlock` ([#58](https://github.com/GMOD/bbi-js/issues/58))
+  ([eb3f7a4](https://github.com/GMOD/bbi-js/commit/eb3f7a4885c4e8262c6e3e63696b533e53072463))
 
+* Small perf improvement (#58)
+
 ## [4.0.2](https://github.com/GMOD/bbi-js/compare/v4.0.1...v4.0.2) (2023-07-30)
@@ -13,0 +17,0 @@

dist/block-view.js

@@ -206,4 +206,4 @@ "use strict";
                     try {
-                        const length = fr.max() - fr.min();
-                        const offset = fr.min();
+                        const length = fr.max - fr.min;
+                        const offset = fr.min;
                         const resultBuffer = yield this.featureCache.get(`${length}_${offset}`, { length, offset }, opts === null || opts === void 0 ? void 0 : opts.signal);
@@ -215,3 +215,3 @@ for (const element of off) {
                                 if (outstanding === 0) {
-                                    this.readFeatures(observer, blocksToFetch, Object.assign(Object.assign({}, opts), { request }));
+                                    this.readFeatures(observer, blocksToFetch, Object.assign(Object.assign({}, opts), { request })).catch(e => observer.error(e));
                                 }
@@ -230,5 +230,9 @@ }
                         const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32;
-                        let spans = new range_1.default(offset[0], offset[0] + maxCirBlockSpan);
+                        let spans = new range_1.default([
+                            { min: offset[0], max: offset[0] + maxCirBlockSpan },
+                        ]);
                         for (let i = 1; i < offset.length; i += 1) {
-                            const blockSpan = new range_1.default(offset[i], offset[i] + maxCirBlockSpan);
+                            const blockSpan = new range_1.default([
+                                { min: offset[i], max: offset[i] + maxCirBlockSpan },
+                            ]);
                             spans = spans.union(blockSpan);
@@ -235,0 +239,0 @@ }

dist/range.d.ts

@@ -5,7 +5,11 @@ /**
  */
+export interface IRange {
+    min: number;
+    max: number;
+}
 export default class Range {
-    ranges: any;
-    constructor(arg1: any, arg2?: any);
-    min(): number;
-    max(): number;
+    ranges: IRange[];
+    constructor(arg1: IRange[]);
+    get min(): number;
+    get max(): number;
     contains(pos: number): boolean;
@@ -16,5 +20,2 @@ isContiguous(): boolean;
     union(s1: Range): Range;
-    intersection(arg: Range): Range;
-    coverage(): number;
-    rangeOrder(tmpa: Range, tmpb: Range): number;
 }

dist/range.js

 "use strict";
 /* eslint prefer-rest-params:0, no-nested-ternary:0 */
 Object.defineProperty(exports, "__esModule", { value: true });
-/**
- * Adapted from a combination of Range and _Compound in the
- * Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
- */
 class Range {
-    constructor(arg1, arg2) {
-        this.ranges =
-            arguments.length === 2
-                ? [{ min: arg1, max: arg2 }]
-                : 0 in arg1
-                    ? Object.assign({}, arg1)
-                    : [arg1];
+    constructor(arg1) {
+        this.ranges = arg1;
     }
-    min() {
+    get min() {
         return this.ranges[0].min;
     }
-    max() {
+    get max() {
         return this.ranges[this.ranges.length - 1].max;
     }
     contains(pos) {
-        for (let s = 0; s < this.ranges.length; s += 1) {
-            const r = this.ranges[s];
+        for (const r of this.ranges) {
             if (r.min <= pos && r.max >= pos) {
@@ -36,9 +26,25 @@ return true;
     getRanges() {
-        return this.ranges.map((r) => new Range(r.min, r.max));
+        return this.ranges.map(r => new Range([{ min: r.min, max: r.max }]));
     }
     toString() {
-        return this.ranges.map((r) => `[${r.min}-${r.max}]`).join(',');
+        return this.ranges.map(r => `[${r.min}-${r.max}]`).join(',');
     }
     union(s1) {
-        const ranges = this.getRanges().concat(s1.getRanges()).sort(this.rangeOrder);
+        const ranges = [...this.getRanges(), ...s1.getRanges()].sort((a, b) => {
+            if (a.min < b.min) {
+                return -1;
+            }
+            else if (a.min > b.min) {
+                return 1;
+            }
+            else if (a.max < b.max) {
+                return -1;
+            }
+            else if (b.max > a.max) {
+                return 1;
+            }
+            else {
+                return 0;
+            }
+        });
         const oranges = [];
@@ -48,82 +54,15 @@ let current = ranges[0];
             const nxt = ranges[i];
-            if (nxt.min() > current.max() + 1) {
+            if (nxt.min > current.max + 1) {
                 oranges.push(current);
                 current = nxt;
             }
-            else if (nxt.max() > current.max()) {
-                current = new Range(current.min(), nxt.max());
+            else if (nxt.max > current.max) {
+                current = new Range([{ min: current.min, max: nxt.max }]);
             }
         }
         oranges.push(current);
-        if (oranges.length === 1) {
-            return oranges[0];
-        }
-        return new Range(oranges);
+        return oranges.length === 1 ? oranges[0] : new Range(oranges);
     }
-    intersection(arg) {
-        // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
-        let s0 = this;
-        let s1 = arg;
-        const r0 = this.ranges();
-        const r1 = s1.ranges();
-        const l0 = r0.length;
-        const l1 = r1.length;
-        let i0 = 0;
-        let i1 = 0;
-        const or = [];
-        while (i0 < l0 && i1 < l1) {
-            s0 = r0[i0];
-            s1 = r1[i1];
-            const lapMin = Math.max(s0.min(), s1.min());
-            const lapMax = Math.min(s0.max(), s1.max());
-            if (lapMax >= lapMin) {
-                or.push(new Range(lapMin, lapMax));
-            }
-            if (s0.max() > s1.max()) {
-                i1 += 1;
-            }
-            else {
-                i0 += 1;
-            }
-        }
-        if (or.length === 0) {
-            throw new Error('found range of length 0');
-        }
-        if (or.length === 1) {
-            return or[0];
-        }
-        return new Range(or);
-    }
-    coverage() {
-        let tot = 0;
-        const rl = this.ranges();
-        for (const r of rl) {
-            tot += r.max() - r.min() + 1;
-        }
-        return tot;
-    }
-    rangeOrder(tmpa, tmpb) {
-        let a = tmpa;
-        let b = tmpb;
-        if (arguments.length < 2) {
-            b = a;
-            // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
-            a = this;
-        }
-        if (a.min() < b.min()) {
-            return -1;
-        }
-        if (a.min() > b.min()) {
-            return 1;
-        }
-        if (a.max() < b.max()) {
-            return -1;
-        }
-        if (b.max() > a.max()) {
-            return 1;
-        }
-        return 0;
-    }
 }
 exports.default = Range;
 //# sourceMappingURL=range.js.map

esm/block-view.js

@@ -190,4 +190,4 @@ import { Buffer } from 'buffer';
                 try {
-                    const length = fr.max() - fr.min();
-                    const offset = fr.min();
+                    const length = fr.max - fr.min;
+                    const offset = fr.min;
                     const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts === null || opts === void 0 ? void 0 : opts.signal);
@@ -199,3 +199,6 @@ for (const element of off) {
                             if (outstanding === 0) {
-                                this.readFeatures(observer, blocksToFetch, { ...opts, request });
+                                this.readFeatures(observer, blocksToFetch, {
+                                    ...opts,
+                                    request,
+                                }).catch(e => observer.error(e));
                             }
@@ -214,5 +217,9 @@ }
                     const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32;
-                    let spans = new Range(offset[0], offset[0] + maxCirBlockSpan);
+                    let spans = new Range([
+                        { min: offset[0], max: offset[0] + maxCirBlockSpan },
+                    ]);
                     for (let i = 1; i < offset.length; i += 1) {
-                        const blockSpan = new Range(offset[i], offset[i] + maxCirBlockSpan);
+                        const blockSpan = new Range([
+                            { min: offset[i], max: offset[i] + maxCirBlockSpan },
+                        ]);
                         spans = spans.union(blockSpan);
@@ -219,0 +226,0 @@ }

esm/range.d.ts

@@ -5,7 +5,11 @@ /**
  */
+export interface IRange {
+    min: number;
+    max: number;
+}
 export default class Range {
-    ranges: any;
-    constructor(arg1: any, arg2?: any);
-    min(): number;
-    max(): number;
+    ranges: IRange[];
+    constructor(arg1: IRange[]);
+    get min(): number;
+    get max(): number;
     contains(pos: number): boolean;
@@ -16,5 +20,2 @@ isContiguous(): boolean;
     union(s1: Range): Range;
-    intersection(arg: Range): Range;
-    coverage(): number;
-    rangeOrder(tmpa: Range, tmpb: Range): number;
 }

esm/range.js

 /* 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 {
-    constructor(arg1, arg2) {
-        this.ranges =
-            arguments.length === 2
-                ? [{ min: arg1, max: arg2 }]
-                : 0 in arg1
-                    ? Object.assign({}, arg1)
-                    : [arg1];
+    constructor(arg1) {
+        this.ranges = arg1;
     }
-    min() {
+    get min() {
         return this.ranges[0].min;
     }
-    max() {
+    get max() {
         return this.ranges[this.ranges.length - 1].max;
     }
     contains(pos) {
-        for (let s = 0; s < this.ranges.length; s += 1) {
-            const r = this.ranges[s];
+        for (const r of this.ranges) {
             if (r.min <= pos && r.max >= pos) {
@@ -34,9 +24,25 @@ return true;
     getRanges() {
-        return this.ranges.map((r) => new Range(r.min, r.max));
+        return this.ranges.map(r => new Range([{ min: r.min, max: r.max }]));
     }
     toString() {
-        return this.ranges.map((r) => `[${r.min}-${r.max}]`).join(',');
+        return this.ranges.map(r => `[${r.min}-${r.max}]`).join(',');
     }
     union(s1) {
-        const ranges = this.getRanges().concat(s1.getRanges()).sort(this.rangeOrder);
+        const ranges = [...this.getRanges(), ...s1.getRanges()].sort((a, b) => {
+            if (a.min < b.min) {
+                return -1;
+            }
+            else if (a.min > b.min) {
+                return 1;
+            }
+            else if (a.max < b.max) {
+                return -1;
+            }
+            else if (b.max > a.max) {
+                return 1;
+            }
+            else {
+                return 0;
+            }
+        });
         const oranges = [];
@@ -46,81 +52,14 @@ let current = ranges[0];
             const nxt = ranges[i];
-            if (nxt.min() > current.max() + 1) {
+            if (nxt.min > current.max + 1) {
                 oranges.push(current);
                 current = nxt;
             }
-            else if (nxt.max() > current.max()) {
-                current = new Range(current.min(), nxt.max());
+            else if (nxt.max > current.max) {
+                current = new Range([{ min: current.min, max: nxt.max }]);
             }
         }
         oranges.push(current);
-        if (oranges.length === 1) {
-            return oranges[0];
-        }
-        return new Range(oranges);
+        return oranges.length === 1 ? oranges[0] : new Range(oranges);
     }
-    intersection(arg) {
-        // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
-        let s0 = this;
-        let s1 = arg;
-        const r0 = this.ranges();
-        const r1 = s1.ranges();
-        const l0 = r0.length;
-        const l1 = r1.length;
-        let i0 = 0;
-        let i1 = 0;
-        const or = [];
-        while (i0 < l0 && i1 < l1) {
-            s0 = r0[i0];
-            s1 = r1[i1];
-            const lapMin = Math.max(s0.min(), s1.min());
-            const lapMax = Math.min(s0.max(), s1.max());
-            if (lapMax >= lapMin) {
-                or.push(new Range(lapMin, lapMax));
-            }
-            if (s0.max() > s1.max()) {
-                i1 += 1;
-            }
-            else {
-                i0 += 1;
-            }
-        }
-        if (or.length === 0) {
-            throw new Error('found range of length 0');
-        }
-        if (or.length === 1) {
-            return or[0];
-        }
-        return new Range(or);
-    }
-    coverage() {
-        let tot = 0;
-        const rl = this.ranges();
-        for (const r of rl) {
-            tot += r.max() - r.min() + 1;
-        }
-        return tot;
-    }
-    rangeOrder(tmpa, tmpb) {
-        let a = tmpa;
-        let b = tmpb;
-        if (arguments.length < 2) {
-            b = a;
-            // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
-            a = this;
-        }
-        if (a.min() < b.min()) {
-            return -1;
-        }
-        if (a.min() > b.min()) {
-            return 1;
-        }
-        if (a.max() < b.max()) {
-            return -1;
-        }
-        if (b.max() > a.max()) {
-            return 1;
-        }
-        return 0;
-    }
 }
 //# sourceMappingURL=range.js.map

package.json

 {
   "name": "@gmod/bbi",
-  "version": "4.0.3",
+  "version": "4.0.4",
   "description": "Parser for BigWig/BigBed files",
@@ -54,17 +54,17 @@ "license": "MIT",
     "@gmod/bed": "^2.1.2",
-    "@types/jest": "^29.5.3",
-    "@types/node": "^20.4.5",
+    "@types/jest": "^29.5.12",
+    "@types/node": "^20.11.16",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^6.2.0",
-    "@typescript-eslint/parser": "^6.2.0",
+    "@typescript-eslint/eslint-plugin": "^6.21.0",
+    "@typescript-eslint/parser": "^6.21.0",
     "eslint": "^8.46.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^50.0.1",
+    "eslint-plugin-unicorn": "^51.0.0",
     "jest": "^29.6.2",
     "jest-environment-jsdom": "^29.6.2",
-    "prettier": "^3.0.0",
+    "prettier": "^3.2.5",
     "rimraf": "^5.0.1",
-    "standard-changelog": "^3.0.0",
-    "ts-jest": "^29.1.1",
+    "standard-changelog": "^5.0.0",
+    "ts-jest": "^29.1.2",
     "typescript": "^5.1.6"
@@ -71,0 +71,0 @@ },

README.md

@@ -32,3 +32,4 @@ # bbi-js
 
-// if running in the browser, RemoteFile will use the the global fetch
+// if running in the browser or newer versions of node.js, RemoteFile will use
+// the the global fetch
 const file = new BigWig({
@@ -38,3 +39,3 @@ filehandle: new RemoteFile('volvox.bw'),
 
-// if running under node.js you must supply the fetch function to RemoteFile
+// old versions of node.js without a global fetch, supply custom fetch function
 const fetch = require('node-fetch')
@@ -41,0 +42,0 @@ const file = new BigWig({

src/block-view.ts

@@ -271,4 +271,4 @@ import { Buffer } from 'buffer'
         try {
-          const length = fr.max() - fr.min()
-          const offset = fr.min()
+          const length = fr.max - fr.min
+          const offset = fr.min
           const resultBuffer: Buffer = await this.featureCache.get(
@@ -284,3 +284,6 @@ `${length}_${offset}`,
               if (outstanding === 0) {
-                this.readFeatures(observer, blocksToFetch, { ...opts, request })
+                this.readFeatures(observer, blocksToFetch, {
+                  ...opts,
+                  request,
+                }).catch(e => observer.error(e))
               }
@@ -299,5 +302,9 @@ }
           const maxCirBlockSpan = 4 + Number(cirBlockSize) * 32
-          let spans = new Range(offset[0], offset[0] + maxCirBlockSpan)
+          let spans = new Range([
+            { min: offset[0], max: offset[0] + maxCirBlockSpan },
+          ])
           for (let i = 1; i < offset.length; i += 1) {
-            const blockSpan = new Range(offset[i], offset[i] + maxCirBlockSpan)
+            const blockSpan = new Range([
+              { min: offset[i], max: offset[i] + maxCirBlockSpan },
+            ])
             spans = spans.union(blockSpan)
@@ -304,0 +311,0 @@ }

src/range.ts

@@ -7,25 +7,24 @@ /* eslint prefer-rest-params:0, no-nested-ternary:0 */
  */
+
+export interface IRange {
+  min: number
+  max: number
+}
 export default class Range {
-  public ranges: any
+  public ranges: IRange[]
 
-  public constructor(arg1: any, arg2?: any) {
-    this.ranges =
-      arguments.length === 2
-        ? [{ min: arg1, max: arg2 }]
-        : 0 in arg1
-          ? Object.assign({}, arg1)
-          : [arg1]
+  public constructor(arg1: IRange[]) {
+    this.ranges = arg1
   }
 
-  public min(): number {
+  get min() {
     return this.ranges[0].min
   }
 
-  public max(): number {
+  get max() {
     return this.ranges[this.ranges.length - 1].max
   }
 
-  public contains(pos: number): boolean {
-    for (let s = 0; s < this.ranges.length; s += 1) {
-      const r = this.ranges[s]
+  public contains(pos: number) {
+    for (const r of this.ranges) {
       if (r.min <= pos && r.max >= pos) {
@@ -42,12 +41,24 @@ return true
 
-  public getRanges(): Range[] {
-    return this.ranges.map((r: Range) => new Range(r.min, r.max))
+  public getRanges() {
+    return this.ranges.map(r => new Range([{ min: r.min, max: r.max }]))
   }
 
   public toString(): string {
-    return this.ranges.map((r: Range) => `[${r.min}-${r.max}]`).join(',')
+    return this.ranges.map(r => `[${r.min}-${r.max}]`).join(',')
   }
 
   public union(s1: Range): Range {
-    const ranges = this.getRanges().concat(s1.getRanges()).sort(this.rangeOrder)
+    const ranges = [...this.getRanges(), ...s1.getRanges()].sort((a, b) => {
+      if (a.min < b.min) {
+        return -1
+      } else if (a.min > b.min) {
+        return 1
+      } else if (a.max < b.max) {
+        return -1
+      } else if (b.max > a.max) {
+        return 1
+      } else {
+        return 0
+      }
+    })
     const oranges = []
@@ -58,7 +69,7 @@ let current = ranges[0]
       const nxt = ranges[i]
-      if (nxt.min() > current.max() + 1) {
+      if (nxt.min > current.max + 1) {
         oranges.push(current)
         current = nxt
-      } else if (nxt.max() > current.max()) {
-        current = new Range(current.min(), nxt.max())
+      } else if (nxt.max > current.max) {
+        current = new Range([{ min: current.min, max: nxt.max }])
       }
@@ -68,78 +79,4 @@ }
 
-    if (oranges.length === 1) {
-      return oranges[0]
-    }
-    return new Range(oranges)
+    return oranges.length === 1 ? oranges[0] : new Range(oranges)
   }
-
-  public intersection(arg: Range): Range {
-    // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
-    let s0 = this
-    let s1 = arg
-    const r0 = this.ranges()
-    const r1 = s1.ranges()
-    const l0 = r0.length
-
-    const l1 = r1.length
-    let i0 = 0
-
-    let i1 = 0
-    const or = []
-
-    while (i0 < l0 && i1 < l1) {
-      s0 = r0[i0]
-      s1 = r1[i1]
-      const lapMin = Math.max(s0.min(), s1.min())
-      const lapMax = Math.min(s0.max(), s1.max())
-      if (lapMax >= lapMin) {
-        or.push(new Range(lapMin, lapMax))
-      }
-      if (s0.max() > s1.max()) {
-        i1 += 1
-      } else {
-        i0 += 1
-      }
-    }
-
-    if (or.length === 0) {
-      throw new Error('found range of length 0')
-    }
-    if (or.length === 1) {
-      return or[0]
-    }
-    return new Range(or)
-  }
-
-  public coverage(): number {
-    let tot = 0
-    const rl = this.ranges()
-    for (const r of rl) {
-      tot += r.max() - r.min() + 1
-    }
-    return tot
-  }
-
-  public rangeOrder(tmpa: Range, tmpb: Range): number {
-    let a = tmpa
-    let b = tmpb
-    if (arguments.length < 2) {
-      b = a
-      // eslint-disable-next-line @typescript-eslint/no-this-alias,unicorn/no-this-assignment
-      a = this
-    }
-
-    if (a.min() < b.min()) {
-      return -1
-    }
-    if (a.min() > b.min()) {
-      return 1
-    }
-    if (a.max() < b.max()) {
-      return -1
-    }
-    if (b.max() > a.max()) {
-      return 1
-    }
-    return 0
-  }
 }

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Number of lines in readme file

226

increased by0.44%

Worsened metrics

Total package byte prevSize

240218

decreased by-3.15%

Lines of code

4007

decreased by-3.79%

No dependency changes