npm - @gmod/bbi - Versions diffs - 4.0.3 → 4.0.4 - Mend

@gmod/bbi 4.0.3 → 4.0.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (15) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -1,13 +1,17 @@
-## [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
+- optimize `parseBigBedBlock` ([#58](https://github.com/GMOD/bbi-js/issues/58))
+  ([eb3f7a4](https://github.com/GMOD/bbi-js/commit/eb3f7a4885c4e8262c6e3e63696b533e53072463))
-- Small perf improvement (#58)
+* Small perf improvement (#58)
 ## [4.0.2](https://github.com/GMOD/bbi-js/compare/v4.0.1...v4.0.2) (2023-07-30)

package/README.md CHANGED Viewed

@@ -29,12 +29,13 @@ https://github.com/GMOD/generic-filehandle/
 const { BigWig } = require('@gmod/bbi')
 const { RemoteFile } = require('generic-filehandle')
-// 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({
   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')
 const file = new BigWig({
   filehandle: new RemoteFile('volvox.bw', { fetch }),

package/dist/block-view.js CHANGED Viewed

@@ -203,15 +203,15 @@ class BlockView {
                 };
                 const cirFobStartFetch = (off, fr, level) => __awaiter(this, void 0, void 0, function* () {
                     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);
                         for (const element of off) {
                             if (fr.contains(element)) {
                                 cirFobRecur2(resultBuffer, element - offset, level);
                                 outstanding -= 1;
                                 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));
                                 }
                             }
                         }
@@ -225,9 +225,13 @@ class BlockView {
                         outstanding += offset.length;
                         // Upper bound on size, based on a completely full leaf node.
                         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);
                         }
                         spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));

package/dist/block-view.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/range.d.ts CHANGED Viewed

@@ -2,17 +2,18 @@
  * Adapted from a combination of Range and _Compound in the
  * Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
  */
+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;
     isContiguous(): boolean;
     getRanges(): Range[];
     toString(): string;
     union(s1: Range): Range;
-    intersection(arg: Range): Range;
-    coverage(): number;
-    rangeOrder(tmpa: Range, tmpb: Range): number;
 }

package/dist/range.js CHANGED Viewed

@@ -1,28 +1,18 @@
 "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) {
                 return true;
             }
@@ -33,94 +23,43 @@ class Range {
         return this.ranges.length > 1;
     }
     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 = [];
         let current = ranges[0];
         for (let i = 1; i < ranges.length; i += 1) {
             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);
-    }
-    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;
+        return oranges.length === 1 ? oranges[0] : new Range(oranges);
     }
 }
 exports.default = Range;

package/dist/range.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"range.js","sourceRoot":"","sources":["../src/range.ts"],"names":[],"mappings":";AAAA,sDAAsD;;AAWtD,MAAqB,KAAK;IAGxB,YAAmB,IAAc;QAC/B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;IACpB,CAAC;IAED,IAAI,GAAG;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC3B,CAAC;IAED,IAAI,GAAG;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,CAAA;IAChD,CAAC;IAEM,QAAQ,CAAC,GAAW;QACzB,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;YAC5B,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC;gBACjC,OAAO,IAAI,CAAA;YACb,CAAC;QACH,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;IAEM,YAAY;QACjB,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAA;IAC/B,CAAC;IAEM,SAAS;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAA;IACtE,CAAC;IAEM,QAAQ;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IAC9D,CAAC;IAEM,KAAK,CAAC,EAAS;QACpB,MAAM,MAAM,GAAG,CAAC,GAAG,IAAI,CAAC,SAAS,EAAE,EAAE,GAAG,EAAE,CAAC,SAAS,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACpE,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBAClB,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,OAAO,CAAC,CAAA;YACV,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,OAAO,CAAC,CAAC,CAAA;YACX,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC;gBACzB,OAAO,CAAC,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,OAAO,CAAC,CAAA;YACV,CAAC;QACH,CAAC,CAAC,CAAA;QACF,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,IAAI,OAAO,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAEvB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC1C,MAAM,GAAG,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;YACrB,IAAI,GAAG,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,GAAG,CAAC,EAAE,CAAC;gBAC9B,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,OAAO,GAAG,GAAG,CAAA;YACf,CAAC;iBAAM,IAAI,GAAG,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;gBACjC,OAAO,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,GAAG,EAAE,OAAO,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC3D,CAAC;QACH,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAErB,OAAO,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,OAAO,CAAC,CAAA;IAC/D,CAAC;CACF;AAlED,wBAkEC"}

package/esm/block-view.js CHANGED Viewed

@@ -187,15 +187,18 @@ export class BlockView {
             };
             const cirFobStartFetch = async (off, fr, level) => {
                 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);
                     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 });
+                                this.readFeatures(observer, blocksToFetch, {
+                                    ...opts,
+                                    request,
+                                }).catch(e => observer.error(e));
                             }
                         }
                     }
@@ -209,9 +212,13 @@ export class BlockView {
                     outstanding += offset.length;
                     // 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);
+                    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);
                     }
                     spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));

package/esm/block-view.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/range.d.ts CHANGED Viewed

@@ -2,17 +2,18 @@
  * Adapted from a combination of Range and _Compound in the
  * Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
  */
+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;
     isContiguous(): boolean;
     getRanges(): Range[];
     toString(): string;
     union(s1: Range): Range;
-    intersection(arg: Range): Range;
-    coverage(): number;
-    rangeOrder(tmpa: Range, tmpb: Range): number;
 }

package/esm/range.js CHANGED Viewed

@@ -1,26 +1,16 @@
 /* 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) {
                 return true;
             }
@@ -31,94 +21,43 @@ export default class Range {
         return this.ranges.length > 1;
     }
     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 = [];
         let current = ranges[0];
         for (let i = 1; i < ranges.length; i += 1) {
             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);
-    }
-    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;
+        return oranges.length === 1 ? oranges[0] : new Range(oranges);
     }
 }
 //# sourceMappingURL=range.js.map

package/esm/range.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "4.0.3",
+  "version": "4.0.4",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -51,21 +51,21 @@
   },
   "devDependencies": {
     "@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"
   },
   "publishConfig": {

package/src/block-view.ts CHANGED Viewed

@@ -268,8 +268,8 @@ export class BlockView {
         level: number,
       ) => {
         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(
             `${length}_${offset}`,
             { length, offset },
@@ -280,7 +280,10 @@ export class BlockView {
               cirFobRecur2(resultBuffer, element - offset, level)
               outstanding -= 1
               if (outstanding === 0) {
-                this.readFeatures(observer, blocksToFetch, { ...opts, request })
+                this.readFeatures(observer, blocksToFetch, {
+                  ...opts,
+                  request,
+                }).catch(e => observer.error(e))
               }
             }
           }
@@ -294,9 +297,13 @@ export class BlockView {
           // 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)
+          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)
           }
           spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level))

package/src/range.ts CHANGED Viewed

@@ -4,29 +4,28 @@
  * Adapted from a combination of Range and _Compound in the
  * Dalliance Genome Explorer, (c) Thomas Down 2006-2010.
  */
+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) {
         return true
       }
@@ -38,104 +37,42 @@ export default class Range {
     return this.ranges.length > 1
   }
-  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 = []
     let current = ranges[0]
     for (let i = 1; i < ranges.length; i += 1) {
       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)
-  }
-  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
+    return oranges.length === 1 ? oranges[0] : new Range(oranges)
   }
 }