@gmod/bbi 4.0.2 → 4.0.4

package/CHANGELOG.md

@@ -1,6 +1,19 @@
-## [4.0.2](https://github.com/GMOD/bbi-js/compare/v4.0.1...v4.0.2) (2023-07-30)
+## [4.0.4](https://github.com/GMOD/bbi-js/compare/v4.0.3...v4.0.4) (2024-3-5)
+
+
+
+- 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)
+
+## [4.0.2](https://github.com/GMOD/bbi-js/compare/v4.0.1...v4.0.2) (2023-07-30)
 
 - Fix issue with fetching headers that are large in certain cases
 

package/README.md

@@ -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 }),
@@ -164,18 +165,18 @@ can be parsed by the @gmod/bed module, which is not by default integrated with
 this module, but can be combined with it as follows
 
 ```typescript
-import {BigBed} from '@gmod/bbi'
+import { BigBed } from '@gmod/bbi'
 import BED from '@gmod/bed'
 
 const ti = new BigBed({
   filehandle: new LocalFile(require.resolve('./data/hg18.bb')),
 })
-const {autoSql} = await ti.getHeader()
+const { autoSql } = await ti.getHeader()
 const feats = await ti.getFeatures('chr7', 0, 100000)
-const parser = new BED({autoSql})
+const parser = new BED({ autoSql })
 const lines = feats.map(f => {
-    const { start, end, rest, uniqueId } = f
-    return parser.parseLine(`chr7\t${start}\t${end}\t${rest}, { uniqueId })\
+  const { start, end, rest, uniqueId } = f
+  return parser.parseLine(`chr7\t${start}\t${end}\t${rest}`, { uniqueId })
 })
 // @gmod/bbi returns features with {uniqueId, start, end, rest}
 // we reconstitute this as a line for @gmod/bed with a template string

package/dist/bbi.js.map

@@ -1 +1 @@
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package/dist/bigbed.js.map

@@ -1 +1 @@
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package/dist/bigint-polyfill/polyfill.js.map

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package/dist/bigint-polyfill/pure.js.map

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+{"version":3,"file":"pure.js","sourceRoot":"","sources":["../../src/bigint-polyfill/pure.ts"],"names":[],"mappings":";;;AAAA,MAAM,QAAQ,GAAG,MAAM,CAAC,EAAE,CAAC,CAAA;AAE3B,SAAgB,WAAW,CACzB,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,MAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,OAAO,CACL,CAAC,MAAM,CACL,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,aAAa;QACzD,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,gBAAgB,CACrE;QACC,QAAQ,CAAC;QACX,MAAM,CACJ,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,GAAG,gBAAgB;YAC7D,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,GAAG,aAAa,CACnE,CACF,CAAA;AACH,CAAC;AAnBD,kCAmBC;AAED,SAAgB,YAAY,CAC1B,QAAkB,EAClB,UAAkB,EAClB,YAAiC;IAEjC,MAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,YAAY,CAAC,CAAA;IACtD,MAAM,CAAC,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,YAAY,CAAC,CAAA;IAE1D,MAAM,gBAAgB,GAAG,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAA;IAC/C,MAAM,aAAa,GAAG,MAAM,CAAC,CAAC,YAAY,CAAC,CAAA;IAE3C,4EAA4E;IAC5E,gDAAgD;IAChD,kCAAkC;IAClC,OAAO,CACL,CAAC,MAAM,CAAC,CAAC,GAAG,aAAa,GAAG,CAAC,GAAG,gBAAgB,CAAC,IAAI,QAAQ,CAAC;QAC9D,MAAM,CAAC,CAAC,GAAG,gBAAgB,GAAG,CAAC,GAAG,aAAa,CAAC,CACjD,CAAA;AACH,CAAC;AAlBD,oCAkBC;AAED,SAAgB,WAAW,CACzB,QAAkB,EAClB,UAAkB,EAClB,KAAa,EACb,YAAiC;IAEjC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,IAAI,QAAQ,CAAC,CAAA;IACpC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,CAAA;IAE7C,IAAI,YAAY,EAAE,CAAC;QACjB,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QACnD,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;IAClD,CAAC;SAAM,CAAC;QACN,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QAC/C,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;IACtD,CAAC;AACH,CAAC;AAhBD,kCAgBC;AAED,SAAgB,YAAY,CAC1B,QAAkB,EAClB,UAAkB,EAClB,KAAa,EACb,YAAiC;IAEjC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,IAAI,QAAQ,CAAC,CAAA;IACpC,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,GAAG,MAAM,CAAC,UAAU,CAAC,CAAC,CAAA;IAE7C,IAAI,YAAY,EAAE,CAAC;QACjB,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QACpD,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;IAClD,CAAC;SAAM,CAAC;QACN,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;QAChD,QAAQ,CAAC,SAAS,CAAC,UAAU,GAAG,CAAC,EAAE,EAAE,EAAE,YAAY,CAAC,CAAA;IACtD,CAAC;AACH,CAAC;AAhBD,oCAgBC"}

package/dist/bigwig.js.map

@@ -1 +1 @@
-{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,6CAAwC;AACxC,+BAA2C;AAE3C,MAAa,MAAO,SAAQ,SAAG;IAC7B;;;;;OAKG;IACa,OAAO,CAAC,KAAa,EAAE,IAAoB;;YACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;YAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;YAChC,IAAI,CAAC,QAAQ,EAAE;gBACb,4EAA4E;gBAC5E,QAAQ,IAAI,CAAC,CAAA;aACd;YAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;gBACrC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;gBACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE;oBAC7C,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;oBAE1C,OAAO,IAAI,sBAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;iBACF;aACF;YACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QACnC,CAAC;KAAA;CACF;AAlCD,wBAkCC"}
+{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,6CAAwC;AACxC,+BAA2C;AAE3C,MAAa,MAAO,SAAQ,SAAG;IAC7B;;;;;OAKG;IACa,OAAO,CAAC,KAAa,EAAE,IAAoB;;YACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;YAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;YAChC,IAAI,CAAC,QAAQ,EAAE,CAAC;gBACd,4EAA4E;gBAC5E,QAAQ,IAAI,CAAC,CAAA;YACf,CAAC;YAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;gBACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;oBAC9C,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;oBAE1C,OAAO,IAAI,sBAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;gBACH,CAAC;YACH,CAAC;YACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QACnC,CAAC;KAAA;CACF;AAlCD,wBAkCC"}

package/dist/block-view.js

@@ -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));
@@ -288,7 +292,8 @@ class BlockView {
         let currOffset = startOffset;
         while (currOffset < data.byteLength) {
             const res = this.bigBedParser.parse(data.subarray(currOffset));
-            items.push(Object.assign(Object.assign({}, res), { uniqueId: `bb-${offset + currOffset}` }));
+            res.uniqueId = `bb-${offset + currOffset}`;
+            items.push(res);
             currOffset += res.offset;
         }
         return request

package/dist/block-view.js.map

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

@@ -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

@@ -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

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package/dist/unzip.d.ts

@@ -1 +1,2 @@
+/// <reference types="node" />
 export { inflateSync as unzip } from 'zlib';

package/dist/util.js

@@ -10,7 +10,6 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.abortBreakPoint = exports.checkAbortSignal = exports.groupBlocks = exports.AbortError = void 0;
-/* eslint no-bitwise: ["error", { "allow": ["|"] }] */
 class AbortError extends Error {
     constructor(message) {
         super(message);

package/dist/util.js.map

@@ -1 +1 @@
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package/esm/bbi.js.map

@@ -1 +1 @@
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package/esm/bigbed.js.map

@@ -1 +1 @@
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package/esm/bigint-polyfill/polyfill.js.map

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package/esm/bigint-polyfill/pure.js.map

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