npm - @gmod/bbi - Versions diffs - 4.0.2 → 4.0.3 - Mend

@gmod/bbi 4.0.2 → 4.0.3

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 (28) hide show

package/CHANGELOG.md +10 -1
package/README.md +5 -5
package/dist/bbi.js.map +1 -1
package/dist/bigbed.js.map +1 -1
package/dist/bigint-polyfill/polyfill.js.map +1 -1
package/dist/bigint-polyfill/pure.js.map +1 -1
package/dist/bigwig.js.map +1 -1
package/dist/block-view.js +2 -1
package/dist/block-view.js.map +1 -1
package/dist/range.js.map +1 -1
package/dist/unzip.d.ts +1 -0
package/dist/util.js +0 -1
package/dist/util.js.map +1 -1
package/esm/bbi.js.map +1 -1
package/esm/bigbed.js.map +1 -1
package/esm/bigint-polyfill/polyfill.js.map +1 -1
package/esm/bigint-polyfill/pure.js.map +1 -1
package/esm/bigwig.js.map +1 -1
package/esm/block-view.js +2 -1
package/esm/block-view.js.map +1 -1
package/esm/range.js.map +1 -1
package/esm/unzip.d.ts +1 -0
package/esm/util.js +0 -1
package/esm/util.js.map +1 -1
package/package.json +17 -18
package/src/block-view.ts +2 -1
package/src/range.ts +2 -2
package/src/util.ts +0 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,7 +1,16 @@
-## [4.0.2](https://github.com/GMOD/bbi-js/compare/v4.0.1...v4.0.2) (2023-07-30)
+## [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
 ## [4.0.1](https://github.com/GMOD/bbi-js/compare/v4.0.0...v4.0.1) (2023-07-13)

package/README.md CHANGED Viewed

@@ -164,18 +164,18 @@ 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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/bigwig.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/block-view.js CHANGED Viewed

@@ -288,7 +288,8 @@ 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 CHANGED Viewed

	@@ -1 +1 @@
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package/dist/range.js.map CHANGED Viewed

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

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

package/dist/util.js CHANGED Viewed

@@ -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);

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package/esm/bigwig.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;OAKG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;QAChC,IAAI,CAAC,QAAQ,EAAE;~~YACb~~,4EAA4E;YAC5E,QAAQ,IAAI,CAAC,CAAA;~~SACd~~;QAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;~~YACrC~~,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE;~~gBAC7C~~,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;gBAE1C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;~~aACF~~;~~SACF~~;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}
1	+ {"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACxC,OAAO,EAAE,GAAG,EAAkB,MAAM,OAAO,CAAA;AAE3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;OAKG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,EAAE,GACxE,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,IAAI,QAAQ,GAAG,UAAU,CAAC,MAAM,CAAA;QAChC,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,4EAA4E;YAC5E,QAAQ,IAAI,CAAC,CAAA;QACf,CAAC;QAED,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,CAAA;gBAE1C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,WAAW,EACX,WAAW,EACX,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}

package/esm/block-view.js CHANGED Viewed

@@ -271,7 +271,8 @@ export class BlockView {
         let currOffset = startOffset;
         while (currOffset < data.byteLength) {
             const res = this.bigBedParser.parse(data.subarray(currOffset));
-            items.push({ ...res, uniqueId: `bb-${offset + currOffset}` });
+            res.uniqueId = `bb-${offset + currOffset}`;
+            items.push(res);
             currOffset += res.offset;
         }
         return request

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

	@@ -1 +1 @@
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package/esm/range.js.map CHANGED Viewed

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

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

package/esm/util.js CHANGED Viewed

@@ -1,4 +1,3 @@
-/* eslint no-bitwise: ["error", { "allow": ["|"] }] */
 export class AbortError extends Error {
     constructor(message) {
         super(message);

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "4.0.2",
+  "version": "4.0.3",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -23,6 +23,7 @@
     "test": "jest",
     "coverage": "npm test -- --coverage",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts src",
+    "format": "prettier",
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean",
     "build:esm": "tsc --target es2018 --outDir esm --module es2020",
@@ -50,24 +51,22 @@
   },
   "devDependencies": {
     "@gmod/bed": "^2.1.2",
-    "@types/jest": "^29.5.0",
-    "@types/long": "^5.0.0",
-    "@types/node": "^18.15.7",
+    "@types/jest": "^29.5.3",
+    "@types/node": "^20.4.5",
     "@types/pako": "^2.0.0",
-    "@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",
-    "eslint-plugin-unicorn": "^46.0.0",
-    "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": "^29.0.5",
-    "typescript": "^5.0.2"
+    "@typescript-eslint/eslint-plugin": "^6.2.0",
+    "@typescript-eslint/parser": "^6.2.0",
+    "eslint": "^8.46.0",
+    "eslint-config-prettier": "^9.1.0",
+    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-unicorn": "^50.0.1",
+    "jest": "^29.6.2",
+    "jest-environment-jsdom": "^29.6.2",
+    "prettier": "^3.0.0",
+    "rimraf": "^5.0.1",
+    "standard-changelog": "^3.0.0",
+    "ts-jest": "^29.1.1",
+    "typescript": "^5.1.6"
   },
   "publishConfig": {
     "access": "public"

package/src/block-view.ts CHANGED Viewed

@@ -375,7 +375,8 @@ export class BlockView {
     let currOffset = startOffset
     while (currOffset < data.byteLength) {
       const res = this.bigBedParser.parse(data.subarray(currOffset))
-      items.push({ ...res, uniqueId: `bb-${offset + currOffset}` })
+      res.uniqueId = `bb-${offset + currOffset}`
+      items.push(res)
       currOffset += res.offset
     }

package/src/range.ts CHANGED Viewed

@@ -12,8 +12,8 @@ export default class Range {
       arguments.length === 2
         ? [{ min: arg1, max: arg2 }]
         : 0 in arg1
-        ? Object.assign({}, arg1)
-        : [arg1]
+          ? Object.assign({}, arg1)
+          : [arg1]
   }
   public min(): number {

package/src/util.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/* eslint no-bitwise: ["error", { "allow": ["|"] }] */
 export class AbortError extends Error {
   public code: string