Remove long

CHANGELOG.md

@@ -1,34 +1,28 @@
 ## [1.1.14](https://github.com/GMOD/twobit-js/compare/v1.1.13...v1.1.14) (2022-07-18)
 
-
-
 - Update generic-filehandle 2->3
 
 <a name="1.1.13"></a>
-## [1.1.13](https://github.com/GMOD/twobit-js/compare/v1.1.12...v1.1.13) (2022-03-30)
-
 
+## [1.1.13](https://github.com/GMOD/twobit-js/compare/v1.1.12...v1.1.13) (2022-03-30)
 
 - Publish src directory for better source maps
 
 <a name="1.1.12"></a>
-## [1.1.12](https://github.com/GMOD/twobit-js/compare/v1.1.11...v1.1.12) (2021-12-14)
-
 
+## [1.1.12](https://github.com/GMOD/twobit-js/compare/v1.1.11...v1.1.12) (2021-12-14)
 
 - Remove es6-promisify dependency
 
 <a name="1.1.11"></a>
-## [1.1.11](https://github.com/GMOD/twobit-js/compare/v1.1.10...v1.1.11) (2021-12-14)
-
 
+## [1.1.11](https://github.com/GMOD/twobit-js/compare/v1.1.10...v1.1.11) (2021-12-14)
 
 - Typescriptify codebase and add esm build
 
 <a name="1.1.10"></a>
-## [1.1.10](https://github.com/GMOD/twobit-js/compare/v1.1.9...v1.1.10) (2019-10-06)
-
 
+## [1.1.10](https://github.com/GMOD/twobit-js/compare/v1.1.9...v1.1.10) (2019-10-06)
 
 - Small refactor of `filehandle.read()` to make it more robust
 
@@ -38,13 +32,10 @@
 
 ## [1.1.8](https://github.com/GMOD/twobit-js/compare/v1.1.6...v1.1.8) (2019-04-04)
 
-
-
 - Add @babel/runtime-corejs2 as a runtime dependency
 
 ## [1.1.7](https://github.com/GMOD/twobit-js/compare/v1.1.6...v1.1.7) (2019-04-03)
 
-
 - Use core-js to polyfill Object.values instead of polyfill library
 
 ## [1.1.6](https://github.com/GMOD/twobit-js/compare/v1.1.5...v1.1.6) (2019-04-03)
@@ -67,7 +58,6 @@
 
 - Use @gmod/binary-parser
 
-
 ## 1.1.1
 
 - Use babel-plugin-transform-runtime

README.md

@@ -44,26 +44,26 @@ const seqNames = await t.getSequenceNames()
 
 ##### Table of Contents
 
-*   [constructor](#constructor)
-    *   [Parameters](#parameters)
-*   [getHeader](#getheader)
-*   [getIndex](#getindex)
-*   [getSequenceNames](#getsequencenames)
-*   [getSequenceSizes](#getsequencesizes)
-*   [getSequenceSize](#getsequencesize)
-    *   [Parameters](#parameters-1)
-*   [getSequence](#getsequence)
-    *   [Parameters](#parameters-2)
+- [constructor](#constructor)
+  - [Parameters](#parameters)
+- [getHeader](#getheader)
+- [getIndex](#getindex)
+- [getSequenceNames](#getsequencenames)
+- [getSequenceSizes](#getsequencesizes)
+- [getSequenceSize](#getsequencesize)
+  - [Parameters](#parameters-1)
+- [getSequence](#getsequence)
+  - [Parameters](#parameters-2)
 
 #### constructor
 
 ##### Parameters
 
-*   `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
+- `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
 
-    *   `args.filehandle` **Filehandle?** node fs.promises-like filehandle for the .2bit file.
-        Only needs to support `filehandle.read(buffer, offset, length, position)`
-    *   `args.path` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** filesystem path for the .2bit file to open
+  - `args.filehandle` **Filehandle?** node fs.promises-like filehandle for the .2bit file.
+    Only needs to support `filehandle.read(buffer, offset, length, position)`
+  - `args.path` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** filesystem path for the .2bit file to open
 
 #### getHeader
 
@@ -90,17 +90,17 @@ faster
 
 ##### Parameters
 
-*   `seqName` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** name of the sequence
+- `seqName` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** name of the sequence
 
 Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** for the sequence's length, or undefined if it is not in the file
 
 #### getSequence
 
 ##### Parameters
 
-*   `seqName` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** name of the sequence you want
-*   `regionStart` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional 0-based half-open start of the sequence region to fetch. (optional, default `0`)
-*   `regionEnd` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional 0-based half-open end of the sequence region to fetch. defaults to end of the sequence
+- `seqName` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** name of the sequence you want
+- `regionStart` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional 0-based half-open start of the sequence region to fetch. (optional, default `0`)
+- `regionEnd` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional 0-based half-open end of the sequence region to fetch. defaults to end of the sequence
 
 Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** for a string of sequence bases
 

jest.config.js

@@ -2,4 +2,4 @@
 module.exports = {
   preset: 'ts-jest',
   testEnvironment: 'node',
-};
+}

package.json

@@ -39,24 +39,23 @@
   ],
   "dependencies": {
     "@gmod/binary-parser": "^1.3.5",
-    "generic-filehandle": "^3.0.0",
-    "long": "^4.0.0"
+    "generic-filehandle": "^3.0.0"
   },
   "devDependencies": {
-    "@types/jest": "^29.2.4",
-    "@typescript-eslint/eslint-plugin": "^5.46.1",
-    "@typescript-eslint/parser": "^5.46.1",
-    "documentation": "^14.0.1",
-    "eslint": "^8.30.0",
-    "eslint-config-prettier": "^8.3.0",
-    "eslint-plugin-import": "^2.26.0",
-    "eslint-plugin-prettier": "^4.2.1",
-    "jest": "^29.3.1",
-    "prettier": "^2.8.1",
-    "rimraf": "^3.0.2",
-    "standard-changelog": "^2.0.27",
-    "ts-jest": "^29.0.3",
-    "typescript": "^4.9.4"
+    "@types/jest": "^29.5.3",
+    "@typescript-eslint/eslint-plugin": "^6.2.0",
+    "@typescript-eslint/parser": "^6.2.0",
+    "documentation": "^14.0.2",
+    "eslint": "^8.46.0",
+    "eslint-config-prettier": "^9.0.0",
+    "eslint-plugin-import": "^2.28.0",
+    "eslint-plugin-prettier": "^5.0.0",
+    "jest": "^29.6.2",
+    "prettier": "^3.1.0",
+    "rimraf": "^5.0.1",
+    "standard-changelog": "^5.0.0",
+    "ts-jest": "^29.1.1",
+    "typescript": "^5.1.6"
   },
   "publishConfig": {
     "access": "public"

src/declare.d.ts

@@ -1,2 +1 @@
 declare module '@gmod/binary-parser'
-declare module 'long'

src/twoBitFile.ts

@@ -1,4 +1,3 @@
-import Long from 'long'
 import { LocalFile, GenericFilehandle } from 'generic-filehandle'
 import { Parser } from '@gmod/binary-parser'
 
@@ -97,9 +96,7 @@ export default class TwoBitFile {
       .uint8('nameLength')
       .string('name', { length: 'nameLength' })
     if (this.version === 1) {
-      indexEntryParser = indexEntryParser.buffer('offsetBytes', {
-        length: 8,
-      })
+      indexEntryParser = indexEntryParser.buffer('buf', { length: 8 })
     } else {
       indexEntryParser = indexEntryParser.uint32('offset')
     }
@@ -197,17 +194,9 @@ export default class TwoBitFile {
     const indexData = indexParser.parse(buffer).result.index
     const index = {} as { [key: string]: number }
     if (this.version === 1) {
-      indexData.forEach(
-        ({ name, offsetBytes }: { name: string; offsetBytes: number }) => {
-          const long = Long.fromBytes(offsetBytes, true, !this.isBigEndian)
-          if (long.greaterThan(Number.MAX_SAFE_INTEGER)) {
-            throw new Error(
-              'integer overflow. File offset greater than 2^53-1 encountered. This library can only handle offsets up to 2^53-1.',
-            )
-          }
-          index[name] = long.toNumber()
-        },
-      )
+      indexData.forEach(({ name, buf }: { name: string; buf: Buffer }) => {
+        index[name] = Number(buf.readBigUInt64LE())
+      })
     } else {
       indexData.forEach(
         ({ name, offset }: { name: string; offset: number }) => {