Remove dependency on long package (#99)

GMOD · Aug 30, 2024 · 3636c75 · 3636c75
1 parent d90afd4
commit 3636c75
Show file tree

Hide file tree

Showing 9 changed files with 197 additions and 213 deletions.
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -1,43 +1,32 @@
-import prettier from 'eslint-plugin-prettier'
-import typescriptEslint from '@typescript-eslint/eslint-plugin'
-import tsParser from '@typescript-eslint/parser'
-import path from 'node:path'
-import { fileURLToPath } from 'node:url'
-import js from '@eslint/js'
-import { FlatCompat } from '@eslint/eslintrc'
+import eslint from '@eslint/js'
+import eslintPluginUnicorn from 'eslint-plugin-unicorn'
+import tseslint from 'typescript-eslint'
 
-const __filename = fileURLToPath(import.meta.url)
-const __dirname = path.dirname(__filename)
-const compat = new FlatCompat({
-  baseDirectory: __dirname,
-  recommendedConfig: js.configs.recommended,
-  allConfig: js.configs.all,
-})
-
-export default [
-  ...compat.extends(
-    'plugin:@typescript-eslint/recommended',
-    'plugin:@typescript-eslint/recommended-type-checked',
-    'plugin:@typescript-eslint/stylistic-type-checked',
-    'plugin:prettier/recommended',
-    'plugin:unicorn/recommended',
-  ),
+export default tseslint.config(
+  {
+    ignores: [
+      'webpack.config.js',
+      'dist/*',
+      'esm/*',
+      'example/*',
+      'eslint.config.mjs',
+    ],
+  },
   {
-    plugins: {
-      prettier,
-      '@typescript-eslint': typescriptEslint,
-    },
-
     languageOptions: {
-      parser: tsParser,
-      ecmaVersion: 5,
-      sourceType: 'script',
-
       parserOptions: {
-        project: './tsconfig.lint.json',
+        project: ['./tsconfig.lint.json'],
+        tsconfigRootDir: import.meta.dirname,
       },
     },
+  },
+  eslint.configs.recommended,
+  ...tseslint.configs.recommended,
+  ...tseslint.configs.stylisticTypeChecked,
+  ...tseslint.configs.strictTypeChecked,
 
+  eslintPluginUnicorn.configs['flat/recommended'],
+  {
     rules: {
       '@typescript-eslint/no-unused-vars': [
         'warn',
@@ -101,6 +90,9 @@ export default [
       '@typescript-eslint/no-unsafe-return': 'off',
       '@typescript-eslint/prefer-nullish-coalescing': 'off',
       '@typescript-eslint/require-await': 'off',
+      '@typescript-eslint/restrict-template-expressions': 'off',
+      '@typescript-eslint/restrict-plus-operands': 'off',
+      'no-empty': 'off',
     },
   },
-]
+)
diff --git a/package.json b/package.json
@@ -20,15 +20,14 @@
     "src"
   ],
   "scripts": {
-    "test": "vitest run",
-    "coverage": "npm test -- --coverage",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
+    "test": "vitest",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "clean": "rimraf dist esm",
     "build:esm": "tsc --target es2018 --outDir esm",
     "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "prebuild": "npm run clean && npm run lint",
-    "preversion": "npm run lint && npm test && npm run build",
+    "preversion": "npm run lint && npm test run && npm run build",
     "version": "standard-changelog && git add CHANGELOG.md",
     "postversion": "git push --follow-tags"
   },
@@ -43,7 +42,6 @@
     "@gmod/bgzf-filehandle": "^1.4.4",
     "crc": "^4.3.2",
     "generic-filehandle": "^3.0.0",
-    "long": "^4.0.0",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {

diff --git a/src/bai.ts b/src/bai.ts
@@ -22,7 +22,7 @@ function reg2bins(beg: number, end: number) {
     [73 + (beg >> 20), 73 + (end >> 20)],
     [585 + (beg >> 17), 585 + (end >> 17)],
     [4681 + (beg >> 14), 4681 + (end >> 14)],
-  ]
+  ] as const
 }
 
 export default class BAI extends IndexFile {
@@ -125,6 +125,7 @@ export default class BAI extends IndexFile {
     const range = start !== undefined
     const indexData = await this.parse(opts)
     const seqIdx = indexData.indices[seqId]
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (!seqIdx) {
       return []
     }
@@ -167,10 +168,12 @@ export default class BAI extends IndexFile {
     }
 
     const indexData = await this.parse(opts)
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (!indexData) {
       return []
     }
     const ba = indexData.indices[refId]
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (!ba) {
       return []
     }
@@ -182,6 +185,7 @@ export default class BAI extends IndexFile {
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (ba.binIndex[bin]) {
           const binChunks = ba.binIndex[bin]
           for (const binChunk of binChunks) {
@@ -199,6 +203,7 @@ export default class BAI extends IndexFile {
     const maxLin = Math.min(max >> 14, nintv - 1)
     for (let i = minLin; i <= maxLin; ++i) {
       const vp = ba.linearIndex[i]
+      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
         lowest = vp
       }
@@ -209,7 +214,7 @@ export default class BAI extends IndexFile {
 
   async parse(opts: BaseOpts = {}) {
     if (!this.setupP) {
-      this.setupP = this._parse(opts).catch(e => {
+      this.setupP = this._parse(opts).catch((e: unknown) => {
         this.setupP = undefined
         throw e
       })

diff --git a/src/bamFile.ts b/src/bamFile.ts
@@ -178,7 +178,7 @@ export default class BamFile {
 
   getHeader(opts?: BaseOpts) {
     if (!this.headerP) {
-      this.headerP = this.getHeaderPre(opts).catch(e => {
+      this.headerP = this.getHeaderPre(opts).catch((e: unknown) => {
         this.headerP = undefined
         throw e
       })
@@ -430,6 +430,7 @@ export default class BamFile {
       const blockEnd = blockStart + 4 + blockSize - 1
 
       // increment position to the current decompressed status
+      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       if (dpositions) {
         while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]) {}
         pos--
@@ -470,6 +471,7 @@ export default class BamFile {
                 chunk.minv.dataPosition +
                 1
               : // must be slice, not subarray for buffer polyfill on web
+                // eslint-disable-next-line @typescript-eslint/no-deprecated
                 crc32.signed(ba.slice(blockStart, blockEnd)),
         })
 

diff --git a/src/csi.ts b/src/csi.ts
@@ -159,7 +159,8 @@ export default class CSI extends IndexFile {
     }
 
     const indexData = await this.parse(opts)
-    const ba = indexData?.indices[refId]
+    const ba = indexData.indices[refId]
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (!ba) {
       return []
     }
@@ -173,6 +174,7 @@ export default class CSI extends IndexFile {
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (ba.binIndex[bin]) {
           const binChunks = ba.binIndex[bin]
           for (const c of binChunks) {
@@ -210,14 +212,14 @@ export default class CSI extends IndexFile {
           `query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`,
         )
       }
-      bins.push([b, e])
+      bins.push([b, e] as const)
     }
     return bins
   }
 
   async parse(opts: BaseOpts = {}) {
     if (!this.setupP) {
-      this.setupP = this._parse(opts).catch(e => {
+      this.setupP = this._parse(opts).catch((e: unknown) => {
         this.setupP = undefined
         throw e
       })

diff --git a/src/record.ts b/src/record.ts
@@ -79,7 +79,7 @@ export default class BamRecord {
     if (this.isPaired()) {
       tags.push('next_segment_position', 'pair_orientation')
     }
-    tags = tags.concat(this._tagList || [])
+    tags = tags.concat(this._tagList)
 
     for (const k of Object.keys(this.data)) {
       if (!k.startsWith('_') && k !== 'next_seq_id') {

diff --git a/src/util.ts b/src/util.ts
@@ -1,21 +1,10 @@
-import Long from 'long'
 import Chunk from './chunk'
 import VirtualOffset from './virtualOffset'
 
 export function timeout(ms: number) {
   return new Promise(resolve => setTimeout(resolve, ms))
 }
 
-export function longToNumber(long: Long) {
-  if (
-    long.greaterThan(Number.MAX_SAFE_INTEGER) ||
-    long.lessThan(Number.MIN_SAFE_INTEGER)
-  ) {
-    throw new Error('integer overflow')
-  }
-  return long.toNumber()
-}
-
 /**
  * Properly check if the given AbortSignal is aborted.
  * Per the standard, if the signal reads as aborted,
@@ -113,13 +102,9 @@ export function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset) {
 }
 
 export function parsePseudoBin(bytes: Buffer, offset: number) {
-  const lineCount = longToNumber(
-    Long.fromBytesLE(
-      Array.prototype.slice.call(bytes, offset, offset + 8),
-      true,
-    ),
-  )
-  return { lineCount }
+  return {
+    lineCount: Number(bytes.readBigInt64LE(offset)),
+  }
 }
 
 export function findFirstData(

diff --git a/tsconfig.json b/tsconfig.json
@@ -2,7 +2,7 @@
   "include": ["src"],
   "compilerOptions": {
     "outDir": "dist",
-    "target":"es2018",
+    "target": "es2018",
     "types": ["node"],
     "lib": ["dom", "esnext"],
     "declaration": true,