Updates

eslint.config.mjs

@@ -0,0 +1,114 @@
+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'
+
+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 [
+  {
+    ignores: ['src/binary-parser/*.js'],
+  },
+  ...compat.extends(
+    'plugin:@typescript-eslint/recommended',
+    'plugin:@typescript-eslint/recommended-type-checked',
+    'plugin:@typescript-eslint/stylistic-type-checked',
+    'plugin:prettier/recommended',
+    'plugin:unicorn/recommended',
+  ),
+  {
+    plugins: {
+      prettier,
+      '@typescript-eslint': typescriptEslint,
+    },
+
+    languageOptions: {
+      parser: tsParser,
+      ecmaVersion: 5,
+      sourceType: 'script',
+
+      parserOptions: {
+        tsconfigRootDir: '/home/cdiesh/src/gmod/cram-js',
+        project: './tsconfig.lint.json',
+      },
+    },
+
+    rules: {
+      '@typescript-eslint/no-unused-vars': [
+        'warn',
+        {
+          argsIgnorePattern: '^_',
+          ignoreRestSiblings: true,
+        },
+      ],
+
+      'no-underscore-dangle': 0,
+      curly: 'error',
+      '@typescript-eslint/no-explicit-any': 0,
+      '@typescript-eslint/explicit-module-boundary-types': 0,
+      '@typescript-eslint/ban-ts-comment': 0,
+      semi: ['error', 'never'],
+      'unicorn/no-new-array': 'off',
+      'unicorn/no-empty-file': 'off',
+      'unicorn/prefer-type-error': 'off',
+      'unicorn/prefer-modern-math-apis': 'off',
+      'unicorn/prefer-node-protocol': 'off',
+      'unicorn/no-unreadable-array-destructuring': 'off',
+      'unicorn/no-abusive-eslint-disable': 'off',
+      'unicorn/no-array-callback-reference': 'off',
+      'unicorn/number-literal-case': 'off',
+      'unicorn/prefer-add-event-listener': 'off',
+      'unicorn/prefer-top-level-await': 'off',
+      'unicorn/consistent-function-scoping': 'off',
+      'unicorn/no-await-expression-member': 'off',
+      'unicorn/no-lonely-if': 'off',
+      'unicorn/consistent-destructuring': 'off',
+      'unicorn/prefer-module': 'off',
+      'unicorn/prefer-optional-catch-binding': 'off',
+      'unicorn/no-useless-undefined': 'off',
+      'unicorn/no-null': 'off',
+      'unicorn/no-nested-ternary': 'off',
+      'unicorn/filename-case': 'off',
+      'unicorn/catch-error-name': 'off',
+      'unicorn/prevent-abbreviations': 'off',
+      'unicorn/prefer-code-point': 'off',
+      'unicorn/numeric-separators-style': 'off',
+      'unicorn/no-array-for-each': 'off',
+      'unicorn/prefer-spread': 'off',
+      'unicorn/explicit-length-check': 'off',
+      'unicorn/prefer-regexp-test': 'off',
+      'unicorn/relative-url-style': 'off',
+      'unicorn/prefer-math-trunc': 'off',
+      'unicorn/prefer-query-selector': 'off',
+      'unicorn/no-negated-condition': 'off',
+      'unicorn/switch-case-braces': 'off',
+      'unicorn/prefer-switch': 'off',
+      'unicorn/better-regex': 'off',
+      'unicorn/no-for-loop': 'off',
+      'unicorn/escape-case': 'off',
+      'unicorn/prefer-number-properties': 'off',
+      'unicorn/no-process-exit': 'off',
+      'unicorn/prefer-at': 'off',
+      'unicorn/prefer-string-replace-all': 'off',
+      'unicorn/no-array-reduce': 'off',
+      '@typescript-eslint/no-base-to-string': 'off',
+      '@typescript-eslint/no-unsafe-member-access': 'off',
+      '@typescript-eslint/no-unsafe-argument': 'off',
+      '@typescript-eslint/no-unsafe-assignment': 'off',
+      '@typescript-eslint/no-unsafe-call': 'off',
+      '@typescript-eslint/no-unsafe-return': 'off',
+      '@typescript-eslint/prefer-nullish-coalescing': 'off',
+      '@typescript-eslint/require-await': 'off',
+      '@typescript-eslint/restrict-template-expressions': 'off',
+    },
+  },
+]

package.json

@@ -54,30 +54,25 @@
     "xz-decompress": "^0.2.1"
   },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.18.2",
-    "@babel/preset-typescript": "^7.17.12",
     "@gmod/indexedfasta": "^2.1.0",
     "@types/jest": "^29.5.12",
-    "@types/long": "^4.0.2",
+    "@types/long": "^4.0.0",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
     "@typescript-eslint/eslint-plugin": "^7.0.2",
     "@typescript-eslint/parser": "^7.0.2",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
-    "eslint": "^8.30.0",
+    "eslint": "^9.0.0",
     "eslint-config-prettier": "^9.0.0",
-    "eslint-plugin-import": "^2.25.4",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^51.0.1",
-    "glob": "^10.3.1",
+    "eslint-plugin-unicorn": "^54.0.0",
     "jest": "^29.3.1",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
     "rimraf": "^5.0.1",
     "ts-jest": "^29.1.2",
     "typescript": "^5.0.3",
-    "url": "^0.11.0",
     "webpack": "^5.90.3",
     "webpack-cli": "^5.0.1"
   },

src/indexedCramFile.ts

@@ -1,5 +1,4 @@
-import { CramSizeLimitError, CramUnimplementedError } from './errors'
-
+import { CramUnimplementedError } from './errors'
 import CramFile from './cramFile'
 import CramRecord from './cramFile/record'
 import { SeqFetch } from './cramFile/file'
@@ -98,7 +97,6 @@ export default class IndexedCramFile {
     }
     const seqId = seq
     const slices = await this.index.getEntriesForRange(seqId, start, end)
-    const totalSize = slices.map(s => s.sliceBytes).reduce((a, b) => a + b, 0)
 
     // TODO: do we need to merge or de-duplicate the blocks?
 

test/cram2sam.ts

@@ -151,12 +151,12 @@ function tags2str(record: CramRecord, RG: string[]) {
   for (const type in record.tags) {
     str += '\t'
     if (typeof record.tags[type] === 'number') {
-      str += type + ':i:' + record.tags[type]
+      str += `${type}:i:${record.tags[type]}`
     } else if (typeof record.tags[type] === 'string') {
       str +=
         record.tags[type].length === 1
-          ? type + ':A:' + record.tags[type]
-          : type + ':Z:' + record.tags[type]
+          ? `${type}:A:${record.tags[type]}`
+          : `${type}:Z:${record.tags[type]}`
     } else {
       console.error(
         type,

test/lib/syncLocalFile.ts

@@ -1,6 +1,6 @@
 //@ts-nocheck
 // don't load fs native module if running in webpacked code
-const fs = typeof __webpack_require__ !== 'function' ? require('fs') : null // eslint-disable-line camelcase
+const fs = typeof __webpack_require__ !== 'function' ? require('fs') : null
 
 const fsOpen = fs.openSync
 const fsRead = fs.readSync