Bump deps

.github/workflows/push.yml

@@ -4,14 +4,14 @@ on: push
 
 jobs:
   test:
-    name: Lint, build, and test on node 14.x and ubuntu-latest
+    name: Lint, build, and test on node 20.x and ubuntu-latest
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Use Node.js 14.x
-        uses: actions/setup-node@v1
+      - uses: actions/checkout@v4
+      - name: Use Node.js 20.x
+        uses: actions/setup-node@v4
         with:
-          node-version: 14.x
+          node-version: 20.x
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Lint codebase

CHANGELOG.md

@@ -1,19 +1,13 @@
 ## [5.0.10](https://github.com/GMOD/vcf-js/compare/v5.0.9...v5.0.10) (2022-12-17)
 
-
-
 - Use es2015 for nodejs build
 
 ## [5.0.9](https://github.com/GMOD/vcf-js/compare/v5.0.8...v5.0.9) (2022-11-23)
 
-
-
 - Fix erroneous parsing of symbolic alleles as breakends
 
 ## [5.0.8](https://github.com/GMOD/vcf-js/compare/v5.0.7...v5.0.8) (2022-11-20)
 
-
-
 - Parse single breakends and large insertion shorthand notation (#95)
 
 <a name="5.0.7"></a>

eslint.config.mjs

@@ -0,0 +1,58 @@
+import typescriptEslint from "@typescript-eslint/eslint-plugin";
+import prettier from "eslint-plugin-prettier";
+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 [...compat.extends(
+    "eslint:recommended",
+    "plugin:@typescript-eslint/recommended",
+    "plugin:@typescript-eslint/recommended-type-checked",
+    "plugin:@typescript-eslint/stylistic-type-checked",
+    "prettier",
+), {
+    plugins: {
+        "@typescript-eslint": typescriptEslint,
+        prettier,
+    },
+
+    languageOptions: {
+        parser: tsParser,
+        ecmaVersion: 5,
+        sourceType: "script",
+
+        parserOptions: {
+            tsconfigRootDir: "/home/cdiesh/src/gmod/vcf-js",
+            project: "./tsconfig.lint.json",
+        },
+    },
+
+    rules: {
+        curly: "error",
+
+        "@typescript-eslint/no-unused-vars": ["warn", {
+            argsIgnorePattern: "^_",
+            ignoreRestSiblings: true,
+        }],
+
+        "@typescript-eslint/ban-ts-comment": "off",
+        "@typescript-eslint/no-this-alias": "off",
+        "@typescript-eslint/no-unsafe-member-access": "off",
+        "@typescript-eslint/no-unsafe-argument": "off",
+        "@typescript-eslint/no-explicit-any": "off",
+        "@typescript-eslint/no-unsafe-assignment": "off",
+        "@typescript-eslint/no-unsafe-call": "off",
+        "@typescript-eslint/no-unsafe-return": "off",
+        "prettier/prettier": "error",
+    },
+}];

jest.config.js

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

package.json

@@ -26,7 +26,7 @@
   "scripts": {
     "test": "jest",
     "coverage": "npm test -- --coverage",
-    "lint": "eslint . --ext .ts,.js",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
     "docs": "documentation readme src/parse.ts --section=API  --shallow",
     "postdocs": "prettier --write README.md",
     "clean": "rimraf dist esm",
@@ -40,19 +40,21 @@
   },
   "devDependencies": {
     "@babel/core": "^7.20.5",
+    "@eslint/eslintrc": "^3.1.0",
+    "@eslint/js": "^9.7.0",
     "@types/jest": "^29.2.4",
-    "@typescript-eslint/eslint-plugin": "^5.46.1",
-    "@typescript-eslint/parser": "^5.46.1",
+    "@typescript-eslint/eslint-plugin": "^7.17.0",
+    "@typescript-eslint/parser": "^7.17.0",
     "documentation": "^14.0.1",
-    "eslint": "^8.30.0",
-    "eslint-config-prettier": "^8.3.0",
-    "eslint-plugin-prettier": "^4.0.0",
+    "eslint": "^9.7.0",
+    "eslint-config-prettier": "^9.1.0",
+    "eslint-plugin-prettier": "^5.1.3",
     "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"
+    "prettier": "^3.2.4",
+    "rimraf": "^6.0.1",
+    "standard-changelog": "^6.0.0",
+    "ts-jest": "^29.1.2",
+    "typescript": "^5.3.3"
   },
   "keywords": [
     "vcf",

src/index.ts

@@ -15,8 +15,7 @@ export function parseBreakend(breakendString: string): Breakend | undefined {
     let Join
     let Replacement
     let MatePosition
-    for (let i = 0; i < tokens.length; i += 1) {
-      const tok = tokens[i]
+    for (const tok of tokens) {
       if (tok) {
         if (tok.includes(':')) {
           // this is the remote location
@@ -45,7 +44,7 @@ export function parseBreakend(breakendString: string): Breakend | undefined {
         SingleBreakend: true,
         Replacement: breakendString.slice(0, breakendString.length - 1),
       }
-    } else if (breakendString[0] === '<') {
+    } else if (breakendString.startsWith('<')) {
       const res = breakendString.match('<(.*)>(.*)')
       if (!res) {
         throw new Error(`failed to parse ${breakendString}`)

src/parse.ts

@@ -33,7 +33,7 @@ export default class VCF {
     header: string
     strict?: boolean
   }) {
-    if (!header || !header.length) {
+    if (!header?.length) {
       throw new Error('empty header received')
     }
     const headerLines = header.split(/[\r\n]+/).filter(line => line)
@@ -183,8 +183,8 @@ export default class VCF {
    */
   getMetadata(...args: string[]) {
     let filteredMetadata: any = this.metadata
-    for (let i = 0; i < args.length; i += 1) {
-      filteredMetadata = filteredMetadata[args[i]]
+    for (const arg of args) {
+      filteredMetadata = filteredMetadata[arg]
       if (!filteredMetadata) {
         return filteredMetadata
       }
@@ -211,33 +211,33 @@ export default class VCF {
     let currKey = ''
     let currValue = ''
     let state = 1 // states: 1: read key to = or pair sep, 2: read value to sep or quote, 3: read value to quote
-    for (let i = 0; i < str.length; i += 1) {
+    for (const s of str) {
       if (state === 1) {
         // read key to = or pair sep
-        if (str[i] === '=') {
+        if (s === '=') {
           state = 2
-        } else if (str[i] !== pairSeparator) {
-          currKey += str[i]
+        } else if (s !== pairSeparator) {
+          currKey += s
         } else if (currValue === '') {
           data[currKey] = null
           currKey = ''
         }
       } else if (state === 2) {
         // read value to pair sep or quote
-        if (str[i] === pairSeparator) {
+        if (s === pairSeparator) {
           data[currKey] = currValue
           currKey = ''
           currValue = ''
           state = 1
-        } else if (str[i] === '"') {
+        } else if (s === '"') {
           state = 3
         } else {
-          currValue += str[i]
+          currValue += s
         }
       } else if (state === 3) {
         // read value to quote
-        if (str[i] !== '"') {
-          currValue += str[i]
+        if (s !== '"') {
+          currValue += s
         } else {
           state = 2
         }
@@ -258,7 +258,6 @@ export default class VCF {
    * CRLF newlines.
    */
   parseLine(line: string) {
-    // eslint-disable-next-line no-param-reassign
     line = line.trim()
     if (!line.length) {
       return undefined
@@ -320,7 +319,6 @@ export default class VCF {
           })
         } else if (itemType === 'Flag') {
           if (info[key]) {
-            // eslint-disable-next-line no-console
             console.warn(
               `Info field ${key} is a Flag and should not have a value (got value ${info[key]})`,
             )

test/parse.test.ts

@@ -324,7 +324,7 @@ test('shortcut parsing with 1000 genomes', () => {
   expect(Object.keys(variants[0].SAMPLES).slice(0, 5)).toMatchSnapshot()
   expect(Object.keys(variants[0].SAMPLES).slice(-5)).toMatchSnapshot()
   const ret = variants.map(v => {
-    const { SAMPLES, ...rest } = v
+    const { SAMPLES: _, ...rest } = v
     return rest
   })
   expect(ret).toMatchSnapshot()

tsconfig.lint.json

@@ -0,0 +1,4 @@
+{
+  "extends": "./tsconfig",
+  "include": ["src", "test"]
+}