diff --git a/eslint.config.mjs b/eslint.config.mjs index db0c4a5..bcb3c45 100644 --- 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 index 8b70e77..ce28a49 100644 --- 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 index f369b03..3394183 100644 --- 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 index 368db39..0c61ba0 100644 --- 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 index f0e4ffb..072114c 100644 --- 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 index 2703bf0..4ca8cd9 100644 --- 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 index 7c12c61..1793eef 100644 --- a/src/util.ts +++ b/src/util.ts @@ -1,4 +1,3 @@ -import Long from 'long' import Chunk from './chunk' import VirtualOffset from './virtualOffset' @@ -6,16 +5,6 @@ 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 index cc3ec2c..70ad94c 100644 --- 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, diff --git a/yarn.lock b/yarn.lock index 6cc0ea2..e3c73b5 100644 --- a/yarn.lock +++ b/yarn.lock @@ -39,16 +39,16 @@ picocolors "^1.0.0" "@babel/parser@^7.25.4": - version "7.25.4" - resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.25.4.tgz#af4f2df7d02440286b7de57b1c21acfb2a6f257a" - integrity sha512-nq+eWrOgdtu3jG5Os4TQP3x3cLA8hR8TvJNjD8vnPa20WGycimcparWnLK4jJhElTK6SDyuJo1weMKO/5LpmLA== 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