Reverts

.eslintrc.json

@@ -0,0 +1,16 @@
+{
+  "parser": "@typescript-eslint/parser",
+  "plugins": ["prettier", "@typescript-eslint"],
+  "extends": [
+    "plugin:@typescript-eslint/recommended",
+    "plugin:prettier/recommended"
+  ],
+  "rules": {
+    "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"]
+  }
+}

.github/workflows/push.yml

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

README.md

@@ -2,7 +2,7 @@
 [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/bgzf-filehandle/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/bgzf-filehandle/branch/master)
 [![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bgzf-filehandle/push.yml?branch=master)](https://github.com/GMOD/bgzf-filehandle/actions)
 
-Transparently read [indexed block-gzipped (BGZF)](http://www.htslib.org/doc/bgzip.html) files, such as those created by bgzip, using coordinates from the uncompressed file. The module is used in @gmod/indexedfasta to read bgzip-indexed fasta files (with gzi index, fai index, and fa).
+Transparently read [indexed block-gzipped (BGZF)](http://www.htslib.org/doc/bgzip.html) files, such as those created by bgzip, using coordinates from the uncompressed file. The module is used in @gmod/indexedfasta to read bgzip-indexed fasta files (with gzi index, fai index, and fa). 
 
 Users can also use the `unzip` function to unzip bgzip files whole (which pako has trouble with natively)
 

jest.config.js

@@ -0,0 +1,5 @@
+/** @type {import('ts-jest/dist/types').InitialOptionsTsJest} */
+module.exports = {
+  preset: 'ts-jest',
+  testEnvironment: 'node',
+};

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bgzf-filehandle",
-  "version": "1.5.2",
+  "version": "1.4.7",
   "description": "read from a compressed bgzip file (with .gzi) as if it were uncompressed",
   "license": "MIT",
   "repository": "gmod/bgzf-filehandle",
@@ -20,14 +20,14 @@
     "src"
   ],
   "scripts": {
-    "test": "vitest",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
+    "test": "jest",
+    "lint": "eslint src test",
     "clean": "rimraf dist esm",
-    "prebuild": "yarn clean",
+    "prebuild": "npm run clean",
     "build:esm": "tsc --target es2018 --outDir esm",
-    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
-    "build": "yarn build:esm && yarn build:es5",
-    "prepublishOnly": "yarn test --run && yarn build",
+    "build:es5": "tsc --target es5 --outDir dist",
+    "build": "npm run build:esm && npm run build:es5",
+    "prepublishOnly": "npm test && npm run build",
     "postversion": "git push --follow-tags"
   },
   "keywords": [
@@ -42,25 +42,26 @@
   },
   "devDependencies": {
     "@types/es6-promisify": "^6.0.0",
+    "@types/jest": "^29.5.2",
     "@types/long": "^4.0.1",
-    "@types/node": "^22.10.1",
+    "@types/node": "^18.11.16",
     "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^8.16.0",
-    "@typescript-eslint/parser": "^8.16.0",
-    "eslint": "^9.7.0",
+    "@typescript-eslint/eslint-plugin": "^5.59.9",
+    "@typescript-eslint/parser": "^5.59.9",
+    "eslint": "^8.42.0",
+    "eslint-config-prettier": "^8.8.0",
     "eslint-plugin-import": "^2.27.5",
-    "eslint-plugin-unicorn": "^56.0.1",
-    "prettier": "^3.2.5",
-    "rimraf": "^6.0.1",
-    "typescript": "^5.1.3",
-    "typescript-eslint": "^8.16.0",
-    "vitest": "^2.1.6"
+    "eslint-plugin-prettier": "^4.2.1",
+    "jest": "^29.5.0",
+    "prettier": "^2.8.8",
+    "rimraf": "^5.0.1",
+    "ts-jest": "^29.1.0",
+    "typescript": "^5.1.3"
   },
   "publishConfig": {
     "access": "public"
   },
   "browser": {
-    "./esm/unzip.js": "./esm/unzip-pako.js",
-    "./dist/unzip.js": "./dist/unzip-pako.js"
+    "./esm/unzip.js": "./esm/unzip-pako.js"
   }
 }

src/bgzFilehandle.ts

@@ -50,12 +50,7 @@ export default class BgzFilehandle {
   async getUncompressedFileSize() {
     // read the last block's ISIZE (see gzip RFC),
     // and add it to its uncompressedPosition
-    const ret = await this.gzi.getLastBlock()
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-    if (!ret) {
-      throw new Error('no blocks')
-    }
-    const [, uncompressedPosition] = ret
+    const [, uncompressedPosition] = await this.gzi.getLastBlock()
 
     const { size } = await this.filehandle.stat()
 
@@ -72,13 +67,12 @@ export default class BgzFilehandle {
 
   async _readAndUncompressBlock(
     blockBuffer: Buffer,
-    [compressedPosition]: [number, number],
-    [nextCompressedPosition]: [number, number],
+    [compressedPosition]: [number],
+    [nextCompressedPosition]: [number],
   ) {
     let next = nextCompressedPosition
     if (!next) {
-      const stat = await this.filehandle.stat()
-      next = stat.size
+      next = (await this.filehandle.stat()).size
     }
 
     // read the compressed data into the block buffer
@@ -96,7 +90,7 @@ export default class BgzFilehandle {
       blockBuffer.slice(0, blockCompressedLength),
     )
 
-    return unzippedBuffer
+    return unzippedBuffer as Buffer
   }
 
   async read(buf: Buffer, offset: number, length: number, position: number) {
@@ -114,6 +108,7 @@ export default class BgzFilehandle {
       blockNum < blockPositions.length - 1;
       blockNum += 1
     ) {
+      // eslint-disable-next-line no-await-in-loop
       const uncompressedBuffer = await this._readAndUncompressBlock(
         blockBuffer,
         blockPositions[blockNum],

src/gziIndex.ts

@@ -8,7 +8,7 @@ const UNCOMPRESSED_POSITION = 1
 export default class GziIndex {
   filehandle: GenericFilehandle
 
-  index?: Promise<[number, number][]>
+  index?: any
 
   constructor({
     filehandle,
@@ -46,15 +46,15 @@ export default class GziIndex {
     return this.index
   }
 
-  async _readIndex(): Promise<[number, number][]> {
+  async _readIndex() {
     let buf = Buffer.allocUnsafe(8)
     await this.filehandle.read(buf, 0, 8, 0)
     const numEntries = this._readLongWithOverflow(buf, 0, true)
     if (!numEntries) {
       return [[0, 0]]
     }
 
-    const entries = new Array(numEntries + 1) as [number, number][]
+    const entries = new Array(numEntries + 1)
     entries[0] = [0, 0]
 
     // TODO rewrite this to make an index-index that stays in memory
@@ -81,7 +81,10 @@ export default class GziIndex {
 
   async getLastBlock() {
     const entries = await this._getIndex()
-    return entries.at(-1)!
+    if (!entries.length) {
+      return undefined
+    }
+    return entries[entries.length - 1]
   }
 
   async getRelevantBlocksForRead(length: number, position: number) {
@@ -90,13 +93,12 @@ export default class GziIndex {
       return []
     }
     const entries = await this._getIndex()
-    const relevant = [] as [number, number][]
+    const relevant = []
 
     // binary search to find the block that the
     // read starts in and extend forward from that
-    const compare = (entry: number[], nextEntry: number[]) => {
+    const compare = (entry: any, nextEntry: any) => {
       const uncompressedPosition = entry[UNCOMPRESSED_POSITION]
-      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       const nextUncompressedPosition = nextEntry
         ? nextEntry[UNCOMPRESSED_POSITION]
         : Infinity
@@ -142,9 +144,9 @@ export default class GziIndex {
         break
       }
     }
-    // if (relevant.at(-1)![UNCOMPRESSED_POSITION] < endPosition) {
-    //   relevant.push([])
-    // }
+    if (relevant[relevant.length - 1][UNCOMPRESSED_POSITION] < endPosition) {
+      relevant.push([])
+    }
     return relevant
   }
 }

src/index.ts

@@ -1,2 +1,4 @@
-export { default as BgzfFilehandle } from './bgzFilehandle'
-export { unzip, unzipChunkSlice, unzipChunk } from './unzip'
+import BgzfFilehandle from './bgzFilehandle'
+import { unzip, unzipChunk, unzipChunkSlice } from './unzip'
+
+export { BgzfFilehandle, unzip, unzipChunk, unzipChunkSlice }

src/unzip-pako.ts

@@ -12,12 +12,9 @@ interface Chunk {
 }
 
 // browserify-zlib, which is the zlib shim used by default in webpacked code,
-// does not properly uncompress bgzf chunks that contain more than one bgzf
-// block, so export an unzip function that uses pako directly if we are running
-// in a browser.
-//
-//
-
+// does not properly uncompress bgzf chunks that contain more than
+// one bgzf block, so export an unzip function that uses pako directly
+// if we are running in a browser.
 async function unzip(inputData: Buffer) {
   try {
     let strm
@@ -31,7 +28,6 @@ async function unzip(inputData: Buffer) {
       inflator = new Inflate()
       //@ts-ignore
       ;({ strm } = inflator)
-
       inflator.push(remainingInput, Z_SYNC_FLUSH)
       if (inflator.err) {
         throw new Error(inflator.msg)
@@ -49,21 +45,20 @@ async function unzip(inputData: Buffer) {
       offset += chunks[i].length
     }
     return Buffer.from(result)
-  } catch (error) {
+  } catch (e) {
     //cleanup error message
-    if (`${error}`.includes('incorrect header check')) {
+    if (`${e}`.match(/incorrect header check/)) {
       throw new Error(
         'problem decompressing block: incorrect gzip header check',
       )
     }
-    throw error
+    throw e
   }
 }
 
-// similar to pakounzip, except it does extra counting to return the positions
-// of compressed and decompressed data offsets
-//
-
+// similar to pakounzip, except it does extra counting
+// to return the positions of compressed and decompressed
+// data offsets
 async function unzipChunk(inputData: Buffer) {
   try {
     let strm
@@ -77,7 +72,6 @@ async function unzipChunk(inputData: Buffer) {
       const inflator = new Inflate()
       // @ts-ignore
       ;({ strm } = inflator)
-
       inflator.push(remainingInput, Z_SYNC_FLUSH)
       if (inflator.err) {
         throw new Error(inflator.msg)
@@ -95,21 +89,19 @@ async function unzipChunk(inputData: Buffer) {
 
     const buffer = Buffer.concat(blocks)
     return { buffer, cpositions, dpositions }
-  } catch (error) {
+  } catch (e) {
     //cleanup error message
-    if (`${error}`.includes('incorrect header check')) {
+    if (`${e}`.match(/incorrect header check/)) {
       throw new Error(
         'problem decompressing block: incorrect gzip header check',
       )
     }
-    throw error
+    throw e
   }
 }
 
 // similar to unzipChunk above but slices (0,minv.dataPosition) and
 // (maxv.dataPosition,end) off
-//
-
 async function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {
   try {
     let strm
@@ -127,7 +119,6 @@ async function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {
       const inflator = new Inflate()
       // @ts-ignore
       ;({ strm } = inflator)
-
       inflator.push(remainingInput, Z_SYNC_FLUSH)
       if (inflator.err) {
         throw new Error(inflator.msg)
@@ -145,7 +136,6 @@ async function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {
         len = chunks[0].length
       }
       const origCpos = cpos
-
       cpos += strm.next_in
       dpos += len
 
@@ -178,14 +168,14 @@ async function unzipChunkSlice(inputData: Buffer, chunk: Chunk) {
     const buffer = Buffer.from(result)
 
     return { buffer, cpositions, dpositions }
-  } catch (error) {
+  } catch (e) {
     //cleanup error message
-    if (`${error}`.includes('incorrect header check')) {
+    if (`${e}`.match(/incorrect header check/)) {
       throw new Error(
         'problem decompressing block: incorrect gzip header check',
       )
     }
-    throw error
+    throw e
   }
 }
 

src/unzip.ts

@@ -1,18 +1,16 @@
 import zlib from 'zlib'
 import { Buffer } from 'buffer'
 import { promisify } from 'es6-promisify'
+import { pakoUnzip, unzipChunk, unzipChunkSlice } from './unzip-pako'
 
 const gunzip = promisify(zlib.gunzip)
 
 // in node, just use the native unzipping with Z_SYNC_FLUSH
 function nodeUnzip(input: Buffer): Promise<Buffer> {
   //@ts-ignore
   return gunzip(input, {
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     finishFlush: (zlib.constants || zlib).Z_SYNC_FLUSH,
   })
 }
 
-export { nodeUnzip as unzip, nodeUnzip }
-
-export { pakoUnzip, unzipChunkSlice, unzipChunk } from './unzip-pako'
+export { nodeUnzip as unzip, unzipChunk, unzipChunkSlice, nodeUnzip, pakoUnzip }