Wow

package.json

@@ -39,32 +39,32 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^1.4.4",
+    "@gmod/bgzf-filehandle": "^1.4.7",
     "abortable-promise-cache": "^1.5.0",
     "buffer-crc32": "^0.2.13",
-    "generic-filehandle": "^3.0.0",
+    "generic-filehandle": "^3.1.1",
     "long": "^4.0.0",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/buffer-crc32": "^0.2.2",
-    "@types/jest": "^29.5.1",
+    "@types/buffer-crc32": "^0.2.4",
+    "@types/jest": "^29.5.11",
     "@types/long": "^4.0.0",
-    "@types/node": "^18.16.0",
-    "@typescript-eslint/eslint-plugin": "^5.59.6",
-    "@typescript-eslint/parser": "^5.59.6",
-    "eslint": "^8.40.0",
-    "eslint-config-prettier": "^8.7.0",
-    "eslint-plugin-import": "^2.27.5",
-    "eslint-plugin-prettier": "^4.2.1",
-    "eslint-plugin-unicorn": "^47.0.0",
-    "jest": "^29.5.0",
+    "@types/node": "^20.10.4",
+    "@typescript-eslint/eslint-plugin": "^6.13.2",
+    "@typescript-eslint/parser": "^6.13.2",
+    "eslint": "^8.55.0",
+    "eslint-config-prettier": "^9.1.0",
+    "eslint-plugin-import": "^2.29.0",
+    "eslint-plugin-prettier": "^5.0.1",
+    "eslint-plugin-unicorn": "^49.0.0",
+    "jest": "^29.7.0",
     "jest-fetch-mock": "^3.0.3",
-    "prettier": "^2.8.8",
-    "rimraf": "^5.0.0",
-    "standard-changelog": "^2.0.27",
-    "ts-jest": "^29.1.0",
-    "typescript": "^5.0.4"
+    "prettier": "^3.1.1",
+    "rimraf": "^5.0.5",
+    "standard-changelog": "^5.0.0",
+    "ts-jest": "^29.1.1",
+    "typescript": "^5.3.3"
   },
   "publishConfig": {
     "access": "public"

src/bamFile.ts

@@ -17,6 +17,10 @@ export const BAM_MAGIC = 21840194
 
 const blockLen = 1 << 16
 
+function isGzip(buf: Buffer) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
+}
+
 async function gen2array<T>(gen: AsyncIterable<T[]>): Promise<T[]> {
   let out: T[] = []
   for await (const x of gen) {
@@ -157,7 +161,7 @@ export default class BamFile {
       buffer = (await this.bam.readFile(opts)) as Buffer
     }
 
-    const uncba = await unzip(buffer)
+    const uncba = isGzip(buffer) ? await unzip(buffer) : buffer
 
     if (uncba.readInt32LE(0) !== BAM_MAGIC) {
       throw new Error('Not a BAM file')
@@ -215,9 +219,8 @@ export default class BamFile {
     if (!bytesRead) {
       throw new Error('Error reading refseqs from header')
     }
-    const uncba = await unzip(
-      buffer.subarray(0, Math.min(bytesRead, refSeqBytes)),
-    )
+    const ret = buffer.subarray(0, Math.min(bytesRead, refSeqBytes))
+    const uncba = isGzip(ret) ? await unzip(ret) : ret
     const nRef = uncba.readInt32LE(start)
     let p = start + 4
     const chrToIndex: { [key: string]: number } = {}

src/record.ts

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-empty-function */
 import Constants from './constants'
 
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('')