Update deps

package.json

@@ -21,7 +21,7 @@
     "esm"
   ],
   "scripts": {
-    "test": "vitest run",
+    "test": "vitest",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "format": "prettier --write .",
     "docs": "documentation readme --shallow src/indexedCramFile.ts --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/craiIndex.ts --section=CraiIndex;  documentation readme --shallow errors.ts '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
@@ -31,7 +31,7 @@
     "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "postbuild": "webpack",
-    "prepack": "npm test && npm run build && cp dist/errors.js errors.js",
+    "prepack": "npm test run && npm run build && cp dist/errors.js errors.js",
     "postpublish": "rm errors.js",
     "postversion": "git push --follow-tags"
   },

src/craiIndex.ts

@@ -1,5 +1,3 @@
-import AbortablePromiseCache from '@gmod/abortable-promise-cache'
-import QuickLRU from 'quick-lru'
 import { unzip } from './unzip'
 import { open } from './io'
 import { CramMalformedError } from './errors'
@@ -68,9 +66,9 @@ export default class CraiIndex {
     this.filehandle = open(args.url, args.path, args.filehandle)
   }
 
-  async parseIndex(opts: { signal?: AbortSignal } = {}) {
+  async parseIndex() {
     const index: ParsedIndex = {}
-    const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile(opts))
+    const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile())
     if (
       uncompressedBuffer.length > 4 &&
       uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC
@@ -122,9 +120,9 @@ export default class CraiIndex {
     return index
   }
 
-  getIndex(opts?: { signal?: AbortSignal }) {
+  getIndex() {
     if (!this.parseIndexP) {
-      this.parseIndexP = this.parseIndex(opts).catch(e => {
+      this.parseIndexP = this.parseIndex().catch((e: unknown) => {
         this.parseIndexP = undefined
         throw e
       })

src/cramFile/file.ts

@@ -90,10 +90,9 @@ export default class CramFile {
       cacheSize: args.cacheSize ?? 20000,
     }
 
-    // cache of features in a slice, keyed by the
-    // slice offset. caches all of the features in a slice, or none.
-    // the cache is actually used by the slice object, it's just
-    // kept here at the level of the file
+    // cache of features in a slice, keyed by the slice offset. caches all of
+    // the features in a slice, or none. the cache is actually used by the
+    // slice object, it's just kept here at the level of the file
     this.featureCache = new QuickLRU({
       maxSize: this.options.cacheSize,
     })

src/cramFile/slice/decodeRecord.ts

@@ -84,7 +84,7 @@ function parseTagData(tagType: string, buffer: Uint8Array) {
     return readNullTerminatedString(buffer)
   }
   if (tagType === 'A') {
-    return String.fromCharCode(buffer[0])
+    return String.fromCharCode(buffer[0]!)
   }
   if (tagType === 'I') {
     return new Uint32Array(buffer.buffer)[0]
@@ -102,7 +102,7 @@ function parseTagData(tagType: string, buffer: Uint8Array) {
     return new Int8Array(buffer.buffer)[0]
   }
   if (tagType === 'C') {
-    return buffer[0] as number
+    return buffer[0]!
   }
   if (tagType === 'f') {
     return new Float32Array(buffer.buffer)[0]
@@ -312,7 +312,6 @@ export default function decodeRecord(
   // TN = tag names
   const TN = compressionScheme.getTagNames(TLindex)!
   const ntags = TN.length
-
   for (let i = 0; i < ntags; i += 1) {
     const tagId = TN[i]!
     const tagName = tagId.slice(0, 2)
@@ -321,7 +320,8 @@ export default function decodeRecord(
     const tagData = compressionScheme
       .getCodecForTag(tagId)
       .decode(slice, coreDataBlock, blocksByContentId, cursors)
-    tags[tagName] = parseTagData(tagType, tagData)
+    tags[tagName] =
+      typeof tagData === 'number' ? tagData : parseTagData(tagType, tagData)
   }
 
   let readFeatures: ReadFeature[] | undefined

test/parse.test.ts

@@ -128,7 +128,6 @@ describe('CRAM reader', () => {
       refSeqStart: 0,
     })
     const {
-      // eslint-disable-next-line @typescript-eslint/no-unused-vars
       content,
       parsedContent: compressionBlockData,
       ...compressionBlock