Remove dependency on long, abortable-promise-cache (#128)

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'
@@ -35,6 +33,13 @@ function addRecordToIndex(index: ParsedIndex, record: number[]) {
   })
 }
 
+function maybeUnzip(data: Buffer) {
+  if (data[0] === 31 && data[1] === 139) {
+    return unzip(data)
+  }
+  return data
+}
+
 export default class CraiIndex {
   // A CRAM index (.crai) is a gzipped tab delimited file containing the
   // following columns:
@@ -45,10 +50,9 @@ export default class CraiIndex {
   // 4. Container start byte position in the file
   // 5. Slice start byte position in the container data (‘blocks’)
   // 6. Slice size in bytes
-  //
-  // Each line represents a slice in the CRAM file. Please note that all slices
-  // must be listed in index file.
-  private _parseCache: AbortablePromiseCache<unknown, ParsedIndex>
+  // Each line represents a slice in the CRAM file. Please note that all slices must be listed in index file.
+  private parseIndexP?: Promise<ParsedIndex>
+
   private filehandle: Filehandle
 
   /**
@@ -60,17 +64,11 @@ export default class CraiIndex {
    */
   constructor(args: CramFileSource) {
     this.filehandle = open(args.url, args.path, args.filehandle)
-    this._parseCache = new AbortablePromiseCache<unknown, ParsedIndex>({
-      cache: new QuickLRU({ maxSize: 1 }),
-      fill: (_data, _signal) => this.parseIndex(),
-    })
   }
 
   async parseIndex() {
     const index: ParsedIndex = {}
-    const data = await this.filehandle.readFile()
-    const uncompressedBuffer =
-      data[0] === 31 && data[1] === 139 ? unzip(data) : data
+    const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile())
     if (
       uncompressedBuffer.length > 4 &&
       uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC
@@ -122,8 +120,14 @@ export default class CraiIndex {
     return index
   }
 
-  getIndex(opts: { signal?: AbortSignal } = {}) {
-    return this._parseCache.get('index', null, opts.signal)
+  getIndex() {
+    if (!this.parseIndexP) {
+      this.parseIndexP = this.parseIndex().catch((e: unknown) => {
+        this.parseIndexP = undefined
+        throw e
+      })
+    }
+    return this.parseIndexP
   }
 
   /**

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

@@ -1,4 +1,3 @@
-import Long from 'long'
 import { CramMalformedError } from '../../errors'
 import {
   BamFlagsDecoder,
@@ -31,7 +30,7 @@ function readNullTerminatedString(buffer: Uint8Array) {
  * parse a BAM tag's array value from a binary buffer
  * @private
  */
-function parseTagValueArray(buffer: Buffer) {
+function parseTagValueArray(buffer: Uint8Array) {
   const arrayType = String.fromCharCode(buffer[0]!)
   const length = Int32Array.from(buffer.slice(1))[0]!
 
@@ -80,15 +79,15 @@ function parseTagValueArray(buffer: Buffer) {
   return array
 }
 
-function parseTagData(tagType: string, buffer: any) {
+function parseTagData(tagType: string, buffer: Uint8Array) {
   if (tagType === 'Z') {
     return readNullTerminatedString(buffer)
   }
   if (tagType === 'A') {
-    return String.fromCharCode(buffer[0])
+    return String.fromCharCode(buffer[0]!)
   }
   if (tagType === 'I') {
-    return Long.fromBytesLE(buffer).toNumber()
+    return new Uint32Array(buffer.buffer)[0]
   }
   if (tagType === 'i') {
     return new Int32Array(buffer.buffer)[0]
@@ -103,7 +102,7 @@ function parseTagData(tagType: string, buffer: any) {
     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]
@@ -313,7 +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)
@@ -322,7 +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

src/cramFile/slice/index.ts

@@ -181,7 +181,7 @@ export default class CramSlice {
   constructor(
     public container: CramContainer,
     public containerPosition: number,
-    _unused: number,
+    public sliceSize: number,
   ) {
     this.file = container.file
   }