Misc

package.json

@@ -44,10 +44,8 @@
   "dependencies": {
     "@gmod/binary-parser": "^1.3.5",
     "@jkbonfield/htscodecs": "^0.5.1",
-    "abortable-promise-cache": "^1.2.0",
     "buffer-crc32": "^1.0.0",
     "bzip2": "^0.1.1",
-    "long": "^4.0.0",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
     "quick-lru": "^4.0.1",
@@ -58,7 +56,6 @@
     "@babel/preset-typescript": "^7.17.12",
     "@gmod/indexedfasta": "^2.1.0",
     "@types/jest": "^29.5.12",
-    "@types/long": "^4.0.2",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
     "@typescript-eslint/eslint-plugin": "^7.0.2",

src/craiIndex.ts

@@ -1,5 +1,3 @@
-import AbortablePromiseCache from 'abortable-promise-cache'
-import QuickLRU from 'quick-lru'
 import { unzip } from './unzip'
 import { open } from './io'
 import { CramMalformedError } from './errors'
@@ -34,6 +32,13 @@ 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:
   // 1. Sequence id
@@ -43,7 +48,7 @@ export default class CraiIndex {
   // 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>
+  private parseIndexP?: Promise<ParsedIndex>
   private filehandle: Filehandle
 
   /**
@@ -55,57 +60,45 @@ 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(),
-    })
   }
 
-  parseIndex() {
+  async parseIndex(opts: { signal?: AbortSignal } = {}) {
     const index: ParsedIndex = {}
-    return this.filehandle
-      .readFile()
-      .then(data => {
-        if (data[0] === 31 && data[1] === 139) {
-          return unzip(data)
-        }
-        return data
-      })
-      .then(uncompressedBuffer => {
-        if (
-          uncompressedBuffer.length > 4 &&
-          uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC
-        ) {
-          throw new CramMalformedError(
-            'invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support',
-          )
-        }
-        // interpret the text as regular ascii, since it is
-        // supposed to be only digits and whitespace characters
-        // this is written in a deliberately low-level fashion for performance,
-        // because some .crai files can be pretty large.
-        let currentRecord: number[] = []
-        let currentString = ''
+    const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile(opts))
+    if (
+      uncompressedBuffer.length > 4 &&
+      uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC
+    ) {
+      throw new CramMalformedError(
+        'invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support',
+      )
+    }
+    // interpret the text as regular ascii, since it is
+    // supposed to be only digits and whitespace characters
+    // this is written in a deliberately low-level fashion for performance,
+    // because some .crai files can be pretty large.
+    let currentRecord: number[] = []
+    let currentString = ''
         for (const charCode of uncompressedBuffer) {
-          if (
-            (charCode >= 48 && charCode <= 57) /* 0-9 */ ||
-            (!currentString && charCode === 45) /* leading - */
-          ) {
-            currentString += String.fromCharCode(charCode)
-          } else if (charCode === 9 /* \t */) {
-            currentRecord.push(Number.parseInt(currentString, 10))
-            currentString = ''
-          } else if (charCode === 10 /* \n */) {
-            currentRecord.push(Number.parseInt(currentString, 10))
-            currentString = ''
-            addRecordToIndex(index, currentRecord)
-            currentRecord = []
-          } else if (charCode !== 13 /* \r */ && charCode !== 32 /* space */) {
-            // if there are other characters in the file besides
-            // space and \r, something is wrong.
-            throw new CramMalformedError('invalid .crai index file')
-          }
-        }
+      if (
+        (charCode >= 48 && charCode <= 57) /* 0-9 */ ||
+        (!currentString && charCode === 45) /* leading - */
+      ) {
+        currentString += String.fromCharCode(charCode)
+      } else if (charCode === 9 /* \t */) {
+        currentRecord.push(Number.parseInt(currentString, 10))
+        currentString = ''
+      } else if (charCode === 10 /* \n */) {
+        currentRecord.push(Number.parseInt(currentString, 10))
+        currentString = ''
+        addRecordToIndex(index, currentRecord)
+        currentRecord = []
+      } else if (charCode !== 13 /* \r */ && charCode !== 32 /* space */) {
+        // if there are other characters in the file besides
+        // space and \r, something is wrong.
+        throw new CramMalformedError('invalid .crai index file')
+      }
+    }
 
         // if the file ends without a \n, we need to flush our buffers
         if (currentString) {
@@ -125,14 +118,20 @@ export default class CraiIndex {
       })
   }
 
-  getIndex(opts: { signal?: AbortSignal } = {}) {
-    return this._parseCache.get('index', null, opts.signal)
+  getIndex(opts?: { signal?: AbortSignal }) {
+    if (!this.parseIndexP) {
+      this.parseIndexP = this.parseIndex(opts).catch(e => {
+        this.parseIndexP = undefined
+        throw e
+      })
+    }
+    return this.parseIndexP
   }
 
   /**
    * @param {number} seqId
-   * @returns {Promise} true if the index contains entries for
-   * the given reference sequence ID, false otherwise
+   * @returns true if the index contains entries for the given reference
+   * sequence ID, false otherwise
    */
   async hasDataForReferenceSequence(seqId: number) {
     return !!(await this.getIndex())[seqId]

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])
   }
   if (tagType === 'I') {
-    return Long.fromBytesLE(buffer).toNumber()
+    return new Uint32Array(buffer.buffer)[0]
   }
   if (tagType === 'i') {
     return new Int32Array(buffer.buffer)[0]
@@ -259,8 +258,8 @@ export default function decodeRecord(
   let mateRecordNumber
   // mate record
   if (CramFlagsDecoder.isDetached(cramFlags)) {
-    // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
-    // const mate: any = {}
+    // note: the MF is a byte in 1.0, int32 in 2+,
+    // but once again this doesn't matter for javascript
     const mateFlags = decodeDataSeries('MF')
     let mateReadName
     if (!compressionScheme.readNamesIncluded) {