@gmod/cram 2.0.3 → 3.0.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "2.0.3",
+  "version": "3.0.0",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -22,7 +22,7 @@
   ],
   "scripts": {
     "test": "jest",
-    "lint": "eslint src test",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
     "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",
     "prebuild": "npm run clean",
     "clean": "rimraf dist esm",
@@ -42,9 +42,8 @@
     "biojs"
   ],
   "dependencies": {
-    "@gmod/binary-parser": "^1.3.5",
+    "@gmod/abortable-promise-cache": "^2.0.0",
     "@jkbonfield/htscodecs": "^0.5.1",
-    "abortable-promise-cache": "^1.2.0",
     "buffer-crc32": "^1.0.0",
     "bzip2": "^0.1.1",
     "long": "^4.0.0",
@@ -54,30 +53,25 @@
     "xz-decompress": "^0.2.1"
   },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.18.2",
-    "@babel/preset-typescript": "^7.17.12",
     "@gmod/indexedfasta": "^2.1.0",
     "@types/jest": "^29.5.12",
-    "@types/long": "^4.0.2",
+    "@types/long": "^4.0.0",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@typescript-eslint/eslint-plugin": "^7.0.2",
-    "@typescript-eslint/parser": "^7.0.2",
+    "@typescript-eslint/eslint-plugin": "^8.0.0",
+    "@typescript-eslint/parser": "^8.0.0",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
-    "eslint": "^8.30.0",
+    "eslint": "^9.8.0",
     "eslint-config-prettier": "^9.0.0",
-    "eslint-plugin-import": "^2.25.4",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^51.0.1",
-    "glob": "^10.3.1",
+    "eslint-plugin-unicorn": "^55.0.0",
     "jest": "^29.3.1",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
-    "rimraf": "^5.0.1",
+    "rimraf": "^6.0.1",
     "ts-jest": "^29.1.2",
     "typescript": "^5.0.3",
-    "url": "^0.11.0",
     "webpack": "^5.90.3",
     "webpack-cli": "^5.0.1"
   },

package/src/craiIndex.ts

@@ -1,4 +1,4 @@
-import AbortablePromiseCache from 'abortable-promise-cache'
+import AbortablePromiseCache from '@gmod/abortable-promise-cache'
 import QuickLRU from 'quick-lru'
 import { unzip } from './unzip'
 import { open } from './io'

package/src/cramFile/codecs/byteArrayLength.ts

@@ -1,10 +1,9 @@
-import { tinyMemoize } from '../util'
-
 import CramCodec, { Cursors } from './_base'
 import { ByteArrayLengthEncoding, CramEncoding } from '../encoding'
 import CramSlice from '../slice'
 import { CramFileBlock } from '../file'
 import { DataType } from './dataSeriesTypes'
+import { tinyMemoize } from '../util'
 
 type CramCodecFactory = <TData extends DataType = DataType>(
   encodingData: CramEncoding,

package/src/cramFile/codecs/external.ts

@@ -42,7 +42,7 @@ export default class ExternalCodec extends CramCodec<
     const contentBlock = blocksByContentId[blockContentId]
     if (!contentBlock) {
       throw new CramMalformedError(
-        `no block found with content ID ${blockContentId}`,
+        `no block found with content ID ${blockContentId}}`,
       )
     }
     const cursor = cursors.externalBlocks.getCursor(blockContentId)

package/src/cramFile/codecs/huffman.ts

@@ -46,7 +46,8 @@ export default class HuffmanIntCodec extends CramCodec<
     this.buildCodes()
     this.buildCaches()
 
-    // if this is a degenerate zero-length huffman code, special-case the decoding
+    // if this is a degenerate zero-length huffman code, special-case the
+    // decoding
     if (this.sortedCodes[0].bitLength === 0) {
       this._decode = this._decodeZeroLengthCode
     }

package/src/cramFile/container/compressionScheme.ts

@@ -1,6 +1,6 @@
 import { instantiateCodec } from '../codecs'
 import CramCodec from '../codecs/_base'
-import { CramCompressionHeader, CramPreservationMap } from '../sectionParsers'
+import { CramCompressionHeader } from '../sectionParsers'
 import { CramEncoding } from '../encoding'
 import { CramMalformedError } from '../../errors'
 import {
@@ -95,12 +95,8 @@ export default class CramContainerCompressionScheme {
   public tagCodecCache: Record<string, CramCodec> = {}
   public tagEncoding: Record<string, CramEncoding> = {}
   public dataSeriesEncoding: DataSeriesEncodingMap
-  private preservation: CramPreservationMap
-  private _endPosition: number
-  private _size: number
 
   constructor(content: CramCompressionHeader) {
-    // Object.assign(this, content)
     // interpret some of the preservation map tags for convenient use
     this.readNamesIncluded = content.preservation.RN
     this.APdelta = content.preservation.AP
@@ -109,9 +105,6 @@ export default class CramContainerCompressionScheme {
     this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM)
     this.dataSeriesEncoding = content.dataSeriesEncoding
     this.tagEncoding = content.tagEncoding
-    this.preservation = content.preservation
-    this._size = content._size
-    this._endPosition = content._endPosition
   }
 
   /**

package/src/cramFile/container/index.ts

@@ -4,6 +4,7 @@ import { itf8Size, parseItem, tinyMemoize } from '../util'
 import CramSlice from '../slice'
 import CramContainerCompressionScheme from './compressionScheme'
 import CramFile from '../file'
+import { getSectionParsers } from '../sectionParsers'
 
 export default class CramContainer {
   constructor(
@@ -11,20 +12,21 @@ export default class CramContainer {
     public filePosition: number,
   ) {}
 
-  // memoize
   getHeader() {
     return this._readContainerHeader(this.filePosition)
   }
 
-  // memoize
   async getCompressionHeaderBlock() {
     const containerHeader = await this.getHeader()
 
-    // if there are no records in the container, there will be no compression header
-    if (!containerHeader.numRecords) {
+    // if there are no records in the container, there will be no compression
+    // header
+    if (!containerHeader?.numRecords) {
       return null
     }
-    const sectionParsers = await this.file.getSectionParsers()
+    const { majorVersion } = await this.file.getDefinition()
+    const sectionParsers = getSectionParsers(majorVersion)
+
     const block = await this.getFirstBlock()
     if (block === undefined) {
       return undefined
@@ -34,6 +36,7 @@ export default class CramContainer {
         `invalid content type ${block.contentType} in what is supposed to be the compression header block`,
       )
     }
+
     const content = parseItem(
       block.content,
       sectionParsers.cramCompressionHeader.parser,
@@ -48,16 +51,20 @@ export default class CramContainer {
 
   async getFirstBlock() {
     const containerHeader = await this.getHeader()
+    if (!containerHeader) {
+      return undefined
+    }
     return this.file.readBlock(containerHeader._endPosition)
   }
 
-  // parses the compression header data into a CramContainerCompressionScheme object
-  // memoize
+  // parses the compression header data into a CramContainerCompressionScheme
+  // object
   async getCompressionScheme() {
     const header = await this.getCompressionHeaderBlock()
     if (!header) {
       return undefined
     }
+
     return new CramContainerCompressionScheme(header.parsedContent)
   }
 
@@ -68,11 +75,15 @@ export default class CramContainer {
   }
 
   async _readContainerHeader(position: number) {
-    const sectionParsers = await this.file.getSectionParsers()
+    const { majorVersion } = await this.file.getDefinition()
+    const sectionParsers = getSectionParsers(majorVersion)
     const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers
     const { size: fileSize } = await this.file.stat()
 
     if (position >= fileSize) {
+      console.warn(
+        `position:${position}>=fileSize:${fileSize} in cram container`,
+      )
       return undefined
     }
 
@@ -80,11 +91,11 @@ export default class CramContainer {
     // how much to buffer until you read numLandmarks
     const bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength)
     await this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position)
-    const header1 = parseItem(bytes1, cramContainerHeader1.parser) as any
+    const header1 = parseItem(bytes1, cramContainerHeader1.parser)
     const numLandmarksSize = itf8Size(header1.numLandmarks)
     if (position + header1.length >= fileSize) {
       console.warn(
-        `${this.file}: container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`,
+        `container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`,
       )
       return undefined
     }

package/src/cramFile/file.ts

@@ -2,7 +2,6 @@ import { unzip } from '../unzip'
 import crc32 from 'buffer-crc32'
 import QuickLRU from 'quick-lru'
 import htscodecs from '@jkbonfield/htscodecs'
-import { Parser } from '@gmod/binary-parser'
 // @ts-expect-error
 import bzip2 from 'bzip2'
 import { XzReadableStream } from 'xz-decompress'
@@ -11,7 +10,7 @@ import ransuncompress from '../rans'
 import {
   BlockHeader,
   CompressionMethod,
-  cramFileDefinition as cramFileDefinitionParser,
+  cramFileDefinition,
   getSectionParsers,
 } from './sectionParsers'
 
@@ -32,25 +31,20 @@ function bufferToStream(buf: Buffer) {
   })
 }
 
-//source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
+// source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
   const uInt32 = new Uint32Array([0x11223344])
   const uInt8 = new Uint8Array(uInt32.buffer)
 
   if (uInt8[0] === 0x44) {
-    return 0 //little-endian
+    return 0 // little-endian
   } else if (uInt8[0] === 0x11) {
-    return 1 //big-endian
+    return 1 // big-endian
   } else {
-    return 2 //mixed-endian?
+    return 2 // mixed-endian?
   }
 }
 
-// export type CramFileSource =
-//   | { url: string; path?: undefined; filehandle?: undefined }
-//   | { path: string; url?: undefined; filehandle?: undefined }
-//   | { filehandle: Filehandle; url?: undefined; path?: undefined }
-
 export interface CramFileSource {
   filehandle?: Filehandle
   url?: string
@@ -110,15 +104,7 @@ export default class CramFile {
   }
 
   // can just read this object like a filehandle
-  read(
-    buffer: Buffer,
-    offset: number,
-    length: number,
-    position: number,
-  ): Promise<{
-    bytesRead: number
-    buffer: Buffer
-  }> {
+  read(buffer: Buffer, offset: number, length: number, position: number) {
     return this.file.read(buffer, offset, length, position)
   }
 
@@ -129,10 +115,10 @@ export default class CramFile {
 
   // memoized
   async getDefinition() {
-    const headbytes = Buffer.allocUnsafe(cramFileDefinitionParser.maxLength)
-    await this.file.read(headbytes, 0, cramFileDefinitionParser.maxLength, 0)
-    const definition = cramFileDefinitionParser.parser.parse(headbytes)
-      .result as any
+    const { maxLength, parser } = cramFileDefinition()
+    const headbytes = Buffer.allocUnsafe(maxLength)
+    await this.file.read(headbytes, 0, maxLength, 0)
+    const definition = parser(headbytes).value
     if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
       throw new CramUnimplementedError(
         `CRAM version ${definition.majorVersion} not supported`,
@@ -169,21 +155,16 @@ export default class CramFile {
     return this.header
   }
 
-  // memoize
-  async getSectionParsers() {
-    const { majorVersion } = await this.getDefinition()
-    return getSectionParsers(majorVersion)
-  }
-
   async getContainerById(containerNumber: number) {
-    const sectionParsers = await this.getSectionParsers()
+    const { majorVersion } = await this.getDefinition()
+    const sectionParsers = getSectionParsers(majorVersion)
     let position = sectionParsers.cramFileDefinition.maxLength
     const { size: fileSize } = await this.file.stat()
     const { cramContainerHeader1 } = sectionParsers
 
     // skip with a series of reads to the proper container
     let currentContainer
-    for (let i = 0; i <= containerNumber; i += 1) {
+    for (let i = 0; i <= containerNumber; i++) {
       // if we are about to go off the end of the file
       // and have not found that container, it does not exist
       if (position + cramContainerHeader1.maxLength + 8 >= fileSize) {
@@ -197,13 +178,12 @@ export default class CramFile {
           `container ${containerNumber} not found in file`,
         )
       }
-      // if this is the first container, read all the blocks in the
-      // container to determine its length, because we cannot trust
-      // the container header's given length due to a bug somewhere
-      // in htslib
+      // if this is the first container, read all the blocks in the container
+      // to determine its length, because we cannot trust the container
+      // header's given length due to a bug somewhere in htslib
       if (i === 0) {
         position = currentHeader._endPosition
-        for (let j = 0; j < currentHeader.numBlocks; j += 1) {
+        for (let j = 0; j < currentHeader.numBlocks; j++) {
           const block = await this.readBlock(position)
           if (block === undefined) {
             return undefined
@@ -239,7 +219,8 @@ export default class CramFile {
    * @returns {Promise[number]} the number of containers in the file
    */
   async containerCount(): Promise<number | undefined> {
-    const sectionParsers = await this.getSectionParsers()
+    const { majorVersion } = await this.getDefinition()
+    const sectionParsers = getSectionParsers(majorVersion)
     const { size: fileSize } = await this.file.stat()
     const { cramContainerHeader1 } = sectionParsers
 
@@ -256,7 +237,7 @@ export default class CramFile {
       // header's given length due to a bug somewhere in htslib
       if (containerCount === 0) {
         position = currentHeader._endPosition
-        for (let j = 0; j < currentHeader.numBlocks; j += 1) {
+        for (let j = 0; j < currentHeader.numBlocks; j++) {
           const block = await this.readBlock(position)
           if (block === undefined) {
             return undefined
@@ -278,7 +259,8 @@ export default class CramFile {
   }
 
   async readBlockHeader(position: number) {
-    const sectionParsers = await this.getSectionParsers()
+    const { majorVersion } = await this.getDefinition()
+    const sectionParsers = getSectionParsers(majorVersion)
     const { cramBlockHeader } = sectionParsers
     const { size: fileSize } = await this.file.stat()
 
@@ -292,7 +274,10 @@ export default class CramFile {
   }
 
   async _parseSection<T>(
-    section: { parser: Parser<T>; maxLength: number },
+    section: {
+      maxLength: number
+      parser: (buffer: Buffer, offset: number) => { offset: number; value: T }
+    },
     position: number,
     size = section.maxLength,
     preReadBuffer = undefined,
@@ -363,9 +348,9 @@ export default class CramFile {
     }
   }
 
-  async readBlock(position: number): Promise<CramFileBlock | undefined> {
+  async readBlock(position: number) {
     const { majorVersion } = await this.getDefinition()
-    const sectionParsers = await this.getSectionParsers()
+    const sectionParsers = getSectionParsers(majorVersion)
     const blockHeader = await this.readBlockHeader(position)
     if (blockHeader === undefined) {
       return undefined

package/src/cramFile/record.ts

@@ -1,6 +1,6 @@
 import Constants from './constants'
 import CramContainerCompressionScheme from './container/compressionScheme'
-import decodeRecord from './slice/decodeRecord'
+import type decodeRecord from './slice/decodeRecord'
 
 export interface RefRegion {
   start: number