@gmod/cram 3.0.4 → 3.0.5

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "3.0.4",
+  "version": "3.0.5",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -21,8 +21,9 @@
     "esm"
   ],
   "scripts": {
-    "test": "jest",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
+    "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",
     "prebuild": "npm run clean",
     "clean": "rimraf dist esm",
@@ -30,7 +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"
   },
@@ -41,7 +42,6 @@
     "biojs"
   ],
   "dependencies": {
-    "@gmod/abortable-promise-cache": "^2.0.0",
     "@jkbonfield/htscodecs": "^0.5.1",
     "bzip2": "^0.1.1",
     "crc": "^4.3.2",
@@ -53,24 +53,24 @@
   },
   "devDependencies": {
     "@gmod/indexedfasta": "^2.1.0",
-    "@types/jest": "^29.5.12",
     "@types/long": "^4.0.0",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
     "@typescript-eslint/eslint-plugin": "^8.0.0",
     "@typescript-eslint/parser": "^8.0.0",
+    "@vitest/coverage-v8": "^2.0.5",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
-    "eslint": "^9.8.0",
+    "eslint": "^9.9.0",
     "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-prettier": "^5.1.3",
     "eslint-plugin-unicorn": "^55.0.0",
-    "jest": "^29.3.1",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
     "rimraf": "^6.0.1",
-    "ts-jest": "^29.1.2",
     "typescript": "^5.0.3",
+    "typescript-eslint": "^8.0.1",
+    "vitest": "^2.0.5",
     "webpack": "^5.90.3",
     "webpack-cli": "^5.0.1"
   },

package/src/craiIndex.ts

@@ -1,12 +1,10 @@
-import AbortablePromiseCache from '@gmod/abortable-promise-cache'
-import QuickLRU from 'quick-lru'
 import { unzip } from './unzip'
 import { open } from './io'
 import { CramMalformedError } from './errors'
 import { CramFileSource } from './cramFile/file'
 import { Filehandle } from './cramFile/filehandle'
 
-const BAI_MAGIC = 21578050 // BAI\1
+const BAI_MAGIC = 21_578_050 // BAI\1
 
 export interface Slice {
   start: number
@@ -16,26 +14,36 @@ export interface Slice {
   sliceBytes: number
 }
 
-type ParsedIndex = Record<string, Slice[]>
+type ParsedIndex = Record<string, Slice[] | undefined>
 
 function addRecordToIndex(index: ParsedIndex, record: number[]) {
   const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record
 
-  if (!index[seqId]) {
-    index[seqId] = []
+  const s = seqId!
+  if (!index[s]) {
+    index[s] = []
   }
 
-  index[seqId].push({
-    start,
-    span,
-    containerStart,
-    sliceStart,
-    sliceBytes,
+  index[s].push({
+    start: start!,
+    span: span!,
+    containerStart: containerStart!,
+    sliceStart: sliceStart!,
+    sliceBytes: sliceBytes!,
   })
 }
 
+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:
+  // A CRAM index (.crai) is a gzipped tab delimited file containing the
+  // following columns:
+  //
   // 1. Sequence id
   // 2. Alignment start
   // 3. Alignment span
@@ -43,7 +51,8 @@ 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
 
   /**
@@ -55,78 +64,70 @@ 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() {
     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 = ''
-        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 the file ends without a \n, we need to flush our buffers
-        if (currentString) {
-          currentRecord.push(Number.parseInt(currentString, 10))
-        }
-        if (currentRecord.length === 6) {
-          addRecordToIndex(index, currentRecord)
-        }
-
-        // sort each of them by start
-        Object.entries(index).forEach(([seqId, ent]) => {
-          index[seqId] = ent.sort(
-            (a, b) => a.start - b.start || a.span - b.span,
-          )
-        })
-        return index
-      })
+    const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile())
+    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 the file ends without a \n, we need to flush our buffers
+    if (currentString) {
+      currentRecord.push(Number.parseInt(currentString, 10))
+    }
+    if (currentRecord.length === 6) {
+      addRecordToIndex(index, currentRecord)
+    }
+
+    // sort each of them by start
+    Object.entries(index).forEach(([seqId, ent]) => {
+      const e2 = ent!
+      index[seqId] = e2.sort((a, b) => a.start - b.start || a.span - b.span)
+    })
+    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
   }
 
   /**

package/src/cramFile/codecs/byteArrayLength.ts

@@ -23,11 +23,6 @@ export default class ByteArrayStopCodec extends CramCodec<
   ) {
     super(parameters, dataType)
     this.instantiateCodec = instantiateCodec
-    if (dataType !== 'byteArray') {
-      throw new TypeError(
-        `byteArrayLength does not support data type ${dataType}`,
-      )
-    }
   }
 
   decode(
@@ -71,6 +66,6 @@ export default class ByteArrayStopCodec extends CramCodec<
   }
 }
 
-'_getLengthCodec _getDataCodec'
-  .split(' ')
-  .forEach(method => tinyMemoize(ByteArrayStopCodec, method))
+'_getLengthCodec _getDataCodec'.split(' ').forEach(method => {
+  tinyMemoize(ByteArrayStopCodec, method)
+})

package/src/cramFile/codecs/byteArrayStop.ts

@@ -10,18 +10,6 @@ export default class ByteArrayStopCodec extends CramCodec<
   'byteArray',
   ByteArrayStopCramEncoding['parameters']
 > {
-  constructor(
-    parameters: ByteArrayStopCramEncoding['parameters'],
-    dataType: 'byteArray',
-  ) {
-    super(parameters, dataType)
-    if (dataType !== 'byteArray') {
-      throw new TypeError(
-        `byteArrayStop codec does not support data type ${dataType}`,
-      )
-    }
-  }
-
   decode(
     slice: CramSlice,
     coreDataBlock: CramFileBlock,

package/src/cramFile/codecs/external.ts

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError, CramUnimplementedError } from '../../errors'
 import CramCodec, { Cursor, Cursors } from './_base'
 import { parseItf8 } from '../util'
@@ -64,6 +63,6 @@ export default class ExternalCodec extends CramCodec<
         'attempted to read beyond end of block. this file seems truncated.',
       )
     }
-    return contentBlock.content[cursor.bytePosition++]
+    return contentBlock.content[cursor.bytePosition++]!
   }
 }

package/src/cramFile/codecs/getBits.ts

@@ -17,7 +17,7 @@ export function getBits(
   for (let dlen = numBits; dlen; dlen--) {
     // get the next `dlen` bits in the input, put them in val
     val <<= 1
-    val |= (data[cursor.bytePosition] >> cursor.bitPosition) & 1
+    val |= (data[cursor.bytePosition]! >> cursor.bitPosition) & 1
     cursor.bitPosition -= 1
     if (cursor.bitPosition < 0) {
       cursor.bytePosition += 1

package/src/cramFile/codecs/huffman.ts

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError } from '../../errors'
 import CramCodec, { Cursor, Cursors } from './_base'
 import { getBits } from './getBits'
@@ -48,7 +47,7 @@ export default class HuffmanIntCodec extends CramCodec<
 
     // if this is a degenerate zero-length huffman code, special-case the
     // decoding
-    if (this.sortedCodes[0].bitLength === 0) {
+    if (this.sortedCodes[0]!.bitLength === 0) {
       this._decode = this._decodeZeroLengthCode
     }
   }
@@ -58,10 +57,10 @@ export default class HuffmanIntCodec extends CramCodec<
     let codes = new Array<{ symbol: number; bitLength: number }>(
       this.parameters.numCodes,
     )
-    for (let i = 0; i < this.parameters.numCodes; i += 1) {
+    for (let i = 0; i < this.parameters.numCodes; i++) {
       codes[i] = {
-        symbol: this.parameters.symbols[i],
-        bitLength: this.parameters.bitLengths[i],
+        symbol: this.parameters.symbols[i]!,
+        bitLength: this.parameters.bitLengths[i]!,
       }
     }
     // sort the codes by bit length and symbol value
@@ -74,7 +73,7 @@ export default class HuffmanIntCodec extends CramCodec<
       if (!this.codeBook[code.bitLength]) {
         this.codeBook[code.bitLength] = []
       }
-      this.codeBook[code.bitLength].push(code.symbol)
+      this.codeBook[code.bitLength]!.push(code.symbol)
     })
   }
 
@@ -117,7 +116,7 @@ export default class HuffmanIntCodec extends CramCodec<
 
     this.bitCodeToValue = new Array(maxBitCode + 1).fill(-1)
     for (let i = 0; i < this.sortedBitCodes.length; i += 1) {
-      this.bitCodeToValue[this.sortedCodes[i].bitCode] = i
+      this.bitCodeToValue[this.sortedCodes[i]!.bitCode] = i
     }
   }
 
@@ -136,7 +135,7 @@ export default class HuffmanIntCodec extends CramCodec<
 
   // the special case for zero-length codes
   _decodeZeroLengthCode() {
-    return this.sortedCodes[0].value
+    return this.sortedCodes[0]!.value
   }
 
   _decode(slice: CramSlice, coreDataBlock: CramFileBlock, coreCursor: Cursor) {
@@ -145,19 +144,19 @@ export default class HuffmanIntCodec extends CramCodec<
     let prevLen = 0
     let bits = 0
     for (let i = 0; i < this.sortedCodes.length; i += 1) {
-      const length = this.sortedCodes[i].bitLength
+      const length = this.sortedCodes[i]!.bitLength
       bits <<= length - prevLen
       bits |= getBits(input, coreCursor, length - prevLen)
       prevLen = length
       {
-        const index = this.bitCodeToValue[bits]
+        const index = this.bitCodeToValue[bits]!
         if (index > -1 && this.sortedBitLengthsByBitCode[index] === length) {
-          return this.sortedValuesByBitCode[index]
+          return this.sortedValuesByBitCode[index]!
         }
 
         for (
           let j = i;
-          this.sortedCodes[j + 1].bitLength === length &&
+          this.sortedCodes[j + 1]!.bitLength === length &&
           j < this.sortedCodes.length;
           j += 1
         ) {

package/src/cramFile/container/compressionScheme.ts

@@ -53,30 +53,30 @@ function parseSubstitutionMatrix(byteArray: number[]) {
     matrix[i] = new Array(4)
   }
 
-  matrix[0][(byteArray[0] >> 6) & 3] = 'C'
-  matrix[0][(byteArray[0] >> 4) & 3] = 'G'
-  matrix[0][(byteArray[0] >> 2) & 3] = 'T'
-  matrix[0][(byteArray[0] >> 0) & 3] = 'N'
-
-  matrix[1][(byteArray[1] >> 6) & 3] = 'A'
-  matrix[1][(byteArray[1] >> 4) & 3] = 'G'
-  matrix[1][(byteArray[1] >> 2) & 3] = 'T'
-  matrix[1][(byteArray[1] >> 0) & 3] = 'N'
-
-  matrix[2][(byteArray[2] >> 6) & 3] = 'A'
-  matrix[2][(byteArray[2] >> 4) & 3] = 'C'
-  matrix[2][(byteArray[2] >> 2) & 3] = 'T'
-  matrix[2][(byteArray[2] >> 0) & 3] = 'N'
-
-  matrix[3][(byteArray[3] >> 6) & 3] = 'A'
-  matrix[3][(byteArray[3] >> 4) & 3] = 'C'
-  matrix[3][(byteArray[3] >> 2) & 3] = 'G'
-  matrix[3][(byteArray[3] >> 0) & 3] = 'N'
-
-  matrix[4][(byteArray[4] >> 6) & 3] = 'A'
-  matrix[4][(byteArray[4] >> 4) & 3] = 'C'
-  matrix[4][(byteArray[4] >> 2) & 3] = 'G'
-  matrix[4][(byteArray[4] >> 0) & 3] = 'T'
+  matrix[0]![(byteArray[0]! >> 6) & 3] = 'C'
+  matrix[0]![(byteArray[0]! >> 4) & 3] = 'G'
+  matrix[0]![(byteArray[0]! >> 2) & 3] = 'T'
+  matrix[0]![(byteArray[0]! >> 0) & 3] = 'N'
+
+  matrix[1]![(byteArray[1]! >> 6) & 3] = 'A'
+  matrix[1]![(byteArray[1]! >> 4) & 3] = 'G'
+  matrix[1]![(byteArray[1]! >> 2) & 3] = 'T'
+  matrix[1]![(byteArray[1]! >> 0) & 3] = 'N'
+
+  matrix[2]![(byteArray[2]! >> 6) & 3] = 'A'
+  matrix[2]![(byteArray[2]! >> 4) & 3] = 'C'
+  matrix[2]![(byteArray[2]! >> 2) & 3] = 'T'
+  matrix[2]![(byteArray[2]! >> 0) & 3] = 'N'
+
+  matrix[3]![(byteArray[3]! >> 6) & 3] = 'A'
+  matrix[3]![(byteArray[3]! >> 4) & 3] = 'C'
+  matrix[3]![(byteArray[3]! >> 2) & 3] = 'G'
+  matrix[3]![(byteArray[3]! >> 0) & 3] = 'N'
+
+  matrix[4]![(byteArray[4]! >> 6) & 3] = 'A'
+  matrix[4]![(byteArray[4]! >> 4) & 3] = 'C'
+  matrix[4]![(byteArray[4]! >> 2) & 3] = 'G'
+  matrix[4]![(byteArray[4]! >> 0) & 3] = 'T'
 
   return matrix
 }
@@ -112,16 +112,21 @@ export default class CramContainerCompressionScheme {
    * @private
    */
   getCodecForTag(tagName: string): CramCodec {
-    if (!this.tagCodecCache[tagName]) {
+    const test = this.tagCodecCache[tagName]
+    if (!test) {
       const encodingData = this.tagEncoding[tagName]
-      if (encodingData) {
-        this.tagCodecCache[tagName] = instantiateCodec(
-          encodingData,
-          'byteArray', // all tags are byte array data
-        )
+      if (!encodingData) {
+        throw new Error('Error, no tag encoding')
       }
+      const ret = instantiateCodec(
+        encodingData,
+        'byteArray', // all tags are byte array data
+      )
+      this.tagCodecCache[tagName] = ret
+      return ret
+    } else {
+      return test
     }
-    return this.tagCodecCache[tagName]
   }
 
   /**
@@ -140,8 +145,10 @@ export default class CramContainerCompressionScheme {
       this.dataSeriesCodecCache[dataSeriesName]
     if (r === undefined) {
       const encodingData = this.dataSeriesEncoding[dataSeriesName]
+      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       if (encodingData) {
         const dataType = dataSeriesTypes[dataSeriesName]
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!dataType) {
           throw new CramMalformedError(
             `data series name ${dataSeriesName} not defined in file compression header`,

package/src/cramFile/container/index.ts

@@ -130,4 +130,6 @@ export default class CramContainer {
 
 'getHeader getCompressionHeaderBlock getCompressionScheme'
   .split(' ')
-  .forEach(method => tinyMemoize(CramContainer, method))
+  .forEach(method => {
+    tinyMemoize(CramContainer, method)
+  })

package/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,
     })
@@ -279,7 +278,7 @@ export default class CramFile {
     },
     position: number,
     size = section.maxLength,
-    preReadBuffer = undefined,
+    preReadBuffer?: Buffer,
   ) {
     let buffer: Buffer
     if (preReadBuffer) {
@@ -330,8 +329,8 @@ export default class CramFile {
       ret.copy(outputBuffer)
     } else if (compressionMethod === 'rans') {
       ransuncompress(inputBuffer, outputBuffer)
-      //htscodecs r4x8 is slower, but compatible.
-      //htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
+      // htscodecs r4x8 is slower, but compatible.
+      // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
     } else if (compressionMethod === 'rans4x16') {
       htscodecs.r4x16_uncompress(inputBuffer, outputBuffer)
     } else if (compressionMethod === 'arith') {
@@ -422,6 +421,6 @@ export default class CramFile {
   }
 }
 
-'getDefinition getSectionParsers getSamHeader'
-  .split(' ')
-  .forEach(method => tinyMemoize(CramFile, method))
+'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
+  tinyMemoize(CramFile, method)
+})

package/src/cramFile/record.ts

@@ -42,7 +42,7 @@ function decodeReadSequence(cramRecord: CramRecord, refRegion: RefRegion) {
   let currentReadFeature = 0
   while (bases.length < cramRecord.readLength) {
     if (currentReadFeature < cramRecord.readFeatures.length) {
-      const feature = cramRecord.readFeatures[currentReadFeature]
+      const feature = cramRecord.readFeatures[currentReadFeature]!
       if (feature.code === 'Q' || feature.code === 'q') {
         currentReadFeature += 1
       } else if (feature.pos === bases.length + 1) {
@@ -90,10 +90,7 @@ function decodeReadSequence(cramRecord: CramRecord, refRegion: RefRegion) {
         // put down a chunk of sequence up to the next read feature
         const chunk = refRegion.seq.slice(
           regionPos,
-          regionPos +
-            cramRecord.readFeatures[currentReadFeature].pos -
-            bases.length -
-            1,
+          regionPos + feature.pos - bases.length - 1,
         )
         bases += chunk
         regionPos += chunk.length
@@ -131,10 +128,6 @@ function decodeBaseSubstitution(
   compressionScheme: CramContainerCompressionScheme,
   readFeature: ReadFeature,
 ) {
-  if (!refRegion) {
-    return
-  }
-
   // decode base substitution code using the substitution matrix
   const refCoord = readFeature.refPos - refRegion.start
   const refBase = refRegion.seq.charAt(refCoord)
@@ -145,7 +138,7 @@ function decodeBaseSubstitution(
   if (baseNumber === undefined) {
     baseNumber = 4
   }
-  const substitutionScheme = compressionScheme.substitutionMatrix[baseNumber]
+  const substitutionScheme = compressionScheme.substitutionMatrix[baseNumber]!
   const base = substitutionScheme[readFeature.data]
   if (base) {
     readFeature.sub = base

package/src/cramFile/sectionParsers.ts

@@ -179,8 +179,8 @@ export function cramPreservationMap() {
       const ents = []
       for (let i = 0; i < mapCount; i++) {
         const key =
-          String.fromCharCode(buffer[offset]) +
-          String.fromCharCode(buffer[offset + 1])
+          String.fromCharCode(buffer[offset]!) +
+          String.fromCharCode(buffer[offset + 1]!)
         offset += 2
 
         if (
@@ -550,8 +550,8 @@ function cramDataSeriesEncodingMap() {
       const ents = []
       for (let i = 0; i < mapCount; i++) {
         const key =
-          String.fromCharCode(buffer[offset]) +
-          String.fromCharCode(buffer[offset + 1])
+          String.fromCharCode(buffer[offset]!) +
+          String.fromCharCode(buffer[offset + 1]!)
         offset += 2
 
         const { value, offset: newOffset4 } = cramEncodingSub(buffer, offset)