Misc

eslint.config.mjs

@@ -4,7 +4,7 @@ import tseslint from 'typescript-eslint'
 
 export default tseslint.config(
   {
-    ignores: ['**/dist/**/*', '**/esm/**/*'],
+    ignores: ['esm/**/*', 'dist/**/*', '*.js', '*.mjs', 'example/*'],
   },
   {
     languageOptions: {

src/craiIndex.ts

@@ -21,16 +21,17 @@ 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!,
   })
 }
 

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(

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,

src/cramFile/codecs/external.ts

@@ -64,6 +64,6 @@ 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++]!
   }
 }

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

src/cramFile/codecs/huffman.ts

@@ -48,7 +48,7 @@ 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 +58,10 @@ 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 +74,7 @@ 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 +117,7 @@ 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 +136,7 @@ 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 +145,19 @@ 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
         ) {

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
 }
@@ -145,8 +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`,

src/cramFile/file.ts

@@ -279,7 +279,7 @@ export default class CramFile {
     },
     position: number,
     size = section.maxLength,
-    preReadBuffer = undefined,
+    preReadBuffer?: Buffer,
   ) {
     let buffer: Buffer
     if (preReadBuffer) {

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

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)

src/cramFile/slice/decodeRecord.ts

@@ -22,7 +22,7 @@ import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes'
 function readNullTerminatedString(buffer: Uint8Array) {
   let r = ''
   for (let i = 0; i < buffer.length && buffer[i] !== 0; i++) {
-    r += String.fromCharCode(buffer[i])
+    r += String.fromCharCode(buffer[i]!)
   }
   return r
 }
@@ -32,46 +32,46 @@ function readNullTerminatedString(buffer: Uint8Array) {
  * @private
  */
 function parseTagValueArray(buffer: Buffer) {
-  const arrayType = String.fromCharCode(buffer[0])
-  const length = Int32Array.from(buffer.slice(1))[0]
+  const arrayType = String.fromCharCode(buffer[0]!)
+  const length = Int32Array.from(buffer.slice(1))[0]!
 
   const array: number[] = new Array(length)
   buffer = buffer.slice(5)
 
   if (arrayType === 'c') {
     const arr = new Int8Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'C') {
     const arr = new Uint8Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 's') {
     const arr = new Int16Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'S') {
     const arr = new Uint16Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'i') {
     const arr = new Int32Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'I') {
     const arr = new Uint32Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else if (arrayType === 'f') {
     const arr = new Float32Array(buffer.buffer)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
   } else {
     throw new Error(`unknown type: ${arrayType}`)
@@ -311,26 +311,17 @@ export default function decodeRecord(
 
   const tags: Record<string, any> = {}
   // TN = tag names
-  const TN = compressionScheme.getTagNames(TLindex)
+  const TN = compressionScheme.getTagNames(TLindex)!
   const ntags = TN.length
 
   for (let i = 0; i < ntags; i += 1) {
-    const tagId = TN[i]
+    const tagId = TN[i]!
     const tagName = tagId.slice(0, 2)
     const tagType = tagId.slice(2, 3)
 
-    const tagCodec = compressionScheme.getCodecForTag(tagId)
-    if (!tagCodec) {
-      throw new CramMalformedError(
-        `no codec defined for auxiliary tag ${tagId}`,
-      )
-    }
-    const tagData = tagCodec.decode(
-      slice,
-      coreDataBlock,
-      blocksByContentId,
-      cursors,
-    )
+    const tagData = compressionScheme
+      .getCodecForTag(tagId)
+      .decode(slice, coreDataBlock, blocksByContentId, cursors)
     tags[tagName] = parseTagData(tagType, tagData)
   }