@gmod/cram 2.0.0 → 2.0.2

package/esm/sam.js

@@ -1,16 +1,29 @@
 export function parseHeaderText(text) {
     const lines = text.split(/\r?\n/);
     const data = [];
-    lines.forEach(line => {
+    for (const line of lines) {
         const [tag, ...fields] = line.split(/\t/);
-        const parsedFields = fields.map(f => {
-            const [fieldTag, value] = f.split(':', 2);
-            return { tag: fieldTag, value };
-        });
         if (tag) {
-            data.push({ tag: tag.substr(1), data: parsedFields });
+            data.push({
+                tag: tag.slice(1),
+                data: fields.map(f => {
+                    const r = f.indexOf(':');
+                    return r !== -1
+                        ? {
+                            tag: f.slice(0, r),
+                            value: f.slice(r + 1),
+                        }
+                        : // @CO lines are not comma separated.
+                            // See "samtools view -H c2\#pad.3.0.cram"
+                            // so, just store value tag itself
+                            {
+                                tag: f,
+                                value: undefined,
+                            };
+                }),
+            });
         }
-    });
+    }
     return data;
 }
 //# sourceMappingURL=sam.js.map

package/esm/sam.js.map

@@ -1 +1 @@
-{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAKA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAAqB,EAAE,CAAA;IACjC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,MAAM,YAAY,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAClC,MAAM,CAAC,QAAQ,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YACzC,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACjC,CAAC,CAAC,CAAA;QACF,IAAI,GAAG,EAAE;YACP,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAA;SACtD;IACH,CAAC,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAMJ,EAAE,CAAA;IACR,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,OAAO,CAAC,KAAK,CAAC,CAAC;wBACb,CAAC,CAAC;4BACE,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;4BAClB,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;yBACtB;wBACH,CAAC,CAAC,qCAAqC;4BACrC,0CAA0C;4BAC1C,kCAAkC;4BAClC;gCACE,GAAG,EAAE,CAAC;gCACN,KAAK,EAAE,SAAS;6BACjB,CAAA;gBACP,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/esm/typescript.js.map

@@ -1 +1 @@
-{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,gBAAgB,CAAI,CAAuB;IACzD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,SAAS,EAAE;QACjC,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;KAC9C;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}
+{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,gBAAgB,CAAI,CAAuB;IACzD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;QAClC,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;IAC/C,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}

package/esm/unzip.d.ts

@@ -1,2 +1,2 @@
-import { gunzipSync } from 'zlib';
-export { gunzipSync as unzip };
+/// <reference types="node" />
+export { gunzipSync as unzip } from 'zlib';

package/esm/unzip.js

@@ -1,3 +1,2 @@
-import { gunzipSync } from 'zlib';
-export { gunzipSync as unzip };
+export { gunzipSync as unzip } from 'zlib';
 //# sourceMappingURL=unzip.js.map

package/esm/unzip.js.map

@@ -1 +1 @@
-{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjC,OAAO,EAAE,UAAU,IAAI,KAAK,EAAE,CAAA"}
+{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,IAAI,KAAK,EAAE,MAAM,MAAM,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "2.0.0",
+  "version": "2.0.2",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -45,7 +45,7 @@
     "@gmod/binary-parser": "^1.3.5",
     "@jkbonfield/htscodecs": "^0.5.1",
     "abortable-promise-cache": "^1.2.0",
-    "buffer-crc32": "^0.2.13",
+    "buffer-crc32": "^1.0.0",
     "bzip2": "^0.1.1",
     "long": "^4.0.0",
     "md5": "^2.2.1",
@@ -57,28 +57,28 @@
     "@babel/plugin-transform-modules-commonjs": "^7.18.2",
     "@babel/preset-typescript": "^7.17.12",
     "@gmod/indexedfasta": "^2.1.0",
-    "@types/buffer-crc32": "^0.2.2",
-    "@types/jest": "^29.2.4",
+    "@types/jest": "^29.5.12",
     "@types/long": "^4.0.2",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@typescript-eslint/eslint-plugin": "^6.9.1",
-    "@typescript-eslint/parser": "^6.9.1",
+    "@typescript-eslint/eslint-plugin": "^7.0.2",
+    "@typescript-eslint/parser": "^7.0.2",
     "buffer": "^6.0.3",
-    "documentation": "^14.0.1",
+    "documentation": "^14.0.3",
     "eslint": "^8.30.0",
     "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-import": "^2.25.4",
-    "eslint-plugin-prettier": "^5.0.1",
+    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-unicorn": "^51.0.1",
     "glob": "^10.3.1",
     "jest": "^29.3.1",
     "mock-fs": "^5.2.0",
-    "prettier": "^3.0.3",
+    "prettier": "^3.2.5",
     "rimraf": "^5.0.1",
-    "ts-jest": "^29.0.3",
+    "ts-jest": "^29.1.2",
     "typescript": "^5.0.3",
     "url": "^0.11.0",
-    "webpack": "5.89.0",
+    "webpack": "^5.90.3",
     "webpack-cli": "^5.0.1"
   },
   "publishConfig": {

package/src/craiIndex.ts

@@ -8,7 +8,7 @@ import { Filehandle } from './cramFile/filehandle'
 
 const BAI_MAGIC = 21578050 // BAI\1
 
-export type Slice = {
+export interface Slice {
   start: number
   span: number
   containerStart: number
@@ -19,10 +19,6 @@ export type Slice = {
 type ParsedIndex = Record<string, Slice[]>
 
 function addRecordToIndex(index: ParsedIndex, record: number[]) {
-  if (record.some(el => el === undefined)) {
-    throw new CramMalformedError('invalid .crai index file')
-  }
-
   const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record
 
   if (!index[seqId]) {
@@ -61,7 +57,7 @@ export default class CraiIndex {
     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(),
+      fill: (_data, _signal) => this.parseIndex(),
     })
   }
 
@@ -90,8 +86,7 @@ export default class CraiIndex {
         // because some .crai files can be pretty large.
         let currentRecord: number[] = []
         let currentString = ''
-        for (let i = 0; i < uncompressedBuffer.length; i += 1) {
-          const charCode = uncompressedBuffer[i]
+        for (const charCode of uncompressedBuffer) {
           if (
             (charCode >= 48 && charCode <= 57) /* 0-9 */ ||
             (!currentString && charCode === 45) /* leading - */
@@ -158,7 +153,7 @@ export default class CraiIndex {
     seqId: number,
     queryStart: number,
     queryEnd: number,
-  ) {
+  ): Promise<Slice[]> {
     const seqEntries = (await this.getIndex())[seqId]
     if (!seqEntries) {
       return []
@@ -175,10 +170,10 @@ export default class CraiIndex {
       } // entry is behind query
       return 0 // entry overlaps query
     }
-    const bins = []
-    for (let i = 0; i < seqEntries.length; i += 1) {
-      if (compare(seqEntries[i]) === 0) {
-        bins.push(seqEntries[i])
+    const bins = [] as Slice[]
+    for (const entry of seqEntries) {
+      if (compare(entry) === 0) {
+        bins.push(entry)
       }
     }
     return bins

package/src/cramFile/codecs/_base.ts

@@ -2,19 +2,19 @@ import CramSlice from '../slice'
 import { CramFileBlock } from '../file'
 import { DataType } from './dataSeriesTypes'
 
-export type DataTypeMapping = {
+export interface DataTypeMapping {
   byte: number
   int: number
   long: number
   byteArray: Uint8Array
 }
 
-export type Cursor = {
+export interface Cursor {
   bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7
   bytePosition: number
 }
 
-export type Cursors = {
+export interface Cursors {
   lastAlignmentStart: number
   coreBlock: Cursor
   externalBlocks: {

package/src/cramFile/codecs/external.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError, CramUnimplementedError } from '../../errors'
 import CramCodec, { Cursor, Cursors } from './_base'
 import { parseItf8 } from '../util'

package/src/cramFile/codecs/huffman.ts

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError } from '../../errors'
 import CramCodec, { Cursor, Cursors } from './_base'
 import { getBits } from './getBits'
@@ -12,7 +13,11 @@ function numberOfSetBits(ii: number) {
   return (((i + (i >> 4)) & 0x0f0f0f0f) * 0x01010101) >> 24
 }
 
-type Code = { bitLength: number; value: number; bitCode: number }
+interface Code {
+  bitLength: number
+  value: number
+  bitCode: number
+}
 
 export default class HuffmanIntCodec extends CramCodec<
   'byte' | 'int',
@@ -20,7 +25,6 @@ export default class HuffmanIntCodec extends CramCodec<
 > {
   private codes: Record<number, Code> = {}
   private codeBook: Record<number, number[]> = {}
-  private sortedByValue: Code[] = []
   private sortedCodes: Code[] = []
   private sortedValuesByBitCode: number[] = []
   private sortedBitCodes: number[] = []
@@ -50,7 +54,7 @@ export default class HuffmanIntCodec extends CramCodec<
 
   buildCodeBook() {
     // parse the parameters together into a `codes` data structure
-    let codes: Array<{ symbol: number; bitLength: number }> = new Array(
+    let codes = new Array<{ symbol: number; bitLength: number }>(
       this.parameters.numCodes,
     )
     for (let i = 0; i < this.parameters.numCodes; i += 1) {
@@ -105,11 +109,6 @@ export default class HuffmanIntCodec extends CramCodec<
       (a, b) => a.bitLength - b.bitLength || a.bitCode - b.bitCode,
     )
 
-    // this.sortedValues = this.parameters.values.sort((a,b) => a-b)
-    this.sortedByValue = Object.values(this.codes).sort(
-      (a, b) => a.value - b.value,
-    )
-
     this.sortedValuesByBitCode = this.sortedCodes.map(c => c.value)
     this.sortedBitCodes = this.sortedCodes.map(c => c.bitCode)
     this.sortedBitLengthsByBitCode = this.sortedCodes.map(c => c.bitLength)

package/src/cramFile/container/compressionScheme.ts

@@ -165,7 +165,7 @@ export default class CramContainerCompressionScheme {
   toJSON() {
     const data: any = {}
     Object.keys(this).forEach(k => {
-      if (/Cache$/.test(k)) {
+      if (k.endsWith('Cache')) {
         return
       }
       data[k] = (this as any)[k]

package/src/cramFile/encoding.ts

@@ -1,10 +1,10 @@
-export type NullEncoding = {
+export interface NullEncoding {
   codecId: 0
   parametersBytes: number
   parameters: Record<string, never>
 }
 
-export type ExternalCramEncoding = {
+export interface ExternalCramEncoding {
   codecId: 1
   parametersBytes: number
   parameters: {
@@ -12,7 +12,7 @@ export type ExternalCramEncoding = {
   }
 }
 
-export type GolombEncoding = {
+export interface GolombEncoding {
   codecId: 2
   parametersBytes: number
   parameters: {
@@ -21,7 +21,7 @@ export type GolombEncoding = {
   }
 }
 
-export type HuffmanEncoding = {
+export interface HuffmanEncoding {
   codecId: 3
   parametersBytes: number
   parameters: {
@@ -32,7 +32,7 @@ export type HuffmanEncoding = {
   }
 }
 
-export type ByteArrayLengthEncoding = {
+export interface ByteArrayLengthEncoding {
   codecId: 4
   parametersBytes: number
   parameters: {
@@ -41,7 +41,7 @@ export type ByteArrayLengthEncoding = {
   }
 }
 
-export type ByteArrayStopCramEncoding = {
+export interface ByteArrayStopCramEncoding {
   codecId: 5
   parametersBytes: number
   parameters: {
@@ -50,7 +50,7 @@ export type ByteArrayStopCramEncoding = {
   }
 }
 
-export type BetaEncoding = {
+export interface BetaEncoding {
   codecId: 6
   parametersBytes: number
   parameters: {
@@ -59,7 +59,7 @@ export type BetaEncoding = {
   }
 }
 
-export type SubexpEncoding = {
+export interface SubexpEncoding {
   codecId: 7
   parametersBytes: number
   parameters: {
@@ -68,7 +68,7 @@ export type SubexpEncoding = {
   }
 }
 
-export type GolombRiceEncoding = {
+export interface GolombRiceEncoding {
   codecId: 8
   parametersBytes: number
   parameters: {
@@ -77,7 +77,7 @@ export type GolombRiceEncoding = {
   }
 }
 
-export type GammaEncoding = {
+export interface GammaEncoding {
   codecId: 9
   parametersBytes: number
   parameters: {

package/src/cramFile/file.ts

@@ -51,7 +51,7 @@ function getEndianness() {
 //   | { path: string; url?: undefined; filehandle?: undefined }
 //   | { filehandle: Filehandle; url?: undefined; path?: undefined }
 
-export type CramFileSource = {
+export interface CramFileSource {
   filehandle?: Filehandle
   url?: string
   path?: string
@@ -64,9 +64,9 @@ export type SeqFetch = (
 ) => Promise<string>
 
 export type CramFileArgs = CramFileSource & {
-  checkSequenceMD5: boolean
+  checkSequenceMD5?: boolean
   cacheSize?: number
-  seqFetch: SeqFetch
+  seqFetch?: SeqFetch
 }
 
 export type CramFileBlock = BlockHeader & {
@@ -80,9 +80,9 @@ export type CramFileBlock = BlockHeader & {
 export default class CramFile {
   private file: Filehandle
   public validateChecksums: boolean
-  public fetchReferenceSequenceCallback: SeqFetch
+  public fetchReferenceSequenceCallback?: SeqFetch
   public options: {
-    checkSequenceMD5: boolean
+    checkSequenceMD5?: boolean
     cacheSize: number
   }
   public featureCache: QuickLRU<string, Promise<CramRecord[]>>

package/src/cramFile/filehandle.ts

@@ -1,3 +1 @@
-import { GenericFilehandle } from 'generic-filehandle'
-
-export { GenericFilehandle as Filehandle }
+export { GenericFilehandle as Filehandle } from 'generic-filehandle'

package/src/cramFile/index.ts

@@ -1,4 +1,3 @@
-import CramFile from './file'
 export { default as CramRecord } from './record'
 
-export default CramFile
+export { default } from './file'

package/src/cramFile/record.ts

@@ -2,13 +2,13 @@ import Constants from './constants'
 import CramContainerCompressionScheme from './container/compressionScheme'
 import decodeRecord from './slice/decodeRecord'
 
-export type RefRegion = {
+export interface RefRegion {
   start: number
   end: number
   seq: string
 }
 
-export type ReadFeature = {
+export interface ReadFeature {
   code: string
   pos: number
   refPos: number
@@ -36,7 +36,7 @@ function decodeReadSequence(
 
   if (!cramRecord.readFeatures) {
     return refRegion.seq
-      .substr(regionSeqOffset, cramRecord.lengthOnRef)
+      .slice(regionSeqOffset, regionSeqOffset + (cramRecord.lengthOnRef || 0))
       .toUpperCase()
   }
 
@@ -91,18 +91,21 @@ function decodeReadSequence(
         }
       } else if (currentReadFeature < cramRecord.readFeatures.length) {
         // put down a chunk of sequence up to the next read feature
-        const chunk = refRegion.seq.substr(
+        const chunk = refRegion.seq.slice(
           regionPos,
-          cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1,
+          regionPos +
+            cramRecord.readFeatures[currentReadFeature].pos -
+            bases.length -
+            1,
         )
         bases += chunk
         regionPos += chunk.length
       }
     } else {
       // put down a chunk of reference up to the full read length
-      const chunk = refRegion.seq.substr(
+      const chunk = refRegion.seq.slice(
         regionPos,
-        cramRecord.readLength - bases.length,
+        regionPos + cramRecord.readLength - bases.length,
       )
       bases += chunk
       regionPos += chunk.length
@@ -152,7 +155,7 @@ function decodeBaseSubstitution(
   }
 }
 
-export type MateRecord = {
+export interface MateRecord {
   readName?: string
   sequenceId: number
   alignmentStart: number
@@ -208,7 +211,7 @@ type FlagsEncoder<Type> = {
 }
 
 function makeFlagsHelper<T>(
-  x: ReadonlyArray<readonly [number, T]>,
+  x: readonly (readonly [number, T])[],
 ): FlagsDecoder<T> & FlagsEncoder<T> {
   const r: any = {}
   for (const [code, name] of x) {
@@ -494,7 +497,7 @@ export default class CramRecord {
   toJSON() {
     const data: any = {}
     Object.keys(this).forEach(k => {
-      if (k.charAt(0) === '_') {
+      if (k.startsWith('_')) {
         return
       }
       data[k] = (this as any)[k]

package/src/cramFile/sectionParsers.ts

@@ -85,7 +85,7 @@ const cramTagDictionary = new Parser().itf8('size').buffer('ents', {
       const str = buffer.toString('utf8', stringStart, stringEnd)
       const tags = []
       for (let i = 0; i < str.length; i += 3) {
-        tags.push(str.substr(i, 3))
+        tags.push(str.slice(i, i + 3))
       }
       return tags
     }
@@ -113,7 +113,7 @@ const parseByteAsBool = new Parser().uint8(null, {
   formatter: /* istanbul ignore next */ val => !!val,
 })
 
-export type CramPreservationMap = {
+export interface CramPreservationMap {
   MI: boolean
   UI: boolean
   PI: boolean
@@ -155,9 +155,8 @@ const cramPreservationMap = new Parser()
 
 /* istanbul ignore next */
 function formatMap<T>(data: { ents: { key: string; value: T }[] }) {
-  const map: { [x: string]: T } = {}
-  for (let i = 0; i < data.ents.length; i += 1) {
-    const { key, value } = data.ents[i]
+  const map: Record<string, T> = {}
+  for (const { key, value } of data.ents) {
     if (map[key]) {
       console.warn(`duplicate key ${key} in map`)
     }
@@ -172,7 +171,7 @@ const unversionedParsers = {
   cramBlockCrc32,
 }
 
-export type MappedSliceHeader = {
+export interface MappedSliceHeader {
   refSeqId: number
   refSeqStart: number
   refSeqSpan: number
@@ -185,7 +184,7 @@ export type MappedSliceHeader = {
   md5: TupleOf<number, 16>
 }
 
-export type UnmappedSliceHeader = {
+export interface UnmappedSliceHeader {
   numRecords: number
   recordCounter: number
   numBlocks: number
@@ -279,7 +278,7 @@ const versionedParsers = {
     return { parser, maxLength: maxLengthFunc }
   },
 
-  cramEncoding(majorVersion: number) {
+  cramEncoding(_majorVersion: number) {
     const parser = new Parser()
       .namely('cramEncoding')
       .itf8('codecId')
@@ -425,7 +424,7 @@ export type CompressionMethod =
   | 'fqzcomp'
   | 'tok3'
 
-export type BlockHeader = {
+export interface BlockHeader {
   compressionMethod: CompressionMethod
   contentType:
     | 'FILE_HEADER'

package/src/cramFile/slice/decodeRecord.ts

@@ -224,23 +224,21 @@ export default function decodeRecord(
   majorVersion: number,
   recordNumber: number,
 ) {
-  let flags = decodeDataSeries('BF') as number
+  let flags = decodeDataSeries('BF')
 
   // note: the C data type of compressionFlags is byte in cram v1
   // and int32 in cram v2+, but that does not matter for us here
   // in javascript land.
-  const cramFlags = decodeDataSeries('CF') as number
+  const cramFlags = decodeDataSeries('CF')
 
   if (!isMappedSliceHeader(sliceHeader.parsedContent)) {
-    throw new Error()
+    throw new Error('slice header not mapped')
   }
 
-  let sequenceId
-  if (majorVersion > 1 && sliceHeader.parsedContent.refSeqId === -2) {
-    sequenceId = decodeDataSeries('RI')
-  } else {
-    sequenceId = sliceHeader.parsedContent.refSeqId
-  }
+  const sequenceId =
+    majorVersion > 1 && sliceHeader.parsedContent.refSeqId === -2
+      ? decodeDataSeries('RI')
+      : sliceHeader.parsedContent.refSeqId
 
   const readLength = decodeDataSeries('RL')
   // if APDelta, will calculate the true start in a second pass
@@ -263,14 +261,14 @@ export default function decodeRecord(
   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 = {}
-    const mateFlags = decodeDataSeries('MF') as number
+    const mateFlags = decodeDataSeries('MF')
     let mateReadName
     if (!compressionScheme.readNamesIncluded) {
       mateReadName = readNullTerminatedString(decodeDataSeries('RN'))
       readName = mateReadName
     }
-    const mateSequenceId = decodeDataSeries('NS') as number
-    const mateAlignmentStart = decodeDataSeries('NP') as number
+    const mateSequenceId = decodeDataSeries('NS')
+    const mateAlignmentStart = decodeDataSeries('NP')
     if (mateFlags || mateSequenceId > -1) {
       mateToUse = {
         mateFlags,
@@ -293,7 +291,7 @@ export default function decodeRecord(
 
     // detachedCount++
   } else if (CramFlagsDecoder.isWithMateDownstream(cramFlags)) {
-    mateRecordNumber = (decodeDataSeries('NF') as number) + recordNumber + 1
+    mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1
   }
 
   // TODO: the aux tag parsing will have to be refactored if we want to support
@@ -311,8 +309,8 @@ export default function decodeRecord(
 
   for (let i = 0; i < ntags; i += 1) {
     const tagId = TN[i]
-    const tagName = tagId.substr(0, 2)
-    const tagType = tagId.substr(2, 1)
+    const tagName = tagId.slice(0, 2)
+    const tagType = tagId.slice(2, 3)
 
     const tagCodec = compressionScheme.getCodecForTag(tagId)
     if (!tagCodec) {
@@ -336,7 +334,7 @@ export default function decodeRecord(
   let readBases = undefined
   if (!BamFlagsDecoder.isSegmentUnmapped(flags)) {
     // reading read features
-    const readFeatureCount = decodeDataSeries('FN') as number
+    const readFeatureCount = decodeDataSeries('FN')
     if (readFeatureCount) {
       readFeatures = decodeReadFeatures(
         alignmentStart,
@@ -370,7 +368,7 @@ export default function decodeRecord(
     }
 
     // mapping quality
-    mappingQuality = decodeDataSeries('MQ') as number
+    mappingQuality = decodeDataSeries('MQ')
     if (CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
       qualityScores = new Array(readLength)
       for (let i = 0; i < qualityScores.length; i++) {