@gmod/cram 1.6.3 → 1.7.0

package/esm/indexedCramFile.d.ts

@@ -1,4 +1,21 @@
+import CramFile from './cramFile';
+import CramRecord from './cramFile/record';
+import { SeqFetch } from './cramFile/file';
+import { Filehandle } from './cramFile/filehandle';
+import { Slice } from './craiIndex';
+export declare type CramFileSource = {
+    cramFilehandle?: Filehandle;
+    cramUrl?: string;
+    cramPath?: string;
+};
+export declare type CramIndexLike = {
+    getEntriesForRange: (seqId: number, start: number, end: number) => Promise<Slice[]>;
+    hasDataForReferenceSequence: (seqId: number) => Promise<boolean>;
+};
 export default class IndexedCramFile {
+    cram: CramFile;
+    index: CramIndexLike;
+    private fetchSizeLimit;
     /**
      *
      * @param {object} args
@@ -10,11 +27,16 @@ export default class IndexedCramFile {
      * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
      */
     constructor(args: {
+        index: CramIndexLike;
+        fetchSizeLimit?: number;
+    } & ({
         cram: CramFile;
-    });
-    cram: CramFile;
-    index: any;
-    fetchSizeLimit: any;
+    } | ({
+        cram?: undefined;
+        seqFetch: SeqFetch;
+        checkSequenceMD5: boolean;
+        cacheSize?: number;
+    } & CramFileSource)));
     /**
      *
      * @param {number} seq numeric ID of the reference sequence
@@ -22,18 +44,21 @@ export default class IndexedCramFile {
      * @param {number} end end of the range of interest. 1-based closed coordinates.
      * @returns {Promise[Array[CramRecord]]}
      */
-    getRecordsForRange(seq: number, start: number, end: number, opts?: {}): Promise<any>[any[][CramRecord]];
-    getRecordsInSlice({ containerStart, sliceStart, sliceBytes }: {
-        containerStart: any;
-        sliceStart: any;
-        sliceBytes: any;
-    }, filterFunction: any): Promise<any>;
+    getRecordsForRange(seq: number, start: number, end: number, opts?: {
+        viewAsPairs?: boolean;
+        pairAcrossChr?: boolean;
+        maxInsertSize?: number;
+    }): Promise<CramRecord[]>;
+    getRecordsInSlice({ containerStart, sliceStart, sliceBytes, }: {
+        containerStart: number;
+        sliceStart: number;
+        sliceBytes: number;
+    }, filterFunction: (r: CramRecord) => boolean): Promise<CramRecord[]>;
     /**
      *
      * @param {number} seqId
      * @returns {Promise} true if the CRAM file contains data for the given
      * reference sequence numerical ID
      */
-    hasDataForReferenceSequence(seqId: number): Promise<any>;
+    hasDataForReferenceSequence(seqId: number): Promise<boolean>;
 }
-import CramFile from "./cramFile";

package/esm/indexedCramFile.js

@@ -1,4 +1,4 @@
-import { CramUnimplementedError, CramSizeLimitError } from './errors';
+import { CramSizeLimitError, CramUnimplementedError } from './errors';
 import CramFile from './cramFile';
 export default class IndexedCramFile {
     /**
@@ -58,8 +58,9 @@ export default class IndexedCramFile {
         }
         // TODO: do we need to merge or de-duplicate the blocks?
         // fetch all the slices and parse the feature data
-        const filter = feature => feature.sequenceId === seq &&
+        const filter = (feature) => feature.sequenceId === seq &&
             feature.alignmentStart <= end &&
+            feature.lengthOnRef !== undefined &&
             feature.alignmentStart + feature.lengthOnRef - 1 >= start;
         const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, filter)));
         let ret = Array.prototype.concat(...sliceResults);
@@ -68,6 +69,9 @@ export default class IndexedCramFile {
             const readIds = {};
             for (let i = 0; i < ret.length; i += 1) {
                 const name = ret[i].readName;
+                if (name === undefined) {
+                    throw new Error();
+                }
                 const id = ret[i].uniqueId;
                 if (!readNames[name]) {
                     readNames[name] = 0;
@@ -83,13 +87,17 @@ export default class IndexedCramFile {
             });
             const matePromises = [];
             for (let i = 0; i < ret.length; i += 1) {
-                const name = ret[i].readName;
+                const cramRecord = ret[i];
+                const name = cramRecord.readName;
+                if (name === undefined) {
+                    throw new Error();
+                }
                 if (unmatedPairs[name] &&
-                    ret[i].mate &&
-                    (ret[i].mate.sequenceId === seqId || opts.pairAcrossChr) &&
-                    Math.abs(ret[i].alignmentStart - ret[i].mate.alignmentStart) <
+                    cramRecord.mate &&
+                    (cramRecord.mate.sequenceId === seqId || opts.pairAcrossChr) &&
+                    Math.abs(cramRecord.alignmentStart - cramRecord.mate.alignmentStart) <
                         opts.maxInsertSize) {
-                    const mateSlices = this.index.getEntriesForRange(ret[i].mate.sequenceId, ret[i].mate.alignmentStart, ret[i].mate.alignmentStart + 1);
+                    const mateSlices = this.index.getEntriesForRange(cramRecord.mate.sequenceId, cramRecord.mate.alignmentStart, cramRecord.mate.alignmentStart + 1);
                     matePromises.push(mateSlices);
                 }
             }
@@ -121,6 +129,9 @@ export default class IndexedCramFile {
                     const mateRecs = [];
                     for (let i = 0; i < feats.length; i += 1) {
                         const feature = feats[i];
+                        if (feature.readName === undefined) {
+                            throw new Error();
+                        }
                         if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
                             mateRecs.push(feature);
                         }
@@ -137,7 +148,7 @@ export default class IndexedCramFile {
         }
         return ret;
     }
-    getRecordsInSlice({ containerStart, sliceStart, sliceBytes }, filterFunction) {
+    getRecordsInSlice({ containerStart, sliceStart, sliceBytes, }, filterFunction) {
         const container = this.cram.getContainerAtPosition(containerStart);
         const slice = container.getSlice(sliceStart, sliceBytes);
         return slice.getRecords(filterFunction);

package/esm/indexedCramFile.js.map

@@ -1 +1 @@
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package/esm/io/index.d.ts

@@ -1,5 +1,5 @@
-import LocalFile from "./localFile";
-import RemoteFile from "./remoteFile";
-export function fromUrl(source: any): RemoteFile | LocalFile;
-export function open(maybeUrl: any, maybePath: any, maybeFilehandle: any): any;
-export { LocalFile, RemoteFile };
+import { Filehandle } from '../cramFile/filehandle';
+import { LocalFile, RemoteFile } from 'generic-filehandle';
+declare function fromUrl(source: string): LocalFile | RemoteFile;
+declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
+export { LocalFile, RemoteFile, fromUrl, open };

package/esm/io/index.js

@@ -1,10 +1,10 @@
 import url from 'url';
-import RemoteFile from './remoteFile';
-import LocalFile from './localFile';
+import { ensureNotNullish } from '../typescript';
+import { LocalFile, RemoteFile } from 'generic-filehandle';
 function fromUrl(source) {
     const { protocol, pathname } = url.parse(source);
     if (protocol === 'file:') {
-        return new LocalFile(unescape(pathname));
+        return new LocalFile(unescape(ensureNotNullish(pathname)));
     }
     return new RemoteFile(source);
 }

package/esm/io/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.js"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,KAAK,CAAA;AACrB,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,SAAS,OAAO,CAAC,MAAM;IACrB,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAChD,IAAI,QAAQ,KAAK,OAAO,EAAE;QACxB,OAAO,IAAI,SAAS,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,CAAA;KACzC;IACD,OAAO,IAAI,UAAU,CAAC,MAAM,CAAC,CAAA;AAC/B,CAAC;AAED,SAAS,IAAI,CAAC,QAAQ,EAAE,SAAS,EAAE,eAAe;IAChD,IAAI,eAAe,EAAE;QACnB,OAAO,eAAe,CAAA;KACvB;IACD,IAAI,QAAQ,EAAE;QACZ,OAAO,OAAO,CAAC,QAAQ,CAAC,CAAA;KACzB;IACD,IAAI,SAAS,EAAE;QACb,OAAO,IAAI,SAAS,CAAC,SAAS,CAAC,CAAA;KAChC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAED,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,OAAO,EAAE,IAAI,EAAE,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,KAAK,CAAA;AACrB,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAA;AAEhD,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE1D,SAAS,OAAO,CAAC,MAAc;IAC7B,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAChD,IAAI,QAAQ,KAAK,OAAO,EAAE;QACxB,OAAO,IAAI,SAAS,CAAC,QAAQ,CAAC,gBAAgB,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;KAC3D;IACD,OAAO,IAAI,UAAU,CAAC,MAAM,CAAC,CAAA;AAC/B,CAAC;AAED,SAAS,IAAI,CACX,QAAiB,EACjB,SAAkB,EAClB,eAA4B;IAE5B,IAAI,eAAe,EAAE;QACnB,OAAO,eAAe,CAAA;KACvB;IACD,IAAI,QAAQ,EAAE;QACZ,OAAO,OAAO,CAAC,QAAQ,CAAC,CAAA;KACzB;IACD,IAAI,SAAS,EAAE;QACb,OAAO,IAAI,SAAS,CAAC,SAAS,CAAC,CAAA;KAChC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAED,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,OAAO,EAAE,IAAI,EAAE,CAAA"}

package/esm/sam.d.ts

@@ -1 +1,8 @@
-export function parseHeaderText(text: any): any[];
+export declare type HeaderDataItem = {
+    tag: string;
+    data: Array<{
+        tag: string;
+        value: string;
+    }>;
+};
+export declare function parseHeaderText(text: string): HeaderDataItem[];

package/esm/sam.js.map

@@ -1 +1 @@
-{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.js"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAI;IAClC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,EAAE,CAAA;IACf,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":"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"}

package/esm/typescript.d.ts

@@ -0,0 +1,3 @@
+export declare function ensureNotNullish<T>(x: T | null | undefined): T;
+export declare type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
+export declare type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;

package/esm/typescript.js

@@ -0,0 +1,7 @@
+export function ensureNotNullish(x) {
+    if (x === null || x === undefined) {
+        throw new Error('Value must not be nullish.');
+    }
+    return x;
+}
+//# sourceMappingURL=typescript.js.map

package/esm/typescript.js.map

@@ -0,0 +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"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "1.6.3",
+  "version": "1.7.0",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -27,10 +27,11 @@
     "prebuild": "npm run clean",
     "clean": "rimraf dist esm",
     "build:esm": "tsc --target es2018 --outDir esm",
-    "build:es5": "tsc --target es5 --outDir dist",
+    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "postbuild": "webpack",
     "prepublishOnly": "npm test && npm run build && cp dist/errors.js errors.js",
+    "prepack": "npm test && npm run build && cp dist/errors.js errors.js",
     "postpublish": "rm errors.js",
     "postversion": "git push --follow-tags"
   },
@@ -47,32 +48,38 @@
     "buffer-crc32": "^0.2.13",
     "bzip2": "^0.1.1",
     "cross-fetch": "^3.0.0",
-    "es6-promisify": "^6.0.1",
     "long": "^4.0.0",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
-    "quick-lru": "^2.0.0"
+    "quick-lru": "^4.0.1"
   },
   "devDependencies": {
+    "@babel/plugin-transform-modules-commonjs": "^7.18.2",
+    "@babel/preset-typescript": "^7.17.12",
     "@gmod/indexedfasta": "^2.0.2",
+    "@types/buffer-crc32": "^0.2.0",
     "@types/jest": "^27.4.0",
+    "@types/long": "^4.0.2",
+    "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
     "@typescript-eslint/eslint-plugin": "^5.9.1",
     "@typescript-eslint/parser": "^5.9.1",
+    "buffer": "^6.0.3",
     "documentation": "^13.2.5",
-    "eslint": "^7.0.0",
-    "eslint-config-prettier": "^8.3.0",
+    "eslint": "^8.15.0",
+    "eslint-config-prettier": "^8.5.0",
     "eslint-plugin-import": "^2.25.4",
     "eslint-plugin-prettier": "^4.0.0",
-    "glob": "^7.2.0",
-    "jest": "^27.4.7",
+    "glob": "^8.0.3",
+    "jest": "^28.1.0",
     "mock-fs": "^5.1.2",
     "prettier": "^2.5.1",
     "rimraf": "^3.0.2",
-    "ts-jest": "^27.1.2",
+    "ts-jest": "^28.0.2",
     "typescript": "^4.5.4",
-    "webpack": "4",
-    "webpack-cli": "^3.2.1"
+    "url": "^0.11.0",
+    "webpack": "5.72.1",
+    "webpack-cli": "^4.9.2"
   },
   "publishConfig": {
     "access": "public"

package/src/{craiIndex.js → craiIndex.ts}

@@ -3,20 +3,22 @@ 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
 
-class Slice {
-  constructor(args) {
-    Object.assign(this, args)
-  }
-
-  toString() {
-    return `${this.start}:${this.span}:${this.containerStart}:${this.sliceStart}:${this.sliceBytes}`
-  }
+export type Slice = {
+  start: number
+  span: number
+  containerStart: number
+  sliceStart: number
+  sliceBytes: number
 }
 
-function addRecordToIndex(index, record) {
+type ParsedIndex = Record<string, Slice[]>
+
+function addRecordToIndex(index: ParsedIndex, record: number[]) {
   if (record.some(el => el === undefined)) {
     throw new CramMalformedError('invalid .crai index file')
   }
@@ -27,15 +29,13 @@ function addRecordToIndex(index, record) {
     index[seqId] = []
   }
 
-  index[seqId].push(
-    new Slice({
-      start,
-      span,
-      containerStart,
-      sliceStart,
-      sliceBytes,
-    }),
-  )
+  index[seqId].push({
+    start,
+    span,
+    containerStart,
+    sliceStart,
+    sliceBytes,
+  })
 }
 
 export default class CraiIndex {
@@ -47,6 +47,8 @@ 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 filehandle: Filehandle
 
   /**
    *
@@ -55,18 +57,18 @@ export default class CraiIndex {
    * @param {string} [args.url]
    * @param {FileHandle} [args.filehandle]
    */
-  constructor(args) {
-    const filehandle = open(args.url, args.path, args.filehandle)
-    this._parseCache = new AbortablePromiseCache({
+  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({ signal }),
+      fill: (data, signal) => this.parseIndex(),
     })
-    this.readFile = filehandle.readFile.bind(filehandle)
   }
 
   parseIndex() {
-    const index = {}
-    return this.readFile()
+    const index: ParsedIndex = {}
+    return this.filehandle
+      .readFile()
       .then(data => {
         if (data[0] === 31 && data[1] === 139) {
           return unzip(data)
@@ -86,7 +88,7 @@ export default class CraiIndex {
         // 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 = []
+        let currentRecord: number[] = []
         let currentString = ''
         for (let i = 0; i < uncompressedBuffer.length; i += 1) {
           const charCode = uncompressedBuffer[i]
@@ -128,7 +130,7 @@ export default class CraiIndex {
       })
   }
 
-  getIndex(opts = {}) {
+  getIndex(opts: { signal?: AbortSignal } = {}) {
     return this._parseCache.get('index', null, opts.signal)
   }
 
@@ -137,7 +139,7 @@ export default class CraiIndex {
    * @returns {Promise} true if the index contains entries for
    * the given reference sequence ID, false otherwise
    */
-  async hasDataForReferenceSequence(seqId) {
+  async hasDataForReferenceSequence(seqId: number) {
     return !!(await this.getIndex())[seqId]
   }
 
@@ -152,16 +154,20 @@ export default class CraiIndex {
    * an array of objects of the form
    * `{start, span, containerStart, sliceStart, sliceBytes }`
    */
-  async getEntriesForRange(seqId, queryStart, queryEnd) {
+  async getEntriesForRange(
+    seqId: number,
+    queryStart: number,
+    queryEnd: number,
+  ) {
     const seqEntries = (await this.getIndex())[seqId]
     if (!seqEntries) {
       return []
     }
 
-    const compare = entry => {
+    const compare = (entry: Slice) => {
       const entryStart = entry.start
       const entryEnd = entry.start + entry.span
-      if (entryStart >= queryEnd) {
+      if (entryStart > queryEnd) {
         return -1
       } // entry is ahead of query
       if (entryEnd <= queryStart) {

package/src/cramFile/codecs/_base.ts

@@ -0,0 +1,45 @@
+import CramSlice from '../slice'
+import { CramFileBlock } from '../file'
+import { DataType } from './dataSeriesTypes'
+
+export type DataTypeMapping = {
+  byte: number
+  int: number
+  long: number
+  byteArray: Uint8Array
+}
+
+export type Cursor = {
+  bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7
+  bytePosition: number
+}
+
+export type Cursors = {
+  lastAlignmentStart: number
+  coreBlock: Cursor
+  externalBlocks: {
+    map: Map<any, any>
+    getCursor: (contentId: number) => Cursor
+  }
+}
+
+// codec base class
+export default abstract class CramCodec<
+  TResult extends DataType = DataType,
+  TParameters = unknown,
+> {
+  public parameters: TParameters
+  public dataType: DataType
+
+  constructor(parameters: TParameters, dataType: TResult) {
+    this.parameters = parameters
+    this.dataType = dataType
+  }
+
+  abstract decode(
+    slice: CramSlice,
+    coreDataBlock: CramFileBlock,
+    blocksByContentId: Record<number, CramFileBlock>,
+    cursors: Cursors,
+  ): DataTypeMapping[TResult]
+}

package/src/cramFile/codecs/beta.ts

@@ -0,0 +1,34 @@
+import { CramUnimplementedError } from '../../errors'
+import CramCodec, { Cursors } from './_base'
+import { getBits } from './getBits'
+import CramSlice from '../slice'
+import { CramFileBlock } from '../file'
+import { BetaEncoding } from '../encoding'
+
+export default class BetaCodec extends CramCodec<
+  'int',
+  BetaEncoding['parameters']
+> {
+  constructor(parameters: BetaEncoding['parameters'], dataType: 'int') {
+    super(parameters, dataType)
+    if (this.dataType !== 'int') {
+      throw new CramUnimplementedError(
+        `${this.dataType} decoding not yet implemented by BETA codec`,
+      )
+    }
+  }
+
+  decode(
+    slice: CramSlice,
+    coreDataBlock: CramFileBlock,
+    blocksByContentId: Record<number, CramFileBlock>,
+    cursors: Cursors,
+  ) {
+    const fromBits = getBits(
+      coreDataBlock.content,
+      cursors.coreBlock,
+      this.parameters.length,
+    )
+    return fromBits - this.parameters.offset
+  }
+}

package/src/cramFile/codecs/{byteArrayLength.js → byteArrayLength.ts}

@@ -1,9 +1,27 @@
 import { tinyMemoize } from '../util'
 
-import CramCodec from './_base'
+import CramCodec, { Cursors } from './_base'
+import { ByteArrayLengthEncoding, CramEncoding } from '../encoding'
+import CramSlice from '../slice'
+import { CramFileBlock } from '../file'
+import { DataType } from './dataSeriesTypes'
 
-export default class ByteArrayStopCodec extends CramCodec {
-  constructor(parameters = {}, dataType, instantiateCodec) {
+type CramCodecFactory = <TData extends DataType = DataType>(
+  encodingData: CramEncoding,
+  dataType: TData | 'ignore',
+) => CramCodec<TData>
+
+export default class ByteArrayStopCodec extends CramCodec<
+  'byteArray',
+  ByteArrayLengthEncoding['parameters']
+> {
+  private instantiateCodec: CramCodecFactory
+
+  constructor(
+    parameters: ByteArrayLengthEncoding['parameters'],
+    dataType: 'byteArray',
+    instantiateCodec: CramCodecFactory,
+  ) {
     super(parameters, dataType)
     this.instantiateCodec = instantiateCodec
     if (dataType !== 'byteArray') {
@@ -13,7 +31,12 @@ export default class ByteArrayStopCodec extends CramCodec {
     }
   }
 
-  decode(slice, coreDataBlock, blocksByContentId, cursors) {
+  decode(
+    slice: CramSlice,
+    coreDataBlock: CramFileBlock,
+    blocksByContentId: Record<number, CramFileBlock>,
+    cursors: Cursors,
+  ) {
     const lengthCodec = this._getLengthCodec()
     const arrayLength = lengthCodec.decode(
       slice,
@@ -45,7 +68,6 @@ export default class ByteArrayStopCodec extends CramCodec {
   // memoize
   _getDataCodec() {
     const encodingParams = this.parameters.valuesEncoding
-
     return this.instantiateCodec(encodingParams, 'byte')
   }
 }

package/src/cramFile/codecs/{byteArrayStop.js → byteArrayStop.ts}

@@ -1,20 +1,33 @@
-import { CramBufferOverrunError, CramMalformedError } from '../../errors'
+import { CramMalformedError } from '../../errors'
 
-import CramCodec from './_base'
+import CramCodec, { Cursor, Cursors } from './_base'
+import CramSlice from '../slice'
+import { CramFileBlock } from '../file'
+import { ByteArrayStopCramEncoding } from '../encoding'
+import { CramBufferOverrunError } from './getBits'
 
-export default class ByteArrayStopCodec extends CramCodec {
-  constructor(parameters = {}, dataType) {
+export default class ByteArrayStopCodec extends CramCodec<
+  'byteArray',
+  ByteArrayStopCramEncoding['parameters']
+> {
+  constructor(
+    parameters: ByteArrayStopCramEncoding['parameters'],
+    dataType: 'byteArray',
+  ) {
     super(parameters, dataType)
-    if (dataType === 'byteArray') {
-      this._decode = this._decodeByteArray
-    } else {
+    if (dataType !== 'byteArray') {
       throw new TypeError(
         `byteArrayStop codec does not support data type ${dataType}`,
       )
     }
   }
 
-  decode(slice, coreDataBlock, blocksByContentId, cursors) {
+  decode(
+    slice: CramSlice,
+    coreDataBlock: CramFileBlock,
+    blocksByContentId: Record<number, CramFileBlock>,
+    cursors: Cursors,
+  ) {
     const { blockContentId } = this.parameters
     const contentBlock = blocksByContentId[blockContentId]
     if (!contentBlock) {
@@ -23,10 +36,10 @@ export default class ByteArrayStopCodec extends CramCodec {
       )
     }
     const cursor = cursors.externalBlocks.getCursor(blockContentId)
-    return this._decode(contentBlock, cursor)
+    return this._decodeByteArray(contentBlock, cursor)
   }
 
-  _decodeByteArray(contentBlock, cursor) {
+  _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor) {
     const dataBuffer = contentBlock.content
     const { stopByte } = this.parameters
     // scan to the next stop byte
@@ -41,9 +54,9 @@ export default class ByteArrayStopCodec extends CramCodec {
           `byteArrayStop reading beyond length of data buffer?`,
         )
       }
-      stopPosition += 1
+      stopPosition = stopPosition + 1
     }
     cursor.bytePosition = stopPosition + 1
-    return dataBuffer.slice(startPosition, stopPosition)
+    return dataBuffer.subarray(startPosition, stopPosition)
   }
 }