@gmod/cram - npm Package Compare versions

Comparing version 3.0.4 to 3.0.5

dist/craiIndex.d.ts

@@ -9,5 +9,5 @@ import { CramFileSource } from './cramFile/file';
 }
-type ParsedIndex = Record<string, Slice[]>;
+type ParsedIndex = Record<string, Slice[] | undefined>;
 export default class CraiIndex {
-    private _parseCache;
+    private parseIndexP?;
     private filehandle;
@@ -23,5 +23,3 @@ /**
     parseIndex(): Promise<ParsedIndex>;
-    getIndex(opts?: {
-        signal?: AbortSignal;
-    }): Promise<ParsedIndex>;
+    getIndex(): Promise<ParsedIndex>;
     /**
@@ -28,0 +26,0 @@ * @param {number} seqId

dist/craiIndex.js

@@ -11,8 +11,3 @@ "use strict";
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
-const quick_lru_1 = __importDefault(require("quick-lru"));
 const unzip_1 = require("./unzip");
@@ -24,13 +19,20 @@ const io_1 = require("./io");
     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) {
+    if (data[0] === 31 && data[1] === 139) {
+        return (0, unzip_1.unzip)(data);
+    }
+    return data;
+}
 class CraiIndex {
@@ -46,18 +48,7 @@ /**
         this.filehandle = (0, io_1.open)(args.url, args.path, args.filehandle);
-        this._parseCache = new abortable_promise_cache_1.default({
-            cache: new quick_lru_1.default({ maxSize: 1 }),
-            fill: (_data, _signal) => this.parseIndex(),
-        });
     }
     parseIndex() {
-        const index = {};
-        return this.filehandle
-            .readFile()
-            .then(data => {
-            if (data[0] === 31 && data[1] === 139) {
-                return (0, unzip_1.unzip)(data);
-            }
-            return data;
-        })
-            .then(uncompressedBuffer => {
+        return __awaiter(this, void 0, void 0, function* () {
+            const index = {};
+            const uncompressedBuffer = maybeUnzip(yield this.filehandle.readFile());
             if (uncompressedBuffer.length > 4 &&
@@ -103,3 +94,4 @@ uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC) {
             Object.entries(index).forEach(([seqId, ent]) => {
-                index[seqId] = ent.sort((a, b) => a.start - b.start || a.span - b.span);
+                const e2 = ent;
+                index[seqId] = e2.sort((a, b) => a.start - b.start || a.span - b.span);
             });
@@ -109,4 +101,10 @@ return index;
     }
-    getIndex(opts = {}) {
-        return this._parseCache.get('index', null, opts.signal);
+    getIndex() {
+        if (!this.parseIndexP) {
+            this.parseIndexP = this.parseIndex().catch((e) => {
+                this.parseIndexP = undefined;
+                throw e;
+            });
+        }
+        return this.parseIndexP;
     }
@@ -113,0 +111,0 @@ /**

dist/cramFile/codecs/byteArrayLength.js

@@ -12,5 +12,2 @@ "use strict";
         this.instantiateCodec = instantiateCodec;
-        if (dataType !== 'byteArray') {
-            throw new TypeError(`byteArrayLength does not support data type ${dataType}`);
-        }
     }
@@ -39,5 +36,5 @@ decode(slice, coreDataBlock, blocksByContentId, cursors) {
 exports.default = ByteArrayStopCodec;
-'_getLengthCodec _getDataCodec'
-    .split(' ')
-    .forEach(method => (0, util_1.tinyMemoize)(ByteArrayStopCodec, method));
+'_getLengthCodec _getDataCodec'.split(' ').forEach(method => {
+    (0, util_1.tinyMemoize)(ByteArrayStopCodec, method);
+});
 //# sourceMappingURL=byteArrayLength.js.map

dist/cramFile/codecs/byteArrayStop.d.ts

@@ -6,5 +6,4 @@ import CramCodec, { Cursor, Cursors } from './_base';
 export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayStopCramEncoding['parameters']> {
-    constructor(parameters: ByteArrayStopCramEncoding['parameters'], dataType: 'byteArray');
     decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Buffer;
     _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Buffer;
 }

dist/cramFile/codecs/byteArrayStop.js

@@ -10,8 +10,2 @@ "use strict";
 class ByteArrayStopCodec extends _base_1.default {
-    constructor(parameters, dataType) {
-        super(parameters, dataType);
-        if (dataType !== 'byteArray') {
-            throw new TypeError(`byteArrayStop codec does not support data type ${dataType}`);
-        }
-    }
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
@@ -18,0 +12,0 @@ const { blockContentId } = this.parameters;

dist/cramFile/codecs/external.js

@@ -6,3 +6,2 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/unbound-method */
 const errors_1 = require("../../errors");
@@ -9,0 +8,0 @@ const _base_1 = __importDefault(require("./_base"));

dist/cramFile/codecs/huffman.js

@@ -6,3 +6,2 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/unbound-method */
 const errors_1 = require("../../errors");
@@ -41,3 +40,3 @@ const _base_1 = __importDefault(require("./_base"));
         let codes = new Array(this.parameters.numCodes);
-        for (let i = 0; i < this.parameters.numCodes; i += 1) {
+        for (let i = 0; i < this.parameters.numCodes; i++) {
             codes[i] = {
@@ -44,0 +43,0 @@ symbol: this.parameters.symbols[i],

dist/cramFile/container/compressionScheme.d.ts

@@ -62,3 +62,3 @@ import CramCodec from '../codecs/_base';
      */
-    getTagNames(tagListId: number): string[];
+    getTagNames(tagListId: number): string[] | undefined;
     getCodecForDataSeries<TDataSeries extends DataSeriesEncodingKey>(dataSeriesName: TDataSeries): CramCodec<DataSeriesTypes[TDataSeries]> | undefined;
@@ -65,0 +65,0 @@ toJSON(): any;

dist/cramFile/container/compressionScheme.js

@@ -87,9 +87,15 @@ "use strict";
     getCodecForTag(tagName) {
-        if (!this.tagCodecCache[tagName]) {
+        const test = this.tagCodecCache[tagName];
+        if (!test) {
             const encodingData = this.tagEncoding[tagName];
-            if (encodingData) {
-                this.tagCodecCache[tagName] = (0, codecs_1.instantiateCodec)(encodingData, 'byteArray');
+            if (!encodingData) {
+                throw new Error('Error, no tag encoding');
             }
+            const ret = (0, codecs_1.instantiateCodec)(encodingData, 'byteArray');
+            this.tagCodecCache[tagName] = ret;
+            return ret;
         }
-        return this.tagCodecCache[tagName];
+        else {
+            return test;
+        }
     }
@@ -108,4 +114,6 @@ /**
             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) {
@@ -112,0 +120,0 @@ throw new errors_1.CramMalformedError(`data series name ${dataSeriesName} not defined in file compression header`);

dist/cramFile/container/index.js

@@ -114,3 +114,5 @@ "use strict";
     .split(' ')
-    .forEach(method => (0, util_1.tinyMemoize)(CramContainer, method));
+    .forEach(method => {
+    (0, util_1.tinyMemoize)(CramContainer, method);
+});
 //# sourceMappingURL=index.js.map

dist/cramFile/file.d.ts

@@ -78,3 +78,3 @@ import { Buffer } from 'buffer';
         };
-    }, position: number, size?: number, preReadBuffer?: undefined): Promise<(T & {
+    }, position: number, size?: number, preReadBuffer?: Buffer): Promise<(T & {
         _endPosition: number;
@@ -81,0 +81,0 @@ _size: number;

dist/cramFile/file.js

@@ -62,6 +62,5 @@ "use strict";
         };
-        // 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 quick_lru_1.default({
@@ -231,3 +230,3 @@ maxSize: this.options.cacheSize,
     _parseSection(section_1, position_1) {
-        return __awaiter(this, arguments, void 0, function* (section, position, size = section.maxLength, preReadBuffer = undefined) {
+        return __awaiter(this, arguments, void 0, function* (section, position, size = section.maxLength, preReadBuffer) {
             let buffer;
@@ -279,4 +278,4 @@ if (preReadBuffer) {
                 (0, rans_1.default)(inputBuffer, outputBuffer);
-                //htscodecs r4x8 is slower, but compatible.
-                //htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
+                // htscodecs r4x8 is slower, but compatible.
+                // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
             }
@@ -344,5 +343,5 @@ else if (compressionMethod === 'rans4x16') {
 exports.default = CramFile;
-'getDefinition getSectionParsers getSamHeader'
-    .split(' ')
-    .forEach(method => (0, util_1.tinyMemoize)(CramFile, method));
+'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
+    (0, util_1.tinyMemoize)(CramFile, method);
+});
 //# sourceMappingURL=file.js.map

dist/cramFile/record.js

@@ -84,6 +84,3 @@ "use strict";
                 // 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);
+                const chunk = refRegion.seq.slice(regionPos, regionPos + feature.pos - bases.length - 1);
                 bases += chunk;
@@ -115,5 +112,2 @@ regionPos += chunk.length;
 function decodeBaseSubstitution(cramRecord, refRegion, compressionScheme, readFeature) {
-    if (!refRegion) {
-        return;
-    }
     // decode base substitution code using the substitution matrix
@@ -120,0 +114,0 @@ const refCoord = readFeature.refPos - refRegion.start;

dist/cramFile/slice/decodeRecord.js

 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = decodeRecord;
-const long_1 = __importDefault(require("long"));
 const errors_1 = require("../../errors");
@@ -86,3 +82,3 @@ const record_1 = require("../record");
     if (tagType === 'I') {
-        return long_1.default.fromBytesLE(buffer).toNumber();
+        return new Uint32Array(buffer.buffer)[0];
     }
@@ -260,8 +256,7 @@ if (tagType === 'i') {
         const tagType = tagId.slice(2, 3);
-        const tagCodec = compressionScheme.getCodecForTag(tagId);
-        if (!tagCodec) {
-            throw new errors_1.CramMalformedError(`no codec defined for auxiliary tag ${tagId}`);
-        }
-        const tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-        tags[tagName] = parseTagData(tagType, tagData);
+        const tagData = compressionScheme
+            .getCodecForTag(tagId)
+            .decode(slice, coreDataBlock, blocksByContentId, cursors);
+        tags[tagName] =
+            typeof tagData === 'number' ? tagData : parseTagData(tagType, tagData);
     }
@@ -268,0 +263,0 @@ let readFeatures;

dist/cramFile/slice/index.d.ts

@@ -11,4 +11,5 @@ import CramRecord from '../record';
     containerPosition: number;
+    sliceSize: number;
     private file;
-    constructor(container: CramContainer, containerPosition: number, _unused: number);
+    constructor(container: CramContainer, containerPosition: number, sliceSize: number);
     getHeader(): Promise<{
@@ -40,3 +41,3 @@ parsedContent: {
     _getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;
-    getBlockByContentId(id: number): Promise<CramFileBlock>;
+    getBlockByContentId(id: number): Promise<CramFileBlock | undefined>;
     getReferenceRegion(): Promise<{
@@ -43,0 +44,0 @@ seq: any;

dist/cramFile/slice/index.js

@@ -72,10 +72,8 @@ "use strict";
 /**
- * @private establishes a mate-pair relationship between two records in the same slice.
- * CRAM compresses mate-pair relationships between records in the same slice down into
- * just one record having the index in the slice of its mate
+ * @private establishes a mate-pair relationship between two records in the
+ * same slice. CRAM compresses mate-pair relationships between records in the
+ * same slice down into just one record having the index in the slice of its
+ * mate
  */
 function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, mateRecord) {
-    if (!mateRecord) {
-        throw new errors_1.CramMalformedError('could not resolve intra-slice mate pairs, file seems truncated or malformed');
-    }
     const complicatedMultiSegment = !!(mateRecord.mate ||
@@ -142,5 +140,6 @@ (mateRecord.mateRecordNumber !== undefined &&
 class CramSlice {
-    constructor(container, containerPosition, _unused) {
+    constructor(container, containerPosition, sliceSize) {
         this.container = container;
         this.containerPosition = containerPosition;
+        this.sliceSize = sliceSize;
         this.file = container.file;
@@ -197,3 +196,2 @@ }
             const blocks = yield this.getBlocks();
-            // the core data block is always the first block in the slice
             return blocks[0];
@@ -283,5 +281,2 @@ });
             const sliceHeader = yield this.getHeader();
-            if (sliceHeader === undefined) {
-                throw new Error('slice header undefined');
-            }
             const blocksByContentId = yield this._getBlocksContentIdIndex();
@@ -335,3 +330,3 @@ // check MD5 of reference if available
             };
-            let records = new Array(sliceHeader.parsedContent.numRecords);
+            const records = new Array(sliceHeader.parsedContent.numRecords);
             for (let i = 0; i < records.length; i += 1) {
@@ -348,3 +343,2 @@ try {
                         console.warn('read attempted beyond end of buffer, file seems truncated.');
-                        records = records.filter(r => !!r);
                         break;
@@ -443,5 +437,5 @@ }
 // memoize several methods in the class for performance
-'getHeader getBlocks _getBlocksContentIdIndex'
-    .split(' ')
-    .forEach(method => (0, util_1.tinyMemoize)(CramSlice, method));
+'getHeader getBlocks _getBlocksContentIdIndex'.split(' ').forEach(method => {
+    (0, util_1.tinyMemoize)(CramSlice, method);
+});
 //# sourceMappingURL=index.js.map

dist/indexedCramFile.js

@@ -43,5 +43,2 @@ "use strict";
         this.index = args.index;
-        if (!this.index.getEntriesForRange) {
-            throw new Error('invalid arguments: not an index');
-        }
     }
@@ -48,0 +45,0 @@ /**

dist/rans/d04.js

@@ -7,3 +7,3 @@ "use strict";
 exports.default = uncompress;
-//@ts-nocheck
+// @ts-nocheck
 const errors_1 = require("../errors");
@@ -10,0 +10,0 @@ const constants_1 = require("./constants");

dist/rans/d14.js

@@ -7,3 +7,3 @@ "use strict";
 exports.default = uncompress;
-//@ts-nocheck
+// @ts-nocheck
 const constants_1 = require("./constants");
@@ -10,0 +10,0 @@ const decoding_1 = __importDefault(require("./decoding"));

dist/rans/decoding.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-//@ts-nocheck
+// @ts-nocheck
 const errors_1 = require("../errors");
@@ -5,0 +5,0 @@ const constants_1 = require("./constants");

dist/rans/frequencies.js

@@ -8,3 +8,3 @@ "use strict";
 exports.readStatsO1 = readStatsO1;
-//@ts-nocheck
+// @ts-nocheck
 const errors_1 = require("../errors");
@@ -11,0 +11,0 @@ const constants_1 = require("./constants");

dist/rans/index.js

@@ -7,3 +7,3 @@ "use strict";
 exports.default = uncompress;
-//@ts-nocheck
+// @ts-nocheck
 const buffer_1 = require("buffer");
@@ -10,0 +10,0 @@ const errors_1 = require("../errors");

esm/craiIndex.d.ts

@@ -9,5 +9,5 @@ import { CramFileSource } from './cramFile/file';
 }
-type ParsedIndex = Record<string, Slice[]>;
+type ParsedIndex = Record<string, Slice[] | undefined>;
 export default class CraiIndex {
-    private _parseCache;
+    private parseIndexP?;
     private filehandle;
@@ -23,5 +23,3 @@ /**
     parseIndex(): Promise<ParsedIndex>;
-    getIndex(opts?: {
-        signal?: AbortSignal;
-    }): Promise<ParsedIndex>;
+    getIndex(): Promise<ParsedIndex>;
     /**
@@ -28,0 +26,0 @@ * @param {number} seqId

esm/craiIndex.js

@@ -1,3 +0,1 @@
-import AbortablePromiseCache from '@gmod/abortable-promise-cache';
-import QuickLRU from 'quick-lru';
 import { unzip } from './unzip';
@@ -9,13 +7,20 @@ import { open } from './io';
     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) {
+    if (data[0] === 31 && data[1] === 139) {
+        return unzip(data);
+    }
+    return data;
+}
 export default class CraiIndex {
@@ -31,65 +36,59 @@ /**
         this.filehandle = open(args.url, args.path, args.filehandle);
-        this._parseCache = new AbortablePromiseCache({
-            cache: new QuickLRU({ maxSize: 1 }),
-            fill: (_data, _signal) => this.parseIndex(),
-        });
     }
-    parseIndex() {
+    async parseIndex() {
         const index = {};
-        return this.filehandle
-            .readFile()
-            .then(data => {
-            if (data[0] === 31 && data[1] === 139) {
-                return unzip(data);
+        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 = [];
+        let currentString = '';
+        for (const charCode of uncompressedBuffer) {
+            if ((charCode >= 48 && charCode <= 57) /* 0-9 */ ||
+                (!currentString && charCode === 45) /* leading - */) {
+                currentString += String.fromCharCode(charCode);
             }
-            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');
+            else if (charCode === 9 /* \t */) {
+                currentRecord.push(Number.parseInt(currentString, 10));
+                currentString = '';
             }
-            // 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 = [];
-            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) {
+            else if (charCode === 10 /* \n */) {
                 currentRecord.push(Number.parseInt(currentString, 10));
-            }
-            if (currentRecord.length === 6) {
+                currentString = '';
                 addRecordToIndex(index, currentRecord);
+                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;
+            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 = {}) {
-        return this._parseCache.get('index', null, opts.signal);
+    getIndex() {
+        if (!this.parseIndexP) {
+            this.parseIndexP = this.parseIndex().catch((e) => {
+                this.parseIndexP = undefined;
+                throw e;
+            });
+        }
+        return this.parseIndexP;
     }
@@ -96,0 +95,0 @@ /**

esm/cramFile/codecs/byteArrayLength.js

@@ -7,5 +7,2 @@ import CramCodec from './_base';
         this.instantiateCodec = instantiateCodec;
-        if (dataType !== 'byteArray') {
-            throw new TypeError(`byteArrayLength does not support data type ${dataType}`);
-        }
     }
@@ -33,5 +30,5 @@ decode(slice, coreDataBlock, blocksByContentId, cursors) {
 }
-'_getLengthCodec _getDataCodec'
-    .split(' ')
-    .forEach(method => tinyMemoize(ByteArrayStopCodec, method));
+'_getLengthCodec _getDataCodec'.split(' ').forEach(method => {
+    tinyMemoize(ByteArrayStopCodec, method);
+});
 //# sourceMappingURL=byteArrayLength.js.map

esm/cramFile/codecs/byteArrayStop.d.ts

@@ -6,5 +6,4 @@ import CramCodec, { Cursor, Cursors } from './_base';
 export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayStopCramEncoding['parameters']> {
-    constructor(parameters: ByteArrayStopCramEncoding['parameters'], dataType: 'byteArray');
     decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Buffer;
     _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Buffer;
 }

esm/cramFile/codecs/byteArrayStop.js

@@ -5,8 +5,2 @@ import { CramMalformedError } from '../../errors';
 export default class ByteArrayStopCodec extends CramCodec {
-    constructor(parameters, dataType) {
-        super(parameters, dataType);
-        if (dataType !== 'byteArray') {
-            throw new TypeError(`byteArrayStop codec does not support data type ${dataType}`);
-        }
-    }
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
@@ -13,0 +7,0 @@ const { blockContentId } = this.parameters;

esm/cramFile/codecs/external.js

@@ -1,2 +0,1 @@
-/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError, CramUnimplementedError } from '../../errors';
@@ -3,0 +2,0 @@ import CramCodec from './_base';

esm/cramFile/codecs/huffman.js

@@ -1,2 +0,1 @@
-/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError } from '../../errors';
@@ -35,3 +34,3 @@ import CramCodec from './_base';
         let codes = new Array(this.parameters.numCodes);
-        for (let i = 0; i < this.parameters.numCodes; i += 1) {
+        for (let i = 0; i < this.parameters.numCodes; i++) {
             codes[i] = {
@@ -38,0 +37,0 @@ symbol: this.parameters.symbols[i],

esm/cramFile/container/compressionScheme.d.ts

@@ -62,3 +62,3 @@ import CramCodec from '../codecs/_base';
      */
-    getTagNames(tagListId: number): string[];
+    getTagNames(tagListId: number): string[] | undefined;
     getCodecForDataSeries<TDataSeries extends DataSeriesEncodingKey>(dataSeriesName: TDataSeries): CramCodec<DataSeriesTypes[TDataSeries]> | undefined;
@@ -65,0 +65,0 @@ toJSON(): any;

esm/cramFile/container/compressionScheme.js

@@ -85,9 +85,15 @@ import { instantiateCodec } from '../codecs';
     getCodecForTag(tagName) {
-        if (!this.tagCodecCache[tagName]) {
+        const test = this.tagCodecCache[tagName];
+        if (!test) {
             const encodingData = this.tagEncoding[tagName];
-            if (encodingData) {
-                this.tagCodecCache[tagName] = instantiateCodec(encodingData, 'byteArray');
+            if (!encodingData) {
+                throw new Error('Error, no tag encoding');
             }
+            const ret = instantiateCodec(encodingData, 'byteArray');
+            this.tagCodecCache[tagName] = ret;
+            return ret;
         }
-        return this.tagCodecCache[tagName];
+        else {
+            return test;
+        }
     }
@@ -106,4 +112,6 @@ /**
             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) {
@@ -110,0 +118,0 @@ throw new CramMalformedError(`data series name ${dataSeriesName} not defined in file compression header`);

esm/cramFile/container/index.js

@@ -94,3 +94,5 @@ import { Buffer } from 'buffer';
     .split(' ')
-    .forEach(method => tinyMemoize(CramContainer, method));
+    .forEach(method => {
+    tinyMemoize(CramContainer, method);
+});
 //# sourceMappingURL=index.js.map

esm/cramFile/file.d.ts

@@ -78,3 +78,3 @@ import { Buffer } from 'buffer';
         };
-    }, position: number, size?: number, preReadBuffer?: undefined): Promise<(T & {
+    }, position: number, size?: number, preReadBuffer?: Buffer): Promise<(T & {
         _endPosition: number;
@@ -81,0 +81,0 @@ _size: number;

esm/cramFile/file.js

@@ -48,6 +48,5 @@ import { Buffer } from 'buffer';
         };
-        // 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({
@@ -202,3 +201,3 @@ maxSize: this.options.cacheSize,
     }
-    async _parseSection(section, position, size = section.maxLength, preReadBuffer = undefined) {
+    async _parseSection(section, position, size = section.maxLength, preReadBuffer) {
         let buffer;
@@ -248,4 +247,4 @@ if (preReadBuffer) {
             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);
         }
@@ -314,5 +313,5 @@ else if (compressionMethod === 'rans4x16') {
 }
-'getDefinition getSectionParsers getSamHeader'
-    .split(' ')
-    .forEach(method => tinyMemoize(CramFile, method));
+'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
+    tinyMemoize(CramFile, method);
+});
 //# sourceMappingURL=file.js.map

esm/cramFile/record.js

@@ -78,6 +78,3 @@ import Constants from './constants';
                 // 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);
+                const chunk = refRegion.seq.slice(regionPos, regionPos + feature.pos - bases.length - 1);
                 bases += chunk;
@@ -109,5 +106,2 @@ regionPos += chunk.length;
 function decodeBaseSubstitution(cramRecord, refRegion, compressionScheme, readFeature) {
-    if (!refRegion) {
-        return;
-    }
     // decode base substitution code using the substitution matrix
@@ -114,0 +108,0 @@ const refCoord = readFeature.refPos - refRegion.start;

esm/cramFile/slice/decodeRecord.js

@@ -1,2 +0,1 @@
-import Long from 'long';
 import { CramMalformedError } from '../../errors';
@@ -80,3 +79,3 @@ import { BamFlagsDecoder, CramFlagsDecoder, MateFlagsDecoder, } from '../record';
     if (tagType === 'I') {
-        return Long.fromBytesLE(buffer).toNumber();
+        return new Uint32Array(buffer.buffer)[0];
     }
@@ -254,8 +253,7 @@ if (tagType === 'i') {
         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);
-        tags[tagName] = parseTagData(tagType, tagData);
+        const tagData = compressionScheme
+            .getCodecForTag(tagId)
+            .decode(slice, coreDataBlock, blocksByContentId, cursors);
+        tags[tagName] =
+            typeof tagData === 'number' ? tagData : parseTagData(tagType, tagData);
     }
@@ -262,0 +260,0 @@ let readFeatures;

esm/cramFile/slice/index.d.ts

@@ -11,4 +11,5 @@ import CramRecord from '../record';
     containerPosition: number;
+    sliceSize: number;
     private file;
-    constructor(container: CramContainer, containerPosition: number, _unused: number);
+    constructor(container: CramContainer, containerPosition: number, sliceSize: number);
     getHeader(): Promise<{
@@ -40,3 +41,3 @@ parsedContent: {
     _getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;
-    getBlockByContentId(id: number): Promise<CramFileBlock>;
+    getBlockByContentId(id: number): Promise<CramFileBlock | undefined>;
     getReferenceRegion(): Promise<{
@@ -43,0 +44,0 @@ seq: any;

esm/cramFile/slice/index.js

@@ -58,10 +58,8 @@ import { CramArgumentError, CramMalformedError } from '../../errors';
 /**
- * @private establishes a mate-pair relationship between two records in the same slice.
- * CRAM compresses mate-pair relationships between records in the same slice down into
- * just one record having the index in the slice of its mate
+ * @private establishes a mate-pair relationship between two records in the
+ * same slice. CRAM compresses mate-pair relationships between records in the
+ * same slice down into just one record having the index in the slice of its
+ * mate
  */
 function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, mateRecord) {
-    if (!mateRecord) {
-        throw new CramMalformedError('could not resolve intra-slice mate pairs, file seems truncated or malformed');
-    }
     const complicatedMultiSegment = !!(mateRecord.mate ||
@@ -128,5 +126,6 @@ (mateRecord.mateRecordNumber !== undefined &&
 export default class CramSlice {
-    constructor(container, containerPosition, _unused) {
+    constructor(container, containerPosition, sliceSize) {
         this.container = container;
         this.containerPosition = containerPosition;
+        this.sliceSize = sliceSize;
         this.file = container.file;
@@ -178,3 +177,2 @@ }
         const blocks = await this.getBlocks();
-        // the core data block is always the first block in the slice
         return blocks[0];
@@ -256,5 +254,2 @@ }
         const sliceHeader = await this.getHeader();
-        if (sliceHeader === undefined) {
-            throw new Error('slice header undefined');
-        }
         const blocksByContentId = await this._getBlocksContentIdIndex();
@@ -308,3 +303,3 @@ // check MD5 of reference if available
         };
-        let records = new Array(sliceHeader.parsedContent.numRecords);
+        const records = new Array(sliceHeader.parsedContent.numRecords);
         for (let i = 0; i < records.length; i += 1) {
@@ -324,3 +319,2 @@ try {
                     console.warn('read attempted beyond end of buffer, file seems truncated.');
-                    records = records.filter(r => !!r);
                     break;
@@ -415,5 +409,5 @@ }
 // memoize several methods in the class for performance
-'getHeader getBlocks _getBlocksContentIdIndex'
-    .split(' ')
-    .forEach(method => tinyMemoize(CramSlice, method));
+'getHeader getBlocks _getBlocksContentIdIndex'.split(' ').forEach(method => {
+    tinyMemoize(CramSlice, method);
+});
 //# sourceMappingURL=index.js.map

esm/indexedCramFile.js

@@ -29,5 +29,2 @@ import { CramUnimplementedError } from './errors';
         this.index = args.index;
-        if (!this.index.getEntriesForRange) {
-            throw new Error('invalid arguments: not an index');
-        }
     }
@@ -34,0 +31,0 @@ /**

esm/rans/d04.js

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors';
@@ -3,0 +3,0 @@ import { TF_SHIFT } from './constants';

esm/rans/d14.js

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { TF_SHIFT } from './constants';
@@ -3,0 +3,0 @@ import Decoding from './decoding';

esm/rans/decoding.js

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors';
@@ -3,0 +3,0 @@ import { RANS_BYTE_L } from './constants';

esm/rans/frequencies.js

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors';
@@ -3,0 +3,0 @@ import { TOTFREQ } from './constants';

esm/rans/index.js

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { Buffer } from 'buffer';
@@ -3,0 +3,0 @@ import { CramMalformedError } from '../errors';

package.json

 {
   "name": "@gmod/cram",
-  "version": "3.0.4",
+  "version": "3.0.5",
   "description": "read CRAM files with pure Javascript",
@@ -24,4 +24,5 @@ "license": "MIT",
   "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",
@@ -34,3 +35,3 @@ "prebuild": "npm run clean",
     "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",
@@ -46,3 +47,2 @@ "postversion": "git push --follow-tags"
   "dependencies": {
-    "@gmod/abortable-promise-cache": "^2.0.0",
     "@jkbonfield/htscodecs": "^0.5.1",
@@ -59,3 +59,2 @@ "bzip2": "^0.1.1",
     "@gmod/indexedfasta": "^2.1.0",
-    "@types/jest": "^29.5.12",
     "@types/long": "^4.0.0",
@@ -66,14 +65,15 @@ "@types/md5": "^2.3.2",
     "@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",
@@ -80,0 +80,0 @@ "webpack-cli": "^5.0.1"

src/craiIndex.ts

@@ -1,3 +0,1 @@
-import AbortablePromiseCache from '@gmod/abortable-promise-cache'
-import QuickLRU from 'quick-lru'
 import { unzip } from './unzip'
@@ -9,3 +7,3 @@ import { open } from './io'
 
-const BAI_MAGIC = 21578050 // BAI\1
+const BAI_MAGIC = 21_578_050 // BAI\1
 
@@ -20,3 +18,3 @@ export interface Slice {
 
-type ParsedIndex = Record<string, Slice[]>
+type ParsedIndex = Record<string, Slice[] | undefined>
 
@@ -26,17 +24,27 @@ function addRecordToIndex(index: ParsedIndex, record: number[]) {
 
-  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
@@ -49,3 +57,4 @@ // 2. Alignment start
   // 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
@@ -62,74 +71,66 @@
     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')
-          }
-        }
+    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)
-        }
+    // 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
-      })
+    // 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
   }
@@ -136,0 +137,0 @@

src/cramFile/codecs/byteArrayLength.ts

@@ -26,7 +26,2 @@ import CramCodec, { Cursors } from './_base'
     this.instantiateCodec = instantiateCodec
-    if (dataType !== 'byteArray') {
-      throw new TypeError(
-        `byteArrayLength does not support data type ${dataType}`,
-      )
-    }
   }
@@ -75,4 +70,4 @@
 
-'_getLengthCodec _getDataCodec'
-  .split(' ')
-  .forEach(method => tinyMemoize(ByteArrayStopCodec, method))
+'_getLengthCodec _getDataCodec'.split(' ').forEach(method => {
+  tinyMemoize(ByteArrayStopCodec, method)
+})

src/cramFile/codecs/byteArrayStop.ts

@@ -13,14 +13,2 @@ import { CramMalformedError } from '../../errors'
 > {
-  constructor(
-    parameters: ByteArrayStopCramEncoding['parameters'],
-    dataType: 'byteArray',
-  ) {
-    super(parameters, dataType)
-    if (dataType !== 'byteArray') {
-      throw new TypeError(
-        `byteArrayStop codec does not support data type ${dataType}`,
-      )
-    }
-  }
-
   decode(
@@ -27,0 +15,0 @@ slice: CramSlice,

src/cramFile/codecs/external.ts

@@ -1,2 +0,1 @@
-/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError, CramUnimplementedError } from '../../errors'
@@ -67,4 +66,4 @@ import CramCodec, { Cursor, Cursors } from './_base'
     }
-    return contentBlock.content[cursor.bytePosition++]
+    return contentBlock.content[cursor.bytePosition++]!
   }
 }

src/cramFile/codecs/getBits.ts

@@ -20,3 +20,3 @@ export class CramBufferOverrunError extends Error {}
     val <<= 1
-    val |= (data[cursor.bytePosition] >> cursor.bitPosition) & 1
+    val |= (data[cursor.bytePosition]! >> cursor.bitPosition) & 1
     cursor.bitPosition -= 1
@@ -23,0 +23,0 @@ if (cursor.bitPosition < 0) {

src/cramFile/codecs/huffman.ts

@@ -1,2 +0,1 @@
-/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError } from '../../errors'
@@ -51,3 +50,3 @@ import CramCodec, { Cursor, Cursors } from './_base'
     // decoding
-    if (this.sortedCodes[0].bitLength === 0) {
+    if (this.sortedCodes[0]!.bitLength === 0) {
       this._decode = this._decodeZeroLengthCode
@@ -62,6 +61,6 @@ }
     )
-    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]!,
       }
@@ -79,3 +78,3 @@ }
       }
-      this.codeBook[code.bitLength].push(code.symbol)
+      this.codeBook[code.bitLength]!.push(code.symbol)
     })
@@ -123,3 +122,3 @@ }
     for (let i = 0; i < this.sortedBitCodes.length; i += 1) {
-      this.bitCodeToValue[this.sortedCodes[i].bitCode] = i
+      this.bitCodeToValue[this.sortedCodes[i]!.bitCode] = i
     }
@@ -143,3 +142,3 @@ }
   _decodeZeroLengthCode() {
-    return this.sortedCodes[0].value
+    return this.sortedCodes[0]!.value
   }
@@ -153,3 +152,3 @@
     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
@@ -159,5 +158,5 @@ bits |= getBits(input, coreCursor, length - prevLen)
       {
-        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]!
         }
@@ -167,3 +166,3 @@
           let j = i;
-          this.sortedCodes[j + 1].bitLength === length &&
+          this.sortedCodes[j + 1]!.bitLength === length &&
           j < this.sortedCodes.length;
@@ -170,0 +169,0 @@ j += 1

src/cramFile/container/compressionScheme.ts

@@ -56,26 +56,26 @@ import { instantiateCodec } from '../codecs'
 
-  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[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[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[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[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[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'
 
@@ -116,12 +116,17 @@ return matrix
   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]
   }
@@ -145,4 +150,6 @@
       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) {
@@ -149,0 +156,0 @@ throw new CramMalformedError(

src/cramFile/container/index.ts

@@ -133,2 +133,4 @@ import { Buffer } from 'buffer'
   .split(' ')
-  .forEach(method => tinyMemoize(CramContainer, method))
+  .forEach(method => {
+    tinyMemoize(CramContainer, method)
+  })

src/cramFile/file.ts

@@ -93,6 +93,5 @@ import { Buffer } from 'buffer'
 
-    // 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({
@@ -283,3 +282,3 @@ maxSize: this.options.cacheSize,
     size = section.maxLength,
-    preReadBuffer = undefined,
+    preReadBuffer?: Buffer,
   ) {
@@ -335,4 +334,4 @@ let buffer: Buffer
       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') {
@@ -428,4 +427,4 @@ htscodecs.r4x16_uncompress(inputBuffer, outputBuffer)
 
-'getDefinition getSectionParsers getSamHeader'
-  .split(' ')
-  .forEach(method => tinyMemoize(CramFile, method))
+'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
+  tinyMemoize(CramFile, method)
+})

src/cramFile/record.ts

@@ -45,3 +45,3 @@ import Constants from './constants'
     if (currentReadFeature < cramRecord.readFeatures.length) {
-      const feature = cramRecord.readFeatures[currentReadFeature]
+      const feature = cramRecord.readFeatures[currentReadFeature]!
       if (feature.code === 'Q' || feature.code === 'q') {
@@ -94,6 +94,3 @@ currentReadFeature += 1
           regionPos,
-          regionPos +
-            cramRecord.readFeatures[currentReadFeature].pos -
-            bases.length -
-            1,
+          regionPos + feature.pos - bases.length - 1,
         )
@@ -136,6 +133,2 @@ bases += chunk
 ) {
-  if (!refRegion) {
-    return
-  }
-
   // decode base substitution code using the substitution matrix
@@ -151,3 +144,3 @@ const refCoord = readFeature.refPos - refRegion.start
   }
-  const substitutionScheme = compressionScheme.substitutionMatrix[baseNumber]
+  const substitutionScheme = compressionScheme.substitutionMatrix[baseNumber]!
   const base = substitutionScheme[readFeature.data]
@@ -154,0 +147,0 @@ if (base) {

src/cramFile/sectionParsers.ts

@@ -182,4 +182,4 @@ import { TupleOf } from '../typescript'
         const key =
-          String.fromCharCode(buffer[offset]) +
-          String.fromCharCode(buffer[offset + 1])
+          String.fromCharCode(buffer[offset]!) +
+          String.fromCharCode(buffer[offset + 1]!)
         offset += 2
@@ -554,4 +554,4 @@
         const key =
-          String.fromCharCode(buffer[offset]) +
-          String.fromCharCode(buffer[offset + 1])
+          String.fromCharCode(buffer[offset]!) +
+          String.fromCharCode(buffer[offset + 1]!)
         offset += 2
@@ -558,0 +558,0 @@

src/cramFile/slice/decodeRecord.ts

@@ -1,2 +0,1 @@
-import Long from 'long'
 import { CramMalformedError } from '../../errors'
@@ -25,3 +24,3 @@ import {
   for (let i = 0; i < buffer.length && buffer[i] !== 0; i++) {
-    r += String.fromCharCode(buffer[i])
+    r += String.fromCharCode(buffer[i]!)
   }
@@ -35,5 +34,5 @@ return r
  */
-function parseTagValueArray(buffer: Buffer) {
-  const arrayType = String.fromCharCode(buffer[0])
-  const length = Int32Array.from(buffer.slice(1))[0]
+function parseTagValueArray(buffer: Uint8Array) {
+  const arrayType = String.fromCharCode(buffer[0]!)
+  const length = Int32Array.from(buffer.slice(1))[0]!
 
@@ -46,3 +45,3 @@ const array: number[] = new Array(length)
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
@@ -52,3 +51,3 @@ } else if (arrayType === 'C') {
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
@@ -58,3 +57,3 @@ } else if (arrayType === 's') {
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
@@ -64,3 +63,3 @@ } else if (arrayType === 'S') {
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
@@ -70,3 +69,3 @@ } else if (arrayType === 'i') {
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
@@ -76,3 +75,3 @@ } else if (arrayType === 'I') {
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
@@ -82,3 +81,3 @@ } else if (arrayType === 'f') {
     for (let i = 0; i < length; i += 1) {
-      array[i] = arr[i]
+      array[i] = arr[i]!
     }
@@ -92,3 +91,3 @@ } else {
 
-function parseTagData(tagType: string, buffer: any) {
+function parseTagData(tagType: string, buffer: Uint8Array) {
   if (tagType === 'Z') {
@@ -98,6 +97,6 @@ return readNullTerminatedString(buffer)
   if (tagType === 'A') {
-    return String.fromCharCode(buffer[0])
+    return String.fromCharCode(buffer[0]!)
   }
   if (tagType === 'I') {
-    return Long.fromBytesLE(buffer).toNumber()
+    return new Uint32Array(buffer.buffer)[0]
   }
@@ -117,3 +116,3 @@ if (tagType === 'i') {
   if (tagType === 'C') {
-    return buffer[0] as number
+    return buffer[0]!
   }
@@ -326,23 +325,14 @@ if (tagType === 'f') {
   // 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,
-    )
-    tags[tagName] = parseTagData(tagType, tagData)
+    const tagData = compressionScheme
+      .getCodecForTag(tagId)
+      .decode(slice, coreDataBlock, blocksByContentId, cursors)
+    tags[tagName] =
+      typeof tagData === 'number' ? tagData : parseTagData(tagType, tagData)
   }
@@ -349,0 +339,0 @@

src/cramFile/slice/index.ts

@@ -93,5 +93,6 @@ import { CramArgumentError, CramMalformedError } from '../../errors'
 /**
- * @private establishes a mate-pair relationship between two records in the same slice.
- * CRAM compresses mate-pair relationships between records in the same slice down into
- * just one record having the index in the slice of its mate
+ * @private establishes a mate-pair relationship between two records in the
+ * same slice. CRAM compresses mate-pair relationships between records in the
+ * same slice down into just one record having the index in the slice of its
+ * mate
  */
@@ -104,8 +105,2 @@ function associateIntraSliceMate(
 ) {
-  if (!mateRecord) {
-    throw new CramMalformedError(
-      'could not resolve intra-slice mate pairs, file seems truncated or malformed',
-    )
-  }
-
   const complicatedMultiSegment = !!(
@@ -191,3 +186,3 @@ mateRecord.mate ||
     public containerPosition: number,
-    _unused: number,
+    public sliceSize: number,
   ) {
@@ -248,3 +243,3 @@ this.file = container.file
       blocks[i] = block
-      blockPosition = blocks[i]._endPosition
+      blockPosition = blocks[i]!._endPosition
     }
@@ -258,4 +253,3 @@
     const blocks = await this.getBlocks()
-    // the core data block is always the first block in the slice
-    return blocks[0]
+    return blocks[0]!
   }
@@ -365,6 +359,2 @@
     const sliceHeader = await this.getHeader()
-    if (sliceHeader === undefined) {
-      throw new Error('slice header undefined')
-    }
-
     const blocksByContentId = await this._getBlocksContentIdIndex()
@@ -438,3 +428,5 @@
     }
-    let records: CramRecord[] = new Array(sliceHeader.parsedContent.numRecords)
+    const records: CramRecord[] = new Array(
+      sliceHeader.parsedContent.numRecords,
+    )
     for (let i = 0; i < records.length; i += 1) {
@@ -466,3 +458,2 @@ try {
           )
-          records = records.filter(r => !!r)
           break
@@ -478,3 +469,3 @@ } else {
     for (let i = 0; i < records.length; i += 1) {
-      const { mateRecordNumber } = records[i]
+      const { mateRecordNumber } = records[i]!
       if (mateRecordNumber !== undefined && mateRecordNumber >= 0) {
@@ -484,4 +475,4 @@ associateIntraSliceMate(
           i,
-          records[i],
-          records[mateRecordNumber],
+          records[i]!,
+          records[mateRecordNumber]!,
         )
@@ -593,4 +584,4 @@ }
 // memoize several methods in the class for performance
-'getHeader getBlocks _getBlocksContentIdIndex'
-  .split(' ')
-  .forEach(method => tinyMemoize(CramSlice, method))
+'getHeader getBlocks _getBlocksContentIdIndex'.split(' ').forEach(method => {
+  tinyMemoize(CramSlice, method)
+})

src/cramFile/util.ts

@@ -23,3 +23,3 @@ import md5 from 'md5'
   let offset = initialOffset
-  const countFlags = buffer[offset]
+  const countFlags = buffer[offset]!
   let result: number
@@ -30,7 +30,7 @@ if (countFlags < 0x80) {
   } else if (countFlags < 0xc0) {
-    result = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff
+    result = ((countFlags << 8) | buffer[offset + 1]!) & 0x3fff
     offset = offset + 2
   } else if (countFlags < 0xe0) {
     result =
-      ((countFlags << 16) | (buffer[offset + 1] << 8) | buffer[offset + 2]) &
+      ((countFlags << 16) | (buffer[offset + 1]! << 8) | buffer[offset + 2]!) &
       0x1fffff
@@ -41,5 +41,5 @@ offset = offset + 3
       ((countFlags << 24) |
-        (buffer[offset + 1] << 16) |
-        (buffer[offset + 2] << 8) |
-        buffer[offset + 3]) &
+        (buffer[offset + 1]! << 16) |
+        (buffer[offset + 2]! << 8) |
+        buffer[offset + 3]!) &
       0x0fffffff
@@ -50,6 +50,6 @@ offset = offset + 4
       ((countFlags & 0x0f) << 28) |
-      (buffer[offset + 1] << 20) |
-      (buffer[offset + 2] << 12) |
-      (buffer[offset + 3] << 4) |
-      (buffer[offset + 4] & 0x0f)
+      (buffer[offset + 1]! << 20) |
+      (buffer[offset + 2]! << 12) |
+      (buffer[offset + 3]! << 4) |
+      (buffer[offset + 4]! & 0x0f)
     // x=((0xff & 0x0f)<<28) | (0xff<<20) | (0xff<<12) | (0xff<<4) | (0x0f & 0x0f);
@@ -69,3 +69,3 @@ // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
   let offset = initialOffset
-  const countFlags = buffer[offset]
+  const countFlags = buffer[offset]!
   let n: number | Long
@@ -76,9 +76,9 @@ if (countFlags < 0x80) {
   } else if (countFlags < 0xc0) {
-    n = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff
+    n = ((buffer[offset]! << 8) | buffer[offset + 1]!) & 0x3fff
     offset += 2
   } else if (countFlags < 0xe0) {
     n =
-      ((buffer[offset] << 16) |
-        (buffer[offset + 1] << 8) |
-        buffer[offset + 2]) &
+      ((buffer[offset]! << 16) |
+        (buffer[offset + 1]! << 8) |
+        buffer[offset + 2]!) &
       0x1fffff
@@ -89,6 +89,6 @@ n = ((countFlags & 63) << 16) | buffer.readUInt16LE(offset + 1)
     n =
-      ((buffer[offset] << 24) |
-        (buffer[offset + 1] << 16) |
-        (buffer[offset + 2] << 8) |
-        buffer[offset + 3]) &
+      ((buffer[offset]! << 24) |
+        (buffer[offset + 1]! << 16) |
+        (buffer[offset + 2]! << 8) |
+        buffer[offset + 3]!) &
       0x0fffffff
@@ -98,6 +98,6 @@ offset += 4
     n =
-      ((buffer[offset] & 15) * 2 ** 32 + (buffer[offset + 1] << 24)) |
-      ((buffer[offset + 2] << 16) |
-        (buffer[offset + 3] << 8) |
-        buffer[offset + 4])
+      ((buffer[offset]! & 15) * 2 ** 32 + (buffer[offset + 1]! << 24)) |
+      ((buffer[offset + 2]! << 16) |
+        (buffer[offset + 3]! << 8) |
+        buffer[offset + 4]!)
     // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
@@ -107,18 +107,18 @@ offset += 5
     n =
-      ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * 2 ** 32 +
-        (buffer[offset + 2] << 24)) |
-      ((buffer[offset + 3] << 16) |
-        (buffer[offset + 4] << 8) |
-        buffer[offset + 5])
+      ((((buffer[offset]! & 7) << 8) | buffer[offset + 1]!) * 2 ** 32 +
+        (buffer[offset + 2]! << 24)) |
+      ((buffer[offset + 3]! << 16) |
+        (buffer[offset + 4]! << 8) |
+        buffer[offset + 5]!)
     offset += 6
   } else if (countFlags < 0xfe) {
     n =
-      ((((buffer[offset] & 3) << 16) |
-        (buffer[offset + 1] << 8) |
-        buffer[offset + 2]) *
+      ((((buffer[offset]! & 3) << 16) |
+        (buffer[offset + 1]! << 8) |
+        buffer[offset + 2]!) *
         2 ** 32 +
-        (buffer[offset + 3] << 24)) |
-      ((buffer[offset + 4] << 16) |
-        (buffer[offset + 5] << 8) |
-        buffer[offset + 6])
+        (buffer[offset + 3]! << 24)) |
+      ((buffer[offset + 4]! << 16) |
+        (buffer[offset + 5]! << 8) |
+        buffer[offset + 6]!)
     offset += 7
@@ -179,2 +179,3 @@ } else if (countFlags < 0xff) {
       Promise.resolve(res).catch(() => {
+         
         delete this[memoAttrName]
@@ -181,0 +182,0 @@ })

src/indexedCramFile.ts

@@ -66,5 +66,2 @@ import { CramUnimplementedError } from './errors'
     this.index = args.index
-    if (!this.index.getEntriesForRange) {
-      throw new Error('invalid arguments: not an index')
-    }
   }
@@ -167,3 +164,3 @@
           (item, pos, ary) =>
-            !pos || item.toString() !== ary[pos - 1].toString(),
+            !pos || item.toString() !== ary[pos - 1]!.toString(),
         )
@@ -170,0 +167,0 @@

src/rans/d04.ts

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors'
@@ -3,0 +3,0 @@

src/rans/d14.ts

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { TF_SHIFT } from './constants'
@@ -3,0 +3,0 @@ import Decoding from './decoding'

src/rans/decoding.ts

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors'
@@ -3,0 +3,0 @@

src/rans/frequencies.ts

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { CramMalformedError } from '../errors'
@@ -3,0 +3,0 @@

src/rans/index.ts

@@ -1,2 +0,2 @@
-//@ts-nocheck
+// @ts-nocheck
 import { Buffer } from 'buffer'
@@ -3,0 +3,0 @@ import { CramMalformedError } from '../errors'

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Improved metrics

Dependency count

8

decreased by-11.11%

Worsened metrics

Total package byte prevSize

1034495

decreased by-0.81%

Lines of code

14711

decreased by-0.57%

Dependency changes

• - Removed@gmod/abortable-promise-cache@^2.0.0

• - Removed@gmod/abortable-promise-cache@2.0.1(transitive)