@gmod/cram 1.5.9 → 1.6.2

package/dist/unzip.d.ts

@@ -0,0 +1,2 @@
+import { gunzipSync } from 'zlib';
+export { gunzipSync as unzip };

package/dist/unzip.js

@@ -0,0 +1,6 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.unzip = void 0;
+var zlib_1 = require("zlib");
+Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.gunzipSync; } });
+//# sourceMappingURL=unzip.js.map

package/dist/unzip.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,6BAAiC;AACV,sFADd,iBAAU,OACS"}

package/errors.js

@@ -1,115 +1,78 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/getPrototypeOf"));
-
-var _inherits2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/inherits"));
-
-var _wrapNativeSuper2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/wrapNativeSuper"));
-
-var CramError =
-/*#__PURE__*/
-function (_Error) {
-  (0, _inherits2.default)(CramError, _Error);
-
-  function CramError() {
-    (0, _classCallCheck2.default)(this, CramError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramError).apply(this, arguments));
-  }
-
-  return CramError;
-}((0, _wrapNativeSuper2.default)(Error));
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.CramArgumentError = exports.CramSizeLimitError = exports.CramBufferOverrunError = exports.CramMalformedError = exports.CramUnimplementedError = exports.CramError = void 0;
+var CramError = /** @class */ (function (_super) {
+    __extends(CramError, _super);
+    function CramError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramError;
+}(Error));
+exports.CramError = CramError;
 /** Error caused by encountering a part of the CRAM spec that has not yet been implemented */
-
-
-var CramUnimplementedError =
-/*#__PURE__*/
-function (_Error2) {
-  (0, _inherits2.default)(CramUnimplementedError, _Error2);
-
-  function CramUnimplementedError() {
-    (0, _classCallCheck2.default)(this, CramUnimplementedError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramUnimplementedError).apply(this, arguments));
-  }
-
-  return CramUnimplementedError;
-}((0, _wrapNativeSuper2.default)(Error));
+var CramUnimplementedError = /** @class */ (function (_super) {
+    __extends(CramUnimplementedError, _super);
+    function CramUnimplementedError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramUnimplementedError;
+}(Error));
+exports.CramUnimplementedError = CramUnimplementedError;
 /** An error caused by malformed data.  */
-
-
-var CramMalformedError =
-/*#__PURE__*/
-function (_CramError) {
-  (0, _inherits2.default)(CramMalformedError, _CramError);
-
-  function CramMalformedError() {
-    (0, _classCallCheck2.default)(this, CramMalformedError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramMalformedError).apply(this, arguments));
-  }
-
-  return CramMalformedError;
-}(CramError);
+var CramMalformedError = /** @class */ (function (_super) {
+    __extends(CramMalformedError, _super);
+    function CramMalformedError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramMalformedError;
+}(CramError));
+exports.CramMalformedError = CramMalformedError;
 /**
  * An error caused by attempting to read beyond the end of the defined data.
  */
-
-
-var CramBufferOverrunError =
-/*#__PURE__*/
-function (_CramMalformedError) {
-  (0, _inherits2.default)(CramBufferOverrunError, _CramMalformedError);
-
-  function CramBufferOverrunError() {
-    (0, _classCallCheck2.default)(this, CramBufferOverrunError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramBufferOverrunError).apply(this, arguments));
-  }
-
-  return CramBufferOverrunError;
-}(CramMalformedError);
+var CramBufferOverrunError = /** @class */ (function (_super) {
+    __extends(CramBufferOverrunError, _super);
+    function CramBufferOverrunError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramBufferOverrunError;
+}(CramMalformedError));
+exports.CramBufferOverrunError = CramBufferOverrunError;
 /**
  * An error caused by data being too big, exceeding a size limit.
  */
-
-
-var CramSizeLimitError =
-/*#__PURE__*/
-function (_CramError2) {
-  (0, _inherits2.default)(CramSizeLimitError, _CramError2);
-
-  function CramSizeLimitError() {
-    (0, _classCallCheck2.default)(this, CramSizeLimitError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramSizeLimitError).apply(this, arguments));
-  }
-
-  return CramSizeLimitError;
-}(CramError);
+var CramSizeLimitError = /** @class */ (function (_super) {
+    __extends(CramSizeLimitError, _super);
+    function CramSizeLimitError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramSizeLimitError;
+}(CramError));
+exports.CramSizeLimitError = CramSizeLimitError;
 /**
  * An invalid argument was supplied to a cram-js method or object.
  */
-
-
-var CramArgumentError =
-/*#__PURE__*/
-function (_CramError3) {
-  (0, _inherits2.default)(CramArgumentError, _CramError3);
-
-  function CramArgumentError() {
-    (0, _classCallCheck2.default)(this, CramArgumentError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramArgumentError).apply(this, arguments));
-  }
-
-  return CramArgumentError;
-}(CramError);
-
-module.exports = {
-  CramBufferOverrunError: CramBufferOverrunError,
-  CramMalformedError: CramMalformedError,
-  CramUnimplementedError: CramUnimplementedError,
-  CramSizeLimitError: CramSizeLimitError,
-  CramArgumentError: CramArgumentError
-};
+var CramArgumentError = /** @class */ (function (_super) {
+    __extends(CramArgumentError, _super);
+    function CramArgumentError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramArgumentError;
+}(CramError));
+exports.CramArgumentError = CramArgumentError;
+//# sourceMappingURL=errors.js.map

package/esm/craiIndex.d.ts

@@ -0,0 +1,37 @@
+export default class CraiIndex {
+    /**
+     *
+     * @param {object} args
+     * @param {string} [args.path]
+     * @param {string} [args.url]
+     * @param {FileHandle} [args.filehandle]
+     */
+    constructor(args: {
+        path?: string | undefined;
+        url?: string | undefined;
+        filehandle?: any;
+    });
+    _parseCache: AbortablePromiseCache<any, any>;
+    readFile: any;
+    parseIndex(): any;
+    getIndex(opts?: {}): Promise<any>;
+    /**
+     * @param {number} seqId
+     * @returns {Promise} true if the index contains entries for
+     * the given reference sequence ID, false otherwise
+     */
+    hasDataForReferenceSequence(seqId: number): Promise<any>;
+    /**
+     * fetch index entries for the given range
+     *
+     * @param {number} seqId
+     * @param {number} queryStart
+     * @param {number} queryEnd
+     *
+     * @returns {Promise} promise for
+     * an array of objects of the form
+     * `{start, span, containerStart, sliceStart, sliceBytes }`
+     */
+    getEntriesForRange(seqId: number, queryStart: number, queryEnd: number): Promise<any>;
+}
+import AbortablePromiseCache from "abortable-promise-cache";

package/esm/craiIndex.js

@@ -0,0 +1,158 @@
+import AbortablePromiseCache from 'abortable-promise-cache';
+import QuickLRU from 'quick-lru';
+import { unzip } from './unzip';
+import { open } from './io';
+import { CramMalformedError } from './errors';
+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}`;
+    }
+}
+function addRecordToIndex(index, record) {
+    if (record.some(el => el === undefined)) {
+        throw new CramMalformedError('invalid .crai index file');
+    }
+    const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;
+    if (!index[seqId]) {
+        index[seqId] = [];
+    }
+    index[seqId].push(new Slice({
+        start,
+        span,
+        containerStart,
+        sliceStart,
+        sliceBytes,
+    }));
+}
+export default class CraiIndex {
+    // A CRAM index (.crai) is a gzipped tab delimited file containing the following columns:
+    // 1. Sequence id
+    // 2. Alignment start
+    // 3. Alignment span
+    // 4. Container start byte position in the file
+    // 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.
+    /**
+     *
+     * @param {object} args
+     * @param {string} [args.path]
+     * @param {string} [args.url]
+     * @param {FileHandle} [args.filehandle]
+     */
+    constructor(args) {
+        const filehandle = open(args.url, args.path, args.filehandle);
+        this._parseCache = new AbortablePromiseCache({
+            cache: new QuickLRU({ maxSize: 1 }),
+            fill: (data, signal) => this.parseIndex({ signal }),
+        });
+        this.readFile = filehandle.readFile.bind(filehandle);
+    }
+    parseIndex() {
+        const index = {};
+        return this.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 = [];
+            let currentString = '';
+            for (let i = 0; i < uncompressedBuffer.length; i += 1) {
+                const charCode = uncompressedBuffer[i];
+                if ((charCode >= 48 && charCode <= 57) /* 0-9 */ ||
+                    (!currentString && charCode === 45) /* leading - */) {
+                    currentString += String.fromCharCode(charCode);
+                }
+                else if (charCode === 9 /* \t */) {
+                    currentRecord.push(Number.parseInt(currentString, 10));
+                    currentString = '';
+                }
+                else if (charCode === 10 /* \n */) {
+                    currentRecord.push(Number.parseInt(currentString, 10));
+                    currentString = '';
+                    addRecordToIndex(index, currentRecord);
+                    currentRecord = [];
+                }
+                else if (charCode !== 13 /* \r */ && charCode !== 32 /* space */) {
+                    // if there are other characters in the file besides
+                    // space and \r, something is wrong.
+                    throw new CramMalformedError('invalid .crai index file');
+                }
+            }
+            // if the file ends without a \n, we need to flush our buffers
+            if (currentString) {
+                currentRecord.push(Number.parseInt(currentString, 10));
+            }
+            if (currentRecord.length === 6) {
+                addRecordToIndex(index, currentRecord);
+            }
+            // sort each of them by start
+            Object.entries(index).forEach(([seqId, ent]) => {
+                index[seqId] = ent.sort((a, b) => a.start - b.start || a.span - b.span);
+            });
+            return index;
+        });
+    }
+    getIndex(opts = {}) {
+        return this._parseCache.get('index', null, opts.signal);
+    }
+    /**
+     * @param {number} seqId
+     * @returns {Promise} true if the index contains entries for
+     * the given reference sequence ID, false otherwise
+     */
+    async hasDataForReferenceSequence(seqId) {
+        return !!(await this.getIndex())[seqId];
+    }
+    /**
+     * fetch index entries for the given range
+     *
+     * @param {number} seqId
+     * @param {number} queryStart
+     * @param {number} queryEnd
+     *
+     * @returns {Promise} promise for
+     * an array of objects of the form
+     * `{start, span, containerStart, sliceStart, sliceBytes }`
+     */
+    async getEntriesForRange(seqId, queryStart, queryEnd) {
+        const seqEntries = (await this.getIndex())[seqId];
+        if (!seqEntries) {
+            return [];
+        }
+        const compare = entry => {
+            const entryStart = entry.start;
+            const entryEnd = entry.start + entry.span;
+            if (entryStart >= queryEnd) {
+                return -1;
+            } // entry is ahead of query
+            if (entryEnd <= queryStart) {
+                return 1;
+            } // entry is behind query
+            return 0; // entry overlaps query
+        };
+        const bins = [];
+        for (let i = 0; i < seqEntries.length; i += 1) {
+            if (compare(seqEntries[i]) === 0) {
+                bins.push(seqEntries[i]);
+            }
+        }
+        return bins;
+    }
+}
+//# sourceMappingURL=craiIndex.js.map

package/esm/craiIndex.js.map

@@ -0,0 +1 @@
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package/esm/cramFile/codecs/_base.d.ts

@@ -0,0 +1,6 @@
+export default class CramCodec {
+    constructor(parameters: {} | undefined, dataType: any);
+    parameters: {};
+    dataType: any;
+    _getBits(data: any, cursor: any, numBits: any): number;
+}

package/esm/cramFile/codecs/_base.js

@@ -0,0 +1,42 @@
+import { CramBufferOverrunError } from '../../errors';
+const validDataTypes = {
+    int: true,
+    byte: true,
+    long: true,
+    byteArray: true,
+    byteArrayBlock: true,
+};
+// codec base class
+export default class CramCodec {
+    constructor(parameters = {}, dataType) {
+        this.parameters = parameters;
+        this.dataType = dataType;
+        if (!dataType) {
+            throw new TypeError('must provide a data type to codec constructor');
+        }
+        if (!validDataTypes[dataType]) {
+            throw new TypeError(`invalid data type ${dataType}`);
+        }
+    }
+    // decode(slice, coreDataBlock, blocksByContentId, cursors) {
+    // }
+    _getBits(data, cursor, numBits) {
+        let val = 0;
+        if (cursor.bytePosition + (7 - cursor.bitPosition + numBits) / 8 >
+            data.length) {
+            throw new CramBufferOverrunError('read error during decoding. the file seems to be truncated.');
+        }
+        for (let dlen = numBits; dlen; dlen -= 1) {
+            // get the next `dlen` bits in the input, put them in val
+            val <<= 1;
+            val |= (data[cursor.bytePosition] >> cursor.bitPosition) & 1;
+            cursor.bitPosition -= 1;
+            if (cursor.bitPosition < 0) {
+                cursor.bytePosition += 1;
+            }
+            cursor.bitPosition &= 7;
+        }
+        return val;
+    }
+}
+//# sourceMappingURL=_base.js.map

package/esm/cramFile/codecs/_base.js.map

@@ -0,0 +1 @@
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package/esm/cramFile/codecs/beta.d.ts

@@ -0,0 +1,4 @@
+export default class BetaCodec extends CramCodec {
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): number;
+}
+import CramCodec from "./_base";

package/esm/cramFile/codecs/beta.js

@@ -0,0 +1,15 @@
+import { CramUnimplementedError } from '../../errors';
+import CramCodec from './_base';
+export default class BetaCodec extends CramCodec {
+    constructor(parameters = {}, dataType) {
+        super(parameters, dataType);
+        if (this.dataType !== 'int') {
+            throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`);
+        }
+    }
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        const data = this._getBits(coreDataBlock.content, cursors.coreBlock, this.parameters.length) - this.parameters.offset;
+        return data;
+    }
+}
+//# sourceMappingURL=beta.js.map

package/esm/cramFile/codecs/beta.js.map

@@ -0,0 +1 @@
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package/esm/cramFile/codecs/byteArrayLength.d.ts

@@ -0,0 +1,8 @@
+export default class ByteArrayStopCodec extends CramCodec {
+    constructor(parameters: {} | undefined, dataType: any, instantiateCodec: any);
+    instantiateCodec: any;
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any[];
+    _getLengthCodec(): any;
+    _getDataCodec(): any;
+}
+import CramCodec from "./_base";

package/esm/cramFile/codecs/byteArrayLength.js

@@ -0,0 +1,35 @@
+import { tinyMemoize } from '../util';
+import CramCodec from './_base';
+export default class ByteArrayStopCodec extends CramCodec {
+    constructor(parameters = {}, dataType, instantiateCodec) {
+        super(parameters, dataType);
+        this.instantiateCodec = instantiateCodec;
+        if (dataType !== 'byteArray') {
+            throw new TypeError(`byteArrayLength does not support data type ${dataType}`);
+        }
+    }
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        const lengthCodec = this._getLengthCodec();
+        const arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+        const dataCodec = this._getDataCodec();
+        const data = new Array(arrayLength);
+        for (let i = 0; i < arrayLength; i += 1) {
+            data[i] = dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+        }
+        return data;
+    }
+    // memoize
+    _getLengthCodec() {
+        const encodingParams = this.parameters.lengthsEncoding;
+        return this.instantiateCodec(encodingParams, 'int');
+    }
+    // memoize
+    _getDataCodec() {
+        const encodingParams = this.parameters.valuesEncoding;
+        return this.instantiateCodec(encodingParams, 'byte');
+    }
+}
+'_getLengthCodec _getDataCodec'
+    .split(' ')
+    .forEach(method => tinyMemoize(ByteArrayStopCodec, method));
+//# sourceMappingURL=byteArrayLength.js.map

package/esm/cramFile/codecs/byteArrayLength.js.map

@@ -0,0 +1 @@
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package/esm/cramFile/codecs/byteArrayStop.d.ts

@@ -0,0 +1,6 @@
+export default class ByteArrayStopCodec extends CramCodec {
+    _decode: (contentBlock: any, cursor: any) => any;
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any;
+    _decodeByteArray(contentBlock: any, cursor: any): any;
+}
+import CramCodec from "./_base";

package/esm/cramFile/codecs/byteArrayStop.js

@@ -0,0 +1,40 @@
+import { CramBufferOverrunError, CramMalformedError } from '../../errors';
+import CramCodec from './_base';
+export default class ByteArrayStopCodec extends CramCodec {
+    constructor(parameters = {}, dataType) {
+        super(parameters, dataType);
+        if (dataType === 'byteArray') {
+            this._decode = this._decodeByteArray;
+        }
+        else {
+            throw new TypeError(`byteArrayStop codec does not support data type ${dataType}`);
+        }
+    }
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        const { blockContentId } = this.parameters;
+        const contentBlock = blocksByContentId[blockContentId];
+        if (!contentBlock) {
+            throw new CramMalformedError(`no block found with content ID ${blockContentId}`);
+        }
+        const cursor = cursors.externalBlocks.getCursor(blockContentId);
+        return this._decode(contentBlock, cursor);
+    }
+    _decodeByteArray(contentBlock, cursor) {
+        const dataBuffer = contentBlock.content;
+        const { stopByte } = this.parameters;
+        // scan to the next stop byte
+        const startPosition = cursor.bytePosition;
+        let stopPosition = cursor.bytePosition;
+        while (dataBuffer[stopPosition] !== stopByte &&
+            stopPosition < dataBuffer.length) {
+            if (stopPosition === dataBuffer.length) {
+                throw new CramBufferOverrunError(`byteArrayStop reading beyond length of data buffer?`);
+            }
+            stopPosition += 1;
+        }
+        cursor.bytePosition = stopPosition + 1;
+        const data = dataBuffer.slice(startPosition, stopPosition);
+        return data;
+    }
+}
+//# sourceMappingURL=byteArrayStop.js.map

package/esm/cramFile/codecs/byteArrayStop.js.map

@@ -0,0 +1 @@
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package/esm/cramFile/codecs/external.d.ts

@@ -0,0 +1,7 @@
+export default class ExternalCodec extends CramCodec {
+    _decodeData: (contentBlock: any, cursor: any) => any;
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any;
+    _decodeInt(contentBlock: any, cursor: any): any;
+    _decodeByte(contentBlock: any, cursor: any): any;
+}
+import CramCodec from "./_base";

package/esm/cramFile/codecs/external.js

@@ -0,0 +1,40 @@
+import { CramUnimplementedError, CramMalformedError, CramBufferOverrunError, } from '../../errors';
+import CramCodec from './_base';
+import { parseItf8 } from '../util';
+export default class ExternalCodec extends CramCodec {
+    constructor(parameters = {}, dataType) {
+        super(parameters, dataType);
+        if (this.dataType === 'int') {
+            this._decodeData = this._decodeInt;
+        }
+        else if (this.dataType === 'byte') {
+            this._decodeData = this._decodeByte;
+        }
+        else {
+            throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by EXTERNAL codec`);
+        }
+    }
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        const { blockContentId } = this.parameters;
+        const contentBlock = blocksByContentId[blockContentId];
+        if (!contentBlock) {
+            throw new CramMalformedError(`no block found with content ID ${blockContentId}`);
+        }
+        const cursor = cursors.externalBlocks.getCursor(blockContentId);
+        return this._decodeData(contentBlock, cursor);
+    }
+    _decodeInt(contentBlock, cursor) {
+        const [result, bytesRead] = parseItf8(contentBlock.content, cursor.bytePosition);
+        cursor.bytePosition += bytesRead;
+        return result;
+    }
+    _decodeByte(contentBlock, cursor) {
+        if (cursor.bytePosition >= contentBlock.content.length) {
+            throw new CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
+        }
+        const result = contentBlock.content[cursor.bytePosition];
+        cursor.bytePosition += 1;
+        return result;
+    }
+}
+//# sourceMappingURL=external.js.map

package/esm/cramFile/codecs/external.js.map

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