@gmod/cram 1.6.3 → 1.7.0

package/dist/cram-bundle.js.LICENSE.txt

@@ -0,0 +1,17 @@
+/*!
+ * Determine if an object is a Buffer
+ *
+ * @author   Feross Aboukhadijeh <https://feross.org>
+ * @license  MIT
+ */
+
+/*!
+ * The buffer module from node.js, for the browser.
+ *
+ * @author   Feross Aboukhadijeh <https://feross.org>
+ * @license  MIT
+ */
+
+/*! https://mths.be/punycode v1.3.2 by @mathias */
+
+/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */

package/dist/cramFile/codecs/_base.d.ts

@@ -1,6 +1,27 @@
-export default class CramCodec {
-    constructor(parameters: {} | undefined, dataType: any);
-    parameters: {};
-    dataType: any;
-    _getBits(data: any, cursor: any, numBits: any): number;
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { DataType } from './dataSeriesTypes';
+export declare type DataTypeMapping = {
+    byte: number;
+    int: number;
+    long: number;
+    byteArray: Uint8Array;
+};
+export declare type Cursor = {
+    bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
+    bytePosition: number;
+};
+export declare type Cursors = {
+    lastAlignmentStart: number;
+    coreBlock: Cursor;
+    externalBlocks: {
+        map: Map<any, any>;
+        getCursor: (contentId: number) => Cursor;
+    };
+};
+export default abstract class CramCodec<TResult extends DataType = DataType, TParameters = unknown> {
+    parameters: TParameters;
+    dataType: DataType;
+    constructor(parameters: TParameters, dataType: TResult);
+    abstract decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): DataTypeMapping[TResult];
 }

package/dist/cramFile/codecs/_base.js

@@ -1,47 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var errors_1 = require("../../errors");
-var validDataTypes = {
-    int: true,
-    byte: true,
-    long: true,
-    byteArray: true,
-    byteArrayBlock: true,
-};
 // codec base class
-var CramCodec = /** @class */ (function () {
-    function CramCodec(parameters, dataType) {
-        if (parameters === void 0) { parameters = {}; }
+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 ".concat(dataType));
-        }
     }
-    // decode(slice, coreDataBlock, blocksByContentId, cursors) {
-    // }
-    CramCodec.prototype._getBits = function (data, cursor, numBits) {
-        var val = 0;
-        if (cursor.bytePosition + (7 - cursor.bitPosition + numBits) / 8 >
-            data.length) {
-            throw new errors_1.CramBufferOverrunError('read error during decoding. the file seems to be truncated.');
-        }
-        for (var 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;
-    };
-    return CramCodec;
-}());
+}
 exports.default = CramCodec;
 //# sourceMappingURL=_base.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"_base.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/_base.ts"],"names":[],"mappings":";;AAyBA,mBAAmB;AACnB,MAA8B,SAAS;IAOrC,YAAY,UAAuB,EAAE,QAAiB;QACpD,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;CAQF;AAlBD,4BAkBC"}

package/dist/cramFile/codecs/beta.d.ts

@@ -1,4 +1,8 @@
-export default class BetaCodec extends CramCodec {
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): number;
+import CramCodec, { Cursors } from './_base';
+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');
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
 }
-import CramCodec from "./_base";

package/dist/cramFile/codecs/beta.js

@@ -1,40 +1,22 @@
 "use strict";
-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 __());
-    };
-})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var errors_1 = require("../../errors");
-var _base_1 = __importDefault(require("./_base"));
-var BetaCodec = /** @class */ (function (_super) {
-    __extends(BetaCodec, _super);
-    function BetaCodec(parameters, dataType) {
-        if (parameters === void 0) { parameters = {}; }
-        var _this = _super.call(this, parameters, dataType) || this;
-        if (_this.dataType !== 'int') {
-            throw new errors_1.CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by BETA codec"));
+const errors_1 = require("../../errors");
+const _base_1 = __importDefault(require("./_base"));
+const getBits_1 = require("./getBits");
+class BetaCodec extends _base_1.default {
+    constructor(parameters, dataType) {
+        super(parameters, dataType);
+        if (this.dataType !== 'int') {
+            throw new errors_1.CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`);
         }
-        return _this;
     }
-    BetaCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
-        var data = this._getBits(coreDataBlock.content, cursors.coreBlock, this.parameters.length) - this.parameters.offset;
-        return data;
-    };
-    return BetaCodec;
-}(_base_1.default));
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        const fromBits = (0, getBits_1.getBits)(coreDataBlock.content, cursors.coreBlock, this.parameters.length);
+        return fromBits - this.parameters.offset;
+    }
+}
 exports.default = BetaCodec;
 //# sourceMappingURL=beta.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,SAAU,SAAQ,eAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;SACF;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;QACD,OAAO,QAAQ,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IAC1C,CAAC;CACF;AA1BD,4BA0BC"}

package/dist/cramFile/codecs/byteArrayLength.d.ts

@@ -1,8 +1,14 @@
-export default class ByteArrayStopCodec extends CramCodec {
-    constructor(parameters: {} | undefined, dataType: any, instantiateCodec: any);
-    instantiateCodec: any;
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): Uint8Array;
-    _getLengthCodec(): any;
-    _getDataCodec(): any;
+import CramCodec, { Cursors } from './_base';
+import { ByteArrayLengthEncoding, CramEncoding } from '../encoding';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { DataType } from './dataSeriesTypes';
+declare type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
+export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {
+    private instantiateCodec;
+    constructor(parameters: ByteArrayLengthEncoding['parameters'], dataType: 'byteArray', instantiateCodec: CramCodecFactory);
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array;
+    _getLengthCodec(): CramCodec<"int", unknown>;
+    _getDataCodec(): CramCodec<"byte", unknown>;
 }
-import CramCodec from "./_base";
+export {};

package/dist/cramFile/codecs/byteArrayLength.js

@@ -1,60 +1,41 @@
 "use strict";
-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 __());
-    };
-})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var util_1 = require("../util");
-var _base_1 = __importDefault(require("./_base"));
-var ByteArrayStopCodec = /** @class */ (function (_super) {
-    __extends(ByteArrayStopCodec, _super);
-    function ByteArrayStopCodec(parameters, dataType, instantiateCodec) {
-        if (parameters === void 0) { parameters = {}; }
-        var _this = _super.call(this, parameters, dataType) || this;
-        _this.instantiateCodec = instantiateCodec;
+const util_1 = require("../util");
+const _base_1 = __importDefault(require("./_base"));
+class ByteArrayStopCodec extends _base_1.default {
+    constructor(parameters, dataType, instantiateCodec) {
+        super(parameters, dataType);
+        this.instantiateCodec = instantiateCodec;
         if (dataType !== 'byteArray') {
-            throw new TypeError("byteArrayLength does not support data type ".concat(dataType));
+            throw new TypeError(`byteArrayLength does not support data type ${dataType}`);
         }
-        return _this;
     }
-    ByteArrayStopCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
-        var lengthCodec = this._getLengthCodec();
-        var arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-        var dataCodec = this._getDataCodec();
-        var data = new Uint8Array(arrayLength);
-        for (var i = 0; i < arrayLength; i += 1) {
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        const lengthCodec = this._getLengthCodec();
+        const arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+        const dataCodec = this._getDataCodec();
+        const data = new Uint8Array(arrayLength);
+        for (let i = 0; i < arrayLength; i += 1) {
             data[i] = dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
         }
         return data;
-    };
+    }
     // memoize
-    ByteArrayStopCodec.prototype._getLengthCodec = function () {
-        var encodingParams = this.parameters.lengthsEncoding;
+    _getLengthCodec() {
+        const encodingParams = this.parameters.lengthsEncoding;
         return this.instantiateCodec(encodingParams, 'int');
-    };
+    }
     // memoize
-    ByteArrayStopCodec.prototype._getDataCodec = function () {
-        var encodingParams = this.parameters.valuesEncoding;
+    _getDataCodec() {
+        const encodingParams = this.parameters.valuesEncoding;
         return this.instantiateCodec(encodingParams, 'byte');
-    };
-    return ByteArrayStopCodec;
-}(_base_1.default));
+    }
+}
 exports.default = ByteArrayStopCodec;
 '_getLengthCodec _getDataCodec'
     .split(' ')
-    .forEach(function (method) { return (0, util_1.tinyMemoize)(ByteArrayStopCodec, method); });
+    .forEach(method => (0, util_1.tinyMemoize)(ByteArrayStopCodec, method));
 //# sourceMappingURL=byteArrayLength.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,kCAAqC;AAErC,oDAA4C;AAW5C,MAAqB,kBAAmB,SAAQ,eAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,MAAM,IAAI,SAAS,CACjB,8CAA8C,QAAQ,EAAE,CACzD,CAAA;SACF;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CACpC,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QAED,MAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;QACtC,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;QACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE;YACvC,IAAI,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,MAAM,CACxB,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;SACF;QAED,OAAO,IAAI,CAAA;IACb,CAAC;IAED,UAAU;IACV,eAAe;QACb,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,aAAa;QACX,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QACrD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AA3DD,qCA2DC;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,IAAA,kBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,CAAC,CAAA"}

package/dist/cramFile/codecs/byteArrayStop.d.ts

@@ -1,6 +1,10 @@
-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;
+/// <reference types="node" />
+import CramCodec, { Cursor, Cursors } from './_base';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { ByteArrayStopCramEncoding } from '../encoding';
+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;
 }
-import CramCodec from "./_base";

package/dist/cramFile/codecs/byteArrayStop.js

@@ -1,64 +1,43 @@
 "use strict";
-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 __());
-    };
-})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var errors_1 = require("../../errors");
-var _base_1 = __importDefault(require("./_base"));
-var ByteArrayStopCodec = /** @class */ (function (_super) {
-    __extends(ByteArrayStopCodec, _super);
-    function ByteArrayStopCodec(parameters, dataType) {
-        if (parameters === void 0) { parameters = {}; }
-        var _this = _super.call(this, parameters, dataType) || this;
-        if (dataType === 'byteArray') {
-            _this._decode = _this._decodeByteArray;
+const errors_1 = require("../../errors");
+const _base_1 = __importDefault(require("./_base"));
+const getBits_1 = require("./getBits");
+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}`);
         }
-        else {
-            throw new TypeError("byteArrayStop codec does not support data type ".concat(dataType));
-        }
-        return _this;
     }
-    ByteArrayStopCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
-        var blockContentId = this.parameters.blockContentId;
-        var contentBlock = blocksByContentId[blockContentId];
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        const { blockContentId } = this.parameters;
+        const contentBlock = blocksByContentId[blockContentId];
         if (!contentBlock) {
-            throw new errors_1.CramMalformedError("no block found with content ID ".concat(blockContentId));
+            throw new errors_1.CramMalformedError(`no block found with content ID ${blockContentId}`);
         }
-        var cursor = cursors.externalBlocks.getCursor(blockContentId);
-        return this._decode(contentBlock, cursor);
-    };
-    ByteArrayStopCodec.prototype._decodeByteArray = function (contentBlock, cursor) {
-        var dataBuffer = contentBlock.content;
-        var stopByte = this.parameters.stopByte;
+        const cursor = cursors.externalBlocks.getCursor(blockContentId);
+        return this._decodeByteArray(contentBlock, cursor);
+    }
+    _decodeByteArray(contentBlock, cursor) {
+        const dataBuffer = contentBlock.content;
+        const { stopByte } = this.parameters;
         // scan to the next stop byte
-        var startPosition = cursor.bytePosition;
-        var stopPosition = cursor.bytePosition;
+        const startPosition = cursor.bytePosition;
+        let stopPosition = cursor.bytePosition;
         while (dataBuffer[stopPosition] !== stopByte &&
             stopPosition < dataBuffer.length) {
             if (stopPosition === dataBuffer.length) {
-                throw new errors_1.CramBufferOverrunError("byteArrayStop reading beyond length of data buffer?");
+                throw new getBits_1.CramBufferOverrunError(`byteArrayStop reading beyond length of data buffer?`);
             }
-            stopPosition += 1;
+            stopPosition = stopPosition + 1;
         }
         cursor.bytePosition = stopPosition + 1;
-        return dataBuffer.slice(startPosition, stopPosition);
-    };
-    return ByteArrayStopCodec;
-}(_base_1.default));
+        return dataBuffer.subarray(startPosition, stopPosition);
+    }
+}
 exports.default = ByteArrayStopCodec;
 //# sourceMappingURL=byteArrayStop.js.map

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

@@ -1 +1 @@
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package/dist/cramFile/codecs/dataSeriesTypes.d.ts

@@ -0,0 +1,4 @@
+import { CramEncoding } from '../encoding';
+export declare type DataType = 'int' | 'byte' | 'long' | 'byteArray';
+export declare type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
+export declare type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;

package/dist/cramFile/codecs/dataSeriesTypes.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=dataSeriesTypes.js.map

package/dist/cramFile/codecs/dataSeriesTypes.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"dataSeriesTypes.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/dataSeriesTypes.ts"],"names":[],"mappings":""}

package/dist/cramFile/codecs/external.d.ts

@@ -1,7 +1,11 @@
-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, { Cursor, Cursors } from './_base';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { ExternalCramEncoding } from '../encoding';
+export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
+    private readonly _decodeData;
+    constructor(parameters: ExternalCramEncoding['parameters'], dataType: 'int' | 'byte');
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
+    _decodeInt(contentBlock: CramFileBlock, cursor: Cursor): number;
+    _decodeByte(contentBlock: CramFileBlock, cursor: Cursor): number;
 }
-import CramCodec from "./_base";

package/dist/cramFile/codecs/external.js

@@ -1,63 +1,45 @@
 "use strict";
-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 __());
-    };
-})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var errors_1 = require("../../errors");
-var _base_1 = __importDefault(require("./_base"));
-var util_1 = require("../util");
-var ExternalCodec = /** @class */ (function (_super) {
-    __extends(ExternalCodec, _super);
-    function ExternalCodec(parameters, dataType) {
-        if (parameters === void 0) { parameters = {}; }
-        var _this = _super.call(this, parameters, dataType) || this;
-        if (_this.dataType === 'int') {
-            _this._decodeData = _this._decodeInt;
+const errors_1 = require("../../errors");
+const _base_1 = __importDefault(require("./_base"));
+const util_1 = require("../util");
+const getBits_1 = require("./getBits");
+class ExternalCodec extends _base_1.default {
+    constructor(parameters, dataType) {
+        super(parameters, dataType);
+        if (this.dataType === 'int') {
+            this._decodeData = this._decodeInt;
         }
-        else if (_this.dataType === 'byte') {
-            _this._decodeData = _this._decodeByte;
+        else if (this.dataType === 'byte') {
+            this._decodeData = this._decodeByte;
         }
         else {
-            throw new errors_1.CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by EXTERNAL codec"));
+            throw new errors_1.CramUnimplementedError(`${this.dataType} decoding not yet implemented by EXTERNAL codec`);
         }
-        return _this;
     }
-    ExternalCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
-        var blockContentId = this.parameters.blockContentId;
-        var contentBlock = blocksByContentId[blockContentId];
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        const { blockContentId } = this.parameters;
+        const contentBlock = blocksByContentId[blockContentId];
         if (!contentBlock) {
-            throw new errors_1.CramMalformedError("no block found with content ID ".concat(blockContentId));
+            throw new errors_1.CramMalformedError(`no block found with content ID ${blockContentId}`);
         }
-        var cursor = cursors.externalBlocks.getCursor(blockContentId);
+        const cursor = cursors.externalBlocks.getCursor(blockContentId);
         return this._decodeData(contentBlock, cursor);
-    };
-    ExternalCodec.prototype._decodeInt = function (contentBlock, cursor) {
-        var _a = (0, util_1.parseItf8)(contentBlock.content, cursor.bytePosition), result = _a[0], bytesRead = _a[1];
-        cursor.bytePosition += bytesRead;
+    }
+    _decodeInt(contentBlock, cursor) {
+        const [result, bytesRead] = (0, util_1.parseItf8)(contentBlock.content, cursor.bytePosition);
+        cursor.bytePosition = cursor.bytePosition + bytesRead;
         return result;
-    };
-    ExternalCodec.prototype._decodeByte = function (contentBlock, cursor) {
+    }
+    _decodeByte(contentBlock, cursor) {
         if (cursor.bytePosition >= contentBlock.content.length) {
-            throw new errors_1.CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
+            throw new getBits_1.CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
         }
         return contentBlock.content[cursor.bytePosition++];
-    };
-    return ExternalCodec;
-}(_base_1.default));
+    }
+}
 exports.default = ExternalCodec;
 //# sourceMappingURL=external.js.map

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

@@ -1 +1 @@
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package/dist/cramFile/codecs/gamma.d.ts

@@ -1,4 +1,8 @@
-export default class GammaCodec extends CramCodec {
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): number;
+import CramCodec, { Cursors } from './_base';
+import { GammaEncoding } from '../encoding';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+export default class GammaCodec extends CramCodec<'int', GammaEncoding['parameters']> {
+    constructor(parameters: GammaEncoding['parameters'], dataType: 'int');
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
 }
-import CramCodec from "./_base";