@gmod/cram 1.5.9 → 1.6.2

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

@@ -1,56 +1,47 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _require = require('../../errors'),
-    CramBufferOverrunError = _require.CramBufferOverrunError;
-
+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 =
-/*#__PURE__*/
-function () {
-  function CramCodec() {
-    var parameters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    var dataType = arguments.length > 1 ? arguments[1] : undefined;
-    (0, _classCallCheck2.default)(this, CramCodec);
-    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) {
-  // }
-
-
-  (0, _createClass2.default)(CramCodec, [{
-    key: "_getBits",
-    value: function _getBits(data, cursor, numBits) {
-      var 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 (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;
+    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 = {}; }
+        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));
+        }
     }
-  }]);
-  return CramCodec;
-}();
-
-module.exports = CramCodec;
+    // 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

@@ -0,0 +1 @@
+{"version":3,"file":"_base.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/_base.js"],"names":[],"mappings":";;AAAA,uCAAqD;AAErD,IAAM,cAAc,GAAG;IACrB,GAAG,EAAE,IAAI;IACT,IAAI,EAAE,IAAI;IACV,IAAI,EAAE,IAAI;IACV,SAAS,EAAE,IAAI;IACf,cAAc,EAAE,IAAI;CACrB,CAAA;AAED,mBAAmB;AACnB;IACE,mBAAY,UAAe,EAAE,QAAQ;QAAzB,2BAAA,EAAA,eAAe;QACzB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;QACxB,IAAI,CAAC,QAAQ,EAAE;YACb,MAAM,IAAI,SAAS,CAAC,+CAA+C,CAAC,CAAA;SACrE;QACD,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,EAAE;YAC7B,MAAM,IAAI,SAAS,CAAC,4BAAqB,QAAQ,CAAE,CAAC,CAAA;SACrD;IACH,CAAC;IAED,6DAA6D;IAC7D,IAAI;IAEJ,4BAAQ,GAAR,UAAS,IAAI,EAAE,MAAM,EAAE,OAAO;QAC5B,IAAI,GAAG,GAAG,CAAC,CAAA;QACX,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;YAC5D,IAAI,CAAC,MAAM,EACX;YACA,MAAM,IAAI,+BAAsB,CAC9B,6DAA6D,CAC9D,CAAA;SACF;QACD,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,IAAI,CAAC,EAAE;YACxC,yDAAyD;YACzD,GAAG,KAAK,CAAC,CAAA;YACT,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;YAC5D,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;YACvB,IAAI,MAAM,CAAC,WAAW,GAAG,CAAC,EAAE;gBAC1B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;aACzB;YACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;SACxB;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IACH,gBAAC;AAAD,CAAC,AArCD,IAqCC"}

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

@@ -1,50 +1,40 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-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 _require = require('../../errors'),
-    CramUnimplementedError = _require.CramUnimplementedError;
-
-var CramCodec = require('./_base');
-
-var BetaCodec =
-/*#__PURE__*/
-function (_CramCodec) {
-  (0, _inherits2.default)(BetaCodec, _CramCodec);
-
-  function BetaCodec() {
-    var _this;
-
-    var parameters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    var dataType = arguments.length > 1 ? arguments[1] : undefined;
-    (0, _classCallCheck2.default)(this, BetaCodec);
-    _this = (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(BetaCodec).call(this, parameters, dataType));
-
-    if (_this.dataType !== 'int') {
-      throw new CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by BETA codec"));
+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"));
+        }
+        return _this;
     }
-
-    return _this;
-  }
-
-  (0, _createClass2.default)(BetaCodec, [{
-    key: "decode",
-    value: function decode(slice, coreDataBlock, blocksByContentId, cursors) {
-      var data = this._getBits(coreDataBlock.content, cursors.coreBlock, this.parameters.length) - this.parameters.offset;
-      return data;
-    }
-  }]);
-  return BetaCodec;
-}(CramCodec);
-
-module.exports = BetaCodec;
+    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));
+exports.default = BetaCodec;
+//# sourceMappingURL=beta.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,uCAAqD;AACrD,kDAA+B;AAE/B;IAAuC,6BAAS;IAC9C,mBAAY,UAAe,EAAE,QAAQ;QAAzB,2BAAA,EAAA,eAAe;QAA3B,YACE,kBAAM,UAAU,EAAE,QAAQ,CAAC,SAM5B;QALC,IAAI,KAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,MAAM,IAAI,+BAAsB,CAC9B,UAAG,KAAI,CAAC,QAAQ,gDAA6C,CAC9D,CAAA;SACF;;IACH,CAAC;IAED,0BAAM,GAAN,UAAO,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,IAAM,IAAI,GACR,IAAI,CAAC,QAAQ,CACX,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;QAC5B,OAAO,IAAI,CAAA;IACb,CAAC;IACH,gBAAC;AAAD,CAAC,AAnBD,CAAuC,eAAS,GAmB/C"}

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

@@ -1,80 +1,60 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-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 _context;
-
-var _require = require('../util'),
-    tinyMemoize = _require.tinyMemoize;
-
-var CramCodec = require('./_base');
-
-var ByteArrayStopCodec =
-/*#__PURE__*/
-function (_CramCodec) {
-  (0, _inherits2.default)(ByteArrayStopCodec, _CramCodec);
-
-  function ByteArrayStopCodec() {
-    var _this;
-
-    var parameters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    var dataType = arguments.length > 1 ? arguments[1] : undefined;
-    var instantiateCodec = arguments.length > 2 ? arguments[2] : undefined;
-    (0, _classCallCheck2.default)(this, ByteArrayStopCodec);
-    _this = (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(ByteArrayStopCodec).call(this, parameters, dataType));
-    _this.instantiateCodec = instantiateCodec;
-    if (dataType !== 'byteArray') throw new TypeError("byteArrayLength does not support data type ".concat(dataType));
-    return _this;
-  }
-
-  (0, _createClass2.default)(ByteArrayStopCodec, [{
-    key: "decode",
-    value: function decode(slice, coreDataBlock, blocksByContentId, cursors) {
-      var lengthCodec = this._getLengthCodec();
-
-      var arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-
-      var dataCodec = this._getDataCodec();
-
-      var data = new Array(arrayLength);
-
-      for (var i = 0; i < arrayLength; i += 1) {
-        data[i] = dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-      }
-
-      return data;
-    } // memoize
-
-  }, {
-    key: "_getLengthCodec",
-    value: function _getLengthCodec() {
-      var encodingParams = this.parameters.lengthsEncoding;
-      return this.instantiateCodec(encodingParams, 'int');
-    } // memoize
-
-  }, {
-    key: "_getDataCodec",
-    value: function _getDataCodec() {
-      var encodingParams = this.parameters.valuesEncoding;
-      return this.instantiateCodec(encodingParams, 'byte');
+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;
+        if (dataType !== 'byteArray') {
+            throw new TypeError("byteArrayLength does not support data type ".concat(dataType));
+        }
+        return _this;
     }
-  }]);
-  return ByteArrayStopCodec;
-}(CramCodec);
-
-(0, _forEach.default)(_context = '_getLengthCodec _getDataCodec'.split(' ')).call(_context, function (method) {
-  return tinyMemoize(ByteArrayStopCodec, method);
-});
-module.exports = ByteArrayStopCodec;
+    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 Array(arrayLength);
+        for (var 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;
+        return this.instantiateCodec(encodingParams, 'int');
+    };
+    // memoize
+    ByteArrayStopCodec.prototype._getDataCodec = function () {
+        var 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); });
+//# sourceMappingURL=byteArrayLength.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,gCAAqC;AAErC,kDAA+B;AAE/B;IAAgD,sCAAS;IACvD,4BAAY,UAAe,EAAE,QAAQ,EAAE,gBAAgB;QAA3C,2BAAA,EAAA,eAAe;QAA3B,YACE,kBAAM,UAAU,EAAE,QAAQ,CAAC,SAO5B;QANC,KAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,MAAM,IAAI,SAAS,CACjB,qDAA8C,QAAQ,CAAE,CACzD,CAAA;SACF;;IACH,CAAC;IAED,mCAAM,GAAN,UAAO,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,IAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,IAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CACpC,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QAED,IAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;QACtC,IAAM,IAAI,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;QACnC,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,4CAAe,GAAf;QACE,IAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,0CAAa,GAAb;QACE,IAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QAErD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;IACH,yBAAC;AAAD,CAAC,AA9CD,CAAgD,eAAS,GA8CxD;;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,UAAA,MAAM,IAAI,OAAA,IAAA,kBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,EAAvC,CAAuC,CAAC,CAAA"}

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

@@ -1,79 +1,65 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _slice = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/slice"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-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 _require = require('../../errors'),
-    CramBufferOverrunError = _require.CramBufferOverrunError,
-    CramMalformedError = _require.CramMalformedError;
-
-var CramCodec = require('./_base');
-
-var ByteArrayStopCodec =
-/*#__PURE__*/
-function (_CramCodec) {
-  (0, _inherits2.default)(ByteArrayStopCodec, _CramCodec);
-
-  function ByteArrayStopCodec() {
-    var _this;
-
-    var parameters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    var dataType = arguments.length > 1 ? arguments[1] : undefined;
-    (0, _classCallCheck2.default)(this, ByteArrayStopCodec);
-    _this = (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(ByteArrayStopCodec).call(this, parameters, dataType));
-
-    if (dataType === 'byteArray') {
-      _this._decode = _this._decodeByteArray;
-    } else {
-      throw new TypeError("byteArrayStop codec does not support data type ".concat(dataType));
-    }
-
-    return _this;
-  }
-
-  (0, _createClass2.default)(ByteArrayStopCodec, [{
-    key: "decode",
-    value: function decode(slice, coreDataBlock, blocksByContentId, cursors) {
-      var blockContentId = this.parameters.blockContentId;
-      var contentBlock = blocksByContentId[blockContentId];
-      if (!contentBlock) throw new CramMalformedError("no block found with content ID ".concat(blockContentId));
-      var cursor = cursors.externalBlocks.getCursor(blockContentId);
-      return this._decode(contentBlock, cursor);
-    }
-  }, {
-    key: "_decodeByteArray",
-    value: function _decodeByteArray(contentBlock, cursor) {
-      var dataBuffer = contentBlock.content;
-      var stopByte = this.parameters.stopByte; // scan to the next stop byte
-
-      var startPosition = cursor.bytePosition;
-      var stopPosition = cursor.bytePosition;
-
-      while (dataBuffer[stopPosition] !== stopByte && stopPosition < dataBuffer.length) {
-        if (stopPosition === dataBuffer.length) {
-          throw new CramBufferOverrunError("byteArrayStop reading beyond length of data buffer?");
+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;
+        }
+        else {
+            throw new TypeError("byteArrayStop codec does not support data type ".concat(dataType));
         }
-
-        stopPosition += 1;
-      }
-
-      cursor.bytePosition = stopPosition + 1;
-      var data = (0, _slice.default)(dataBuffer).call(dataBuffer, startPosition, stopPosition);
-      return data;
+        return _this;
     }
-  }]);
-  return ByteArrayStopCodec;
-}(CramCodec);
-
-module.exports = ByteArrayStopCodec;
+    ByteArrayStopCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
+        var blockContentId = this.parameters.blockContentId;
+        var contentBlock = blocksByContentId[blockContentId];
+        if (!contentBlock) {
+            throw new errors_1.CramMalformedError("no block found with content ID ".concat(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;
+        // scan to the next stop byte
+        var startPosition = cursor.bytePosition;
+        var 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?");
+            }
+            stopPosition += 1;
+        }
+        cursor.bytePosition = stopPosition + 1;
+        var data = dataBuffer.slice(startPosition, stopPosition);
+        return data;
+    };
+    return ByteArrayStopCodec;
+}(_base_1.default));
+exports.default = ByteArrayStopCodec;
+//# sourceMappingURL=byteArrayStop.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,uCAAyE;AAEzE,kDAA+B;AAE/B;IAAgD,sCAAS;IACvD,4BAAY,UAAe,EAAE,QAAQ;QAAzB,2BAAA,EAAA,eAAe;QAA3B,YACE,kBAAM,UAAU,EAAE,QAAQ,CAAC,SAQ5B;QAPC,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,KAAI,CAAC,OAAO,GAAG,KAAI,CAAC,gBAAgB,CAAA;SACrC;aAAM;YACL,MAAM,IAAI,SAAS,CACjB,yDAAkD,QAAQ,CAAE,CAC7D,CAAA;SACF;;IACH,CAAC;IAED,mCAAM,GAAN,UAAO,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QAC7C,IAAA,cAAc,GAAK,IAAI,CAAC,UAAU,eAApB,CAAoB;QAC1C,IAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,2BAAkB,CAC1B,yCAAkC,cAAc,CAAE,CACnD,CAAA;SACF;QACD,IAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,OAAO,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC3C,CAAC;IAED,6CAAgB,GAAhB,UAAiB,YAAY,EAAE,MAAM;QACnC,IAAM,UAAU,GAAG,YAAY,CAAC,OAAO,CAAA;QAC/B,IAAA,QAAQ,GAAK,IAAI,CAAC,UAAU,SAApB,CAAoB;QACpC,6BAA6B;QAC7B,IAAM,aAAa,GAAG,MAAM,CAAC,YAAY,CAAA;QACzC,IAAI,YAAY,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,OACE,UAAU,CAAC,YAAY,CAAC,KAAK,QAAQ;YACrC,YAAY,GAAG,UAAU,CAAC,MAAM,EAChC;YACA,IAAI,YAAY,KAAK,UAAU,CAAC,MAAM,EAAE;gBACtC,MAAM,IAAI,+BAAsB,CAC9B,qDAAqD,CACtD,CAAA;aACF;YACD,YAAY,IAAI,CAAC,CAAA;SAClB;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,IAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;QAC1D,OAAO,IAAI,CAAA;IACb,CAAC;IACH,yBAAC;AAAD,CAAC,AA7CD,CAAgD,eAAS,GA6CxD"}

package/dist/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";